Note: Descriptions are shown in the official language in which they were submitted.
CA 02323761 2000-09-18
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CA 02323761 2000-09-18
WO 99/47540 PCTIUS99/05804
95 Human Secreted Proteins
Field of the Invention
This invention relates to newly identified polynucleotides and the
polypeptides encoded by these polynucleotides, uses of such polynucleotides
and
polypeptides, and their production.
Background of the Invention
Unlike bacterium, which exist as a single compartment surrounded by a
membrane, human cells and other eucaryotes are subdivided by membranes into
many
functionally distinct compartments. Each membrane-bounded compartment, or
organelle, contains different proteins essential for the function of the
organelle. The
cell uses "sorting signals," which are amino acid motifs located within the
protein, to
target proteins to particular cellular organelles.
One type of sorting signal, called a signal sequence, a signal peptide, or a
leader sequence, directs a class of proteins to an organelle called the
endoplasmic
reticulum (ER). The ER separates the membrane-bounded proteins from all other
types of proteins. Once localized to the ER, both groups of proteins can be
further
directed to another organelle called the Golgi apparatus. Here, the Golgi
distributes
the proteins to vesicles, including secretory vesicles, the cell membrane,
lysosomes,
and the other organelles.
Proteins targeted to the ER by a signal sequence can be released into the
extracellular space as a secreted protein. For example, vesicles containing
secreted
proteins can fuse with the cell membrane and release their contents into the
extracellular space - a process called exocytosis. Exocytosis can occur
constitutively
or after receipt of a triggering signal. In the latter case, the proteins are
stored in
secretory vesicles (or secretory granules) until exocytosis is triggered.
Similarly,
proteins residing on the cell membrane can also be secreted into the
extracellular
space by proteolytic cleavage of a "linker" holding the protein to the
membrane.
Despite the great progress made in recent years, only a small number of Genes
encoding human secreted proteins have been identified. These secreted proteins
include the commercially valuable human insulin, interferon, Factor VIII,
human
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2
growth hormone, tissue plasminogen activator, and erythropoeitin. Thus, in
light of
the pervasive role of secreted proteins in human physiology, a need exists for
identifying and characterizing novel human secreted proteins and the genes
that
encode them. This knowledge will allow one to detect, to treat, and to prevent
medical disorders by using secreted proteins or the genes that encode them.
Summary of the Invention
The present invention relates to novel polynucleotides and the encoded
polypeptides. Moreover, the present invention relates to vectors, host cells,
antibodies, and recombinant methods for producing the polypeptides and
polynucleotides. Also provided are diagnostic methods for detecting disorders
related
to the polypeptides, and therapeutic methods for treating such disorders. The
invention further relates to screening methods for identifying binding
partners of the
polypeptides.
Detailed Description
Definitions
The following definitions are provided to facilitate understanding of certain
terms used throughout this specification.
In the present invention, "isolated" refers to material removed from its
original
environment (e.g., the natural environment if it is naturally occurring), and
thus is
altered "by the hand of man" from its natural state. For example, an isolated
polynucleotide could be part of a vector or a composition of matter, or could
be
contained within a cell, and still be "isolated" because that vector,
composition of
matter, or particular cell is not the original environment of the
polynucleotide.
In the present invention, a "secreted" protein refers to those proteins
capable
of being directed to the ER, secretory vesicles, or the extracellular space as
a result of
a signal sequence, as well as those proteins released into the extracellular
space
without necessarily containing a signal sequence. If the secreted protein is
released
into the extracellular space, the secreted protein can undergo extracellular
processing
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3
to produce a "mature" protein. Release into the extracellular space can occur
by many
mechanisms, including exocytosis and proteolytic cleavage.
In specific embodiments, the polynucleotides of the invention are less than
300 kb, 200 kb, 100 kb, 50 kb, 15 kb, 10 kb, or 7.5 kb in length. In a further
embodiment, polynucleotides of the invention comprise at least 15 contiguous
nucleotides of the coding sequence, but do not comprise all or a portion of
any intron.
In another embodiment, the nucleic acid comprising the coding sequence does
not
contain coding sequences of a genomic flanking gene (i.e., 5' or 3' to the
gene in the
genome).
As used herein , a "polynucleotide" refers to a molecule having a nucleic acid
sequence contained in SEQ ID NO:X or the cDNA contained within the clone
deposited with the ATCC. For example, the polynucleotide can contain the
nucleotide sequence of the full length cDNA sequence, including the S' and 3'
untranslated sequences, the coding region, with or without the signal
sequence, the
secreted protein coding region, as well as fragments, epitopes, domains, and
variants
of the nucleic acid sequence. Moreover, as used herein, a "polypeptide" refers
to a
molecule having the translated amino acid sequence generated from the
polynucleotide as broadly defined.
In the present invention, the full length sequence identified as SEQ ID NO:X
was often generated by overlapping sequences contained in multiple clones
(contig
analysis). A representative clone containing all or most of the sequence for
SEQ ID
NO:X was deposited with the American Type Culture Collection ("ATCC"). As
shown in Table l, each clone is identified by a cDNA Clone ID (Identifier) and
the
ATCC Deposit Number. The ATCC is located at 10801 University Boulevard,
Manassas, Virginia 20110-2209, USA. The ATCC deposit was made pursuant to the
terms of the Budapest Treaty on the international recognition of the deposit
of
microorganisms for purposes of patent procedure.
A "polynucleotide" of the present invention also includes those
polynucleotides capable of hybridizing, under stringent hybridization
conditions, to
sequences contained in SEQ ID NO:X, the complement thereof, or the cDNA within
the clone deposited with the ATCC. "Stringent hybridization conditions" refers
to an
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4
overnight incubation at 42° C in a solution comprising 50% formamide,
Sx SSC (750
mM NaCI, 75 mM sodium citrate), 50 mM sodium phosphate (pH 7.6), Sx Denhardt's
solution, 10% dextran sulfate, and 20 p.g/ml denatured, sheared salmon sperm
DNA,
followed by washing the filters in O.lx SSC at about 65°C.
Also contemplated are nucleic acid molecules that hybridize to the
polynucleotides of the present invention at lower stringency hybridization
conditions.
Changes in the stringency of hybridization and signal detection are primarily
accomplished through the manipulation of formamide concentration (lower
percentages of formamide result in lowered stringency); salt conditions, or
temperature. For example, lower stringency conditions include an overnight
incubation at 37°C in a solution comprising 6X SSPE (20X SSPE = 3M
NaCI: 0.2M
NaH,P04; 0.02M EDTA, pH 7.4), 0.5% SDS, 30% formamide, I00 ug/ml salmon
sperm blocking DNA; followed by washes at 50°C with 1XSSPE, 0.1 % SDS.
In
addition, to achieve even lower stringency, washes performed following
stringent
hybridization can be done at higher salt concentrations (e.g. SX SSC).
Note that variations in the above conditions may be accomplished through the
inclusion and/or substitution of alternate blocking reagents used to suppress
background in hybridization experiments. Typical blocking reagents include
Denhardt's reagent, BLOTTO, heparin, denatured salmon sperm DNA, and
commercially available proprietary formulations. The inclusion of specific
blocking
reagents may require modification of the hybridization conditions described
above,
due to problems with compatibility.
Of course, a polynucleotide which hybridizes only to polyA+ sequences (such
as any 3' terminal polyA+ tract of a cDNA shown in the sequence listing), or
to a
complementary stretch of T (or U) residues, would not be included in the
definition of
"polynucleotide," since such a polynucleotide would hybridize to any nucleic
acid
molecule containing a poly (A) stretch or the complement thereof (e.g.,
practically
any double-stranded cDNA clone).
The polynucleotide of the present invention can be composed of any
polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or
DNA or modified RNA or DNA. For example, polynucleotides can be composed of
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single- and double-stranded DNA, DNA that is a mixture of single- and double-
stranded regions, single- and double-stranded RNA, and RNA that is mixture of
single- and double-stranded regions, hybrid molecules comprising DNA and RNA
that may be single-stranded or, more typically, double-stranded or a mixture
of single-
s and double-stranded regions. In addition, the polynucleotide can be composed
of
triple-stranded regions comprising RNA or DNA or both RNA and DNA. A
polynucleotide may also contain one or more modified bases or DNA or RNA
backbones modified for stability or for other reasons. "Modified" bases
include, for
example, tritylated bases and unusual bases such as inosine. A variety of
modifications can be made to DNA and RNA; thus, "polynucleotide" embraces
chemically, enzymatically, or metabolically modified forms.
The polypeptide of the present invention can be composed of amino acids
joined to each other by peptide bonds or modified peptide bonds, i.e., peptide
isosteres, and may contain amino acids other than the 20 gene-encoded amino
acids.
The polypeptides may be modified by either natural processes, such as
posttranslational processing, or by chemical modification techniques which are
well
known in the art. Such modifications are well described in basic texts and in
more
detailed monographs, as well as in a voluminous research literature.
Modifications
can occur anywhere in a polypeptide, including the peptide backbone, the amino
acid
side-chains and the amino or carboxyl termini. It will be appreciated that the
same
type of modification may be present in the same or varying degrees at several
sites in
a given polypeptide. Also, a given polypeptide may contain many types of
modifications. Polypeptides may be branched , for example, as a result of
ubiquitination, and they may be cyclic, with or without branching. Cyclic,
branched,
and branched cyclic polypeptides may result from posttranslation natural
processes or
may be made by synthetic methods. Modifications include acetylation,
acylation,
ADP-ribosylation, amidation, covalent attachment of flavin, covalent
attachment of a
heme moiety, covalent attachment of a nucleotide or nucleotide derivative,
covalent
attachment of a lipid or lipid derivative, covalent attachment of
phosphotidylinositol,
cross-linking, cyclization, disulfide bond formation, demethylation, formation
of
covalent cross-links, formation of cysteine, formation of pyroglutamate,
formylation,
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gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation,
iodination, methylation, myristoylation, oxidation, pegylation, proteolytic
processing,
phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-
RNA
mediated addition of amino acids to proteins such as arginylation, and
ubiquitination.
(See, for instance, PROTEINS - STRUCTURE AND MOLECULAR PROPERTIES,
2nd Ed., T. E. Creighton, W. H. Freeman and Company, New York (1993);
POSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS, B. C.
Johnson, Ed., Academic Press, New York, pgs. 1-12 (1983); Seifter et al., Meth
Enzymol 182:626-646 ( 1990); Rattan et al., Ann NY Acad Sci 663:48-62 (
1992).)
"SEQ ID NO:X" refers to a polynucleotide sequence while "SEQ ID NO:Y"
refers to a polypeptide sequence, both sequences identified by an integer
specified in
Table 1.
"A polypeptide having biological activity" refers to polypeptides exhibiting
activity similar, but not necessarily identical to, an activity of a
polypeptide of the
present invention, including mature forms, as measured in a particular
biological
assay, with or without dose dependency. In the case where dose dependency does
exist, it need not be identical to that of the polypeptide, but rather
substantially similar
to the dose-dependence in a given activity as compared to the polypeptide of
the
present invention (i.e., the candidate polypeptide will exhibit greater
activity or not
more than about 25-fold less and, preferably, not more than about tenfold less
activity, and most preferably, not more than about three-fold less activity
relative to
the polypeptide of the present invention.)
Polynucleotides and Pol~rRgotides of the Invention
FEATURES OF PROTEIN ENCODED BY GENE NO: 1
This gene is expressed primarily in anergic T cells and merkel cells.
Therefore, polynucleotides and polypeptides of the invention are useful as
reagents for differential identification of the tissues) or cell types)
present in a
biological sample and for diagnosis of diseases and conditions which include,
but are
not limited to, immune disorders and inflammatory diseases. Similarly,
polypeptides
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and antibodies directed to these polypeptides are useful in providing
immunological
probes for differential identification of the tissues) or cell type(s). For a
number of
disorders of the above tissues or cells, particularly of the immune system,
expression
of this gene at significantly higher or lower levels may be routinely detected
in certain
tissues or cell types (e.g., immune, cancerous and wounded tissues) or bodily
fluids
(e.g., lymph, serum, plasma, urine, synovial fluid and spinal fluid) or
another tissue or
cell sample taken from an individual having such a disorder, relative to the
standard
gene expression level, i.e., the expression level in healthy tissue or bodily
fluid from
an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO:
108 as residues: Ala-55 to Gln-64.
The tissue distribution in T-cells and merkel cells indicates that the protein
products of this gene are useful for the diagnosis and/or treatment of immune
system
diseases. Furthermore,
Expression of this gene product in T-cells indicates a role in the regulation
of
the proliferation; survival; differentiation; and/or activation of potentially
all
hematopoietic cell lineages, including blood stem cells. This gene product may
be
involved in the regulation of cytokine production, antigen presentation, or
other
processes that may also suggest a usefulness in the treatment of cancer (e.g.
by
boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
deficiency diseases such as AIDS, leukemia, rheumatoid arthritis, inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
commercial utility in the expansion of stem cells and committed progenitors of
various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Protein, as well as, antibodies directed against the protein may show
utility as a
tumor marker and/or immunotherapy targets for the above listed tissues.
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Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID NO:1 l and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence is
cumbersome. Accordingly, preferably excluded from the present invention are
one or
more polynucleotides comprising a nucleotide sequence described by the general
formula of a-b, where a is any integer between 1 to 2329 of SEQ ID NO:I l, b
is an
integer of 15 to 2343, where both a and b correspond to the positions of
nucleotide
residues shown in SEQ ID NO:1 l, and where b is greater than or equal to a +
14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 2
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: IPENRRPASXCTWSMWTSRTTTRRPPWGRFSSVSSASV
SSTRKTWRTRSTSCCRSSRRRVAAPFCTPSASTEPSARMEPPLELPVVHTFSFL
TFVFTYRCSAGDGSITQINCAYEMGEEMPKRQMKAIKFLLFHFYL (SEQ ID
N0:205), IPENRRPASXCTWSMWTSRTTTRRPPWGRFSSVSSASVSST (SEQ ID
N0:206), RKTWRTRSTSCCRSSRRRVAAPFCTPSASTEPSARMEPPLELP (SEQ
ID N0:207), and/or VVHTFSFLTFVFTYRCSAGDGSITQINCAYEMGEEMPKRQ
MKAIKFLLFHFYL (SEQ ID N0:208). Polynucleotides encoding these polypeptides
are also encompassed by the invention.
This gene is expressed primarily in placental, brain and breast tissues, and
to a
lesser extent in T cells and tumors.
Therefore, polynucleotides and polypeptides of the invention are useful as
reagents for differential identification of the tissues) or cell type{s)
present in a
biological sample and for diagnosis of diseases and conditions which include,
but are
not limited to, neurodegenerative and/or endocrine disorders and neoplasias,
or
developmental disorders. Similarly, polypeptides and antibodies directed to
these
polypeptides are useful in providing immunological probes for differential
identification of the tissues) or cell type(s). For a number of disorders of
the above
tissues or cells, particularly of the neurodegenerative, developing, endocrine
and
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9
immune systems, expression of this gene at significantly higher or lower
levels may
be routinely detected in certain tissues or cell types (e.g., brain,
endocrine, immune,
developing, cancerous and wounded tissues) or bodily fluids (e.g., lymph,
serum,
plasma, urine, synovial fluid and spinal fluid) or another tissue or cell
sample taken
from an individual having such a disorder, relative to the standard gene
expression
level, i.e., the expression level in healthy tissue or bodily fluid from an
individual not
having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO:
109 as residues: Ala-55 to Asn-60, Lys-65 to Met-71, Leu-75 to Asn-86, Asp-93
to
Asp-110, Leu-130 to Cys-138, Gln-149 to Glu-154, Thr-172 to Ile-179, Glu-185
to
Arg-192.
The tissue distribution in breast and brain tissues indicates that the protein
products of this gene are useful for the diagnosis and/or treatment of
endocrine
disorders, neurodegenerative disorders, developmental disorders, immune system
diseases and neoplasias. The tissue distribution in placental tissue indicates
that
polynucleotides and polypeptides corresponding to this gene are useful for the
diagnosis and/or treatment of disorders of the placenta. Specific expression
within the
placenta indicates that this gene product may play a role in the proper
establishment
and maintenance of placental function. Alternately, this gene product may be
produced by the placenta and then transported to the embryo, where it may play
a
crucial role in the development and/or survival of the developing embryo or
fetus.
Expression of this gene product in a vascular-rich tissue such as the placenta
also indicates that this gene product may be produced more generally in
endothelial
cells or within the circulation. In such instances, it may play more
generalized roles in
vascular function, such as in angiogenesis. It may also be produced in the
vasculature
and have effects on other cells within the circulation, such as hematopoietic
cells. It
may serve to promote the proliferation, survival, activation, and/or
differentiation of
hematopoietic cells, as well as other cells throughout the body. Likewise,
Expression of this gene product in T-cells indicates a role in the regulation
of
the proliferation; survival; differentiation; and/or activation of potentially
all
hematopoietic cell lineages, including blood stem cells. This gene product may
be
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involved in the regulation of cytokine production, antigen presentation, or
other
processes that may also suggest a usefulness in the treatment of cancer (e.g.
by
boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
5 well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
deficiency diseases such as AIDS, leukemia, rheumatoid arthritis, inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
10 commercial utility in the expansion of stem cells and committed progenitors
of
various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Alternatively, the tissue distribution in brain tissue indicates that
polynucleotides and polypeptides corresponding to this gene are useful for the
detectionltreatment of neurodegenerative disease states and behavioural
disorders
such as Alzheimers Disease, Parkinsons Disease, Huntingtons Disease, Tourette
Syndrome, schizophrenia, mania, dementia, paranoia, obsessive compulsive
disorder,
panic disorder, learning disabilities, ALS, psychoses, autism, and altered
behaviors,
including disorders in feeding, sleep patterns, balance, and perception. In
addition, the
gene or gene product may also play a role in the treatment and/or detection of
developmental disorders associated with the developing embryo, or sexually-
linked
disorders. Protein, as well as, antibodies directed against the protein may
show utility
as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:12 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence is
cumbersome. Accordingly, preferably excluded from the present invention are
one or
more polynucleotides comprising a nucleotide sequence described by the general
formula of a-b, where a is any integer between 1 to 1163 of SEQ ID N0:12, b is
an
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11
integer of 15 to 1177, where both a and b correspond to the positions of
nucleotide
residues shown in SEQ ID N0:12, and where b is greater than or equal to a +
14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 3
The translation product of this gene shares sequence homology with bovine
beta-mannosidase, which is thought to be important in lysosomal catabolism of
glycoproteins. See, for example, J. Biol. Chem. 270, 3841-3848 ( 1995),
incorporated
herein by reference in its entirety. Based on the sequence similarity between
these
proteins the translation product of this gene will sometimes hereinafter be
reffered to
as human beta-mannosidase. Human beta-mannosidase is expected to share certain
biological activities, particularly enzymatic activities, with bovine beta-
mannosidase.
Such activities may be assayed by methods known in the art, described in J.
Biol.
Chem. 270, 3841-3848 (1995), and/or disclosed elsewhere herein.
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: HPSIIIWSGNNENEEALMMNWYHISFTDRPIYIKDYVTL
YVKNIRELVLAGDKSRPFITSSPTNGAETVAEAW VSQNPNSNYFGDVHFYDYI
SDCWNWKVFPKARFASEYGYQSWPSFSTLEKVSSTEDWSFNSKFSLHRQHH
EGGNKQMLYQAGLHFKLPQSTDPLRTFKDTIYLTQVMQAQCVKTETEFYRRS
RSEIVDQQGHTMGALYWQLNDIWQAPSW (SEQ ID N0:209), and/or
VRVHTWS
SLEPVCSRVTERFVMKGGEAVCLYEEPVSELLRRCGNCTRESCVVSFYLSAD
HELLSPTNYHFLSSPKEAVGLCKAQITAIISQQGDIFVFDLETSAVAPFVWLDV
GSIPGRFSDNGFLMTEKTRTILFYPWEPTSKNELEQSFHVTSLTDIY (SEQ ID
N0:210). Polynucleotides encoding these polypeptides are also encompassed by
the
invention. The gene encoding the disclosed cDNA is thought to reside on
chromosome 4. Accordingly, polynucleotides related to this invention are
useful as a
marker in linkage analysis for chromosome 4.
This gene is expressed primarily in colon tissue, and to a lesser extent in
thymus stromal cells and chondrosarcoma tissue.
Therefore, polynucleotides and polypeptides of the invention are useful as
reagents for differential identification of the tissues) or cell types)
present in a
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12
biological sample and for diagnosis of diseases and conditions which include,
but are
not limited to, chondroma and mannosidosis. Similarly, polypeptides and
antibodies
directed to these polypeptides are useful in providing immunological probes
for
differential identification of the tissues) or cell type(s). For a number of
disorders of
the above tissues or cells, particularly of the chondro and immune system. The
expression of this gene at significantly higher or lower levels may be
routinely
detected in certain tissues or cell types (e.g., immune, metabolic, cancerous
and
wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial
fluid
and spinal fluid) or another tissue or cell sample taken from an individual
having such
a disorder, relative to the standard gene expression level, i.e., the
expression level in
healthy tissue or bodily fluid from an individual not having the disorder.
The tissue distribution and homology to bovine beta-mannosidase indicates
that the protein products of this gene are useful for the diagnosis and/or
treatment of
chondroma and mannosidosis. Human beta-mannosidosis is an autosomal recessive,
lysosomal storage disease caused by a deficiency of the enzyme beta-
mannosidase.
Furthermore, the homology of the translation product of this gene to beta-
mannosidase indicates that polynucleotides and polypeptides corresponding to
this
gene are useful for the diagnosis, prevention, and/or treatment of various
metabolic
disorders such as lysosomal storage deficiencies, Tay-Sachs disease,
phenylkenonuria, galactosemia, hyperlipidemias, porphyrias, and Hurler's
syndrome.
Protein, as well as, antibodies directed against the protein may show utility
as a tumor
marker andlor immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:13 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence is
cumbersome. Accordingly, preferably excluded from the present invention are
one or
more polynucleotides comprising a nucleotide sequence described by the general
formula of a-b, where a is any integer between I to 2093 of SEQ ID N0:13, b is
an
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13
integer of 15 to 2107, where both a and b correspond to the positions of
nucleotide
residues shown in SEQ ID N0:13, and where b is greater than or equal to a +
14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 4
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: PRLTPRMKWPTAALASRLLGWTVLRPPYPRVPSLPQVT
LHPTDGLMAVLYTGGEGRTLGEQHFFHETFVTRWLLGPVPVRFGACSPLSFL
APRRGQGAPAGXFCACPRPASRQLCPWPALPGTPYSNSAPLCTGMGHSNTPQ
GPPSPQYALSPTEPTSLSGNSHLPAILVL (SEQ ID N0:211},
PRLTPRMKWPTAAL ASRLLGWTVLRPPYPRVPSLPQVTLHP (SEQ ID
N0:212), TDGLMAVLYTGGE GRTLGEQHFFHETFVTRWLLGPVPVRFG (SEQ
ID N0:213), ACSPLSFLAPRRGQGAPAGXFCACPRPAS RQLCPWPALPGTP
( S E Q I D N O : 2 1 4 ) , a n d / o r
YSNSAPLCTGMGHSNTPQGPPSPQYALSPTEPTSLSGNS HLPAILVL (SEQ ID
N0:215). Polynucleotides encoding these polypeptides are also encompassed by
the
invention.
This gene is expressed primarily in human lung (adult and fetal), and to a
lesser extent in liver and brain tissues.
Therefore, polynucleotides and polypeptides of the invention are useful as
reagents for differential identification of the tissues) or cell types)
present in a
biological sample and for diagnosis of diseases and conditions which include,
but are
not limited to, pulmonary disorders and hemostasis. Similarly, polypeptides
and
antibodies directed to these polypeptides are useful in providing
immunological
probes for differential identification of the tissues) or cell type(s). For a
number of
disorders of the above tissues or cells, particularly of the lung and liver
tissues,
expression of this gene at significantly higher or lower levels may be
routinely
detected in certain tissues or cell types (e.g., pulmonary, cancerous and
wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
and spinal
fluid) or another tissue or cell sample taken from an individual having such a
disorder, relative to the standard gene expression level, i.e., the expression
level in
healthy tissue or bodily fluid from an individual not having the disorder.
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14
Preferred epitopes include those comprising a sequence shown in SEQ ID NO:
111 as residues: Arg-28 to Gln-36.
The tissue distribution in lung and liver tissues indicates that the protein
products of this gene are useful for the diagnosis and/or treatment of
pulmonary
disorders and hematopoietic disorders. The tissue distribution in adult and
fetal lung
tissues indicates that polynucleotides and polypeptides corresponding to this
gene are
useful for the detection and treatment of disorders associated with developing
lungs,
particularly in premature infants where the lungs are the last tissues to
develop. The
tissue distribution indicates that polynucleotides and polypeptides
corresponding to
this gene are useful for the diagnosis and intervention of lung tumors, since
the gene
may be involved in the regulation of cell division, particularly since it is
expressed in
fetal tissue. Alternatively,
Expression of this gene product in liver tissue indicates a role in the
regulation
of the proliferation; survival; differentiation; and/or activation of
potentially all
hematopoietic cell lineages, including blood stem cells. This gene product may
be
involved in the regulation of cytokine production, antigen presentation, or
other
processes that may also suggest a usefulness in the treatment of cancer (e.g.
by
boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
deficiency diseases such as AIDS, leukemia, rheumatoid arthritis, inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
commercial utility in the expansion of stem cells and committed progenitors of
various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Protein, as well as, antibodies directed against the protein may show
utility as a
tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:14 and may have been publicly available prior to
conception of
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IS
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence is
cumbersome. Accordingly, preferably excluded from the present invention are
one or
more polynucleotides comprising a nucleotide sequence described by the general
formula of a-b, where a is any integer between 1 to 1248 of SEQ ID N0:14, b is
an
integer of 15 to 1262, where both a and b correspond to the positions of
nucleotide
residues shown in SEQ ID N0:14, and where b is greater than or equal to a +
14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 5
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: HLLEVTPCRLPVPEFPGRTPRGSRTPD (SEQ ID N0:216).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
This gene is expressed primarily in rapidly dividing liver tissue, (e.g.,
hepatoma, hepatocellular carcinoma, and fetal liver tissue), and to a lesser
extent in
normal liver tissue, and other tumors such as colon cancer and uterine cancer.
Therefore, polynucleotides and polypeptides of the invention are useful as
reagents for differential identification of the tissues) or cell types)
present in a
biological sample and for diagnosis of diseases and conditions which include,
but are
not limited to, cancers, particularly hepatomas, colon cancer, and uterine
cancer.
Similarly, polypeptides and antibodies directed to these polypeptides are
useful in
providing immunological probes for differential identification of the tissues)
or cell
type(s). For a number of disorders of the above tissues or cells, particularly
of the
liver, colon and uterus, expression of this gene at significantly higher or
lower levels
may be routinely detected in certain tissues or cell types (e.g., liver,
colon, uterus,
cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma,
urine,
synovial fluid and spinal fluid) or another tissue or cell sample taken from
an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue or bodily fluid from an individual not
having the
disorder.
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16
Preferred epitopes include those comprising a sequence shown in SEQ ID NO:
112 as residues: Trp-3S to Trp-4S, Pro-S2 to Asp-S7, Thr-73 to Arg-82, Pro-lOS
to
Leu-112, Pro-11 S to Arg-127, Pro-140 to Gln-151.
The tissue distribution in liver tissues and cancers thereof, as well as other
S cancerous tissues, indicates that the protein products of this gene are
useful for the
diagnosis and/or treatment of cancers, particularly, hepatoma, colon cancer
and
uterine cancer, as well as cancers of other tissues where expression has been
observed. Furthermore, expression within cellular sources marked by
proliferating
cells indicates that this protein may play a role in the regulation of
cellular division,
and may show utility in the diagnosis and treatment of cancer and other
proliferative
disorders. Thus, this protein may also be involved in apoptosis or tissue
differentiation and could again be useful in cancer therapy. Protein, as well
as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID NO:1S and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence is
cumbersome. Accordingly, preferably excluded from the present invention are
one or
more polynucleotides comprising a nucleotide sequence described by the general
formula of a-b, where a is any integer between 1 to 74S of SEQ ID NO:1 S, b is
an
integer of I S to 759, where both a and b correspond to the positions of
nucleotide
residues shown in SEQ ID NO:1S, and where b is greater than or equal to a +
14.
2S
FEATURES OF PROTEIN ENCODED BY GENE NO: 6
This gene is expressed primarily in hepatocellular tumors.
Therefore, polynucleotides and polypeptides of the invention are useful as
reagents for differential identification of the tissues) or cell types)
present in a
biological sample and for diagnosis of diseases and conditions which include,
but are
not limited to, hepatomas. Similarly, polypeptides and antibodies directed to
these
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17
polypeptides are useful in providing immunological probes for differential
identification of the tissues) or cell type(s). For a number of disorders of
the above
tissues or cells, particularly of the liver, expression of this gene at
significantly higher
or lower levels may be routinely detected in certain tissues or cell types
(e.g., liver,
cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma,
urine,
synovial fluid and spinal fluid) or another tissue or cell sample taken from
an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue or bodily fluid from an individual not
having the
disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO:
113 as residues: Pro-32 to Gly-40.
The tissue distribution in hepatocellular tumors indicates that the protein
products of this gene are useful for the diagnosis and/or treatment of
hepatomas, as
well as cancers of other tissues where expression has been observed.
Furthermore,
expression within cellular sources marked by proliferating cells indicates
that this
protein may play a role in the regulation of cellular division, and may show
utility in
the diagnosis and treatment of cancer and other proliferative disorders. Thus,
this
protein may also be involved in apoptosis or tissue differentiation and could
again be
useful in cancer therapy. Protein, as well as, antibodies directed against the
protein
may show utility as a tumor marker and/or immunotherapy targets for the above
listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:16 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence is
cumbersome. Accordingly, preferably excluded from the present invention are
one or
more polynucleotides comprising a nucleotide sequence described by the general
formula of a-b, where a is any integer between 1 to 1796 of SEQ ID N0:16, b is
an
integer of 15 to 1810, where both a and b correspond to the positions of
nucleotide
residues shown in SEQ ID N0:16, and where b is greater than or equal to a +
14.
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18
FEATURES OF PROTEIN ENCODED BY GENE NO: 7
This gene is expressed primarily in human rhabdomyosarcoma tissue, as well
as in placental tissue.
S Therefore, polynucleotides and polypeptides of the invention are useful as
reagents for differential identification of the tissues) or cell types)
present in a
biological sample and for diagnosis of diseases and conditions which include,
but are
not limited to, malignant neoplasms and reproductive disorders. Similarly,
polypeptides and antibodies directed to these polypeptides are useful in
providing
immunological probes for differential identification of the tissues) or cell
type(s). For
a number of disorders of the above tissues or cells, particularly of the
skeletal system
and reproductive system, expression of this gene at significantly higher or
lower
levels may be routinely detected in certain tissues or cell types (e.g.,
reproductive,
cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma,
urine,
synovial fluid and spinal fluid) or another tissue or cell sample taken from
an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue or bodily fluid from an individual not
having the
disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO:
114 as residues: Arg-23 to Trp-28, Phe-93 to Lys-98, Arg-199 to Trp-206, GIy-
208 to
Met-213.
The tissue distribution in placental tissue and human rhabdomyosarcoma
tissue indicates that the protein products of this gene are useful for the
diagnosis
and/or treatment of skeletal and reproductive disorders. Furthermore, the
tissue
distribution in placental tissue indicates that polynucleotides and
polypeptides
corresponding to this gene are useful for the diagnosis and/or treatment of
disorders
of the placenta. Specific expression within the placenta indicates that this
gene
product may play a role in the proper establishment and maintenance of
placental
function. Alternately, this gene product may be produced by the placenta and
then
transported to the embryo, where it may play a crucial role in the development
and/or
survival of the developing embryo or fetus.
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19
Expression of this gene product in a vascular-rich tissue such as the placenta
also indicates that this gene product may be produced more generally in
endothelial
cells or within the circulation. In such instances, it may play more
generalized roles in
vascular function, such as in angiogenesis. It may also be produced in the
vasculature
and have effects on other cells within the circulation, such as hematopoietic
cells. It
may serve to promote the proliferation, survival, activation, and/or
differentiation of
hematopoietic cells, as well as other cells throughout the body. Protein, as
well as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:17 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence is
cumbersome. Accordingly, preferably excluded from the present invention are
one or
more polynucleotides comprising a nucleotide sequence described by the general
formula of a-b, where a is any integer between 1 to 1038 of SEQ ID N0:17, b is
an
integer of 15 to 1052, where both a and b correspond to the positions of
nucleotide
residues shown in SEQ ID N0:17, and where b is greater than or equal to a +
14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 8
This gene is expressed primarily in fetal liver/spleen and fetal skin tissues,
and
to a lesser extent in breast cancer tissue.
Therefore, polynucleotides and polypeptides of the invention are useful as
reagents for differential identification of the tissues) or cell types)
present in a
biological sample and for diagnosis of diseases and conditions which include,
but are
not limited to, developmental disorders and neoplasias. Similarly,
polypeptides and
antibodies directed to these polypeptides are useful in providing
immunological
probes for differential identification of the tissues) or cell types}. For a
number of
disorders of the above tissues or cells, particularly of the fetal tissue and
adult
immune system, expression of this gene at significantly higher or lower levels
may be
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routinely detected in certain tissues or cell types (e.g., developing, immune,
cancerous
and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine,
synovial
fluid and spinal fluid) or another tissue or cell sample taken from an
individual having
such a disorder, relative to the standard gene expression level, i.e., the
expression
5 level in healthy tissue or bodily fluid from an individual not having the
disorder.
The tissue distribution in fetal liver/spleen and skin tissues indicates that
the
protein products of this gene are useful for the diagnosis andlor treatment of
developmental disorders and malignant neoplasias. Likewise, expression within
fetal
tissue and other cellular sources marked by proliferating cells indicates that
this
10 protein may play a role in the regulation of cellular division, and may
show utility in
the diagnosis and treatment of cancer and other proliferative disorders.
Similarly, fetal
development also involves decisions involving cell differentiation and/or
apoptosis in
pattern formation. Thus, this protein may also be involved in apoptosis or
tissue
differentiation and could again be useful in cancer therapy.
15 Alternatively, the tissue distribution in fetal skin tissue indicates that
polynucleotides and polypeptides corresponding to this gene are useful for the
treatment, diagnosis, and/or prevention of various skin disorders including
congenital
disorders (i.e. nevi, moles, freckles, Mongolian spots, hemangiomas, port-wine
syndrome), integumentary tumors (i.e. keratoses, Bowen's disease, basal cell
20 carcinoma, squamous cell carcinoma, malignant melanoma, Paget's disease,
mycosis
fungoides, and Kaposi's sarcoma), injuries and inflammation of the skin
(i.e.wounds,
rashes, prickly heat disorder, psoriasis, dermatitis), atherosclerosis,
uticaria, eczema,
photosensitivity, autoimmune disorders (i.e. lupus erythematosus, vitiligo,
dermatomyositis, moiphea, scleroderma, pemphigoid, and pemphigus), keloids,
striae,
erythema, petechiae, purpura, and xanthelasma. Moreover, such disorders may
predispose increased susceptibility to viral and bacterial infections of the
skin (i.e.
cold sores, warts, chickenpox, molluscum contagiosum, herpes zoster, boils,
cellulitis,
erysipelas, impetigo, tinea, althletes foot, and ringworm). Protein, as well
as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
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21
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:18 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence is
cumbersome. Accordingly, preferably excluded from the present invention are
one or
more polynucleotides comprising a nucleotide sequence described by the general
formula of a-b, where a is any integer between 1 to 1116 of SEQ ID N0:18, b is
an
integer of 15 to 1130, where both a and b correspond to the positions of
nucleotide
residues shown in SEQ ID N0:18, and where b is greater than or equal to a +
14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 9
The translation product of this gene shares sequence homology with the
bacterial gufA gene, as well as a C. elegans protein of unknown function.
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: MIPGSDSQTALNFGSTLMKKKSDPEGPALLFPESELSIRI
GRAGLLSDKSENGEAYQRKKAAATGLPEGPAVPVPSRGNLAQPGGSSWRRI
ALLILAITIHNVPEGLAVGVGFGAIEKTASATFESARNLAIGIGIQNFPEGLAVS
LPLRGAGFSTWRAFWYGQLSGMVEPLAGVFGAFAVVLAEPILPYALAFAAG
AMVYVVMDDIIPEAQISGNGKLASWASILGFVVMMSLDVGLG (SEQ ID
N0:217), MIPGSDSQTALNFGSTLMKKKSDPEGPALLFPESELSIRIGRA (SEQ
ID N0:218), GLLSDKSENGEAYQRKKAAATGLPEGPAVPVPSRGNLAQPG
( S E Q I D N O : 2 1 9 ) ,
GSSWRRIALLILAITIHNVPEGLAVGVGFGAIEKTASATFESAR (SEQ ID
N0:220), NLAIGIGIQNFPEGLAVSLPLRGAGFSTWRAFWYGQLS GMVEP
(SEQ ID N0:221), LAGVFGAFAVVLAEPILPYALAFAAGAMVYVVM
DDIIPEAQIS (SEQ ID N0:222), and/or GNGKLASWASILGFVVMMSLDVGLG
(SEQ ID N0:223). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
This gene is expressed primarily in cells of the immune system, particularly
macrophage.
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22
Therefore, polynucleotides and polypeptides of the invention are useful as
reagents for differential identification of the tissues) or cell types)
present in a
biological sample and for diagnosis of diseases and conditions which include,
but are
not limited to, disorders of the immune system, such as AIDS, as well as
inflammatory disorders. Similarly, polypeptides and antibodies directed to
these
polypeptides are useful in providing immunological probes for differential
identification of the tissues) or cell type(s). For a number of disorders of
the above
tissues or cells, particularly of the immune system, expression of this gene
at
significantly higher or lower levels may be routinely detected in certain
tissues or cell
types (e.g., immune, cancerous and wounded tissues) or bodily fluids (e.g.,
lymph,
serum, plasma, urine, synovial fluid and spinal fluid) or another tissue or
cell sample
taken from an individual having such a disorder, relative to the standard gene
expression level, i.e., the expression level in healthy tissue or bodily fluid
from an
individual not having the disorder.
The tissue distribution indicates that polynucleotides and polypeptides
corresponding to this gene are useful for the diagnosis and treatment of a
variety of
immune system disorders. Expression of this gene product in immune cells such
as
macrophage indicates a role in the regulation of the proliferation; survival;
differentiation; and/or activation of potentially all hematopoietic cell
lineages,
including blood stem cells. This gene product may be involved in the
regulation of
cytokine production, antigen presentation, or other processes that may also
suggest a
usefulness in the treatment of cancer (e.g. by boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
deficiency diseases such as AIDS, leukemia, rheumatoid arthritis, inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
commercial utility in the expansion of stem cells and committed progenitors of
various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Expression of this gene product in macrophage also strongly indicates a
role
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23
for this protein in immune function and immune surveillance. Protein, as well
as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:19 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence is
cumbersome. Accordingly, preferably excluded from the present invention are
one or
more polynucleotides comprising a nucleotide sequence described by the general
formula of a-b, where a is any integer between 1 to 869 of SEQ ID N0:19, b is
an
integer of 15 to 883, where both a and b correspond to the positions of
nucleotide
residues shown in SEQ ID N0:19, and where b is greater than or equal to a +
14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 10
This gene is expressed primarily in the spleen metastic melanoma tissue as
well as in embryonic tissues.
Therefore, polynucleotides and polypeptides of the invention are useful as
reagents for differential identification of the tissues) or cell types)
present in a
biological sample and for diagnosis of diseases and conditions which include,
but are
not limited to, disorders affecting the spleen or immune system, developmental
disorders, and cancers. Similarly, polypeptides and antibodies directed to
these
polypeptides are useful in providing immunological probes for differential
identification of the tissues) or cell type(s). For a number of disorders of
the above
tissues or cells, particularly of the immune system, expression of this gene
at
significantly higher or lower levels may be routinely detected in certain
tissues or cell
types (e.g., spleen, developing, cancerous and wounded tissues) or bodily
fluids (e.g.,
lymph, serum, plasma, urine, synovial fluid and spinal fluid) or another
tissue or cell
sample taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue or bodily fluid
from an
individual not having the disorder.
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24
Preferred epitopes include those comprising a sequence shown in SEQ ID NO:
1 I7 as residues: Asn-37 to Lys-44, Ser-73 to Glu-78, Ala-103 to Ser-111.
The tissue distribution in spleen metastic melanoma and embryonic tissues
indicates that the protein products of this gene are useful for the diagnosis
and/or
treatment of disorders affecting the spleen, including cancers of the spleen,
as well as
cancers of other tissues where expression has been observed. Furthermore,
expression
within embryonic tissue and other cellular sources marked by proliferating
cells
indicates that this protein may play a role in the regulation of cellular
division, and
may show utility in the diagnosis and treatment of cancer and other
proliferative
disorders. Similarly, embryonic development also involves decisions involving
cell
differentiation and/or apoptosis in pattern formation. Thus, this protein may
also be
involved in apoptosis or tissue differentiation and could again be useful in
cancer
therapy. Protein, as well as, antibodies directed against the protein may show
utility as
a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:20 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence is
cumbersome. Accordingly, preferably excluded from the present invention are
one or
more polynucleotides comprising a nucleotide sequence described by the general
formula of a-b, where a is any integer between 1 to 975 of SEQ ID N0:20, b is
an
integer of 15 to 989, where both a and b correspond to the positions of
nucleotide
residues shown in SEQ ID N0:20, and where b is greater than or equal to a +
14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 11
It has been discovered that this gene is expressed primarily in cells of the
immune system, including monocytes and neutrophils.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell type{s) present in a biological sample
and for
diagnosis of the following diseases and conditions: disorders affecting the
immune
CA 02323761 2000-09-18
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system, such as AIDS. Similarly, polypeptides and antibodies directed to those
polypeptides are useful to provide immunological probes for differential
identification
of the tissues) or cell type(s). For a number of disorders of the above
tissues or cells,
particularly of the immune system, expression of this gene at significantly
higher or
5 lower levels may be detected in certain tissues or cell types (e.g., immune,
cancerous
and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine,
synovial
fluid or spinal fluid) taken from an individual having such a disorder,
relative to the
standard gene expression level, i.e., the expression level in healthy tissue
from an
individual not having the disorder.
10 Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
118 as residues: Ser-12 to Asp-20, Gly-22 to Gly-32, Ala-49 to Thr-57.
The tissue distribution in monocytes and neutrophils indicates that the
protein
products of this clone are useful for the diagnosis and/or treatment of immune
system
disorders, including AIDS. Furthermore, expression of this gene product in
15 monocytes and neutrophils suggests a role in the regulation of the
proliferation;
survival; differentiation; and/or activation of potentially all hematopoietic
cell
lineages, including blood stem cells. This gene product may be involved in the
regulation of cytokine production, antigen presentation, or other processes
that may
also suggest a usefulness in the treatment of cancer (e.g. by boosting immune
20 responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
25 deficiency diseases such as AIDS, leukemia, rheumatoid arthritis,
inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
commercial utility in the expansion of stem cells and committed progenitors of
various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Expression of this gene product in monocytes and neutrophils also
strongly
suggests a role for this protein in immune function and immune surveillance.
Protein,
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26
as well as, antibodies directed against the protein may show utility as a
tumor marker
and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:21 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 481 of SEQ ID
N0:21, b
is an integer of 15 to 495, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:21, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 12
It has been discovered that this gene is expressed primarily in cells of the
immune system, including monocytes.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: disorders affecting the
immune
system. Similarly, polypeptides and antibodies directed to those polypeptides
are
useful to provide immunological probes for differential identification of the
tissues)
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
the immune system, expression of this gene at significantly higher or lower
levels
may be detected in certain tissues or cell types (e.g., immune, cancerous and
wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
119 as residues: Glu-35 to Trp-42.
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27
The tissue distribution suggests that the protein product of this clone is
useful
for the diagnosis and treatment of a variety of immune system disorders.
Expression
of this gene product in monocytes suggests a role in the regulation of the
proliferation; survival; differentiation; and/or activation of potentially all
hematopoietic cell lineages, including blood stem cells. This gene product may
be
involved in the regulation of cytokine production, antigen presentation, or
other
processes that may also suggest a usefulness in the treatment of cancer (e.g.
by
boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
deficiency diseases such as AIDS, leukemia, rheumatoid arthritis, inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
commercial utility in the expansion of stem cells and committed progenitors of
various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Expression of this gene product in monocytes also strongly suggests a
role for
this protein in immune function and immune surveillance. Protein, as well as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many poiynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:22 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 2303 of SEQ ID
N0:22, b
is an integer of 15 to 2317, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:22, and where b is greater than or
equal to a
+ 14.
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28
FEATURES OF PROTEIN ENCODED BY GENE NO: 13
It has been discovered that this gene is expressed primarily in cells of the
immune system, including monocytes.
S Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: disorders of the immune
system.
Similarly, polypeptides and antibodies directed to those polypeptides are
useful to
provide immunological probes for differential identification of the tissues)
or cell
type(s). For a number of disorders of the above tissues or cells, particularly
of the
immune system, expression of this gene at significantly higher or lower levels
may be
detected in certain tissues or cell types (e.g., immune, cancerous and wounded
tissues)
or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal
fluid)
taken from an individual having such a disorder, relative to the standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
The tissue distribution in monocytes indicates that the protein products of
this
clone are useful for the diagnosis and/or treatment of disorders of the immune
system.
Expression of this gene product in monocytes suggests a role in the regulation
of the
proliferation; survival; differentiation; and/or activation of potentially all
hematopoietic cell lineages, including blood stem cells. This gene product may
be
involved in the regulation of cytokine production, antigen presentation, or
other
processes that may also suggest a usefulness in the treatment of cancer (e.g.
by
boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
deficiency diseases such as AIDS, leukemia, rheumatoid arthritis, inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
commercial utility in the expansion of stem cells and committed progenitors of
CA 02323761 2000-09-18
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29
various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Expression of this gene product in monocytes also strongly suggests a
role for
this protein in immune function and immune surveillance. Protein, as well as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:23 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1712 of SEQ ID
N0:23, b
is an integer of 15 to 1726, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:23, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 14
The translation product of this gene shares sequence homology with a gene
from C. elegans of unknown function.
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: TRPITYVLLAG (SEQ ID N0:224). Polynucleotides encoding
these polypeptides are also encompassed by the invention. The gene encoding
the
disclosed cDNA is thought to reside on chromosome 11. Accordingly,
polynucleotides related to this invention are useful as a marker in linkage
analysis for
chromosome 11.
It has been discovered that this gene is expressed primarily in fetal lung,
liver,
spleen and heart tissues, as well as adult liver, bladder, endometrial stromal
cells,
synovium, colon cancer, smooth muscle, keratinocytes, and the bone marrow
derived
cell line RS4;11.
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Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: disorders of the musculo-
skeletal
system, and cancers of the immune system. Similarly, polypeptides and
antibodies
5 directed to those polypeptides are useful to provide immunological probes
for
differential identification of the tissue{s) or cell type(s). For a number of
disorders of
the above tissues or cells, particularly of the musculo-skeletal and immune
systems,
expression of this gene at significantly higher or lower levels may be
detected in
certain tissues or cell types (e.g., immune, musculo-skeletal, cancerous and
wounded
10 tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial
fluid or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
The tissue distribution in tissues of the immune system indicates that the
15 protein products of this clone are useful for treating proliferative
disorders of immune
system precursor cells. Alternatively, the tissue distribution in smooth
muscle and
heart tissue indicates that the protein product of this gene is useful for the
diagnosis
and treatment of conditions and pathologies of the cardiovascular system, such
as
heart disease, restenosis, atherosclerosis, stoke, angina, thrombosis, and
wound
20 healing. Protein, as well as, antibodies directed against the protein may
show utility as
a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:24 and may have been publicly available prior to
conception of
25 the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to S 15 of SEQ ID
N0:24, b
30 is an integer of 15 to 529, where both a and b correspond to the positions
of
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31
nucleotide residues shown in SEQ ID N0:24, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 15
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: GTSLTAPLLEFLLALYFLFADAMQLNDKWQGLCWP
(SEQ ID N0:225). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
It has been discovered that this gene is expressed primarily in T-cells, fetal
spleen and infant brain tissues, and to a lesser extent in many other tissues
including
melanocytes, lung cancer, macrophages, dendritic cells, stromal cells, adrenal
gland
and others.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: inflammation and
autoimmunity,
developing tissues. Similarly, polypeptides and antibodies directed to those
polypeptides are useful to provide immunological probes for differential
identification
of the tissues) or cell type(s). For a number of disorders of the above
tissues or cells,
particularly of the immune and developing system, expression of this gene at
significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., immune, developing, cancerous and wounded tissues) or bodily fluids
(e.g.,
lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from an
individual
having such a disorder, relative to the standard gene expression level, i.e.,
the
expression level in healthy tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
122 as residues: Ser-46 to Gly-51.
