Note: Descriptions are shown in the official language in which they were submitted.
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METHODS AND MATERIALS RELATING TO
METALLOCARBOXYPEPTIDASE-LIKE POLYPEPTIDES AND
POLYNUCLEOTIDES
1 TECHNICAL FIELD
The present invention provides novel polynucleotides and proteins encoded by
such
polynucleotides, along with uses for these polynucleotides and proteins, for
example in
therapeutic, diagnostic and research methods. In particular, the invention
relates to a novel
metallocarboxypeptidase-like polypeptide.
2 BACKGROUND ART
Identified polynucleotide and polypeptide sequences have numerous applications
in, for
example, diagnostics, forensics, gene mapping; identification of mutations
responsible for
genetic disorders or other traits, to assess biodiversity, and to produce many
other types of
data and products dependent on DNA and amino acid sequences. Proteins are
known to have
biological activity, for example, by virtue of their secreted nature in the
case of leader
sequence cloning, by virtue of their cell or tissue source in the case of PCR-
based techniques,
or by virtue of structural similarity to other genes of known biological
activity. It is to these
polypeptides and the polynucleotides encoding them that the present invention
is directed. In
particular, this invention is directed to novel metallocarboxypeptidase-like
polypeptides and
polynucleotides.
A variety of cellular and tissue processes are regulated by peptide hormones.
These
proteins control processes such as cell growth and division, blood pressure,
development,
metabolism, and blood clotting. Their activity is modified in two ways. First,
most hormones
are synthesized as larger precursor proteins and must be cleaved specifically
by enzymes to
achieve their activated conformation. Second, their activity can be altered,
or terminated, by
additional proteases. Carboxypeptidases are a class of enzymes that may be
involved in either
of these reactions. They are responsible for hydrolyzing peptide bonds at the
C=terminus of
peptides, or proteins.
Two major families of carboxypeptidases have been identified,
metallocarboxypeptidases and serine-carboxypeptidases. The
metallocarboxypeptidases are
classified by the the presence of a tightly bound zinc ion at the motif
HXXE(X)nH, where X is
any amino acid, and n is 105-132 residues (SEQ ID NO: 22). There are several
family
members that are included in this group such as carboxypeptidase A, B, D, E,
M, N, U, X,
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and Z. Carboxypeptidase A is the prototypical metallocarboxypeptidase. It
generally
functions to cleave hydrophobic amino acids from the C-terminus of proteins.
Although the
precise role of this protein is not yet fully understood, it is known to form
macramolecular
complexes with proteoglycans, and to cleave peptide substrates in tandem with
other prateases.
Because it is present in mast cells, it has been implicated in pathogenic
conditions such as
inflammation and allergic response.
Carboxypepddase B is a second metallocarboxypeptidase that is secreted as an
inactive
precursor, or zymogen. These carboxypeptidases catalyze the hydrolysis of
individual basic
amino acids, lysine and arginine, from the C-terminus of peptides. Because
trypsin cleavage of
proteins leaves a lysine or arginine at the C-terminal end, these digestion
products are
favorable cleavage substrates for carboxypeptidase B. To achieve their
activated state,
cleavage of an N-terminal globular domain by trypsin, plasmin, or thrombin
must take place.
Two major forms of this enzyme have been isolated and characterized, plasma
and pancreatic
procarboxypeptidase. The plasma procarboxypeptidase, also known as
carboxypeptidase U, is
secreted by liver and is found in the blood as a zymogen. It is believed to
promote blood
clotting by removing plasminogen-binding sites from partially degraded fibrin,
the major
component of blood clots. It is typically bound to plasminogen in its
inactive, pro-enzyme
state, and following activation remains in the circulation complexed with
a2macroglobulin or
pregnancy zone protein. The pancreatic form is secreted by the pancreas in
zymogen granules.
It is involved in digestion, and participates in the degradation of intake
proteins. In addition,
transcripts of a pancreatic carboxypeptidase have been detected in
extrapancreatic tissues,
including brain, where they appear to be the product of alternative splicing.
This variant of
carboxypeptidase B has been found to degrade brain beta-amyloid precursor
protein, a process
that may be important in preventing the development of Alzheimer's disease. In
addition,
brain tissue of patients suffering from sporadic Alzheimer's have been found
to have decreased
levels of this protein (Itoh MA and Matsumoto R, (2000) Eur. J. Neurosci. 12,
227-238).
Carboxypeptidases D and E are involved in the processing of biologically
active
peptides and are therefore classified as regulatory carboxypeptidases. They
are widely
distributed across tissues, and play a variety of physiological roles.
Carboxypeptidase D acts
mainly on proteins that are secreted via the constitutive pathway, such as
growth factors and
growth factor receptors. Alternatively, carboxypeptidase E, also called
carboxypeptidase H, is
found in secretory granules of endocrine and neuroendocrine tissues such as
pancreatic islets,
pituitary, brain, and intestine. It plays a key role in the processing of
insulin, oxytocin-
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vasopressin, gonadotropin release hormone, gastrin, enkelphalin, dynorphin,
neurotensin, and
many others (Leiter EH, {1997) J. Endocrin. 155, 211-214).
Carboxypeptidase M is a widely distributed membrane-bound ectoenzyme that is
found
at high levels in placenta and lungs. It is associated with membranes due to
the presence of a
glycosylphosphatidylinositol (GPI) anchor. This anchor indicates that
carboxypeptidase M
could participate in control of peptide hormone activity at the cell surface,
or in the modulation
of receptors and extracellular protein processing. It has been implicated as a
regulatory
enzyme for growth factors because it is found coincident with epidermal growth
factor.
Carboxypeptidase N is synthesized in the liver, and is released in the blood
where it is
present at high levels. Its role is believed to be largely protective. It
cleaves a variety of
peptide and protein substrates and is the major blood-borne inactivator of
potent peptides such
as kinins and anaphylotoxins.
Carboxypeptidases X and Z are other members of the regulatory
metallocarboxypeptidases that are less well characterized. Carboxypeptidase Z
prefers to
cleave C-terminal arginines, with an alanine in the penultimate position. 'It
has been detected
in placenta and has been implicated as playing a role in processing
extracellular peptides or
proteins.
Metallocarboxypeptidases are important for the regulation of peptide hormones
and
their activity. They are involved in the cleavage of protein or peptide
substrates, and therefore
control a multitude of biological processes. Modulating the activity of
metallocarboxypeptidases could have a dramatic impact on diseases ranging from
poor
digestion, blood clotting, allergic response, inflammation, high or low blood
pressure, and
excess weight. In addition, because cleavage activity is based on terminal
amino acid residues,
and not specific protein type, they have a great potential for the treatment
of a vast array of
other disorders, such as Alzheimer's disease. It would be beneficial to
identify and
characterizes other carboxypeptidases.
3. SUMMARY OF THE INVENTION
This invention is based on the discovery of novel metallocarboxypeptidase-like
polypeptides, novel isolated polynucleotides encoding such polypeptides,
including
recombinant DNA molecules, cloned genes or degenerate variants thereof,
especially naturally
occurring variants such as allelic variants, antisense polynucleotide
molecules, and antibodies
that specifically recognize one or more epitopes present on such polypeptides,
as well as
hybridomas producing such antibodies. Specifically, the polynucleotides of the
present
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invention are based on a metallocarboxypeptidase-like polynucleotide isolated
from a cDNA
library prepared from small intestine (Hyseq clone identification numbers
11732488 (SEQ ID
NO: 1).
The compositions of the present invention additionally include vectors such as
expression vectors containing the polynucleotides of the invention, cells
genetically engineered
to contain such polynucleotides and cells genetically engineered to express
such
polynucleotides .
The compositions of the invention provide isolated polynucleotides that
include, but are
not limited to, a polynucleotide comprising the nucleotide sequence set forth
in the SEQ ID NO:
1-3, 5, 23, or 26; or a fragment of SEQ ID NO: 1-3, 5, 23, or 26; a
polynucleotide comprising
the full length protein coding sequence of the SEQ ID NO: 1-3, 5, 23, or 26
(for example, SEQ
ID NO: 4 or 24); and a polynucleotide comprising the nucleotide sequence of
the mature protein
coding sequence of any of SEQ ID NO: 1-3, 5, 23, or 26. The polynucleotides of
the present
invention also include, but are not limited to, a polynucleotide that
hybridizes under stringent
1 S hybridization conditions to (a) the complement of any of the nucleotide
sequences set forth in SEQ
ID NO: 1-3, 5, 23, or 26; (b) a nucleotide sequence encoding any of SEQ ID NO:
4, 6-19, or 24
- 25, 27; a polynucleotide which is an allelic variant of any polynucleotides
recited above having
at least 70 % polynucleotide sequence identity to the polynucleotides; a
polynucleotide which
encodes a species homolog (e.g. orthologs) of any of the peptides recited
above; or a
polynucleotide that encodes a polypeptide comprising a specific domain or
truncation of the
polypeptide comprising SEQ ID NO: 4 or 24.
A collection as used in this application can be a collection of only one
polynucleotide.
The collection of sequence information or unique identifying information of
each sequence can be
provided on a nucleic acid array. In one embodiment, segments of sequence
information are
provided on a nucleic acid array to detect the polynucleotide that contains
the segment. The array
can be designed to detect full-match or mismatch to the polynucleotide that
contains the segment.
The collection can also be provided in a computer-readable format.
This invention further provides cloning or expression vectors comprising at
least a
fragment of the polynucleotides set forth above and host cells or organisms
transformed with these
expression vectors. Useful vectors include plasnuds, cosrnids, lambda phage
derivatives,
phagemids, and the like, that are well known in the art. Accordingly, the
invention also provides
a vector including a polynucleotide of the invention and a host cell
containing the polynucleotide.
In general, the vector contains an origin of replication functional in at
least one organism,
convenient restriction endonuclease sites, and a selectable marker for the
host cell. Vectors
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according to the invention include expression vectors, replication vectors,
probe generation
vectors, and sequencing vectors. A host cell according to the invention can be
a prokaryotic or
eukaryotic cell and can be a unicellular organism or part of a multicellular
organism.
The compositions of the present invention include polypeptides comprising, but
not limited
to, an isolated polypeptide selected from the group comprising the amino acid
sequence of SEQ
ID NO: 4, 6-19, 24 - 25,or 27; or the corresponding full length or mature
protein. Polypeptides
of the invention also include polypeptides with biological activity that are
encoded by (a) any of
the polynucleotides having a nucleotide sequence set forth in the SEQ ID NO: 1-
3, 5, 23, or 26 of
(a) under stringent hybridization conditions. Biologically or immunologically
active variants of
any of the protein sequences listed as SEQ ID NO: 4, 6-19, 24 - 25, or 27 and
substantial
equivalents thereof that retain biological or immunological activity are also
contemplated. The
polypeptides of the invention may be wholly or partially chemically
synthesized but are preferably
produced by recombinant means using the genetically engineered cells (e.g.
host cells) of the
invention.
The invention also provides compositions comprising a polypeptide of the
invention.
Pharmaceutical compositions of the invention may comprise a polypeptide of the
invention and
an acceptable carrier, such as a hydrophilic, e.g., pharmaceutically
acceptable, carrier.
The invention also relates to methods for producing a polypeptide of the
invention
comprising culturing host cells comprising an expression vector containing at
least a fragment
of a polynucleotide encoding the polypeptide of the invention in a suitable
culture medium
under conditions permitting expression of the desired polypeptide, and
purifying the protein or
peptide from the culture or from the host cells. Preferred embodiments include
those in which
the protein produced by such a process is a mature form of the protein.
Polynucleotides according to the invention have numerous applications in a
variety of
techniques known to those skilled in the art of molecular biology. These
techniques include
use as hybridization probes, use as oligomers, or primers, for PCR, use in an
array, use in
computer-readable media, use for chromosome and gene mapping, use in the
recombinant
production of protein, and use in generation of antisense DNA or RNA, their
chemical analogs
and the like. For example, when the expression of an mRNA is largely
restricted to a
particular cell or tissue type, polynucleotides of the 'invention can be used
as hybridization
probes to detect the presence of the particular cell or tissue mRNA in a
sample using, e. g., in
situ hybridization.
In other exemplary embodiments, the polynucleotides are used in diagnostics as
expressed sequence tags for identifying expressed genes or, as well known in
the art and
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exemplified by Vollrath et al., Science 258:52-59 (1992), as expressed
sequence tags for
physical mapping of the human genome.
The polypeptides according to the invention can be used in a variety of
conventional
procedures and methods that are currently applied to other proteins. For
example, a
polypeptide of the invention can be used to generate an antibody that
specifically binds the
polypeptide. Such antibodies, particularly monoclonal antibodies, are useful
for detecting or
quantitating the polypeptide in tissue. The polypeptides of the invention can
also be used as
molecular weight markers, and as a food supplement.
Methods are also provided for preventing, treating, or ameliorating a medical
condition
which comprises the step of administering to a mammalian subject a
therapeutically effective
amount of a composition comprising a peptide of the present invention and a
pharmaceutically
acceptable carrier.
In particular, the polypeptides and polynucleotides of the invention can be
utilized, for
example, in modulating inflammation, allergic response, blood clotting, and
high or low blood
pressure. They may also be helpful in treating or diagnosing susceptibility
for Alzheimer's
disease.
The methods of the invention also provides methods for the treatment of
disorders as
recited herein which comprise the administration of a therapeutically
effective amount of a
composition comprising a polynucleotide or polypeptide of the invention and a
pharmaceutically acceptable carrier to a mammalian subject exhibiting symptoms
or tendencies
related to disorders as recited herein. In addition, the invention encompasses
methods for
treating diseases or disorders as recited herein comprising the step of
administering a
composition~comprising compounds and other substances that modulate the
overall activity of
the target gene products and a pharmaceutically acceptable carrier. Compounds
and other
substances can effect such modulation either on the level of target
gene/protein expression or
target protein activity. The modulators maybe agonists or antagonists of the
metallocarboxypeptidase-like polypeptide. Specifically, methods are provided
for preventing,
treating or ameliorating a medical condition, including viral diseases, which
comprises
administering to a mammalian subject, including but not limited to humans, a
therapeutically
effective amount of a composition comprising a polypeptide of the invention or
a
therapeutically effective amount of a composition comprising a binding partner
of (e.g.,
antibody specifically reactive for) metallocarboxypeptidase-like polypeptides
of the invention.
The mechanics of the particular condition or pathology will dictate whether
the polypeptides of
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the invention or binding partners (or inhibitors) of these would be beneficial
to the individual
in need of treatment.
According to this method, polypeptides of the invention can be administered to
produce
an ire vitro or in vivo inhibition of cellular function. A polypeptide of the
invention can be
S administered in vivo alone or as an adjunct to other therapies. Conversely,
protein or other
active ingredients of the present invention may be included in formulations of
a particular
agent to minimize side effects of such an agent.
The invention further provides methods for manufacturing medicaments useful in
the
above-described methods.
The present invention further relates to methods for detecting the presence of
the
polynucleotides or polypeptides of the invention in a sample (e.g.,. tissue or
sample). Such
methods can, for example, be utilized as part of prognostic and diagnostic
evaluation of
disorders as recited herein and for the identification of subjects exhibiting
a predisposition to
such conditions.
The invention provides a method for detecting a polypeptide of the invention
in a
sample comprising contacting the sample with a compound that binds to and
forms a complex
with the polypeptide under conditions and for a period sufficient to form the
complex and
detecting formation of the complex, so that if a complex is formed, the
polypeptide is detected.
The invention also provides kits comprising polynucleotide probes and/or
monoclonal
antibodies, and optionally quantitative standards, for carrying out methods of
the invention.
Furthermore, the invention provides methods for evaluating the efficacy of
drugs, and
monitoring the progress of patients, involved in clinical trials for the
treatment of disorders as
recited above.
The invention also provides methods for the identification of compounds that
modulate
(i.e., increase or decrease) the expression or activity of the polynucleotides
and/or
polypeptides of the invention. Such methods can be utilized, for example, for
the identification
of compounds that can ameliorate symptoms of disorders as recited herein. Such
methods can
include, but are not limited to, assays for identifying compounds and other
substances that
interact with (e. g. , bind to) the polypeptides of the invention.
The invention provides a method for identifying a compound that binds to the
polypeptide of the present invention comprising contacting the compound with
the polypeptide
under conditions and for a time sufficient to form a polypeptide/compound
complex and
detecting the complex, so that if the polypeptide/compound complex is
detected, a compound
that binds to the polypeptide is identified.
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Also provided is a method for identifying a compound that binds to the
polypeptide
comprising contacting the compound with the polypeptide in a cell for a time
sufficient to form
a polypeptide/compound complex wherein the complex drives expression of a
reporter gene
sequence in the cell and detecting the complex by detecting reporter gene
sequence expression
so that if the polypeptide/compound complex is detected a compound that binds
to the
polypeptide is identified.
4. BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 shows the BLASTP amino acid sequence alignment between the protein
encoded by SEQ ID NO: 3 (i.e. SEQ ID NO: 4) metallocarboxypeptidase-like
polypeptide and
Bothrops jararaca carboxypeptidase homolog protein (Murbach et al.,
Biochemistry, submitted)
(SEQ ID NO: 20), indicating that the two sequences share 67 % similarity over
326 amino acid
residues of SEQ ID NO: 4 and 46 % identity over the same 326 amino acid
residues of SEQ ID
NO: 4, wherein A=Alanine, C=Cysteine, D=Aspartic Acid, E= Glutamic Acid,
F=Phenylalanine, G=Glycine, H=Histidine, I=Isoleucine, K=Lysine, L=Leucine,
M=Methionine, N=Asparagine, P=Proline, Q=Glutamine, R=Arginine, S=Serine,
T=Threonine, V=Valine, W=Tryptophan, Y=Tyrosine. Gaps are presented as dashes.
Figure 2 shows the BLASTP amino acid sequence alignment between the protein
encoded by SEQ ID NO: 3 (i.e. SEQ ID NO: 4) metallocarboxypeptidase-like
polypeptide and
a human carboxypeptidase B mutant protein (International Patent Application
No.
WO97/07769) [SEQ ID NO: 21], indicating that the two sequences share 66%
similarity over
312 amino acid residues of SEQ ID NO: 4 and 48 % identity over the same 312
amino acid
residues of SEQ ID NO: 4, wherein A=Alanine, C=Cysteine, D=Aspartic Acid, E=
Glutamic Acid, F=Phenylalanine, G=Glycine, H=Histidine, I=Isoleucine,
K=Lysine,
L=Leucine, M=Methionine, N=Asparagine, P=Proline, Q=Glutamine, R=Arginine,
S=Serine, T=Threonine, V=Valine, W=Tryptophan, Y=Tyrosine. Gaps are presented
as
dashes.
5. DETAILED DESCRIPTION OF THE INVENTION
The metallocarboxypeptidase-like polypeptide of SEQ ID NO: 4 is an
approximately
374-amino acid secreted, glycosylphosphatidylinositol (GPI)-linked protein
with a predicted
molecular mass of approximately 41 kDa unglycosylated. Protein database
searches with the
BLASTP algorithm (Altschul S.F. et al., J. Mol. Evol. 36:290-300 (1993) and
Altschul S.F. et
al., J. Mol. Biol. 21:403-10 (1990), herein incorporated by reference)
indicate that SEQ ID
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NO: 4 is homologous to Bothrops jararaca carboxypeptidase and human
carboxypeptidase B
mutant proteins.