The tissue distribution in T-cells and other immune cells indicates that the
protein products of this clone are useful for treating diseases involving the
activation
of T-cells, including inflammation and autoimmune diseases. Alternatively, the
tissue
distribution in a wide range of fetal tissues suggests that this protein may
play a role
in the regulation of cellular division, and may show utility in the diagnosis
and
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32
treatment of cancer and other proliferative disorders. Similarly, fetal
development
also involves decisions involving cell differentiation and/or apoptosis in
pattern
formation. Thus, this protein may also be involved in apoptosis or tissue
differentiation and could again be useful in cancer therapy. Protein, as well
as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:25 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1741 of SEQ ID
N0:25, b
is an integer of 15 to 1755, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:25, and where b is greater than or
equal to a
+ 14.
' FEATURES OF PROTEIN ENCODED BY GENE NO: 16
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: LANFZCSDCAQTVLFVLZFZILVFTYEIPF (SEQ ID
N0:226). Polynucleotides encoding these polypeptides are also encompassed by
the
invention. The gene encoding the disclosed cDNA is thought to reside on
chromosome 13. Accordingly, polynucleotides related to this invention are
useful as a
marker in linkage analysis for chromosome 13. Recently another group published
this
gene, referring to it as CLNS (See Genbank Accession No.: 3342386).
It has been discovered that this gene is expressed primarily in placental
tissue,
12 week embryos, and tumors including testes, tongue and pharynx, and to a
lesser
extent in adipose tissue, tonsils, melanocytes, fetal spleen, macrophages, T-
cells,
amniotic cells, and brain tissue.
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33
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: tumors, particularly of
the tongue
and throat, and neurodegenerative disorders. Similarly, polypeptides and
antibodies
directed to those polypeptides are useful to provide immunological probes for
differential identification of the tissues) or cell type(s). For a number of
disorders of
the above tissues or cells, particularly of the neural and digestive systems,
expression
of this gene at significantly higher or lower levels may be detected in
certain tissues
or cell types (e.g., tongue, throat, brain, cancerous and wounded tissues) or
bodily
fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid)
taken from an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
123 as residues: Pro-44 to Ala-60, Val-187 to Thr-193, Lys-203 to Ala-210, Thr-
212
to Cys-219.
The tissue distribution in tongue and pharynx carcinoma tissue indicates that
the protein products of this clone are useful for diagnosing and/or treating
oral
cancers, including tumors of the throat and tongue. Furthermore, the tissue
distribution in brain tissue suggests that the protein product of this clone
is useful for
the detection/treatment of neurodegenerative disease states and behavioural
disorders
such as neuronal ceroid lipofuscinoses (NCLs), Alzheimers Disease, Parkinsons
Disease, Huntingtons Disease, Tourette Syndrome, schizophrenia, mania,
dementia,
paranoia, obsessive compulsive disorder, panic disorder, learning
disabilities, ALS,
psychoses, autism, and altered behaviors, including disorders in feeding,
sleep
patterns, balance, and perception. In addition, the gene or gene product may
also play
a role in the treatment and/or detection of developmental disorders associated
with the
developing embryo, or sexually-linked disorders. Protein, as well as,
antibodies
directed against the protein may show utility as a tumor marker and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
CA 02323761 2000-09-18
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34
related to SEQ ID N0:26 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specificaily
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1737 of SEQ ID
N0:26, b
is an integer of 15 to 1751, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:26, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 17
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences:
QAWHEVGGGVRRCWFVLGERRAGSLLSASYGTFAMPG
MVLFGRRWAIASDDLVFPGFFELVVRVLWWIGILTLYL (SEQ ID N0:227),
and/or PGMVLFGRRWAIASDDLVFPGFFELVVRVLWWIGILTLYLMHRGKLD
CAGGALLSSYLIVLMILLAVVICTVSAIMCVSMRGTICNPGPRKSMSKLLYIRL
ALFFPEMVWASLGAAWVADGVQCD (SEQ ID N0:228). Polynucleotides
encoding these polypeptides are also encompassed by the invention.
It has been discovered that this gene is expressed in activated neutrophils,
infant brain tissue and primary dendritic cells.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: disorders of the immune
system,
and neurodegenerative disorders. Similarly, polypeptides and antibodies
directed to
those polypeptides are useful to provide immunological probes for differential
identification of the tissues) or cell type(s). For a number of disorders of
the above
tissues or cells, particularly of the immune and neural systems, expression of
this
gene at significantly higher or lower levels may be detected in certain
tissues or cell
types (e.g., immune, brain, cancerous and wounded tissues) or bodily fluids
(e.g.,
lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from an
individual
CA 02323761 2000-09-18
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having such a disorder, relative to the standard gene expression level, i.e.,
the
expression level in healthy tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
124 as residues: Pro-47 to Met-53, Ser-130 to Ser-138.
5 The tissue distribution in neutrophils and primary dendritic cells indicates
that
the protein products of this clone are useful for diagnosing and/or treating
immune
system disorders. Expression of this gene product in neutrophils and primary
dendritic
cells suggests a role in the regulation of the proliferation; survival;
differentiation;
and/or activation of potentially all hematopoietic cell lineages, including
blood stem
10 cells. This gene product may be involved in the regulation of cytokine
production,
antigen presentation, or other processes that may also suggest a usefulness in
the
treatment of cancer (e.g. by boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
15 and/or immunotherapy targets for the above listed tissues. Therefore it may
be also
used as an agent for immunological disorders including arthritis, asthma,
immune
deficiency diseases such as AIDS, leukemia, rheumatoid arthritis, inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
commercial utility in the expansion of stem cells and committed progenitors of
20 various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Expression of this gene product in neutrophils and primary dendritic
cells also
strongly suggests a role for this protein in immune function and immune
surveillance.
Alternatively, the tissue distribution in brain tissue suggests that the
protein
product of this clone is useful for the detection/treatment of
neurodegenerative
25 disease states and behavioural disorders such as Alzheimers Disease,
Parkinsons
Disease, Huntingtons Disease, Tourette Syndrome, schizophrenia, mania,
dementia,
paranoia, obsessive compulsive disorder, panic disorder, learning
disabilities, ALS,
psychoses, autism, and altered behaviors, including disorders in feeding,
sleep
patterns, balance, and perception. In addition, the gene or gene product may
also play
30 a role in the treatment and/or detection of developmental disorders
associated with the
developing embryo, or sexually-linked disorders. Protein, as well as,
antibodies
CA 02323761 2000-09-18
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36
directed against the protein may show utility as a tumor marker and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:27 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1198 of SEQ ID
N0:27, b
is an integer of 15 to 1212, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:27, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 18
It has been discovered that this gene is expressed primarily in neutrophils,
and
to a lesser extent in other tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune and inflammatory
disorders. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues)
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
the immune system, expression of this gene at significantly higher or lower
levels
may be detected in certain tissues or cell types (e.g., immune, cancerous and
wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
125 as residues: Gln-17 to Ser-24.
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37
The tissue distribution in neutrophils indicates that the protein products of
this
clone are useful for the diagnosis and/or treatment of immune and inflammatory
disorders. Expression of this gene product in neutrophils suggests a role in
the
regulation of the proliferation; survival; differentiation; and/or activation
of
potentially all hematopoietic cell lineages, including blood stem cells. This
gene
product may be involved in the regulation of cytokine production, antigen
presentation, or other processes that may also suggest a usefulness in the
treatment of
cancer (e.g. by boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
deficiency diseases such as AIDS, leukemia, rheumatoid arthritis, inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
commercial utility in the expansion of stem cells and committed progenitors of
various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Expression of this gene product in neutrophils also strongly suggests a
role for
this protein in immune function and immune surveillance. Protein, as well as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:28 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1098 of SEQ ID
N0:28, b
is an integer of 15 to 1112, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:28, and where b is greater than or
equal to a
+ 14.
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38
FEATURES OF PROTEIN ENCODED BY GENE NO: 19
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: HERNCFPMWLNHSAFPPV (SEQ ID N0:229).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
It has been discovered that this gene is expressed primarily in neutrophils,
and
to a lesser extent in other tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune and inflammatory
disorders. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues)
or cell type(s). For a number of disorders of the above tissues 4r cells,
particularly of
the immune system, expression of this gene at significantly higher or lower
levels
may be detected in certain tissues or cell types (e.g., immune, cancerous and
wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
The tissue distribution in neutrophils indicates that the protein products of
this
clone are useful for the diagnosis and/or treatment of immune and inflammatory
disorders. Expression of this gene product in neutrophils suggests a role in
the
regulation of the proliferation; survival; differentiation; and/or activation
of
potentially all hematopoietic cell lineages, including blood stem cells. This
gene
product may be involved in the regulation of cytokine production, antigen
presentation, or other processes that may also suggest a usefulness in the
treatment of
cancer (e.g. by boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
CA 02323761 2000-09-18
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39
deficiency diseases such as AIDS, leukemia, rheumatoid arthritis, inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
commercial utility in the expansion of stem cells and committed progenitors of
various blood lineages, and in the differentiation and/or proliferation of
various cell
S types. Expression of this gene product in neutrophils also strongly suggests
a role for
this protein in immune function and immune surveillance. Protein, as well as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:29 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 734 of SEQ ID
N0:29, b
is an integer of 15 to 748, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:29, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 20
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: GWTRENDHRALSKAGIGSAEIQPSNLRVGSAKDLGKPW
AGKLLLLSSCLLFFSLGVLYRGQMLAPPLQEDWKGGVKDSDLIDDSSASPIPP
SYLEYKAALYPFSEHKSVRNATDSLTFFLVTDHFLDNQDSQ (SEQ ID
N0:230), GWTRENDHRALSKAGIGSAEIQPSNLRVGSAKDLGKPWAGKLLLL
(SEQ iD N0:231),
SSCLLFFSLGVLYRGQMLAPPLQEDWKGGVKDSDLIDDSSASPIPP (SEQ ID
N0:232), and/or SYLEYKAALYPFSEHKSVRNATDSLTFFLVTDHFL DNQDSQ
(SEQ ID N0:233). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
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It has been discovered that this gene is expressed primarily in ovarian cancer
tissue, and to a lesser extent in other tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
S diagnosis of the following diseases and conditions: ovarian cancer.
Similarly,
polypeptides and antibodies directed to those polypeptides are useful to
provide
immunological probes for differential identification of the tissues) or cell
type(s). For
a number of disorders of the above tissues or cells, particularly of the
ovaries,
expression of this gene at significantly higher or lower levels may be
detected in
10 certain tissues or cell types (e.g., reproductive, cancerous and wounded
tissues) or
bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal
fluid) taken
from an individual having such a disorder, relative to the standard gene
expression
level, i.e., the expression level in healthy tissue from an individual not
having the
disorder.
15 Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
127 as residues: Thr-20 to Gly-27, Gly-32 to Phe-41.
The tissue distribution in ovarian cancer tissue indicates that the protein
products of this clone are useful for the diagnosis and/or treatment of
ovarian cancer,
as well as cancers of other tissues where expression has been observed.
Protein, as
20 well as, antibodies directed against the protein may show utility as a
tumor marker
and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:30 and may have been publicly available prior to
conception of
25 the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 764 of SEQ ID
N0:30, b
30 is an integer of 15 to 778, where both a and b correspond to the positions
of
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41
nucleotide residues shown in SEQ ID NO:30, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 2I
When tested against U937 Myeloid cell lines, supernatants removed from cells
containing this gene activated the GAS assay. Thus, it is likely that this
gene activates
myeloid cells, and to a lesser extent other cells, through the Jak-STAT signal
transduction pathway. The gamma activating sequence (GAS) is a promoter
element
found upstream of many genes which are involved in the Jak-STAT pathway. The
Jak-STAT pathway is a large, signal transduction pathway involved in the
differentiation and proliferation of cells. Therefore, activation of the Jak-
STAT
pathway, reflected by the binding of the GAS element, can be used to indicate
proteins involved in the proliferation and differentiation of cells.
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: LKFHQESLSGD (SEQ ID N0:234). Polynucleotides
encoding these polypeptides are also encompassed by the invention.
It has been discovered that this gene is expressed primarily in fast-growing
tissues such as immune/hematopoietic tissues, early developmental stage human
tissues, and tumor tissues, and to a lesser extent in some other tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissue{s) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: growth disorders, immune
and
inflammatory diseases, and tumorigenesis. Similarly, polypeptides and
antibodies
directed to those polypeptides are useful to provide immunological probes for
differential identification of the tissues) or cell type(s). For a number of
disorders of
the above tissues or cells, particularly of the immune/hematopoietic system,
expression of this gene at significantly higher or lower levels may be
detected in
certain tissues or cell types (e.g., immune, cancerous and wounded tissues) or
bodily
fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid)
taken from an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
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42
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
128 as residues: Glu-60 to Arg-65.
The tissue distribution in immune tissues, in conjunction with the biological
activity data, indicates that the protein products of this clone are useful
for the
diagnosis and/or treatment of growth disorders, immune and inflammatory
diseases,
and tumorigenesis. Furthermore, expression within embryonic tissue and other
cellular sources marked by proliferating cells suggests that this protein may
play a
role in the regulation of cellular division, and may show utility in the
diagnosis and
treatment of cancer and other proliferative disorders. Similarly, embryonic
development also involves decisions involving cell differentiation and/or
apoptosis in
pattern formation. Thus, this protein may also be involved in apoptosis or
tissue
differentiation and could again be useful in cancer therapy. Protein, as well
as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:31 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1310 of SEQ ID
N0:31, b
is an integer of 15 to 1324, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:31, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 22
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: EAKSRPVTQAGVQWHDLGSLQPLPP (SEQ ID N0:235).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
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43
It has been discovered that this gene is expressed primarily in ovarian cancer
tissue, and to a lesser extent in fetal liver/spleen and retinal tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: ovarian cancer, immune
disorders,
and retinal disorders. Similarly, polypeptides and antibodies directed to
those
polypeptides are useful to provide immunological probes for differential
identification
of the tissues) or cell type(s). For a number of disorders of the above
tissues or cells,
particularly of the ovaries, immune and ocular systems, expression of this
gene at
significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., reproductive, ovaries, retina, immune, cancerous and wounded tissues)
or bodily
fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid)
taken from an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
The tissue distribution in ovarian cancer tissue indicates that the protein
products of this clone are useful for the diagnosis and/or treatment of
ovarian cancer,
as well as cancers of other tissues where expression has been observed. The
tissue
distribution also suggests that the protein product of this clone is useful
for the
diagnosis and treatment of a variety of immune system disorders. Expression of
this
gene product in fetal liver/spleen suggests a role in the regulation of the
proliferation;
survival; differentiation; and/or activation of potentially all hematopoietic
cell
lineages, including blood stem cells. This gene product may be involved in the
regulation of cytokine production, antigen presentation, or other processes
that may
also suggest a usefulness in the treatment of cancer (e.g. by boosting immune
responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
deficiency diseases such as AIDS, leukemia, rheumatoid arthritis, inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
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44
commercial utility in the expansion of stem cells and committed progenitors of
various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Alternatively, the tissue distribution in retinal tissue suggests that
the protein
product of this clone is useful for the treatment and/or detection of eye
disorders
including blindness, color blindness, impaired vision, short and long
sightedness,
retinitis pigmentosa, retinitis proliferans, and retinoblastoma,
retinochoroiditis,
retinopathy and retinoschisis. Protein, as well as, antibodies directed
against the
protein may show utility as a tumor marker andlor immunotherapy targets for
the
above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:32 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 725 of SEQ ID
N0:32, b
is an integer of 15 to 739, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:32, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 23
The translation product of this gene shares sequence homology with a C.
elegans protein of unknown function (See Genbank Accession No.:
gnIIPIDIe 1348017). When tested against fibroblast cell lines, supernatants
removed
from cells containing this gene activated the EGR 1 assay. Thus, it is likely
that this
gene activates fibroblast cells through a signal transduction pathway. Early
growth
response 1 (EGR1) is a promoter associated with certain genes that induces
various
tissues and cell types upon activation, leading the cells to undergo
differentiation and
proliferation. The gene encoding the disclosed cDNA is thought to reside on
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chromosome 17. Accordingly, polynucleotides related to this invention are
useful as a
marker in linkage analysis for chromosome 17.
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: EAKSRPVTQAGVQWHDLGSLQPLPP (SEQ ID N0:236),
5 and/or ALVLVCRQRYCRPRDLLQRYDSKPIVDLIGAMETQSEPSELELDDVVIT
NPHIEAILENEDWIEDASGLMSHCIAILKICHTLTEKLVAMTMGSGAKMKTSA
SVSDIIVVAKRISPRVDDVVKSMYPPLDPKLLDAR (SEQ ID N0:237).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
It has been discovered that this gene is expressed primarily in fast growing
10 tissues such as early development stage human tissues, immune/hematopoietic
tissues, melanocytes, and tumor tissues, and to a lesser extent in some other
tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: growth disorders, immune
and
15 inflammatory disoders, skin and connective tissue disorders, and
tumorigenesis.
Similarly, polypeptides and antibodies directed to those polypeptides are
useful to
provide immunological probes for differential identification of the tissues)
or cell
type(s). For a number of disorders of the above tissues or cells, particularly
of the fast
growing tissues such as early development stage human tissues,
20 immune/hematopoietic tissues, skin and connective tissue, and tumor
tissues,
expression of this gene at significantly higher or lower levels may be
detected in
certain tissues or cell types (e.g., musculo-skeletal, skin, immune,
developing,
cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma,
urine,
synovial fluid or spinal fluid) taken from an individual having such a
disorder,
25 relative to the standard gene expression level, i.e., the expression level
in healthy
tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
130 as residues: Pro-34 to Ser-43, Glu-54 to Ser-60.
The tissue distribution suggests that the protein product of this clone is
useful
30 for the diagnosis and/or treatment of growth disorders, immune and
inflammatory
disorders, and tumorigenesis. Alternatively, the tissue distribution in
melanocytes, in
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46
conjunction with the observed biological activity data, suggests that the
protein
product of this clone is useful for the treatment, diagnosis, and/or
prevention of
various skin disorders including congenital disorders (i.e. nevi, moles,
freckles,
Mongolian spots, hemangiomas, port-wine syndrome), integumentary tumors (i.e.
keratoses, Bowen's disease, basal cell carcinoma, squamous cell carcinoma,
malignant melanoma, Paget's disease, mycosis fungoides, and Kaposi's sarcoma},
injuries and inflammation of the skin (i.e.wounds, rashes, prickly heat
disorder,
psoriasis, dermatitis), atherosclerosis, uticaria, eczema, photosensitivity,
autoimmune
disorders (i.e. lupus erythematosus, vitiligo, dermatomyositis, morphea,
scleroderma,
pemphigoid, and pemphigus), keloids, striae, erythema, petechiae, purpura, and
xanthelasma.
Moreover, such disorders may predispose increased susceptibility to viral and
bacterial infections of the skin (i.e. cold sores, warts, chickenpox,
molluscum
contagiosum, herpes zoster, boils, cellulitis, erysipelas, impetigo, tinea,
althletes foot,
1 S and ringworm). Protein, as well as, antibodies directed against the
protein may show
utility as a tumor marker and immunotherapy targets for the above listed
tumors and
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:33 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1448 of SEQ ID
N0:33, b
is an integer of 15 to 1462, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:33, and where b is greater than or
equal to a
+ 14.
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47
FEATURES OF PROTEIN ENCODED BY GENE NO: 24
When tested against U937 Myeloid cell lines, supernatants removed from cells
containing this gene activated the GAS assay. Thus, it is likely that this
gene activates
myeloid cells, and to a lesser extent other cells, through the Jak-STAT signal
transduction pathway. The gamma activating sequence (GAS) is a promoter
element
found upstream of many genes which are involved in the Jak-STAT pathway. The
Jak-STAT pathway is a large, signal transduction pathway involved in the
differentiation and proliferation of cells. Therefore, activation of the Jak-
STAT
pathway, reflected by the binding of the GAS element, can be used to indicate
proteins involved in the proliferation and differentiation of cells
In specific embodiments, polypeptides of the invention comprise the following
a m i n o a c i d s a q a a n c a s
DVESRGPSARCLPVVPGSLLPGLEPATKLMPGGLAPGHG
APVRELLLPLLSQPTLGSLWDSLRHCSLLCNPLSCVPALEAPPSLVSLGCSGGC
PRLSLAGSASPFPFLTALLSLLNTLAQIHKGLCGQLAAILAAPGLQNYFLQCVA
PGAAPHLTPFSAWALRHEYHLQYLALALAQKAAALQPLPATHAALYHGMAL
ALLSRLLPGSEYLTHELLLSCVFRLEFLPERTSGGPEAADFSDQLSLGSSRVPR
CGQGTLLAQACQDLPSIRNCYLTHCSPARASLLASQALHRGELQRVPTLLLP
MPTEPLLPTDWPFLH (SEQ ID N0:238),
DVESRGPSARCLPVVPGSLLPGLEPATKLM PGGLAPGHGAPVRE (SEQ ID
N0:239), LLLPLLSQPTLGSLWDSLRHCSLLCNP LSCVPALEAPPSLVSLGC
(SEQ ID N0:240), SGGCPRLSLAGSASPFPFLTALL
SLLNTLAQIHKGLCGQLAAILA (SEQ ID N0:241), APGLQNYFLQCVAPGAAP
HLTPFSAWALRHEYHLQYLALALAQK (SEQ ID N0:242), AAALQPLPATHAA
LYHGMALALLSRLLPGSEYLTHELLLSCVFR (SEQ ID N0:243), LEFLPERTSG
GPEAADFSDQLSLGSSRVPRCGQGTLLAQACQDL (SEQ ID N0:244), and/or
PSIRNCYLTHCSPARASLLASQALHRGELQRVPTLLLPMPTEPLLPTDWPFLH
(SEQ ID N0:245). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
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48
It has been discovered that this gene is expressed primarily in hematopoietic
tissues and fetal heart tissue, and to a lesser extent in brain and gall
bladder tissues,
and some other tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune and inflammatory
disorders, cardiovascular disorders, and growth disorders. Similarly,
polypeptides and
antibodies directed to those poIypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the hematopoietic and vascular
systems,
expression of this gene at significantly higher or lower levels may be
detected in
certain tissues or cell types (e.g., vascular, immune, cancerous and wounded
tissues)
or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal
fluid)
taken from an individual having such a disorder, relative to the standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
131 as residues: Tyr-88 to Trp-102, Asp-105 to Ser-110.
The tissue distribution in hematopoietic tissues, in conjunction with the
observed biological activity data, indicates that the protein products of this
clone are
useful for the diagnosis and/or treatment of immune and inflammatory disorders
and
growth disorders. Alternatively, the tissue distribution in fetal heart tissue
indicates
that the protein product of this gene is useful for the diagnosis and
treatment of
conditions and pathologies of the cardiovascular system, such as heart
disease,
restenosis, atherosclerosis, stoke, angina, thrombosis, and wound healing.
Protein, as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:34 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
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49
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 2801 of SEQ ID
N0:34, b
is an integer of 15 to 2815, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:34, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 25
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: VGSVLGAFLTFPGLRLAQTHRDALT (SEQ ID N0:246).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
The gene encoding the disclosed cDNA is thought to reside on chromosome 19.
Accordingly, polynucleotides related to this invention are useful as a marker
in
linkage analysis for chromosome 19.
It has been discovered that this gene is expressed primarily in human
pituitary
tissue.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: hyperpituitarism and
hypopituitarism. Similarly, polypeptides and antibodies directed to those
polypeptides
are useful to provide immunological probes for differential identification of
the
tissues) or cell type(s). For a number of disorders of the above tissues or
cells,
particularly of the endocrine system, expression of this gene at significantly
higher or
lower levels may be detected in certain tissues or cell types (e.g.,
endocrine,
cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma,
urine,
synovial fluid or spinal fluid) taken from an individual having such a
disorder,
relative to the standard gene expression level, i.e., the expression level in
healthy
tissue from an individual not having the disorder. This gene is found on the
short arm
of chromosome 19 and, therefore, is useful as a chromosome marker.
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Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
132 as residues: Met-1 to Pro-6, Gln-89 to Ala-94, Pro-161 to Cys-173.
The tissue distribution in pituitary tissue indicates that the protein
products of
this clone are useful for the diagnosis and/or treatment of pituitary
disorders. More
5 generally, the tissue distribution in pituitary tissue suggests that the
protein product of
this clone is useful for the detection, treatment, and/or prevention of
various
endocrine disorders and cancers, particularly Addison's disease, Cushing's
Syndrome, and disorders and/or cancers of the pancrease (e.g. diabetes
mellitus),
adrenal cortex, ovaries, pituitary (e.g., hyper-, hypopituitarism), thyroid
(e.g. hyper-,
10 hypothyroidism), parathyroid (e.g. hyper-, hypoparathyroidism) ,
hypothallamus, and
testes. Protein, as well as, antibodies directed against the protein may show
utility as a
tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
15 related to SEQ ID N0:35 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
20 general formula of a-b, where a is any integer between 1 to 1064 of SEQ ID
N0:35, b
is an integer of 15 to 1078, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:35, and where b is greater than or
equal to a
+ 14.
25 FEATURES OF PROTEIN ENCODED BY GENE NO: 26
It has been discovered that this gene is expressed highly and specifically in
placental and bone marrow cDNA libraries, and to a lesser extent in T-cells.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
30 diagnosis of the following diseases and conditions: immune, developmental
and
reproductive disorders. Similarly, polypeptides and antibodies directed to
those
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51
polypeptides are useful to provide immunological probes for differential
identification
of the tissues) or cell type(s). For a number of disorders of the above
tissues or cells,
particularly of the immune and developing systems, expression of this gene at
significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., immune, developmental, reproductive, cancerous and wounded tissues) or
bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal
fluid) taken
from an individual having such a disorder, relative to the standard gene
expression
level, i.e., the expression level in healthy tissue from an individual not
having the
disorder.
The tissue distribution in bone marrow and placental tissue indicates that the
protein products of this clone are useful for the diagnosis and/or treatment
of immune
and reproductive disorders. The tissue distribution in bone marrow suggests
that the
protein product of this clone is useful for the treatment and diagnosis of
hematopoietic related disorders such as anemia, pancytopenia, leukopenia,
thrombocytopenia or leukemia. The uses include bone marrow cell ex vivo
culture,
bone marrow transplantation, bone marrow reconstitution, radiotherapy or
chemotherapy of neoplasia. The gene product may also be involved in
lymphopoiesis,
therefore, it can be used in immune disorders such as infection, inflammation,
allergy,
immunodeficiency etc. In addition, this gene product may have commercial
utility in
the expansion of stem cells and committed progenitors of various blood
lineages, and
in the differentiation and/or proliferation of various cell types.
Alternatively, the tissue distribution in placental tissue suggests that the
protein product of this clone is useful for the diagnosis andlor treatment of
disorders
of the placenta. Specific expression within the placenta suggests that this
gene
product may play a role in the proper establishment and maintenance of
placental
function. Alternately, this gene product may be produced by the placenta and
then
transported to the embryo, where it may play a crucial role in the development
and/or
survival of the developing embryo or fetus.
Expression of this gene product in a vascular-rich tissue such as the placenta
also suggests that this gene product may be produced more generally in
endothelial
cells or within the circulation. In such instances, it may play more
generalized roles in
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52
vascular function, such as in angiogenesis. It may also be produced in the
vasculature
and have effects on other cells within the circulation, such as hematopoietic
cells. It
may serve to promote the proliferation, survival, activation, and/or
differentiation of
hematopoietic cells, as well as other cells throughout the body. Protein, as
well as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:36 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1203 of SEQ ID
N0:36, b
is an integer of 15 to 1217, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:36, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 27
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences:
LECTDTIMVHCSLKLLSPSDXSHSASQVAKTRGVHHXTQ
LIFKVFFVXMGSHSTKYXSIRPGLLP (SEQ ID N0:247). Polynucleotides
encoding these polypeptides are also encompassed by the invention.
It has been discovered that this gene is expressed primarily in human prostate
and smooth muscle tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: disorders in the prostate
gland,
vascular and connective tissues. Similarly, polypeptides and antibodies
directed to
those polypeptides are useful to provide immunological probes for differential
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53
identification of the tissues) or cell type(s). For a number of disorders of
the above
tissues or cells, particularly of the male reproductive and urinary system and
vascular
system, expression of this gene at significantly higher or lower levels may be
detected
in certain tissues or cell types (e.g., reproductive, vascular, cancerous and
wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
The tissue distribution in prostate and smooth muscle tissues indicates that
the
protein products of this clone are useful for the diagnosis and/or treatment
of prostate
gland, vascular and connective tissue disorders. The tissue distribution in
smooth
muscle tissue indicates that the protein product of this gene is useful for
the diagnosis
and treatment of conditions and pathologies of the cardiovascular system, such
as
heart disease, restenosis, atherosclerosis, stoke, angina, thrombosis, and
wound
healing. The expression in the prostate tissue may indicate the gene or its
products
can be used in the disorders of the prostate, including inflammatory
disorders, such as
chronic prostatitis, granulomatous prostatitis and malacoplakia, prostatic
hyperplasia
and prostate neoplastic disorders, including adenocarcinoma, transitional cell
carcinomas, ductal carcinomas, squamous cell carcinomas, or as hormones or
factors
with systemic or reproductive functions. Protein, as well as, antibodies
directed
against the protein may show utility as a tumor marker and/or immunotherapy
targets
for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:37 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1268 of SEQ ID
N0:37, b
is an integer of 15 to 1282, where both a and b correspond to the positions of
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nucleotide residues shown in SEQ ID N0:37, and where b is greater than or
equal to a
+ 14.
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FEATURES OF PROTEIN ENCODED BY GENE NO: 28
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: ESSFVPPAAHSSLC (SEQ ID N0:248). Polynucleotides
encoding these polypeptides are also encompassed by the invention.
5 It has been discovered that this gene is expressed primarily in human
pituitary
tissue.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: hyperpituitarism and
10 hypopituitarism. Similarly, polypeptides and antibodies directed to those
polypeptides
are useful to provide immunological probes for differential identification of
the
tissues) or cell type(s). For a number of disorders of the above tissues or
cells,
particularly of the endocrine system, expression of this gene at significantly
higher or
lower levels may be detected in certain tissues or cell types (e.g.,
endocrine,
15 cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum,
plasma, urine,
synovial fluid or spinal fluid) taken from an individual having such a
disorder,
relative to the standard gene expression level, i.e., the expression level in
healthy
tissue from an individual not having the disorder.
The tissue distribution in pituitary tissue indicates that the protein
products of
20 this clone are useful for the diagnosis and/or treatment of pituitary gland
disorders
such as hypopituitarism and hyperpituitarism. More generally, the tissue
distribution
in pituitary tissue suggests that the protein product of this clone is useful
for the
detection, treatment, and/or prevention of various endocrine disorders and
cancers,
particularly Addison's disease, Cushing's Syndrome, and disorders and/or
cancers of
25 the pancrease (e.g. diabetes mellitus), adrenal cortex, ovaries, pituitary
(e.g., hyper-,
hypopituitarism), thyroid (e.g. hyper-, hypothyroidism), parathyroid (e.g.
hyper-,
hypoparathyroidism) , hypothallamus, and testes. Protein, as well as,
antibodies
directed against the protein may show utility as a tumor marker and/or
immunotherapy targets for the above listed tissues.
30 Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
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56
related to SEQ ID N0:38 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 545 of SEQ ID
N0:38, b
is an integer of 15 to 559, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:38, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 29
In specific embodiments, polypeptides of the invention comprise the following
a m i n o a c i d
LLPGQQEATQCVEAGAGEGALTPMCPCRQEQFVDLYKEF
EPSLVNSTVYIMAMAIQMAPFAINYKVRPGPCXNIHCLPTQPHPMKPSVPHPH
RARPSWRACPRTSPWCGVWQFHSWPSLACSSAPRPTSTASLASWTSLWSSS
WSLPRSCSWTSAWRSWPTASCSSSWGPRS (SEQ ID N0:249),
LLPGQQEATQCV EAGAGEGALTPMCPCRQEQFVDLYKEFEPSLVN (SEQ ID
N0:250), STVYIMAMAIQMAPFAINYKVRPGPCXNIHCLPTQPHPMKPSVP
( S E Q I D N O . 2 5 1 ) ,
HPHRARPSWRACPRTSPWCGVWQFHSWPSLACSSAPRPTSTA (SEQ ID
N0:252), and/or SLASWTSLWSSSWSLPRSCSWTSAWRSWPTASCSSSWG PRS
(SEQ ID N0:253). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
It has been discovered that this gene is expressed primarily in human
pituitary
and breast tissues, and to a lesser extent in endometrial and ovarian cancer
tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: hyperpituitarism and
hypopituitarism, and cancers of the female reproductive system. Similarly,
polypeptides and antibodies directed to those polypeptides are useful to
provide
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57
immunological probes for differential identification of the tissues) or cell
type(s). For
a number of disorders of the above tissues or cells, particularly of the
endocrine and
reproductive systems, expression of this gene at significantly higher or lower
levels
may be detected in certain tissues or cell types (e.g., endocrine,
reproductive,
cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma,
urine,
synovial fluid or spinal fluid) taken from an individual having such a
disorder,
relative to the standard gene expression level, i.e., the expression level in
healthy
tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
136 as residues: Ser-3 to Lys-8.
The tissue distribution in pituitary tissue indicates that the protein
products of
this clone are useful for the diagnosis and/or treatment of disorders in the
pituitary
gland. More generally, the tissue distribution in pituitary tissue suggests
that the
protein product of this clone is useful for the detection, treatment, and/or
prevention
of various endocrine disorders and cancers, particularly Addison's disease,
Cushing's
Syndrome, and disorders and/or cancers of the pancrease (e.g. diabetes
mellitus),
adrenal cortex, ovaries, pituitary (e.g., hyper-, hypopituitarism), thyroid
(e.g. hyper-,
hypothyroidism), parathyroid (e.g. hyper-, hypoparathyroidism) ,
hypothallamus, and
testes. Alternatively, the tissue distribution in breast tissue and cancerous
tissues of
the endometrium and ovaries suggests that the translation product of this gene
is
useful for the detection and/or treatment of disorders and cancers of the
female
reproductive system, as well as cancers of other tissues where expression has
been
observed. Protein, as well as, antibodies directed against the protein may
show utility
as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:39 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
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general formula of a-b, where a is any integer between 1 to 789 of SEQ ID
N0:39, b
is an integer of 15 to 803, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:39, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 30
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: TRNILSFIKCVIHNFWIPKESNEITIIINPYRETVCFSVEP
VKKIFNY (SEQ ID N0:254). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
It has been discovered that this gene is expressed primarily in human synovial
sarcoma tissue.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample.
Similarly,
polypeptides and antibodies directed to those polypeptides are useful to
provide
immunological probes for differential identification of the tissues) or cell
type(s). For
a number of disorders of the above tissues or cells, particularly of the
skeletal system,
expression of this gene at significantly higher or lower levels may be
detected in
certain tissues or cell types (e.g., skeletal, connective, cancerous and
wounded tissues)
or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal
fluid)
taken from an individual having such a disorder, relative to the standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
137 as residues: Thr-29 to Pro-34.
The tissue distribution in synovial sarcoma tissue indicates that the protein
products of this clone are useful for the diagnosis and/or treatment of
diseases of the
synovium. In addition, the
Expression of this gene product in synovium suggests a role in the detection
and treatment of disorders and conditions affecting the skeletal system, in
particular
osteoporosis as well as disorders afflicting connective tissues (e.g.
arthritis, trauma,
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tendonitis, chrondomalacia and inflammation), such as in the diagnosis or
treatment
of various autoimmune disorders such as rheumatoid arthritis, lupus,
scleroderma, and
dermatomyositis as well as dwarfism, spinal deformation, and specific joint
abnormalities as well as chondrodysplasias (ie. spondyloepiphyseal dysplasia
congenita, familial arthritis, Atelosteogenesis type II, metaphyseal
chondrodysplasia
type Schmid). Protein, as well as, antibodies directed against the protein may
show
utility as a tumor marker and/or immunotherapy targets for the above listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:40 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1496 of SEQ ID
N0:40, b
is an integer of 15 to 1510, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:40, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 31
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: LVVLFASSNSRYLKYFFLVPLILGSAW (SEQ ID N0:255).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
It has been discovered that this gene is expressed primarily in human
rhabdomyosarcoma and fetal liver/spleen tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: malignant neoplasms and
hematopoiesis. Similarly, polypeptides and antibodies directed to those
polypeptides
are useful to provide immunological probes for differential identification of
the
tissues) or cell type(s). For a number of disorders of the above tissues or
cells.
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particularly of the skeletal and immune system, expression of this gene at
significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., musculo-skeletal, immune, cancerous and wounded tissues) or bodily
fluids
(e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from
an
5 individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
138 as residues: Gly-29 to Thr-35.
The tissue distribution in rhabdomyosarcoma and fetal liver/spleen tissues
10 indicates that the protein products of this clone are useful for diagnosis
and treatment
of skeletal and immune disorders. The expression in rhabdomyosarcoma tissue
suggests that the protein product of this clone is useful for the detection,
treatment,
and/or prevention of various muscle disorders, such as muscular dystrophy,
cardiomyopathy, fibroids, myomas, and rhabdomyosarcomas. Alternatively,
15 Expression of this gene product in fetal liver/spleen tissue suggests a
role in
the regulation of the proliferation; survival; differentiation; and/or
activation of
potentially all hematopoietic cell lineages, including blood stem cells. This
gene
product may be involved in the regulation of cytokine production, antigen
presentation, or other processes that may also suggest a usefulness in the
treatment of
20 cancer (e.g. by boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
25 deficiency diseases such as AIDS, leukemia, rheumatoid arthritis,
inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
commercial utility in the expansion of stem cells and committed progenitors of
various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Protein, as well as, antibodies directed against the protein may show
utility as a
30 tumor marker and/or immunotherapy targets for the above listed tissues.
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Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:41 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1081 of SEQ ID
N0:41, b
is an integer of 15 to 1095, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:41, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 32
It has been discovered that this gene is expressed primarily in fibrosarcoma
tissue.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: fibrosarcoma. Similarly,
polypeptides and antibodies directed to those polypeptides are useful to
provide
immunological probes for differential identification of the tissues) or cell
type(s). For
a number of disorders of the above tissues or cells, particularly of the
connective
tissue system, expression of this gene at significantly higher or lower levels
may be
detected in certain tissues or cell types (e.g., musculo-skeletal, cancerous
and
wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial
fluid or
spinal fluid) taken from an individual having such a disorder, relative to the
standard
gene expression level, i.e., the expression level in healthy tissue from an
individual
not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
139 as residues: Ser-34 to Gln-40, Gly-42 to Glu-48, Tyr-56 to Leu-62.
The tissue distribution in only fibrosarcoma tissue suggests that the protein
product of this clone is useful for the treatment, diagnosis and/or prognosis
of
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62
fibrosarcoma's or other diorders related with fibrous tissue including
fibroma,
fibromatosis, fibromyoma, fibromyositis, fibrosis and fibrositis. Likewise,
the
expression in fibrosarcoma tissue suggests that the protein product of this
clone is
useful for the detection, treatment, and/or prevention of various muscle
disorders,
such as muscular dystrophy, cardiomyopathy, myomas, and rhabdomyosarcomas.
Protein, as well as, antibodies directed against the protein may show utility
as a tumor
marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:42 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1148 of SEQ ID
N0:42, b
is an integer of 15 to 1162, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:42, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 33
It has been discovered that this gene is expressed primarily in Hodgkins
lymphoma and breast cancer tissues, and to a lesser extent in stromal cells
and brain
tissue.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: lymphoma, breast cancer,
and
neurological disorders. Similarly, polypeptides and antibodies directed to
those
polypeptides are useful to provide immunological probes for differential
identification
of the tissues) or cell type(s). For a number of disorders of the above
tissues or cells,
particularly of the immune amd nervous systems, expression of this gene at
significantly higher or lower levels may be detected in certain tissues or
cell types
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(e.g., immune, neural, cancerous and wounded tissues) or bodily fluids (e.g.,
lymph,
serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual
having
such a disorder, relative to the standard gene expression level, i.e., the
expression
level in healthy tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
140 as residues: Pro-22 to Lys-29.
The tissue distribution in Hodgkins lymphoma, brain and breast cancer tissues
suggests a role in the treatment, diagnosis and/or prognosis of breast cancer,
immune
and hematopoietic disorders including arthritis, asthma, immunodeficiency
diseases,
leukemia and Hodgkin's lymphoma and neurodegenerative disease states and
behavioral disorders such as Alzheimer's Disease, Parkinson's Disease,
Huntington's
Disease, schizophrenia, mania, dementia, paranoia, obsessive compulsive
disorder
and panic disorder. Protein, as well as, antibodies directed against the
protein may
show utility as a tumor marker andlor immunotherapy targets for the above
listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:43 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 643 of SEQ ID
N0:43, b
is an integer of 15 to 657, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:43, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 34
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: HEWKCKQKYSEGSGNTRIGN (SEQ ID N0:256).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
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It has been discovered that this gene is expressed primarily in chronic
synovitis tissue, and to a lesser extent in fetal kidney and testes tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: synovitis, renal disorders
and male
infertility. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues)
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
the connective tissue system, the renal system, and the male reproductive
system,
expression of this gene at significantly higher or lower levels may be
detected in
certain tissues or cell types (e.g., skeletal, renal, reproductive, cancerous
and wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
141 as residues: Met-33 to Pro-39, Ser-74 to Trp-79.
The tissue distribution of this gene in chronic synovitis, testes, and kidneys
suggests a role in the treatment, diagnosis and prognosis of synovial membrane
disorders including synovitis, renal disorders including kidney failure, renal
colic,
renal diabetes, hypertension, osteodystrophy, tubular acidosis and kidney
stones: and
and male infertility. Furthermore, the tissue distribution in testes tissue
indicates that
the protein product of this clone is useful for the treatment and/or diagnosis
of
conditions concerning proper testicular function (e.g. endocrine function,
sperm
maturation), as well as cancer. Therefore, this gene product is useful in the
treatment
of male infertility and/or impotence. This gene product is also useful in
assays
designed to identify binding agents, as such agents (antagonists) are useful
as male
contraceptive agents. Similarly, the protein is believed to be useful in the
treatment
and/or diagnosis of testicular cancer. The testes are also a site of active
gene
expression of transcripts that may be expressed, particularly at low levels,
in other
tissues of the body. Therefore, this gene product may be expressed in other
specific
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tissues or organs where it may play related functional roles in other
processes, such as
hematopoiesis, inflammation, bone formation, and kidney function, to name a
few
possible target indications. In addition, the
Expression of this gene product in synovium suggests a role in the detection
5 and/or treatment of disorders and conditions affecting the skeletal system,
in
particular osteoporosis as well as disorders afflicting connective tissues
(e.g. arthritis,
trauma, tendonitis, chrondomalacia and inflammation), such as in the diagnosis
or
treatment of various autoimmune disorders such as rheumatoid arthritis, lupus,
scleroderma, and dermatomyositis as well as dwarfism, spinal deformation, and
10 specific joint abnormalities as well as chondrodysplasias (ie.
spondyloepiphyseal
dysplasia congenita, familial arthritis, Atelosteogenesis type II, metaphyseal
chondrodysplasia type Schmid). Protein, as well as, antibodies directed
against the
protein may show utility as a tumor marker and/or immunotherapy targets for
the
above listed tissues.
15 Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:44 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
20 would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1141 of SEQ ID
N0:44, b
is an integer of 15 to 1155, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:44, and where b is greater than or
equal to a
25 + 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 35
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: LLPLCFLGPRQVLEEFPSIV (SEQ ID N0:257).
30 Polynucleotides encoding these polypeptides are also encompassed by the
invention.
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It has been discovered that this gene is expressed primarily in brain tissue,
and
to a lesser extent in osteoclastoma and testes tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: neurological disorders and
male
reproductive disorders. Similarly, polypeptides and antibodies directed to
those
polypeptides are useful to provide immunological probes for differential
identification
of the tissues) or cell type(s). For a number of disorders of the above
tissues or cells,
particularly of the nervous system and the male reproductive system,
expression of
this gene at significantly higher or lower levels may be detected in certain
tissues or
cell types (e.g., neural, reproductive, cancerous and wounded tissues) or
bodily fluids
(e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from
an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
The tissue distribution of this gene in brain tissue suggests a role in the
diagnosis, prognosis and/or treatment of neurodegenerative disease states and
behavioural disorders such as Alzheimer's Disease, Parkinson's Disease,
Huntinton's
Disease, schizophrenia, mania, dementia, paranoia, obsessive compulsive
disorder
and panic disorder. In addition, the gene or gene product may also play a role
in the
treatment and/or detection of developmental disorders associated with the
developing
embryo, or sexually-linked disorders. Protein, as well as, antibodies directed
against
the protein may show utility as a tumor marker andlor immunotherapy targets
for the
above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:45 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1098 of SEQ ID
N0:45, b
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is an integer of 15 to 1112, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID'N0:45, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 36
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: PTRPSKHQEAGS (SEQ ID N0:258). Polynucleotides
encoding these polypeptides are also encompassed by the invention. The gene
encoding the disclosed cDNA is thought to reside on chromosome 3. Accordingly,
polynucleotides related to this invention are useful as a marker in linkage
analysis for
chromosome 3.
It has been discovered that this gene is expressed primarily in adult and
fetal
heart tissue, and to a lesser extent in fetal lung and fetal liver/spleen
tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: cardiovascular and immune
disorders. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues)
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
the vascular and immune systems, expression of this gene at significantly
higher or
lower levels may be detected in certain tissues or cell types (e.g., vascular,
immune,
pulmonary, cancerous and wounded tissues) or bodily fluids (e.g., lymph,
serum,
plasma, urine, synovial fluid or spinal fluid) taken from an individual having
such a
disorder, relative to the standard gene expression level, i.e., the expression
level in
healthy tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
143 as residues: Val-2 to Ser-14.
The tissue distribution in heart, fetal liver and fetal spleen tissues
suggests a
role in the treatment and/or diagnosis of cardiovascular disorders including
myocardial infarction, congestive heart failure, coronary failure, as well as
immune
disorders including autoimmune diseases, such as lupus, transplant rejection,
allergic
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68
reactions, arthritis, asthma, immunodeficiency diseases, leukemia, and AIDS.
Furthermore, the tissue distribution in adult and fetal heart tissue indicates
that the
protein product of this gene is useful for the diagnosis and treatment of
conditions and
pathologies of the cardiovascular system, such as heart disease, restenosis,
atherosclerosis, stoke, angina, thrombosis, and wound healing. Protein, as
well as,
antibodies directed against the protein may show utility as a tumor marker
andlor
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:46 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 4009 of SEQ ID
N0:46, b
is an integer of 15 to 4023, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:46, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 37
It has been discovered that this gene is expressed primarily in testes
tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: male infertility and
reproductive
disorders. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues)
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
the male reproductive system, expression of this gene at significantly higher
or lower
levels may be detected in certain tissues or cell types (e.g., reproductive,
cancerous
and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine,
synovial
fluid or spinal fluid) taken from an individual having such a disorder,
relative to the
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69
standard gene expression level, i.e., the expression level in healthy tissue
from an
individual not having the disorder.
The tissue distribution in testes tissues suggests a role in the treatment
and/or
diagnosis of male infertility, and testicular disorders including cancer.
Furthermore,
the tissue distribution in testes tissue indicates that the protein product of
this clone is
useful for the treatment and diagnosis of conditions concerning proper
testicular
function (e.g. endocrine function, sperm maturation), as well as cancer.
Therefore,
this gene product is useful in the treatment of male infertility and/or
impotence. This
gene product is also useful in assays designed to identify binding agents, as
such
agents (antagonists) are useful as male contraceptive agents. Similarly, the
protein is
believed to be useful in the treatment and/or diagnosis of testicular cancer.
The testes
are also a site of active gene expression of transcripts that may be
expressed,
particularly at low levels, in other tissues of the body. Therefore, this gene
product
may be expressed in other specific tissues or organs where it may play related
functional roles in other processes, such as hematopoiesis, inflammation, bone
formation, and kidney function, to name a few possible target indications.
Protein, as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:47 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 528 of SEQ ID
N0:47, b
is an integer of 15 to 542, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:47, and where b is greater than or
equal to a
+ 14.
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FEATURES OF PROTEIN ENCODED BY GENE NO: 38
It has been discovered that this gene is expressed primarily in apoptotic T-
cells, and to a lesser extent in brain tissue.
Therefore, nucleic acids of the invention are useful as reagents for
differential
5 identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune and neurological
disorders. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues)
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
10 the immune and nervous systems, expression of this gene at significantly
higher or
lower levels may be detected in certain tissues or cell types (e.g., immune,
neural,
cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma,
urine,
synovial fluid or spinal fluid) taken from an individual having such a
disorder,
relative to the standard gene expression level, i.e., the expression level in
healthy
15 tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
145 as residues: Glu-33 to Tyr-42.
The tissue distribution in apoptotic T-cells suggests potential roles in the
treatment and/or diagnosis of immune disorders including of immune and
20 autoimmune diseases, such as lupus, transplant rejection, allergic
reactions, arthritis,
asthma, immunodeficiency diseases, leukemia, and AIDS. Alternatively,
expression
in brain tissue suggests a role in the treatment and/or diagnosis of
neurodegenerative
disease states and behavioural disorders such as Alzheimer's Disease,
Parkinson's
Disease, Huntinton's Disease, schizophrenia, mania, dementia, paranoia,
obsessive
25 compulsive disorder and panic disorder. Furthermore, the tissue
distribution in
apoptotic T-cells indicates that the translation product of this gene may also
be
involved in apoptosis or tissue differentiation and could again be useful in
cancer
therapy. Protein, as well as, antibodies directed against the protein may show
utility as
a tumor marker and/or immunotherapy targets for the above listed tissues.
30 Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
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71
related to SEQ ID N0:48 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1481 of SEQ ID
N0:48, b
is an integer of 15 to 1495, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:48, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 39
The translation product of this gene shares sequence homology with
phosphomannomutase, which is thought to be important in mannose matabolism.
It has been discovered that this gene is expressed primarily in meningioma and
testis tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: meningioma related
diseases.
Similarly, polypeptides and antibodies directed to those polypeptides are
useful to
provide immunological probes for differential identification of the tissues)
or cell
type(s). For a number of disorders of the above tissues or cells, particularly
of the
central nervous system, expression of this gene at significantly higher or
lower levels
may be detected in certain tissues or cell types (e.g., neural, cancerous and
wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
146 as residues: Ser-33 to Lys-43.
The tissue distribution in meningioma, and the homology to
phosphomannomutase, suggests that the protein product of this clone is useful
for the
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72
diagnosis and/or intervention of meningioma related diseases. For example, the
gene
product can be used for preventing microbial infection of the meninges, for
imaging
conjugates, or as a secretory factor as a endocrine with systemic, central or
peripheral
nerve functions. Protein, as well as, antibodies directed against the protein
may show
utility as a tumor marker and/or immunotherapy targets for the above listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:49 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 804 of SEQ ID
N0:49, b
is an integer of 15 to 818, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:49, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 40
It has been discovered that this gene is expressed primarily in tonsils,
osteoclastoma and retinoic acid treated teratocarcinoma cells, and to a lesser
extent in
macrophages, female bladder, adipose tissue, myeloid progenitor cells,
prostate tissue,
and number of other tissues and organs.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: tonsils and osteoclast
related
diseases. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues)
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
the immune and bone systems, expression of this gene at significantly higher
or lower
levels may be detected in certain tissues or cell types (e.g., immune,
skeletal,
cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma,
urine,
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73
synovial fluid or spinal fluid) taken from an individual having such a
disorder,
relative to the standard gene expression level, i.e., the expression level in
healthy
tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
147 as residues: Glu-55 to Arg-61, Gln-84 to Ser-92, Ser-99 to Ser-104.
The tissue distribution in tonsils and osteoclastoma suggests that the protein
product of this clone is useful for the diagnosis and/or intervention of
diseases related
to tonsils or osteoclasts. For example, tonsillitis, adenoids, peritonsilar
abscess,
neoplasms, or bone related disorders like rickets, abnormalities of bone
growth and
modelling, facture, osteonecrosis, and osteoporosis etc. Expression of this
gene
product in osteoclastoma suggests that it may play a role in the survival,
proliferation,
and/or growth of osteoclasts. Therefore, it may be useful in influencing bone
mass in
such conditions as osteoporosis.
Alternatively, the expression of this gene product in tonsils suggests a role
in
the regulation of the proliferation; survival; differentiation; and/or
activation of
potentially all hematopoietic cell lineages, including blood stem cells. This
gene
product may be involved in the regulation of cytokine production, antigen
presentation, or other processes that may also suggest a usefulness in the
treatment of
cancer (e.g. by boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
deficiency diseases such as AIDS, leukemia, rheumatoid arthritis, inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
commercial utility in the expansion of stem cells and committed progenitors of
various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Protein, as well as, antibodies directed against the protein may show
utility as a
tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
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74
related to SEQ ID NO:50 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1697 of SEQ ID
NO:50, b
is an integer of 15 to 1711, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID NO:50, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 41
It has been discovered that this gene is expressed primarily in resting T-
cells.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: T-cell related disorders.
Similarly,
polypeptides and antibodies directed to those polypeptides are useful to
provide
immunological probes for differential identification of the tissues) or cell
type(s). For
a number of disorders of the above tissues or cells, particularly of the
immune system,
expression of this gene at significantly higher or lower levels may be
detected in
certain tissues or cell types (e.g., immune, cancerous and wounded tissues) or
bodily
fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid)
taken from an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
The tissue distribution in resting T-cells suggests that the protein product
of
this clone is useful for the diagnosis and/or intervention of T-cell related
disorders,
such as infection, inflammation, allergy, tissue/organ transplantation, immune
deficiency etc. Furthermore, the expression of this gene product in T cells
also
strongly suggests a role for this protein in immune function and immune
surveillance.
Protein, as well as, antibodies directed against the protein may show utility
as a tumor
marker and/or immunotherapy targets for the above listed tissues.
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Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID NO:51 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
5 excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 735 of SEQ ID NO:S
l, b
is an integer of 15 to 749, where both a and b correspond to the positions of
10 nucleotide residues shown in SEQ ID NO:51, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 42
The translation product of this gene shares weak sequence homology with
15 Human metastasis suppressor KISS-1 fragment, which is thought to be
important in
the diagnosis, prevention, staging and/or treatment of cancers, such as
melanoma (See
Accession No. W 15789).
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: GQGPAGRWVRRLPCSRRAGGERGPHWGVWAGPQM
20 SCGLXFGP (SEQ ID N0:259), WRTQGPMVLLWVVTCPATMLTEPQNPHLIGF
VAYSGPSHTTQPHKYWLLLDGQADPAAAEGPVKRKAASV VWWPQALRHLS
LLVHCWEESYEMNIGCQSLWAGGLASSGNGWDLGVAFRRDTCMSSSSLHW
KEFKYAPGSLHYFALSFVLILTEICLVSSGMGFPQEGKHFSVLGSPDCSLWGR
DEHVPREFA (SEQ ID N0:260),
25 WRTQGPMVLLWVVTCPATMLTEPQNPHLIGFVAY SGPSHTTQ (SEQ ID
N0:261), PHKYWLLLDGQADPAAAEGPVKRKAASVVWW PQALRHLSLL
(SEQ ID N0:262), VHCWEESYEMNIGCQSLWAGGLASSGNGW
DLGVAFRRDTCM (SEQ ID N0:263),
SSSSLHWKEFKYAPGSLHYFALSFVLILT EICLVSSGMGFPQEG (SEQ ID
30 N0:264), and/or KHFSVLGSPDCSLWGRDEHV PREFA (SEQ ID N0:265).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
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76
The gene encoding the disclosed cDNA is thought to reside on chromosome 1.
Accordingly, polynucleotides related to this invention are useful as a marker
in
linkage analysis for chromosome 1.
It has been discovered that this gene is expressed primarily in tonsils,
osteoclastoma and teratocarcinoma tissues, and to a lesser extent in female
bladder,
adipose tissue, myeloid progenitor, prostate tissue, and number of other
tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: diseases related to
tonsils and
osteoclasts. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues)
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
the immune and bone system, expression of this gene at significantly higher or
lower
levels may be detected in certain tissues or cell types (e.g., immune,
skeletal,
cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma,
urine,
synovial fluid or spinal fluid) taken from an individual having such a
disorder,
relative to the standard gene expression level, i.e., the expression level in
healthy
tissue from an individual not having the disorder.
The tissue distribution in tonsils and osteoclastoma tissues suggests that the
protein product of this clone is useful for the diagnosis and/or treatment of
diseases
related to tonsils and osteoclasts. For example, tonsillitis, adenoids,
peritonsilar
abscess, neoplasms, or abnormal growth and modelling of the bone,
osteonecrosis,
osteoporosis, osteodystrophy, osteoclastoma etc. Expression of this gene
product in
osteoclastoma suggests that it may play a role in the survival, proliferation,
and/or
growth of osteoclasts. Therefore, it may be useful in influencing bone mass in
such
conditions as osteoporosis.
Moreover, the expression of this gene product in tonsils suggests a role in
the
regulation of the proliferation; survival; differentiation; and/or activation
of
potentially all hematopoietic cell lineages, including blood stem cells. This
gene
product may be involved in the regulation of cytokine production, antigen
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77
presentation, or other processes that may also suggest a usefulness in the
treatment of
cancer (e.g. by boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the gene or protein,
as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues. Therefore it may be
also
used as an agent for immunological disorders including arthritis, asthma,
immune
deficiency diseases such as AIDS, leukemia, rheumatoid arthritis, inflammatory
bowel disease, sepsis, acne, and psoriasis. In addition, this gene product may
have
commercial utility in the expansion of stem cells and committed progenitors of
various blood lineages, and in the differentiation and/or proliferation of
various cell
types. Protein, as well as, antibodies directed against the protein may show
utility as a
tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:52 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1077 of SEQ ID
N0:52, b
is an integer of 15 to 1091, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:52, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 43
The translation product of this gene shares sequence homology with the
Drosophila gene "maleless", which is one of four known regulatory loci
required for
increased transcription (dosage compensation) of X-linked genes (See Genbank
Accession No.: gi1157906).
It has been discovered that this gene is expressed primarily in normal
prostate
tissue, testes tissue, whole 6-week old embryonic tissue, human colon
carcinoma
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(HCC) cell line, and cerebellum tissue, and to a lesser extent in primary
breast cancer,
activated T-cells, and many other tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: diseases of the prostate
or colon,
or male reproductive disorders. Similarly, polypeptides and antibodies
directed to
those polypeptides are useful to provide immunological probes for differential
identification of the tissues) or cell type(s). For a number of disorders of
the above
tissues or cells, particularly of the prostate or colon carcinoma, and male
reproductive
disorders, expression of this gene at significantly higher or lower levels may
be
detected in certain tissues or cell types (e.g., colon, prostate,
reproductive, cancerous
and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine,
synovial
fluid or spinal fluid) taken from an individual having such a disorder,
relative to the
standard gene expression level, i.e., the expression level in healthy tissue
from an
IS individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
150 as residues: Val-39 to Ala-45.
The tissue distribution in colon and prostate tissues suggests that the
protein
product of this clone is useful for the diagnosis and/or treatment of prostate
disorders
such as prostatitis, prostatic hyperplasia, prostate cancers, or human colon
carcinoma,
as well as cancers of other tissues where expression has been observed.
Alternatively,
the tissue distribution in testes tissue, in conjunction with the homology to
the
Drosophila maleless gene, suggests that the translation product of this gene
is useful
for the detection and/or treatment of disorders involving the testes or the
transcription
of X-linked genes. Furthermore, the tissue distribution indicates that the
protein
product of this clone is useful for the treatment and diagnosis of conditions
concerning proper testicular function (e.g. endocrine function, sperm
maturation), as
well as cancer. Therefore, this gene product is useful in the treatment of
male
infertility and/or impotence.
This gene product is also useful in assays designed to identify binding
agents,
as such agents (antagonists) are useful as male contraceptive agents.
Similarly, the
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protein is believed to be useful in the treatment and/or diagnosis of
testicular cancer.
The testes are also a site of active gene expression of transcripts that may
be
expressed, particularly at low levels, in other tissues of the body.
Therefore, this gene
product may be expressed in other specific tissues or organs where it may play
related
functional roles in other processes, such as hematopoiesis, inflammation, bone
formation, and kidney function, to name a few possible target indications.
Protein, as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:53 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 2240 of SEQ ID
N0:53, b
is an integer of 15 to 2254, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID NO:53, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 44
The translation product of this gene shares weak sequence homology with
Eimeria antigen Eam45 M3, which is thought to be important in uses as a
vaccine for
protecting chickens against coccidiosis.
It has been discovered that this gene is expressed primarily in adrenal gland
tissue, and to a lesser extent in activated T-cells.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: adrenal cortical
insufficiency,
adrenal cortical hyperfunction, neoplasia. Similarly, polypeptides and
antibodies
directed to those polypeptides are useful to provide immunological probes for
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differential identification of the tissues) or cell type(s). For a number of
disorders of
the above tissues or cells, particularly of the endocrine system, expression
of this gene
at significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., endocrine, cancerous and wounded tissues) or bodily fluids (e.g.,
lymph, serum, .
5 plasma, urine, synovial fluid or spinal fluid) taken from an individual
having such a
disorder, relative to the standard gene expression level, i.e., the expression
level in
healthy tissue from an individual not having the disorder.
The tissue distribution in adrenal gland tissue suggests that the protein
product
of this clone is useful for the diagnosis and/or intervention of disorders
caused by
10 adrenal gland abnormalities, such as adrenal cortical insufficiency,
adrenal cortical
hyperfunction, and neoplasia. More generally, the tissue distribution suggests
that the
protein product of this clone is useful for the detection, treatment, and/or
prevention
of various endocrine disorders and cancers, particularly Addison's disease,
Cushing's
Syndrome, and disorders andlor cancers of the pancrease (e.g. diabetes
mellitus),
15 adrenal cortex, ovaries, pituitary (e.g., hyper-, hypopituitarism), thyroid
(e.g. hyper-,
hypothyroidism), parathyroid (e.g. hyper-, hypoparathyroidism) ,
hypothallamus, and
testes. Protein, as well as, antibodies directed against the protein may show
utility as a
tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
20 available and accessible through sequence databases. Some of these
sequences are
related to SEQ ID N0:54 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
25 are one or more polynucleotides comprising a nucleotide sequence described
by the
general formula of a-b, where a is any integer between 1 to 472 of SEQ ID
N0:54, b
is an integer of 15 to 486, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:54, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 45
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The translation product of this gene shares sequence homology with neural
thread protein, tumor necrosis factor related gene product, human alpha-1C2
adrenalin receptor, which is thought to be important for diagnosing the
presence of
Alzheimer's disease, neuroectodermal tumours and a malignant astrocytoma, or
diagnosis of hepatocellular carcinomas and preneoplastic or pathological
conditions
of the liver, and tumor immunity.
It has been discovered that this gene is expressed primarily in activated T-
cells
and endothelial cells.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: Alzheimer's disease,
neuroectodermal tumours and a malignant astrocytoma, hepatocellular carcinomas
and tumors of various origins. Similarly, polypeptides and antibodies directed
to those
polypeptides are useful to provide immunological probes for differential
identification
of the tissues) or cell type(s). For a number of disorders of the above
tissues or cells,
particularly of the immune system and endothelial cells, expression of this
gene at
significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., immune, endothelial, cancerous and wounded tissues) or bodily fluids
(e.g.,
lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from an
individual
having such a disorder, relative to the standard gene expression level, i.e.,
the
expression level in healthy tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
152 as residues: Arg-38 to Arg-47.
The tissue distribution in immune and endothelial tissues, and the homology to
neural thread protein, tumor necrosis factor related gene product, human alpha-
1C2
adrenalin receptor, or Smaller hepatocellular oncoprotein (hhcm) gene product
suggests that the protein product of this clone is useful .for the diagnosis
and/or
treatment of tumors of various origins, including neuroectodermal tumours and
a
malignant astrocytoma, hepatocellular carcinomas, as well as syndromes
inflicted by
these cancers. Protein, as well as, antibodies directed against the protein
may show
utility as a tumor marker and/or immunotherapy targets for the above listed
tissues.
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Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID NO:55 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1256 of SEQ ID
NO:55, b
is an integer of 15 to 1270, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID NO:55, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 46
It has been discovered that this gene is expressed primarily in tumor tissues
such as hepatocellular tumor, hemangiopericytoma, chronic lymphocytic
leukemia,
and activated T-cells.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: tumors of various origins.
Similarly, polypeptides and antibodies directed to those polypeptides are
useful to
provide immunological probes for differential identification of the tissues)
or cell
type(s). For a number of disorders of the above tissues or cells, particularly
of the
hepatocellular tumor, expression of this gene at significantly higher or lower
levels
may be detected in certain tissues or cell types (e.g., liver, immune,
cancerous and
wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial
fluid or
spinal fluid) taken from an individual having such a disorder, relative to the
standard
gene expression level, i.e., the expression level in healthy tissue from an
individual
not having the disorder.
The tissue distribution in hepatocellular tumors suggests that the protein
product of this clone is useful for the diagnosis and/or targeting of
hepatocellular
carcinomas, preneoplastic or pathological conditions of the liver, Alzheimer's
disease,
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83
neuroectodermal tumours and malignant astrocytoma. Protein, as well as,
antibodies
directed against the protein may show utility as a tumor marker and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:56 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 2045 of SEQ ID
N0:56, b
is an integer of 15 to 2059, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:56, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 47
It has been discovered that this gene is expressed primarily in glioblastoma,
ulcerative colitis, and hemangiopericytoma.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: glioblastoma,
hemangiopericytoma and their inflicted disorders. Similarly, polypeptides and
antibodies directed to those polypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the brain tissues, expression
of this gene
at significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., neural, cancerous and wounded tissues) or bodily fluids (e.g., lymph,
serum,
plasma, urine, synovial fluid or spinal fluid) taken from an individual having
such a
disorder, relative to the standard gene expression level, i.e., the expression
level in
healthy tissue from an individual not having the disorder.
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Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
154 as residues: Pro-31 to Ala-37.
The tissue distribution suggests that the protein product of this clone would
be
useful for the diagnosis, targeting and/or treatment of tumors in the brain,
such as
glioblastoma and hemangiopericytoma. Additionally, the gene products can be
useful
agent for the diagnosis and treatment of ulcerative colitis. Protein, as well
as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:57 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 854 of SEQ ID
N0:57, b
is an integer of 15 to 868, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:57, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 48
It has been discovered that this gene is expressed primarily in bone marrow.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immunodeficiency, tumor
necrosis, infection, lymphomas, auto-immunities, cancer, inflammation, anemias
(leukemia) and other hematopoeitic disorders. Similarly, polypeptides and
antibodies
directed to those polypeptides are useful to provide immunological probes for
differential identification of the tissues) or cell type(s). For a number of
disorders of
the above tissues or cells, particularly of the immune system, expression of
this gene
at significantly higher or lower levels may be detected in certain tissues or
cell types
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(e.g., immune, cancerous and wounded tissues) or bodily fluids (e.g., lymph,
serum,
plasma, urine, synovial fluid or spinal fluid) taken from an individual having
such a
disorder, relative to the standard gene expression level, i.e., the expression
level in
healthy tissue from an individual not having the disorder.
5 Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
155 as residues: Thr-47 to Val-53.
The tissue distribution in bone marrow suggests that the protein product of
this
clone is useful for the diagnosis and/or treatment of immune disorders
including:
leukemias, lymphomas, auto-immunities, immunodeficiencies (e.g. AIDS), immuno-
10 supressive conditions (transplantation) and hematopoeitic disorders. In
addition this
gene product may be applicable in conditions of general microbial infection,
inflammation or cancer. Furthermore, the tissue distribution in bone marrow
suggests
that the protein product of this clone is useful for the treatment and
diagnosis of
hematopoietic related disorders such as anemia, pancytopenia, leukopenia,
15 thrombocytopenia or leukemia.
The uses include bone marrow cell ex vivo culture, bone marrow
transplantation, bone marrow reconstitution, radiotherapy or chemotherapy of
neoplasia. The gene product may also be involved in lymphopoiesis, therefore,
it can
be used in immune disorders such as infection, inflammation, allergy,
20 immunodeficiency etc. In addition, this gene product may have commercial
utility in
the expansion of stem cells and committed progenitors of various blood
lineages, and
in the differentiation and/or proliferation of various cell types. Protein, as
well as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
25 Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:58 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
30 would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
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86
general formula of a-b, where a is any integer between 1 to 972 of SEQ ID
N0:58, b
is an integer of 15 to 986, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:58, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 49
It has been discovered that this gene is expressed primarily in bone marrow.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immunodeficiency, tumor
necrosis, infection, lymphomas, auto-immunities, cancer, inflammation, anemias
(leukemia) and other hematopoeitic disorders. Similarly, polypeptides and
antibodies
directed to those polypeptides are useful to provide immunological probes for
differential identification of the tissues) or cell type(s). For a number of
disorders of
the above tissues or cells, particularly of the immune system, expression of
this gene
at significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., immune, cancerous and wounded tissues) or bodily fluids (e.g., lymph,
serum,
plasma, urine, synovial fluid or spinal fluid) taken from an individual having
such a
disorder, relative to the standard gene expression level, i.e., the expression
level in
healthy tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
I56 as residues: Leu-40 to Cys-47.
The bone marrow tissue distribution suggests that the protein product of this
clone would be useful for the diagnosis and treatment of immune disorders
including:
leukemias, lymphomas, auto-immunities, immunodeficiencies (e.g. AIDS), immuno-
supressive conditions (transplantation) and hematopoeitic disorders. In
addition this
gene product may be applicable in conditions of general microbial infection,
inflammation or cancer. Furthermore, the tissue distribution in bone marrow
suggests
that the protein product of this clone is useful for the treatment and
diagnosis of
hematopoietic related disorders such as anemia, pancytopenia, leukopenia,
thrombocytopenia or leukemia.
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The uses include bone marrow cell ex vivo culture, bone marrow
transplantation, bone marrow reconstitution, radiotherapy or chemotherapy of
neoplasia. The gene product may also be involved in lymphopoiesis, therefore,
it can
be used in immune disorders such as infection, inflammation, allergy,
immunodeficiency etc. In addition, this gene product may have commercial
utility in
the expansion of stem cells and committed progenitors of various blood
lineages, and
in the differentiation and/or proliferation of various cell types. Protein, as
well as,
antibodies directed against the protein may show utility as a tumor marker
andlor
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:59 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 681 of SEQ ID
N0:59, b
is an integer of 15 to 695, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:59, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 50
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: IAQGTVPLTKRGVQSSGPDYPEGTLTPLPRG (SEQ ID
N0:266 and 267). Polynucleotides encoding these polypeptides are also
encompassed
by the invention.
It has been discovered that this gene is expressed primarily in dendritic
cells.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune disorders and
related
conditions such as leukemias, lymphomas, inflammation, hematopoeitic
disfunction,
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88
arthritis and asthma. Similarly, polypeptides and antibodies directed to those
polypeptides are useful to provide irnmunological probes for differential
identification
of dendritic cells. For a number of disorders of the above tissues or cells,
particularly
of the immune system, expression of this gene at significantly higher or lower
levels
may be detected in certain tissues or cell types (e.g., dendritic cells,
cancerous and
wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial
fluid or
spinal fluid) taken from an individual having such a disorder, relative to the
standard
gene expression level, i.e., the expression level in healthy tissue from an
individual
not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
157 as residues: Ser-25 to Phe-31, Lys-55 to Arg-61.
The tissue distribution in dendritic cells suggests that the protein product
of
this clone is useful for the diagnosis and/or treatment of immune disorders
including:
leukemias, lymphomas, auto-immunities, immunodeficiencies (e.g. AIDS), immuno-
supressive conditions (transplantation) and hematopoeitic disorders. In
addition this
gene product may be applicable in conditions of general microbial infection,
inflammation or cancer.
Moreover, the expression of this gene product in dendritic cells also strongly
suggests a role for this protein in immune function and immune surveillance.
Protein,
as well as, antibodies directed against the protein may show utility as a
tumor marker
and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:60 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 300 of SEQ ID
N0:60, b
is an integer of 15 to 314, where both a and b correspond to the positions of
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89
nucleotide residues shown in SEQ ID N0:60, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 51
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: DCLYLALSFPWHCHCHHHPPSGSLLYPF (SEQ ID
N0:268). Polynucleotides encoding these polypeptides are also encompassed by
the
invention. The translation product of this gene shares sequence homology with
a C.
elegans protein of unknown function (See Genbank Accession No.: gil 1947142
(AF000264)).
It has been discovered that this gene is expressed primarily in healing
abdominal wound tissue.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: tissue necrosis, wound
healing,
ulceration, neoplasms or cancer. Similarly, polypeptides and antibodies
directed to
those polypeptides are useful to provide immunological probes for differential
identification of the tissues) or cell type(s). For a number of disorders of
the above
tissues or cells, particularly of injured tissue, expression of this gene at
significantly
higher or lower levels may be detected in certain tissues or cell types (e.g.,
vascular,
endothelial, cancerous and wounded tissues) or bodily fluids (e.g., lymph,
serum,
plasma, urine, synovial fluid or spinal fluid) taken from an individual having
such a
disorder, relative to the standard gene expression level, i.e., the expression
level in
healthy tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
158 as residues: Pro-34 to Tyr-43, Gln-73 to Cys-86, Pro-98 to Leu-103.
The tissue distribution in healing abdominal wound tissue suggests that the
protein product of this clone is useful for the treatment and/or diagnosis of
conditions
involving tissue repair and wound healing. Tissue repair may be indicated in
cases of
injury to the skin or internal organs, ulceration, cellular necrosis or other
conditions
involving healing of both diseased or non-diseased, traumatized tissue. In
addition,
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because of the implications of tissue regeneration, remoldeling and growth
regulation,
the protein product of this gene may have indications in the diagnosis and
treatment
of neoplasms and cancer.
More generally, the tissue distribution in endothelial tissue indicates that
the
5 protein product of this gene is useful for the diagnosis and treatment of
conditions and
pathologies of the cardiovascular system, such as heart disease, restenosis,
atherosclerosis, stoke, angina, thrombosis, and wound healing. Likewise, the
tissue
distribution further suggests that the protein product of this clone is useful
for the
treatment, diagnosis, and/or prevention of various skin disorders including
congenital
10 disorders (i.e. nevi, moles, freckles, Mongolian spots, hemangiomas, port-
wine
syndrome), integumentary tumors (i.e. keratoses, Bowen's disease, basal cell
carcinoma, squamous cell carcinoma, malignant melanoma, Paget's disease,
mycosis
fungoides, and Kaposi's sarcoma), injuries and inflammation of the skin
(i.e.wounds,
rashes, prickly heat disorder, psoriasis, dermatitis), atherosclerosis,
uticaria, eczema,
15 photosensitivity, autoimmune disorders (i.e. lupus erythematosus, vitiligo,
dermatomyositis, morphea, scleroderma, pemphigoid, and pemphigus), keloids,
striae,
erythema, petechiae, purpura, and xanthelasma. In addition, such disorders may
predispose increased susceptibility to viral and bacterial infections of the
skin (i.e.
cold sores, warts, chickenpox, molluscum contagiosum, herpes zoster, boils,
cellulitis,
20 erysipelas, impetigo, tinea, althletes foot, and ringworm). Moreover, the
protein
product of this clone may also be useful for the treatment or diagnosis of
various
connective tissue disorders such as arthritis, trauma, tendonitis,
chrondomalacia and
inflammation, autoimmune disorders such as rheumatoid arthritis, lupus,
scleroderma,
and dermatomyositis as well as dwarfism, spinal deformation, and specific
joint
25 abnormalities as well as chondrodysplasias (i.e. spondyloepiphyseal
dysplasia
congenita, familial osteoarthritis, Atelosteogenesis type II, metaphyseai
chondrodysplasia type Schmid). Protein, as well as, antibodies directed
against the
protein may show utility as a tumor marker and/or immunotherapy targets for
the
above listed tissues.
30 Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
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91
related to SEQ ID N0:61 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 720 of SEQ ID
N0:61, b
is an integer of 15 to 734, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:61, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 52
The translation product of this gene shares sequence homology with FAR-
17A, which is an androgen induced protein, absent in castrated hamsters (See
Genbank Accession No.: gi1191315), as well as a male hormone-dependent gene
product (See GenSeq Accession No.: R10612). The gene encoding the disclosed
cDNA is thought to reside on chromosome 6. Accordingly, polynucleotides
related to
this invention are useful as a marker in linkage analysis for chromosome 6.
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequences: ASLPPSRSRPLANMALVPCQVLRMAILLSYCSILCNYKA
IEMPSHQTYGGSWKFLTFIDLVIQAVFFGICVLTDLSSLLTRGSGNQEQERQLK
KLISLRDW (SEQ ID N0:269). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
It has been discovered that this gene is expressed primarily in fetal liver
and
spleen tissue, and to a lesser extent in a variety of other fetal tissues and
brain tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune disorders including
leukemias, lymphomas; reproductive and endocrine disorders, including
testicular
cancer; and liver disorders (e.g. hepatoblastoma, metabolic diseases and
conditions
that are attributable to the differentiation of hepatocyte progenitor cells).
Similarly,
polypeptides and antibodies directed to those polypeptides are useful to
provide
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92
immunological probes for differential identification of the tissues) or cell
type(s). For
.a number of disorders of the above tissues or cells, particularly of the
immune and
reproductive systems, expression of this gene at significantly higher or lower
levels
may be detected in certain tissues or cell types (e.g., immune, reproductive,
cancerous
and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine,
synovial
fluid or spinal fluid) taken from an individual having such a disorder,
relative to the
standard gene expression level, i.e., the expression level in healthy tissue
from an
individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
159 as residues; Thr-59 to Gly-70, Tyr-132 to Glu-150.
The tissue distribution and homology to FAR-17A suggests that the protein
product of this clone is useful for the treatment and/or diagnosis of androgen
related
conditions and disorders. Male reproductive and endocrine disorders would be
potential area of application (e.g. endocrine function, sperm maturation). It
may also
prove to be valuable in the diagnosis and treatment of testicular cancer.
More generally, the protein product of this clone may be useful for the
treatment and/or diagnosis of conditions concerning proper testicular function
(e.g.
endocrine function, sperm maturation), as well as cancer. Therefore, this gene
product
is useful in the treatment of male infertility and/or impotence. This gene
product is
also useful in assays designed to identify binding agents, as such agents
(antagonists)
are useful as male contraceptive agents. Similarly, the protein is believed to
be useful
in the treatment and/or diagnosis of testicular cancer. The testes are also a
site of
active gene expression of transcripts that may be expressed, particularly at
low levels,
in other tissues of the body. Therefore, this gene product may be expressed in
other
specific tissues or organs where it may play related functional roles in other
processes, such as hematopoiesis, inflammation, bone formation, and kidney
function,
to name a few possible target indications. Protein, as well as, antibodies
directed
against the protein may show utility as a tumor marker and/or immunotherapy
targets
for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
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93
related to SEQ ID N0:62 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1396 of SEQ ID
N0:62, b
is an integer of 1 S to 1410, where both a and b correspond to the positions
of
nucleotide residues shown in SEQ ID N0:62, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 53
Contact of cells with supernatant expressing the product of this gene has been
shown to increase the permeability of the plasma membrane of THP-1 to calcium.
Thus it is likely that the product of this gene is involved in a signal
transduction
pathway that is initiated when the product binds a receptor on the surface of
the
plasma membrane of monocytes, and to a lesser extent, in immune or
hematopoietic
cells and tissues. Thus, polynucleotides and polypeptides have uses which
include,
but are not limited to, activating monocytes.
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: MSRSSRISGLSCPWLL (SEQ ID N0:270). Polynucleotides
encoding these polypeptides are also encompassed by the invention. The gene
encoding the disclosed cDNA is believed to reside on chromosome 1.
Accordingly,
polynucleotides related to this invention are useful as a marker in linkage
analysis for
chromosome 1.
It has been discovered that this gene is expressed primarily in T-cells.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues} or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune and hematopoietic
diseases and/or disorders. Similarly, polypeptides and antibodies directed to
those
polypeptides are useful to provide immunological probes for differential
identification
of the tissues) or cell type(s). For a number of disorders of the above
tissues or cells,
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94
particularly of the immune and haemopoietic systems, expression of this gene
at
significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., immune, hematopoietic, and cancerous and wounded tissues) or bodily
fluids
(e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from
an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
160 as residues: Pro-42 to Cys-50, Leu-61 to Ala-66.
The tissue distribution in T-cells, combined with the detected calcium flux
activity in monocytes suggests that the protein product of this clone would be
useful
for the treatment and diagnosis of immune and hematopoietic disorders.
Morever, the
expression of this gene product suggests a role in regulating the
proliferation;
survival; differentiation; and/or activation of hematopoietic cell lineages,
including
blood stem cells. This gene product may be involved in the regulation of
cytokine
production, antigen presentation, or other processes suggesting a usefulness
in the
treatment of cancer (e.g. by boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the natural gene
product may be involved in immune functions. Therefore it may be also used as
an
agent for immunological disorders including arthritis, asthma,
immunodeficiency
diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease,
inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia,
psoriasis,
hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to
transplanted organs and tissues, such as host-versus-graft and graft-versus-
host
diseases, or autoimmunity disorders, such as autoimmune infertility, Tense
tissue
injury, demyelination, systemic lupus erythematosis, drug induced hemolytic
anemia,
rheumatoid arthritis, Sjogren's disease, scleroderma and tissues.
Moreover, the protein may represent a secreted factor that influences the
differentiation or behavior of other blood cells, or that recruits
hematopoietic cells to
sites of injury. In addition, this gene product may have commercial utility in
the
expansion of stem cells and committed progenitors of various blood lineages,
and in
the differentiation and/or proliferation of various cell types. Protein, as
well as,
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antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
5 related to SEQ ID N0:63 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
10 general formula of a-b, where a is any integer between 1 to 1217 of SEQ ID
N0:63, b
is an integer of 15 to 1231, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:63, and where b is greater than or
equal to a
+ 14.
15 FEATURES OF PROTEIN ENCODED BY GENE NO: 54
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: DHWPAGFLPPAPGLKFPVALEVFRKVLPAVCPTDCSGS
AGKERNS (SEQ ID N0:271). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
20 It has been discovered that this gene is expressed primarily in liver.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: metabolic diseases and
liver
conditions. Similarly, polypeptides and antibodies directed to those
polypeptides are
25 useful to provide immunological probes for differential identification of
the tissues)
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
the metabolic system, expression of this gene at significantly higher or lower
levels
may be detected in certain tissues or cell types (e.g., hepatic, liver,
metabolic, and
cancerous and wounded tissues) or bodily fluids (e.g., lymph, bile, serum,
plasma,
30 urine, synovial fluid or spinal fluid) taken from an individual having such
a disorder,
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96
relative to the standard gene expression level, i.e., the expression level in
healthy
tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
161 as residues: Ser-31 to Gln-41.
The tissue distribution in liver suggests that the protein product of this
clone
would be useful for treatment and diagnosis of disorders of the metabolic
system and
liver disorders. Morever, the protein product of this clone is useful for the
detection
and treatment of liver disorders and cancers (e.g. hepatoblastoma, jaundice,
hepatitis,
liver metabolic diseases and conditions that are attributable to the
differentiation of
hepatocyte progenitor cells). Protein, as well as, antibodies directed against
the
protein may show utility as a tumor marker and/or immunotherapy targets for
the
above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:64 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 598 of SEQ ID
N0:64, b
is an integer of 15 to 612, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:64, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 55
When tested against PC12 cell lines, supernatants removed from cells
containing this gene activated the EGR1 (early growth response gene 1)
promoter
element. Thus, it is likely that this gene activates sensory neuron cells, and
to a lesser
extent in other neural cells and tissues, through the EGR1 signal transduction
pathway. EGR1 is a separate signal transduction pathway from Jak-STAT, genes
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97
containing the EGR1 promoter are induced in various tissues and cell types
upon
activation, leading the cells to undergo differentiation and proliferation.
It has been discovered that this gene is expressed primarily in T-cells and
monocytes, and to a lesser extent in cancerous tissues, including cancerous
colon
tissue and placenta.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune and haemopoietic
disorders and cancer such as colon cancer, but also such cancers as breast
cancer,
cardiac tumors, pancreatic cancer, melanoma, retinoblastoma, glioblastoma,
lung
cancer, intestinal cancer, testicular cancer, stomach cancer, neuroblastoma,
myxoma,
myoma, lymphoma, endothelioma, osteoblastoma, osteoclastoma, adenoma, and the
like. Similarly, polypeptides and antibodies directed to those polypeptides
are useful
to provide immunological probes for differential identification of the
tissues) or cell
type(s). For a number of disorders of the above tissues or cells, particularly
of the
immune and haemopoietic systems, expression of this gene at significantly
higher or
lower levels may be detected in certain tissues or cell types (e.g., immune,
hematopoietic, and cancerous and wounded tissues) or bodily fluids (e.g.,
lymph,
serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual
having
such a disorder, relative to the standard gene expression level, i.e., the
expression
level in healthy tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
162 as residues: Glu-63 to Trp-72.
The tissue distribution in T-cells and monocytes, combined with the detected
EGR 1 biological activity suggests that the protein product of this clone
would be
useful for treatment and diagnosis of disorders of the immune and haemopoietic
systems and colon and other cancers. This gene product may be involved in the
regulation of cytokine production, antigen presentation, or other processes
suggesting
a usefulness in the treatment of cancer (e.g. by boosting immune responses).
~0
Since the gene is expressed in cells of lymphoid origin, the natural gene
product may be involved in immune functions. Therefore it may be also used as
an
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98
agent for immunological disorders including arthritis, asthma,
immunodeficiency
diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease,
inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia,
psoriasis,
hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to
transplanted organs and tissues, such as host-versus-graft and graft-versus-
host
diseases, or autoimmunity disorders, such as autoimmune infertility, Tense
tissue
injury, demyelination, systemic lupus erythematosis, drug induced hemolytic
anemia,
rheumatoid arthritis, Sjogren's disease, scleroderma and tissues.
Moreover, the protein may represent a secreted factor that influences the
differentiation or behavior of other blood cells, or that recruits
hematopoietic cells to
sites of injury. In addition, this gene product may have commercial utility in
the
expansion of stem cells and committed progenitors of various blood lineages,
and in
the differentiation and/or proliferation of various cell types. Expression
cellular
sources marked by proliferating cells suggests this protein may play a role in
the
regulation of cellular division, and may show utility in the diagnosis and
treatment of
cancer and other proliferative disorders. Similarly, developmental tissues
rely on
decisions involving cell differentiation and/or apoptosis in pattern
formation.
Dysregulation of apoptosis can result in inappropriate suppression of cell
death, as
occurs in the development of some cancers, or in failure to control the extent
of cell
death, as is believed to occur in acquired immunodeficiency and certain
neurodegenerative disorders, such as spinal muscular atrophy (SMA).
Therefore, the polynucleotides and polypeptides of the present invention are
useful in treating, detecting, and/or preventing said disorders and
conditions, in
addition to other types of degenerative conditions. Thus this protein may
modulate
apoptosis or tissue differentiation and would be useful in the detection,
treatment,
and/or prevention of degenerative or proliferative conditions and diseases.
Protein, as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:65 and may have been publicly available prior to
conception of
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99
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 2256 of SEQ ID
N0:65, b
is an integer of 15 to 2270, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:65, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 56
The translation product of this gene has homology with several human keratin
genes at the nucleotide level (see, for example, Troyanovsky, et al., Eur. J.
Cell Biol.
59:127-137 (1992) which is hereby incorporated by reference herein). Based on
the
sequence similarity, the translation product of this clone is expected to
share
biological activities with keratin and growth factor proteins. Such activities
are known
in the art, and some of which are described elsewhere herein.
It has been discovered that this gene is expressed primarily in neutrophils.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune and haemopoietic
disorders. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues}
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
the immune and haemopoietic system, expression of this gene at significantly
higher
or lower levels may be detected in certain tissues or cell types (e.g.,
cancerous and
wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial
fluid or
spinal fluid) taken from an individual having such a disorder, relative to the
standard
gene expression level, i.e., the expression level in healthy tissue from an
individual
not having the disorder.
The tissue distribution in neutrophils suggests that the protein product of
this
clone would be useful for treatment and diagnosis of disorders of the immune
and
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100
haemopoietic system. Furthermore, sequence homology of the polynucleotides and
polypeptides of the present invention with a number of human cytokeratin
molecules,
such as CK-8, CK-1 S, and CK-17, indicate that molecules of the present
invention
can be used diagnostically as markers of basal cell differentiation in complex
epithelia
S and therefore indicative of a certain type of epithelial stem cells, as well
as markers of
the differentiation of other cell types such as neutrophils or other immune
cells.
Molecules of the present invention, or agonists or antagonists thereof, can
also be
used therapeutically to treat differentiation disorders of epithelial,
neutrophil or other
immune cell differentiation or activation. Protein, as well as, antibodies
directed
against the protein may show utility as a tumor marker and/or immunotherapy
targets
for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:66 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1269 of SEQ ID
N0:66, b
is an integer of 15 to 1283, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:66, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 57
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: EEIATSIEPIRDFLAIVFFASIGLHVFPTFVAYELTVLVF
LTLSVVV (SEQ ID N0:272). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
It has been discovered that this gene is expressed primarily in synovium,
placenta, and stromal cells, and to a lesser extent in several other tissues
and organs,
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I 01
including, among others, bone marrow, palate, pituitary gland, and in tissue
derived
from osteosarcoma and chondrosarcoma.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: developmental disorders,
as well
as disorders of the musculoskeletal and haematopoietic systems, and cancers
including especially osteosarcoma and chondrosarcoma, but also other cancers
including breast cancer, colon cancer, cardiac tumors, pancreatic cancer,
melanoma,
retinoblastoma, glioblastoma, lung cancer, intestinal cancer, testicular
cancer,
stomach cancer, neuroblastoma, myxoma, myoma, lymphoma, endothelioma,
osteoblastoma, osteoclastoma, adenoma, and the like. Similarly, polypeptides
and
antibodies directed to those polypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the haemopoietic and
musculoskeletal
systems, as well as developmental disorders, expression of this gene at
significantly
higher or lower levels may be detected in certain tissues or cell types (e.g.,
synovium,
placenta, stromal, immune, hematopoietic, skeletal, and cancerous and wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
164 as residues: Pro-81 to Ser-88.
The tissue distribution in placenta suggests that the protein product of this
clone would be useful for treatment and diagnosis of developmental disorders.
Polynucleotides and polypeptides of the present invention can be used
diagnostically
and therapeutically to detect and treat many cancers, particularly
osteosarcoma and
chondrosarcoma. In addition, the expression of this gene product in synovium
would
suggest a role in the detection and treatment of disorders and conditions
affecting the
skeletal system, in particular osteoporosis, bone cancer, as well as,
disorders afflicting
connective tissues (e.g. arthritis, trauma, tendonitis, chrondomalacia and
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102
inflammation), such as in the diagnosis or treatment of various autoimmune
disorders
such as rheumatoid arthritis, lupus, scleroderma, and dermatomyositis as well
as
dwarfism, spinal deformation, and specific joint abnormalities as well as
chondrodysplasias (i.e. spondyloepiphyseal dysplasia congenita, familial
osteoarthritis, Atelosteogenesis type II, metaphyseal chondrodysplasia type
Schmid).
Moreover, the protein is useful in the detection, treatment, and/or prevention
of a variety of vascular disorders and condtions, which include, but are not
limited to
miscrovascular disease, vascular leak syndrome, aneurysm, stroke, embolism,
thrombosis, coronary artery disease, arteriosclerosis, and/or atherosclerosis.
Protein,
as well as, antibodies directed against the protein may show utility as a
tumor marker
and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:67 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1249 of SEQ ID
N0:67, b
is an integer of 15 to 1263, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:67, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 58
Contact of cells with supernatant expressing the product of this gene has been
shown to increase the permeability of the plasma membrane of renal messiaglia
cells
to calcium. Thus it is likely that the product of this gene is involved in a
signal
transduction pathway that is initiated when the product binds a receptor on
the surface
of the plasma membrane of renal and developing cells and tissues.Thus,
polynucleotides and polypeptides have uses which include, but are not limited
to,
activating renal and developing cells and tissues.
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In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: YCNLQCR (SEQ ID N0:273). Polynucleotides encoding these
polypeptides are also encompassed by the invention.
It has been discovered that this gene is expressed primarily in the whole
developing embryo, as well as in ovarian cancer and placenta.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: developmental or
reproductive
diseases and/or disorders, in addition to the following and ovarian cancer, as
well as
other cancers including breast cancer, colon cancer, cardiac tumors,
pancreatic cancer,
melanoma, retinoblastoma, glioblastoma, lung cancer, intestinal cancer,
testicular
cancer, stomach cancer, neuroblastoma, myxoma, myoma, lymphoma, endothelioma,
osteoblastoma, osteoclastoma, osteosarcoma, chondrosarcoma, adenoma, and the
like.
Similarly, polypeptides and antibodies directed to those polypeptides are
useful to
provide immunological probes for differential identification of the tissues)
or cell
type(s). For a number of disorders of the above tissues or cells, particularly
of the
developing and fetal system, expression of this gene at significantly higher
or lower
levels may be detected in certain tissues or cell types (e.g., developmental,
reproductive, and cancerous and wounded tissues) or bodily fluids (e.g.,
lymph,
amniotic fluid, serum, plasma, urine, synovial fluid or spinal fluid) taken
from an
individual having such a disorder, relative to the standard gene expression
Level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
The tissue distribution in embryonic and ovarian tissue, combined with the
detected calcium flux activity, suggests that the protein product of this
clone would be
useful for tretment and diagnosis of developmental disorders as well as
ovarian and
other cancers. Expression within embryonic tissue and other cellular sources
marked
by proliferating cells suggests this protein may play a role in the regulation
of cellular
division, and may show utility in the diagnosis and treatment of cancer and
other
proliferative disorders. Similarly, developmental tissues rely on decisions
involving
cell differentiation and/or apoptosis in pattern formation. Dysregulation of
apoptosis
can result in inappropriate suppression of cell death, as occurs in the
development of
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104
some cancers, or in failure to control the extent of cell death, as is
believed to occur in
acquired immunodeficiency and certain neurodegenerative disorders, such as
spinal
muscular atrophy (SMA).
Therefore, the polynucleotides and polypeptides of the present invention are
useful in treating, detecting, andlor preventing said disorders and
conditions, in
addition to other types of degenerative conditions. Thus this protein may
modulate
apoptosis or tissue differentiation and would be useful in the detection,
treatment,
and/or prevention of degenerative or proliferative conditions and diseases.