Figure 1 shows the BLASTP amino acid sequence alignment between the protein
encoded by SEQ ID NO: 3 (i.e. SEQ ID NO: 4) and the Bothrops jararaca
carboxypeptidase
homolog protein (Murbach et al., Biochemistry, submitted) (SEQ ID NO: 20)
indicating that
the two sequences share 67 % similarity over 326 amino acid residues of SEQ ID
NO: 4 and
46 % identity over the same 326 amino acid residues of SEQ ID NO: 4. Figure 2
shows the
BLASTP amino acid sequence alignment between the protein encoded by SEQ ID NO:
3 (i.e.
SEQ ID NO: 4) and the human carboxypeptidase B mutant protein (International
Patent
Application No. W097/07769) [SEQ ID NO: 21] indicating that the two sequences
share 66%
similarity over 312 amino acid residues of SEQ ID NO: 4 and 48 % identity over
the same 312
amino acid residues of SEQ ID NO: 4. The sequences of the present invention
are expected to
have secreted or GPI anchored metallocarboxypeptidase-like activity.
A predicted approximately twenty-residue signal peptide is encoded from
approximately
residue 1 through residue 20 inclusive of SEQ ID NO: 4 (SEQ ID NO: 16). The
extracellular
portion is useful on its own. This can be confirmed by expression in mammalian
cells and
sequencing of the cleaved product. The signal peptide region was predicted
using the Kyte-
Doolittle hydrophobicity prediction algorithm (J. Mol Biol, 157, pp. 105-31
(1982),
incorporated herein by reference). One of skill in the art will recognize that
the cleavage site
may be different than that predicted by the computer program.
A predicted approximately fifteen-residue GPI anchor is encoded from
approximately
residue 360 to residue 374 inclusive of SEQ ID NO: 4 (SEQ ID NO: 17). The GPI
anchor
region was predicted using the Kyte-Doolittle hydrophobicity prediction
algorithm (J. Mol
Biol, 157, pp. 105-31 (1982), incorporated herein by reference). One of skill
in the art will
recognize that the linkage site may be different than that predicted by the
computer program.
Using the eMATRIX software package (Stanford University, Stanford, CA) (Wu, et
al., J. Comp. Biol., vol. 6, pp. 219-235 (1999), herein incorporated by
reference), zinc
carboxypeptidase, zinc-binding region 1 protein signature sequences are
predicted. These
include regions encoded from approximately residue 129 to residue169 inclusive
of SEQ ID
NO: 4 (SEQ ID N0:6), approximately residue 99 to 112 inclusive of SEQ ID NO: 4
(SEQ ID
NO: 7), approximately residue 50 to residue 90 inclusive of SEQ ID NO: 4 (SEQ
ID NO: 9),
approximately residue 228 to residue 249 inclusive of SEQ ID NO: 4 (SEQ ID NO:
10),
approximately residue 173 to residue 187 inclusive of SEQ ID NO 4: (SEQ ID NO:
11),
approximately residue 199 to residue 225 inclusive of SEQ ID NO 4: (SEQ ID NO:
12), and
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approximately residue 285 to residue 302 inclusive of SEQ ID NO 4: (SEQ ID
NO:15). The
r eMATRIX software package (Stanford University, Stanford, CA) (Wu, et al., J.
Comp. Biol.,
vol. 6, pp. 219-235 (1999), herein incorporated by reference), has also
predicted
carboxypeptidase A metalloprotease (M14) family signature sequences encoded
from
approximately residue 99 to residue 113 inclusive of SEQ ID N0:4 (SEQ ID NO:
8),
approximately residue 233 to residue 246 inclusive of SEQ ID NO: 4 (SEQ ID NO:
13), and
approximately residue 179 to residue 187 inclusive of SEQ ID NO: 4 (SEQ ID NO:
14). The
domains corresponding to SEQ ID NO: 6 through and including SEQ ID NO: l5.are
as
follows wherein A=Alanine, C=Cysteine, D=Aspartic Acid, E= Glutamic Acid,
F=Phenylalanine, G=Glycine, H=Histidine, I=Isoleucine, K=Lysine, L=Leucine,
M=Methionine, N=Asparagine, P=Proline, Q=Glutamine, R=Arginine, S=Serine,
T=Threonine, V=Valine, W=Tryptophan, Y=Tyrosine:
Zinc carboxypeptidases, zinc-binding region 1 domain
HKDNSRIRKLLRNLDFYVLPVLNIDGYIYTWTTDRLWRKSR
designated as SEQ ID NO: 6, p-value of 3.308e-28, BL00132C (identification
number
correlating to signature); located at residues 129-169 of SEQ ID NO: 4 and
Zinc carboxypeptidases, zinc-binding region 1 domain
KIIWMDCGIHAREW
designated as SEQ ID NO: 7, p-value of 1.871 e-16, BL00132B (identification
number
correlating to signature); located at residues 99-112 of SEQ ID NO: 4 and
Zinc carboxypeptidases, zinc-binding region 1 domain
YHPMGEIYEWMREISEKYKEVVTQHFLGVTYETHPIYYLKI
designated as SEQ ID NO: 9, p-value of 1.682e-14, BL00132A (identification
number
correlating to signature); located at residues 50-90 of SEQ ID NO: 4 and
Zinc carboxypeptidases, zinc-binding region 1 domain
DILCFLTMHSYGQLILTPYGYT
designated as SEQ ID NO: 10, p-value of 7.254e-14, BL00132F (identification
number
correlating to signature); located at residues 228-249 of SEQ ID NO: 4 and
Zinc carboxypeptidases, zinc-binding region 1 domain
NNGTCFGTDLNRNFN
designated as SEQ ID NO: 11, p-value of 2.875e-12, BL00132D (identification
number
correlating to signature); located at residues 173-187 of SEQ ID NO: 4 and
Zinc carboxypeptidases, zinc-binding region 1 domain
CQDQTFCGTGPVSEPETKAVASFIESK
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designated as SEQ ID NO: 12, p-value of 3.552e-12, BL00132E (identification
number
correlating to signature); located at residues 199-225 of SEQ ID NO: 4 and
Zinc carboxypeptidases, zinc-binding region 1 domain DILYASSGSSRDWARDIG
designated as SEQ ID NO: 15, p-value of 4.541e-10, BL00132G (identification
number
correlating to signature); located at residues 285-302 of SEQ ID NO: 4 and
Carboxypeptidase A metalloprotease (M14) family signature domain
KIIWMDCGIHAREWI
designated as SEQ ID NO: 8, p-value of 7.857e-16, PR00765B (identification
number
correlating to signature); located at residues 99-113 of SEQ ID NO: 4 and
Carboxypeptidase A metalloprotease (M14) family signature domain
LTMHSYGQLILTPY
designated as SEQ ID NO: 13, p-value of S.SOOe-1 l, PR00765D (identification
number
correlating to signature); located at residues 233-246 of SEQ ID NO: 4 and
Carboxypeptidase A metalloprotease (M14) family signature domain GTDLNRNFN
designated as SEQ ID NO: 14, p-value of 1.290e-10, PR00765C (identification
number
correlating to signature); located at residues 179-187 of SEQ ID NO: 4.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc. , San
Diego, CA), several regions of the metallocarboxypeptidase-like polypeptide,
SEQ ID NO: 4,
were determined to have procarboxypeptidase characteristic motifs. A region at
residues 7
through 347 was found to have characteristic motifs of the porcine
procarboxypeptidasc B,
with PSI BLAST e-value of 0.0, protein database identification number entry =
lnsa
(Research collaboratory for Structural Bioinformatics
http://www.rcsb.org/pbd), verify score
= 0.93, located at residues 7 -347 of SEQ ID NO: 4.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 4 was
also predicted
to have a region at residues 2 - 349 with characteristic motifs to the human
procarboxypeptidase A2, with PSI BLAST e-value 0.0, protein database
identification number
entry = laye (Research collaboratory for Structural Bioinformatics
http://www.rcsb.org/pbd),
verify score = 0.78, located at residues 2 - 349 of SEQ ID NO: 4.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 4 was
also predicted
to have a region at residues 2 - 347 with characteristic motifs to the porcine
pancreatic
procarboxypeptidase A, with PSI BLAST e-value 0.0, protein database
identification number
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entry = lpca (Research collaboratory for Structural Bioinformatics
http://www.rcsb.org/pbd),
verify score = 0.68, located at residues 2 - 347 of SEQ ID NO: 4.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 4 was
also predicted
to have a region at residues 42 - 347 with characteristic motifs to the bovine
pancreatic
carboxypeptidase B, with PSI BLAST e-value 0.0, protein database
identification number entry
= lcpb (Research collaboratory for Structural Bioinformatics
http://www.rcsb.org/pbd),
verify score = 0.39, located at residues 42 - 347 of SEQ ID NO: 4.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 4 was
also predicted
to have a region at residues 40 - 347 with characteristic motifs to the bovine
pancreatic
procarboxypeptidase A, with PSI BLAST e-value 0.0, protein database
identification number
entry = 2ctc (Research collaboratory for Structural Bioinformatics
http://www.rcsb.org/pbd),
verify score = 0.86, located at residues 40 - 347 of SEQ ID NO: 4.
The metallocarboxypeptidase-like polypeptide of SEQ ID NO: 24 is also an
approximately 374-amino acid secreted, glycosylphosphatidylinositol (GPI)-
linked protein with
a predicted molecular mass of approximately 41 kDa unglycosylated. It is a
variant of the
metallocarboxypeptidase-like polypeptide of SEQ ID NO: 4 that contains a
single nucleotide
base substitution, resulting one amino acid change in the polypeptide. The
metallocarboxypeptidase-like polypeptide of SEQ ID NO: 24 has an identical
signal peptide,
GPI anchor, carboxypeptidase A metalloprotease (M14) family signatures, and
zinc
carboxypeptidases zinc-binding region 1 domains as the peptide of SEQ ID NO:
4, with the
exception of the zinc binding region-1 signature located at residues 50 - 90.
This is the region
of the polypeptides that contains the amino acid change. For SEQ ID NO: 24
this domain is as
follows:
Zinc carboxypeptidases, zinc-binding region 1 domain
YHPMGEIYE WMREI SEKYKEV VTQHFLGVTYETHPMYYLKI
designated as SEQ ID NO: 27, p-value of 8.286e-15, BL00132A (identification
number
correlating to signature); located at residues 50-90 of SEQ ID NO: 24
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA), several regions of the metallocarboxypeptidase-like polypeptide,
SEQ ID NO: 24,
were determined to have procarboxypeptidase characteristic motifs. A region at
residues 7
through 347 was found to have characteristic motifs of the porcine
procarboxypeptidase B,
with PSI BLAST e-value of 0.0, protein database identification number entry =
lnsa
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(Research collaboratory for Structural Bioinformatics
http://www.rcsb.orglpbd), verify score
= 0.75, located at residues 7 -347 of SEQ ID NO: 24.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 24 was
also
predicted to have a region at residues 2 - 349 with characteristic motifs to
the human
procarboxypeptidase A2, with PSI BLAST e-value 0.0, protein database
identification number
entry = laye (Research collaboratory for Structural Bioinformatics
http://www.rcsb.orglpbd),
verify score = 0.71, located at residues 2 - 349 of SEQ ID NO: 24.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 24 was
also
predicted to have a region at residues 2 - 347 with characteristic motifs to
the porcine
pancreatic procarboxypeptidase A, with PSI BLAST e-value 0.0, protein database
identification number entry = lpca (Research collaboratory for Structural
Bioinformatics
http://www.rcsb.org/pbd), verify score = 0.77, located at residues 2 - 347 of
SEQ ID NO:
24.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 24 was
also
predicted to have a region at residues 42 - 347 with characteristic motifs to
the bovine
pancreatic carboxypeptidase B, with PSI BLAST e-value 0.0, protein database
identification
number entry = lcpb (Research collaboratory for Structural Bioinformatics
http://www.rcsb.org/pbd), verify score = 0.39, located at residues 42 - 347 of
SEQ ID NO:
24.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 24 was
also
predicted to have a region at residues 40 - 347 with characteristic motifs to
the bovine
pancreatic procarboxypeptidase A, with PSI BLAST e-value 0.0, protein database
identification number entry = 2ctc (Research collaboratory for Structural
Bioinformatics
http://www.rcsb.org/pbd), verify score = 0.91, located at residues 40 - 347 of
SEQ ID NO:
24.
The polypeptides and polynucleotides of the invention and molecules capable of
modulating the polypeptides and polynucleotides of the invention can be
utilized, for example,
in modulating high or low blood pressure, treating excess weight, digestive
disorders, and
autoimmunity. They may also be helpful in treating and diagnosing inflammatory
disorders
and Alzheimer's disease.
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5.1 DEFINITIONS
It must be noted that as used herein and in the appended claims, the singular
forms "a",
"an" and "the" include plural references unless the context clearly dictates
otherwise.
The term "active" refers to those forms of the polypeptide that retain the
biologic
and/or immunologic activities of any naturally occurring polypeptide.
According to the
invention, the terms "biologically active" or "biological activity" refer to a
protein or peptide
having structural, regulatory or biochemical functions of a naturally
occurring molecule.
Likewise "biologically active" or "biological activity" refers to the
capability of the natural,
recombinant or synthetic metallocarboxypeptidase-like peptide, or any peptide
thereof, to
induce a specific biological response in appropriate animals or cells and to
bind with specific
antibodies. The term "metallocarboxypeptidase-like biological activity" refers
to biological
activity that is similar to the biological activity of a
metallocarboxypeptidase protein.
The term "activated cells" as used in this application are those cells which
are engaged
in extracellular or intracellular membrane trafficking, including the export
of secretory or
enzymatic molecules as part of a normal or disease process.
The terms "complementary" or "complementarity" refer to the natural binding of
polynucleotides by base pairing. For example, the sequence 5'-AGT-3' binds to
the
complementary sequence 3'-TCA-5' . Complementarity between two single-stranded
molecules
may be "partial" such that only some of the nucleic acids bind or it may be
"complete" such
that total complementarity exists between the single stranded molecules. The
degree of
complementarity between the nucleic acid strands has significant effects on
the efficiency and
strength of the hybridization between the nucleic acid strands.
The term "embryonic stem cells (ES)" refers to a cell that can give rise to
many
differentiated cell types in an embryo or an adult, including the germ cells.
The term "germ
line stem cells (GSCs)" refers to stem cells derived from primordial stem
cells that provide a
steady and continuous source of germ cells for the production of gametes. The
term
"primordial germ cells (PGCs)" refers to a small population of cells set aside
from other cell
lineages particularly from the yolk sac, mesenteries, or gonadal ridges during
embryogenesis
that have the potential to differentiate into germ cells and other cells. PGCs
are the source
from which GSCs and ES cells are derived The PGCs, the GSCs and the ES cells
are capable
of self renewal. Thus these cells not only populate the germ line and give
rise to a plurality of
terminally differentiated cells that comprise the adult specialized organs,
but are able to
regenerate themselves.
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The term "expression modulating fragment, " EMF, means a series of nucleotides
that
modulates the expression of an operably linked ORF or another EMF.
As used herein, a sequence is said to "modulate the expression of an operably
linked
sequence" when the expression of the sequence is altered by the presence of
the EMF. EMFs
include, but are not limited to, promoters, and promoter modulating sequences
(inducible
elements). One class of EMFs is nucleic acid fragments which induce the
expression of an
operably linked ORF in response to a specific regulatory factor or
physiological event.
The terms "nucleotide sequence" or "nucleic acid" or "polynucleotide" or
"oligonculeotide" are used interchangeably and refer to a heteropolymer of
nucleotides or the
sequence of these nucleotides. These phrases also refer to DNA or RNA of
genomic or
synthetic origin which may be single-stranded or double-stranded and may
represent the sense
or the antisense strand, to peptide nucleic acid (PNA) or to any DNA-like or
RNA-like
material. It its understood that where the nucleic acid is RNA, the T's in the
nucleic acid
sequences provided herein will be substituted with U's. Generally, nucleic
acid segments
provided by this invention may be assembled from fragments of the genome and
short
oligonucleotide linkers, or from a series of oligonucleotides, or from
individual nucleotides, to
provide a synthetic nucleic acid which is capable of being expressed in a
recombinant
transcriptional unit comprising regulatory elements derived from a microbial
or viral operon,
or a eukaryotic gene.
The terms "oligonucleotide fragment" or a "polynucleotide fragment",
"portion," or
"segment" or "probe" or "primer" are used interchangeably and refer to a
sequence of
nucleotide residues which axe at least about 5 nucleotides, more preferably at
least about 7
nucleotides, more preferably at least about 9 nucleotides, more preferably at
least about 11
nucleotides and most preferably at least about 17 nucleotides. The fragment is
preferably less
than about 500 nucleotides, preferably less than about 200 nucleotides, more
preferably less
than about 100 nucleotides, more preferably less than about 50 nucleotides and
most preferably
less than 30 nucleotides. Preferably the probe is from about 6 nucleotides to
about 200
nucleotides, preferably from about 15 to about 50 nucleotides, more preferably
from about 17
to 30 nucleotides and most preferably from about 20 to 25 nucleotides.
Preferably the
fragments can be used in polymerise chain reaction (PCR), various
hybridization procedures
or microarray procedures to identify or amplify identical or related parts of
mRNA or DNA
molecules. A fragment or segment may uniquely identify each polynucleotide
sequence of the
present invention. Preferably the fragment comprises a sequence substantially
similar to a
portion of SEQ ID NO: 1-3, 5, 23, or 26.
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Probes may, for example, be used to determine whether specific mRNA molecules
are
present in a cell or tissue or to isolate similar nucleic acid sequences from
chromosomal DNA
as described by Walsh et al. (Walsh, P.S. et al., 1992, PCR Methods Appl 1:241-
250). They
may be labeled by nick translation, Klenow fill-in reaction, PCR, or other
methods well known
in the art. Probes of the present invention, their preparation and/or labeling
are elaborated in
Sambrook, J. et al., 1989, Molecular Cloning: A Laboratory Manual, Cold Spring
Harbor
Laboratory, NY; or Ausubel, F.M. et al., 1989, Current Protocols in Molecular
Biology, John
Wiley & Sons, New York NY, both of which are incorporated herein by reference
in their
entirety.
The nucleic acid sequences of the present invention also include the sequence
information from any of the nucleic acid sequences of SEQ ID NO: 1-3, 5, 23,
or 26. The
sequence information can be a segment of SEQ ID NO: 1-3, 5, 23, or 26 that
uniquely
identifies or represents the sequence information of SEQ ID NO: 1-3, 5, 23, or
26. One such
segment can be a twenty-mer nucleic acid sequence because the probability that
a twenty-mer
is fully matched in the human genome is 1 in 300. In the human genome, there
are three
billion base pairs in one set of chromosomes. Because 42° possible
twenty-mers exist, there are
300 times more twenty-mers than there are base pairs in a set of human
chromosome. Using
the same analysis, the probability for a seventeen-mer to be fully matched in
the human
genome is approximately 1 in 5. When these segments are used in arrays for
expression
studies, fifteen-mer segments can be used. The probability that the fifteen-
mer is fully
matched in the expressed sequences is also approximately one in five because
expressed
sequences comprise less than approximately 5 % of the entire genome sequence.
Similarly, when using sequence information for detecting a single mismatch, a
segment
can be a twenty-five mer. The probability that the twenty-five mer would
appear in a human
genome with a single mismatch is calculated by multiplying the probability for
a full match
(1-4'~) times the increased probability for mismatch at each nucleotide
position (3 x 25). The
probability that an eighteen mer with a single mismatch can be detected in an
array for expression
studies is approximately one in five. The probability that a twenty-mer with a
single mismatch
can be detected in a human genome is approximately one in five.
The term "open reading frame," ORF, means a series of nucleotide triplets
coding for
amino acids without any termination codons and is a sequence translatable into
protein.
The terms "operably linked" or "operably associated" refer to functionally
related
nucleic acid sequences. For example, a promoter is operably associated or
operably linked
with a coding sequence if the promoter controls the transcription of the
coding sequence.
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While operably linked nucleic acid sequences can be contiguous and in the same
reading
frame, certain genetic elements e.g. repressor genes are not contiguously
linked to the coding
sequence but still control transcription/translation of the coding sequence.
The term "pluripotent" refers to the capability of a cell to differentiate
into a number of
differentiated cell types that are present in an adult organism. A pluripotent
cell is restricted in
its differentiation capability in comparison to a totipotent cell.
The terms "polypeptide" or "peptide" or "amino acid sequence" refer to an
oligopeptide, peptide, polypeptide or protein sequence or fragment thereof and
to naturally
occurring or synthetic molecules. A polypeptide "fragment," "portion," or
"segment" is a
stretch of amino acid residues of at least about 5 amino acids, preferably at
least about 7 amino
acids, more preferably at least about 9 amino acids and most preferably at
least about 17 or
more amino acids. The peptide preferably is not greater than about 200 amino
acids, more
preferably less than 150 amino acids and most preferably less than 100 amino
acids.
Preferably the peptide is from about 5 to about 200 amino acids. To be active,
any
1 S polypeptide must have sufficient length to display biological and/or
irnmunological activity.
The term "naturally occurring polypeptide" refers to polypeptides produced by
cells
that have not been genetically engineered and specifically contemplates
various polypeptides
arising from post-translational modifications of the polypeptide including,
but not limited to,
acetylation, carboxylation, glycosylation, phosphorylation, lipidation and
acylation.
The term "translated protein coding portion" means a sequence which encodes
for the
full length protein which may include any leader sequence or a processing
sequence.
The term "mature protein coding sequence" refers to a sequence which encodes a
peptide or protein without any leader/signal sequence. The peptide may have
the leader
sequences removed during processing in the cell or the protein may have been
produced
synthetically or using a polynucleotide only encoding for the mature protein
coding sequence.
The term "derivative" refers to polypeptides chemically modified by such
techniques as
ubiquitination, labeling (e.g., with radionuclides or various enzymes),
covalent polymer
attachment such as pegylation (derivatization with polyethylene glycol) and
insertion or
substitution by chemical synthesis of amino acids such as ornithine, which do
not normally
occur in human proteins.
The term "variant"(or "analog") refers to any polypeptide differing from
naturally
occurring polypeptides by amino acid insertions, deletions, and substitutions,
created using, a
g., recombinant DNA techniques. Guidance in determining which amino acid
residues may be
replaced, added or deleted without abolishing activities of interest, may be
found by comparing
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the sequence of the particular polypeptide with that of homologous peptides
and minimizing the
number of amino acid sequence changes made in regions of high homology
(conserved
regions) or by replacing amino acids with consensus sequence.
Alternatively, recombinant variants encoding these same or similar
polypeptides may be
synthesized or selected by making use of the "redundancy" in the genetic code.
Various codon
substitutions, such as the silent changes which produce various restriction
sites, may be
introduced to optimize cloning into a plasmid or viral vector or expression in
a particular
prokaryotic or eukaryotic system. Mutations in the polynucleotide sequence may
be reflected
in the polypeptide or domains of other peptides added to the polypeptide to
modify the
properties of any part of the polypeptide, to change characteristics such as
ligand-binding
affinities, interchain affinities, or degradationlturnover rate.
Preferably, amino acid "substitutions" are the result of replacing one amino
acid with
another amino acid having similar structural and/or chemical properties, i. e.
, conservative
amino acid replacements. "Conservative" amino acid substitutions may be made
on the basis
of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity,
andlor the
amphipathic nature of the residues involved. For example, nonpolar
(hydrophobic) amino
acids include alanine, leucine, isoleucine, valine, proline, phenylalanine,
tryptophan, and
methionine; polar neutral amino acids include glycine, serine, threonine,
cysteine, tyrosine,
asparagine, and glutamine; positively charged (basic) amino acids include
arginine, lysine, and
histidine; and negatively charged (acidic) amino acids include aspartic acid
and glutamic acid.
"Insertions" or "deletions" are preferably in the range of about 1 to 20 amino
acids, more
preferably 1 to 10 amino acids. The variation allowed may be experimentally
determined by
systematically making insertions, deletions, or substitutions of amino acids
in a polypeptide
molecule using recombinant DNA techniques and assaying the resulting
recombinant variants
for activity.
Alternatively, where alteration of function is desired, insertions, deletions
or non-
conservative alterations can be engineered to produce altered polypeptides.
Such alterations
can, for example, alter one or more of the biological functions or biochemical
characteristics
of the polypeptides of the invention. For example, such alterations may change
polypeptide
characteristics such as ligand-binding affinities, interchain affinities, or
degradation/turnover
rate. Further, such alterations can be selected so as to generate polypeptides
that are better
suited for expression, scale up and the like in the host cells chosen for
expression. For
example, cysteine residues can be deleted or substituted with another amino
acid residue in
order to eliminate disulfide bridges.
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The terms "purified" or "substantially purified" as used herein denotes that
the
indicated nucleic acid or polypeptide is present in the substantial absence of
other biological
macromolecules, e. g. , polynucleotides, proteins, and the like. In one
embodiment, the
polynucleotide or polypeptide is purified such that it constitutes at least 95
% by weight, more
preferably at least 99 % by weight, of the indicated biological macromolecules
present (but
water, buffers, and other small molecules, especially molecules having a
molecular weight of
less than 1000 daltons, can be present).
The term "isolated" as used herein refers to a nucleic acid or polypeptide
separated
from at least one other component (e.g., nucleic acid or polypeptide) present
with the nucleic
acid or polypeptide in its natural source. In one embodiment, the nucleic acid
or polypeptide
is found in the' presence of (if anything) only a solvent, buffer, ion, or
other components
normally present in a solution of the same. The terms "isolated" and
"purified" do not
encompass nucleic acids or polypeptides present in their natural source.
The term "recombinant," when used herein to refer to a polypeptide or protein,
means
that a polypeptide or protein is derived from recombinant (e. g. , microbial,
insect, or
mammalian) expression systems. "Microbial" refers to recombinant polypeptides
or proteins
made in bacterial or fungal (e.g., yeast) expression systems. As a product,
"recombinant
microbial" defines a polypeptide or protein essentially free of native
endogenous substances
and unaccompanied by associated native glycosylation. Polypeptides or proteins
expressed in
most bacterial cultures, e.g., E. coli, will be free of glycosylation
modifications; polypeptides
or proteins expressed in yeast will have a glycosylation pattern in general
different from those
expressed in mammalian cells.
The term "recombinant expression vehicle or vector" refers to a plasmid or
phage or
virus or vector, for expressing a polypeptide from a DNA (RNA) sequence. An
expression
vehicle can comprise a transeriptional unit comprising an assembly of (1) a
genetic element or
elements having a regulatory role in gene expression, for example, promoters
or enhancers, (2)
a structural or coding sequence which is transcribed into mRNA and translated
into protein,
and (3) appropriate transcription initiation and termination sequences.
Structural units intended
for use in yeast or eukaryotic expression systems preferably include a leader
sequence enabling
extraeellular secretion of translated protein by a host cell. Alternatively,
where recombinant
protein is expressed without a leader or transport sequence, it may include an
amino terminal
methionine residue. This residue may or may not be subsequently cleaved from
the expressed
recombinant protein to provide a final product.
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The term "recombinant expression system" means host cells which have stably
integrated a recombinant transcriptional unit into chromosomal DNA or carry
the recombinant
transcriptional unit extrachromosomally. Recombinant expression systems as
defined herein
will express heterologous polypeptides or proteins upon induction of the
regulatory elements
linked to the DNA segment or synthetic gene to be expressed. This term also
means host cells
which have stably integrated a recombinant genetic element or elements having
a regulatory
role in gene expression, for example, promoters or enhancers. Recombinant
expression
systems as defined herein will express polypeptides or proteins endogenous to
the cell upon
induction of the regulatory elements linked to the endogenous DNA segment or
gene to be
expressed. The cells can be prokaryotic or eukaryotic.
The term "secreted" includes a protein that is transported across or through a
membrane, including transport as a result of signal sequences in its amino
acid sequence when
it is expressed in a suitable host cell. "Secreted" proteins include without
limitation proteins
secreted wholly (e. g. , soluble proteins) or partially (e. g. , receptors)
from the cell in which
they are expressed. "Secreted" proteins also include without limitation
proteins that are
transported across the membrane of the endoplasmic reticulum. "Secreted"
proteins are also
intended to include proteins containing non-typical signal sequences (e.g.
Interleukin-1 Beta,
see Krasney, P.A. and Young, P.R. (1992) Cytokine 4(2):134 -143) and factors
released from
damaged cells (e.g. Interleukin-1 Receptor Antagonist, see Arend, W.P. et. al.
(1998) Annu.
Rev.Immuno1.16:27-55)
Where desired, an expression vector may be designed to contain a "signal or
leader
sequence" which will direct the polypeptide through the membrane of a cell.
Such a sequence
may be naturally present on the polypeptides of the present invention or
provided from
heterologous protein sources by recombinant DNA techniques.
The term "stringent" is used to refer to conditions that are commonly
understood in the
art as stringent. Stringent conditions can include highly stringent conditions
(i.e.,
hybridization to filter-bound DNA in 0.5 M NaHP04, 7 % sodium dodecyl sulfate
(SDS), 1
mM EDTA at 65°C, and washing in O.1X SSClO.l % SDS at 68°C), and
moderately stringent
conditions (i.e., washing in 0.2X SSC/0.1 % SDS at 42°C). Other
exemplary hybridization
conditions are described herein in the examples.
In instances of hybridization of deoxyoligonucleotides, additional exemplary
stringent
hybridization conditions include washing in 6X SSC/0.05 % sodium pyrophosphate
at 37°C (for
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14-base oligonucleotides), 48°C (for 17-base oligonucleotides),
55°C (for 20-base
oligonucleotides), and 60°C (for 23-base oligonucleotides).
As used herein, "substantially equivalent" or "substantially similar" can
refer both to .
nucleotide and amino acid sequences, for example a mutant sequence, that
varies from a
reference sequence by one or more substitutions, deletions, or additions, the
net effect of
which does not result in an adverse functional dissimilarity between the
reference and subject
sequences. Typically, such a substantially equivalent sequence varies from one
of those listed
herein by no more than about 35 % (i. e. , the number of individual residue
substitutions,
additions, and/or deletions in a substantially equivalent sequence, as
compared to the
corresponding reference sequence, divided by the total number of residues in
the substantially
equivalent sequence is about 0.35 or less). Such a sequence is said to have 65
% sequence
identity to the listed sequence. In one embodiment, a substantially
equivalent, e. g. , mutant,
sequence of the invention varies from a listed sequence by no more than 30%
(70% sequence
identity); in a variation of this embodiment, by no more than 25 % (75 %
sequence identity);
and in a further variation of this embodiment, by no more than 20 % (80 %
sequence identity)
and in a further variation of this embodiment, by no more than 10% (90%
sequence identity)
and in a further variation of this embodiment, by no more that 5 % (95 %
sequence identity).
Substantially equivalent, e. g. , mutant, amino acid sequences according to
the invention
preferably have at least 80 % sequence identity with a listed amino acid
sequence, more
preferably at least 85 % sequence identity, more preferably at least 90 %
sequence identity,
more preferably at least 95 % sequence identity, more preferably at least 98 %
sequence
identity, and most preferably at least 99% sequence identity. Substantially
equivalent
nucleotide sequence of the invention can have lower percent sequence
identities, taking into
account, for example, the redundancy or degeneracy of the genetic code.
Preferably, the
nucleotide sequence has at least about 65 % identity, more preferably at least
about 75
identity, more preferably at least about 80% sequence identity, more
preferably at least 85%
sequence identity, more preferably at least 90 % sequence identity, more
preferably at least
about 95 % sequence identity, more preferably at least 98 % sequence identity,
and most
preferably at least 99 % sequence identity. For the purposes of the present
invention,
sequences having substantially equivalent biological activity and
substantially equivalent
r
expression characteristics are considered substantially equivalent. For the
purposes of
determining equivalence, truncation of the mature sequence (e. g. , via a
mutation which creates
a spurious stop codon) should be disregarded. Sequence identity may be
determined, e.g.,
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using the Jotun Hein method (Hero, J. (1990) Methods Enzymol. 183:626-645).
Identity
between sequences can also be determined by other methods known in the art,
e.g. by varying
hybridization conditions.
The term "totipotent" refers to the capability of a cell to differentiate into
all of the cell
types of an adult organism.
The term "transformation" means introducing DNA into a suitable host cell so
that the
DNA is replicable, either as an extrachromosomal element, or by chromosomal
integration.
The term "transfection" refers to the taking up of an expression vector by a
suitable host cell,
whether or not any coding sequences are in fact expressed. The term
"infection" refers to the
introduction of nucleic acids into a suitable host cell by use of a virus or
viral vector.
As used herein, an "uptake modulating fragment," UMF, means a series of
nucleotides
which mediate the uptake of a linked DNA fragment into a cell. UMFs can be
readily
identified using known UMFs as a target sequence or target motif with the
computer-based
systems described below. The presence and activity of a UMF can be confirmed
by attaching
the suspected UMF to a marker sequence. The resulting nucleic acid molecule is
then
incubated with an appropriate host under appropriate conditions and the uptake
of the marker
sequence is determined. As described above, a UMF will increase the frequency
of uptake of
a linked marker sequence.
Each of the above terms is meant to encompass all that is described for each,
unless the
context dictates otherwise.
5.2 NUCLEIC ACIDS OF THE INVENTION
The invention is based on the discovery of a novel secreted
metallocarboxypeptidase-
like polypeptide, the polynucleotides encoding the metallocarboxypeptidase-
like polypeptide
and the use of these compositions for the diagnosis, treatment or prevention
of conditions and
disorders relating to peptide hormone imbalances and disorders.
The isolated polynucleotides of the invention include, but are not limited to
a
polynucleotide comprising any of the nucleotide sequences of SEQ ID NO: 1-3,
5, 23, or 26; a
fragment of SEQ ID NO: 1-3, 5, 23, or 26; a polynucleotide comprising the full
length protein
coding sequence of SEQ ID NO: 1-3, 5, 23, or 26 (for example SEQ ID NO: 4 or
24); and a
polynucleotide comprising the nucleotide sequence encoding the mature protein
coding
sequence of the polynucleotides of any one of SEQ ID NO: 1-3, 5, 23, or 26.
The
polynucleotides of the present invention also include, but are not limited to,
a polynucleotide
that hybridizes under stringent conditions to (a) the complement of any of the
nucleotides
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sequences of the SEQ ID NO: 1-3, 5, 23, or 26; (b) a polynucleotide encoding
any one of the
polypeptides of SEQ ID NO: 4, 6-19, 24 - 25, or 27; (c) a polynucleotide which
is an allelic
variant of any polynucleotides recited above; (d) a polynucleotide which
encodes a species
homolog of any of the proteins recited above; or (e) a polynucleotide that
encodes a
polypeptide comprising a specific domain or truncation of the polypeptides of
SEQ ID NO: 4,
6-19, 24 - 25, or 27. Domains of interest may depend on the nature of the
encoded
polypeptide; e.g., domains in receptor-like polypeptides include ligand-
binding, extracellular,
transmembrane, or cytoplasmic domains, or combinations thereof; domains in
immunoglobulin-like proteins include the variable immunoglobulin-like domains;
domains in
enzyme-like polypeptides include catalytic and substrate binding domains; and
domains in
ligand polypeptides include receptor-binding domains.
The polynucleotides of the invention include naturally occurring or wholly or
partially
synthetic DNA, e.g., cDNA and genomic DNA, and RNA, e.g., mRNA. The
polynucleotides
may include all of the coding region of the cDNA or may represent a portion of
the coding
region of the cDNA.
The present invention also provides genes corresponding to the cDNA sequences
disclosed
herein. The corresponding genes can be isolated in accordance with known
methods using the
sequence information disclosed herein. Such methods include the preparation of
probes or
primers from the disclosed sequence information for identification and/or
amplification of genes
in appropriate genomic libraries or other sources of genomic materials.
Further 5' and 3'
sequence can be obtained using methods known in the art. For example, full
length cDNA or
genomic DNA that corresponds to any of the polynucleotides of the SEQ ID NO: 1-
3, 5, 23, or
26 can be obtained by screening appropriate cDNA or genomic DNA libraries
under suitable
hybridization conditions using any of the polynucleoddes of the SEQ ID NO: 1-
3, 5, 23, or 26 or
a portion thereof as a probe. Alternatively, the polynucleotides of the SEQ ID
NO: 1-3, 5, 23, or
26 may be used as the basis for suitable primers) that allow identification
and/or amplification of
genes in appropriate genomic DNA or cDNA libraries.
The nucleic acid sequences of the invention can be assembled from ESTs and
sequences
(including cDNA and genomic sequences) obtained from one or more public
databases, such as
dbEST, gbpri, and UniGene. The EST sequences can provide identifying sequence
information,
representative fragment or segment information, or novel segment information
for the full-length
gene.
The polynucleotides of the invention also provide polynucleotides including
nucleotide
sequences that are substantially equivalent to the polynucleotides recited
above.
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Polynucleotides according to the invention can have, e. g. , at least about 65
% , at least about
70 % , at least about 75 % , at least about 80 %o , 81 % , 82 % , 83 % , 84 %
, more typically at least
about 85 %o , 86 % , 87 % , 88 % , 89 % , more typically at least about 90 % ,
91 % , 92 % , 93 % ,
94 % , and even more typically at least about 95 % , 96 % , 97 % , 98 % , 99 %
sequence identity to
a polynucleotide recited above.
Included within the scope of the nucleic acid sequences of the invention are
nucleic acid
sequence fragments that hybridize under stringent conditions to any of the
nucleotide sequences
of the SEQ ID NO: 1-3, 5, 23, or 26, or complements thereof, which fragment is
greater than
about 5 nucleotides, preferably 7 nucleotides, more preferably greater than 9
nucleotides and
most preferably greater than 17 nucleotides. Fragments of, e.g. 15, 17, or 20
nucleotides or
more that are selective for (i.e. specifically hybridize to any one of the
polynucleotides of the
invention) are contemplated. Probes capable of specifically hybridizing to a
polynucleotide can
differentiate polynucleotide sequences of the invention from other
polynucleotide sequences in
the same family of genes or can differentiate human genes from genes of other
species, and are
preferably based on unique nucleotide sequences.