Alternatively, the protein is useful in the detection, treatment, and/or
prevention of
vascular conditions, which include, but are not limited to, microvascular
disease,
vascular leak syndrome, aneurysm, stroke, atherosclerosis, arteriosclerosis,
or
embolism. Protein, as well as, antibodies directed against the protein may
show utility
as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:68 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1603 of SEQ ID
N0:68, b
is an integer of 15 to 1617, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:68, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 59
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: SALIGNPKGCFGCFSPVVLREWSVESWKSLRPFQAICK
LKTNFR {SEQ ID N0:274). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
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It has been discovered that this gene is expressed primarily in hypothalamus
and anergic T cells.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: neurological and
inflammatory
defects, diseases, and/or disorders. Similarly, polypeptides and antibodies
directed to
those polypeptides are useful to provide immunological probes for differential
identification of the tissues) or cell type(s). For a number of disorders of
the above
tissues or cells, particularly of the central nervous and immune systems,
expression of
this gene at significantly higher or lower levels may be detected in certain
tissues
(e.g., neural, immune, hematopoietic, and cancerous and wounded tissues) or
bodily
fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid)
taken from an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
166 as residues: His-33 to Trp-38.
The tissue distribution in hypothalamus and T-cells suggests that the protein
product of this clone would be useful for study and treatment of immune and
nervous
system disorders. The protein product of this clone is useful for the
detection,
treatment, and/or prevention of neurodegenerative disease states, behavioral
disorders, or inflammatory conditions which include, but are not limited to
Alzheimer's Disease, Parkinson's Disease, Huntington's Disease, Tourette
Syndrome,
meningitis, encephalitis, demyelinating diseases, peripheral neuropathies,
neoplasia,
trauma, congenital malformations, spinal cord injuries, ischemia and
infarction,
aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive
compulsive disorder, depression, panic disorder, learning disabilities, ALS,
psychoses, autism, and altered behaviors, including disorders in feeding,
sleep
patterns, balance, and perception. In addition, elevated
Expression of this gene product in regions of the brain suggests it plays a
role
in normal neural function. Potentially, this gene product is involved in
synapse
formation, neurotransmission, learning, cognition, homeostasis, or neuronal
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106
differentiation or survival. Morever, the expression of this gene product
suggests a
role in regulating the proliferation; survival; differentiation; and/or
activation of
hematopoietic cell lineages, including blood stem cells. This gene product may
be
involved in the regulation of cytokine production, antigen presentation, or
other
processes suggesting a usefulness in the treatment of cancer (e.g. by boosting
immune
responses).
Since the gene is expressed in cells of lymphoid origin, the natural gene
product may be involved in immune functions. Therefore it may be also used as
an
agent for immunological disorders including arthritis, asthma,
immunodeficiency
diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease,
inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia,
psoriasis,
hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to
transplanted organs and tissues, such as host-versus-graft and graft-versus-
host
diseases, or autoimmunity disorders, such as autoimmune infertility, Tense
tissue
injury, demyelination, systemic lupus erythematosis, drug induced hemolytic
anemia,
rheumatoid arthritis, Sjogren's disease, scleroderma and tissues. Moreover,
the protein
may represent a secreted factor that influences the differentiation or
behavior of other
blood cells, or that recruits hematopoietic cells to sites of injury. In
addition, this gene
product may have commercial utility in the expansion of stem cells and
committed
progenitors of various blood lineages, and in the differentiation and/or
proliferation of
various cell types. Protein, as well as, antibodies directed against the
protein may
show utility as a tumor marker and/or immunotherapy targets for the above
listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:69 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1375 of SEQ ID
N0:69, b
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is an integer of 15 to 1389, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:69, and where b is greater than or
equal to a
+ 14.
S FEATURES OF PROTEIN ENCODED BY GENE NO: 60
The translation product of this gene shares nucleotide sequence homology
with the human PKDI gene which is thought to be important in polycystic kidney
disease.
This gene is expressed widely with a predominant expression exhibited in
liver, pediatric kidney, and in the whole 8 week old developing human embryo.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: cancer, growth, renal, and
metabolic defects, diseases, and/or disorders. Similarly, polypeptides and
antibodies
directed to those polypeptides are useful to provide immunological probes for
differential identification of the tissues) or cell type(s). For a number of
disorders of
the above tissues or cells, particularly of the endocrine, digestive and
immune
systems, expression of this gene at significantly higher or lower levels may
be
detected in certain tissues or cell types (e.g., renal, metabolic, hepatic,
developmental,
and cancerous and wounded tissues) or bodily fluids (e.g., lymph, amniotic
fluid, bile,
serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual
having
such a disorder, relative to the standard gene expression level, i.e., the
expression
level in healthy tissue from an individual not having the disorder.
The tissue distribution in pediatric kidney suggests that the protein product
of
this clone would be useful for study and treatment of renal and general
neoplasias and
growth and development disorders. The protein product of this clone could be
used in
the treatment and/or detection of kidney diseases including renal failure,
nephritus,
renal tubular acidosis, proteinuria, pyuria, edema, pyelonephritis,
hydronephritis,
nephrotic syndrome, crush syndrome, glomerulonephritis, hematuria, renal colic
and
kidney stones, in addition to Wilm's Tumor Disease, and congenital kidney
abnormalities such as horseshoe kidney, polycystic kidney, and Falconi's
syndrome.
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Moreover, the expression within embryonic tissue suggests this protein may
play a role in the regulation of cellular division, and may show utility in
the diagnosis
and treatment of cancer and other proliferative disorders, particularly of the
liver and
other organs. Similarly, developmental tissues rely on decisions involving
cell
differentiation and/or apoptosis in pattern formation. Dysregulation of
apoptosis can
result in inappropriate suppression of cell death, as occurs in the
development of some
cancers, or in failure to control the extent of cell death, as is believed to
occur in
acquired immunodeficiency and certain neurodegenerative disorders, such as
spinal
muscular atrophy (SMA). Therefore, the polynucleotides and polypeptides of the
present invention are useful in treating, detecting, and/or preventing said
disorders
and conditions, in addition to other types of degenerative conditions. Thus
this protein
may modulate apoptosis or tissue differentiation and would be useful in the
detection,
treatment, and/or prevention of degenerative or proliferative conditions and
diseases.
Protein, as well as, antibodies directed against the protein may show utility
as a tumor
marker andlor immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:70 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1882 of SEQ ID
N0:70, b
is an integer of 15 to 1896, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:70, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 61
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: HEAALRGP (SEQ ID N0:275). Polynucleotides encoding
these polypeptides are also encompassed by the invention.
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It has been discovered that this gene is expressed primarily in human striatum
depression.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: stroke, in addition to
other,
neurologically-related diseases and/or defects. Similarly, polypeptides and
antibodies
directed to those polypeptides are useful to provide immunological probes for
differential identification of the tissues) or cell type(s). For a number of
disorders of
the above tissues or cells, particularly of the central nervous system,
expression of
this gene at significantly higher or lower levels may be detected in certain
tissues
(e.g., neural, musculoskeletal, and cancerous and wounded tissues) or bodily
fluids
(e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from
an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
168 as residues: Glu-50 to Glu-61.
The tissue distribution in human striatum depression suggests that the protein
product of this clone would be useful for study and treatment of central
nervous
system orders, such as seizures and other neurological conditions. The protein
product
of this clone is useful for the detection, treatment, and/or prevention of
neurodegenerative disease states, behavioral disorders, or inflammatory
conditions
which include, but are not limited to Alzheimer's Disease, Parkinson's
Disease,
Huntington's Disease, Tourette Syndrome, meningitis, encephalitis,
demyelinating
diseases, peripheral neuropathies, neoplasia, trauma, congenital
malformations, spinal
cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia,
mania, dementia, paranoia, obsessive compulsive disorder, depression, panic
disorder,
learning disabilities, ALS, psychoses, autism, and altered behaviors,
including
disorders in feeding, sleep patterns, balance, and perception. In addition,
elevated
Expression of this gene product in regions of the brain suggests it plays a
role
in normal neural function. Potentially, this gene product is involved in
synapse
formation, neurotransmission, learning, cognition, homeostasis, or neuronal
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differentiation or survival. Protein, as well as, antibodies directed against
the protein
may show utility as a tumor marker and/or immunotherapy targets for the above
listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:71 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 294 of SEQ ID
N0:71, b
is an integer of 15 to 308, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:71, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 62
This clone has homology to a cystine rich granulin peptides) from
leucocyte(s) which has been termed Granulin E. Granulins inhibit keratinocytes
and is
useful topically for wound healing. The gene encoding the disclosed cDNA is
believed to reside on chromosome 3. Accordingly, polynucleotides related to
this
invention are useful as a marker in linkage analysis for chromosome 3.
It has been discovered that this gene is expressed primarily in infant brain.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: neurological,
developmental, and
growth defects. Similarly, polypeptides.and antibodies directed to those
polypeptides
are useful to provide immunological probes for differential identification of
the
tissues) or cell type(s). For a number of disorders of the above tissues or
cells.
particularly of the fetus and the nervous system, expression of this gene at
significantly higher or lower levels may be detected in certain tissues (e.g.,
neural,
developmental, growth, and cancerous and wounded tissues) or bodily fluids
(e.g.,
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lymph, amniotic fluid, serum, plasma, urine, synovial fluid or spinal fluid)
taken from
an individual having such a disorder, relative to the standard gene expression
level,
i.e., the expression level in healthy tissue from an individual not having the
disorder.
Based on the strong conservation of cysteine residues, the polypeptide of the
present
invention can be used to inhibit keratinocytes and promote wound healing.
The tissue distribution in infant brain suggests that the protein product of
this
clone would be useful for study and treatment of nervous system,
neurodegenerative
and developmental disorders. The protein product of this clone is useful for
the
detection, treatment, and/or prevention of neurodegenerative disease states,
behavioral disorders, or inflammatory conditions which include, but are not
limited to
Alzheimer's Disease, Parkinson's Disease, Huntington's Disease, Tourette
Syndrome,
meningitis, encephalitis, demyelinating diseases, peripheral neuropathies,
neoplasia,
trauma, congenital malformations, spinal cord injuries, ischemia and
infarction,
aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive
compulsive disorder, depression, panic disorder, learning disabilities, ALS,
psychoses, autism, and altered behaviors, including disorders in feeding,
sleep
patterns, balance, and perception. In addition, elevated
Expression of this gene product in regions of the brain suggests it plays a
role
in normal neural function. Potentially, this gene product is involved in
synapse
formation, neurotransmission, learning, cognition, homeostasis, or neuronal
differentiation or survival. Protein, as well as, antibodies directed against
the protein
may show utility as a tumor marker and/or immunotherapy targets for the above
listed
tissues. The homology to granulin proteins suggest the protein product of this
clone is
useful for the treatment, diagnosis, and/or prevention of various skin
disorders
including congenital disorders (i.e. nevi, moles, freckles, Mongolian spots,
hemangiomas, port-wine syndrome), integumentary tumors (i.e. keratoses,
Bowen's
disease, basal cell carcinoma, squamous cell carcinoma, malignant melanoma,
Paget's
disease, mycosis fungoides, and Kaposi's sarcoma), injuries and inflammation
of the
skin (i.e.wounds, rashes, prickly heat disorder, psoriasis, dermatitis),
atherosclerosis,
uticaria, eczema, photosensitivity, autoimmune disorders {i.e. lupus
erythematosus,
vitiligo, dermatomyositis, morphea, scleroderma, pemphigoid, and pemphigus),
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keloids, striae, erythema, petechiae, purpura, and xanthelasma. In addition,
such
disorders may predispose increased susceptibility to viral and bacterial
infections of
the skin (i.e. cold sores, warts, chickenpox, molluscum contagiosum, herpes
zoster,
boils, cellulitis, erysipelas, impetigo, tinea, althletes foot, and ringworm).
Moreover,
the protein product of this clone may also be useful for the treatment or
diagnosis of
various connective tissue disorders such as arthritis, trauma, tendonitis,
chrondomalacia and inflammation, autoimmune disorders such as rheumatoid
arthritis, lupus, scleroderma, and dermatomyositis as well as dwarfism, spinal
deformation, and specific joint abnormalities as well as chondrodysplasias
(i.e.
spondyloepiphyseal dysplasia congenita, familial osteoarthritis,
Atelosteogenesis type
II, metaphyseal chondrodysplasia type Schmid). Protein, as well as, antibodies
directed against the protein may show utility as a tumor marker and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:72 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1674 of SEQ ID
N0:72, b
is an integer of 15 to 1688, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:72, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 63
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: SNAAGNVVRAFLYINHLKL GCKVGLA (SEQ ID N0:276}.
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
It has been discovered that this gene is expressed primarily in prostate
cancer
and dendritic cells.
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Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: reproductive, immune, and
hematopoietic diseases, defects and/or disorders. Similarly, polypeptides and
antibodies directed to those polypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the endocrine and immune
systems,
expression of this gene at significantly higher or lower levels may be
detected in
certain tissues or cell types (e.g., reproductive, immune, hematopoietic, and
cancerous
and wounded tissues) or bodily fluids (e.g., lymph, seminal fluid, serum,
plasma,
urine, synovial fluid or spinal fluid) taken from an individual having such a
disorder,
relative to the standard gene expression level, i.e., the expression level in
healthy
tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
170 as residues: Trp-47 to Thr-54.
The tissue distribution in prostate cells and tissues indicates that the
protein
products of this clone are useful for study, diagnosis and treatment of
neoplasias, esp.
of the prostate, and hormonal and metabolic disorders. Moreover, the protein
product
of this clone is useful for the treatment and diagnosis of hematopoietic
related
disorders such as anemia, pancytopenia, leukopenia, thrombocytopenia or
leukemia
since stromal cells are important in the production of cells of hematopoietic
lineages.
The uses include bone marrow cell ex- vivo culture, bone marrow
transplantation,
bone marrow reconstitution, radiotherapy or chemotherapy of neoplasia. The
gene
product may also be involved in lymphopoiesis, therefore, it can be used in
immune
disorders such as infection, inflammation, allergy, immunodeficiency etc. In
addition,
this gene product may have commercial utility in the expansion of stem cells
and
committed progenitors of various blood lineages, and in the differentiation
and/or
proliferation of various cell types. Protein, as well as, antibodies directed
against the
protein may show utility as a tumor marker and/or immunotherapy targets for
the
above listed tissues.
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Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:73 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1124 of SEQ ID
N0:73, b
is an integer of 15 to 1138, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:73, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 64
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: NWAVLNMLLSKGKITIFLGPLECGS (SEQ ID N0:277).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
It has been discovered that this gene is expressed primarily in B cell
lymphoma.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune and hematopoietic
diseases, disorders, andJor defects, particularly cancers. Similarly,
polypeptides and
antibodies directed to those polypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the hemopoietic and immune
systems,
expression of this gene at significantly higher or lower levels may be
detected in
certain tissues or cell types (e.g., immune, hematopoietic, and cancerous and
wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
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The tissue distribution in B cell lymphoma suggests that the protein product
of
this clone would be useful for study and treatment of blood and immune
disorders and
neoplasias, esp. of the lymphatic system. The protein product of this clone is
useful
for the treatment and diagnosis of hematopoietic related disorders such as
anemia,
pancytopenia, leukopenia, thrombocytopenia or leukemia since stromal cells are
important in the production of cells of hematopoietic lineages. The uses
include bone
marrow cell ex- vivo culture, bone marrow transplantation, bone marrow
reconstitution, radiotherapy or chemotherapy of neoplasia. The gene product
may also
be involved in lymphopoiesis, therefore, it can be used in immune disorders
such as
infection, inflammation, allergy, immunodeficiency etc. In addition, this gene
product
may have commercial utility in the expansion of stem cells and committed
progenitors of various blood lineages, and in the differentiation and/or
proliferation of
various cell types. Protein, as well as, antibodies directed against the
protein may
show utility as a tumor marker and/or immunotherapy targets for the above
listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:74 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 763 of SEQ ID
N0:74, b
is an integer of 15 to 777, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:74, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 65
It has been discovered that this gene is expressed primarily in B cell
lymphoma.
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Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune and hematopoietic
diseases, disorders, and/or defects, particularly cancer. Similarly,
poIypeptides and
antibodies directed to those polypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the hemopoietic and immune
systems,
expression of this gene at significantly higher or lower levels may be
detected in
certain tissues or cell types {e.g., immune, hematopoietic, and cancerous and
wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
The tissue distribution in B cell lymphoma suggests that the protein product
of
this clone would be useful for study and treatment of neplasias, esp. of
lymphatic
organs, and immune disorders. The protein product of this clone is useful for
the
treatment and diagnosis of hematopoietic related disorders such as anemia,
pancytopenia, leukopenia, thrombocytopenia or leukemia since stromal cells are
important in the production of cells of hematopoietic Iineages. The uses
include bone
marrow cell ex- vivo culture, bone marrow transplantation, bone marrow
reconstitution, radiotherapy or chemotherapy of neoplasia. The gene product
may also
be involved in lymphopoiesis, therefore, it can be used in immune disorders
such as
infection, inflammation, allergy, immunodeficiency etc. In addition, this gene
product
may have commercial utility in the expansion of stem cells and committed
progenitors of various blood lineages, and in the differentiation and/or
proliferation of
various cell types. Protein, as well as, antibodies directed against the
protein may
show utility as a tumor marker and/or immunotherapy targets for the above
listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:75 and may have been publicly available prior to
conception of
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the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1046 of SEQ ID
N0:75, b
is an integer of 15 to 1060, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:75, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 66
The translation product of this gene shares sequence homology with a rat
protein phosphatase, in addition to, a human heterogeneous nuclear
ribonucleoprotein
R (See Genbank Accession No.gi12697103 (AF000364)). When tested against PC12
cell lines, supernatants removed from cells containing this gene activated the
EGR1
(early growth response gene 1) promoter element. Thus, it is likely that this
gene
activates sensory neuron cells through the EGRI signal transduction pathway.
EGR1
is a separate signal transduction pathway from Jak-STAT, genes containing the
EGR1
promoter are induced in various tissues and cell types upon activation,
leading the
cells to undergo differentiation and proliferation. This gene also showed
activity in
sensory neurons using the EGR assay described in the Example section.
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: PSHQTRKGKSAKLLDRPPEALRMKIITTTLLLACHLQLEV
GVVVGGEVD (SEQ ID N0:278),
FQASSANNQQNWGSQPIAQQPLQQGGDYSG
NYGYNNDNQEFYQDTYGQQWK (SEQ ID N0:279), WXPLLXTSGSPGLXGFG
TRMNGKEIEGEEIEIVLAKPPDKKRKERQAARQASRSTAYEDYYYHPPPRMPP
PIRGRGRGGGRGGYGYPPDYYGYEDYYDDYYGYDYHDYRGGYEDPYYGYD
DGYAVRGRGGGRGGRGAPPPPRGRGAPPPRGRAGYSQRGAPLGPPRGSRGG
RGGPAQQQRGRGSRGSRGNRGGNVGGKRKADGYNQPDSKRRQPTTNRTGV
PNPSLSSRFSKVVTILVTMVTIMTTRNFIRILMGNSGSRQVRA (SEQ ID
N0:280), RMNGKEIEGEEIEIVLAKPPDKKRKER (SEQ ID N0:281 ), YYHPPP
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RMPP PIRGRGRGGGRGGYG (SEQ ID N0:282), DYRGGYEDPYYGYDDGYAV
RGRGGGR (SEQ ID N0:283), PPPRGRAGYSQRGAPLGPPRGSRGGRGG (SEQ
ID N0:284), and/or ADGYNQPDSK RRQPTTNRTGVPNPSLSSRFSKVVT (SEQ
ID N0:285). Polynucleotides encoding these polypeptides are also encompassed
by
the invention. The gene encoding the disclosed cDNA is believed to reside on
chromosome 1. Accordingly, polynucleotides related to this invention are
useful as
a marker in linkage analysis for chromosome 1.
It has been discovered that this gene is expressed primarily in human primary
breast cancer, lung, and leukocytes.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: reproductive, immune, or
pulmonary diseases and/or disorders, particularly breast cancer. Similarly,
polypeptides and antibodies directed to those polypeptides are useful to
provide
immunological probes for differential identification of the tissues) or cell
type(s). For
a number of disorders of the above tissues or cells, particularly of the
reproductive,
immune and respiratory systems, expression of this gene at significantly
higher or
lower levels may be detected in certain tissues or cell types (e.g.,
reproductive,
immune, pulmonary, and cancerous and wounded tissues) or bodily fluids (e.g.,
lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from an
individual
having such a disorder, relative to the standard gene expression level, i.e.,
the
expression level in healthy tissue from an individual not having the disorder.
The tissue distribution in breast cancer cells and tissues, in addition to
immune
cells, combined with the homology to a protein phosphatase suggests that the
protein
product of this clone would be useful for diagnosis and treatment of breast
cancer and
abnormalities of the lung and the immune system. Morever, the expression of
this
gene product suggests a role in regulating the proliferation; survival;
differentiation;
and/or activation of hematopoietic cell lineages, including blood stem cells.
This gene
product may be involved in the regulation of cytokine production, antigen
presentation, or other processes suggesting a usefulness in the treatment of
cancer
(e.g. by boosting immune responses).
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Since the gene is expressed in cells of lymphoid origin, the natural gene
product may be involved in immune functions. Therefore it may be also used as
an
agent for immunological disorders including arthritis, asthma,
immunodeflciency
diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease.
inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia,
psoriasis,
hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to
transplanted organs and tissues, such as host-versus-graft and graft-versus-
host
diseases, or autoimmunity disorders, such as autoimmune infertility, tense
tissue
injury, demyelination, systemic lupus erythematosis, drug induced hemolytic
anemia,
rheumatoid arthritis, Sjogren's disease, scleroderma and tissues.
Moreover, the protein may represent a secreted factor that influences the
differentiation or behavior of other blood cells, or that recruits
hematopoietic cells to
sites of injury. In addition, this gene product may have commercial utility in
the
expansion of stem cells and committed progenitors of various blood lineages,
and in
the differentiation and/or proliferation of various cell types. The protein is
useful in
modulating the immune response to aberrant cells and cell types, particularly
proliferative cells (e.g. protein may increase the immunogenicity of tumor
antigens
either directly or indirectly, or may activate apoptosis). The protein is
useful in
treating, detecting, and/or preventing various pulmonary disorders, which
include, but
are not limited to, ARDS, emphysema, and cystic fibrosis. Protein, as well as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:76 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To Iist every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1489 of SEQ ID
N0:76, b
is an integer of 15 to 1503, where both a and b correspond to the positions of
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nucleotide residues shown in SEQ ID N0:76, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 67
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: LQIPPSSQSLGLKNADSSI (SEQ ID N0:286), GGPPESAPW
LPAVLRAPVLTSRCASSDSEGPVWFCQPGSGPSSTEMSCHCILGPGSSCLCVL
RGSMWTPSVPGWPQPAKETGASSCSVFSANNGSCPLPLHNHQRQASLDTGL
SLEHVPGESYFYSPVG (SEQ ID N0:287), SSDSEGPVWFCQPGSGPSSTEMSC
HCILGPGSSC (SEQ ID N0:288), WTPSVPGWPQPAKETGASSCSVFSANNG
(SEQ ID N0:289), and/or QRQASLDTGL SLEHVPGESYF (SEQ ID N0:290).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
It has been discovered that this gene is expressed primarily in human B cell
lymphoma.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune or hematopoietic
diseases
and/or disorders, particularly B cell lymphoma. Similarly, polypeptides and
antibodies directed to those polypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the immune system, expression
of this
gene at significantly higher or lower levels may be detected in certain
tissues or cell
types (e.g., immune, hematopoietic, and cancerous and wounded tissues) or
bodily
fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid)
taken from an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
The tissue distribution in B-cell lymphoma suggests that the protein product
of
this clone would be useful for diagnosis and treatment of immune or
hematopoietic
diseases and/or disorders, particularly proliferative conditions. Morever, the
expression of this gene product suggests a role in regulating the
proliferation;
survival; differentiation; and/or activation of hematopoietic cell lineages,
including
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blood stem cells. This gene product may be involved in the regulation of
cytokine
production, antigen presentation, or other processes suggesting a usefulness
in the
treatment of cancer (e.g. by boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the natural gene
product may be involved in immune functions. Therefore it may be also used as
an
agent for immunological disorders including arthritis, asthma,
immunodeficiency
diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease,
inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia,
psoriasis,
hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to
transplanted organs and tissues, such as host-versus-graft and graft-versus-
host
diseases, or autoimmunity disorders, such as autoimmune infertility, Tense
tissue
injury, demyelination, systemic lupus erythematosis, drug induced hemolytic
anemia,
rheumatoid arthritis, Sjogren's disease, scleroderma and tissues. Moreover,
the protein
may represent a secreted factor that influences the differentiation or
behavior of other
blood cells, or that recruits hematopoietic cells to sites of injury. In
addition, this gene
product may have commercial utility in the expansion of stem cells and
committed
progenitors of various blood lineages, and in the differentiation andlor
proliferation of
various cell types. The uses include bone marrow cell ex- vivo culture, bone
marrow
transplantation, bone marrow reconstitution, radiotherapy or chemotherapy of
neoplasia. The gene product may also be involved in lymphopoiesis, therefore,
it can
be used in immune disorders such as infection, inflammation, allergy,
immunodeficiency etc. In addition, this gene product may have commercial
utility in
the expansion of stem cells and committed progenitors of various blood
lineages, and
in the differentiation and/or proliferation of various cell types. Protein, as
well as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:77 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
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would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 858 of SEQ ID
N0:77, b
is an integer of 15 to 872, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:77, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 68
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: SSSLVLTIRSQTLFLASFIHSTSIFCALN (SEQ ID N0:291 ).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
It has been discovered that this gene is expressed primarily in osteoarthritic
cartilage.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: osteoarthritis and other
bone/cartilage disorders, particularly degenerative conditions. Similarly,
polypeptides
and antibodies directed to those polypeptides are useful to provide
immunological
probes for differential identification of these tissues) or cell type(s). For
a number of
disorders of the above tissues or cells, particularly of the skelatal system,
expression
of this gene at significantly higher or lower levels may be detected in
certain tissues
or cell types (e.g., skeletal, joint, autoimmune, and cancerous and wounded
tissues) or
bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal
fluid) taken
from an individual having such a disorder, relative to the standard gene
expression
level, i.e., the expression level in healthy tissue from an individual not
having the
disorder.
The tissue distribution in osteoarthritic cartilage suggests that the protein
product of this clone would be useful for the diagnosis, treatment, and/or
prevention
of osteoarthritis. Moreover, the gene product is useful in the detection and
treatment
of disorders and conditions affecting the skeletal system, in particular
osteoporosis,
bone cancer, as well as, disorders afflicting connective tissues (e.g.
arthritis, trauma,
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tendonitis, chrondomalacia and inflammation), such as in the diagnosis or
treatment
of various autoimmune disorders such as rheumatoid arthritis, lupus,
scleroderma, and
dermatomyositis as well as dwarfism, spinal deformation, and specific joint
abnormalities as well as chondrodysplasias (i.e. spondyloepiphyseal dysplasia
congenita, familial osteoarthritis, Atelosteogenesis type II, metaphyseal
chondrodysplasia type Schmid). Protein, as well as, antibodies directed
against the
protein may show utility as a tumor marker and/or immunotherapy targets for
the
above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:78 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 559 of SEQ ID
N0:78, b
is an integer of 15 to 573, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:78, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 69
The gene encoding the disclosed cDNA is believed to reside on chromosome
17. Accordingly, polynucleotides related to this invention are useful as a
marker in
linkage analysis for chromosome 17.
It has been discovered that this gene is expressed primarily in fetal brain,
pharynx carcinoma, and Hodgkin's lymphoma.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: developmental and/or
proliferative
diseases and disorders, particularly pharynx carcinoma, and Hodgkin's
lymphoma.
Similarly, polypeptides and antibodies directed to those polypeptides are
useful to
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provide immunological probes for differential identification of the tissues)
or cell
type(s). For a number of disorders of the above tissues or cells, particularly
of the
digestive and immune systems, expression of this gene at significantly higher
or
lower levels may be detected in certain tissues or cell types (e.g.,
developmental,
proliferative cancerous and wounded tissues) or bodily fluids (e.g., lymph,
serum,
plasma, urine, amniotic fluid, synovial fluid or spinal fluid) taken from an
individual
having such a disorder, relative to the standard gene expression level, i.e.,
the
expression level in healthy tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
176 as residues: Tyr-30 to Ser-40.
The tissue distribution in pharynx carcinoma and Hodgkin's lymphoma
suggests that the protein product of this clone would be useful for diagnosis
and
treatment of immune and proliferative conditions. Moreover, expression within
fetal
tissue and other cellular sources marked by proliferating cells suggests this
protein
may play a role in the regulation of cellular division, and may show utility
in the
diagnosis and treatment of cancer and other proliferative disorders.
Similarly,
developmental tissues rely on decisions involving cell differentiation and/or
apoptosis
in pattern formation. Dysregulation of apoptosis can result in inappropriate
suppression of cell death, as occurs in the development of some cancers, or in
failure
to control the extent of cell death, as is believed to occur in acquired
immunodeficiency and certain neurodegenerative disorders, such as spinal
muscular
atrophy (SMA). Therefore, the polynucleotides and polypeptides of the present
invention are useful in treating, detecting, and/or preventing said disorders
and
conditions, in addition to other types of degenerative conditions. Thus this
protein
may modulate apoptosis or tissue differentiation and would be useful in the
detection,
treatment, and/or prevention of degenerative or proliferative conditions and
diseases.
Alternatively, the protein product of this clone is useful for the detection,
treatment, and/or prevention of neurodegenerative disease states, behavioral
disorders, or inflammatory conditions which include, but are not limited to
Alzheimer's Disease, Parkinson's Disease, Huntington's Disease, Tourette
Syndrome,
meningitis, encephalitis, demyelinating diseases, peripheral neuropathies,
neoplasia,
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trauma, congenital malformations, spinal cord injuries, ischenua and
infarction,
aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive
compulsive disorder, depression, panic disorder, learning disabilities, ALS,
psychoses, autism, and altered behaviors, including disorders in feeding,
sleep
patterns, balance, and perception. In addition, elevated
Expression of this gene product in regions of the brain suggests it plays a
role
in normal neural function. Potentially, this gene product is involved in
synapse
formation, neurotransmission, learning, cognition, homeostasis, or neuronal
differentiation or survival. Protein, as well as, antibodies directed against
the protein
may show utility as a tumor marker and/or immunotherapy targets for the above
listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:79 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1495 of SEQ ID
N0:79, b
is an integer of 15 to 1509, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:79, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 70
The translation product of this gene shares sequence homology with insuIin-
like growth factor binding protein. Moreover, the protein has homology to the
human
Slit-1 protein (See Genbank Accession No. gnIIPIDId1036170 (AB0171b7)), which
is
thought to play an integral role in neural development. In Drosophila
embryogenesis,
the slit gene has been shown to play a critical role in CNS midline formation.
Each
Slit gene encodes a putative secreted protein, which contains conserved
protein-
protein interaction domains including leucine-rich repeats (LRR) and epidermal
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growth factor (EGF)-like motifs, like that of the Drosophila protein. The Slit
genes
form an evolutionary conserved group in vertebrates and invertebrates, and the
mammalian Slit proteins may participate in the formation and maintenance of
the
nervous and endocrine systems by protein-protein interactions.
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: the EGF-like domain: CCCRLGLSGPKC (SEQ ID N0:292); in
addition to the following: RAFWGLGALQLLDLSANQLEAL (SEQ ID N0:293),
HASGRRTGSADDGLQGRTGSGPPTAGAGGGGAAP (SEQ ID N0:294),
VSAAAGARLAPRAPGAPAGCRPMRGCAARAAARKSLVPVLPAGWRSGPAA
AARPGPRRLAHAPSAARSRAGPGAVARPLPRRHLAAAHGRGCGPAAARAGA
GSGPGARRAARVPTAGRPPGTHVHTSGQSGAPRDPEGEALADTWAQTGQGD
SSSNSSSSGRGRDQEGPRMGAAPPPPAPAVGGPLPVRPWSPSSAEPVLRPDAW
( S E Q I D N O : 2 9 5 ) ,
TRPAAERAPRTTGSRDAQAAGLPPRVPGAGGLPPCGALPGR
GLGRCCCCCCCCRLGLSGPKCRPGPRPRGPWAPRTAPRCARACREACQLSAL
SLPAVPPGLSLRLRALLLDHNRVRALPPGAFAGAGALQRLDLRENGLHSVHV
RAFWGLGALQLLDLSANQLEALAPGTFAPLRALRNLSLAGNRLARLEPAALG
ALPLLRSLSLQDNELAALAPGLLGRLPALDALHLRGNPWGCGCALRPLCAWL
RRHPLPASEAETVLCV WPGRLTLSPLTAFSDAAFSHCAQPLALRDLARGLHA
RAGLLPRQPGFLPGAGLWAHRLPCAPPPPPHRRPPPAETVQTRTPIPTPTAVPR
PRTRGAPSAAAQA (SEQ ID N0:296),
GCRPMRGCAARAAARKSLVPVLPAGWRSGP AAAARPGPRRLAHAPSA (SEQ
ID N0:297), PGAVARPLPRRHLAAAHGRGCG PAAARAGA (SEQ ID N0:298),
SGQSGAPRDPEGEALADTWAQTGQ (SEQ ID N0:299),
PPAPAVGGPLPVRPWSPSSAEPV (SEQ ID N0:300), APRTTGSRD
AQAAGLPPRVPGAGGLP (SEQ ID N0:301 ), GPRPRGPWAPRTAPRCARACRE
(SEQ ID N0:302), AVPPGLSLRLRALLLDHNRVRALPPGAFAGA (SEQ ID
N0:303), LGALQLLDLSANQLEALAPGTFAP (SEQ ID N0:304), PPGAFAGAG
ALQRLDLRENGLHSVHVRAFWGLGALQ (SEQ ID N0:305), RNLSLAGNRLA
RLEPAALGALPLLRSLS (SEQ ID N0:306), LPALDALHLRGNPWGCGCALRP
LCAW (SEQ ID N0:307), TVLCVWPGRLTLSPLTAFSDAAFSHCAQPLALRD
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(SEQ ID N0:308), LHARAGLLPRQPGFLPGAGLWAHR (SEQ ID N0:309),
and/or TVQTRTPIPTPTAVPRPRTRGAPS (SEQ ID N0:310). Polynucleotides
encoding these polypeptides are also encompassed by the invention.
It has been discovered that this gene is expressed primarily in a breast
cancer
cell line, MDA36.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: neural, reproductive, and
proliferative diseases and/or disorders, particularly breast cancer and
degenerative
conditions. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues)
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
the reproductive system, expression of this gene at significantly higher or
lower levels
may be detected in certain tissues or cell types (e.g., neural, reproductive,
and
proliferative cancerous and wounded tissues) or bodily fluids (e.g., lymph,
serum,
plasma, urine, synovial fluid or spinal fluid) taken from an individual having
such a
disorder, relative to the standard gene expression level, i.e., the expression
level in
healthy tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
177 as residues: Met-1 to Arg-10, Arg-64 to Ala-71, Gly-124 to Gly-131, Pro-
189 to
Arg-194, Val-223 to Gly-228.
The tissue distribution in a breast cancer cells and tissues and homology to
insulin-like growth factor binding protien suggests that the protein product
of this
clone would be useful for diagnosis and treatment of breast cancer, and other
forms of
cancer. Moreover, the homology to the conserved human slit-1 protein suggests
that
the protein is useful in the treatment, diagnosis, and/or prevention of neural
disorders,
particularly developmental and degenerative conditions. Similarly, the protein
is
useful for the treatment and/or diagnosis of neurodegenerative disease states,
behavioral disorders, or inflammatory conditions which include, but are not
limited to
Alzheimer's Disease, Parkinson's Disease, Huntington's Disease, Tourette
Syndrome,
meningitis, encephalitis, demyelinating diseases, peripheral neuropathies,
neoplasia,
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trauma, congenital malformations, spinal cord injuries, ischemia and
infarction,
aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive
compulsive disorder, depression, panic disorder, learning disabilities, ALS,
psychoses, autism, and altered behaviors, including disorders in feeding,
sleep
patterns, balance, and perception. In addition, elevated
Expression of this gene product in regions of the brain suggests it plays a
role
in normal neural function. Potentially, this gene product is involved in
synapse
formation, neurotransmission, learning, cognition, homeostasis, or neuronal
differentiation or survival. Protein, as well as, antibodies directed against
the protein
may show utility as a tumor marker and/or immunotherapy targets for the above
listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:80 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1095 of SEQ ID
N0:80, b
is an integer of 15 to 1109, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:80, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 71
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: HASGRPDRSSAPIGNSGLPCPDLEPLGGLQSKCRLCAPTE
ARGLWSRSLCSDRCDTWRS (SEQ ID N0:311), and/or GLPCPDLEPLGGLQSK
CRLCAPTEARGLW (SEQ ID N0:312). Polynucleotides encoding these
polypeptides are also encompassed by the invention. This gene also maps to
chromosome 1, and therefore can be used in linkage analysis as a marker for
chromosome 1.
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It has been discovered that this gene is expressed primarily in salivary gland
and colon carcinoma.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: colon carcinoma and other
digestive system or gastrointestinal diseases and/or disorders. Similarly,
polypeptides
and antibodies directed to those polypeptides are useful to provide
immunological
probes for differential identification of the tissues) or cell type(s). For a
number of
disorders of the above tissues or cells, particularly of the digestive system,
expression
of this gene at significantly higher or lower levels may be detected in
certain tissues
or cell types (e.g., digestive system, gastrointestinal, metabolic, and
cancerous and
wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, chyme,
bile,
synovial fluid or spinal fluid) taken from an individual having such a
disorder,
relative to the standard gene expression level, i.e., the expression level in
healthy
tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
178 as residues: Val-34 to Leu-39, Ser-64 to Cys-74, Ser-86 to Ser-95, Arg-128
to
Ala-136.
The tissue distribution in salivary gland and colon carcinoma suggests that
the
protein product of this clone would be useful for the treatment and diagnosis
colon
cancer and other digestive system diseases and/or disorders, such as ulcers,
and other
proliferative conditions. Protein, as well as, antibodies directed against the
protein
may show utility as a tumor marker and/or immunotherapy targets for the above
listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:81 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
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general formula of a-b, where a is any integer between 1 to 793 of SEQ ID
N0:81, b
is an integer of 15 to 807, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:81, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 72
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: QEWESELGERRKPLQA (SEQ ID N0:313). Polynucleotides
encoding these polypeptides are also encompassed by the invention.
It has been discovered that this gene is expressed primarily in 6 week old
human embryos.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: embryological defects;
aberrant
development; aberrant cellular proliferation (e.g. cancers), and other
developmentally
related or proliferative diseases and/or disorders. Similarly, polypeptides
and
antibodies directed to those polypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the developing human embryo,
expression
of this gene at significantly higher or lower levels may be detected in
certain tissues
or cell types (e.g., developmental, and cancerous and wounded tissues) or
bodily
fluids (e.g., lymph, serum, plasma, amniotic fluid, urine, synovial fluid or
spinal fluid)
taken from an individual having such a disorder, relative to the standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
The tissue distribution in 6 week old human embryos suggests that the protein
product of this clone would be useful for the diagnosis and/or treatment of
defects in
embryonic development. Elevated expression of this gene product in early 6
week
human embryos suggests that this gene product plays a critical role in normal
human
development. Alternatively, this gene product may be involved in the pattern
of
cellular proliferation that accompanies early embryogenesis. Thus, aberrant
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Expression of this gene product in tissues - particularly adult tissues - may
correlate with patterns of abnormal cellular proliferation, such as found in
various
cancers. Moreover, this protein may play a role in the regulation of cellular
division,
and may show utility in the diagnosis and treatment of cancer and other
proliferative
disorders. Similarly, developmental tissues rely on decisions involving cell
differentiation and/or apoptosis in pattern formation. Dysregulation of
apoptosis can
result in inappropriate suppression of cell death, as occurs in the
development of some
cancers, or in failure to control the extent of cell death, as is believed to
occur in
acquired imrnunodeficiency and certain neurodegenerative disorders, such as
spinal
muscular atrophy (SMA). Therefore, the polynucleotides and polypeptides of the
present invention are useful in treating, detecting, and/or preventing said
disorders
and conditions, in addition to other types of degenerative conditions. Thus
this protein
may modulate apoptosis or tissue differentiation and would be useful in the
detection,
treatment, and/or prevention of degenerative or proliferative conditions and
diseases.
Protein, as well as, antibodies directed against the protein may show utility
as a tumor
marker and/or imlnunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:82 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1029 of SEQ ID
N0:82, b
is an integer of 15 to 1043, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:82, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 73
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: CQSSNLIFFQFVNILFNLMMDILVDFSITKMPINSIFSLYF
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CYEII (SEQ ID N0:314). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
It has been discovered that this gene is expressed primarily in 6 week old
human embryo.
S Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: abnormal embryonic
development; abnormal cellular proliferation; developmental defects, and other
developmentally related or proliferative diseases and/or conditions.
Similarly,
polypeptides and antibodies directed to those polypeptides are useful to
provide
immunological probes for differential identification of the tissues) or cell
type(s). For
a number of disorders of the above tissues or cells, particularly of the
developing
human embryo, expression of this gene at significantly higher or lower levels
may be
detected in certain tissues or cell types (e.g., developmental, and cancerous
and
wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, amniotic fluid,
urine,
synovial fluid or spinal fluid) taken from an individual having such a
disorder,
relative to the standard gene expression level, i.e., the expression level in
healthy
tissue from an individual not having the disorder.
The tissue distribution in 6 week old human embryo suggests that the protein
product of this clone would be useful for the diagnosis and treatment of
disorders of
human embryonic development. Expression of this clone in developing embryos
suggests that it plays a critical role in early human development.
Alternatively, it may
be involved in key cellular proliferation events that occur during
embryogenesis.
Therefore misexpression of this gene in adult tissues may lead to abnormal
patterns of
cellular proliferation and cancer. Moreover, expression within embryonic
tissue and
other cellular sources marked by proliferating cells suggests this protein may
play a
role in the regulation of cellular division, and may show utility in the
diagnosis and
treatment of cancer and other proliferative disorders. Similarly,
developmental tissues
rely on decisions involving cell differentiation and/or apoptosis in pattern
formation.
Dysregulation of apoptosis can result in inappropriate suppression of cell
death, as
occurs in the development of some cancers, or in failure to control the extent
of cell
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death, as is believed to occur in acquired immunodeficiency and certain
neurodegenerative disorders, such as spinal muscular atrophy (SMA). Therefore,
the
polynucleotides and polypeptides of the present invention are useful in
treating,
detecting, and/or preventing said disorders and conditions, in addition to
other types
of degenerative conditions. Thus this protein may modulate apoptosis or tissue
differentiation and would be useful in the detection, treatment, and/or
prevention of
degenerative or proliferative conditions and diseases. Protein, as well as,
antibodies
directed against the protein may show utility as a tumor marker and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:83 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
1 S would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1159 of SEQ ID
N0:83, b
is an integer of 15 to 1173, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:83, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 74
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: GPVWLFCFLTLCRKPSQLFSQENSCMDVAGGVTTCLPP
WFSRGAPAQMSQWPPSSDHGAVRAGRDSRVGPVQPSHLTCEGGKEEREKNK
KAEVNPPTGMGLANRIPRDDITLKLRNQGKLRTKENRTQSAKRHP (SEQ ID
N0:315), VACKPENRTKTHFASSPACDGHALGGQVGFAICFLSCLFPPM (SEQ
ID N0:316), and/or SHPMPNTPQKQLLFSEDNELLVSLRTGRKPTLQAALRVTG
(SEQ ID N0:317). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
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It has been discovered that this gene is expressed primarily in pleural cancer
and endometrial tumors, and, to a lesser extent, in bone marrow & apoptotic T
cells.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: pleural cancer;
endometrial
tumors; hematopoietic disorders; immune dysfunction. Similarly, polypeptides
and
antibodies directed to those polypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the lungs and immune system,
expression
of this gene at significantly higher or lower levels may be detected in
certain tissues
or cell types (e.g., immune, hematopoietic, reproductive, and cancerous and
wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
The tissue distribution in pleural cancer and endometrial tumors indicates
that
the protein products of this clone are useful for the diagnosis and treatment
of various
reproductive cancers, including pleural cancer and endometrial tumors. In
addition,
Expression of this gene product within T cells & bone marrow suggests that it
may play a role in normal hematopoiesis. Therefore, this gene product may also
be
useful in the diagnosis andlor treatment of a variety of hematopoietic
disorders,
including defects in immune surveillance, inflammation, impaired immune
function,
and T cell lymphomas. Use of this gene product may be appropriate in
situations
designed to affect the proliferation, survival, and/or differentiation of
various
hematopoietic cell lineages, including blood stem cells.
Moreover, this protein may play a role in the regulation of cellular division,
and may show utility in the diagnosis and treatment of cancer and other
proliferative
disorders. Similarly, developmental tissues rely on decisions involving cell
differentiation and/or apoptosis in pattern formation. Dysregulation of
apoptosis can
result in inappropriate suppression of cell death, as occurs in the
development of some
cancers, or in failure to control the extent of cell death, as is believed to
occur in
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acquired immunodeficiency and certain neurodegenerative disorders, such as
spinal
muscular atrophy (SMA). Therefore, the polynucleotides and polypeptides of the
present invention are useful in treating, detecting, and/or preventing said
disorders
and conditions, in addition to other types of degenerative conditions. Thus
this protein
may modulate apoptosis or tissue differentiation and would be useful in the
detection,
treatment, and/or prevention of degenerative or proliferative conditions and
diseases.
Protein, as well as, antibodies directed against the protein may show utility
as a tumor
marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:84 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1547 of SEQ ID
N0:84, b
is an integer of 15 to 1561, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:84, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 75
The translation product of this gene shares low sequence homology with dreg-
2, a gene product originally identified in Drosophila that shows an
oscillating pattern
of expression tied into a circadian clock rhythm.
In specific embodiments, polypeptides of the invention comprise the following
a m i n o a c i d s a q a a n c a
AHRLQIRLLTWDVKDTLLRLRHPLGEAYATKARAHGLEV
EPSALEQGFRQAYRAQSHSFPNYGLSHGLTSRQWWLDV VLQTFHLAGV QDA
QAVAPIAEQLYKDFSHPCTWQVLDGAEDTLRECRTRGLRLAVISNFDRRLEGI
LXGLGLREHFDFVLTSEAAGWPKPDPRIFQEALRLAHMEPVVAAHVGDNYL
CDYQGPRAVGMHSFLV VGPQALDPV VRDS VPKEHILPSLAHLLPALDCLEGS
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T P G L ( S E Q I D N 0:319),
EGDPRGRPRPRPLGPPPQLTLPTALXDILRQVRAPGLRLSRA
LEVGRKGSPIFKIQIYL (SEQ ID N0:318), IRLLTWDVKDTLLRLRHPLGEAYA
TKA (SEQ ID N0:320), LEQGFRQAYRAQSHSFPNYGLSHG (SEQ ID N0:321),
HLAGVQDAQAVAPIAEQLYKDFSHPC (SEQ ID N0:322), VLDGAEDTLRECR
TRGLRLAVIS (SEQ ID N0:323), REHFDFVLTSEAAGWPKPDPRIFQEA (SEQ
ID N0:324), EPVVAAHVGDNYLCDYQGPRAVGMHSFL (SEQ ID N0:325),
and/or VVRDSVPKEHILPSLAHLLPALD (SEQ ID N0:326). Polynucleotides
encoding these polypeptides are also encompassed by the invention.