The sequences falling within the scope of the present invention are not
limited to these
specific sequences, but also include allelic and species variations thereof.
Allelic and species
variations can be routinely determined by comparing the sequence provided in
SEQ ID NO: 1-3,
5, 23, or 26, a representative fragment thereof, or a nucleotide sequence at
least 90% identical,
preferably 95 % identical, to SEQ ID NO: 1-3, 5, 23, or 26 with a sequence
from another isolate
of the same species. Furthermore, to accommodate codon variability, the
invention includes
nucleic acid molecules coding for the same amino acid sequences as do the
specific ORFs
disclosed herein. In other words, in the coding region of an ORF, substitution
of one codon for
another codon that encodes the same amino acid is expressly contemplated.
The nearest neighbor result for the nucleic acids of the present invention,
including SEQ
ID NO: 1-3, 5, 23, or 26, can be obtained by searching a database using an
algorithm or a
program. Preferably, a BLAST which stands for Basic Local Alignment Search
Tool is used to
search for local sequence alignments (Altshul, S.F. J Mol. Evol. 36 290-300
(1993) and Altschul
S.F. et al. J. Mol. Biol. 21:403-410 (1990))
Species homologs (or orthologs) of the disclosed polynucleotides and proteins
are also
provided by the present invention. 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 from the desired species.
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The invention also encompasses allelic variants of the disclosed
polynucleotides or
proteins; that is, naturally-occurring alternative forms of the isolated
polynucleotide which also
encode proteins which are identical, homologous or related to that encoded by
the
polynucleotides .
The nucleic acid sequences of the invention are further directed to sequences
which
encode variants of the described nucleic acids. These amino acid sequence
variants may be
prepared by methods known in the art by introducing appropriate nucleotide
changes into a
native or variant polynucleotide. There are two variables in the construction
of amino acid
sequence variants: the location of the mutation and the nature of the
mutation. Nucleic acids
encoding the amino acid sequence variants are preferably constructed by
mutating the
polynucleotide to encode an amino acid sequence that does not occur in nature.
These nucleic
acid alterations can be made at sites that differ in the nucleic acids from
different species
(variable positions) or in highly conserved regions (constant regions). Sites
at such locations
will typically be modified in series, e. g., by substituting first with
conservative choices (e. g. ,
hydrophobic amino acid to a different hydrophobic amino acid) and then with
more distant
choices (e. g. , hydrophobic amino acid to a charged amino acid), and then
deletions or
insertions may be made at the target site. Amino acid sequence deletions
generally range from
about 1 to 30 residues, preferably about 1 to 10 residues, and are typically
contiguous. Amino
acid insertions include amino- and/or carboxyl-terminal fusions ranging in
length from one to
one hundred or more residues, as well as intrasequence insertions of single or
multiple amino
acid residues. Intrasequence insertions may range generally from about 1 to 10
amino
residues, preferably from 1 to 5 residues. Examples of terminal insertions
include the
heterologous signal sequences necessary for secretion or for intracellular
targeting in different
host cells and sequences such as FLAG or poly-histidine sequences useful for
purifying the
expressed protein.
In a preferred method, polynucleotides encoding the novel amino acid sequences
are
changed via site-directed mutagenesis. This method uses oligonucleotide
sequences to alter a
polynucleotide to encode the desired amino acid variant, as well as sufficient
adjacent
nucleotides on both sides of the changed amino acid to form a stable duplex on
either side of
the site being changed. In general, the techniques of site-directed
mutagenesis are well known
to those of skill in the art and this technique is exemplified by publications
such as, Edelman et
al., DNA 2:183 (1983). A versatile and efficient method for producing site-
specific changes in
a polynucleotide sequence was published by Zoller and Smith, Nucleic Acids
Res. 10:6487-
6500 (1982). PCR may also be used to create amino acid sequence variants of
the novel
CA 02399672 2002-08-02
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nucleic acids. When small amounts of template DNA are used as starting
material, primers)
that differs slightly in sequence from the corresponding region in the
template DNA can °
generate the desired amino acid variant. PCR amplification results in a
population of product
DNA fragments that differ from the polynucleotide template encoding the
polypeptide at the
position specified by the primer. The product DNA fragments replace the
corresponding
region in the plasmid and this gives a polynucleotide encoding the desired
amino acid variant.
A further technique for generating amino acid variants is the cassette
mutagenesis
technique described in Wells et al., Gene 34:315 (1985); and other mutagenesis
techniques
well known in the art, such as, for example, the techniques in Sambrook et
al., supra, and
Current Protocols in Molecular Biology, Ausubel et al. Due to the inherent
degeneracy of the
genetic code, other DNA sequences which encode substantially the same or a
functionally
equivalent amino acid sequence may be used in the practice of the invention
for the cloning and
expression of these novel nucleic acids. Such DNA sequences include those
which are capable
of hybridizing to the appropriate novel nucleic acid sequence under stringent
conditions.
Polynucleotides encoding preferred polypeptide truncations of the invention
can be used
to generate polynucleotides encoding chimeric or fusion proteins comprising
one or more
domains of the invention and heterologous protein sequences.
The polynucleotides of the invention additionally include the complement of
any of the
polynucleotides recited above. The polynucleotide can be DNA (genomic, cDNA,
amplified,
or synthetic) or RNA. Methods and algorithms for obtaining such
polynucleotides are well
known to those of skill in the art and can include, for example, methods for
determining
hybridization conditions that can routinely isolate polynucleotides of the
desired sequence
identities.
In accordance with the invention, polynucleotide sequences comprising the
mature
protein coding sequences corresponding to any one of SEQ ID NO: 4, 6-19, 24 -
25, or 27 or
functional equivalents thereof, may be used to generate recombinant DNA
molecules that
direct the expression of that nucleic acid, or a functional equivalent
thereof, in appropriate host
cells. Also included are the cDNA inserts of any of the clones identified
herein.
A polynucleotide according to the invention can be joined to any of a variety
of other
nucleotide sequences by well-established recombinant DNA techniques (see
Sambrook J et al.
(1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory,
NY).
Useful nucleotide sequences for joining to polynucleotides include an
assortment of vectors,
e.g., plasmids, cosmids, lambda phage derivatives, phagemids, and the like,
that are well
known in the art. Accordingly, the invention also provides a vector including
a polynucleotide
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of the invention and a host cell containing the polynucleotide. In general,
the vector contains
an origin of replication functional in at least one organism, convenient
restriction endonuclease
sites, and a selectable marker for the host cell. Vectors according to the
invention include
expression vectors, replication vectors, probe generation vectors, and
sequencing vectors. A
host cell according to the invention can be a prokaryotic or eukaryotic cell
and can be a
unicellular organism or part of a multicellular organism.
The present invention further provides recombinant constructs comprising a
nucleic
acid having any of the nucleotide sequences of the SEQ ID NO: 1-3, 5, 23, or
26 or a
fragment thereof or any other polynucleotides of the invention. In one
embodiment, the
recombinant constructs of the present invention comprise a vector, such as a
plasmid or viral
vector, into which a nucleic acid having any of the nucleotide sequences of
the SEQ ID NO: 1-
3, 5, 23, or 26 or a fragment thereof is inserted, in a forward or reverse
orientation. In the
case of a vector comprising one of the ORFs of the present invention, the
vector may further
comprise regulatory sequences, including for example, a promoter, operably
linked to the
ORF. Large numbers of suitable vectors and promoters are known to those of
skill in the art
and are commercially available for generating the recombinant constructs of
the present
invention. The following vectors are provided by way of example. Bacterial:
pBs,
phagescript, PsiX174, pBluescript SK, pBs KS, pNHBa, pNHl6a, pNHl8a, pNH46a
(Stratagene); pTrc99A, pKK223-3, pKK233-3, pDR540, pRITS (Pharmacia).
Eukaryotic:
pWLneo, pSV2cat, pOG44, PXTI, pSG (Stratagene) pSVK3, pBPV, pMSG, pSVL
(Pharmacia) .
The isolated polynucleotide of the invention may be operably linked to an
expression
control sequence such as the pMT2 or pED expression vectors disclosed in
Kaufman et al.,
Nucleic Acids Res. 19, 4485-4490 (1991), in order to produce the protein
recombinantly.
Many suitable expression control sequences are known in the art. General
methods of
expressing recombinant proteins are also known and are exemplified in R.
Kaufman, Methods
i~ Enzymology 185, 537-566 (1990). As defined herein "operably linked" means
that the
isolated polynucleotide of the invention and an expression control sequence
are situated within
a vector or cell in such a way that the protein is expressed by a host cell
which has been
transformed (transfected) with the ligated polynucleotidelexpression control
sequence.
Promoter regions can be selected from any desired gene using CAT
(chloramphenicol
transferase) vectors or other vectors with selectable markers. Two appropriate
vectors are
pKK232-8 and pCM7. Particular named bacterial promoters include lacI, lacZ,
T3, T7, gpt,
lambda PR, and trc. Eukaryotic promoters include CMV immediate early, HSV
thymidine
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kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-
I. Selection of
the appropriate vector and promoter is well within the level of ordinary skill
in the art.
Generally, recombinant expression vectors will include origins of replication
and selectable
markers permitting transformation of the host cell, e. g. , the ampicillin
resistance gene of E.
coli and S. cerevisiae TRPl gene, and a promoter derived from a highly
expressed gene to
direct transcription of a downstream structural sequence. Such promoters can
be derived from
operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), a-
factor, acid
phosphatase, or heat shock proteins, among others. The heterologous structural
sequence is
assembled in appropriate phase with translation initiation and termination
sequences, and
preferably, a leader sequence capable of directing secretion of translated
protein into the
periplasmic space or extracellular medium. Optionally, the heterologous
sequence can encode
a fusion protein including an amino terminal identification peptide imparting
desired
characteristics, e. g. , stabilization or simplified purification of expressed
recombinant product. ,
Useful expression vectors for bacterial use are constructed by inserting a
structural DNA
sequence encoding a desired protein together with suitable translation
initiation and termination
signals in operable reading phase with a functional promoter. The vector will
comprise one or
more phenotypic selectable markers and an origin of replication to ensure
maintenance of the
vector and to, if desirable, provide amplification within the host. Suitable
prokaryotic hosts
for transformation include E. coli, Bacillus subtilis, Salmonella typhimurium
and various
species within the genera Pseudomonas, Streptomyces, and Staphylococcus,
although others
may also be employed as a matter of choice.
As a representative but non-limiting example, useful expression vectors for
bacterial
use can comprise a selectable marker and bacterial origin of replication
derived from
commercially available plasmids comprising genetic elements of the well known
cloning vector
pBR322 (ATCC 37017). Such commercial vectors include, for example, pKK223-3
(Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM 1 (Promega Biotech,
Madison, WI,
USA). These pBR322 "backbone" sections are combined with an appropriate
promoter and
the structural sequence to be expressed. Following transformation of a
suitable host strain and
growth of the host strain to an appropriate cell density, the selected
promoter is induced or
3 0 derepressed by appropriate means (e. g. , temperature shift or chemical
induction) and cells are
cultured for an additional period. Cells are typically harvested by
centrifugation, disrupted by
physical or chemical means, and the resulting crude extract retained for
further purification.
Polynucleotides of the invention can also be used to induce immune responses.
For
example, as described in Fan et al., Nat. Biotech. 17:870-872 (1999),
incorporated herein by
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reference, nucleic acid sequences encoding a polypeptide may be used to
generate antibodies
against the encoded polypeptide following topical administration of naked
plasmid DNA or
following injection, and preferably intramuscular injection of the DNA. The
nucleic acid
sequences are preferably inserted in a recombinant expression vector and may
be in the form
of naked DNA.
5.3 ANTISENSE
Another aspect of the invention pertains to isolated antisense nucleic acid
molecules that
are hybridizable to or complementary to the nucleic acid molecule comprising
the nucleotide
sequence of SEQ ID NO: 1-3, 5, 23, or 26, or fragments, analogs or derivatives
thereof. An
"antisense" nucleic acid comprises a nucleotide sequence that is complementary
to a "sense"
nucleic acid encoding a protein, e. g. , complementary to the coding strand of
a double-stranded
cDNA molecule or complementary to an mRNA sequence. In specific aspects,
antisense
nucleic acid molecules are provided that comprise a sequence complementary to
at least about
10, 25, 50, 100, 250 or 500 nucleotides or an entire coding strand, or to only
a portion
thereof. Nucleic acid molecules encoding fragments, homologs, derivatives and
analogs of a
protein of any of SEQ ID NO: 1-3, 5, ~23, or 26 or antisense nucleic acids
complementary to a
nucleic acid sequence of SEQ ID NO: 1-3, 5, 23, or 26 are additionally
provided.
In one embodiment, an antisense nucleic acid molecule is antisense to a
"coding region"
of the coding strand of a nucleotide sequence of the invention. The term
"coding region"
refers to the region of the nucleotide sequence comprising codons which are
translated into
amino acid residues. In another embodiment, the antisense nucleic acid
molecule is antisense to
a "noncoding region" of the coding strand of a nucleotide sequence of the
invention. The term
"noncoding region" refers to 5' and 3' sequences that flank the coding region
that are not
translated into amino acids (i. e. , also referred to as 5' and 3'
untranslated regions).
Given the coding strand sequences encoding a nucleic acid disclosed herein
(e.g., SEQ
ID NO: 1-3, 5, 23, or 26, antisense nucleic acids of the invention can be
designed according to
the rules of Watson and Crick or Hoogsteen base pairing. The antisense nucleic
acid molecule
can be complementary to the entire coding region of an mRNA, but more
preferably is an
oligonucleotide that is antisense to only a portion of the coding or noncoding
region of an
mRNA. For example, the antisense oligonucleotide can be complementary to the
region
surrounding the translation start site of an mRNA. An antisense
oligonucleotide can be, for
example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length.
An antisense
nucleic acid of the invention can be constructed using chemical synthesis or
enzymatic ligation
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reactions using procedures known in the art. For example, an antisense nucleic
acid (e. g. , an
antisense oligonucleotide) can be chemically synthesized using naturally
occurring nucleotides
or variously modified nucleotides designed to increase the biological
stability of the molecules
or to increase the physical stability of the duplex formed between the
antisense and sense
nucleic acids, e.g., phosphorothioate derivatives and acridine substituted
nucleotides can be
used.
Examples of modified nucleotides that can be used to generate the antisense
nucleic acid
include: 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil,
hypoxanthine, xanthine,
4-acetylcytosine, 5-(carboxyhydroxylinethyl) uracil, 5-
carboxymethylaminomethyl-
2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-
galactosylqueosine,
inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-
dimethylguanine,
2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-
adenine,
7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil,
beta-D-mannosylqueosine, 5'-methoxycarboxymethyluracil, 5-methoxyuracil,
2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine,
pseudouracil,
queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-
methyluracil,
uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-
thiouracil,
3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine.
Alternatively, the
antisense nucleic acid can be produced biologically using an expression vector
into which a
nucleic acid has been subcloned in an antisense orientation (i. e. , RNA
transcribed from the
inserted nucleic acid will be of an antisense orientation to a target nucleic
acid of interest,
described further in the following subsection).
The antisense nucleic acid molecules of the invention are typically
administered to a
subject or generated in situ such that they hybridize with or bind to cellular
mRNA and/or
genomic DNA encoding a protein according to the invention to thereby inhibit
expression of
the protein, e. g. , by inhibiting transcription and/or translation. The
hybridization can be by
conventional nucleotide complementarity to form a stable duplex, or, for
example, in the case
of an antisense nucleic acid molecule that binds to DNA duplexes, through
specific interactions
in the major groove of the double helix. An example of a route of
administration of antisense
nucleic acid molecules of the invention includes direct injection at a tissue
site. Alternatively,
antisense nucleic acid molecules can be modified to target selected cells and
then administered
systemically. For example, for systemic administration, antisense molecules
can be modified
such that they specifically bind to receptors or antigens expressed on a
selected cell surface,
e.g. , by linking the antisense nucleic acid molecules to peptides or
antibodies that bind to cell
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surface receptors or antigens. The antisense nucleic acid molecules can also
be delivered to
cells using the vectors described herein. To achieve sufficient intracellular
concentrations of
antisense molecules, vector constructs in which the antisense nucleic acid
molecule is placed
under the control of a strong pol II or pol III promoter are preferred.
In yet another embodiment, the antisense nucleic acid molecule of the
invention is an
a-anomeric nucleic acid molecule. An a-anomeric nucleic acid molecule forms
specific
double-stranded hybrids with complementary RNA in which, contrary to the usual
a -units, the
strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids Res
15: 6625-6641). The
antisense nucleic acid molecule can also comprise a 2'-o-methylribonucleotide
(moue et al.
(1987) Nucleic Acids Res 15: 6131-6148) or a chimeric RNA -DNA analogue (moue
et al.
(1987) FEBS Lett 215: 327-330).
5.4 RIBOZYMES AND PNA MOIETIES
In still another embodiment, an antisense nucleic acid of the invention is a
ribozyme.
Ribozymes are catalytic RNA molecules with ribonuclease activity that are
capable of cleaving
a single-stranded nucleic acid, such as an mRNA, to which they have a
complementary region.
Thus, ribozymes (e. g. , hammerhead ribozymes (described in Haselhoff and
Gerlach ( 1988)
Nature 334:585-591)) can be used to catalytically cleave mRNA transcripts to
thereby inhibit
translation of an mRNA. A ribozyme having specificity for a nucleic acid of
the invention can
be designed based upon the nucleotide sequence of a DNA disclosed herein (i.
e. , SEQ ID NO:
1-3, 5, 23, or 26). For example, a derivative of Tetrahymena L-19 IVS RNA can
be
constructed in which the nucleotide sequence of the active site is
complementary to the
nucleotide sequence to be cleaved in a SECX-encoding mRNA. See, e. g. , Cech
et al. U. S.
Pat. No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742. Alternatively,
SECX mRNA
can be used to select a catalytic RNA having a specific ribonuclease activity
from a pool of
RNA molecules. See, e.g., Bartel et al., (1993) Science 261:1411-1418.
Alternatively, gene expression can be inhibited by targeting nucleotide
sequences
complementary to the regulatory region (e. g. , promoter and/or enhancers) to
form triple
helical structures that prevent transcription of the gene in target cells. See
generally, Helene.
(1991) Anticancer Drug Des. 6: 569-84; Helene. et al. (1992) Ann. N. Y. Acad.
Sci.
660:27-36; and Maher (1992) Bioassays 14: 807-15.
In various embodiments, the nucleic acids of the invention can be modified at
the base
moiety, sugar moiety or phosphate backbone to improve, e. g. , the stability,
hybridization, or
solubility of the molecule. For example, the deoxyribose phosphate backbone of
the nucleic
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acids can be modified to generate peptide nucleic acids (see Hyrup et al.
(1996) Bioorg Med
Chem 4: 5-231. As used herein, the terms "peptide nucleic acids" or "PNAs"
refer to nucleic
acid mimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone is
replaced by
a pseudopeptide backbone and only the four natural nucleobases are retained.
The neutral
backbone of PNAs has been shown to allow for specific hybridization to DNA and
RNA under
conditions of low ionic strength. The synthesis of PNA oligomers can be
performed using
standard solid phase peptide synthesis protocols as described in Hyrup et al.
(1996) above;
Perry-O'Keefe et al. (1996) PNAS 93: 14670-675.
PNAs of the invention can be used in therapeutic and diagnostic applications.
For
example, PNAs can be used as antisense or antigens agents for sequence-
specific modulation
of gene expression by, e. g. , inducing transcription or translation arrest or
inhibiting
replication. PNAs of the invention can also be used, e. g. , in the analysis
of single base pair
mutations in a gene by, e. g. , PNA directed PCR clamping; as artificial
restriction enzymes
when used in combination with other enzymes, e.g. , Sl nucleases (Hyrup B.
(1996) above); or
as probes or primers for DNA sequence and hybridization (Hyrup et al. (1996),
above;
Perry-O'Keefe (1996), above).
In another embodiment, PNAs of the invention can be modified, e. g. , to
enhance their
stability or cellular uptake, by attaching lipophilic or other helper groups
to PNA, by the
formation of PNA-DNA chimeras, or by the use of liposomes or other techniques
of drug
delivery known in the art. For example, PNA-DNA chimeras can be generated that
may
combine the advantageous properties of PNA and DNA. Such chimeras allow DNA
recognition enzymes, e.g., RNase H and DNA polymerases, to interact with the
DNA portion
while the PNA portion would provide high binding affinity and specificity. PNA-
DNA
chimeras can be linked using linkers of appropriate lengths selected in terms
of base stacking,
number of bonds between the nucleobases, and orientation (Hyrup (1996) above).
The
synthesis of PNA-DNA chimeras can be performed as described in Hyrup (1996)
above and
Finn et al. (1996) Nucl Acids Res 24: 3357-63. For example, a DNA chain can be
synthesized
on a solid support using standard phosphoramidite coupling chemistry, and
modified
nucleoside analogs, e.g., 5'-(4-methoxytrityl)amino-5'-deoxy-thymidine
phosphoramidite, can
be used between the PNA and the 5' end of DNA (Mag et al. (1989) Nucl Acid Res
17:
5973-88). PNA monomers are then coupled in a stepwise manner to produce a
chimeric
molecule with a 5' ,PNA segment and a 3' DNA segment (Finn et al. (1996)
above).
Alternatively, chimeric molecules can be synthesized with a 5' DNA segment and
a 3' PNA
segment. See, Petersen et al. (1975) Bioorg Med Chem Lett 5: 1119-11124.
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In other embodiments, the oligonucleotide may include other appended groups
such as
peptides (e. g. , for targeting host cell receptors in vivo), or agents
facilitating transport across
the cell membrane (see, e. g. , Letsinger et al., 1989, Proc. Natl. Acad. Sci.
U. S.A.
86:6553-6556; Lemaitre et al., 1987, Proc. Natl. Acad. Sci. 84:648-652; PCT
Publication No.
W088109810) or the blood-brain barrier (see, e.g., PCT Publication No.
W089/10134). In
addition, oligonucleotides can be modified with hybridization triggered
cleavage agents (See,
e. g. , Krol et al. , 1988, BioTechniques 6:958-976) or intercalating agents.
(See, e. g. , Zon,
1988, Pharm. Res. 5: 539-549). To this end, the oligonucleotide may be
conjugated to another
molecule, e.g., a peptide, a hybridization triggered cross-linking agent, a
transport agent, a
hybridization-triggered cleavage agent, etc.
5.5 HOSTS
The present invention further provides host cells genetically engineered to
contain the
polynucleotides of the invention. For example, such host cells may contain
nucleic acids of the
invention introduced into the host cell using known transformation,
transfection or infection
methods. The present invention still further provides host cells genetically
engineered to
express the polynucleotides of the invention, wherein such polynucleotides are
in operative
association with a regulatory sequence heterologous to the host cell which
drives expression of
the polynucleotides in the cell.
Knowledge of metallocarboxypeptidase-like DNA sequences allows for
modification of
cells to permit, or increase, expression of metallocarboxypeptidase-like
polypeptide. Cells can
be modified (e.g., by homologous recombination) to provide increased
metallocarboxypeptidase-like polypeptide expression by replacing, in whole or
in part, the
naturally occurring metallocarboxypeptidase-like promoter with all or part of
a heterologous
promoter so that the cells metallocarboxypeptidase-like polypeptide is
expressed at higher
levels. The heterologous promoter is inserted in such a manner that it is
operatively linked to
metallocarboxypeptidase-like encoding sequences. See, for example, PCT
International
Publication No. W094/12650, PCT International Publication No. W092/20808, and
PCT
International Publication No. W091/09955. It is also contemplated that, in
addition to
heterologous promoter DNA, amplifiable marker DNA (e.g., ada, dhfr, and the
multifunctional CAD gene which encodes carbamyl phosphate synthase, aspartate
transcarbamylase, and dihydroorotase) andlor intron DNA may be inserted along
with the
heterologous promoter DNA. If linked to the metallocarboxypeptidase-like
coding sequence,
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amplification of the marker DNA by standard selection methods results in co-
amplification of
the metallocarboxypeptidase-like coding sequences in the cells.
The host cell can be a higher eukaryotic host cell, such as a mammalian cell,
a lower
eukaryotic host cell., such as a yeast cell, or the host cell can be a
prokaryotic cell, such as a
bacterial cell. Introduction of the recombinant construct into the host cell
can be effected by
calcium phosphate transfection, DEAF, dextran-mediated transfection, or
electroporation
(Davis, L. et al., Basic Methods ih MoleculaY Biology (1986)). The host cells
containing one
of the polynucleotides of the invention, can be used in conventional manners
to produce the
gene product encoded by the isolated fragment (in the case of an ORF) or can
be used to
produce a heterologous protein under the control of the EMF.
Any hostlvector system can be used to express one or more of the ORFs of the
present
invention. These .include, but are not limited to, eukaryotic hosts such as
HeLa cells, Cv-1
cell, COS cells, 293 cells, and Sf9 cells, as well as prokaryotic host such as
E. coli and B.
subtilis. The most preferred cells are those which do not normally express the
particular
polypeptide or protein or which expresses the polypeptide or protein at low
natural level.
Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other
cells under the
control of appropriate promoters. Cell-free translation systems can also be
employed to
produce such proteins using RNAs derived from the DNA constructs of the
present invention.
Appropriate cloning and expression vectors for use with prokaryotic and
eukaryotic hosts are
described by Sambrook, et al. , in Molecular Cloning: A Laboratory Manual,
Second Edition,
Cold Spring Harbor, New York (1989), the disclosure of which is hereby
incorporated by
reference.
Various mammalian cell culture systems can also be employed to express
recombinant
protein. Examples of mammalian expression systems include the COS-7 lines of
monkey
kidney fibroblasts, described by Gluzman, Cell 23:175 (1981). Other cell lines
capable of
expressing a compatible vector are, for example, the C127, monkey COS cells,
Chinese
Hamster Ovary (CHO) cells, human kidney 293 cells, human epidermal A431 cells,
human
Co1o205 cells, 3T3 cells, CV-1 cells, other transformed primate cell lines,
normal diploid
cells, cell strains derived from in vitro culture of primary tissue, primary
explants, HeLa cells,
mouse L cells, BHK, HL-60, U937, HaK or Jurkat cells. Mammalian expression
vectors will
comprise an origin of replication, a suitable promoter and also any necessary
ribosome binding
sites, polyadenylation site, splice donor and acceptor sites, transcriptional
termination
sequences, and 5' flanking nontranscribed sequences. DNA sequences derived
from the SV40
viral genome, for example, SV40 origin, early promoter, enhancer, splice, and
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polyadenylation sites may be used to provide the required nontranscribed
genetic elements.
Recombinant polypeptides and proteins produced in bacterial culture are
usually isolated by
initial extraction from cell pellets, followed by one or more salting-out,
aqueous ion exchange
or size exclusion chromatography steps. Protein refolding steps can be used,
as necessary, in
completing configuration of the mature protein. Finally, high performance
liquid
chromatography (HPLC) can be employed for final purification steps. Microbial
cells
employed in expression of proteins can be disrupted by any convenient method,
including
freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing
agents.
Alternatively, it may be possible to produce the protein in lower eukaryotes
such as
yeast or insects or in prokaryotes such as bacteria. Potentially suitable
yeast strains include
Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces strains,
Cahdida, or
any yeast strain capable of expressing heterologous proteins. Potentially
suitable bacterial
strains include Escherichia coli, Bacillus subtilis, Salmonella typhimurium,
or any bacterial
strain capable of expressing heterologous proteins. If the protein is made in
yeast or bacteria,
it may be necessary to modify the protein produced therein, for example by
phosphorylation or
glycosylation of the appropriate sites, in order to obtain the functional
protein. Such covalent
attachments may be accomplished using known chemical or enzymatic methods.
In another embodiment of the present invention, cells and tissues may be
engineered to
express an endogenous gene comprising the polynucleotides of the invention
under the control
of inducible regulatory elements, in which case the regulatory sequences of
the endogenous
gene may be replaced by homologous recombination. As described herein, gene
targeting can
be used to replace a gene's existing regulatory region with a regulatory
sequence isolated from
a different gene or a novel regulatory sequence synthesized by genetic
engineering methods.
Such regulatory sequences may be comprised of promoters, enhancers, scaffold-
attachment
regions, negative regulatory elements, transcriptional initiation sites,
regulatory protein binding
sites or combinations of said sequences. Alternatively, sequences which affect
the structure or
stability of the RNA or protein produced may be replaced, removed, added, or
otherwise
modified by targeting. These sequence include polyadenylation signals, mRNA
stability
elements, splice sites, leader sequences for enhancing or modifying transport
or secretion
properties of the protein, or other sequences which alter or improve the
function or stability of
protein or RNA molecules.
The targeting event may be a simple insertion of the regulatory sequence,
placing the
gene under the control of the new regulatory sequence, e.g., inserting a new
promoter or
enhancer or both upstream of a gene. Alternatively, the targeting event may be
a simple
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deletion of a regulatory element, such as the deletion of a tissue-specific
negative regulatory
element. Alternatively, the targeting event may replace an existing element;
for example, a
tissue-specific enhancer can be replaced by an enhancer that has broader or
different cell-type
specificity than the naturally occurring elements. Here, the naturally
occurring sequences are
deleted and new sequences are added. In all cases, the identification of the
targeting event may
be facilitated by the use of one or more selectable marker genes that are
contiguous with the
targeting DNA, allowing for the selection of cells in which the exogenous DNA
has integrated
into the host cell genome. The identification of the targeting event may also
be facilitated by
the use of one or more marker genes exhibiting the property of negative
selection, such that the
negatively selectable marker is linked to the exogenous DNA, but configured
such that the
negatively selectable marker flanks the targeting sequence, and such that a
correct homologous
recombination event with sequences in the host cell genome does not result in
the stable
integration of the negatively selectable marker. Markers useful for this
purpose include the
Herpes Simplex Virus thymidine kinase (TK) gene or the bacterial xanthine-
guanine
phosphoribosyl-transferase (gpt) gene.
The gene targeting or gene activation techniques which can be used in
accordance with
this aspect of the invention are more particularly described in U.S. Patent
No. 5,272,071 to
Chappel; U.S. Patent No. 5,578,461 to Sherwin et al.; International
Application No.
PCT/US92/09627 (W093/09222) by Selden et al.; and International Application
No.
PCT/US90/06436 (W091/06667) by Skoultchi et al., each of which is incorporated
by
reference herein in its entirety.
5.6 POLYPEPTIDES OF THE INVENTION
The isolated polypeptides of the invention include, but are not limited to, a
polypeptide
comprising: the amino acid sequence set forth as any one of SEQ ID NO: 4, 6-
19, 24 - 25, or
27 or an amino acid sequence encoded by any one of the nucleotide sequences
SEQ ID NO: 1
3, 5, 23, or 26 or the corresponding full length or mature protein.
Polypeptides of the
invention also include polypeptides preferably with biological or
immunological activity that
are encoded by: (a) a polynucleotide having any one of the nucleotide
sequences set forth in the
SEQ ID NO: 1-3, 5, 23, or 26 or (b) polynucleotides encoding any one of the
amino acid
sequences set forth as SEQ ID NO: 4, 6-19, 24 - 25, 27 or (c) polynucleotides
that hybridize
to the complement of the polynucleotides of either (a) or (b) under stringent
hybridization
conditions. The invention also provides biologically active or immunologically
active variants
of any of the amino acid sequences set forth as SEQ ID NO: 4, 6-19, 24 - 25,
or 27 or the
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corresponding full length or mature protein; and "substantial equivalents"
thereof (e.g., with at
least about 65 % , at least about 70 % , at least about 75 % , at least about
80 % , at least about
85 % , 86 % , 87 % , 88 % , 89 % , at least about 90 % , 91 % , 92 % , 93 % ,
94 % , typically at least
about 95 % , 96 % , 97 % , more typically at least about 98 % , or most
typically at least about
99% amino acid identity) that retain biological activity. Polypeptides encoded
by allelic
variants may have a similar, increased, or decreased activity compared to
polypeptides
comprising SEQ ID NO: 4, 6-19, 24 - 25, or 27.
Fragments of the proteins of the present invention which are capable of
exhibiting
biological activity are also encompassed by the present invention. Fragments
of the protein
may be in linear form or they may be cyclized using known methods, for
example, as
described in H. U. Saragovi, et al., Bio/Technology 10, 773-778 (1992) and in
R. S.
McDowell, et al., J. Amer. Chem. Soc. 114, 9245-9253 (1992), both of which are
incorporated herein by reference. Such fragments may be fused to carrier
molecules such as
immunoglobulins for many purposes, including increasing the valency of protein
binding sites.
The present invention also provides both full-length and mature forms (for
example,
without a signal sequence or precursor sequence) of the disclosed proteins.
The protein coding
sequence is identified in the sequence listing by translation of the disclosed
nucleotide
sequences. The mature form of such protein may be obtained by expression of a
full-length
polynucleotide in a suitable mammalian cell or other host cell. The sequence
of the mature
form of the protein is also determinable from the amino acid sequence of the
full-length form.
Where proteins of the present invention are membrane bound, soluble forms of
the proteins are
also provided. In such forms, part or all of the regions causing the proteins
to be membrane
bound are deleted so that the proteins are fully secreted from the cell in
which it is expressed.
Protein compositions of the present invention may further comprise an
acceptable
carrier, such as a hydrophilic, e.g., pharmaceutically acceptable, carrier.
The present invention further provides isolated polypeptides encoded by the
nucleic
acid fragments of the present invention or by degenerate variants of the
nucleic acid fragments
of the present invention. By "degenerate variant" is intended nucleotide
fragments which
differ from a nucleic acid fragment of the present invention (e. g. , an ORF)
by nucleotide
sequence but, due to the degeneracy of the genetic code, encode an identical
polypeptide
sequence. Preferred nucleic acid fragments of the present invention are the
ORFs that encode
proteins.
A variety of methodologies known in the art can be utilized to obtain any one
of the
isolated polypeptides or proteins of the present invention. At the simplest
level, the amino acid
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sequence can be synthesized using commercially available peptide synthesizers.
The
synthetically-constructed protein sequences, by virtue of sharing primary,
secondary or tertiary
structural and/or conformational characteristics with proteins may possess
biological properties
in common therewith, including protein activity. This technique is
particularly useful in
producing small peptides and fragments of larger polypeptides. Fragments are
useful, for
example, in generating antibodies against the native polypeptide. Thus, they
may be employed
as biologically active or immunological substitutes for natural, purified
proteins in screening of
therapeutic compounds and in immunological processes for the development of
antibodies.
The polypeptides and proteins of the present invention can alternatively be
purified
from cells which have been altered to express the desired polypeptide or
protein. As used
herein, a cell is said to be altered to express a desired polypeptide or
protein when the cell,
through genetic manipulation, is made to produce a polypeptide or protein
which it normally
does not produce or which the cell normally produces at a lower level. One
skilled in the art
can readily adapt procedures for introducing and expressing either recombinant
or synthetic
sequences into eukaryotic or prokaryotic cells in order to generate a cell
which produces one of
the polypeptides or proteins of the present invention.
The invention also relates to methods for producing a polypeptide comprising
growing
a culture of host cells of the invention in a suitable culture medium, and
purifying the protein
from the cells or the culture in which the cells are grown. For example, the
methods of the
invention include a process for producing a polypeptide in which a host cell
containing a
suitable expression vector that includes a polynucleotide of the invention is
cultured under
conditions that allow expression of the encoded polypeptide. The polypeptide
can be recovered
from the culture, conveniently from the culture medium, or from a lysate
prepared from the
host cells and further purified. Preferred embodiments include those in which
the protein
produced by such process is a full length or mature form of the protein.
In an alternative method, the polypeptide or protein is purified from
bacterial cells
which naturally produce the polypeptide or protein. One skilled in the art can
readily follow
known methods for isolating polypeptides and proteins in order to obtain one
of the isolated
polypeptides or proteins of the present invention. These include, but are not
limited to,
immunochromatography, HPLC, size-exclusion chromatography, ion-exchange
chromatography, and immuno-affinity chromatography. See, e.g., Scopes, Protein
Purification: Principles and Practice, Springer-Verlag (1994); Sambrook, et
al., in Molecular
Cloning: A Laboratory Manual; Ausubel et al., Current Protocols in Molecular
Biology.
Polypeptide fragments that retain biological/immunological activity include
fragments
3S
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comprising greater than about 100 amino acids, or greater than about 200 amino
acids, and
fragments that encode specific protein domains.
The purified polypeptides can be used in ih vitro binding assays which are
well known
in the art to identify molecules which bind to the polypeptides. These
molecules include but
are not limited to, for e.g., small molecules, molecules from combinatorial
libraries,
antibodies or other proteins. The molecules identified in the binding assay
are then tested for
antagonist or agonist activity in in vivo tissue culture or animal models that
are well known in
the art. In brief, the molecules are titrated into a plurality of cell
cultures or animals and then
tested for either cell/animal death or prolonged survival of the animal/cells.
In addition, the peptides of the invention or molecules capable of binding to
the
peptides may be complexed with toxins, e.g., ricin or cholera, or with other
compounds that
are toxic to cells. The toxin-binding molecule complex is then targeted to a
tumor or other cell
by the specificity of the binding molecule for SEQ ID NO: 4, 6-19, 24 - 25, or
27.
The protein of the invention may also be expressed as a product of transgenic
animals,
e.g., as a component of the milk of transgenic cows, goats, pigs, or sheep
which are
characterized by somatic or germ cells containing a nucleotide sequence
encoding the protein.
The proteins provided herein also include proteins characterized by amino acid
sequences similar to those of purified proteins but into which modification
are naturally
provided or deliberately engineered. For example, modifications, in the
peptide or DNA
sequence, can be made by those skilled in the art using known techniques.
Modifications of
interest in the protein sequences may include the alteration, substitution,
replacement, insertion
or deletion of a selected amino acid residue in the coding sequence. For
example, one or more
of the cysteine residues may be deleted or replaced with another amino acid to
alter the
conformation of the molecule. Techniques for such alteration, substitution,
replacement,
insertion or deletion are well known to those skilled in the art (see, e. g.,
U.S. Pat. No.