It has been discovered that this gene is expressed primarily in tumors of the
pancreas & thymus and to a lesser extent in a variety of fetal tissues,
including fetal
brain, liver, spleen, and kidney.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: pancreatic cancer; thymic
cancer;
disorders of fetal development; abnormal cellular proliferation; hematopoietic
disorders. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues)
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
the pancreas and immune system, expression of this gene at significantly
higher or
lower levels may be detected in certain tissues or cell types (e.g.,
developmental,
metabolic, immune, hematopoietic, and cancerous and wounded tissues) or bodily
fluids (e.g., lymph, serum, plasma, amniotic fluid, urine, synovial fluid or
spinal fluid)
taken from an individual having such a disorder, relative to the standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
The tissue distribution in proliferative and developmental cells and tissues
indicates that the protein products of this clone are useful for the diagnosis
and
treatment of cancers, particularly pancreatic and thymic cancer. Expression of
this
gene product within various fetal tissues also indicates that it is useful in
the diagnosis
and/or treatment of human developmental disorders. Taken together, the
observation
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that this gene product is expressed in cancers and in fetal tissues indicates
that it plays
a role in proliferation and/or differentiation events that are associated with
early
development. Misexpression of this gene product in adult tissues, therefore,
may
directly contribute to abnormal cellular proliferation and/or
dedifferentiation that
accompanies cancer. Finally,
Moreover, the expression of this gene product in fetal liver/spleen also
suggests that it plays a role in hematopoiesis, and is useful in the diagnosis
and/or
treatment of a variety of disorders of the immune system. Protein, as well as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:85 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1419 of SEQ ID
N0:85, b
is an integer of 15 to 1433, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:85, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 76
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: IRKLGPGLAPCSCRSGQVFPRV (SEQ ID N0:327).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
It has been discovered that this gene is expressed primarily in frontal
cortex,
particularly derived from epileptic patients.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: epilepsy;
neurodegenerative
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diseases and disorders, particularly learning disorders. Similarly,
polypeptides and
antibodies directed to those polypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the brain, CNS, andJor PNS,
expression of
this gene at significantly higher or lower levels may be detected in certain
tissues or
cell types (e.g., neural, and cancerous and wounded tissues) or bodily fluids
(e.g.,
lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from an
individual
having such a disorder, relative to the standard gene expression level, i.e.,
the
expression level in healthy tissue from an individual not having the disorder.
The tissue distribution in frontal cortex tissue suggests that the protein
product
of this clone would be useful for the diagnosis and/or treatment of disorders
of the
brain and nervous system, particularly epilepsy. Moreover, the expression of
this gene
product suggests that it may play a role in various critical processes of the
nervous
system, including nerve survival, pathfinding, signal conductance, and/or
synapse
formation. It may have effects on various processes including homeostasis,
learning,
motor function, language, etc. Potentially, this gene product is involved in
synapse
formation, neurotransmission, learning, cognition, homeostasis, or neuronal
differentiation or survival. Protein, as well as, antibodies directed against
the protein
may show utility as a tumor marker and/or immunotherapy targets for the above
listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:86 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1363 of SEQ ID
N0:86, b
is an integer of 15 to 1377, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:86, and where b is greater than or
equal to a
+ 14.
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FEATURES OF PROTEIN ENCODED BY GENE NO: 77
In specific embodiments, polypeptides of the invention comprise the following
a m i n o a c i d s a q a a n c a
KPLRMARPGGPEHNEYALVSAWHSSGSYLDSEGLRHQDD
FDVSLLVCHCAAPFEEQGEAERH VLRLQFFV VLTS QRELFPRLTADMRRFRK
PPRLPPEPEAPGSSAGSPGEASGLILAPGPAPLFPPLAAEVGMARARLAQLVRL
AGGHCRRDTLWKRLFLLEPPGPDRLRLGGRLALAELEELLEAVHAKSIGDIDP
QLDCFLSMTVSWYQSLIKVLLSRFPRAVAISKAQTWELSTWLR (SEQ ID
N0:328), ARGTLELPTPLIAAHQLYNYVADHASSYHM (SEQ ID N0:329),
SHCEWPGQG AQNTTSMPWCRHGTVLAPTWTLRDFDTR (SEQ ID N0:330),
PLTTVSHLCPL
SLRVFTSHLDITAGHSHRDDTWVPIPALPLKHLRPPSSPFALGPWVSHPLMRW
VQKLSHLHSNPGTGFSMGGKSAEKLKC (SEQ ID N0:331 ), STAARGAPGPGR
AGGTPRSSPCQIHWGHRPPAGLLPIHDGLLVPEPDQSSPKPLPQSCRHFQSPDL
GTQYLVALNQKFTDCSALVFWTPLRKDVSEV VFREALPVQPQDTRSPPAQLV
STYHHLESVINTACFTLLDPPPLKGVDWTTECHCSLNHGPTRLPARGRTDQPF
WAPGQARH (SEQ ID N0:332),
HQRLCNYVLRVCCPSLAAGTALPKHPQPLTHPGL
QRVRSTPRTPWALLGYSFRPPW (SEQ ID N0:333),
PGGPEHNEYALVSAWHSS GSYLDSEGLR (SEQ ID N0:334),
DVSLLVCHCAAPFEEQGEAERHVLR (SEQ ID N0:335),
RLTADMRRFRKPPRLPPEPEAPGSSAGS (SEQ ID N0:336), GEASGLI
LAPGPAPLFPPLAAEVGM (SEQ ID N0:337),
TLWKRLFLLEPPGPDRLRLGGRL (SEQ ID N0:338), and/or
LAELEELLEAVHAKSIGDIDPQLDCFLS (SEQ ID N0:339). Polynucleotides
encoding these polypeptides are also encompassed by the invention.
It has been discovered that this gene is expressed primarily in fetal
liver/spleen
and leukocytes, and to a lesser extent in a colon adenocarcinoma cell line.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
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diagnosis of the following diseases and conditions: hematopoietic disorders;
immune
dysfunction; colon cancer; colorectal adenocarcinoma. Similarly, polypeptides
and
antibodies directed to those polypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the immune system and colon,
expression
of this gene at significantly higher or lower levels may be detected in
certain tissues
or cell types (e.g., hematopoietic, immune, gastrointestinal, and cancerous
and
wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial
fluid or
spinal fluid) taken from an individual having such a disorder, relative to the
standard
gene expression level, i.e., the expression level in healthy tissue from an
individual
not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
184 as residues: Leu-16 to Ser-23, Ser-38 to Pro-43, Gly-53 to Leu-60.
The tissue distribution in colon adenocarcinoma suggests that the protein
product of this clone would be useful for the diagnosis and/or treatment of
gastrointestinal diseases and/or disorders, particularly proliferative
conditions.
Expression of this gene product in fetal and proliferative cells and tissues
suggests
that it may be a marker cancers, and that it's misregulated expression may in
fact
contribute to the development or progression of the types of cancers dictated
by its
expression.
Similarly, the expression of this gene product in fetal liver/spleen - a
primary
site of early hematopoiesis - taken together with its expression in peripheral
blood
leukocytes suggests that this gene product may play a role in a variety of
hematopoietic processes, including the survival, proliferation, activation,
and/or
differentiation of all blood cell lineages, including the totipotent
hematopoietic stem
cell. Such a gene product may therefore play a role in a variety of
hematopoietic
disorders including inflammation; immune dysfunction; defects in immune
surveillance; and hematopoietic cancers and lymphomas. Similarly,
developmental
tissues rely on decisions involving cell differentiation and/or apoptosis in
pattern
formation. Dysregulation of apoptosis can result in inappropriate suppression
of cell
death, as occurs in the development of some cancers, or in failure to control
the extent
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of cell death, as is believed to occur in acquired immunodeficiency and
certain
neurodegenerative disorders, such as spinal muscular atrophy (SMA).
Therefore, the polynucieotides and polypeptides of the present invention are
useful in treating, detecting, and/or preventing said disorders and
conditions, in
addition to other types of degenerative conditions. Thus this protein may
modulate
apoptosis or tissue differentiation and would be useful in the detection,
treatment,
and/or prevention of degenerative or proliferative conditions and diseases.
Protein, as
well as, antibodies directed against the protein may show utility as a tumor
marker
and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:87 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1701 of SEQ ID
N0:87, b
is an integer of 15 to 1715, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:87, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 78
The gene encoding the disclosed cDNA is believed to reside on chromosome
20. Accordingly, polynucleotides related to this invention are useful as a
marker in
linkage analysis for chromosome 20.
It has been discovered that this gene is expressed primarily in brain.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: neurodegenerative diseases
and/or
disorders. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues)
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or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
the central nervous system, expression of this gene at significantly higher or
lower
levels may be detected in certain tissues or cell types (e.g., neural, and
cancerous and
wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial
fluid or
spinal fluid) taken from an individual having such a disorder, relative to the
standard
gene expression Ievel, i.e., the expression level in healthy tissue from an
individual
not having the disorder. This gene is believed to reside on chromosome 20,
D20S 111-
D20S 195. Polynucleotides corresponding to this gene are useful, therefore, as
chromosome markers.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
185 as residues: Met-1 to Tyr-6, Thr-38 to Ala-44.
The tissue distribution in brain tissue indicates that the protein products of
this
clone are useful for diagnosis and treatment of disorders of the central
nervous
system. Moreover, the protein product of this clone is useful for the
detection,
treatment, and/or prevention of neurodegenerative disease states, behavioral
disorders, or inflammatory conditions which include, but are not limited to
Alzheimer's Disease, Parkinson's Disease, Huntington's Disease, Tourette
Syndrome,
meningitis, encephalitis, demyelinating diseases, peripheral neuropathies,
neoplasia,
trauma, congenital malformations, spinal cord injuries, ischemia and
infarction,
aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive
compulsive disorder, depression, panic disorder, learning disabilities, ALS,
psychoses, autism, and altered behaviors, including disorders in feeding,
sleep
patterns, balance, and perception.
In addition, elevated expression of this gene product in regions of the brain
suggests it plays a role in normal neural function. Potentially, this gene
product is
involved in synapse formation, neurotransmission, learning, cognition,
homeostasis,
or neuronal differentiation or survival. Protein, as well as, antibodies
directed against
the protein may show utility as a tumor marker and/or immunotherapy targets
for the
above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
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related to SEQ ID N0:88 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 403 of SEQ ID
N0:88, b
is an integer of 15 to 417, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:88, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 79
When tested against U937 cell lines, supernatants removed from cells
containing this gene activated the GAS (gamma activating sequence) promoter
element. Thus, it is likely that this gene activates myeloid cells, and to a
lesser extent,
other immune and hematopoietic cells or cell types, through the JAK-STAT
signal
transduction pathway. GAS is a promoter element found upstream of many genes
which are involved in the Jak-STAT pathway. The Jak-STAT pathway is a Jarge,
signal transduction pathway involved in the differentiation and proliferation
of cells.
Therefore, activation of the Jak-STAT pathway, reflected by the binding of the
GAS
element, can be used to indicate proteins involved in the proliferation and
differentiation of cells.
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: FQLYFNPELIFKHFQIWRLITNFLFFGPVGFNFLFNMIFLY
RYCRMLEEGSFRGRTADFVFMFLFGGFLMTLFGLFVSLVFLGQAFTIMLVYV
WSRXNPYVRMNFFGLLNFQAPFLPWVLMGFSLLLGNSIIVDLLGIAVGHIYFF
LEDVFPNQPGGIRILKTPSILKAIFDTPDEDPNYNPLPEERPGGFAWGEGQ SEQ
I D N O : 3 4 0 ) ,
GVGQATVGKMAYQSLRLEYLQIPPVSRAYTTACVLTTAAVQLELITPF
QLYFNPELIFKHFQIWRLITNFLFFGPVGFNFLFNMIFLYRYCRMLEEGSFRGR
TADFVF (SEQ ID N0:341), LIFKHFQIWRLITNFLFFGPVGF (SEQ ID N0:342),
FLYRYCRMLEEGSFRGRTADFVFMF (SEQ ID N0:343), LVFLGQAFTIMLVYV
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WSRXNPYV (SEQ ID N0:344), VLMGFSLLLGNSIIVDLLGIA (SEQ ID N0:345),
NQPGGIRILKTPSILKAIFDTPDED (SEQ ID N0:346), RLEYLQIPPVSRAYTTAC
VLTTAAVQLE (SEQ ID N0:347), and/or RLITNFLFFGPVGFNFLFNMIFLYRYC
RMLE (SEQ ID N0:348). Polynucleotides encoding these polypeptides are also
encompassed by the invention. The gene encoding the disclosed cDNA is believed
to
reside on chromosome 17. Accordingly, polynucleotides related to this
invention are
useful as a marker in linkage analysis for chromosome 17.
It has been discovered that this gene is expressed primarily in smooth muscle,
fetal brain, fetal liver and to a lesser extent in activated macrophage, colon
cancer.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: developmental diseases,
immune-
related diseases, neural disorders, and vascular diseases and conditions.
Similarly,
polypeptides and antibodies directed to those polypeptides are useful to
provide
immunological probes for differential identification of the tissues) or cell
type(s). For
a number of disorders of the above tissues or cells, particularly of the
immune system
and central nervous system, expression of this gene at significantly higher or
lower
levels may be detected in certain tissues or cell types (e.g., developmental,
vascular,
immune, and cancerous and wounded tissues) or bodily fluids (e.g., lymph,
serum,
plasma, amniotic fluid, urine, synovial fluid or spinal fluid) taken from an
individual
having such a disorder, relative to the standard gene expression level, i.e.,
the
expression level in healthy tissue from an individual not having the disorder.
The tissue distribution in fetal liver, macrophage, and fetal brain indicates
that
the protein products of this clone are useful for treating and diagosis of
immune
system-related diseases and CNS diseases. Moreover, the protein product of
this clone
is useful for the treatment and diagnosis of hematopoietic related disorders
such as
anemia, pancytopenia, leukopenia, thrombocytopenia or leukemia since stromal
cells
are important in the production of cells of hematopoietic lineages. The uses
include
bone marrow cell ex- vivo culture, bone marrow transplantation, bone marrow
reconstitution, radiotherapy or chemotherapy of neoplasia. The gene product
may also
be involved in lymphopoiesis, therefore, it can be used in immune disorders
such as
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infection, inflammation, allergy, immunodeficiency etc. In addition, this gene
product
may have commercial utility in the expansion of stem cells and committed
progenitors of various blood lineages, and in the differentiation and/or
proliferation of
various cell types. Alternatively, the protein is useful in the detection,
treatment,
and/or prevention of vascular conditions, which include, but are not limited
to,
microvascular disease, vascular leak syndrome, aneurysm, stroke,
atherosclerosis,
arteriosclerosis, or embolism.
Moreover, the expression within fetal tissue and other cellular sources marked
by proliferating cells, combined with the GAS biological activity, suggests
this
protein may play a role in the regulation of cellular division, and may show
utility in
the diagnosis and treatment of cancer and other proliferative disorders.
Similarly,
developmental tissues rely on decisions involving cell differentiation and/or
apoptosis
in pattern formation. Dysregulation of apoptosis can result in inappropriate
suppression of cell death, as occurs in the development of some cancers, or in
failure
to control the extent of cell death, as is believed to occur in acquired
immunodeficiency and certain neurodegenerative disorders, such as spinal
muscular
atrophy (SMA). Therefore, the polynucleotides and polypeptides of the present
invention are useful in treating, detecting, and/or preventing said disorders
and
conditions, in addition to other types of degenerative conditions. Thus this
protein
may modulate apoptosis or tissue differentiation and would be useful in the
detection,
treatment, and/or prevention of degenerative or proliferative conditions and
diseases.
Protein, as well as, antibodies directed against the protein may show utility
as a tumor
marker and/or immunotherapy targets for the above listed tissues. Protein, as
well as,
antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:89 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
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are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1153 of SEQ ID
N0:89, b
is an integer of 15 to 1167, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:89, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 80
The translation product of this gene shares sequence homology with
proacrosin binding proteins (sp32) from non-human mammalian species. The
binding
of sp32 to proacrosin may be involved in packaging the acrosin zymogen into
the
acrosomal matrix. See, for example, J Biol Chem. 1994 Apr l; 269( 13): 10133-
10140, incorporated herein by reference. Accordingly, the inventors have
termed the
translation product of this gene human sp32 or "h-sp32". Contact of cells with
supernatant expressing the product of this gene has been shown to increase the
permeability of the plasma membrane of PMN to calcium. Thus it is likely that
the
product of this gene is involved in a signal transduction pathway that is
initiated when
the product binds a receptor on the surface of the plasma membrane of both
neutrophils, and to a lesser extent in other immune and hematopoietic cells.
Thus,
polynucleotides and polypeptides have uses which include, but are not limited
to,
activating
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: HASAGPDGSSPA (SEQ ID N0:349),
ELLLEKPKPWQPPAAAPHRALLVLCYSIVENTCIITPTAKAWKYMEEEILGFG
KS VCDSLGRRHMSTCALCDFCSLKLEQCHSEASLQRQQCDTSHKTPFAAPCL
PPRACPSATR (SEQ ID N0:350),
LPGWGFPTKICDTDYIQYPNYCSFKSQQCLMR
NRNRKVSRMRCLQNETYSALSPGKSEDVVLRWSQEFSTLTLGQFG (SEQ ID
N0:351), SPVLLPAFPPLPVPLLALPVSAPLPACVLVSAPACAPLLAPACAL
ALAPGFPGTRRIVGALPRCC (SEQ ID N0:352), LLVLCYSIVENTCIITPTAK
AWKYMEEEILGFGKS (SEQ ID N0:353), and/or LKLEQCHSEASLQRQQC
DTSHKTPFA (SEQ ID N0:354). Polynucleotides encoding these polypeptides are
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also encompassed by the invention. The gene encoding the disclosed cDNA is
believed to reside on chromosome 12. Accordingly, polynucleotides related to
this
invention are useful as a marker in linkage analysis for chromosome 12.
It has been discovered that this gene is expressed primarily in testis.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: reproductive disorders.
Similarly,
polypeptides and antibodies directed to those polypeptides are useful to
provide
immunological probes for differential identification of the tissues) or cell
type(s). For
a number of disorders of the above tissues or cells, particularly of the
reproductive
diseases, expression of this gene at significantly higher or lower levels may
be
detected in certain tissues or cell types (e.g., reproductive, testis,
prostate, epidiymus,
and cancerous and wounded tissues) or bodily fluids (e.g., lymph, seminal
fluid,
serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual
having
such a disorder, relative to the standard gene expression level, i.e., the
expression
level in healthy tissue from an individual not having the disorder. This gene
is
believed to map to chromosome 12 and is thought to be useful as a chromosome
marker.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
187 as residues: Asp-27 to Ser-32, Pro-52 to Thr-58, Arg-63 to Asn-70, Gln-78
to
Gly-83, Thr-107 to Asn-113, Thr-160 to Val-176, Ser-188 to Gly-241, Leu-248 to
Pro-265, Tyr-302 to Gly-314.
The tissue distribution in testis, combined with the specific homology to the
sp32 protein indicates that the protein products of this clone are useful for
the
diagnosis, treating, and/or prevention of reproductive diseases and/or
disorders.
Moreover, polynucleotides and polypeptides corresponding to this gene are
useful for
the treatment and diagnosis of conditions concerning proper testicular
function (e.g.
endocrine function, sperm maturation), as well as cancer. Therefore, this gene
product
is useful in the treatment of male infertility and/or impotence. This gene
product is
also useful in assays designed to identify binding agents, as such agents
(antagonists)
are useful as male contraceptive agents.
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Similarly, the protein is believed to be useful in the treatment and/or
diagnosis
of testicular cancer. The testes are also a site of active gene expression of
transcripts
that may be expressed, particularly at low levels, in other tissues of the
body.
Therefore, this gene product may be expressed in other specific tissues or
organs
where it may play related functional roles in other processes, such as
hematopoiesis,
inflammation, bone formation, and kidney function, to name a few possible
target
indications. The protein is useful in application and utility as a
contraceptive, either
directly or indirectly. Based upon the detected calcium flux activity, the
protein may
also be useful as an effect treatment for infertility (i.e. for inhibiting
autoimmune
disorders). Protein, as well as, antibodies directed against the protein may
show utility
as a tumor marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:90 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1878 of SEQ ID
N0:90, b
is an integer of 15 to 1892, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:90, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 81
The translation product of this contig has consistent sequence homology with
a number of previously described viral tat proteins (see, for example,
Stevens, et al., J.
Virol. 64:3716-3725 (1990), which is hereby incorporated by reference,
herein).
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: QVSGLILSLSCGMDGLALDGSPSPSPXTEKAGRCISQTSL
(SEQ ID N0:355), QVSGLILSLSCGMDGLALDGSPSPSPXTEKAGRCISQTSLP
GKWEV (SEQ ID N0:356), RASKTVPRMPPNWPAKMPCLCHIRTVEHLGTIS
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SGAPGRPTGQQAARTYHICWIHPGQKIDSLPPSSQHPRSQQLAPGTWPSTSTT
KPAEETLGSSASLPISQARKSEKCTFQPSPWXVRGKESHQVPAHPSHRTETES
D HSPVRKPPSRGTRTGDFTVGDWSEAWLLELALL (SEQ ID N0:357), RMPPN
WPAKMPCLCHIRTVEHLG (SEQ ID N0:358), GRPTGQQAARTYHICWIHPG
QKIDS (SEQ ID N0:359), WPSTSTTKPAEETLGSSASLPISQA (SEQ ID N0:360),
KSEKCTFQPSPWXVRGKESHQVP (SEQ ID N0:361 ), andlor KPPSRGTRTGDF
TVGDWSEAWLLE (SEQ ID N0:362). Polynucleotides encoding these polypeptides
are also encompassed by the invention.
It has been discovered that this gene is expressed almost exclusively in
neutrophils.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of immune disorders. Similarly, polypeptides and antibodies directed
to
those polypeptides are useful to provide immunological probes for differential
identification of the tissues) or cell type(s). For a number of disorders of
the immune
system, expression of this gene at significantly higher or lower levels may be
detected
in certain tissues or cell types (e.g., immune, hematopoietic, and cancerous
and
wounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial
fluid or
spinal fluid) taken from an individual having such a disorder, relative to the
standard
gene expression level, i.e., the expression level in healthy tissue from an
individual
not having the disorder. In addition, molecules of the present invention can
be used to
regulate transcription and translation of genes in cells of the immune system,
as well
as in other cell types. Such transcriptional and translation regulation is
useful for
diagnosing and treating a number of disorders in which an alterred state of
transcription and translation may be a factor in the disorder. Such disorders
include
many viral infections, particularly of immune cells, including HIV-1, HIV-2,
human
T-cell lymphotropic virus (HTLV)-I, and HTLV-II, as well as other DNA and RNA
viruses such as herpes simplex virus (HSV)-1, HSV-2, HSV-6, cytomegalovirus
(CMV), Epstein-Barr virus (EBV), herpes samirii, adenoviruses, rhinoviruses,
influenza viruses, reoviruses, and the like. In addition, the ability to use
molecules of
the present invention to molecularly regulate the processes of transcription
and
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translation is useful in the diagnosis and treatment of many types of cancers,
particularly those of the immune system, including ovarian cancer, breast
cancer,
colon cancer, cardiac tumors, pancreatic cancer, melanoma, retinoblastoma,
glioblastoma, lung cancer, intestinal cancer, testicular cancer, stomach
cancer,
neuroblastoma, myxoma, myoma, lymphoma, endothelioma, osteoblastoma,
osteoclastoma, osteosarcoma, chondrosarcoma, adenoma, and the like.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
188 as residues: Gln-2 to Trp-12, Ala-30 to Glu-35, Gln-42 to Ser-51.
The tissue distribution in neutrophils, combined with the homology to viral
tat
proteins suggests that the protein product of this clone is useful for the
diagnosis and
treatment of immune disorders, particularly viral infections and proliferative
disorders. Further, since this clone has a high degree of sequence relatedness
to
factors which are involved in the regulation of transcription and translation,
this clone
is useful as a regulator of such processes. Protein, as well as, antibodies
directed
against the protein may show utility as a tumor marker and/or immunotherapy
targets
for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:91 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 509 of SEQ ID
N0:9I, b
is an integer of 15 to 523, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:91, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 82
The translation product of this contig has clear sequence identity with a
number of thioredoxins and endoplasmic reticulum resident proteins (see, for
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example, Shorrosh and Dixon, Plant J. 2:51-58 (1992), which is hereby
incorporated
by reference, herein).
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: PCADCLSAWA (SEQ ID N0:363). Polynucleotides encoding
these polypeptides are also encompassed by the invention.The gene encoding the
disclosed cDNA is believed to reside on chromosome 5. Accordingly,
polynucleotides related to this invention are useful as a marker in linkage
analysis for
chromosome 5.
It has been discovered that this gene is expressed primarily in adipocytes and
striatum depression, and in lower abundance in prostate, whole brain, fetal
liver, and
spleen.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: Prostate cancer, CNS
diseases,
immune disorders . Similarly, polypeptides and antibodies directed to those
polypeptides are useful to provide immunological probes for differential
identification
of the tissues) or cell type(s). For a number of disorders of the above
tissues or cells,
particularly of the immune, expression of this gene at significantly higher or
lower
levels may be detected in certain tissues or cell types (e.g., neural,
hematopoietic,
immune, and cancerous and wounded tissues) or bodily fluids (e.g., seminal
fluid,
amniotic fluid, serum, plasma, urine, synovial fluid or spinal fluid) taken
from an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
Since the translation product of this clone has a high degree of sequence
relatedness
to many thioredoxins, it can be used as a food additive to improve flour
quality or to
suppress the anti-nutritional effects of leguminous plants. Molecules of the
present
invention can further used to inactivate toxins, for example, bee or snake
venom.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
189 as residues: Trp-43 to Ala-49, Pro-68 to Ala-74, Glu-100 to Gly-11 l, Glu-
120 to
Asn-125, Pro-141 to Ala-154, Asp-157 to Lys-17I, Cys-177 to Ile-182, Ser-248
to
Leu-253, Thr-280 to Glu-285, Gly-353 to Val-359.
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The tissue distribution in whole brain suggests that the protein product of
this
clone would be useful for the detection, treatment, and/or prevention of
neurodegenerative disease states, behavioral disorders, or inflammatory
conditions
which include, but are not limited to Alzheimer's Disease, Parkinson's
Disease,
Huntington's Disease, Tourette Syndrome, meningitis, encephalitis,
demyelinating
diseases, peripheral neuropathies, neoplasia, trauma, congenital
malformations, spinal
cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia,
mania, dementia, paranoia, obsessive compulsive disorder, depression, panic
disorder,
learning disabilities, ALS, psychoses, autism, and altered behaviors,
including
disorders in feeding, sleep patterns, balance, and perception. In addition,
elevated
Expression of this gene product in regions of the brain suggests it plays a
role
in normal neural function. Potentially, this gene product is involved in
synapse
formation, neurotransmission, learning, cognition, homeostasis, or neuronal
differentiation or survival. The secreted protein can also be used to
determine
1 S biological activity, to raise antibodies, as tissue markers, to isolate
cognate ligands or
receptors, to identify agents that modulate their interactions, and as
nutritional
supplements. It may also have a very wide range of biological activities.
Typical of
these are cytokine, cell proliferation/differentiation modulating activity or
induction
of other cytokines; immunostimulating/immunosuppressant activities (e.g. for
treating
human immunodeficiency virus infection, cancer, autoimmune diseases and
allergy);
regulation of hematopoiesis (e.g. for treating anemia or as adjunct to
chemotherapy);
stimulation or growth of bone, cartilage, tendons, ligaments and/or nerves
(e.g. for
treating wounds, stimulation of follicle stimulating hormone (for control of
fertility);
chemotactic and chemokinetic activities (e.g. for treating infections,
tumors);
hemostatic or thrombolytic activity (e.g. for treating hemophilia, cardiac
infarction
etc.); anti-inflammatory activity (e.g. for treating septic shock, Crohn's
disease); as
antimicrobials; for treating psoriasis or other hyperproliferative diseases;
for
regulation of metabolism, and behavior. Also contemplated is the use of the
corresponding nucleic acid in gene therapy procedures. Protein, as well as,
antibodies
directed against the protein may show utility as a tumor marker and/or
immunotherapy targets for the above listed tissues.
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Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:92 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1368 of SEQ ID
N0:92, b
is an integer of 15 to 1382, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:92, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 83
When tested against TF-1 cell lines, supernatants removed from cells
containing this gene activated the ISRE (interferon-sensitive responsive
element )
promoter element. Thus, it is likely that this gene activates myeloid cells,
and to a
lesser extent, in immune and hematopoietic cells or tissues, through the JAK-
STAT
signal transduction pathway. ISRE is a promoter element found upstream in many
genes which are involved in the Jak-STAT pathway. The Jak-STAT pathway is a
large, signal transduction pathway involved in the differentiation and
proliferation of
cells. Therefore, activation of the Jak-STAT pathway, reflected by the binding
of the
ISRE element, can be used to indicate proteins involved in the proliferation
and
differentiation of cells.
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: HASGYLCIVLL (SEQ ID N0:364). Polynucleotides encoding
these polypeptides are also encompassed by the invention.
It has been discovered that this gene is expressed exclusively in Rejected
Kidney.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: kidney and other urinary
tract
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disorders and disorders related to, or resulting from, transplantation.
Similarly,
polypeptides and antibodies directed to those polypeptides are useful to
provide
immunological probes for differential identification of the tissues) or cell
type(s). For
a number of disorders of the above tissues or cells, particularly of the
immune and
renal systems, expression of this gene at significantly higher or lower levels
may be
detected in certain tissues or cell types (e.g., renal, kidney, urogenital,
immune,
hematopoietic, and cancerous and wounded tissues) or bodily fluids (e.g.,
lymph,
serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual
having
such a disorder, relative to the standard gene expression level, i.e., the
expression
level in healthy tissue from an individual not having the disorder. Molecules
of the
present invention are particularly useful in the diagnosis and treatment of
disorders
related to transplantation, particularly kidney transplantation.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
190 as residues: Asn-49 to Gln-54, Glu-150 to Asp-159.
The tissue distribution in rejected kidney tissue suggests that the protein
product of this clone would be useful for diagnosis and treatment of disorders
related
to or resulting from rejection of transplanted organs, particularly the
kidney.
Moreover, the protein product of this clone could be used in the treatment
and/or
detection of kidney diseases including renal failure, nephritus, renal tubular
acidosis,
proteinuria, pyuria, edema, pyelonephritis, hydronephritis, nephrotic
syndrome, crush
syndrome, glomerulonephritis, hematuria, renal colic and kidney stones, in
addition to
Wilm's Tumor Disease, and congenital kidney abnormalities such as horseshoe
kidney, polycystic kidney, and Falconi's syndrome. Considering the tissue
distribution
and detected ISRE biological activity, the protein is useful in modulating the
immune
response to aberrant kidney proteins, including autoantigens and aberrant
proteins
which are often present in degenerative and proliferative conditions. Protein,
as well
as, antibodies directed against the protein may show utility as a tumor marker
and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:93 and may have been publicly available prior to
conception of
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the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1733 of SEQ ID
N0:93, b
is an integer of 15 to 1747, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:93, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 84
The translation product of this gene shares sequence homology with the
conserved MAL and plasmolipin protein (Magyar, et al, Gene 189:269-275 (
1997);
See Genbank Accession No.gnIIPIDIe 183885), which are thought to be important
in
modulating T cell function, and proper CNS function, respectively. When tested
against Jurkat cell lines, supernatants removed from cells containing this
gene
activated the GAS (gamma activating sequence) promoter element. Thus, it is
likely
that this gene activates myeloid cells, and to a lesser extent, immune or
hematopoietic
cells and tissues, through the JAK-STAT signal transduction pathway. GAS is a
promoter element found upstream of many genes which are involved in the Jak-
STAT
pathway. The Jak-STAT pathway is a large, signal transduction pathway involved
in
the differentiation and proliferation of cells. Therefore, activation of the
Jak-STAT
pathway, reflected by the binding of the GAS element, can be used to indicate
proteins involved in the proliferation and differentiation of cells.
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: NSARAARAEIVLGLLVWTLIAGTEYFRVPAFGWV (SEQ
ID N0:365). Polynucleotides encoding these polypeptides are also encompassed
by
the invention.
It has been discovered that this gene is expressed primarily in T cells.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of immune, hematopoietic, and neural diseases and/or disorders.
Similarly,
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polypeptides and antibodies directed to those polypeptides are useful to
provide
immunological probes for differential identification of the tissues) or cell
type(s). For
a number of disorders of the above tissues or cells, particularly of the
immune system,
expression of this gene at significantly higher or lower levels may be
detected in
certain tissues or cell types (e.g., immune, hematopoietic, and cancerous and
wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder. Nucleic acids of the present invention are useful as
probes for
detecting traumatic and pathological changes in the central and peripheral
nervous
systems. Molecules of the present invention may be involved in regulating the
growth
of Schwann cells and other neural cells. Molecules of the present invention
are also
useful as modulators of the interaction between Schwann cells and other neural
cells
and the extracellular matrix and is therefore useful for the therapeutic
intervention in
nerve damage primarily by facilitating regeneration of damaged axons and
regenerating nerve cells in damaged nervous system tissues.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
191 as residues: Ser-58 to His-64.
The tissue distribution in T-cells, combined with the homology to the MAL
and plasmolipin proteins and the detected GAS biological activity suggests
that the
protein product of this clone would be useful for the diagnosis and treatment
of
immune disorders including, but not limited to, AIDS and other
immunodeficiencies.
Morever, the expression of this gene product suggests a role in regulating the
proliferation; survival; differentiation; and/or activation of hematopoietic
cell
lineages, including blood stem cells. This gene product may be involved in the
regulation of cytokine production, antigen presentation, or other processes
suggesting
a usefulness in the treatment of cancer (e.g. by boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the natural gene
product may be involved in immune functions. Therefore it may be also used as
an
agent for immunological disorders including arthritis, asthma, leukemia,
rheumatoid
arthritis, granulomatous disease, inflammatory bowel disease, sepsis, acne,
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neutropenia, neutrophilia, psoriasis, hypersensitivities, such as T-cell
mediated
cytotoxicity; immune reactions to transplanted organs and tissues, such as
host-
versus-graft and graft-versus-host diseases, or autoimmunity disorders, such
as
autoimmune infertility, Tense tissue injury, demyelination, systemic lupus
erythematosis, drug induced hemolytic anemia, rheumatoid arthritis, Sjogren's
disease, scleroderma and tissues. Moreover, the protein may represent a
secreted
factor that influences the differentiation or behavior of other blood cells,
or that
recruits hematopoietic cells to sites of injury. In addition, this gene
product may have
commercial utility in the expansion of stem cells and committed progenitors of
various blood lineages, and in the differentiation and/or proliferation of
various cell
types.
The secreted protein can also be used to determine biological activity, to
raise
antibodies, as tissue markers, to isolate cognate ligands or receptors, to
identify agents
that modulate their interactions, and as nutritional supplements. It may also
have a
very wide range of biological activities. Typical of these are cytokine, cell
proliferation/differentiation modulating activity or induction of other
cytokines;
immunostimulating/immunosuppressant activities (e.g. for treating human
immunodeficiency virus infection, cancer, autoimmune diseases and allergy);
regulation of hematopoiesis (e.g. for treating anemia or as adjunct to
chemotherapy);
stimulation or growth of bone, cartilage, tendons, ligaments and/or nerves
(e.g. for
treating wounds, stimulation of follicle stimulating hormone (for control of
fertility);
chemotactic and chemokinetic activities (e.g. for treating infections,
tumors);
hemostatic or thrombolytic activity (e.g. for treating hemophilia, cardiac
infarction
etc.); anti-inflammatory activity (e.g. for treating septic shock, Crohn's
disease); as
antimicrobials; for treating psoriasis or other hyperproliferative diseases;
for
regulation of metabolism, and behavior. Also contemplated is the use of the
corresponding nucleic acid in gene therapy procedures. Protein, as well as,
antibodies
directed against the protein may show utility as a tumor marker and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
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related to SEQ ID N0:94 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 586 of SEQ ID
N0:94, b
is an integer of 15 to 600, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:94, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 85
The translation product of this clone has sequence identity to a protein
tyrosine kinase reported by Oates and Wilks (The Worm Breeders Gazette 14:87-
87
(1995), which is hereby incorporated by reference herein). The gene encoding
the
disclosed cDNA is believed to reside on chromosome 2. Accordingly,
polynucleotides related to this invention are useful as a marker in linkage
analysis for
chromosome 2.
It has been discovered that this gene is expressed primarily in cerebellum,
adult brain, retina, spinal cord, and kidney cortex.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: neural, visual, and renal
diseases
andlor disorders. Similarly, polypeptides and antibodies directed to those
polypeptides are useful to provide immunological probes for differential
identification
of the tissues) or cell type(s). For a number of disorders of the above
tissues or cells,
particularly of the CNS, retina, and kidney cortex. Expression of this gene at
significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., neural, visual, renal, and cancerous and wounded tissues) or bodily
fluids (e.g.,
lymph, serum, plasma, urine, synovial fluid or spinal fluid) taken from an
individual
having such a disorder, relative to the standard gene expression level, i.e.,
the
expression level in healthy tissue from an individual not having the disorder.
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The tissue distribution in cerebellum, adult brain, and spinal cord tissue
suggests that the protein product of this clone would be useful for the
diagnosis and
treatment of neural diseases and disorders. The protein product of this clone
is useful
for the detection, treatment, and/or prevention of neurodegenerative disease
states,
behavioral disorders, or inflammatory conditions which include, but are not
limited to
Alzheimer's Disease, Parkinson's Disease, Huntington's Disease, Tourette
Syndrome,
meningitis, encephalitis, demyelinating diseases, peripheral neuropathies,
neoplasia,
trauma, congenital malformations, spinal cord injuries, ischemia and
infarction,
aneurysms, hemorrhages, schizophrenia, mania, dementia, paranoia, obsessive
compulsive disorder, depression, panic disorder, learning disabilities, ALS,
psychoses, autism, and altered behaviors, including disorders in feeding,
sleep
patterns, balance, and perception. In addition, elevated
Expression of this gene product in regions of the brain suggests it plays a
role
in normal neural function. Potentially, this gene product is involved in
synapse
formation, neurotransmission, learning, cognition, homeostasis, or neuronal
differentiation or survival. Moreover, the protein product of this clone could
be used
in the treatment and/or detection of kidney diseases including renal failure,
nephritus,
renal tubular acidosis, proteinuria, pyuria, edema, pyelonephritis,
hydronephritis,
nephrotic syndrome, crush syndrome, glomerulonephritis, hematuria, renal colic
and
kidney stones, in addition to Wilm's Tumor Disease, and congenital kidney
abnormalities such as horseshoe kidney, polycystic kidney, and Falconi's
syndrome.
Protein, as well as, antibodies directed against the protein may show utility
as a tumor
marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:95 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 572 of SEQ ID
N0:95, b
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is an integer of 15 to 586, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:95, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 86
The translation product of this clone has homology to trkB, and it is thought
that the protein of the present invention is a novel novel neural receptor
protein-
tyrosine kinase, a trkB homolog (See for example, ). This protein is likely to
be
derived from a gene for a ligand-regulated receptor closely related to the
human trk
oncogene. Northern (RNA) analysis showed that the trkB gene is expressed
predominantly in the brain and that trkB expresses multiple mRNAs, ranging
from 0.7
to 9 kb. Hybridization of cerebral mRNAs with a variety of probes indicates
that there
are mRNAs encoding truncated trkB receptors.
In specific embodiments, polypeptides of the invention comprise the sequence
PCSPPDSPPLPGAFVWRVLWVC (SEQ ID N0:366). Polynucleotides encoding this
polypeptide are also encompassed by the invention.
It has been discovered that this gene is expressed primarily in breast cancer,
colon tumor, and B-cell lymphoma.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: breast cancer, colon
tumor. B-cell
lymphoma. Similarly, polypeptides and antibodies directed to those
polypeptides are
useful to provide immunological probes for differential identification of the
tissues)
or cell type(s). For a number of disorders of the above tissues or cells,
particularly of
2S the immune, expression of this gene at significantly higher or lower levels
may be
detected in certain tissues or cell types (e.g., neural, gastrointestinal,
immune, and
cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum, plasma,
urine,
synovial fluid or spinal fluid) taken from an individual having such a
disorder,
relative to the standard gene expression level, i.e., the expression level in
healthy
tissue from an individual not having the disorder.
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Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
193 as residues: Ser-29 to Asn-40.
The tissue distribution in proliferative cells and tissues suggests that the
protein product of this clone would be useful for the treatment, detection,
and/or
prevention of cancer, particularly in the indicated tissues. The expression
within
cellular sources marked by proliferating cells suggests this protein may play
a role in
the regulation of cellular division, and may show utility in the diagnosis and
treatment
of cancer and other proliferative disorders. Similarly, developmental tissues
rely on
decisions involving cell differentiation and/or apoptosis in pattern
formation.
Dysregulation of apoptosis can result in inappropriate suppression of cell
death, as
occurs in the development of some cancers, or in failure to control the extent
of cell
death, as is believed to occur in acquired immunodeficiency and certain
neurodegenerative disorders, such as spinal muscular atrophy (SMA). Therefore,
the
polynucleotides and polypeptides of the present invention are useful in
treating,
detecting, and/or preventing said disorders and conditions, in addition to
other types
of degenerative conditions. Thus this protein may modulate apoptosis or tissue
differentiation and would be useful in the detection, treatment, and/or
prevention of
degenerative or proliferative conditions and diseases.
Alternatively, the homology to the trkB protein suggests the protein product
of
this clone is useful for the detection, treatment, and/or prevention of
neurodegenerative disease states, behavioral disorders, or inflammatory
conditions
which include, but are not limited to Alzheimer's Disease, Parkinson's
Disease,
Huntington's Disease, Tourette Syndrome, meningitis, encephalitis,
demyelinating
diseases, peripheral neuropathies, neoplasia, trauma, congenital
malformations, spinal
cord injuries, ischemia and infarction, aneurysms, hemorrhages, schizophrenia,
mania, dementia, paranoia, obsessive compulsive disorder, depression, panic
disorder,
learning disabilities, ALS, psychoses, autism, and altered behaviors,
including
disorders in feeding, sleep patterns, balance, and perception. In addition,
elevated
expression of this gene product in regions of the brain suggests it plays a
role in
normal neural function. Potentially, this gene product is involved in synapse
formation, neurotransmission, learning, cognition, homeostasis, or neuronal
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differentiation or survival. Protein, as well as, antibodies directed against
the protein
may show utility as a tumor marker and/or immunotherapy targets for the above
listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:96 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 788 of SEQ ID
N0:96, b
is an integer of 15 to 802, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:96, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 87
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: ARACFAYNGVCSEGRCWDSHFHGSV (SEQ ID N0:367),
MSNMGKIPSLSLHIPINKYICSRIPKFIQKVNKSTVLQICLKRQIILNKNKMSDH
SKIGKANLVQIDIHSLGIVETGCVPSKRYCTLLTEQSGFPFLSHP (SEQ ID
N0:368),
MAGCCLKLFGVLSLCFLCGLISIERVICNPVSADFQVSTFCQRHCLLR
SKVMFXIKGXTATIEVINENCTLVAAPPIGFPIXFL (SEQ ID N0:369), MSDHS
KIGKANLVQIDIHSLGIVETGCVPSKRYCTLLTEQSGFPFLSHP (SEQ ID
N0:370), MAGCCLKLFGVLSLCFLCGLISIERVICNPVSADFQVSTFCQRHCL
LRSK (SEQ ID N0:371), VMFXIKGXTATIEVINENCTLVAAPPIGFPIXFL (SEQ
ID N0:372). Polynucleotides encoding these polypeptides are also encompassed
by
the invention.
It has been discovered that this gene is expressed primarily in dendritic
cells,
and smooth muscle.
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Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune, hematopoietic, and
vascular diseases and/or disorders. Similarly, polypeptides and antibodies
directed to
those polypeptides are useful to provide immunological probes for differential
identification of the tissues) or cell type(s). For a number of disorders of
the above
tissues or cells, particularly of the immune, expression of this gene at
significantly
higher or lower levels may be detected in certain tissues (e.g., immune,
hematopoietic, smooth muscle vascular, and cancerous and wounded tissues) or
bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal
fluid) taken
from an individual having such a disorder, relative to the standard gene
expression
level, i.e., the expression level in healthy tissue from an individual not
having the
disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
194 as residues: Asp-40 to Ser-52.
The tissue distribution in dendritic cells suggests that the protein product
of
this clone would be useful for immune disorders.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:97 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1212 of SEQ ID
N0:97, b
is an integer of I S to 1226, where both a and b correspond to the positions
of
nucleotide residues shown in SEQ ID N0:97, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 88
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The translation product of this gene shares sequence homology with androgen-
dependant expressed protein from golden hamster hair follicles which is
thought to be
important in regulating the secretions from glands in the skin (See GenBank
Accession No. gi1191315).
S In specific embodiments, polypeptides of the invention comprise the
following
amino acid sequence: PTEGRQKVLKTFTVPRSALAMTKTSTCIYHFLVLSWYTF
LNYYISQEGKDEVKPKILANGARWKY (SEQ ID N0:373), PTEGRQKVLKTF
TVPRSALAMTKT (SEQ ID N0:375), PRSALAMTKTSTCIYHFLVLSWYTFLN
YYISQEGK (SEQ ID N0:374), and/or FLNYYISQEGKDEVKPKILANGARWKY
(SEQ ID N0:376). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
It has been discovered that this gene is expressed primarily in lung, colon
cancer, and testis.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: disorders of secretory
cells
including cells in the lung, colon, testis and the skin. Similarly,
polypeptides and
antibodies directed to those polypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the secretory epithelial cells
in the lung,
intestine, testis and skin, expression of this gene at significantly higher or
lower levels
may be detected in certain tissues (e.g., cancerous and wounded tissues) or
bodily
fluids (e.g., serum, plasma, urine, synovial fluid or spinal fluid) taken from
an
individual having such a disorder, relative to the standard gene expression
level, i.e.,
the expression level in healthy tissue from an individual not having the
disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
195 as residues: Val-21 to Asp-30, Pro-101 to Thr-109.
The tissue distribution and homology to androgen regulated protein suggests
that the protein product of this clone would be useful for treating disorders
that
involve highly secretory cells including those in the colon, testis, and skin.
It may be
useful for diagnosing disorders such as colon, lung, or testicular cancer and
may be
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used to treat pulmonary conditions in patients with compromised respiratory
function.
In addition, the polynucleotides and polypeptides corresponding to this gene
are
useful for the treatment and diagnosis of conditions concerning proper
testicular
function (e.g. endocrine function, sperm maturation), as well as cancer.
Therefore,
S this gene product is useful in the treatment of male infertility and/or
impotence. This
gene product is also useful in assays designed to identify binding agents, as
such
agents (antagonists) are useful as male contraceptive agents.
Similarly, the protein is believed to be useful in the treatment and/or
diagnosis
of testicular cancer. The testes are also a site of active gene expression of
transcripts
that may be expressed, particularly at low levels, in other tissues of the
body.
Therefore, this gene product may be expressed in other specific tissues or
organs
where it may play related functional roles in other processes, such as
hematopoiesis,
inflammation, bone formation, and kidney function, to name a few possible
target
indications. Protein, as well as, antibodies directed against the protein may
show
utility as a tumor marker and/or immunotherapy targets for the above listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:98 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1106 of SEQ ID
N0:98, b
is an integer of 15 to 1120, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:98, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 89
The translation product of this gene shares sequence homology with dec-205 a
transmembrane protein which is thought to be important in antigen presentation
in
dendritic cells and T-cells.
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It has been discovered that this gene is expressed primarily in macrophage,
dendritic cells, lung and ulcerative colitis.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: inflammatory diseases such
as
ulcerative colitis. Similarly, polypeptides and antibodies directed to those
polypeptides are useful to provide immunological probes for differential
identification
of the tissues) or cell type(s). For a number of disorders of the above
tissues or cells,
particularly of the immune system, expression of this gene at significantly
higher or
lower levels may be detected in certain tissues (e.g., cancerous and wounded
tissues)
or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinal
fluid)
taken from an individual having such a disorder, relative to the standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
196 as residues: Asp-30 to Arg-36, Gln-59 to Val-65.