4,518,584). Preferably, such alteration, substitution, replacement, insertion
or deletion retains
the desired activity of the protein. Regions of the protein that are important
for the protein
function can be determined by various methods known in the art including the
alanine-scanning
method which involved systematic substitution of single or strings of amino
acids with alanine,
followed by testing the resulting alanine-containing variant for biological
activity. This type of
analysis determines the importance of the substituted amino acids) in
biological activity.
Regions of the protein that are important for protein function may be
determined by the
eMATRIX program.
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Other fragments and derivatives of the sequences of proteins which would be
expected
to retain protein activity in whole or in part and are useful for screening or
other
immunological methodologies may also be easily made by those skilled in the
art given the
disclosures herein. Such modifications are encompassed by the present
invention.
The protein may also be produced by operably linking the isolated
polynucleotide of the
invention to suitable control sequences in one or more insect expression
vectors, and
employing an insect expression system. Materials and methods for
baculovirus/insect cell
expression systems are commercially available in kit form from, e. g. ,
Invitrogen, San Diego,
Calif. , U. S. A. (the MaxBat~' kit), and such methods are well known in the
art, as described in
Summers and Smith, Texas Agricultural Experiment Station Bulletin No. 1555
(1987),
incorporated herein by reference. As used herein, an insect cell capable of
expressing a
polynucleotide of the present invention is "transformed."
The protein of the invention may be prepared by culturing transformed host
cells under
culture conditions suitable to express the recombinant protein. The resulting
expressed protein
may then be purified from such culture (i. e. , from culture medium or cell
extracts) using
known purification processes, such as gel filtration and ion exchange
chromatography. The
purification of the protein may also include an affinity column containing
agents which will
bind to the protein; one or more column steps over such affinity resins as
concanavalin A-
agarose, heparin-toyopearlT"' or Cibacrom blue 3GA SepharoseTM; one or more
steps involving
hydrophobic interaction chromatography using such resins as phenyl ether,
butyl ether, or
propyl ether; or immunoaffinity chromatography.
Alternatively, the protein of the invention may also be expressed in a form
which will
facilitate purification. For example, it may be expressed as a fusion protein,
such as those of
maltose binding protein (MBP), glutathione-S-transferase (GST) or thioredoxin
(TRX), or as a
His tag. Kits for expression and purification of such fusion proteins are
commercially
available from New England BioLab (Beverly, Mass.), Pharmacia (Piscataway,
N.J.) and
Invitrogen, respectively. The protein can also be tagged with an epitope and
subsequently
purified by using a specific antibody directed to such epitope. One such
epitope ("FLAG~")
is commercially available from Kodak (New Haven, Conn.).
Finally, one or more reverse-phase high performance liquid chromatography (RP-
HPLC) steps employing hydrophobic 1ZP-HPLC media, e. g. , silica gel having
pendant methyl
or other aliphatic groups, can be employed to further purify the protein. Some
or all of the
foregoing purification steps, in various combinations, can also be employed to
provide a
substantially homogeneous isolated recombinant protein. The protein thus
purified is
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substantially free of other mammalian proteins and is defined in accordance
with the present
invention as an "isolated protein. "
The polypeptides of the invention include analogs (variants). The polypeptides
of the
invention include metallocarboxypeptidase-like analogs. This embraces
fragments of
metallocarboxypeptidase-like polypeptide of the invention, as well
metallocarboxypeptidase-
like polypeptides which comprise one or more amino acids deleted, inserted, or
substituted.
Also, analogs of the metallocarboxypeptidase-like polypeptide of the invention
embrace fusions
of the metallocarboxypeptidase-like polypeptides or modifications of the
metallocarboxypeptidase-like polypeptides, wherein the metallocarboxypeptidase-
like
polypeptide or analog is fused to another moiety or moieties, e.g., targeting
moiety or another
therapeutic agent. Such analogs may exhibit improved properties such as
activity and/or
stability. Examples of moieties which may be fused to the
metallocarboxypeptidase-like
polypeptide or an analog include, for example, targeting moieties which
provide for the
delivery of polypeptide to neurons, e.g., antibodies to central nervous
system, or antibodies to
receptor and ligands expressed on neuronal cells. Other moieties which may be
fused to
metallocarboxypeptidase-like polypeptide include therapeutic agents which are
used for
treatment, for example anti-depressant drugs or other medications for
neurological disorders.
Also, metallocarboxypeptidase-like polypeptides may be fused to neuron growth
modulators,
and other chemokines for targeted delivery.
5.6.1 DETERMINING POLYPEPTIDE AND POLYNUCLEOTIDE IDENTITY
AND SIMILARITY
Preferred identity and/or similarity are designed to give the largest match
between the
sequences tested. Methods to determine identity and similarity are codified in
computer
programs including, but are not limited to, the GCG program package, including
GAP
(Devereux, J., et al., Nucleic Acids Research 12(1):387 (1984); Genetics
Computer Group,
University of Wisconsin, Madison, WI), BLASTP, BLASTN, BLASTX, PASTA
(Altschul,
S.F. et al., J. Molec. Biol. 215:403-410 (1990), PSI-BLAST (Altschul S.F. et
al., Nucleic
Acids Res. vol. 25, pp. 3389-3402, herein incorporated by reference), eMatrix
software (Wu
et al., J. Comp. Biol., vol. 6, pp. 219-235 (1999), herein incorporated by
reference), eMotif
software (Nevill-Manning et al, ISMB-97, vol 4, pp. 202-209, herein
incorporated by
reference) and the Kyte-Doolittle hydrophobicity prediction algorithm (J. Mol
Biol, 157, pp.
105-31 (1982), incorporated herein by reference). The BLAST programs are
publicly
available from the National Center for Biotechnology Information (NCBI) and
other sources
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(BLAST Manual, Altschul, S., et al. NCB NLM NIH Bethesda, MD 20894; Altschul,
S., et
al., J. Mol. Biol. 215:403-410 (1990).
5.7 CHIMERIC AND FUSION PROTEINS
The invention also provides chimeric or fusion proteins. As used herein, a
"chimeric
protein" or "fusion protein" comprises a polypeptide of the invention
operatively linked to
another polypeptide. Within a fusion protein the polypeptide according to the
invention can
correspond to all or a portion of a protein according to the invention. In one
embodiment, a
. fusion protein comprises at least one biologically active portion of a
protein according to the
invention. In another embodiment, a fusion protein comprises at least two
biologically active
portions of a protein according to the invention. Within the fusion protein,
the term
"operatively linked" is intended to indicate that the polypeptide according to
the invention and
the other polypeptide are fused in-frame to each other. The polypeptide can be
fused to the
N-terminus or C-terminus, or to the middle.
For example, in one embodiment a fusion protein comprises a polypeptide
according to
the invention operably linked to the extracellular domain of a second protein.
In another embodiment, the fusion protein is a GST-fusion protein in which the
polypeptide sequences of the invention are fused to the C-terminus of the GST
(i.e.,
glutathione S-transferase) sequences.
In another embodiment, the fusion protein is an immunoglobulin fusion protein
in
which the polypeptide sequences according to the invention comprise one or
more domains
fused to sequences derived from a member of the immunoglobulin protein family.
The
immunoglobulin fusion proteins of the invention can be incorporated into
pharmaceutical
compositions and administered to a subject to inhibit an interaction between a
ligand and a
protein of the invention on the surface of a cell, to thereby suppress signal
transduction ih vavo.
The immunoglobulin fusion proteins can be used to affect the bioavailability
of a cognate
ligand. Inhibition of the ligand/protein interaction may be useful
therapeutically for both the
treatment of proliferative and differentiative disorders, e.g., cancer as well
as modulating
(e. g. , promoting or inhibiting) cell survival. Moreover, the immunoglobulin
fusion proteins of
the invention can be used as immunogens to produce antibodies in a subject, to
purify ligands,
and in screening assays to identify molecules that inhibit the interaction of
a polypeptide of the
invention with a ligand.
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A chimeric or fusion protein of the invention can be produced by standard
recombinant
DNA techniques. For example, DNA fragments coding for the different
polypeptide
sequences are ligated together in-frame in accordance with conventional
techniques, e. g. , by
employing blunt-ended or stagger-ended termini for ligation, restriction
enzyme digestion to
provide for appropriate termini, filling-in of cohesive ends as appropriate,
alkaline phosphatase
treatment to avoid undesirable joining, and enzymatic ligation. In another
embodiment, the
fusion gene can be synthesized by conventional techniques including automated
DNA
synthesizers. Alternatively, PCR amplification of gene fragments can be
carried out using
anchor primers that give rise to complementary overhangs between two
consecutive gene
fragments that can subsequently be annealed and reamplified to generate a
chimeric gene
sequence (see, for example, Ausubel et al. (eds.) CURRENT PROTOCOLS IN
MOLECULAR
BIOLOGY, John Wiley & Sons, 1992). Moreover, many expression vectors are
commercially
available that already encode a fusion moiety (e. g. , a GST polypeptide). A
nucleic acid
encoding a polypeptide of the invention can be cloned into such an expression
vector such that
the fusion moiety is linked in-frame to the protein of the invention.
5.8 GENE THERAPY
Mutations in the polynucleotides of the invention gene may result in loss of
normal
function of the encoded protein. The invention thus provides gene therapy to
restore normal
activity of the polypeptides of the invention; or to treat disease states
involving polypeptides of
the invention. Delivery of a functional gene encoding polypeptides of the
invention to
appropriate cells is effected ex vivo, its situ, or in vivo by use of vectors,
and more particularly
viral vectors (e.g., adenovirus, adeno-associated virus, or a retrovirus), or
ex vivo by use of
physical DNA transfer methods (e.g., liposomes or chemical treatments). See,
for example,
Anderson, Nature, supplement to vol. 392, no. 6679, pp.25-20 (1998). For
additional reviews
of gene therapy technology see Friedmann, Science, 244: 1275-1281 (1989);
Verma, Scientific
American: 68-84 (1990); and Miller, Nature, 357: 455-460 (1992). Introduction
of any one of
the nucleotides of the present invention or a gene encoding the polypeptides
of the present
invention can also be accomplished with extrachromosomal substrates (transient
expression) or
artificial chromosomes (stable expression). Cells may also be cultured ex vivo
in the presence
of proteins of the present invention in order to proliferate or to produce a
desired effect on or
activity in such cells. Treated cells can then be introduced ih vivo for
therapeutic purposes.
Alternatively, it is contemplated that in other human disease states,
preventing the expression
of or inhibiting the activity of polypeptides of the invention will be useful
in treating the
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disease states. It is contemplated that antisense therapy or gene therapy
could be applied to
negatively regulate the expression of polypeptides of the invention.
Other methods inhibiting expression of a protein include the introduction of
antisense
molecules to the nucleic acids of the present invention, their complements, or
their translated
RNA sequences, by methods known in the art. Further, the polypeptides of the
present invention
can be inhibited by using targeted deletion methods, or the insertion of a
negative regulatory
element such as a silencer, which is tissue specific.
The present invention still further provides cells genetically engineered in
vivo to express
the polynucleotides of the invention, wherein such polynucleotides are in
operative association
with a regulatory sequence heterologous to the host cell which drives
expression of the
polynucleotides in the cell. These methods can be used to increase or decrease
the expression of
the polynucleotides of the present invention.
Knowledge of DNA sequences provided by the invention allows for modification
of cells
to permit, increase, or decrease, expression of endogenous polypeptide. Cells
can be modified
(e.g., by homologous recombination) to provide increased polypeptide
expression by replacing, in
whole or in part, the naturally occurring promoter with all or part of a
heterologous promoter so
that the cells express the protein" at higher levels. The heterologous
promoter is inserted in such a
manner that it is operatively linked to the desired protein encoding
sequences. See, for example,
PCT International Publication No. WO 94/12650, PCT International Publication
No. WO
92/20808, and PCT International Publication No. WO 91109955. It is also
contemplated that, in
addition to heterologous promoter DNA, amplifiable marker DNA (e.g., ada,
dhfr, and the
multifunctional CAD gene which encodes carbamyl phosphate synthase, aspartate
transcarbamylase, and dihydroorotase) and/or intron DNA may be inserted along
with the
heterologous promoter DNA. If linked to the desired protein coding sequence,
amplification of
the marker DNA by standard selection methods results in co-amplification of
the desired protein
coding sequences in the cells.
In another embodiment of the present invention, cells and tissues may be
engineered to
express an endogenous gene comprising the polynucleotides of the invention
under the control of
inducible regulatory elements, in which case the regulatory sequences of the
endogenous gene
may be replaced by homologous recombination. As described herein, gene
targeting can be used
to replace a gene's existing regulatory region with a regulatory sequence
isolated from a different
gene or a novel regulatory sequence synthesized by genetic engineering
methods. Such regulatory
sequences may be comprised of promoters, enhancers, scaffold-
attachmentregions, negative
regulatory elements, transcriptional initiation sites, regulatory protein
binding sites or
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combinations of said sequences. Alternatively, sequences which affect the
structure or stability of
the RNA or protein produced may be replaced, removed, added, or otherwise
modified by
targeting. These sequences include polyadenylation signals, mRNA stability
elements, splice
sites, leader sequences for enhancing or modifying transport or secretion
properties of the protein,
or other sequences which alter or improve the function or stability of protein
or RNA molecules.
The targeting event may be a simple insertion of the regulatory sequence,
placing the gene
under the control of the new regulatory sequence, e.g., inserting a new
promoter or enhancer or
both upstream of a gene. Alternatively, the targeting event may be a simple
deletion of a
regulatory element, such as the deletion of a tissue-specific negative
regulatory element.
Alternatively, the targeting event may replace an existing element; for
example, a tissue-specific
enhancer can be replaced by an enhancer that has broader or different cell-
type specificity than the
naturally occurring elements. Here, the naturally occurring sequences are
deleted and new
sequences are added. In all cases, the identification of the targeting event
may be facilitated by
the use of one or more selectable marker genes that are contiguous with the
targeting DNA,
allowing for the selection of cells in which the exogenous DNA has integrated
into the cell
genome. The identification of the targeting event may also be facilitated by
the use of one or
more marker genes exhibiting the property of negative selection, such that the
negatively
selectable marker is linked to the exogenous DNA, but configured such that the
negatively
selectable marker flanks the targeting sequence, and such that a correct
homologous
recombination event with sequences in the host cell genome does not result in
the stable
integration of the negatively selectable marker. Markers useful for this
purpose include the
Herpes Simplex Virus thymidine kinase (TK) gene or the bacterial xanthine-
guanine
phosphoribosyl-transferase (gpt) gene.
The gene targeting or gene activation techniques which can be used in
accordance with
this aspect of the invention are more particularly described in U.S. Patent
No. 5,272,071 to
Chappel; U.S. Patent No. 5,578,461 to Sherwin et al.; International
Application No.
PCT/US92/09627 (W093/09222) by Selden et al.; and International Application
No.
PCT/US90/06436 (W091/06667) by Skoultchi et al., each of which is incorporated
by reference
herein in its entirety.
5.9 TRANSGENIC ANIMALS
In preferred methods to determine biological functions of the polypeptides of
the
invention in vivo, one or more genes provided by the invention are either over
expressed or
inactivated in the germ line of animals using homologous recombination
[Capecchi, Science
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244:1288-1292 (1989)) . Animals in which the gene is over expressed, under the
regulatory
control of exogenous or endogenous promoter elements, are known as transgenic
animals.
Animals in which an endogenous gene has been inactivated by homologous
recombination are
referred to as "knockout" animals. Knockout animals, preferably non-human
mammals, can be
prepared as described in U.S. Patent No. 5,557,032, incorporated herein by
reference.
Transgenic animals are useful to determine the roles polypeptides of the
invention play in
biological processes, and preferably in disease states. Transgenic animals are
useful as model
systems to identify compounds that modulate lipid metabolism. Transgenic
animals, preferably
non-human mammals, are produced using methods as described in U.S. Patent No
5,489,743
and PCT Publication No. W094/28122, incorporated herein by reference.
Transgenic animals can be prepared wherein all or part of a promoter of the
polynucleotides of the invention is either activated or inactivated to alter
the level of expression
of the polypeptides of the invention. Inactivation can be carried out using
homologous
recombination methods described above. Activation can be achieved by
supplementing or even
replacing the homologous.promoter to provide for increased protein expression.
The
homologous promoter can be supplemented by insertion of one or more
heterologous enhancer
elements known to confer promoter activation in a particular tissue.
The polynucleotides of the present invention also make possible the
development,
through, e.g., homologous recombination or knock out strategies, of animals
that fail to
express functional metallocarboxypeptidase-like polypeptide or that express a
variant of
metallocarboxypeptidase-like polypeptide. Such animals are useful as models
for studying the
in vivo activities of metallocarboxypeptidase-like polypeptide as well as for
studying
modulators of the metallocarboxypeptidase-like polypeptide.
In preferred methods to determine biological functions of the polypeptides of
the
invention ih vivo, one or more genes provided by the invention are either over
expressed or
inactivated in the germ line of animals using homologous recombination
[Capecchi, Science
244:1288-1292 (1989)]. Animals in which the gene is over expressed, under the
regulatory
control of exogenous or endogenous promoter elements, are known as transgen.ic
animals.
Animals in which an endogenous gene has been inactivated by homologous
recombination are
referred to as "knockout" animals. Knockout animals, preferably non-human
mammals, can be
prepared as described in U.S. Patent No. 5,557,032, incorporated herein by
reference.
Transgenic animals are useful to determine the roles polypeptides of the
invention play in
biological processes, and preferably in disease states. Transgenic animals are
useful as model
systems to identify compounds that modulate lipid metabolism. Transgenic
animals, preferably
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non-human mammals, are produced using methods as described in U.S. Patent No
5,489,743
and PCT Publication No. W094/28122, incorporated herein by reference.
Transgenic animals can be prepared wherein all or part of the polynucleotides
of the
invention promoter is either activated or inactivated to alter the level of
expression of the
polypeptides of the invention. Inactivation can be carried out using
homologous recombination
methods described above. Activation can be achieved by supplementing or even
replacing the
homologous promoter to provide for increased protein expression. The
homologous promoter
can be supplemented by insertion of one or more heterologous enhancer elements
known to
confer promoter activation in a particular tissue.
5.10 USES AND BIOLOGICAL ACTIVITY OF HUMAN
METALLOCARBOXYPEPTIDASE-LIKE POLYPEPTIDE
The polynucleotides and proteins of the present invention are expected to
exhibit one or
more of the uses or biological activities (including those associated with
assays cited herein)
identified herein. Uses or activities described for proteins of the present
invention may be
provided by administration or use of such proteins or of polynucleotides
encoding such
proteins (such as, for example, in gene therapies or vectors suitable for
introduction of DNA).
The mechanism underlying the particular condition or pathology will dictate
whether the
polypeptides of the invention, the polynucleotides of the invention or
modulators (activators or
inhibitors) thereof would be beneficial to the subject in need of treatment.
Thus, "therapeutic
compositions of the invention" include compositions comprising isolated
polynucleotides
(including recombinant DNA molecules, cloned genes and degenerate variants
thereof) or
polypeptides of the invention (including full length protein, mature protein
and truncations or
domains thereof), or compounds and other substances that modulate the overall
activity of the
target gene products, either at the level of target gene/protein expression or
target protein
activity. Such modulators include polypeptides, analogs, (variants), including
fragments and
fusion proteins, antibodies and other binding proteins; chemical compounds
that directly or
indirectly activate or inhibit the polypeptides of the invention (identified,
e.g., via drug
screening assays as described herein); antisense polynucleotides and
polynucleotides suitable
for triple helix formation; and in particular antibodies or other binding
partners that
specifically recognize one or more epitopes of the polypeptides of the
invention.
The polypeptides of the present invention may likewise be involved in cellular
activation or in one of the other physiological pathways described herein.
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5.10.1 RESEARCH USES AND UTILITIES
The polynucleotides provided by the present invention can be used by the
research
community for various purposes. The polynucleotides can be used to express
recombinant
protein for analysis, characterization or therapeutic use; as markers for
tissues in which the
corresponding protein is preferentially expressed (either constitutively or at
a particular stage
of tissue differentiation or development or in disease states); as molecular
weight markers on
gels; as chromosome markers or tags (when labeled) to identify chromosomes or
to map
related gene positions; to compare with endogenous DNA sequences in patients
to identify
potential genetic disorders; as probes to hybridize and thus discover novel,
related DNA
sequences; as a source of information to derive PCR primers for genetic
fingerprinting; as a
probe to "subtract-out" known sequences in the process of discovering other
novel
polynucleotides; for selecting and making oligomers for attachment to a "gene
chip" or other
support, including for examination of expression patterns; to raise anti-
protein antibodies using
DNA immunization techniques; and as an antigen to raise anti-DNA antibodies or
elicit another
immune response. Where the polynucleotide encodes a protein which binds or
potentially
binds to another protein (such as, for example, in a receptor-ligand
interaction), the
polynucleotide can also be used in interaction trap assays (such as, for
example, that described
in Gyuris et al., Cell 75:791-803 (1993)) to identify polynucleotides encoding
the other protein
with which binding occurs or to identify inhibitors of the binding
interaction.
The polypeptides provided by the present invention can similarly be used in
assays to
determine biological activity, including in a panel of multiple proteins for
high-throughput
screening; to raise antibodies or to elicit another immune response; as a
reagent (including the
labeled reagent) in assays designed to quantitatively determine levels of the
protein (or its
receptor) in biological fluids; as markers for tissues in which the
corresponding polypeptide is
preferentially expressed (either constitutively or at a particular stage of
tissue differentiation or
development or in a disease state); and, of course, to isolate correlative
receptors or ligands.
Proteins involved in these binding interactions can also be used to screen for
peptide or small
molecule inhibitors or agonists of the binding interaction.
The polypeptides of the invention are also useful for making antibody
substances that
are specifically immunoreactive with°metallocarboxypeptidase-like
proteins. Antibodies and
portions thereof (e.g., Fab fragments) which bind to the polypeptides of the
invention can be
used to identify the presence of such polypeptides in a sample. Such
determinations are
carried out using any suitable immunoassay format, and any polypeptide of the
invention that is
specifically bound by the antibody can be employed as a positive control.
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Any or all of these research utilities are capable of being developed into
reagent grade
or kit format for commercialization as research products.
Methods for performing the uses listed above are well known to those skilled
in the art.
References disclosing such methods include without limitation "Molecular
Cloning: A
Laboratory Manual", 2d ed., Cold Spring Harbor Laboratory Press, Sambrook, J.,
E. F. '
Fritsch and T. Maniatis eds., 1989, and "Methods in Enzymology: Guide to
Molecular
Cloning Techniques", Academic Press, Berger, S. L. and A. R. Kimmel eds.,
1987.
5.10.2 NUTRITIONAL USES
Polynucleotides and polypeptides of the present invention can also be used as
nutritional
sources or supplements. Such uses include without limitation use as a protein
or amino acid
supplement, use as a carbon source, use as a nitrogen source and use as a
source of carbohydrate.
In such cases the polypeptide or polynucleotide of the invention can be added
to the feed of a
particular organism or can be administered as a separate solid or liquid
preparation, such as in the
form of powder, pills, solutions, suspensions or capsules. In the case of
microorganisms, the
polypeptide or polynucleotide of the invention can be added to the medium in
or on which the
microorganism is cultured.
Additionally, the polypeptides of the invention can be used as molecular
weight markers,
and as a food supplement. A polypeptide consisting of SEQ ID NO: 4 or 24, for
example,has a
molecular mass of approximately 41 kDa in its unprocessed and unglycosylated
state. Protein
food supplements are well known and the formulation of suitable food
supplements including
polypeptides of the invention is within the level of skill in the food
preparation art.
5.10.3 CYTOKINE AND CELL PROLIFERATION/DIFFERENTIATION
ACTIVITY
A polypeptide of the present invention may exhibit activity relating to
cytokine, cell
proliferation (either inducing or inhibiting) or cell differentiation (either
inducing or inhibiting)
activity or may induce production of other cytokines in certain cell
populations. A
polynucleotide of the invention can encode a polypeptide exhibiting such
attributes. Many
protein factors discovered to date, including all known cytokines, have
exhibited activity in one
or more factor-dependent cell proliferation assays, and hence the assays serve
as a convenient
confirmation of cytokine activity. The activity of therapeutic compositions of
the present
invention is evidenced by any one of a number of routine factor dependent cell
proliferation
assays for cell lines including, without limitation, 32D, DA2, DA1G, T10, B9,
B9/11, BaF3,
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MC9/G, M+(preB M+), 2E8, RBS, DAl, 123, T1165, HT2, CTLL2, TF-1, Mole, CMK,
HUVEC, and Caco. Therapeutic compositions of the invention can be used in the
following:
Assays for T-cell or thymocyte proliferation include without limitation those
described
in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D.
H.
Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and
Wiley-
Interscience (Chapter 3, Ih VLtYO assays for Mouse Lymphocyte Function 3.1-
3.19; Chapter 7,
Immunologic studies in Humans); Takai et al., J. Immunol. 137:3494-3500, 1986;
Bertagnolli
et al., J. Immunol. 145:1706-1712, 1990; Bertagnolli et al., Cellular
Immunology 133:327-
341, 1991; Bertagnolli, et al., I. Immunol. 149:3778-3783, 1992; Bowman et
al., I. Immunol.
152:1756-1761, 1994.
Assays for cytokine production and/or proliferation of spleen cells, lymph
node cells or
thymocytes include, without limitation, those described in: Polyclonal T cell
stimulation,
Kruisbeek, A. M. and Shevach, E. M. In Current Protocols in Immunology. J. E.
e.a. Coligan
eds. Vol 1 pp. 3.12.1-3.12.14, John Wiley and Sons, Toronto. 1994; and
Measurement of
mouse and human interleukin-y, Schreiber, R. D. In Current Protocols in
Immunology. J. E.
e.a. Coligan eds. Vol 1 pp. 6.8.1-6.8.8, John Wiley and Sons, Toronto. 1994.
Assays for proliferation and differentiation of hematopoietic and
lymphopoietic cells
include, without limitation, those described in: Measurement of Human and
Murine Interleukin
2 and Interleukin 4, Bottomly, K., Davis, L. S. and Lipsky, P. E. In Current
Protocols in
Immunology. J. E. e.a. Coligan eds. Vol 1 pp. 6.3.1-6.3.12, John Wiley and
Sons, Toronto.
1991; deVries et al., J. Exp. Med. 173:1205-1211, 1991; Moreau et al., Nature
336:690-692,
1988; Greenberger et al., Proc. Natl. Acad. Sci. U.S.A. 80:2931-2938, 1983;
Measurement of
mouse and human interleukin 6--Nordan, R. In Current Protocols in Immunology.
J. E.
Coligan eds. Vol 1 pp. 6.6.1-6.6.5, John Wiley and Sons, Toronto. 1991; Smith
et al., Proc.
Natl. Aced. Sci. U.S.A. 83:1857-1861, 1986; Measurement of human Interleukin
11--Bennett,
F., Giannotti, J., Clark, S. C. and Turner, K. J. In Current Protocols in
Immunology. J. E.
Coligan eds. Vol 1 pp. 6.15.1 John Wiley and Sons, Toronto. 1991; Measurement
of mouse
and human Interleulan 9-Ciarletta, A., Giannotti, J., Clark, S. C. and Turner,
K. J. In Current
Protocols in Immunology. J. E. Coligan eds. Vol 1 pp. 6.13.1, John Wiley and
Sons, Toronto.
1991.
Assays for T-cell clone responses to antigens (which will identify, among
others,
proteins that affect APC-T cell interactions as well as direct T-cell effects
by measuring
proliferation and cytokine production) include, without limitation, those
described in: Current
Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D. H.
Margulies, E. M.
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Shevach, W Strober, Pub. Greene Publishing Associates and Wiley-Interscience
(Chapter 3, In
Vitro assays for Mouse Lymphocyte Function; Chapter 6, Cytokines and their
cellular
receptors; Chapter 7, hnniunologic studies in Humans); Weinberger et al.,
Proc. Natl. Acad.
Sci. USA 77:6091-6095, 1980; Weinberger et al., Eur. J. Immun. 11:405-411,
1981; Takai et
al., J. Irnmunol. 137:3494-3500, 1986; Takai et al., J. Immunol. 140:508-512,
1988.
5.10.4 STEM CELL GROWTH FACTOR ACTIVITY
A polypeptide of the present invention may exhibit stem cell growth factor
activity and
be involved in the proliferation, differentiation and survival of pluripotent
and totipotent stem
cells including primordial germ cells, embryonic stem cells, hematopoietic
stem cells, neuronal
stem cells and/or germ line stem cells. Administration of the polypeptide of
the invention to
stem cells in vivo or ex vivo may maintain and expand cell populations in a
totipotential or
pluripotential state which would be useful for re-engineering damaged or
diseased tissues,
transplantation, manufacture of bio-pharmaceuticals and the development of bio-
sensors. The
ability to produce large quantities of human cells has important working
applications for the
production of human proteins which currently must be obtained from non-human
sources or
donors, implantation of cells to treat diseases such as Parkinson's,
Alzheimer's and other
neurodegenerative diseases; tissues for grafting such as bone marrow, skin,
cartilage, tendons,
bone, muscle (including cardiac muscle), blood vessels, cornea, neural cells,
gastrointestinal
cells and others; and organs for transplantation such as kidney, liver,
pancreas (including islet
cells), heart and lung.
It is contemplated that the polypeptide of the present invention may inhibit
the growth
of neural stem cells. Accordingly, administration of a polypeptide antagonist
to stem cells may
result in the proliferation, differentiation and survival of the stem cells.
It is also contemplated that multiple different exogenous growth factors
and/or
cytokines may be administered in combination with the polypeptide of the
invention to achieve
the desired effect, including any of the growth factors listed herein, other
stem cell
maintenance factors, and specifically including stem cell factor (SCF),
leukemia inhibitory
factor (LIF), Flt-3 ligand (Flt-3L), any of the interleukins, recombinant
soluble IL-6 receptor
fused to IL-6, macrophage inflammatory protein 1-alpha (MIP-1-alpha), G-CSF,
GM-CSF,
thrombopoietin (TPO), platelet factor 4 (PF-4), platelet-derived growth factor
(PDGF), neural
growth factors and basic fibroblast growth factor (bFGF).
Since totipotent stem cells can give rise to virtually any mature cell type,
expansion of
these cells in culture will facilitate the production of large quantities of
mature cells.
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Techniques for culturing stem cells are known in the art and administration of
polypeptides of
the invention, optionally with other growth factors and/or cytokines, is
expected to enhance the
survival and proliferation of the stem cell populations. This can be
accomplished by direct
administration of the polypeptide of the invention to the culture medium.
Alternatively, stroma
cells transfected with a polynucleotide that encodes for the polypeptide of
the invention can be
used as a feeder layer for the stem cell populations in culture or in vivo.
Stromal support cells
for feeder layers may include embryonic bone marrow fibroblasts, bone marrow
stromal cells,
fetal liver cells, or cultured embryonic fibroblasts (see U.S. Patent No.
5,690,926).
Stem cells themselves can be transfected with a polynucleotide of the
invention to
induce autocrine expression of the polypeptide of the invention. This will
allow for
generation of undifferentiated totipotentiallpluripotential stem cell lines
that are useful as is or
that can then be differentiated into the desired mature cell types. These
stable cell lines can
also serve as a source of undifferentiated totipotential/pluripotential mlRlVA
to create cDNA
libraries and templates for polymerase chain reaction experiments. These
studies would allow
for the isolation and identification of differentially expressed genes in stem
cell populations that
regulate stem cell proliferation andlor maintenance.
Expansion and maintenance of totipotent stem cell populations will be useful
in the
treatment of many pathological conditions. For example, polypeptides of the
present invention
may be used to manipulate stem cells in culture to give rise to
neuroepithelial cells that can be
used to augment or replace cells damaged by illness, autoimmune disease,
accidental damage
or genetic disorders. The polypeptide of the invention may be useful for
inducing the
proliferation of neural cells and for the regeneration of nerve and brain
tissue, i.e. for the
treatment of central and peripheral nervous system diseases and neuropathies,
as well as
mechanical and traumatic disorders which involve degeneration, death or trauma
to neural cells
or nerve tissue. In addition, the expanded stem cell populations can also be
genetically altered
for gene therapy purposes and to decrease host rejection of replacement
tissues after grafting or
implantation.
Expression of the polypeptide of the invention and its effect on stem cells
can also be
manipulated to achieve controlled differentiation of the stem cells into more
differentiated cell
types. A broadly applicable method of obtaining pure populations of a specific
differentiated
cell type from undifferentiated stem cell populations involves the use of a
cell-type specific
promoter driving a selectable marker. The selectable marker allows only cells
of the desired
type to survive. For example, stem cells can be induced to differentiate into
cardiomyocytes
(Wobus et al., Differentiation, 48: 173-182, (1991); Klug et al., J. Clin.
Invest., 98(1): 216-
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224, (1998)) or skeletal muscle cells (Browder, L. W. In: Principles of Tissue
Engineering
eds. Lanza et al. , Academic Press (1997)). Alternatively, directed
differentiation of stem
cells can be accomplished by culturing the stem cells in the presence of a
differentiation factor
such as retinoic acid and an antagonist of the polypeptide of the invention
which would inhibit
the effects of endogenous stem cell factor activity and allow differentiation
to proceed.
In vitro cultures of stem cells can be used to determine if the polypeptide of
the
invention exhibits stem cell growth factor activity. Stem cells are isolated
from any one of
various cell sources (including hematopoietic stem cells and embryonic stem
cells) and cultured
on a feeder layer, as described by Thompson et al. Proc. Natl. Acad. Sci,
U.S.A., 92: 7844-
7848 (1995), in the presence of the polypeptide of the invention alone or in
combination with
other growth factors or cytokines. The ability of the polypeptide of the
invention to induce
stem cells proliferation is determined by colony formation on semi-solid
support e.g. as
described by Bernstein et al., Blood, 77: 2316-2321 (1991).
5.10.5 HEMATOPOIESIS REGULATING ACTIVITY
A polypeptide of the present invention may be involved in regulation of
hematopoiesis
and, consequently, in the treatment of myeloid or lymphoid cell disorders.
Even marginal
biological activity in support of colony forming cells or of factor-dependent
cell lines indicates
involvement in regulating hematopoiesis, e.g. in supporting the growth and
proliferation of
erythroid progenitor cells alone or in combination with other cytokines,
thereby indicating
utility, for example, in treating various anemias or for use in conjunction
with
irradiation/chemotherapy to stimulate the production of erythroid precursors
and/or erythroid
cells; in supporting the growth and proliferation of myeloid cells such as
granulocytes and
monocytes/macrophages (i.e., traditional CSF activity) useful, for example, in
conjunction
with chemotherapy to prevent or treat consequent myelo-suppression; in
supporting the growth
and proliferation of megakaryocytes and consequently of platelets thereby
allowing prevention
or treatment of various platelet disorders such as thrombocytopenia, and
generally for use in
place of or complimentary to platelet transfusions; and/or in supporting the
growth and
proliferation of hematopoietic stem cells which are capable of maturing to any
and all of the
above-mentioned hematopoietic cells and therefore find therapeutic utility in
various stem cell
disorders (such as those usually treated with transplantation, including,
without limitation,
aplastic anemia and paroxysmal nocturnal hemoglobinuria), as well as in
repopulating the stem
cell compartment post irradiation/chemotherapy, either in-vivo or ex-vivo
(i.e., in conjunction
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with bone marrow transplantation or with peripheral progenitor cell
transplantation
(homologous or heterologous)) as normal cells or genetically manipulated for
gene therapy.
Therapeutic compositions of the invention can be used in the following:
Suitable assays for proliferation and differentiation of various hematopoietic
lines are
cited above.
Assays for embryonic stem cell differentiation (which will identify, among
others,
proteins that influence embryonic differentiation hematopoiesis) include,
without limitation,
those described in: Johansson et al. Cellular Biology 15:141-151, 1995; Keller
et al., -
Molecular and Cellular Biology 13:473-486, 1993; McClanahan et al., Blood
81:2903-2915,
1993.
Assays for stem cell survival and differentiation (which will identify, among
others,
proteins that regulate lympho-hematopoiesis) include, without limitation,
those described in:
Methylcellulose colony forming assays, Freshney, M. G. In Culture of
Hematopoietic Cells.
R. I. Freshney, et al. eds. Vol pp. 265-268, Wiley-Liss, Inc., New York, N.Y.
1994;
Hirayama et al., Proc. Natl. Acad. Sci. USA 89:5907-5911, 1992; Primitive
hematopoietic
colony forming cells with high proliferative potential, McNiece, I. K. and
Briddell, R. A. In
Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 23-39,
Wiley-Liss, Inc.,
New York, N.Y. 1994; Neben et al., Experimental Hematology 22:353-359, 1994;
Cobblestone area forming cell assay, Ploemacher, R. E. In Culture of
Hematopoietic Cells. R.
I. Freshney, et al. eds. Vol pp. 1-21, Wiley-Liss, Inc., New York, N.Y. 1994;
Long term
bone marrow cultures in the presence of stromal cells, Spooncer, E., Dexter,
M. and Allen, T.
In Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 163-
179, Wiley-Liss,
Inc., New York, N.Y. 1994; Long term culture initiating cell assay,
Sutherland, H. J. In
Culture of Hematopoietic Cells. R. I. Freshney, et al. eds. Vol pp. 139-162,
Wiley-Liss, Inc.,
New York, N.Y. 1994.
5.10.6 TISSUE GROWTH ACTIVITY
A polypeptide of the present invention also may be involved in bone,
cartilage, tendon,
ligament and/or nerve tissue growth or regeneration, as well as in wound
healing and tissue
repair and replacement, and in healing of burns, incisions and ulcers.
A polypeptide of the present invention which induces cartilage and/or bone
growth in
circumstances where bone is not normally formed, has application in the
healing of bone
fractures and cartilage damage or defects in humans and other animals.
Compositions of a
polypeptide, antibody, binding partner, or other modulator of the invention
may have
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prophylactic use in closed as well as open fracture reduction and also in the
improved fixation
of artificial joints. De novo bone formation induced by an osteogenic agent
contributes to the
repair of congenital, trauma induced, or oncologic resection induced
craniofacial defects, and
also is useful in cosmetic plastic surgery.