The distribution in macrophage, dendritic cells, lung and ulcerative colitis
tissues, and homology to antigen presenting receptors suggests that the
protein
product of this clone would be useful for modulating the immune response in
both
acute and chronic inflammatory conditions. Protein, as well as, antibodies
directed
against the protein may show utility as a tumor marker and/or immunotherapy
targets
for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:99 and may have been publicly available prior to
conception of
the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 2582 of SEQ ID
N0:99, b
is an integer of 1 S to 2596, where both a and b correspond to the positions
of
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nucleotide residues shown in SEQ ID N0:99, and where b is greater than or
equal to a
+ 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 90
This gene maps to chromosome 22 and therefore polynucleotides of the
present invention can be used in linkage analysis as a marker for chromosome
22.
In specific embodiments, polypeptides of the invention comprise the sequence
FKDQLVYPLLAFT (SEQ ID N0:377) and/or RQALNLPDVFGLV (SEQ ID
N0:379). Polnucleotides encoding these polypeptides are also encompassed by
the
invention.
It has been discovered that this gene is expressed primarily in fetal spleen
and
liver as well as cd34 positive cells and to a lesser extent in several tissues
suggesting a
presence in blood or blood forming tissues.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: developmental defects in
the
blood and blood forming cells. Similarly, polypeptides and antibodies directed
to
those polypeptides are useful to provide immunological probes for differential
identification of the tissues) or cell type(s). For a number of disorders of
the above
tissues or cells, particularly of the immune system, expression of this gene
at
significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., fetal spleen and liver as well as cd34 positive cells, cancerous and
wounded
tissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
197 as residues: Gln-54 to Gly-61, Asn-79 to Leu-91, Glu-99 to Thr-105, Pro-
120 to
Gln-126, Pro-128 to Phe-134, Arg-150 to Arg-156, Arg-160 to Arg-170.
The tissue distribution in fetal spleen and liver as well as cd34 positive
cells
suggests that the protein product of this clone would be useful for treating
disorders in
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the development, proliferation, or regulation of blood forming cells including
diseases
such as lymphomas, granulomas, leukemias, and in the preservation and or
replenishment of stem cells in the blood.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID NO:100 and may have been publicly available prior to
conception
of the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1006 of SEQ ID
NO:100,
b is an integer of 15 to 1020, where both a and b correspond to the positions
of
nucleotide residues shown in SEQ ID NO:100, and where b is greater than or
equal to
a + 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 91
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: ATASHDLLLF (SEQ ID N0:379), MSINICLMQSKTQGSCQ
YLLLPHPVPIILKVSTVFSLLSLFRLLFLSFCPHPKKCSYLLKYYGPLEGHKTLX
YLRTNLGVIQPPLRMYAAEDCNGIG (SEQ ID N0:380), MSINICLMQSKTQG
SCQYLLLPHPVPIILKVSTVFSLLSLFRLLFL (SEQ ID N0:381), and/or
SFCPHPK KCSYLLKYYGPLEGHKTLXYLRTNLGVIQPPLRMYAAEDCNGIG
(SEQ ID N0:382). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
It has been discovered that this gene is expressed primarily in T cells, fetal
heart and chronic lymphocytic leukemia and to a lesser extent in kidney, lung,
and 16
week embryos.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: disorders of the blood
including
abnormalities in T cell function or blood cell proliferation such as leukemia
.
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169
Similarly, polypeptides and antibodies directed to those polypeptides are
useful to
provide immunological probes for differential identification of the tissues)
or cell
type(s). For a number of disorders of the above tissues or cells, particularly
of the
immune system, expression of this gene at significantly higher or lower levels
may be
detected in certain tissues or cell types (e.g., T cells, fetal heart and
chronic
lymphocytic leukemia, cancerous and wounded tissues) or bodily fluids (e.g.,
lymph,
serum, plasma, urine, synovial fluid or spinal fluid) taken from an individual
having
such a disorder, relative to the standard gene expression level, i.e., the
expression
level in healthy tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
198 as residues: Leu-45 to Val-S0.
The tissue distribution in T cells, fetal heart and chronic lymphocytic
leukemia
suggests that the protein product of this clone would be useful for treating
abnormalities of the blood particularly those involving T-cells and the
abnormal
proliferation of blood cells such as lymphocytic leukemia. In addition, it
suggests the
protein product of this clone is useful for the diagnosis and treatment of a
variety of
immune system disorders. Morever, the expression of this gene product suggests
a
role in regulating the proliferation; survival; differentiation; and/or
activation of
hematopoietic cell lineages, including blood stem cells. This gene product may
be
involved in the regulation of cytokine production, antigen presentation, or
other
processes suggesting a usefulness in the treatment of cancer (e.g. by boosting
immune
responses).
Since the gene is expressed in cells of lymphoid origin, the natural gene
product may be involved in immune functions. Therefore it may be also used as
an
agent for immunological disorders including arthritis, asthma,
immunodeficiency
diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease,
inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia,
psoriasis,
hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to
transplanted organs and tissues, such as host-versus-graft and graft-versus-
host
diseases, or autoimmunity disorders, such as autoimmune infertility, Tense
tissue
injury, demyelination, systemic lupus erythematosis, drug induced hemolytic
anemia,
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rheumatoid arthritis, Sjogren's disease, scleroderm~ and tissues. Moreover,
the protein
may represent a secreted factor that influences the differentiation or
behavior of other
blood cells, or that recruits hematopoietic cells to sites of injury. In
addition, this gene
product may have commercial utility in the expansion of stem cells and
committed
progenitors of various blood lineages, and in the differentiation andlor
proliferation of
various cell types.
The expression in fetal heart tissue would suggest a useful role for the
protein
product in developmental abnormalities, fetal deficiencies, pre-natal
disorders and
variouswould-healing models and/or tissue trauma. The tissue distribution in
kidney
suggests the protein product of this clone could be used in the treatment
and/or
detection of kidney diseases including renal failure, nephritus, renal tubular
acidosis,
proteinuria, pyuria, edema, pyelonephritis, hydronephritis, nephrotic
syndrome, crush
syndrome, glomerulonephritis, hematuria, renal colic and kidney stones, in
addition to
Wilm's Tumor Disease, and congenital kidney abnormalities such as horseshoe
kidney, polycystic kidney, and Falconi's syndrome.
In addition, the tissue distribution in embryonic tissue suggests the protein
product of this clone is useful for the diagnosis, detection, and/or treatment
of
developmental disorders. Expression within embryonic tissue and other cellular
sources marked by proliferating cells suggests this protein may play a role in
the
regulation of cellular division, and may show utility in the diagnosis and
treatment of
cancer and other proliferative disorders. Similarly, developmental tissues
rely on
decisions involving cell differentiation and/or apoptosis in pattern
formation.
Dysregulation of apoptosis can result in inappropriate suppression of cell
death, as
occurs in the development of some cancers, or in failure to control the extent
of cell
death, as is believed to occur in acquired immunodeficiency and certain
neurodegenerative disorders, such as spinal muscular atrophy (SMA). Therefore,
the
polynucleotides and polypeptides of the present invention are useful in
treating,
detecting, andlor preventing said disorders and conditions, in addition to
other types
of degenerative conditions. Thus this protein may modulate apoptosis or tissue
differentiation and would be useful in the detection, treatment, andlor
prevention of
degenerative or proliferative conditions and diseases. Protein, as well as,
antibodies
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171
directed against the protein may show utility as a tumor marker and/or
immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID NO:101 and may have been publicly available prior to
conception
of the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1506 of SEQ ID
NO:101,
b is an integer of 15 to 1520, where both a and b correspond to the positions
of
nucleotide residues shown in SEQ ID NO:101, and where b is greater than or
equal to
a + 14.
1 S FEATURES OF PROTEIN ENCODED BY GENE NO: 92
The translation product of this gene shares sequence homology with ctg4
which is a glutamine repeat containing gene thought to be a candidate genetic
disease
locus.
In specific embodiments, polypeptides of the invention comprise the sequence
KEEDDDTERLPSKCEVCKLLSTE (SEQ ID N0:383 and 384) LQAELSRTGRSR
EVLELGQ (SEQ ID N0:385 and 386), RQAVIVCRRRFV (SEQ ID N0:387),
PPRWAHPKAPEGSPDPPSPPSALGLSVLPWSDSDPWHISVSPCAQREHYSPGS
AHINSLRPLPALSLKRCKARVSSSCLYPAPAPAPAPLEIDRCDSVPPVALCSAA
YTLRICWASVLCHRPPPSTSQPKPRARPKKGKAIFPTAQVP (SEQ ID N0:388),
PPRWAHPKAPEGSPDPPSPPSALGLSVLPWSDSDPWHISVSPCAQREHYSPGS
AHINSLRPLPALSLKRCK (SEQ ID N0:389), and/or ARVSSSCLYPAPAPAPAPL
EIDRCDS VPPVALCSAAYTLRICWASVLCHRPPPSTSQPKPRARPKKGKAIFPT
AQVP (SEQ ID N0:390). Polynucleotides encoding these polypeptides are also
encompassed by the invention.
It has been discovered that this gene is expressed in several tissues
including
lung, heart, kidney, adrenal gland, smooth muscle, cerebellum, and embryonic
tissue.
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I72
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: inherited developmental
disorders
possibly with a neuropsychiatric component. Similarly, polypeptides and
antibodies
directed to those polypeptides are useful to provide immunological probes for
differential identification of the tissues) or cell type(s). For a number of
disorders of
the above tissues or cells, particularly of the nervous system, expression of
this gene
at significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum,
plasma,
urine, synovial fluid or spinal fluid) taken from an individual having such a
disorder,
relative to the standard gene expression level, i.e., the expression level in
healthy
tissue from an individual not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
199 as residues: Lys-25 to Ser-36, Ser-53 to Glu-60, Thr-70 to Arg-75, Arg-111
to
Thr-119, Glu-161 to Leu-189.
The tissue distribution and homology to glutamine repeat family member
CTG4 suggests that the protein product of this clone would be useful for
identifying
and treating specific diseases related to nucleotide triplet expansion. The
tissue
distribution in embryonic tissue suggests the protein product of this clone is
useful for
the diagnosis, detection, and/or treatment of developmental disorders. The
relatively
specific expression of this gene product during embryogenesis suggests it may
be a
key player in the proliferation, maintenance, and/or differentiation of
various cell
types during development. It may also act as a morphogen to control cell and
tissue
type specification. Because of potential roles in proliferation and
differentiation, this
gene product may have applications in the adult for tissue regeneration and
the
treatment of cancers. Expression within embryonic tissue and other cellular
sources
marked by proliferating cells suggests this protein may play a role in the
regulation of
cellular division, and may show utility in the diagnosis and treatment of
cancer and
other proliferative disorders.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
CA 02323761 2000-09-18
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173
related to SEQ ID N0:102 and may have been publicly available prior to
conception
of the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 1292 of SEQ ID
N0:102,
b is an integer of 15 to 1306, where both a and b correspond to the positions
of
nucleotide residues shown in SEQ ID N0:102, and where b is greater than or
equal to
a + 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 93
In specific embodiments, polypeptides of the invention comprise the following
amino acid sequence: EEKLFTSAPGRDFWVMGETRDGNEEN (SEQ ID N0:391).
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
The gene encoding the disclosed cDNA is believed to reside on chromosome 16.
Accordingly, polynucleotides related to this invention are useful as a marker
in
linkage analysis for chromosome 16.
It has been discovered that this gene is expressed primarily in cancerous and
fetal tissue.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: cancer, developmental
anomalies
or fetal deficiencies. Similarly, polypeptides and antibodies directed to
those
polypeptides are useful to provide immunological probes for differential
identification
of the tissues) or cell type(s). For a number of disorders of the above
tissues or cells,
particularly of the reproductive system and developing fetus, expression of
this gene
at significantly higher or lower levels may be detected in certain tissues or
cell types
(e.g., developmental, reproductive, and cancerous and wounded tissues) or
bodily
fluids (e.g., lymph, amniotic fluid, serum, plasma, urine, synovial fluid or
spinal fluid)
taken from an individual having such a disorder, relative to the standard gene
CA 02323761 2000-09-18
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174
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
200 as residues: Met-1 to Ser-6.
The tissue distribution in fetal tissue suggests that the protein product of
this
clone would be useful for the treatment and diagnosis of developmental
anomalies or
fetal deficiencies. In addition to fetal tissue, expression in a variety of
cancerous
tissues suggests a role in the treatment and diagnosis of uncontrolled cell
proliferation
and/or differentiation (e.g. cancer). Moreover, the expression within
embryonic tissue
and other cellular sources marked by proliferating cells suggests this protein
may play
a role in the regulation of cellular division, and may show utility in the
diagnosis and
treatment of cancer and other proliferative disorders.
Similarly, developmental tissues rely on decisions involving cell
differentiation and/or apoptosis in pattern formation. Dysregulation of
apoptosis can
result in inappropriate suppression of cell death, as occurs in the
development of some
cancers, or in failure to control the extent of cell death, as is believed to
occur in
acquired immunodeficiency and certain neurodegenerative disorders, such as
spinal
muscular atrophy (SMA). Therefore, the polynucleotides and polypeptides of the
present invention are useful in treating, detecting, and/or preventing said
disorders
and conditions, in addition to other types of degenerative conditions. Thus
this protein
may modulate apoptosis or tissue differentiation and would be useful in the
detection,
treatment, and/or prevention of degenerative or proliferative conditions and
diseases.
Protein, as well as, antibodies directed against the protein may show utility
as a tumor
marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:103 and may have been publicly available prior to
conception
of the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
CA 02323761 2000-09-18
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175
general formula of a-b, where a is any integer between 1 to 771 of SEQ ID NO:
I03, b
is an integer of 15 to 785, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID N0:103, and where b is greater than or
equal to
a + 14.
S
FEATURES OF PROTEIN ENCODED BY GENE NO: 94
The gene encoding the disclosed cDNA is believed to reside on chromosome
10. Accordingly, polynucleotides related to this invention are useful as a
marker in
linkage analysis for chromosome 10.
IO This gene is expressed primarily in hypothalamus, T-cells, and adipose
tissue.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immune (e.g.
immunodeflciencies,
autoimmunities, inflammation, leukemias & lymphomas) and neurological (e.g.
15 Alzheimer's disease, dementia, schizophrenia) disorders. Similarly,
polypeptides and
antibodies directed to those polypeptides are useful to provide immunological
probes
for differential identification of the tissues) or cell type(s). For a number
of disorders
of the above tissues or cells, particularly of the central nervous,
hematopoietic and
immune systems, expression of this gene at significantly higher or lower
levels may
20 be detected in certain tissues (e.g., immune, neural, metabolic, and
cancerous and
wounded tissues) or bodily fluids (e.g., serum, plasma, urine, synovial fluid
or spinal
fluid) taken from an individual having such a disorder, relative to the
standard gene
expression level, i.e., the expression level in healthy tissue from an
individual not
having the disorder. The tissue distribution suggests that the protein product
of this
25 clone would be useful in the intervention or detection of pathologies
associated with
the hematopoietic and immune systems, such as anemias (leukemias). In
addition, the
expression in brain {including fetal) might suggest a role in developmental
brain
defects, neuro-degenerative diseases or behavioral abnomalities (e.g.
schizophrenia,
Alzheimer's, dementia, depression, etc.).
30 Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
201 as residues: Phe-64 to Gly-77, Pro-83 to Asp-99.
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The tissue distribution in hypothallamus suggests the protein product of this
clone is useful for the detection, treatment, and/or prevention of
neurodegenerative
disease states, behavioral disorders, or inflammatory conditions which
include, but
are not limited to Alzheimer's Disease, Parkinson's Disease, Huntington's
Disease,
Tourette Syndrome, meningitis, encephalitis, demyelinating diseases,
peripheral
neuropathies, neoplasia, trauma, congenital malformations, spinal cord
injuries,
ischemia and infarction, aneurysms, hemorrhages, schizophrenia, mania,
dementia,
paranoia, obsessive compulsive disorder, depression, panic disorder, learning
disabilities, ALS, psychoses, autism, and altered behaviors, including
disorders in
feeding, sleep patterns, balance, and perception. In addition, elevated
expression of
this gene product in regions of the brain suggests it plays a role in normal
neural
function. Potentially, this gene product is involved in synapse formation,
neurotransmission, learning, cognition, homeostasis, or neuronal
differentiation or
survival. This gene product may be involved in the regulation of cytokine
production,
antigen presentation, or other processes suggesting a usefulness in the
treatment of
cancer (e.g. by boosting immune responses).
Since the gene is expressed in cells of lymphoid origin, the natural gene
product may be involved in immune functions. Therefore it may be also used as
an
agent for immunological disorders including arthritis, asthma,
immunodeficiency
diseases such as AIDS, leukemia, rheumatoid arthritis, granulomatous disease,
inflammatory bowel disease, sepsis, acne, neutropenia, neutrophilia,
psoriasis,
hypersensitivities, such as T-cell mediated cytotoxicity; immune reactions to
transplanted organs and tissues, such as host-versus-graft and graft-versus-
host
diseases, or autoimmunity disorders, such as autoimmune infertility, tense
tissue
injury, demyelination, systemic lupus erythematosis, drug induced hemolytic
anemia,
rheumatoid arthritis, Sjogren's disease, scleroderma and tissues.
Moreover, the protein may represent a secreted factor that influences the
differentiation or behavior of other blood cells, or that recruits
hematopoietic cells to
sites of injury. In addition, this gene product may have commercial utility in
the
expansion of stem cells and committed progenitors of various blood lineages,
and in
the differentiation and/or proliferation of various cell types. Moreover, the
protein
CA 02323761 2000-09-18
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177
product of this clone is useful for the diagnosis, prevention, and/or
treatment of
various metabolic disorders which include, but are not limited to, Tay-Sachs
disease,
phenylkenonuria, galactosemia, hyperlipidemias, porphyrias, and Hurler's
syndrome.
The protein is useful in the treatment and/or prevention of neurodegenerative
conditions, particularly those which occur secondary to aberrant fatty acid
metabolism (i.e. defects which affect the synthesis and integrity of the
myelin sheath).
Protein, as well as, antibodies directed against the protein may show utility
as a tumor
marker and/or immunotherapy targets for the above listed tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID N0:104 and may have been publicly available prior to
conception
of the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 2001 of SEQ ID
N0:104,
b is an integer of 15 to 2015, where both a and b correspond to the positions
of
nucleotide residues shown in SEQ ID N0:104, and where b is greater than or
equal to
a + 14.
FEATURES OF PROTEIN ENCODED BY GENE NO: 95
The translation product of this gene was shown to have homology to the
murine leucine-rich repeat protein (See Genbank Accession No. gi12880079),
which is
thought to be important in neural development.
In specific embodiments, the polypeptides of the invention comprise the
sequence:QKPTFALGELYPPLINLWEAGKEKSTSLKVKATVIGLPTNMS (SEQ
ID N0:392). Polynucleotides encoding this polypeptide are also encompassed by
the
invention. The gene encoding the disclosed cDNA is believed to reside on
chromosome 7. Accordingly, polynucleotides related to this invention are
useful as
a marker in linkage analysis for chromosome 7.
CA 02323761 2000-09-18
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178
It has been discovered that this gene is expressed primarily in T-cells and
brain.
Therefore, nucleic acids of the invention are useful as reagents for
differential
identification of the tissues) or cell types) present in a biological sample
and for
diagnosis of the following diseases and conditions: immunodeflciency, tumor
necrosis, infection, lymphomas, auto-immunities, cancer, inflammation, anemias
(leukemia) and other hematopoeitic disorders, neurological diseases of the
brain such
as depression, schizophrenia, Alzheimer's disease, Parkinson's disease,
Huntington's
disease, dementia and specific brain tumors. Similarly, polypeptides and
antibodies
directed to those polypeptides are useful to provide immunological probes for
differential identification of the tissues) or cell type(s). For a number of
disorders of
the above tissues or cells, particularly of the brain and immune system,
expression of
this gene at significantly higher or lower levels may be detected in certain
tissues or
cell types (e.g., neural, immune, hematopoietic, and cancerous and wounded
tissues)
or bodily fluids (e.g., lymph, amniotic fluid, serum, plasma, urine, synovial
fluid or
spinal fluid) taken from an individual having such a disorder, relative to the
standard
gene expression level, i.e., the expression level in healthy tissue from an
individual
not having the disorder.
Preferred epitopes include those comprising a sequence shown in SEQ ID NO.
202 as residues: Met-24 to Gly-29, Ala-57 to Thr-63.
The tissue distribution in T-cells suggests that the protein product of this
clone
would be useful for the diagnosis and treatment of immune disorders including:
leukemias, lymphomas, auto-immunities, immunodeficiencies (e.g. AIDS), immuno-
supressive conditions (transplantation) and hematopoeitic disorders. In
addition this
gene product may be applicable in conditions of general microbial infection,
inflammation or cancer. The expression in brain, combined with the homology to
the
leucine-rich repeat protein suggests that the protein product of this clone
would be
useful for the treatment and diagnosis of developmental, degenerative and
behavioral
conditions of the brain and nervous system, such as depression, schizophrenia,
Alzheimer's disease, Parkinson's disease, Huntington's disease, Tourette
Syndrome,
mania, dementia, paranoia, addictive behavior, obsessive-compulsisve disorder
and
CA 02323761 2000-09-18
WO 99/47540 PCTNS99/05804
179
sleep disorders. Protein, as well as, antibodies directed against the protein
may show
utility as a tumor marker and/or immunotherapy targets for the above listed
tissues.
Many polynucleotide sequences, such as EST sequences, are publicly
available and accessible through sequence databases. Some of these sequences
are
related to SEQ ID NO:105 and may have been publicly available prior to
conception
of the present invention. Preferably, such related polynucleotides are
specifically
excluded from the scope of the present invention. To list every related
sequence
would be cumbersome. Accordingly, preferably excluded from the present
invention
are one or more polynucleotides comprising a nucleotide sequence described by
the
general formula of a-b, where a is any integer between 1 to 353 of SEQ ID
NO:105, b
is an integer of 15 to 367, where both a and b correspond to the positions of
nucleotide residues shown in SEQ ID NO:105, and where b is greater than or
equal to
a + 14.
CA 02323761 2000-09-18
WO 99/47540 PCT/US99/05804
180
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CA 02323761 2000-09-18
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CA 02323761 2000-09-18
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CA 02323761 2000-09-18
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CA 02323761 2000-09-18
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CA 02323761 2000-09-18
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CA 02323761 2000-09-18
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00 ~n
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M ~ ~ ~ i o
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Table 1 summarizes the information corresponding to each "Gene No." described
above. The nucleotide sequence identified as "NT SEQ ID NO:X" was assembled
from partially homologous ("overlapping") sequences obtained from the "cDNA
clone ID" identified in Table 1 and, in some cases, from additional related
DNA
clones. The overlapping sequences were assembled into a single contiguous
sequence
of high redundancy (usually three to five overlapping sequences at each
nucleotide
position), resulting in a final sequence identified as SEQ ID NO:X.
The cDNA Clone ID was deposited on the date and given the corresponding
deposit number listed in "ATCC Deposit No:Z and Date." Some of the deposits
contain multiple different clones corresponding to the same gene. "Vector"
refers to
the type of vector contained in the cDNA Clone ID.
"Total NT Seq." refers to the total number of nucleotides in the contig
identified by "Gene No." The deposited clone may contain all or most of these
sequences, reflected by the nucleotide position indicated as "5' NT of Clone
Seq."
and the "3' NT of Clone Seq." of SEQ ID NO:X. The nucleotide position of SEQ
ID
NO:X of the putative start codon (methionine) is identified as "5' NT of Start
Codon."
Similarly , the nucleotide position of SEQ ID NO:X of the predicted signal
sequence
is identified as "5' NT of First AA of Signal Pep."
The translated amino acid sequence, beginning with the methionine, is
identified as "AA SEQ ID NO:Y," although other reading frames can also be
easily
translated using known molecular biology techniques. The polypeptides produced
by
these alternative open reading frames are specifically contemplated by the
present
mventlon.
The first and last amino acid position of SEQ ID NO:Y of the predicted signal
peptide is identified as "First AA of Sig Pep" and "Last AA of Sig Pep." The
predicted first amino acid position of SEQ ID NO:Y of the secreted portion is
identified as "Predicted First AA of Secreted Portion." Finally, the amino
acid
position of SEQ ID NO:Y of the last anuno acid in the open reading frame is
identified as "Last AA of ORF."
SEQ ID NO:X and the translated SEQ ID NO:Y are sufficiently accurate and
otherwise suitable for a variety of uses well known in the art and described
further
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below. For instance, SEQ ID NO:X is useful for designing nucleic acid
hybridization
probes that will detect nucleic acid sequences contained in SEQ ID NO:X or the
cDNA contained in the deposited clone. These probes will also hybridize to
nucleic
acid molecules in biological samples, thereby enabling a variety of forensic
and
diagnostic methods of the invention. Similarly, polypeptides identified from
SEQ ID
NO:Y may be used to generate antibodies which bind specifically to the
secreted
proteins encoded by the cDNA clones identified in Table 1.
Nevertheless, DNA sequences generated by sequencing reactions can contain
sequencing errors. The errors exist as misidentified nucleotides, or as
insertions or
deletions of nucleotides in the generated DNA sequence. The erroneously
inserted or
deleted nucleotides cause frame shifts in the reading frames of the predicted
amino
acid sequence. In these cases, the predicted amino acid sequence diverges from
the
actual amino acid sequence, even though the generated DNA sequence may be
greater
than 99.9% identical to the actual DNA sequence (for example, one base
insertion or
deletion in an open reading frame of over 1000 bases).
Accordingly, for those applications requiring precision in the nucleotide
sequence or the amino acid sequence, the present invention provides not only
the
generated nucleotide sequence identified as SEQ ID NO:X and the predicted
translated amino acid sequence identified as SEQ ID NO:Y, but also a sample of
plasmid DNA containing a human cDNA of the invention deposited with the ATCC,
as set forth in Table 1. The nucleotide sequence of each deposited clone can
readily
be determined by sequencing the deposited clone in accordance with known
methods.
The predicted amino acid sequence can then be verified from such deposits.
Moreover, the amino acid sequence of the protein encoded by a particular clone
can
also be directly determined by peptide sequencing or by expressing the protein
in a
suitable host cell containing the deposited human cDNA, collecting the
protein, and
determining its sequence.
The present invention also relates to the genes corresponding to SEQ ID
NO:X, SEQ ID NO:Y, or the deposited clone. The corresponding gene can be
isolated in accordance with known methods using the sequence information
disclosed
herein. Such methods include preparing probes or primers from the disclosed
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sequence and identifying or amplifying the corresponding gene from appropriate
sources of genomic material.
Also provided in the present invention are species homologs. Species
homologs may be isolated and identified by making suitable probes or primers
from
the sequences provided herein and screening a suitable nucleic acid source for
the
desired homologue.
The polypeptides of the invention can be prepared in any suitable manner.
Such polypeptides include isolated naturally occurring polypeptides,
recombinantly
produced polypeptides, synthetically produced polypeptides, or polypeptides
produced by a combination of these methods. Means for preparing such
polypeptides
are well understood in the art.
The polypeptides may be in the form of the secreted protein, including the
mature form, or may be a part of a larger protein, such as a fusion protein
(see below).
It is often advantageous to include an additional amino acid sequence which
contains
secretory or leader sequences, pro-sequences, sequences which aid in
purification ,
such as multiple histidine residues, or an additional sequence for stability
during
recombinant production.
The polypeptides of the present invention are preferably provided in an
isolated form, and preferably are substantially purified. A recombinantly
produced
version of a polypeptide, including the secreted polypeptide, can be
substantially
purified by the one-step method described in Smith and Johnson, Gene 67:31-40
( 1988). Polypeptides of the invention also can be purified from natural or
recombinant sources using antibodies of the invention raised against the
secreted
protein in methods which are well known in the art.
,~i final Sequences
Methods for predicting whether a protein has a signal sequence, as well as the
cleavage point for that sequence, are available. For instance, the method of
McGeoch, Virus Res. 3:271-286 (1985), uses the information from a short N-
terminal
charged region and a subsequent uncharged region of the complete (uncleaved)
protein. The method of von Heinje, Nucleic Acids Res. 14:4683-4690 ( 1986)
uses the
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information from the residues surrounding the cleavage site, typically
residues -13 to
+2, where +1 indicates the amino terminus of the secreted protein. The
accuracy of
predicting the cleavage points of known mammalian secretory proteins for each
of
these methods is in the range of 75-80%. (von Heinje, supra.) However, the two
methods do not always produce the same predicted cleavage points) for a given
protein.
In the present case, the deduced amino acid sequence of the secreted
polypeptide was analyzed by a computer program called SignalP (Henrik Nielsen
et
al., Protein Engineering 10:1-6 ( 1997)), which predicts the cellular location
of a
protein based on the amino acid sequence. As part of this computational
prediction of
localization, the methods of McGeoch and von Heinje are incorporated. The
analysis
of the amino acid sequences of the secreted proteins described herein by this
program
provided the results shown in Table 1.
As one of ordinary skill would appreciate, however, cleavage sites sometimes
vary from organism to organism and cannot be predicted with absolute
certainty.
Accordingly, the present invention provides secreted polypeptides having a
sequence
shown in SEQ ID NO:Y which have an N-terminus beginning within 5 residues
(i.e.,
+ or - 5 residues) of the predicted cleavage point. Similarly, it is also
recognized that
in some cases, cleavage of the signal sequence from a secreted protein is not
entirely
uniform, resulting in more than one secreted species. These polypeptides, and
the
polynucleotides encoding such polypeptides, are contemplated by the present
lnventlon.
Moreover, the signal sequence identified by the above analysis may not
necessarily predict the naturally occurring signal sequence. For example, the
naturally occurring signal sequence may be further upstream from the predicted
signal
sequence. However, it is likely that the predicted signal sequence will be
capable of
directing the secreted protein to the ER. These polypeptides, and the
polynucleotides
encoding such polypeptides, are contemplated by the present invention.
Polynucleotide and Pol~r~eptide Variants
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"Variant" refers to a polynucleotide or polypeptide differing from the
polynucleotide or polypeptide of the present invention, but retaining
essential
properties thereof. Generally, variants are overall closely similar, and, in
many
regions, identical to the polynucleotide or polypeptide of the present
invention.
By a polynucleotide having a nucleotide sequence at least, for example, 95%
"identical" to a reference nucleotide sequence of the present invention, it is
intended
that the nucleotide sequence of the polynucleotide is identical to the
reference
sequence except that the polynucleotide sequence may include up to five point
mutations per each 100 nucleotides of the reference nucleotide sequence
encoding the
polypeptide. In other words, to obtain a polynucleotide having a nucleotide
sequence
at least 95% identical to a reference nucleotide sequence, up to 5% of the
nucleotides
in the reference sequence may be deleted or substituted with another
nucleotide, or a
number of nucleotides up to 5% of the total nucleotides in the reference
sequence may
be inserted into the reference sequence. The query sequence may be an entire
sequence shown inTable l, the ORF (open reading frame), or any fragement
specified
as described herein.
As a practical matter, whether any particular nucleic acid molecule or
polypeptide is at least 90%, 95%, 96%, 97%, 98% or 99% identical to a
nucleotide
sequence of the presence invention can be determined conventionally using
known
computer programs. A preferred method for determing the best overall match
between a query sequence (a sequence of the present invention) and a subject
sequence, also referred to as a global sequence alignment, can be determined
using
the FASTDB computer program based on the algorithm of Brutlag et al. (Comp.
App.
Biosci. (1990) 6:237-245). In a sequence alignment the query and subject
sequences
are both DNA sequences. An RNA sequence can be compared by converting U's to
T's. The result of said global sequence alignment is in percent identity.
Preferred
parameters used in a FASTDB alignment of DNA sequences to calculate percent
identiy are: Matrix=Unitary, k-tuple=4, Mismatch Penalty=1, Joining
Penalty=30,
Randomization Group Length=0, Cutoff Score=l, Gap Penalty=5, Gap Size Penalty
0.05, Window Size=500 or the lenght of the subject nucleotide sequence,
whichever is
shorter.
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If the subject sequence is shorter than the query sequence because of 5' or 3'
deletions, not because of internal deletions, a manual correction must be made
to the
results. This is because the FASTDB program does not account for 5' and 3'
truncations of the subject sequence when calculating percent identity. For
subject
sequences truncated at the 5' or 3' ends, relative to the the query sequence,
the
percent identity is corrected by calculating the number of bases of the query
sequence
that are 5' and 3' of the subject sequence, which are not matched/aligned, as
a percent
of the total bases of the query sequence. Whether a nucleotide is
matched/aligned is
determined by results of the FASTDB sequence alignment. This percentage is
then
subtracted from the percent identity, calculated by the above FASTDB program
using
the specified parameters, to arrive at a final percent identity score. This
corrected
score is what is used for the purposes of the present invention. Only bases
outside the
5' and 3' bases of the subject sequence, as displayed by the FASTDB alignment,
which are not matched/aligned with the query sequence, are calculated for the
purposes of manually adjusting the percent identity score.
For example, a 90 base subject sequence is aligned to a 100 base query
sequence to determine percent identity. The deletions occur at the 5' end of
the
subject sequence and therefore, the FASTDB alignment does not show a
matched/alignement of the first 10 bases at 5' end. The 10 unpaired bases
represent
10% of the sequence (number of bases at the 5' and 3' ends not matched/total
number
of bases in the query sequence) so 10% is subtracted from the percent identity
score
calculated by the FASTDB program. If the remaining 90 bases were perfectly
matched the final percent identity would be 90%. In another example, a 90 base
subject sequence is compared with a 100 base query sequence. This time the
deletions are internal deletions so that there are no bases on the S' or 3' of
the subject
sequence which are not matched/aligned with the query. In this case the
percent
identity calculated by FASTDB is not manually corrected. Once again, only
bases 5'
and 3' of the subject sequence which are not matched/aligned with the query
sequnce
are manually corrected for. No other manual corrections are to made for the
purposes
of the present invention.
By a polypeptide having an amino acid sequence at least, for example, 95%
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"identical" to a query amino acid sequence of the present invention, it is
intended that
the amino acid sequence of the subject polypeptide is identical to the query
sequence
except that the subject polypeptide sequence may include up to five amino acid
alterations per each 100 amino acids of the query amino acid sequence. In
other
words, to obtain a polypeptide having an amino acid sequence at least 95%
identical
to a query amino acid sequence, up to 5% of the amino acid residues in the
subject
sequence may be inserted, deleted, (indels) or substituted with another amino
acid.
These alterations of the reference sequence may occur at the amino or carboxy
terminal positions of the reference amino acid sequence or anywhere between
those
terminal positions, interspersed either individually among residues in the
reference
sequence or in one or more contiguous groups within the reference sequence.
As a practical matter, whether any particular polypeptide is at least 90%,
95%,
96%, 97%, 98% or 99% identical to, for instance, the amino acid sequences
shown in
Table 1 or to the amino acid sequence encoded by deposited DNA clone can be
determined conventionally using known computer programs. A preferred method
for
determing the best overall match between a query sequence (a sequence of the
present
invention) and a subject sequence, also referred to as a global sequence
alignment,
can be determined using the FASTDB computer program based on the algorithm of
Brutlag et al. (Comp. App. Biosci. ( 1990) 6:237-245). In a sequence alignment
the
query and subject sequences are either both nucleotide sequences or both amino
acid
sequences. The result of said global sequence alignment is in percent
identity.
Preferred parameters used in a FASTDB amino acid alignment are: Matrix=PAM 0,
k-tuple=2, Mismatch Penalty=1, Joining Penalty=20, Randomization Group
Length=0, Cutoff Score=1, Window Size=sequence length, Gap Penalty=5, Gap Size
Penalty=0.05, Window Size=500 or the length of the subject amino acid
sequence,
whichever is shorter.
If the subject sequence is shorter than the query sequence due to N- or C-
terminal deletions, not because of internal deletions, a manual correction
must be
made to the results. This is becuase the FASTDB program does not account for N-
and C-terminal truncations of the subject sequence when calculating global
percent
identity. For subject sequences truncated at the N- and C-termini, relative to
the the
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query sequence, the percent identity is corrected by calculating the number of
residues
of the query sequence that are N- and C-terminal of the subject sequence,
which are
not matched/aligned with a corresponding subject residue, as a percent of the
total
bases of the query sequence. Whether a residue is matched/aligned is
determined by
results of the FASTDB sequence alignment. This percentage is then subtracted
from
the percent identity, calculated by the above FASTDB program using the
specified
parameters, to arrive at a final percent identity score. This final percent
identity score
is what is used for the purposes of the present invention. Only residues to
the N- and
C-termini of the subject sequence, which are not matched/aligned with the
query
sequence, are considered for the purposes of manually adjusting the percent
identity
score. That is, only query residue positions outside the farthest N- and C-
terminal
residues of the subject sequence.
For example, a 90 amino acid residue subject sequence is aligned with a 100
residue query sequence to determine percent identity. The deletion occurs at
the N-
terminus of the subject sequence and therefore, the FASTDB alignment does not
show a matching/alignment of the first 10 residues at the N-terminus. The 10
unpaired residues represent 10% of the sequence (number of residues at the N-
and C-
termini not matched/total number of residues in the query sequence) so 10% is
subtracted from the percent identity score calculated by the FASTDB program.
If the
remaining 90 residues were perfectly matched the final percent identity would
be
90%. In another example, a 90 residue subject sequence is compared with a 100
residue query sequence. This time the deletions are internal deletions so
there are no
residues at the N- or C-termini of the subject sequence which are not
matchedlaligned
with the query. In this case the percent identity calculated by FASTDB is not
manually corrected. Once again, only residue positions outside the N- and C-
terminal
ends of the subject sequence, as displayed in the FASTDB alignment, which are
not
matched/aligned with the query sequnce are manually corrected for. No other
manual
corrections are to made for the purposes of the present invention.
The variants may contain alterations in the coding regions, non-coding
regions, or both. Especially preferred are polynucleotide variants containing
alterations which produce silent substitutions, additions, or deletions, but
do not alter
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the properties or activities of the encoded polypeptide. Nucleotide variants
produced
by silent substitutions due to the degeneracy of the genetic code are
preferred.
Moreover, variants in which 5-10, 1-S, or 1-2 amino acids are substituted,
deleted, or
added in any combination are also preferred. Polynucleotide variants can be
produced
for a variety of reasons, e.g., to optimize codon expression for a particular
host
(change codons in the human mRNA to those preferred by a bacterial host such
as E.
coli).
Naturally occurring variants are called "allelic variants," and refer to one
of
several alternate forms of a gene occupying a given locus on a chromosome of
an
organism. (Genes II, Lewin, B., ed., John Wiley & Sons, New York (1985).)
These
allelic variants can vary at either the polynucleotide and/or polypeptide
level.
Alternatively, non-naturally occurring variants may be produced by mutagenesis
techniques or by direct synthesis.
Using known methods of protein engineering and recombinant DNA
technology, variants may be generated to improve or alter the characteristics
of the
polypeptides of the present invention. For instance, one or more amino acids
can be
deleted from the N-terminus or C-terminus of the secreted protein without
substantial
loss of biological function. The authors of Ron et al., J. Biol. Chem. 268:
2984-2988
( 1993), reported variant KGF proteins having heparin binding activity even
after
deleting 3, 8, or 27 amino-terminal amino acid residues. Similarly, Interferon
gamma
exhibited up to ten times higher activity after deleting 8-10 amino acid
residues from
the carboxy terminus of this protein. (Dobeli et al., J. Biotechnology 7:199-
216
( 1988).)
Moreover, ample evidence demonstrates that variants often retain a biological
activity similar to that of the naturally occurring protein. For example,
Gayle and
coworkers (J. Biol. Chem 268:22105-22111 ( 1993)) conducted extensive
mutational
analysis of human cytokine IL-la. They used random mutagenesis to generate
over
3,500 individual IL-la mutants that averaged 2.5 amino acid changes per
variant over
the entire length of the molecule. Multiple mutations were examined at every
possible amino acid position. The investigators found that "[m]ost of the
molecule
could be altered with little effect on either [binding or biological
activity)." (See,
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Abstract.) In fact, only 23 unique amino acid sequences, out of more than
3,500
nucleotide sequences examined, produced a protein that significantly differed
in
activity from wild-type.
Furthermore, even if deleting one or more amino acids from the N-terminus or
C-terminus of a polypeptide results in modification or loss of one or more
biological
functions, other biological activities may still be retained. For example, the
ability of
a deletion variant to induce and/or to bind antibodies which recognize the
secreted
form will likely be retained when less than the majority of the residues of
the secreted
form are removed from the N-terminus or C-ternvnus. Whether a particular
polypeptide lacking N- or C-terminal residues of a protein retains such
immunogenic
activities can readily be determined by routine methods described herein and
otherwise known in the art.
Thus, the invention further includes polypeptide variants which show
substantial biological activity. Such variants include deletions, insertions,
inversions, repeats, and substitutions selected according to general rules
known in the
art so as have little effect on activity. For example, guidance concerning how
to make
phenotypically silent amino acid substitutions is provided in Bowie, J. U. et
al.,
Science 247:1306-1310 (1990), wherein the authors indicate that there are two
main
strategies for studying the tolerance of an amino acid sequence to change.
The first strategy exploits the tolerance of amino acid substitutions by
natural
selection during the process of evolution. By comparing amino acid sequences
in
different species, conserved amino acids can be identified. These conserved
amino
acids are likely important for protein function. In contrast, the amino acid
positions
where substitutions have been tolerated by natural selection indicates that
these
positions are not critical for protein function. Thus, positions tolerating
amino acid
substitution could be modified while still maintaining biological activity of
the
protein.
The second strategy uses genetic engineering to introduce amino acid changes
at specific positions of a cloned gene to identify regions critical for
protein function.
For example, site directed mutagenesis or alanine-scanning mutagenesis
(introduction
of single alanine mutations at every residue in the molecule) can be used.
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(Cunningham and Wells, Science 244:1081-1085 (1989).) The resulting mutant
molecules can then be tested for biological activity.
As the authors state, these two strategies have revealed that proteins are
surprisingly tolerant of amino acid substitutions. The authors further
indicate which
amino acid changes are likely to be permissive at certain amino acid positions
in the
protein. For example, most buried (within the tertiary structure of the
protein) amino
acid residues require nonpolar side chains, whereas few features of surface
side chains
are generally conserved. Moreover, tolerated conservative amino acid
substitutions
involve replacement of the aliphatic or hydrophobic amino acids Ala, Val, Leu
and
Ile; replacement of the hydroxyl residues Ser and Thr; replacement of the
acidic
residues Asp and Glu; replacement of the amide residues Asn and Gln,
replacement of
the basic residues Lys, Arg, and His; replacement of the aromatic residues
Phe, Tyr,
and Trp, and replacement of the small-sized amino acids Ala, Ser, Thr, Met,
and Gly.
Besides conservative amino acid substitution, variants of the present
invention
include (i) substitutions with one or more of the non-conserved amino acid
residues,
where the substituted amino acid residues may or may not be one encoded by the
genetic code, or (ii) substitution with one or more of amino acid residues
having a
substituent group, or {iii) fusion of the mature polypeptide with another
compound,
such as a compound to increase the stability and/or solubility of the
polypeptide (for
example, polyethylene glycol), or (iv) fusion of the polypeptide with
additional amino
acids, such as an IgG Fc fusion region peptide, or leader or secretory
sequence, or a
sequence facilitating purification. Such variant polypeptides are deemed to be
within
the scope of those skilled in the art from the teachings herein.
For example, polypeptide variants containing amino acid substitutions of
charged amino acids with other charged or neutral amino acids may produce
proteins
with improved characteristics, such as less aggregation. Aggregation of
pharmaceutical formulations both reduces activity and increases clearance due
to the
aggregate's immunogenic activity. (Pinckard et al., Clin. Exp. Immunol. 2:331-
340
( 1967); Robbins et al., Diabetes 36: 838-845 ( 1987); Cleland et al., Crit.
Rev.
Therapeutic Drug Carrier Systems 10:307-377 ( 1993).)
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A further embodiment of the invention relates to a polypeptide which
comprises the amino acid sequence of the present invention having an amino
acid
sequence which contains at least one amino acid substitution, but not more
than 50
amino acid substitutions, even more preferably, not more than 40 amino acid
substitutions, still more preferably, not more than 30 amino acid
substitutions, and
still even more preferably, not more than 20 amino acid substitutions. Of
course, in
order of ever-increasing preference, it is highly preferable for a polypeptide
to have
an amino acid sequence which comprises the amino acid sequence of the present
invention, which contains at least one, but not more than 10, 9, 8, 7, 6, 5,
4, 3, 2 or 1
amino acid substitutions. In specific embodiments, the number of additions,
substitutions, and/or deletions in the amino acid sequence of the present
invention or
fragments thereof (e.g., the mature form and/or other fragments described
herein), is
1-5, 5-10, 5-25, 5-50, 10-SO or SO-150, conservative amino acid substitutions
are
preferable.
Potvnucleotide and Polypeptide Fraements
In the present invention, a "polynucleotide fragment" refers to a short
polynucleotide having a nucleic acid sequence contained in the deposited clone
or
shown in SEQ ID NO:X. The short nucleotide fragments are preferably at least
about
15 nt, and more preferably at least about 20 nt, still more preferably at
least about 30
nt, and even more preferably, at least about 40 nt in length. A fragment "at
least 20 nt
in length," for example, is intended to include 20 or more contiguous bases
from the
cDNA sequence contained in the deposited clone or the nucleotide sequence
shown in
SEQ ID NO:X. These nucleotide fragments are useful as diagnostic probes and
primers as discussed herein. Of course, larger fragments (e.g., 50, 150, 500,
600,
2000 nucleotides) are preferred.
Moreover, representative examples of polynucleotide fragments of the
invention, include, for example, fragments having a sequence from about
nucleotide
number 1-50, S1-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-
450, 451-500, 501-550, 551-600, 651-700, 701-750, 751-8(?0, 800-850, 851-900,
901
950, 951-1000, 1001-1050, 1051-1100, l 101-1150, 1151-1200, 1201-1250, 1251
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1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-
1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-
2000, or 2001 to the end of SEQ ID NO:X or the cDNA contained in the deposited
clone. In this context "about" includes the particularly recited ranges,
larger or
smaller by several (5, 4, 3, 2, or 1 ) nucleotides, at either terminus or at
both termini.
Preferably, these fragments encode a polypeptide which has biological
activity. More
preferably, these polynucleotides can be used as probes or primers as
discussed
herein.
In the present invention, a "polypeptide fragment" refers to a short amino
acid
sequence contained in SEQ ID NO:Y or encoded by the cDNA contained in the
deposited clone. Protein fragments may be "free-standing," or comprised within
a
larger polypeptide of which the fragment forms a part or region, most
preferably as a
single continuous region. Representative examples of polypeptide fragments of
the
invention, include, for example, fragments from about amino acid number 1-20,
21-
40, 41-60, 61-80, 81-100, 102-120, 121-140, 141-160, or 161 to the end of the
coding
region. Moreover, polypeptide fragments can be about 20, 30, 40, 50, 60, 70,
80, 90,
100, 110, 120, 130, 140, or 150 amino acids in length. In this context "about"
includes the particularly recited ranges, larger or smaller by several (5, 4,
3, 2, or 1 )
amino acids, at either extreme or at both extremes.
Preferred polypeptide fragments include the secreted protein as well as the
mature form. Further preferred polypeptide fragments include the secreted
protein or
the mature form having a continuous series of deleted residues from the amino
or the
carboxy terminus, or both. For example, any number of amino acids, ranging
from 1-
60, can be deleted from the amino terminus of either the secreted polypeptide
or the
mature form. Similarly, any number of amino acids, ranging from 1-30, can be
deleted from the carboxy terminus of the secreted protein or mature form.
Furthermore, any combination of the above amino and carboxy terminus deletions
are
preferred. Similarly, polynucleotide fragments encoding these polypeptide
fragments
are also preferred.
Also preferred are polypeptide and polynucleotide fragments characterized by
structural or functional domains, such as fragments that comprise alpha-helix
and
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alpha-helix forming regions, beta-sheet and beta-sheet-forming regions, turn
and turn-
forming regions, coil and coil-forming regions, hydrophilic regions,
hydrophobic
regions, alpha amphipathic regions, beta amphipathic regions, flexible
regions,
surface-forming regions, substrate binding region, and high antigenic index
regions.
Polypeptide fragments of SEQ ID NO:Y falling within conserved domains are
specifically contemplated by the present invention. Moreover, polynucleotide
fragments encoding these domains are also contemplated.
Other preferred fragments are biologically active fragments. Biologically
active fragments are those exhibiting activity similar, but not necessarily
identical, to
an activity of the polypeptide of the present invention. The biological
activity of the
fragments may include an improved desired activity, or a decreased undesirable
activity.
Epitomes & Antibodies
In the present invention, "epitopes" refer to polypeptide fragments having
antigenic or immunogenic activity in an animal, especially in a human. A
preferred
embodiment of the present invention relates to a polypeptide fragment
comprising an
epitope, as well as the polynucleotide encoding this fragment. A region of a
protein
molecule to which an antibody can bind is defined as an "antigenic epitope."
In
contrast, an "immunogenic epitope" is defined as a part of a protein that
elicits an
antibody response. (See, for instance, Geysen et aL, Proc. Natl. Acad. Sci.
USA
81:3998- 40(?2 ( 1983).)
Fragments which function as epitopes may be produced by any conventional
means. (See, e.g., Houghten, R. A., Proc. Natl. Acad. Sci. USA 82:5131-S 135 (
1985)
further described in U.S. Patent No. 4,631,211.)
In the present invention, antigenic epitopes preferably contain a sequence of
at
least seven, more preferably at least nine, and most preferably between about
15 to
about 30 amino acids. Antigenic epitopes are useful to raise antibodies,
including
monoclonal antibodies, that specifically bind the epitope. (See, for instance,
Wilson
et al., Cell 37:767-778 ( 1984); Sutcliffe, J. G. et al., Science 219:660-666
( 1983).)
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Similarly, immunogenic epitopes can be used to induce antibodies according
to methods well known in the art. (See, for instance, Sutcliffe et al., supra;
Wilson et
al., supra; Chow, M. et al., Proc. Natl. Acad. Sci. USA 82:910-914; and
Bittle, F. J. et
al., J. Gen. Virol. 66:2347-2354 (1985).) A preferred immunogenic epitope
includes
the secreted protein. The immunogenic epitopes may be presented together with
a
carrier protein, such as an albumin, to an animal system (such as rabbit or
mouse) or,
if it is long enough (at least about 25 amino acids), without a carrier.
However,
immunogenic epitopes comprising as few as 8 to 10 amino acids have been shown
to
be sufficient to raise antibodies capable of binding to, at the very least,
linear epitopes
in a denatured polypeptide (e.g., in Western blotting.)
As used herein, the term "antibody" (Ab) or "monoclonal antibody" (Mab) is
meant to include intact molecules as well as antibody fragments (such as, for
example, Fab and F(ab')2 fragments) which are capable of specifically binding
to
protein. Fab and F(ab')2 fragments lack the Fc fragment of intact antibody,
clear
more rapidly from the circulation, and may have less non-specific tissue
binding than
an intact antibody. (Wahl et al., J. Nucl. Med. 24:316-325 ( 1983).) Thus,
these '
fragments are preferred, as well as the products of a FAB or other
immunoglobulin
expression library. Moreover, antibodies of the present invention include
chimeric,
single chain, and humanized antibodies.
Fusion Proteins
Any polypeptide of the present invention can be used to generate fusion
proteins. For example, the polypeptide of the present invention, when fused to
a
second protein, can be used as an antigenic tag. Antibodies raised against the
polypeptide of the present invention can be used to indirectly detect the
second
protein by binding to the polypeptide. Moreover, because secreted proteins
target
cellular locations based on trafficking signals, the polypeptides of the
present
invention can be used as targeting molecules once fused to other proteins.
Examples of domains that can be fused to polypeptides of the present
invention include not only heterologous signal sequences, but also other
heterologous
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functional regions. The fusion does not necessarily need to be direct, but may
occur
through linker sequences.
Moreover, fusion proteins may also be engineered to improve characteristics
of the polypeptide of the present invention. For instance, a region of
additional amino
S acids, particularly charged amino acids, may be added to the N-terminus of
the
polypeptide to improve stability and persistence during purification from the
host cell
or subsequent handling and storage. Also, peptide moieties may be added to the
polypeptide to facilitate purification. Such regions may be removed prior to
final
preparation of the polypeptide. The addition of peptide moieties to facilitate
handling
of polypeptides are familiar and routine techniques in the art.
Moreover, polypeptides of the present invention, including fragments, and
specifically epitopes, can be combined with parts of the constant domain of
immunoglobulins (IgG), resulting in chimeric polypeptides. These fusion
proteins
facilitate purification and show an increased half-life in vivo. One reported
example
describes chimeric proteins consisting of the first two domains of the human
CD4-
polypeptide and various domains of the constant regions of the heavy or light
chains
of mammalian immunoglobulins. (EP A 394,827; Traunecker et al., Nature 331:84-
86 (1988).) Fusion proteins having disulfide-linked dimeric structures (due to
the
IgG) can also be more efficient in binding and neutralizing other molecules,
than the
monomeric secreted protein or protein fragment alone. (Fountoulakis et al., J.
Biochem. 270:3958-3964 ( 1995).)
Similarly, EP-A-O 464 533 (Canadian counterpart 2045869) discloses fusion
proteins comprising various portions of constant region of immunoglobulin
molecules
together with another human protein or part thereof. In many cases, the Fc
part in a
fusion protein is beneficial in therapy and diagnosis, and thus can result in,
for
example, improved pharmacokinetic properties. (EP-A 0232 262.) Alternatively,
deleting the Fc part after the fusion protein has been expressed, detected,
and purified,
would be desired. For example, the Fc portion may hinder therapy and diagnosis
if
the fusion protein is used as an antigen for immunizations. In drug discovery,
for
example, human proteins, such as hIL-5, have been fused with Fc portions for
the
purpose of high-throughput screening assays to identify antagonists of hIL-5.
(See,
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D. Bennett et al., J. Molecular Recognition 8:52-58 ( 1995); K. Johanson et
al., J. Biol.
Chem. 270:9459-9471 (1995).)
Moreover, the polypeptides of the present invention can be fused to marker
sequences, such as a peptide which facilitates purification of the fused
polypeptide.
In preferred embodiments, the marker amino acid sequence is a hexa-histidine
peptide, such as the tag provided in a pQE vector (QIAGEN, Inc., 9259 Eton
Avenue,
Chatsworth, CA, 91311), among others, many of which are commercially
available.
As described in Gentz et al., Proc. Natl. Acad. Sci. USA 86:821-824 ( 1989),
for
instance, hexa-histidine provides for convenient purification of the fusion
protein.
Another peptide tag useful for purification, the "HA" tag, corresponds to an
epitope
derived from the influenza hemagglutinin protein. (Wilson et al., Cell 37:767
( 1984).)
Thus, any of these above fusions can be engineered using the polynucleotides
or the polypeptides of the present invention.
Vector, Host Cells. and Protein Production
The present invention also relates to vectors containing the polynucleotide of
the present invention, host cells, and the production of polypeptides by
recombinant
techniques. The vector may be, for example, a phage, plasmid, viral, or
retroviral
vector. Retroviral vectors may be replication competent or replication
defective. In
the latter case, viral propagation generally will occur only in complementing
host
cells.
The polynucleotides may be joined to a vector containing a selectable marker
for propagation in a host. Generally, a plasmid vector is introduced in a
precipitate,
such as a calcium phosphate precipitate, or in a complex with a charged lipid.
If the
vector is a virus, it may be packaged in vitro using an appropriate packaging
cell line
and then transduced into host cells.
The polynucleotide insert should be operatively linked to an appropriate
promoter, such as the phage lambda PL promoter, the E. coli lac, trp, phoA and
tac
promoters, the SV40 early and late promoters and promoters of retroviral LTRs,
to
name a few. Other suitable promoters will be known to the skilled artisan. The
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expression constructs will further contain sites for transcription initiation,
termination,
and, in the transcribed region, a ribosome binding site for translation. The
coding
portion of the transcripts expressed by the constructs will preferably include
a
translation initiating codon at the beginning and a termination codon (UAA,
UGA or
UAG) appropriately positioned at the end of the polypeptide to be translated.
As indicated, the expression vectors will preferably include at least one
selectable marker. Such markers include dihydrofolate reductase, 6418 or
neomycin
resistance for eukaryotic cell culture and tetracycline, kanamycin or
ampicillin
resistance genes for culturing in E. coli and other bacteria. Representative
examples
of appropriate hosts include, but are not limited to, bacterial cells, such as
E. coli,
Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast
cells;
insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such
as
CHO, COS, 293, and Bowes melanoma cells; and plant cells. Appropriate culture
mediums and conditions for the above-described host cells are known in the
art.
1 S Among vectors preferred for use in bacteria include pQE70, pQE60 and pQE-
9, available from QIAGEN, Inc.; pBluescript vectors, Phagescript vectors,
pNHBA,
pNHl6a, pNHIBA, pNH46A, available from Stratagene Cloning Systems, Inc.; and
ptrc99a, pKK223-3, pKK233-3, pDR540, pRITS available from Pharmacia Biotech,
Inc. Among preferred eukaryotic vectors are pWLNEO, pSV2CAT, pOG44, pXTI
and pSG available from Stratagene; and pSVK3, pBPV, pMSG and pSVL available
from Pharmacia. Other suitable vectors will be readily apparent to the skilled
artisan.
Introduction of the construct into the host cell can be effected by calcium
phosphate transfection, DEAE-dextran mediated transfection, cationic lipid-
mediated
transfection, electroporation, transduction, infection, or other methods. Such
methods
are described in many standard laboratory manuals, such as Davis et al., Basic
Methods In Molecular Biology ( 1986). It is specifically contemplated that the
polypeptides of the present invention may in fact be expressed by a host cell
lacking a
recombinant vector.
A polypeptide of this invention can be recovered and purified from
recombinant cell cultures by well-known methods including ammonium sulfate or
ethanol precipitation, acid extraction, anion or cation exchange
chromatography,
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phosphocellulose chromatography, hydrophobic interaction chromatography,
affinity
chromatography, hydroxylapatite chromatography and lectin chromatography. Most
preferably, high performance liquid chromatography ("HPLC") is employed for
purification.
Polypeptides of the present invention, and preferably the secreted form, can
also be recovered from: products purified from natural sources, including
bodily
fluids, tissues and cells, whether directly isolated or cultured; products of
chemical
synthetic procedures; and products produced by recombinant techniques from a
prokaryotic or eukaryotic host, including, for example, bacterial, yeast,
higher plant,
insect, and mammalian cells. Depending upon the host employed in a recombinant
production procedure, the polypeptides of the present invention may be
glycosylated
or may be non-glycosylated. In addition, polypeptides of the invention may
also
include an initial modified methionine residue, in some cases as a result of
host-
mediated processes. Thus, it is well known in the art that the N-terminal
methionine
encoded by the translation initiation codon generally is removed with high
efficiency
from any protein after translation in all eukaryotic cells. While the N-
ternunal
methionine on most proteins also is efficiently removed in most prokaryotes,
for some
proteins, this prokaryotic removal process is inefficient, depending on the
nature of
the amino acid to which the N-terminal methionine is covalently linked.
In addition to encompassing host cells containing the vector constructs
discussed herein, the invention also encompasses primary, secondary, and
immortalized host cells of vertebrate origin, particularly mammalian origin,
that have
been engineered to delete or replace endogenous genetic material (e.g., coding
sequence), and/or to include genetic material (e.g., heterologous
polynucleotide
sequences) that is operably associated with the poiynucleotides of the
invention, and
which activates, alters, and/or amplifies endogenous polynucleotides. For
example,
techniques known in the art may be used to operably associate heterologous
control
regions (e.g., promoter and/or enhancer) and endogenous polynucleotide
sequences
via homologous recombination (see, e.g., U.S. Patent No. 5,641,670, issued
June 24,
1997; International Publication No. WO 96/29411, published September 26, 1996;
International Publication No. WO 94/12650, published August 4, 1994; Koller et
al.,
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Proc. Natl. Acad. Sci. USA 86:8932-8935 (1989); and Zijlstra et al., Nature
342:435-
438 ( 1989), the disclosures of each of which are incorporated by reference in
their
entireties).
Uses of the PolynucJ_eotides
Each of the polynucleotides identified herein can be used in numerous ways as
reagents. The following description should be considered exemplary and
utilizes
known techniques.
The polynucleotides of the present invention are useful for chromosome
identification. There exists an ongoing need to identify new chromosome
markers,
since few chromosome marking reagents, based on actual sequence data (repeat
polymorphisms), are presently available. Each polynucleotide of the present
invention can be used as a chromosome marker.
Briefly, sequences can be mapped to chromosomes by preparing PCR primers
(preferably 15-25 bp) from the sequences shown in SEQ ID NO:X. Primers can be
selected using computer analysis so that primers do not span more than one
predicted
exon in the genomic DNA. These primers are then used for PCR screening of
somatic cell hybrids containing individual human chromosomes. Only those
hybrids
containing the human gene corresponding to the SEQ ID NO:X will yield an
amplified fragment.
Similarly, somatic hybrids provide a rapid method of PCR mapping the
polynucleotides to particular chromosomes. Three or more clones can be
assigned per
day using a single thermal cycler. Moreover, sublocalization of the
polynucleotides
can be achieved with panels of specific chromosome fragments. Other gene
mapping
strategies that can be used include in situ hybridization, prescreening with
labeled
flow-sorted chromosomes, and preselection by hybridization to construct
chromosome specific-cDNA libraries.
Precise chromosomal location of the polynucleotides can also be achieved
using fluorescence in situ hybridization (FISH) of a metaphase chromosomal
spread.
This technique uses polynucleotides as short as 500 or 600 bases; however,
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polynucleotides 2,000-4,000 by are preferred. For a review of this technique,
see
Verma et al., "Human Chromosomes: a Manual of Basic Techniques," Pergamon
Press, New York ( 1988).
For chromosome mapping, the polynucleotides can be used individually (to
mark a single chromosome or a single site on that chromosome) or in panels
(for
marking multiple sites and/or multiple chromosomes). Preferred polynucleotides
correspond to the noncoding regions of the cDNAs because the coding sequences
are
more likely conserved within gene families, thus increasing the chance of
cross
hybridization during chromosomal mapping.
Once a polynucleotide has been mapped to a precise chromosomal location,
the physical position of the polynucleotide can be used in linkage analysis.
Linkage
analysis establishes coinheritance between a chromosomal location and
presentation
of a particular disease. (Disease mapping data are found, for example, in V.
McKusick, Mendelian Inheritance in Man (available on line through Johns
Hopkins
University Welch Medical Library) .) Assuming 1 megabase mapping resolution
and
one gene per 20 kb, a cDNA precisely localized to a chromosomal region
associated
with the disease could be one of 50-500 potential causative genes.
Thus, once coinheritance is established, differences in the polynucleotide and
the corresponding gene between affected and unaffected individuals can be
examined.
First, visible structural alterations in the chromosomes, such as deletions or
translocations, are examined in chromosome spreads or by PCR. If no structural
alterations exist, the presence of point mutations are ascertained. Mutations
observed
in some or all affected individuals, but not in normal individuals, indicates
that the
mutation may cause the disease. However, complete sequencing of the
polypeptide
and the corresponding gene from several normal individuals is required to
distinguish
the mutation from a polymorphism. If a new polymorphism is identified, this
polymorphic polypeptide can be used for further linkage analysis.
Furthermore, increased or decreased expression of the gene in affected
individuals as compared to unaffected individuals can be assessed using
polynucleotides of the present invention. Any of these alterations (altered
expression,
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chromosomal rearrangement, or mutation) can be used as a diagnostic or
prognostic
marker.
In addition to the foregoing, a polynucleotide can be used to control gene
expression through triple helix formation or antisense DNA or RNA. Both
methods
rely on binding of the polynucleotide to DNA or RNA. For these techniques,
preferred polynucleotides are usually 20 to 40 bases in length and
complementary to
either the region of the gene involved in transcription (triple helix - see
Lee et al.,
Nucl. Acids Res. 6:3073 ( 1979); Cooney et al., Science 241:456 ( 1988); and
Dervan
et al., Science 251:1360 ( 1991 ) ) or to the mRNA itself (antisense - Okano,
J.
Neurochem. 56:560 ( 1991 ); Oligodeoxy-nucleotides as Antisense Inhibitors of
Gene
Expression, CRC Press, Boca Raton, FL (1988).) Triple helix formation
optimally
results in a shut-off of RNA transcription from DNA, while antisense RNA
hybridization blocks translation of an mRNA molecule into polypeptide. Both
techniques are effective in model systems, and the information disclosed
herein can
be used to design antisense or triple helix polynucleotides in an effort to
treat disease.
Polynucleotides of the present invention are also useful in gene therapy. One
goal of gene therapy is to insert a normal gene into an organism having a
defective
gene, in an effort to correct the genetic defect. The polynucleotides
disclosed in the
present invention offer a means of targeting such genetic defects in a highly
accurate
manner. Another goal is to insert a new gene that was not present in the host
genome,
thereby producing a new trait in the host cell.
The polynucleotides are also useful for identifying individuals from minute
biological samples. The United States military, for example, is considering
the use of
restriction fragment length polymorphism (RFLP) for identification of its
personnel.
In this technique, an individual's genomic DNA is digested with one or more
restriction enzymes, and probed on a Southern blot to yield unique bands for
identifying personnel. This method does not suffer from the current
limitations of
"Dog Tags" which can be lost, switched, or stolen, making positive
identification
difficult. The polynucleotides of the present invention can be used as
additional DNA
markers for RFLP.
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The polynucleotides of the present invention can also be used as an
alternative
to RFLP, by determining the actual base-by-base DNA sequence of selected
portions
of an individual's genome. These sequences can be used to prepare PCR primers
for
amplifying and isolating such selected DNA, which can then be sequenced. Using
this technique, individuals can be identified because each individual will
have a
unique set of DNA sequences. Once an unique ID database is established for an
individual, positive identification of that individual, living or dead, can be
made from
extremely small tissue samples.
Forensic biology also benefits from using DNA-based identification
techniques as disclosed herein. DNA sequences taken from very small biological
samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood,
saliva, semen,
etc., can be amplified using PCR. In one prior art technique, gene sequences
amplified from polymorphic loci, such as DQa class II HLA gene, are used in
forensic
biology to identify individuals. (Erlich, H., PCR Technology, Freeman and Co.
( 1992).) Once these specific polymorphic loci are amplified, they are
digested with
one or more restriction enzymes, yielding an identifying set of bands on a
Southern
blot probed with DNA corresponding to the DQa class II HLA gene. Similarly,
polynucleotides of the present invention can be used as polymorphic markers
for
forensic purposes.
There is also a need for reagents capable of identifying the source of a
particular tissue. Such need arises, for example, in forensics when presented
with
tissue of unknown origin. Appropriate reagents can comprise, for example, DNA
probes or primers specific to particular tissue prepared from the sequences of
the
present invention. Panels of such reagents can identify tissue by species
and/or by
organ type. In a similar fashion, these reagents can be used to screen tissue
cultures
for contamination.
In the very least, the polynucleotides of the present invention can be used as
molecular weight markers on Southern gels, as diagnostic probes for the
presence of a
specific mRNA in a particular cell type, as a probe to "subtract-out" known
sequences
in the process of discovering novel polynucleotides, for selecting and making
oligomers for attachment to a "gene chip" or other support, to raise anti-DNA
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antibodies using DNA immunization techniques, and as an antigen to elicit an
immune response.
Uses of the Poly a tides
Each of the polypeptides identified herein can be used in numerous ways. The
following description should be considered exemplary and utilizes known
techniques.
A polypeptide of the present invention can be used to assay protein levels in
a
biological sample using antibody-based techniques. For example, protein
expression
in tissues can be studied with classical immunohistological methods.
(Jalkanen, M.,
et al., J. Cell. Biol. 101:976-985 (1985); Jalkanen, M., et al., J. Cell .
Biol. 105:3087-
3096 (1987).) Other antibody-based methods useful for detecting protein gene
expression include immunoassays, such as the enzyme linked immunosorbent assay
(ELISA) and the radioimmunoassay (RIA). Suitable antibody assay labels are
known
in the art and include enzyme labels, such as, glucose oxidase, and
radioisotopes, such
as iodine ( 125I, 121 I), carbon ( 14C), sulfur (35S), tritium (3H), indium (
1 l2In), and
technetium (99mTc), and fluorescent labels, such as fluorescein and rhodamine,
and
biotin.
In addition to assaying secreted protein levels in a biological sample,
proteins
can also be detected in vivo by imaging. Antibody labels or markers for in
vivo
imaging of protein include those detectable by X-radiography, NMR or ESR. For
X-
radiography, suitable labels include radioisotopes such as barium or cesium,
which
emit detectable radiation but are not overtly harmful to the subject. Suitable
markers
for NMR and ESR include those with a detectable characteristic spin, such as
deuterium, which may be incorporated into the antibody by labeling of
nutrients for
the relevant hybridoma.
A protein-specific antibody or antibody fragment which has been labeled with
an appropriate detectable imaging moiety, such as a radioisotope (for example,
131I,
1 l2In, 99mTc), a radio-opaque substance, or a material detectable by nuclear
magnetic resonance, is introduced (for example, parenterally, subcutaneously,
or
intraperitoneally) into the mammal. It will be understood in the art that the
size of the
subject and the imaging system used will determine the quantity of imaging
moiety
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needed to produce diagnostic images. In the case of a radioisotope moiety, for
a
human subject, the quantity of radioactivity injected will normally range from
about 5
to 20 millicuries of 99mTc. The labeled antibody or antibody fragment will
then
preferentially accumulate at the location of cells which contain the specific
protein.
In vivo tumor imaging is described in S.W. Burchiel et al.,
"Immunopharmacokinetics
of Radiolabeled Antibodies and Their Fragments." (Chapter 13 in Tumor Imaging:
The Radiochemical Detection of Cancer, S.W. Burchiel and B. A. Rhodes, eds.,
Masson Publishing Inc. ( 1982).)
Thus, the invention provides a diagnostic method of a disorder, which
involves (a) assaying the expression of a polypeptide of the present invention
in cells
or body fluid of an individual; (b) comparing the level of gene expression
with a
standard gene expression level, whereby an increase or decrease in the assayed
polypeptide gene expression level compared to the standard expression level is
indicative of a disorder.
Moreover, polypeptides of the present invention can be used to treat disease.
For example, patients can be administered a polypeptide of the present
invention in an
effort to replace absent or decreased levels of the polypeptide (e.g.,
insulin), to
supplement absent or decreased levels of a different polypeptide (e.g.,
hemoglobin S
for hemoglobin B), to inhibit the activity of a polypeptide (e.g., an
oncogene), to
activate the activity of a polypeptide (e.g., by binding to a receptor), to
reduce the
activity of a membrane bound receptor by competing with it for free ligand
(e.g.,
soluble TNF receptors used in reducing inflammation), or to bring about a
desired
response (e.g., blood vessel growth).
Similarly, antibodies directed to a polypeptide of the present invention can
also be used to treat disease. For example, administration of an antibody
directed to a
polypeptide of the present invention can bind and reduce overproduction of the
polypeptide. Similarly, administration of an antibody can activate the
polypeptide,
such as by binding to a polypeptide bound to a membrane (receptor).
At the very least, the polypeptides of the present invention can be used as
molecular weight markers on SDS-PAGE gels or on molecular sieve gel filtration
columns using methods well known to those of skill in the art. Polypeptides
can also
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be used to raise antibodies, which in turn are used to measure protein
expression from
a recombinant cell, as a way of assessing transformation of the host cell.
Moreover,
the polypeptides of the present invention can be used to test the following
biological
activities.
Biological Activities
The polynucleotides and polypeptides of the present invention can be used in
assays to test for one or more biological activities. If these polynucleotides
and
polypeptides do exhibit activity in a particular assay, it is likely that
these molecules
may be involved in the diseases associated with the biological activity. Thus,
the
polynucleotides and polypeptides could be used to treat the associated
disease.
Immune Activity
A polypeptide or polynucleotide of the present invention may be useful in
treating deficiencies or disorders of the immune system, by activating or
inhibiting the
proliferation, differentiation, or mobilization (chemotaxis) of immune cells.
Immune
cells develop through a process called hematopoiesis, producing myeloid
(platelets,
red blood cells, neutrophils, and macrophages) and lymphoid (B and T
lymphocytes)
cells from pluripotent stem cells. The etiology of these immune deficiencies
or
disorders may be genetic, somatic, such as cancer or some autoimmune
disorders,
acquired (e.g., by chemotherapy or toxins), or infectious. Moreover, a
polynucleotide
or polypeptide of the present invention can be used as a marker or detector of
a
particular immune system disease or disorder.
A polynucleotide or polypeptide of the present invention may be useful in
treating or detecting deficiencies or disorders of hematopoietic cells. A
polypeptide or polynucleotide of the present invention could be used to
increase
differentiation and proliferation of hematopoietic cells, including the
pluripotent stem
cells, in an effort to treat those disorders associated with a decrease in
certain (or
many) types hematopoietic cells. Examples of immunologic deficiency syndromes
include, but are not limited to: blood protein disorders (e.g.
agammaglobulinemia,
dysgammaglobulinemia), ataxia telangiectasia, common variable
immunodeficiency,
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Digeorge Syndrome, HIV infection, HTLV-BLV infection, leukocyte adhesion
deficiency syndrome, lymphopenia, phagocyte bactericidal dysfunction, severe
combined immunodeficiency (SCIDs), Wiskott-Aldrich Disorder, anemia,
thrombocytopenia, or hemoglobinuria.
Moreover, a polypeptide or polynucleotide of the present invention could also
be used to modulate hemostatic (the stopping of bleeding) or thrombolytic
activity
(clot formation). For example, by increasing hemostatic or thrombolytic
activity, a
polynucleotide or polypeptide of the present invention could be used to treat
blood
coagulation disorders (e.g., afibrinogenemia, factor deficiencies), blood
platelet
disorders (e.g. thrombocytopenia), or wounds resulting from trauma, surgery,
or other
causes. Alternatively, a polynucleotide or polypeptide of the present
invention that
can decrease hemostatic or thrombolytic activity could be used to inhibit or
dissolve
clotting. These molecules could be important in the treatment of heart attacks
(infarction), strokes, or scarring.
1 S A polynucleotide or polypeptide of the present invention may also be
useful in
treating or detecting autoimmune disorders. Many autoimmune disorders result
from
inappropriate recognition of self as foreign material by immune cells. This
inappropriate recognition results in an immune response leading to the
destruction of
the host tissue. Therefore, the administration of a polypeptide or
polynucleotide of the
present invention that inhibits an immune response, particularly the
proliferation,
differentiation, or chemotaxis of T-cells, may be an effective therapy in
preventing
autoimmune disorders.
Examples of autoimmune disorders that can be treated or detected by the
present invention include, but are not limited to: Addison's Disease,
hemolytic
anemia, antiphospholipid syndrome, rheumatoid arthritis, dermatitis, allergic
encephalomyelitis, glomerulonephritis, Goodpasture's Syndrome, Graves'
Disease,
Multiple Sclerosis, Myasthenia Gravis, Neuritis, Ophthalmia, Bullous
Pemphigoid,
Pemphigus, Polyendocrinopathies, Purpura, Reiter's Disease, Stiff Man
Syndrome,
Autoimmune Thyroiditis, Systemic Lupus Erythematosus, Autoimmune Pulmonary
Inflammation, Guillain-Barre Syndrome, insulin dependent diabetes mellitis,
and
autoimmune inflammatory eye disease.
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Similarly, allergic reactions and conditions, such as asthma (particularly
allergic asthma) or other respiratory problems, may also be treated by a
polypeptide
or polynucleotide of the present invention. Moreover, these molecules can be
used to
treat anaphylaxis, hypersensitivity to an antigenic molecule, or blood group
S incompatibility.
A polynucleotide or polypeptide of the present invention may also be used to
treat and/or prevent organ rejection or graft-versus-host disease (GVHD).
Organ
rejection occurs by host immune cell destruction of the transplanted tissue
through an
immune response. Similarly, an immune response is also involved in GVHD, but,
in
this case, the foreign transplanted immune cells destroy the host tissues. The
administration of a polypeptide or polynucleotide of the present invention
that inhibits
an immune response, particularly the proliferation, differentiation, or
chemotaxis of
T-cells, may be an effective therapy in preventing organ rejection or GVHD.
Similarly, a polypeptide or polynucleotide of the present invention may also
be used to modulate inflammation. For example, the polypeptide or
polynucleotide
may inhibit the proliferation and differentiation of cells involved in an
inflammatory
response. These molecules can be used to treat inflammatory conditions, both
chronic
and acute conditions, including inflammation associated with infection (e.g.,
septic
shock, sepsis, or systemic inflammatory response syndrome (SIRS)), ischemia-
reperfusion injury, endotoxin lethality, arthritis, complement-mediated
hyperacute
rejection, nephritis, cytokine or chemokine induced lung injury, inflammatory
bowel
disease, Crohn's disease, or resulting from over production of cytokines
(e.g., TNF or
IL-1.)
H~roernroliferative Disorders
A polypeptide. or polynucleotide can be used to treat or detect
hyperproliferative disorders, including neoplasms. A polypeptide or
polynucleotide
of the present invention may inhibit the proliferation of the disorder through
direct or
indirect interactions. Alternatively, a polypeptide or polynucleotide of the
present
invention may proliferate other cells which can inhibit the hyperproliferative
disorder.
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For example, by increasing an immune response, particularly increasing
antigenic qualities of the hyperproliferative disorder or by proliferating,
differentiating, or mobilizing T-cells, hyperproliferative disorders can be
treated.
This immune response may be increased by either enhancing an existing immune
response, or by initiating a new immune response. Alternatively, decreasing an
immune response may also be a method of treating hyperproliferative disorders,
such
as a chemotherapeutic agent.
Examples of hyperproliferative disorders that can be treated or detected by a
polynucleotide or polypeptide of the present invention include, but are not
limited to
neoplasms located in the: abdomen, bone, breast, digestive system, liver,
pancreas,
peritoneum, endocrine glands (adrenal, parathyroid, pituitary, testicles,
ovary, thymus,
thyroid), eye, head and neck, nervous (central and peripheral), lymphatic
system,
pelvic, skin, soft tissue, spleen, thoracic, and urogenital.
Similarly, other hyperproliferative disorders can also be treated or detected
by
a polynucleotide or polypeptide of the present invention. Examples of such
hyperproliferative disorders include, but are not limited to:
hypergammaglobulinemia, lymphoproliferative disorders, paraproteinenuas,
purpura,
sarcoidosis, Sezary Syndrome, Waldenstron's Macroglobulinemia, Gaucher's
Disease, histiocytosis, and any other hyperproliferative disease, besides
neoplasia,
located in an organ system listed above.
Infectious Disease
A polypeptide or polynucleotide of the present invention can be used to treat
or detect infectious agents. For example, by increasing the immune response,
particularly increasing the proliferation and differentiation of B and/or T
cells,
infectious diseases may be treated. The immune response may be increased by
either
enhancing an existing immune response, or by initiating a new immune response.
Alternatively, the polypeptide or polynucleotide of the present invention may
also
directly inhibit the infectious agent, without necessarily eliciting an immune
response.
Viruses are one example of an infectious agent that can cause disease or
symptoms that can be treated or detected by a polynucleotide or polypeptide of
the
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present invention. Examples of viruses, include, but are not limited to the
following
DNA and RNA viral families: Arbovirus, Adenoviridae, Arenaviridae,
Arterivirus,
Birnaviridae, Bunyaviridae, Caliciviridae, Circoviridae, Coronaviridae,
Flaviviridae,
Hepadnaviridae (Hepatitis), Herpesviridae (such as, Cytomegalovirus, Herpes
Simplex, Herpes Zoster), Mononegavirus (e.g., Paramyxoviridae, Morbillivirus,
Rhabdoviridae), Orthomyxoviridae (e.g., Influenza), Papovaviridae,
Parvoviridae,
Picornaviridae, Poxviridae (such as Smallpox or Vaccinia), Reoviridae (e.g.,
Rotavirus), Retroviridae (HTLV-I, HTLV-II, Lentivirus), and Togaviridae (e.g.,
Rubivirus). Viruses falling within these families can cause a variety of
diseases or
symptoms, including, but not limited to: arthritis, bronchiollitis,
encephalitis, eye
infections (e.g., conjunctivitis, keratitis), chronic fatigue syndrome,
hepatitis (A, B, C,
E, Chronic Active, Delta), meningitis, opportunistic infections (e.g., AIDS),
pneumonia, Burkitt's Lymphoma, chickenpox , hemorrhagic fever, Measles, Mumps,
Parainfluenza, Rabies, the common cold, Polio, leukemia, Rubella, sexually
transmitted diseases, skin diseases (e.g., Kaposi's, warts), and viremia. A
polypeptide
or polynucleotide of the present invention can be used to treat or detect any
of these
symptoms or diseases.
Similarly, bacterial or fungal agents that can cause disease or symptoms and
that can be treated or detected by a polynucleotide or polypeptide of the
present
invention include, but not limited to, the following Gram-Negative and Gram-
positive
bacterial families and fungi: Actinomycetales (e.g., Corynebacterium,
Mycobacterium, Norcardia}, Aspergillosis, Bacillaceae (e.g., Anthrax,
Clostridium),
Bacteroidaceae, Blastomycosis, Bordetella, Borrelia, Brucellosis, Candidiasis,
Campylobacter, Coccidioidomycosis, Cryptococcosis, Dermatocycoses,
Enterobacteriaceae (Klebsiella, Salmonella, Serratia, Yersinia),
Erysipelothrix,
Helicobacter, Legionellosis, Leptospirosis, Listeria, Mycoplasmatales,
Neisseriaceae
(e.g., Acinetobacter, Gonorrhea, Menigococcal), Pasteurellacea Infections
(e.g.,
Actinobacillus, Heamophilus, Pasteurella), Pseudomonas, Rickettsiaceae,
Chlamydiaceae, Syphilis, and Staphylococcal. These bacterial or fungal
families can
cause the following diseases or symptoms, including, but not limited to:
bacteremia,
endocarditis, eye infections (conjunctivitis, tuberculosis, uveitis),
gingivitis,
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opportunistic infections (e.g., AIDS related infections), paronychia,
prosthesis-related
infections, Reiter's Disease, respiratory tract infections, such as Whooping
Cough or
Empyema, sepsis, Lyme Disease, Cat-Scratch Disease, Dysentery, Paratyphoid
Fever,
food poisoning, Typhoid, pneumonia, Gonorrhea, meningitis, Chlamydia,
Syphilis,
Diphtheria, Leprosy, Paratuberculosis, Tuberculosis, Lupus, Botulism,
gangrene,
tetanus, impetigo, Rheumatic Fever, Scarlet Fever, sexually transmitted
diseases, skin
diseases (e.g., cellulitis, dermatocycoses), toxemia, urinary tract
infections, wound
infections. A polypeptide or polynucleotide of the present invention can be
used to
treat or detect any of these symptoms or diseases.
Moreover, parasitic agents causing disease or symptoms that can be treated or
detected by a polynucleotide or polypeptide of the present invention include,
but not
limited to, the following families: Amebiasis, Babesiosis, Coccidiosis,
Cryptosporidiosis, Dientamoebiasis, Dourine, Ectoparasitic, Giardiasis,
Helminthiasis, Leishmaniasis, Theileriasis, Toxoplasmosis, Trypanosomiasis,
and
Trichomonas. These parasites can cause a variety of diseases or symptoms,
including,
but not limited to: Scabies, Trombiculiasis, eye infections, intestinal
disease (e.g.,
dysentery, giardiasis), liver disease, lung disease, opportunistic infections
(e.g., AIDS
related), Malaria, pregnancy complications, and toxoplasmosis. A polypeptide
or
polynucleotide of the present invention can be used to treat or detect any of
these
symptoms or diseases.
Preferably, treatment using a polypeptide or polynucleotide of the present
invention could either be by administering an effective amount of a
polypeptide to the
patient, or by removing cells from the patient, supplying the cells with a
polynucleotide of the present invention, and returning the engineered cells to
the
patient (ex vivo therapy). Moreover, the polypeptide or polynucleotide of the
present
invention can be used as an antigen in a vaccine to raise an immune response
against
infectious disease.
Regeneration
A polynucleotide or polypeptide of the present invention can be used to
differentiate, proliferate, and attract cells, leading to the regeneration of
tissues. (See,
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Science 276:59-87 (1997).) The regeneration of tissues could be used to
repair,
replace, or protect tissue damaged by congenital defects, trauma (wounds,
burns,
incisions, or ulcers), age, disease (e.g. osteoporosis, osteocarthritis,
periodontal
disease, liver failure), surgery, including cosmetic plastic surgery,
fibrosis,
S reperfusion injury, or systemic cytokine damage.
Tissues that could be regenerated using the present invention include organs
(e.g., pancreas, liver, intestine, kidney, skin, endothelium), muscle (smooth,
skeletal
or cardiac), vasculature (including vascular and lymphatics), nervous,
hematopoietic,
and skeletal (bone, cartilage, tendon, and ligament) tissue. Preferably,
regeneration
occurs without or decreased scarring. Regeneration also may include
angiogenesis.
Moreover, a polynucleotide or polypeptide of the present invention may
increase regeneration of tissues difficult to heal. For example, increased
tendon/ligament regeneration would quicken recovery time after damage. A
polynucleotide or polypeptide of the present invention could also be used
prophylactically in an effort to avoid damage. Specific diseases that could be
treated
include of tendinitis, carpal tunnel syndrome, and other tendon or ligament
defects. A
further example of tissue regeneration of non-healing wounds includes pressure
ulcers, ulcers associated with vascular insufficiency, surgical, and traumatic
wounds.
Similarly, nerve and brain tissue could also be regenerated by using a
polynucleotide or polypeptide of the present invention to proliferate and
differentiate
nerve cells. Diseases that could be treated using this method include central
and
peripheral nervous system diseases, neuropathies, or mechanical and traumatic
disorders (e.g., spinal cord disorders, head trauma, cerebrovascular disease,
and
stoke). Specifically, diseases associated with peripheral nerve injuries,
peripheral
neuropathy (e.g., resulting from chemotherapy or other medical therapies),
localized
neuropathies, and central nervous system diseases (e.g., Alzheimer's disease,
Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and
Shy-
Drager syndrome), could all be treated using the polynucleotide or polypeptide
of the
present mventlon.
ChemQtaxis
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A polynucleotide or polypeptide of the present invention may have
chemotaxis activity. A chemotaxic molecule attracts or mobilizes cells (e.g.,
monocytes, flbroblasts, neutrophils, T-cells, mast cells, eosinophils,
epithelial and/or
endothelial cells) to a particular site in the body, such as inflammation,
infection, or
site of hyperproliferation. The mobilized cells can then fight off and/or heal
the
particular trauma or abnormality.
A polynucleotide or polypeptide of the present invention may increase
chemotaxic activity of particular cells. These chemotactic molecules can then
be used
to treat inflammation, infection, hyperproliferative disorders, or any immune
system
disorder by increasing the number of cells targeted to a particular location
in the body.
For example, chemotaxic molecules can be used to treat wounds and other trauma
to
tissues by attracting immune cells to the injured location. Chemotactic
molecules of
the present invention can also attract fibroblasts, which can be used to treat
wounds.
It is also contemplated that a polynucleotide or polypeptide of the present
invention may inhibit chemotactic activity. These molecules could also be used
to
treat disorders. Thus, a polynucleotide or polypeptide of the present
invention could
be used as an inhibitor of chemotaxis.
Binding Activity
A polypeptide of the present invention may be used to screen for molecules
that bind to the polypeptide or for molecules to which the polypeptide binds.
The
binding of the polypeptide and the molecule may activate (agonist), increase,
inhibit
(antagonist), or decrease activity of the polypeptide or the molecule bound.
Examples
of such molecules include antibodies, oligonucleotides, proteins (e.g.,
receptors),or
small molecules.
Preferably, the molecule is closely related to the natural ligand of the
polypeptide, e.g., a fragment of the ligand, or a natural substrate, a ligand,
a structural
or functional mimetic. (See, Coligan et al., Current Protocols in Immunology
1(2):Chapter S (1991).) Similarly, the molecule can be closely related to the
natural
receptor to which the polypeptide binds, or at least, a fragment of the
receptor capable
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of being bound by the polypeptide (e.g., active site). In either case, the
molecule can
be rationally designed using known techniques.
Preferably, the screening for these molecules involves producing appropriate
cells which express the polypeptide, either as a secreted protein or on the
cell
membrane. Preferred cells include cells from mammals, yeast, Drosophila, or E.
coli.
Cells expressing the polypeptide (or cell membrane containing the expressed
polypeptide) are then preferably contacted with a test compound potentially
containing the molecule to observe binding, stimulation, or inhibition of
activity of
either the polypeptide or the molecule.
The assay may simply test binding of a candidate compound to the
polypeptide, wherein binding is detected by a label, or in an assay involving
competition with a labeled competitor. Further, the assay may test whether the
candidate compound results in a signal generated by binding to the
polypeptide.
Alternatively, the assay can be carried out using cell-free preparations,
polypeptide/molecule affixed to a solid support, chemical libraries, or
natural product
mixtures. The assay may also simply comprise the steps of mixing a candidate
compound with a solution containing a polypeptide, measuring
polypeptide/molecule
activity or binding, and comparing the polypeptide/molecule activity or
binding to a
standard.
Preferably, an ELISA assay can measure polypeptide level or activity in a
sample (e.g., biological sample) using a monoclonal or polyclonal antibody.
The
antibody can measure polypeptide level or activity by either binding, directly
or
indirectly, to the polypeptide or by competing with the polypeptide for a
substrate.
All of these above assays can be used as diagnostic or prognostic markers.
The molecules discovered using these assays can be used to treat disease or to
bring
about a particular result in a patient (e.g., blood vessel growth) by
activating or
inhibiting the polypeptide/molecule. Moreover, the assays can discover agents
which
may inhibit or enhance the production of the polypeptide from suitably
manipulated
cells or tissues.
Therefore, the invention includes a method of identifying compounds which
bind to a polypeptide of the invention comprising the steps of: (a) incubating
a
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candidate binding compound with a polypeptide of the invention; and (b)
determining
if binding has occurred. Moreover, the invention includes a method of
identifying
agonists/antagonists comprising the steps of: (a) incubating a candidate
compound
with a polypeptide of the invention, (b) assaying a biological activity , and
(b)
determining if a biological activity of the polypeptide has been altered.
Other Activities
A polypeptide or polynucleotide of the present invention may also increase or
decrease the differentiation or proliferation of embryonic stem cells,
besides, as
discussed above, hematopoietic lineage.
A polypeptide or polynucleotide of the present invention may also be used to
modulate mammalian characteristics, such as body height, weight, hair color,
eye
color, skin, percentage of adipose tissue, pigmentation, size, and shape
(e.g., cosmetic
surgery). Similarly, a polypeptide or polynucleotide of the present invention
may be
used to modulate mammalian metabolism affecting catabolism, anabolism,
processing, utilization, and storage of energy.
A polypeptide or polynucleotide of the present invention may be used to
change a mammal's mental state or physical state by influencing biorhythms,
caricadic rhythms, depression (including depressive disorders), tendency for
violence,
tolerance for pain, reproductive capabilities (preferably by Activin or
Inhibin-like
activity), hormonal or endocrine levels, appetite, libido, memory, stress, or
other
cognitive qualities.
A polypeptide or polynucleotide of the present invention may also be used as a
food additive or preservative, such as to increase or decrease storage
capabilities, fat
content, lipid, protein, carbohydrate, vitamins, minerals, cofactors or other
nutritional
components.
Other Preferred Embodiments
Other preferred embodiments of the claimed invention include an isolated
nucleic acid molecule comprising a nucleotide sequence which is at least 95%
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identical to a sequence of at least about 50 contiguous nucleotides in the
nucleotide
sequence of SEQ ID NO:X wherein X is any integer as defined in Table 1.
Also preferred is a nucleic acid molecule wherein said sequence of contiguous
nucleotides is included in the nucleotide sequence of SEQ ID NO:X in the range
of
positions beginning with the nucleotide at about the position of the 5'
Nucleotide of
the Clone Sequence and ending with the nucleotide at about the position of the
3'
Nucleotide of the Clone Sequence as defined for SEQ ID NO:X in Table 1.
Also preferred is a nucleic acid molecule wherein said sequence of contiguous
nucleotides is included in the nucleotide sequence of SEQ ID NO:X in the range
of
positions beginning with the nucleotide at about the position of the S'
Nucleotide of
the Start Codon and ending with the nucleotide at about the position of the 3'
Nucleotide of the Clone Sequence as defined for SEQ ID NO:X in Table 1.
Similarly preferred is a nucleic acid molecule wherein said sequence of
contiguous nucleotides is included in the nucleotide sequence of SEQ ID NO:X.
in the
range of positions beginning with the nucleotide at about the position of the
5'
Nucleotide of the First Amino Acid of the Signal Peptide and ending with the
nucleotide at about the position of the 3' Nucleotide of the Clone Sequence as
defined
for SEQ ID NO:X in Table 1.
Also preferred is an isolated nucleic acid molecule comprising a nucleotide
sequence which is at least 95% identical to a sequence of at least about 150
contiguous nucleotides in the nucleotide sequence of SEQ ID NO:X.
Further preferred is an isolated nucleic acid molecule comprising a nucleotide
sequence which is at least 95% identical to a sequence of at least about 500
contiguous nucleotides in the nucleotide sequence of SEQ ID NO:X.
A further preferred embodiment is a nucleic acid molecule comprising a
nucleotide sequence which is at.least 95% identical to the nucleotide sequence
of SEQ
ID NO:X beginning with the nucleotide at about the position of the 5'
Nucleotide of
the First Amino Acid of the Signal Peptide and ending with the nucleotide at
about
the position of the 3' Nucleotide of the Clone Sequence as defined for SEQ ID
NO:X
in Table 1.
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A further preferred embodiment is an isolated nucleic acid molecule
comprising a nucleotide sequence which is at least 95% identical to the
complete
nucleotide sequence of SEQ ID NO:X.
Also preferred is an isolated nucleic acid molecule which hybridizes under
stringent hybridization conditions to a nucleic acid molecule, wherein said
nucleic
acid molecule which hybridizes does not hybridize under stringent
hybridization
conditions to a nucleic acid molecule having a nucleotide sequence consisting
of only
A residues or of only T residues.
Also preferred is a composition of matter comprising a DNA molecule which
comprises a human cDNA clone identified by a cDNA Clone Identifier in Table 1,
which DNA molecule is contained in the material deposited with the American
Type
Culture Collection and given the ATCC Deposit Number shown in Table 1 for said
cDNA Clone Identifier.
Also preferred is an isolated nucleic acid molecule comprising a nucleotide
sequence which is at least 95% identical to a sequence of at least 50
contiguous
nucleotides in the nucleotide sequence of a human cDNA clone identified by a
cDNA
Clone Identifier in Table 1, which DNA molecule is contained in the deposit
given the
ATCC Deposit Number shown in Table 1.
Also preferred is an isolated nucleic acid molecule, wherein said sequence of
at least 50 contiguous nucleotides is included in the nucleotide sequence of
the
complete open reading frame sequence encoded by said human cDNA clone.
Also preferred is an isolated nucleic acid molecule comprising a nucleotide
sequence which is at least 95% identical to sequence of at least 150
contiguous
nucleotides in the nucleotide sequence encoded by said human cDNA clone.
A further preferred embodiment is an isolated nucleic acid molecule
comprising a nucleotide sequence which is at least 95% identical to sequence
of at
least 500 contiguous nucleotides in the nucleotide sequence encoded by said
human
cDNA clone.
A further preferred embodiment is an isolated nucleic acid molecule
comprising a nucleotide sequence which is at least 95% identical to the
complete
nucleotide sequence encoded by said human cDNA clone.
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A further preferred embodiment is a method for detecting in a biological
sample a nucleic acid molecule comprising a nucleotide sequence which is at
least
95% identical to a sequence of at least 50 contiguous nucleotides in a
sequence
selected from the group consisting of: a nucleotide sequence of SEQ ID NO:X
wherein X is any integer as defined in Table l; and a nucleotide sequence
encoded by
a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and
contained
in the deposit with the ATCC Deposit Number shown for said cDNA clone in Table
1; which method comprises a step of comparing a nucleotide sequence of at
least one
nucleic acid molecule in said sample with a sequence selected from said group
and
determining whether the sequence of said nucleic acid molecule in said sample
is at
least 95% identical to said selected sequence.
Also preferred is the above method wherein said step of comparing sequences
comprises determining the extent of nucleic acid hybridization between nucleic
acid
molecules in said sample and a nucleic acid molecule comprising said sequence
selected from said group. Similarly, also preferred is the above method
wherein said
step of comparing sequences is performed by comparing the nucleotide sequence
determined from a nucleic acid molecule in said sample with said sequence
selected
from said group. The nucleic acid molecules can comprise DNA molecules or RNA
molecules.
A further preferred embodiment is a method for identifying the species, tissue
or cell type of a biological sample which method comprises a step of detecting
nucleic
acid molecules in said sample, if any, comprising a nucleotide sequence that
is at least
95% identical to a sequence of at least 50 contiguous nucleotides in a
sequence
selected from the group consisting of: a nucleotide sequence of SEQ ID NO:X
wherein X is any integer as defined in Table 1; and a nucleotide sequence
encoded by
a human cDNA clone identified by a cDNA Clone Identifier in Table 1 and
contained
in the deposit with the ATCC Deposit Number shown for said cDNA clone in Table
1.
The method for identifying the species, tissue or cell type of a biological
sample can comprise a step of detecting nucleic acid molecules comprising a
nucleotide sequence in a panel of at least two nucleotide sequences, wherein
at least
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one sequence in said panel is at least 95% identical to a sequence of at least
50
contiguous nucleotides in a sequence selected from said group.
Also preferred is a method for diagnosing in a subject a pathological
condition
associated with abnormal structure or expression of a gene encoding a secreted
protein identified in Table 1, which method comprises a step of detecting in a
biological sample obtained from said subject nucleic acid molecules, if any,
comprising a nucleotide sequence that is at least 95% identical to a sequence
of at
least 50 contiguous nucleotides in a sequence selected from the group
consisting of: a
nucleotide sequence of SEQ ID NO:X wherein X is any integer as defined in
Table 1;
and a nucleotide sequence encoded by a human cDNA clone identified by a cDNA
Clone Identifier in Table 1 and contained in the deposit with the ATCC Deposit
Number shown for said cDNA clone in Table 1.
The method for diagnosing a pathological condition can comprise a step of
detecting nucleic acid molecules comprising a nucleotide sequence in a panel
of at
least two nucleotide sequences, wherein at least one sequence in said panel is
at least
95% identical to a sequence of at least 50 contiguous nucleotides in a
sequence
selected from said group.
Also preferred is a composition of matter comprising isolated nucleic acid
molecules wherein the nucleotide sequences of said nucleic acid molecules
comprise
a panel of at least two nucleotide sequences, wherein at least one sequence in
said
panel is at least 95% identical to a sequence of at least 50 contiguous
nucleotides in a
sequence selected from the group consisting of: a nucleotide sequence of SEQ
ID
NO:X wherein X is any integer as defined in Table 1; and a nucleotide sequence
encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1
and contained in the deposit with the ATCC Deposit Number shown for said cDNA
clone in Table 1. The nucleic acid molecules can comprise DNA molecules or RNA
molecules.
Also preferred is an isolated polypeptide comprising an amino acid sequence
at least 90% identical to a sequence of at least about 10 contiguous amino
acids in the
amino acid sequence of SEQ ID NO:Y wherein Y is any integer as defined in
Table 1.
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Also preferred is a polypeptide, wherein said sequence of contiguous amino
acids is included in the amino acid sequence of SEQ ID NO:Y in the range of
positions beginning with the residue at about the position of the First Amino
Acid of
the Secreted Portion and ending with the residue at about the Last Amino Acid
of the
Open Reading Frame as set forth for SEQ ID NO:Y in Table 1.
Also preferred is an isolated polypeptide comprising an amino acid sequence
at least 95% identical to a sequence of at least about 30 contiguous amino
acids in the
amino acid sequence of SEQ ID NO:Y.
Further preferred is an isolated polypeptide comprising an amino acid
sequence at least 95% identical to a sequence of at least about 100 contiguous
amino
acids in the amino acid sequence of SEQ ID NO:Y.
Further preferred is an isolated polypeptide comprising an amino acid
sequence at least 95% identical to the complete amino acid sequence of SEQ ID
NO:Y.
Further preferred is an isolated polypeptide comprising an amino acid
sequence at least 90% identical to a sequence of at least about 10 contiguous
amino
acids in the complete amino acid sequence of a secreted protein encoded by a
human
cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in
the
deposit with the ATCC Deposit Number shown for said cDNA clone in Table 1.
Also preferred is a polypeptide wherein said sequence of contiguous amino
acids is included in the amino acid sequence of a secreted portion of the
secreted
protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in
Table 1 and contained in the deposit with the ATCC Deposit Number shown for
said
cDNA clone in Table 1.
Also preferred is an isolated polypeptide comprising an amino acid sequence
at least 95% identical to a sequence of at least about 30 contiguous amino
acids in the
amino acid sequence of the secreted portion of the protein encoded by a human
cDNA
clone identified by a cDNA Clone Identifier in Table 1 and contained in the
deposit
with the ATCC Deposit Number shown for said cDNA clone in Table 1.
Also preferred is an isolated polypeptide comprising an amino acid sequence
at least 95% identical to a sequence of at least about 100 contiguous amino
acids in
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the amino acid sequence of the secreted portion of the protein encoded by a
human
cDNA clone identified by a cDNA Clone Identifier in Table 1 and contained in
the
deposit with the ATCC Deposit Number shown for said cDNA clone in Table I .
Also preferred is an isolated polypeptide comprising an amino acid sequence
at least 95% identical to the amino acid sequence of the secreted portion of
the protein
encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1
and contained in the deposit with the ATCC Deposit Number shown for said cDNA
clone in Table 1.
Further preferred is an isolated antibody which binds specifically to a
polypeptide comprising an amino acid sequence that is at least 90% identical
to a
sequence of at least 10 contiguous amino acids in a sequence selected from the
group
consisting of: an amino acid sequence of SEQ ID NO:Y wherein Y is any integer
as
defined in Table l; and a complete amino acid sequence of a protein encoded by
a
human cDNA clone identified by a cDNA Clone Identifier in Table 1 and
contained
in the deposit with the ATCC Deposit Number shown for said cDNA clone in Table
1.
Further preferred is a method for detecting in a biological sample a
polypeptide comprising an amino acid sequence which is at least 90% identical
to a
sequence of at least 10 contiguous amino acids in a sequence selected from the
group
consisting of: an amino acid sequence of SEQ ID NO:Y wherein Y is any integer
as
defined in Table 1; and a complete amino acid sequence of a protein encoded by
a
human cDNA clone identified by a cDNA Clone Identifier in Table 1 and
contained
in the deposit with the ATCC Deposit Number shown for said cDNA clone in Table
1; which method comprises a step of comparing an amino acid sequence of at
least
one polypeptide molecule in said sample with a sequence selected from said
group
and determining whether the sequence of said polypeptide molecule in said
sample is
at least 90% identical to said sequence of at least 10 contiguous amino acids.
Also preferred is the above method wherein said step of comparing an amino
acid sequence of at least one polypeptide molecule in said sample with a
sequence
selected from said group comprises determining the extent of specific binding
of
polypeptides in said sample to an antibody which binds specifically to a
polypeptide
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comprising an amino acid sequence that is at least 90% identical to a sequence
of at
least 10 contiguous amino acids in a sequence selected from the group
consisting of:
an amino acid sequence of SEQ ID NO:Y wherein Y is any integer as defined in
Table l; and a complete amino acid sequence of a protein encoded by a human
cDNA
clone identified by a cDNA Clone Identifier in Table 1 and contained in the
deposit
with the ATCC Deposit Number shown for said cDNA clone in Table 1.
Also preferred is the above method wherein said step of comparing sequences
is performed by comparing the amino acid sequence determined from a
polypeptide
molecule in said sample with said sequence selected from said group.
Also preferred is a method for identifying the species, tissue or cell type of
a
biological sample which method comprises a step of detecting polypeptide
molecules
in said sample, if any, comprising an amino acid sequence that is at least 90%
identical to a sequence of at least 10 contiguous amino acids in a sequence
selected
from the group consisting of: an amino acid sequence of SEQ ID NO:Y wherein Y
is
any integer as defined in Table 1; and a complete amino acid sequence of a
secreted
protein encoded by a human cDNA clone identified by a cDNA Clone Identifier in
Table 1 and contained in the deposit with the ATCC Deposit Number shown for
said
cDNA clone in Table 1.
Also preferred is the above method for identifying the species, tissue or cell
type of a biological sample, which method comprises a step of detecting
polypeptide
molecules comprising an amino acid sequence in a panel of at least two amino
acid
sequences, wherein at least one sequence in said panel is at least 90%
identical to a
sequence of at least 10 contiguous amino acids in a sequence selected from the
above
group.
Also preferred is a method for diagnosing in a subject a pathological
condition
associated with abnormal structure or expression of a gene encoding a secreted
protein identified in Table l, which method comprises a step of detecting in a
biological sample obtained from said subject polypeptide molecules comprising
an
amino acid sequence in a panel of at least two amino acid sequences, wherein
at least
one sequence in said panel is at least 90% identical to a sequence of at least
10
contiguous amino acids in a sequence selected from the group consisting of: an
amino
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acid sequence of SEQ ID NO:Y wherein Y is any integer as defined in Table l;
and a
complete amino acid sequence of a secreted protein encoded by a human cDNA
clone
identified by a cDNA Clone Identifier in Table 1 and contained in the deposit
with the
ATCC Deposit Number shown for said cDNA clone in Table 1.
In any of these methods, the step of detecting said polypeptide molecules
includes using an antibody.
Also preferred is an isolated nucleic acid molecule comprising a nucleotide
sequence which is at least 95% identical to a nucleotide sequence encoding a
polypeptide wherein said polypeptide comprises an amino acid sequence that is
at
least 90% identical to a sequence of at least 10 contiguous amino acids in a
sequence
selected from the group consisting of: an amino acid sequence of SEQ ID NO:Y
wherein Y is any integer as defined in Table 1; and a complete amino acid
sequence
of a secreted protein encoded by a human cDNA clone identified by a cDNA Clone
Identifier in Table 1 and contained in the deposit with the ATCC Deposit
Number
shown for said cDNA clone in Table 1.
Also preferred is an isolated nucleic acid molecule, wherein said nucleotide
sequence encoding a polypeptide has been optimized for expression of said
polypeptide in a prokaryotic host.
Also preferred is an isolated nucleic acid molecule, wherein said polypeptide
comprises an amino acid sequence selected from the group consisting of: an
amino
acid sequence of SEQ ID NO:Y wherein Y is any integer as defined in Table 1;
and a
complete amino acid sequence of a secreted protein encoded by a human cDNA
clone
identified by a cDNA Clone Identifier in Table 1 and contained in the deposit
with the
ATCC Deposit Number shown for said cDNA clone in Table I.
Further preferred is a method of making a recombinant vector comprising
inserting any of the above isolated nucleic acid molecule into a vector. Also
preferred
is the recombinant vector produced by this method. Also preferred is a method
of
making a recombinant host cell comprising introducing the vector into a host
cell, as
well as the recombinant host cell produced by this method.
Also preferred is a method of making an isolated polypeptide comprising
culturing this recombinant host cell under conditions such that said
polypeptide is
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expressed and recovering said polypeptide. Also preferred is this method of
making
an isolated polypeptide, wherein said recombinant host cell is a eukaryotic
cell and
said polypeptide is a secreted portion of a human secreted protein comprising
an
amino acid sequence selected from the group consisting of: an amino acid
sequence of
SEQ ID NO:Y beginning with the residue at the position of the First Amino Acid
of
the Secreted Portion of SEQ ID NO:Y wherein Y is an integer set forth in Table
1 and
said position of the First Amino Acid of the Secreted Portion of SEQ ID NO:Y
is
defined in Table 1; and an amino acid sequence of a secreted portion of a
protein
encoded by a human cDNA clone identified by a cDNA Clone Identifier in Table 1
and contained in the deposit with the ATCC Deposit Number shown for said cDNA
clone in Table 1. The isolated polypeptide produced by this method is also
preferred.
Also preferred is a method of treatment of an individual in need of an
increased level of a secreted protein activity, which method comprises
administering
to such an individual a pharmaceutical composition comprising an amount of an
isolated polypeptide, polynucleotide, or antibody of the claimed invention
effective to
increase the level of said protein activity in said individual.
Having generally described the invention, the same will be more readily
understood by reference to the following examples, which are provided by way
of
illustration and are not intended as limiting.
xa les
Examule 1~ Isolation of a Selected cDNA Clone From the Deno ited am~~le
Each cDNA clone in a cited ATCC deposit is contained in a plasmid vector.
Table 1 identifies the vectors used to construct the cDNA library from which
each
clone was isolated. In many cases, the vector used to construct the library is
a phage
vector from which a plasmid has been excised. The table immediately below
correlates the related plasmid for each phage vector used in constructing the
cDNA
library. For example, where a particular clone is identified in Table 1 as
being
isolated in the vector "Lambda Zap," the corresponding deposited clone is in
"pBluescript."
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Vector Used to Construct Library Corresponding, Deposited
Plasmid
Lambda Zap pBluescript (pBS)
Uni-Zap XR pBluescript (pBS)
S Zap Express pBK
lafmid BA plafmid BA
pSport 1 pSport 1
pCMVSport 2.0 pCMVSport 2.0
pCMVSport 3.0 pCMVSport 3.0
pCR~2.1 pCR~2.1
Vectors Lambda Zap (U.S. Patent Nos. 5,128,256 and 5,286,636), Uni-Zap
XR (U.S. Patent Nos. 5,128, 256 and 5,286,636), Zap Express (U.S. Patent Nos.
5,128,256 and 5,286,636), pBluescript (pBS) (Short, J. M. et al., Nucleic
Acids Res.
16:7583-7600 ( 1988); Alting-Mees, M. A. and Short, J. M., Nucleic Acids Res.
1S 17:9494 (1989)) and pBK (Alting-Mees, M. A. et al., Strategies S:SB-61
(I992)) are
commercially available from Stratagene Cloning Systems, Inc., 11011 N. Torrey
Pines Road, La Jolla, CA, 92037. pBS contains an ampicillin resistance gene
and
pBK contains a neomycin resistance gene. Both can be transformed into E. coli
strain
XL-1 Blue, also available from Stratagene. pBS comes in 4 forms SK+, SK-, KS+
and KS. The S and K refers to the orientation of the polylinker to the T7 and
T3
primer sequences which flank the polylinker region ("S" is for SacI and "K" is
for
KpnI which are the first sites on each respective end of the linker). "+" or "-
" refer to
the orientation of the f 1 origin of replication ("ori"), such that in one
orientation,
single stranded rescue initiated from the fl on generates sense strand DNA and
in the
2S other, antisense.
Vectors pSportl, pCMVSport 2.0 and pCMVSport 3.0, were obtained from
Life Technologies, Inc., P. O. Box 6009, Gaithersburg, MD 20897. All Sport
vectors
contain an ampicillin resistance gene and may be transformed into E. coli
strain
DHIOB, also available from Life Technologies. (See, for instance, Gruber, C.
E., et
al., Focus 15:59 (1993).) Vector lafmid BA (Bento Soares, Columbia University,
NY) contains an ampicillin resistance gene and can be transformed into E. coli
strain
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XL-1 Blue. Vector pCR~2.1, which is available from Invitrogen, 1600 Faraday
Avenue, Carlsbad, CA 92008, contains an ampicillin resistance gene and may be
transformed into E. coli strain DH10B, available from Life Technologies. (See,
for
instance, Clark, J. M., Nuc. Acids Res. I 6:9677-9686 ( 1988) and Mead, D. et
al.,
S Bio/Technology 9: (1991).) Preferably, a polynucleotide of the present
invention
does not comprise the phage vector sequences identified for the particular
clone in
Table I, as well as the corresponding plasmid vector sequences designated
above.
The deposited material in the sample assigned the ATCC Deposit Number
cited in Table 1 for any given cDNA clone also may contain one or more
additional
plasmids, each comprising a cDNA clone different from that given clone. Thus,
deposits sharing the same ATCC Deposit Number contain at least a plasmid for
each
cDNA clone identified in Table 1. Typically, each ATCC deposit sample cited in
Table 1 comprises a mixture of approximately equal amounts (by weight) of
about 50
plasmid DNAs, each containing a different cDNA clone; but such a deposit
sample
may include plasmids for more or less than 50 cDNA clones, up to about 500
cDNA
clones.
Two approaches can be used to isolate a particular clone from the deposited
sample of plasmid DNAs cited for that clone in Table 1. First, a plasmid is
directly
isolated by screening the clones using a polynucleotide probe corresponding to
SEQ
ID NO:X.
Particularly, a specific polynucleotide with 30-40 nucleotides is synthesized
using an Applied Biosystems DNA synthesizer according to the sequence
reported.
The oligonucleotide is labeled, for instance, with 3zP-y ATP using T4
polynucleotide
kinase and purified according to routine methods. (E.g., Maniatis et al.,
Molecular
Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring, NY (
1982).)
The plasmid mixture is transformed into a suitable host, as indicated above
(such as
XL-1 Blue (Stratagene)) using techniques known to those of skill in the art,
such as
those provided by the vector supplier or in related publications or patents
cited above.
The transformants are plated on 1.5% agar plates (containing the appropriate
selection
agent, e.g., ampicillin) to a density of about 150 transformants (colonies)
per plate.
These plates are screened using Nylon membranes according to routine methods
for
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bacterial colony screening (e.g., Sambrook et al., Molecular Cloning: A
Laboratory
Manual, 2nd Edit., ( 1989), Cold Spring Harbor Laboratory Press, pages 1.93 to
1.104), or other techniques known to those of skill in the art.
Alternatively, two primers of 17-20 nucleotides derived from both ends of the
SEQ ID NO:X (i.e., within the region of SEQ ID NO:X bounded by the 5' NT and
the
3' NT of the clone defined in Table 1) are synthesized and used to amplify the
desired
cDNA using the deposited cDNA plasmid as a template. The polymerase chain
reaction is carried out under routine conditions, for instance, in 25 p,1 of
reaction
mixture with 0.5 ug of the above cDNA template. A convenient reaction mixture
is
1.5-5 mM MgCl2, 0.01 % (w/v) gelatin, 20 p.M each of dATP, dCTP, dGTP, dTTP,
25
pmol of each primer and 0.25 Unit of Taq polymerase. Thirty five cycles of PCR
{denaturation at 94°C for 1 min; annealing at 55°C for 1 min;
elongation at 72°C for 1
min) are performed with a Perkin-Elmer Cetus automated thermal cycIer. The
amplified product is analyzed by agarose gel electrophoresis and the DNA band
with
expected molecular weight is excised and purified. The PCR product is verified
to be
the selected sequence by subcloning and sequencing the DNA product.
Several methods are available for the identification of the 5' or 3' non-
coding
portions of a gene which may not be present in the deposited clone. These
methods
include but are not limited to, filter probing, clone enrichment using
specific probes,
and protocols similar or identical to 5' and 3' "RACE" protocols which are
well
known in the art. For instance, a method similar to 5' RACE is available for
generating the missing 5' end of a desired full-length transcript. (Fromont-
Racine et
al., Nucleic Acids Res. 21(7):1683-1684 (1993).)
Briefly, a specific RNA oligonucleotide is ligated to the 5' ends of a
population of RNA presumably containing full-length gene RNA transcripts. A
primer set containing a primer specific to the ligated RNA oligonucleotide and
a
primer specific to a known sequence of the gene of interest is used to PCR
amplify
the S' portion of the desired full-length gene. This amplified product may
then be
sequenced and used to generate the full length gene.
This above method starts with total RNA isolated from the desired source,
although poly-A+ RNA can be used. The RNA preparation can then be treated with
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phosphatase if necessary to eliminate 5' phosphate groups on degraded or
damaged
RNA which may interfere with the later RNA ligase step. The phosphatase should
then be inactivated and the RNA treated with tobacco acid pyrophosphatase in
order
to remove the cap structure present at the 5' ends of messenger RNAs. This
reaction
S leaves a 5' phosphate group at the S' end of the cap cleaved RNA which can
then be
ligated to an RNA oligonucleotide using T4 RNA ligase.
This modified RNA preparation is used as a template for first strand cDNA
synthesis using a gene specific oligonucleotide. The first strand synthesis
reaction is
used as a template for PCR amplification of the desired 5' end using a primer
specific
to the ligated RNA oligonucleotide and a primer specific to the known sequence
of
the gene of interest. The resultant product is then sequenced and analyzed to
confirm
that the 5' end sequence belongs to the desired gene.
Fxamnle 2: Isolation of enomic Clones Corresponding to a Po~nucleotide
A human genomic P1 library (Genomic Systems, Inc.) is screened by PCR
using primers selected for the cDNA sequence corresponding to SEQ ID NO:X.,
according to the method described in Example 1. (See also, Sambrook.)
Example 3~ Tisslte Distribution of Poly~ep~g
Tissue distribution of mRNA expression of polynucleotides of the present
invention is determined using protocols for Northern blot analysis, described
by,
among others, Sambrook et al. For example, a cDNA probe produced by the method
described in Example 1 is labeled with P32 using the rediprimeTM DNA labeling
system (Amersham Life Science), according to manufacturer's instructions.
After
labeling, the probe is purified using CHROMA SPIN-100TM column (Clontech
Laboratories, Inc.), according to manufacturer's protocol number PT 1200-1.
The
purified labeled probe is then used to examine various human tissues for mRNA
expression.
Multiple Tissue Northern (MTN) blots containing various human tissues (H)
or human immune system tissues (IM) (Clontech) are examined with the labeled
probe using ExpressHybTM hybridization solution (Clontech) according to
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manufacturer's protocol number PT1190-1. Following hybridization and washing,
the
blots are mounted and exposed to film at -70°C overnight, and the films
developed
according to standard procedures.
Examale 4: Chromosomal MaR~ig~ of the Polynucleotides
An oligonucleotide primer set is designed according to the sequence at the 5'
end of SEQ ID NO:X. This primer preferably spans about 100 nucleotides. This
primer set is then used in a polymerase chain reaction under the following set
of
conditions : 30 seconds, 95°C; 1 minute, 56°C; 1 minute,
70°C. This cycle is
repeated 32 times followed by one 5 minute cycle at 70°C. Human, mouse,
and
hamster DNA is used as template in addition to a somatic cell hybrid panel
containing
individual chromosomes or chromosome fragments (Bios, Inc). The reactions is
analyzed on either 8% polyacrylamide gels or 3.5 % agarose gels. Chromosome
mapping is determined by the presence of an approximately 100 by PCR fragment
in
the particular somatic cell hybrid.
Example 5~ Bacterial Expression of a Polypgp ide
A polynucleotide encoding a polypeptide of the present invention is amplified
using PCR oligonucleotide primers corresponding to the 5' and 3' ends of the
DNA
sequence, as outlined in Example 1, to synthesize insertion fragments. The
primers
used to amplify the cDNA insert should preferably contain restriction sites,
such as
BamHI and XbaI, at the 5' end of the primers in order to clone the amplified
product
into the expression vector. For example, BamHI and XbaI correspond to the
restriction enzyme sites on the bacterial expression vector pQE-9. (Qiagen,
Inc.,
Chatsworth, CA). This plasmid vector encodes antibiotic resistance (Ampr), a
bacterial origin of replication (ori), an IPTG-regulatable promoter/operator
(P/O), a
ribosome binding site (RBS), a 6-histidine tag (6-His), and restriction enzyme
cloning
sites.
The pQE-9 vector is digested with BamHI and XbaI and the amplified
fragment is ligated into the pQE-9 vector maintaining the reading frame
initiated at
the bacterial RBS. The ligation mixture is then used to transform the E. coli
strain
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M15/rep4 (Qiagen, Inc.) which contains multiple copies of the plasmid pREP4,
which
expresses the lacI repressor and also confers kanamycin resistance (Kanr).
Transformants are identified by their ability to grow on LB plates and
ampicillin/kanamycin resistant colonies are selected. Plasmid DNA is isolated
anyl
confirmed by restriction analysis.
Clones containing the desired constructs are grown overnight (O/N) in liquid
culture in LB media supplemented with both Amp (100 ug/ml) and Kan (25 ug/ml).
The O/N culture is used to inoculate a large culture at a ratio of 1:100 to
1:250. The
cells are grown to an optical density 600 (O.D.''°°) of between
0.4 and 0.6. IPTG
(Isopropyl-B-D-thiogalacto pyranoside) is then added to a final concentration
of 1
mM. IPTG induces by inactivating the lacI repressor, clearing the P/O leading
to
increased gene expression.
Cells are grown for an extra 3 to 4 hours. Cells are then harvested by
centrifugation (20 rains at 6000Xg). The cell pellet is solubilized in the
chaotropic
agent 6 Molar Guanidine HCI by stirring for 3-4 hours at 4°C. The cell
debris is
removed by centrifugation, and the supernatant containing the polypeptide is
loaded
onto a nickel-nitrilo-tri-acetic acid ("Ni-NTA") affinity resin column
(available from
QIAGEN, Inc., supra). Proteins with a 6 x His tag bind to the Ni-NTA resin
with
high affinity and can be purified in a simple one-step procedure (for details
see: The
QIAexpressionist ( 1995) QIAGEN, Inc., supra).
Briefly, the supernatant is loaded onto the column in 6 M guanidine-HCI, pH
8, the column is first washed with 10 volumes of 6 M guanidine-HCI, pH 8, then
washed with 10 volumes of 6 M guanidine-HCl pH 6, and finally the polypeptide
is
eluted with 6 M guanidine-HCl, pH 5.
The purified protein is then renatured by dialyzing it against phosphate-
buffered saline (PBS) or 50 mM Na-acetate, pH 6 buffer plus 200 mM NaCI.
Alternatively, the protein can be successfully refolded while immobilized on
the Ni-
NTA column. The recommended conditions are as follows: renature using a linear
6M-1M urea gradient in 500 mM NaCI, 20% glycerol, 20 mM Tris/HCl pH 7.4,
containing protease inhibitors. The renaturation should be performed over a
period of
1.5 hours or more. After renaturation the proteins are eluted by the addition
of 250
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mM immidazole. Immidazole is removed by a final dialyzing step against PBS or
50
mM sodium acetate pH 6 buffer plus 200 mM NaCI. The purified protein is stored
at
4° C or frozen at -80° C.
In addition to the above expression vector, the present invention further
S includes an expression vector comprising phage operator and promoter
elements
operatively linked to a polynucleotide of the present invention, called pHE4a.
(ATCC
Accession Number 209645, deposited on February 25, 1998.) This vector
contains:
1 ) a neomycinphosphotransferase gene as a selection marker, 2) an E. coli
origin of
replication, 3) a TS phage promoter sequence, 4) two lac operator sequences,
5) a
Shine-Delgarno sequence, and 6) the lactose operon repressor gene (lacIq). The
origin of replication (oriC) is derived from pUC 19 (LTI, Gaithersburg, MD).
The
promoter sequence and operator sequences are made synthetically.
DNA can be inserted into the pHEa by restricting the vector with NdeI and
XbaI, BamHI, XhoI, or Asp718, running the restricted product on a gel, and
isolating
the larger fragment (the stuffer fragment should be about 310 base pairs). The
DNA
insert is generated according to the PCR protocol described in Example I,
using PCR
primers having restriction sites for NdeI (5' primer) and XbaI, BamHI, XhoI,
or
Asp718 (3' primer). The PCR insert is gel purified and restricted with
compatible
enzymes. The insert and vector are ligated according to standard protocols.
The engineered vector could easily be substituted in the above protocol to
express protein in a bacterial system.
Example 6: Purification of a Polypeptide from an Inclusion Bodv
. The following alternative method can be used to purify a polypeptide
expressed in E coli when it is present in the form of inclusion bodies. Unless
otherwise specified, all of the following steps are conducted at 4-
10°C.
Upon completion of the production phase of the E. coli fermentation, the cell
culture is cooled to 4-10°C and the cells harvested by continuous
centrifugation at
15,000 rpm (Heraeus Sepatech). On the basis of the expected yield of protein
per unit
weight of cell paste and the amount of purified protein required, an
appropriate
amount of cell paste, by weight, is suspended in a buffer solution containing
100 mM
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Tris, 50 mM EDTA, pH 7.4. The cells are dispersed to a homogeneous suspension
using a high shear mixer.
The cells are then lysed by passing the solution through a microfluidizer
(Microfuidics, Corp, or APV Gaulin, Inc.) twice at 4000-6000 psi. The
homogenate
is then mixed with NaCI solution to a final concentration of 0.5 M NaCI,
followed by
centrifugation at 7000 xg for 15 min. The resultant pellet is washed again
using O.SM
NaCI, 100 mM Tris, 50 mM EDTA, pH 7.4.
The resulting washed inclusion bodies are solubilized with 1.5 M guanidine
hydrochloride (GuHCI) for 2-4 hours. After 7000 xg centrifugation for 15 min.,
the
pellet is discarded and the polypeptide containing supernatant is incubated at
4°C
overnight to allow further GuHCI extraction.
Following high speed centrifugation (30,000 xg) to remove insoluble particles,
the GuHCI solubilized protein is refolded by quickly mixing the GuHCI extract
with
volumes of buffer containing 50 mM sodium, pH 4.5, 150 mM NaCI, 2 mM EDTA
15 by vigorous stirring. The refolded diluted protein solution is kept at
4°C without
mixing for 12 hours prior to further purification steps.
To clarify the refolded polypeptide solution, a previously prepared tangential
filtration unit equipped with 0.16 p,m membrane filter with appropriate
surface area
(e.g., Filtron), equilibrated with 40 mM sodium acetate, pH 6.0 is employed.
The
20 filtered sample is loaded onto a cation exchange resin (e.g., Poros HS-50,
Perseptive
Biosystems). The column is washed with 40 mM sodium acetate, pH 6.0 and eluted
with 250 mM, 500 mM, 1000 mM, and 1500 mM NaCI in the same buffer, in a
stepwise manner. The absorbance at 280 nm of the effluent is continuously
monitored. Fractions are collected and further analyzed by SDS-PAGE.
Fractions containing the polypeptide are then pooled and mixed with 4
volumes of water. The diluted sample is then loaded onto a previously prepared
set of
tandem columns of strong anion (Poros HQ-50, Perseptive Biosystems) and weak
anion (Poros CM-20, Perseptive Biosystems) exchange resins. The columns are
equilibrated with 40 mM sodium acetate, pH 6Ø Both columns are washed with
40
mM sodium acetate, pH 6.0, 200 mM NaCI. The CM-20 column is then eluted using
a 10 column volume linear gradient ranging from 0.2 M NaCI, 50 mM sodium
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241
acetate, pH 6.0 to i.0 M NaCI, 50 mM sodium acetate, pH 6.5. Fractions are
collected under constant A2~ monitoring of the effluent. Fractions containing
the
polypeptide (determined, for instance, by 16% SDS-PAGE) are then pooled.
The resultant polypeptide should exhibit greater than 95% purity after the
above refolding and purification steps. No major contaminant bands should be
observed from Commassie blue stained 16% SDS-PAGE gel when S p.g of purified
protein is loaded. The purified protein can also be tested for endotoxin/LPS
contamination, and typically the LPS content is less than 0.1 ng/ml according
to LAL
assays.
Example 7: Cloning and Expression of a Polyneptide in a Baculovirus
Expression System
In this example, the plasmid shuttle vector pA2 is used to insert a
polynucleotide into a baculovirus to express a polypeptide. This expression
vector
contains the strong polyhedrin promoter of the Autographa californica nuclear
polyhedrosis virus (AcMNPV) followed by convenient restriction sites such as
BamHI, Xba I and Asp718. The polyadenylation site of the simian virus 40
{"SV40")
is used for efficient polyadenylation. For easy selection of recombinant
virus, the
plasmid contains the beta-galactosidase gene from E. coli under control of a
weak
Drosophila promoter in the same orientation, followed by the polyadenylation
signal
of the polyhedrin gene. The inserted genes are flanked on both sides by viral
sequences for cell-mediated homologous recombination with wild-type viral DNA
to
generate a viable virus that express the cloned polynucleotide.
Many other baculovirus vectors can be used in place of the vector above, such
as pAc373, pVL941, and pAcIMI, as one skilled in the art would readily
appreciate,
as long as the construct provides appropriately located signals for
transcription,
translation, secretion and the like, including a signal peptide and an in-
frame AUG as
required. Such vectors are described, for instance, in Luckow et al., Virology
170:31-
39 (1989).
Specifically, the cDNA sequence contained in the deposited clone, including
the AUG initiation codon and the naturally associated leader sequence
identified in
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Table l, is amplified using the PCR protocol described in Example 1. If the
naturally
occurring signal sequence is used to produce the secreted protein, the pA2
vector does
not need a second signal peptide. Alternatively, the vector can be modified
(pA2 GP)
to include a baculovirus leader sequence, using the standard methods described
in
Summers et al., "A Manual of Methods for Baculovirus Vectors and Insect Cell
Culture Procedures," Texas Agricultural Experimental Station Bulletin No. 1555
( 1987).
The amplified fragment is isolated from a 1 % agarose gel using a
commercially available kit ("Geneclean," BIO 101 Inc., La Jolla, Ca.). The
fragment
then is digested with appropriate restriction enzymes and again purified on a
1
agarose gel.
The plasmid is digested with the corresponding restriction enzymes and
optionally, can be dephosphorylated using calf intestinal phosphatase, using
routine
procedures known in the art. The DNA is then isolated from a 1 % agarose gel
using a
commercially available kit ("Geneclean" BIO 101 Inc., La Jolla, Ca.).
The fragment and the dephosphorylated plasmid are ligated together with T4
DNA ligase. E. coli HB 101 or other suitable E. coli hosts such as XL-1 Blue
(Stratagene Cloning Systems, La Jolla, CA) cells are transformed with the
ligation
mixture and spread on culture plates. Bacteria containing the plasmid are
identified
by digesting DNA from individual colonies and analyzing the digestion product
by
gel electrophoresis. The sequence of the cloned fragment is confirmed by DNA
sequencing.
Five p.g of a plasmid containing the polynucleotide is co-transfected with 1.0
p,g of a commercially available linearized baculovirus DNA ("BaculoGoldTM
baculovirus DNA", Pharmingen, San Diego, CA), using the lipofection method
described by Felgner et al., Proc. Natl. Acad. Sci. USA 84:7413-7417 (1987).
One p,g
of BaculoGoldTM virus DNA and 5 p,g of the plasmid are mixed in a sterile well
of a
microtiter plate containing 50 p.l of serum-free Grace's medium (Life
Technologies
Inc., Gaithersburg, MD). Afterwards, 10 p,l Lipofectin plus 90 pl Grace's
medium are
added, mixed and incubated for 15 minutes at room temperature. Then the
transfection mixture is added drop-wise to Sf9 insect cells {ATCC CRL 1711)
seeded
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in a 35 mm tissue culture plate with 1 ml Grace's medium without serum. The
plate is
then incubated for 5 hours at 27° C. The transfection solution is then
removed from
the plate and 1 ml of Grace's insect medium supplemented with 10% fetal calf
serum
is added. Cultivation is then continued at 27° C for four days.
After four days the supernatant is collected and a plaque assay is performed,
as described by Summers and Smith, supra. An agarose gel with "Blue Gal" (Life
Technologies Inc., Gaithersburg) is used to allow easy identification and
isolation of
gal-expressing clones, which produce blue-stained plaques. (A detailed
description of
a "plaque assay" of this type can also be found in the user's guide for insect
cell
culture and baculovirology distributed by Life Technologies Inc.,
Gaithersburg, page
9-10.) After appropriate incubation, blue stained plaques are picked with the
tip of a
micropipettor (e.g., Eppendorf). The agar containing the recombinant viruses
is then
resuspended in a microcentrifuge tube containing 200 p,l of Grace's medium and
the
suspension containing the recombinant baculovirus is used to infect Sf9 cells
seeded
in 35 mm dishes. Four days later the supernatants of these culture dishes are
harvested and then they are stored at 4° C.
To verify the expression of the polypeptide, Sf9 cells are grown in Grace's
medium supplemented with 10% heat-inactivated FBS. The cells are infected with
the recombinant baculovirus containing the polynucleotide at a multiplicity of
infection ("MOI") of about 2. If radiolabeled proteins are desired, 6 hours
later the
medium is removed and is replaced with SF900 II medium minus methionine and
cysteine (available from Life Technologies Inc., Rockville, MD). After 42
hours, S
p.Ci of 35S-methionine and 5 pCi 35S-cysteine (available from Amersham) are
added.
The cells are further incubated for 16 hours and then are harvested by
centrifugation.
The proteins in the supernatant as well as the intracellular proteins are
analyzed by
SDS-PAGE followed by autoradiography (if radiolabeled).
Microsequencing of the amino acid sequence of the amino terminus of
purified protein may be used to determine the amino terminal sequence of the
produced protein.
Example 8: Expression of a Polvpentide in Mammalian Cells
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The polypeptide of the present invention can be expressed in a mammalian
cell. A typical mammalian expression vector contains a promoter element, which
mediates the initiation of transcription of mRNA, a protein coding sequence,
and
signals required for the termination of transcription and polyadenylation of
the
transcript. Additional elements include enhancers, Kozak sequences and
intervening
sequences flanked by donor and acceptor sites for RNA splicing. Highly
efficient
transcription is achieved with the early and late promoters from SV40, the
long
terminal repeats (LTRs) from Retroviruses, e.g., RSV, HTLVI, HIVI and the
early
promoter of the cytomegalovirus (CMV). However, cellular elements can also be
used (e.g., the human actin promoter).
Suitable expression vectors for use in practicing the present invention
include,
for example, vectors such as pSVL and pMSG (Pharmacia, Uppsala, Sweden),
pRSVcat (ATCC 37152), pSV2dhfr (ATCC 37146), pBCI2MI (ATCC 67109),
pCMVSport 2.0, and pCMVSport 3Ø Mammalian host cells that could be used
include, human Hela, 293, H9 and Jurkat cells, mouse NIH3T3 and C127 cells,
Cos 1,
Cos 7 and CV1, quail QC1-3 cells, mouse L cells and Chinese hamster ovary
(CHO)
cells.
Alternatively, the polypeptide can be expressed in stable cell lines
containing
the polynucleotide integrated into a chromosome. The co-transfection with a
selectable marker such as dhfr, gpt, neomycin, hygromycin allows the
identification
and isolation of the transfected cells.
The transfected gene can also be amplified to express large amounts of the
encoded protein. The DHFR (dihydrofolate reductase) marker is useful in
developing
cell lines that carry several hundred or even several thousand copies of the
gene of
interest. (See, e.g., Alt, F. W., et al., J. Biol. Chem. 253:1357-1370 (1978);
Hamlin, J.
L. and Ma, C., Biochem. et Biophys. Acta, 1097:107-143 (1990); Page, M. J. and
Sydenham, M. A., Biotechnology 9:64-68 (1991).) Another useful selection
marker
is the enzyme glutamine synthase (GS) (Murphy et al., Biochem J. 227:277-279
(1991); Bebbington et al., BiofTechnology 10:169-175 (1992). Using these
markers,
the mammalian cells are grown in selective medium and the cells with the
highest
resistance are selected. These cell lines contain the amplified genes)
integrated into a
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chromosome. Chinese hamster ovary (CHO) and NSO cells are often used for the
production of proteins.
Derivatives of the plasmid pS V2-dhfr (ATCC Accession No. 37146), the
expression vectors pC4 (ATCC Accession No. 209646) and pC6 (ATCC Accession
No.209647) contain the strong promoter (LTR) of the Rous Sarcoma Virus (Cullen
et
al., Molecular and Cellular Biology, 438-447 (March, 1985)) plus a fragment of
the
CMV-enhancer (Boshart et al., Cell 41:521-530 (1985).) Multiple cloning sites,
e.g.,
with the restriction enzyme cleavage sites BamHI, XbaI and Asp718, facilitate
the
cloning of the gene of interest. The vectors also contain the 3' intron, the
polyadenylation and termination signal of the rat preproinsulin gene, and the
mouse
DHFR gene under control of the SV40 early promoter.
Specifically, the plasmid pC6, for example, is digested with appropriate
restriction enzymes and then dephosphorylated using calf intestinal phosphates
by
procedures known in the art. The vector is then isolated from a 1 % agarose
gel.
A polynucleotide of the present invention is amplified according to the
protocol outlined in Example 1. If the naturally occurring signal sequence is
used to
produce the secreted protein, the vector does not need a second signal
peptide.
Alternatively, if the naturally occurring signal sequence is not used, the
vector can be
modified to include a heterologous signal sequence. (See, e.g., WO 96/34891.)
The amplified fragment is isolated from a 1 % agarose gel using a
commercially available kit ("Geneclean," BIO 101 Inc., La Jolla, Ca.). The
fragment
then is digested with appropriate restriction enzymes and again purified on a
1 %
agarose gel.
The amplified fragment is then digested with the same restriction enzyme and
purified on a 1 % agarose gel. The isolated fragment and the dephosphorylated
vector
are then ligated with T4 .DNA ligase. E. coli HB 101 or XL-1 Blue cells are
then
transformed and bacteria are identified that contain the fragment inserted
into plasmid
pC6 using, for instance, restriction enzyme analysis.
Chinese hamster ovary cells lacking an active DHFR gene is used for
transfection. Five p.g of the expression plasmid pC6 is cotransfected with 0.5
~tg of
the plasmid pSVneo using lipofectin (Felgner et al., supra). The plasmid pSV2-
neo
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246
contains a dominant selectable marker, the neo gene from Tn5 encoding an
enzyme
that confers resistance to a group of antibiotics including 6418. The cells
are seeded
in alpha minus MEM supplemented with 1 mg/ml 6418. After 2 days, the cells are
trypsinized and seeded in hybridoma cloning plates (Greiner, Germany) in alpha
minus MEM supplemented with 10, 25, or SO ng/ml of metothrexate plus 1 mg/ml
6418. After about 10-14 days single clones are trypsinized and then seeded in
6-well
petri dishes or 10 ml flasks using different concentrations of methotrexate
(50 nM,
100 nM, 200 nM, 400 nM, 800 nM). Clones growing at the highest concentrations
of
methotrexate are then transferred to new 6-well plates containing even higher
concentrations of methotrexate ( 1 ~,M, 2 ~1M, 5 p.M, 10 mM, 20 mM). The same
procedure is repeated until clones are obtained which grow at a concentration
of 100 -
200 p.M. Expression of the desired gene product is analyzed, for instance, by
SDS-
PAGE and Western blot or by reversed phase HPLC analysis.
F~mple 9- Protein Fusion~s
The polypeptides of the present invention are preferably fused to other
proteins. These fusion proteins can be used for a variety of applications. For
example, fusion of the present polypeptides to His-tag, HA-tag, protein A, IgG
domains, and maltose binding protein facilitates purification. (See Example 5;
see
also EP A 394,827; Traunecker, et al., Nature 331:84-86 ( 1988).) Similarly,
fusion to
IgG-l, IgG-3, and albumin increases the halflife time in vivo. Nuclear
localization
signals fused to the polypeptides of the present invention can target the
protein to a
specific subcellular localization, while covalent heterodimer or homodimers
can
increase or decrease the activity of a fusion protein. Fusion proteins can
also create
chimeric molecules having more than one function. Finally, fusion proteins can
increase solubility and/or stability of the fused protein compared to the non-
fused
protein. All of the types of fusion proteins described above can be made by
modifying the following protocol, which outlines the fusion of a polypeptide
to an
IgG molecule, or the protocol described in Example 5.
Briefly, the human Fc portion of the IgG molecule can be PCR amplified,
using primers that span the 5' and 3' ends of the sequence described below.
These
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247
primers also should have convenient restriction enzyme sites that will
facilitate
cloning into an expression vector, preferably a mammalian expression vector.
For example, if pC4 (Accession No. 209646) is used, the human Fc portion
can be ligated into the BamHI cloning site. Note that the 3' BamHI site should
be
destroyed. Next, the vector containing the human Fc portion is re-restricted
with
BamHI, linearizing the vector, and a polynucleotide of the present invention,
isolated
by the PCR protocol described in Example 1, is ligated into this BamHI site.
Note
that the polynucleotide is cloned without a stop codon, otherwise a fusion
protein will
not be produced.
If the naturally occurring signal sequence is used to produce the secreted
protein, pC4 does not need a second signal peptide. Alternatively, if the
naturally
occurring signal sequence is not used, the vector can be modified to include a
heterologous signal sequence. (See, e.g., WO 96/34891
Human IgG Fc region:
GGGATCCGGAGCCCAAATCTTCTGACAAAACTCACACATGCCCACCGTGC
CCAGCACCTGAATTCGAGGGTGCACCGTCAGTCTTCCTCTTCCCCCCAAAA
CCCAAGGACACCCTCATGATCTCCCGGACTCCTGAGGTCACATGCGTGGT
GGTGGACGTAAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGG
ACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTA
CAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACT
GGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCCCA
ACCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAAC
CACAGGTGTACACCCTGCCCCCATCCCGGGATGAGCTGACCAAGAACCAG
GTCAGCCTGACCTGCCTGGTCAAAGGCTTCTATCCAAGCGACATCGCCGT
GGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACGCCT
CCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCTACAGCAAGCTCACCGTG
GACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCA
TGAGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTCCGG
GTAAATGAGTGCGACGGCCGCGACTCTAGAGGAT (SEQ ID NO:1 )
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~xamnle 10~ Production of an Antibody from a Polype tp ide
The antibodies of the present invention can be prepared by a variety of
methods. (See, Current Protocols, Chapter 2.) For example, cells expressing a
polypeptide of the present invention is administered to an animal to induce
the
production of sera containing polyclonal antibodies. In a preferred method, a
preparation of the secreted protein is prepared and purified to render it
substantially
free of natural contaminants. Such a preparation is then introduced into an
animal in
order to produce polyclonal antisera of greater specific activity.
In the most preferred method, the antibodies of the present invention are
monoclonal antibodies (or protein binding fragments thereof). Such monoclonal
antibodies can be prepared using hybridoma technology. (Kohler et al., Nature
256:495 ( 1975); Kohler et al., Eur. J. Immunol. 6:511 ( 1976); Kohler et al.,
Eur. J.
Immunol. 6:292 ( 1976); Hammerling et al., in: Monoclonal Antibodies and T-
Cell
Hybridomas, Elsevier, N.Y., pp. 563-681 ( 1981 ).) In general, such procedures
involve immunizing an animal (preferably a mouse) with polypeptide or, more
preferably, with a secreted polypeptide-expressing cell. Such cells may be
cultured in
any suitable tissue culture medium; however, it is preferable to culture cells
in Earle's
modified Eagle's medium supplemented with 10% fetal bovine serum (inactivated
at
about 56°C), and supplemented with about 10 g/1 of nonessential amino
acids, about
1,000 U/ml of penicillin, and about 100 p,g/ml of streptomycin.
The splenocytes of such mice are extracted and fused with a suitable myeloma
cell line. Any suitable myeloma cell line may be employed in accordance with
the
present invention; however, it is preferable to employ the parent myeloma cell
line
(SP20), available from the ATCC. After fusion, the resulting hybridoma cells
are
selectively maintained in HAT medium, and then cloned by limiting dilution as
described by Wands et al. (Gastroenterology 80:225-232 (1981).) The hybridoma
cells obtained through such a selection are then assayed to identify clones
which
secrete antibodies capable of binding the polypeptide.
Alternatively, additional antibodies capable of binding to the polypeptide can
be produced in a two-step procedure using anti-idiotypic antibodies. Such a
method
makes use of the fact that antibodies are themselves antigens, and therefore,
it is
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