A polypeptide of this invention may also be involved in attracting bone-
forming cells,
stimulating growth of bone-forming cells, or inducing differentiation of
progenitors of bone-
forming cells. Treatment of osteoporosis, osteoarthritis, bone degenerative
disorders, or
periodontal disease, such as through stimulation of bone and/or cartilage
repair or by blocking
inflammation or processes of tissue destruction (collagenase activity,
osteoclast activity, etc.)
mediated by inflammatory processes may also be possible using the composition
of the
invention.
Another category of tissue regeneration activity that may involve the
polypeptide of the
present invention is tendon/ligament formation. Induction of tendon/ligament-
like tissue or
other tissue formation in circumstances where such tissue is not normally
formed, has
application in the healing of tendon or ligament tears, deformities and other
tendon or ligament
defects in humans and other animals. Such a preparation employing a
tendon/ligament-like
tissue inducing protein may have prophylactic use in preventing damage to
tendon or ligament
tissue, as well as use in the improved fixation of tendon or ligament to bone
or other tissues,
and in repairing defects to tendon or ligament tissue. De novo tendon/ligament-
like tissue
formation induced by a composition of the present invention contributes to the
repair of
congenital, trauma induced, or other tendon or ligament defects of other
origin, and is also
useful in cosmetic plastic surgery for attachment or repair of tendons or
ligaments. The
compositions of the present invention may provide environment to attract
tendon- or ligament-
forming cells, stimulate growth of tendon- or ligament-forming cells, induce
differentiation of
progenitors of tendon- or ligament-forming cells, or induce growth of
tendon/ligament cells or
progenitors ex vivo for return in vivo to effect tissue repair. The
compositions of the invention
may also be useful in the treatment of tendinitis, carpal tunnel syndrome and
other tendon or
ligament defects. The compositions may also include an appropriate matrix
and/or sequestering
agent as a carrier as is well known in the art.
The compositions of the present invention may also be useful for proliferation
of neural
stem cells and for regeneration of nerve and brain tissue, i.e. for the
treatment of central and
peripheral nervous system diseases and neuropathies, as well as mechanical and
traumatic
disorders, which involve degeneration, death or trauma to neural cells or
nerve tissue. More
specifically, a composition may be used in the treatment of peripheral and
central nerve
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injuries and of diseases of the peripheral nervous system, such as peripheral
neuropathy and
localized neuropathies, and central nervous system diseases, such as
Alzheimer's, Parkinson's
disease, Huntington's disease, amyotrophic lateral sclerosis, and Shy-Drager
syndrome.
Further conditions which may be treated in accordance with the present
invention include
mechanical and traumatic disorders, such as spinal cord disorders, head trauma
and
cerebrovascular diseases such as stroke. Peripheral neuropathies resulting
from chemotherapy
or other medical therapies may also be treatable using a composition of the
invention.
Compositions of the invention may also be useful to promote better or faster
closure of
non-healing wounds, including without limitation pressure ulcers, ulcers
associated with
vascular insufficiency, surgical and traumatic wounds, and the like.
Compositions of the present invention may also be involved in the generation
or'
regeneration of other tissues, such as organs (including, for example,
pancreas, liver, intestine,
kidney, skin, endothelium), muscle (smooth, skeletal or cardiac) and vascular
(including
vascular endothelium) tissue, or for promoting the growth of cells comprising
such tissues.
Part of the desired effects may be by inhibition or modulation of fibrotic
scarring rnay allow
normal tissue to regenerate. A polypeptide of the present invention may also
exhibit
angiogenic activity.
A composition of the present invention may also be useful for gut protection
or
regeneration and treatment of lung or liver fibrosis, reperfusion injury in
various tissues, and
conditions resulting from systemic cytokine damage.
A composition of the present invention may also be useful for promoting or
inhibiting
differentiation of tissues described above from precursor tissues or cells; or
for inhibiting the
growth of tissues described above.
Therapeutic compositions of the invention can be used in the following:
Assays for tissue generation activity include, without limitation, those
described in:
International Patent Publication No. W095/16035 (bone, cartilage, tendon);
International
Patent Publication No. W095/05846 (nerve, neuronal); International Patent
Publication No.
W091/07491 (skin, endothelium).
Assays for wound healing activity include, without limitation, those described
in:
Winter, Epidermal Wound Healing, pp. 71-112 (Maibach, H. I. and Rovee, D. T.,
eds.), Year
Book Medical Publishers, Inc., Chicago, as modified by Eaglstein and Mertz, J.
Invest.
Dermatol 71:382-84 (1978).
5.10.7 I).VIMUNE FUNCTION STIMULATING OR SUPPRESSING ACTIVITY
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,A polypeptide of the present invention may also exhibit immune stimulating or
immune
suppressing activity, including without limitation the activities for which
assays are described
herein. A polynucleotide of the invention can encode a polypeptide exhibiting
such activities.
A protein may be useful in the treatment of various immune deficiencies and
disorders
(including severe combined immunodeficiency (SCID)), e.g., in regulating (up
or down)
growth and proliferation of T andlor B lymphocytes, as well as effecting the
cytolytic activity
of NK cells and other cell populations. These immune deficiencies may be
genetic or be caused
by viral (e.g., HIV) as well as bacterial or fungal infections, or may result
from autoimrnune
disorders. More specifically, infectious diseases causes by viral, bacterial,
fungal or other
infection may be treatable using a protein of the present invention, including
infections by
HIV, hepatitis viruses, herpes viruses, mycobacteria, Leishmania spp., malaria
spp. and
various fungal infections such as candidiasis. Of course, in this regard,
proteins of the present
invention may also be useful where a boost to the immune system generally may
be desirable,
i.e., in the treatment of cancer.
Autoimmune disorders which may be treated using a protein of the present
invention
include, for example, connective tissue disease, multiple sclerosis, systemic
lupus
erythematosus, rheumatoid arthritis, autoimmune pulmonary inflammation,
Guillain-Barre
syndrome, autoimmune thyroiditis, insulin dependent diabetes mellitis,
myasthenia gravis,
graft-versus-host disease and autoirnrnune inflammatory eye disease. Such a
protein (or
antagonists thereof, including antibodies) of the present invention may also
to be useful in the
treatment of allergic reactions and conditions (e. g. , anaphylaxis, serum
sickness, drug
reactions, food allergies, insect venom allergies, mastocytosis, allergic
rhinitis,
hypersensitivity pneumonitis, urticaria, angioedema, eczema, atopic
dermatitis, allergic contact
dermatitis, erythema multiforme, Stevens-Johnson syndrome, allergic
conjunctivitis, atopic
keratoconjunctivitis, venereal keratoconjunctivitis, giant papillary
conjunctivitis and contact
allergies), such as asthma (particularly allergic asthma) or other respiratory
problems. Other
conditions, in which immune suppression is desired (including, for example,
organ
transplantation), may also be treatable using a protein (or antagonists
thereof) of the present
invention. The therapeutic effects of the polypeptides or antagonists thereof
on allergic
reactions can be evaluated by in vivo animals models such as the cumulative
contact
enhancement test (Lastbom et al., Toxicology 125: 59-66, 1995), skin prick
test (Hoffinann et
al., Allergy 54: 446-54, 1999), guinea pig skin sensitization test (Voter et
al., Arch. Toxocol.
73: 501-9), and murine local lymph node assay (Kimber et al., J. Toxicol.
Environ. Health
53: 563-79).
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Using the proteins of the invention it may also be possible to modulate immune
responses, in a number of ways. Down regulation may be in the form of
inhibiting or blocking
an immune response already in progress or may involve preventing the induction
of an immune
response. The functions of activated T cells may be inhibited by suppressing T
cell responses
or by inducing specific tolerance in T cells, or both. Immunosuppression of T
cell responses is
generally an active, non-antigen-specific, process which requires continuous
exposure of the T
cells to the suppressive agent. Tolerance, which involves inducing non-
responsiveness or
anergy in T cells, is distinguishable from immunosuppression in that it is
generally antigen-
specific and persists after exposure to the tolerizing agent has ceased.
Operationally, tolerance
can be demonstrated by the lack of a T cell response upon reexposure to
specific antigen in the
absence of the tolerizing agent.
Down regulating or preventing one or more antigen functions (including without
limitation B lymphocyte antigen functions (such as, for example, B7)), e.g.,
preventing high
level lymphokine synthesis by activated T cells, will be useful in situations
of tissue, skin and
organ transplantation and in graft-versus-host disease (GVHD). For example,
blockage of T
cell function should result in reduced tissue destruction in tissue
transplantation. Typically, in
tissue transplants, rejection of the transplant is initiated through its
recognition as foreign by T
cells, followed by an immune reaction that destroys the transplant. The
administration of a
therapeutic composition of the invention may prevent cytokine synthesis by
immune cells, such
as T cells, and thus acts as an immunosuppressant. Moreover, a lack of
costimulation may also
be sufficient to anergize the T cells, thereby inducing tolerance in a
subject. Induction of long-
term tolerance by B lymphocyte antigen-blocking reagents may avoid the
necessity of repeated
administration of these blocking reagents. To achieve sufficient
immunosuppression or
tolerance in a subject, it may also be necessary to block the function of a
combination of B
lymphocyte antigens.
The efficacy of particular therapeutic compositions in preventing organ
transplant
rejection or GVHD can be assessed using animal models that are predictive of
efficacy in
humans. Examples of appropriate systems which can be used include allogeneic
cardiac grafts
in rats and xenogeneic pancreatic islet cell grafts in mice, both of which
have been used to
examine the immunosuppressive effects of CTLA4Ig fusion proteins in vivo as
described in
Lenschow et al., Science 257:789-792 (1992) and Turka et al., Proc. Natl.
Acad. Sci USA,
89:11102-11105 (1992). In addition, murine models of GVHD (see Paul ed.,
Fundamental
Immunology, Raven Press, New York, 1989, pp. 846-847) can be used to determine
the effect
of therapeutic compositions of the invention on the development of that
disease.
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Blocking antigen function may also be therapeutically useful for treating
autoimmune
diseases. Many autoimmune disorders are the result of inappropriate activation
of T cells that
are reactive against self tissue and which promote the production of cytokines
and
autoantibodies involved in the pathology of the diseases. Preventing,the
activation of
autoreactive T cells may reduce or eliminate disease symptoms. Administration
of reagents
which block stimulation of T cells can be used to inhibit T cell activation
and prevent
production of autoantibodies or T cell-derived cytokines which may be involved
in the disease
process. Additionally, blocking reagents may induce antigen-specific tolerance
of autoreactive
T cells which could lead to long-term relief from the disease. The efficacy of
blocking reagents
in preventing or alleviating autoimmune disorders can be determined using a
number of well-
characterized animal models of human autoimmune diseases. Examples include
marine
experimental autoirnmune encephalitis, systemic lupus erythematosus in
MRL/lpr/lpr mice or
NZB hybrid mice, marine autoimmune collagen arthritis, diabetes mellitus in
NOD mice and
BB rats, and marine experimental myasthenia gravis (see Paul ed. , Fundamental
Immunology,
Raven Press, New York, 1989, pp. 840-856).
Upregulation of an antigen function (e.g., a B lymphocyte antigen function),
as a means
of up regulating immune responses, may also be useful in therapy. Upregulation
of immune
responses may be in the form of enhancing an existing immune response or
eliciting an initial
immune response. For example, enhancing an immune response may be useful in
cases of viral
infection, including systemic viral diseases such as influenza, the common
cold, and
encephalitis.
Alternatively, anti-viral immune responses may be enhanced in an infected
patient by
removing T cells from the patient, costimulating the T cells in vitro with
viral antigen-pulsed
APCs either expressing a peptide of the present invention or together with a
stimulatory form
of a soluble peptide of the present invention and reintroducing the in vitro
activated T cells into
the patient. Another method of enhancing anti-viral immune responses would be
to isolate
infected cells from a patient, transfect them with a nucleic acid encoding a
protein of the
present invention as described herein such that the cells express all or a
portion of the protein
on their surface, and reintroduce the transfected cells into the patient. The
infected cells would
now be capable of delivering a costimulatory signal to, and thereby activate,
T cells in vivo.
A polypeptide of the present invention may provide the necessary stimulation
signal to
T cells to induce a T cell mediated immune response against the transfected
tumor cells. In
addition, tumor cells which lack MHC class I or MHC class II molecules, or
which fail to
reexpress sufficient mounts of MHC class I or MHC class II molecules, can be
transfected
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with nucleic acid encoding all or a portion of (e. g. , a cytoplasrnic-domain
truncated portion) of
an MHC class I alpha chain protein and (3a microglobulin protein or an MHC
class II alpha
chain protein and an MHC class II beta chain protein to thereby express MHC
class I or MHC
class II proteins on the cell surface. Expression of the appropriate class I
or class II MHC in
conjunction with a peptide having the activity of a B lymphocyte antigen
(e.g., B7-1, B7-2,
B7-3) induces a T cell mediated immune response against the transfected tumor
cell.
Optionally, a gene encoding an antisense construct which blocks expression of
an MHC class
II associated protein, such as the invariant chain, can also be cotransfected
with a DNA
encoding a peptide having the activity of a B lymphocyte antigen to promote
presentation of
tumor associated antigens and induce tumor specific immunity. Thus, the
induction of a T cell
mediated immune response in a human subject may be sufficient to overcome
tumor-specific
tolerance in the subject.
The activity of a protein of the invention may, among other means, be measured
by the
following methods:
Suitable assays for thymocyte or splenocyte cytotoxicity include, without
limitation,
those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A.
M. Kruisbeek,
D. H. Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates
and Wiley
Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function 3.1-
3.19; Chapter 7,
Immunologic studies in Humans); Herrmann et al., Proc. Natl. Acid. Sci. USA
78:2488-2492,
1981; Herrmann et al., J. Immunol. 128:1968-1974, 1982; Handa et al., J.
Immunol.
135:1564-1572, 1985; Takai et al., I. Immunol. 137:3494-3500, 1986; Takai et
al., J.
Immunol. 140:508-512, 1988; Bowman et al., J. Virology 61:1992-1998;
Bertagnolli et al.,
Cellular Immunology 133:327-341, 1991; Brown et al., J. Immunol. 153:3079-
3092, 1994.
Assays for T-cell-dependent immunoglobulin responses and isotype switching
(which
will identify, among others, proteins that modulate T-cell dependent antibody
responses and
that affect ThllTh2 profiles) include, without limitation, those described in:
Maliszewski, J.
Immunol. 144:3028-3033, 1990; and Assays for B cell function: In vitro
antibody production,
Mond, J. J. and Brunswick, M. In Current Protocols in Immunology. J. E. e.a.
Coligan eds.
Vol 1 pp. 3.8.1-3.8.16, John Wiley and Sons, Toronto. 1994.
Mixed lymphocyte reaction (MLR) assays (which will identify, among others,
proteins
that generate predominantly Thl and CTL responses) include, without
limitation, those
described in: Current Protocols in Immunology, Ed by J. E: Coligan, A. M.
Kruisbeek, D. H.
Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and
Wiley-
Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function 3.1-
3.19; Chapter 7,
CA 02399672 2002-08-02
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Immunologic studies in Humans); Takai et al., J. Immunol. 137:3494-3500, 1986;
Takai et
al., J. Immunol. 140:508-512, 1988; Bertagnolli et al., J. Immunol. 149:3778-
3783, 1992.
Dendritic cell-dependent assays (which will identify, among others, proteins
expressed
by dendritic cells that activate naive T-cells) include, without limitation,
those described in:
Guery et al., J. Immunol. 134:536-544, 1995; Inaba et al., Journal of
Experimental Medicine
173:549-559, 1991; Macatonia et al., Journal of Immunology 154:5071-5079,
1995; Porgador
et al., Journal of Experimental Medicine 182:255-260, 1995; Nair et al.,
Journal of Virology
67:4062-4069, 1993; Huang et al., Science 264:961-965, 1994; Macatonia et al.,
Journal of
Experimental Medicine 169:1255-1264, 1989; Bhardwaj et al., Journal of
Clinical
Investigation 94:797-807, 1994; and Inaba et al. , Journal of Experimental
Medicine 172:631-
640, 1990.
Assays for lymphocyte survival/apoptosis (which will identify, among others,
proteins
that prevent apoptosis after superantigen induction and proteins that regulate
lymphocyte
homeostasis) include, without limitation, those described in: Darzynkiewicz et
al., Cytometry
13:795-808, 1992; Gorczyca et al., Leukemia 7:659-670, 1993; Gorczyca et al.,
Cancer
Research 53:1945-1951, 1993; Itoh et al., Cell 66:233-243, 1991; Zacharchuk,
Journal of
Immunology 145:4037-4045, 1990;' Zamai et al., Cytometry 14:891-897, 1993;
Gorczyca et
al. , International Journal of Oncology 1:639-648, 1992.
Assays for proteins that influence early steps of T-cell commitment and
development
include, without limitation, those described in: Antica et al. , Blood 84:111-
117, 1994; Fine et
al., Cellular Immunology 155:111-122, 1994; Galy et al., Blood 85:2770-2778,
1995; Toki et
al., Proc. Nat. Acad Sci. USA 88:7548-7551, 1991.
5.10.8 ACTIVIN/INHIBIN ACTIVITY
A polypeptide of the present invention may also exhibit activin- or inhibin-
related
activities. A polynucleotide of the invention may encode a polypeptide
exhibiting such
characteristics. Inhibins are characterized by their ability to inhibit the
release of follicle
stimulating hormone (FSH), while activins and are characterized by their
ability to stimulate
the release of follicle stimulating hormone (FSH). Thus, a polypeptide of the
present
invention, alone or in heterodimers with a member of the inhibinfamily, may be
useful as a
contraceptive based on the ability of inhibins to decrease fertility in female
mammals and
decrease spermatogenesis in male mammals. Administration of sufficient amounts
of other
inhibins can induce infertility in these mammals. Alternatively, the
polypeptide of the
invention, as a homodimer or as a heterodimer with other protein subunits of
the inhibin
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group, may be useful as a fertility inducing therapeutic, based upon the
ability of activin
molecules in stimulating FSH release from cells of the anterior pituitary.
See, for example,
U.S. Pat. No. 4,798,885. A polypeptide of the invention may also be useful for
advancement
of the onset of fertility in sexually immature mammals, so as to increase the
lifetime
reproductive performance of domestic animals such as, but not limited to,
cows, sheep and
pigs.
The activity of a polypeptide of the invention may, among other means, be
measured by
the following methods.
Assays for activin/inhibin activity include, without limitation, those
described in: Vale
et al., Endocrinology 91:562-572, 1972; Ling et al., Nature 321:779-782, 1986;
Vale et al.,
Nature 321:776-779, 1986; Mason et al., Nature 318:659-663, 1985; Forage et
al., Proc.
Natl. Acad. Sci. USA 83:3091-3095, 1986.
5.10.9 CHEMOTACTIC/CHEMOKINETIC ACTIVITY
A polypeptide of the present invention may be involved in chemotactic or
chemokinetic
activity for mammalian cells, including, for example, monocytes, fibroblasts,
neutrophils, T-
cells, mast cells, eosinophils, epithelial andlor endothelial cells. A
polynucleotide of the
invention can encode a polypeptide exhibiting such attributes. Chemotactic and
chemokinetic
receptor activation can be used to mobilize or attract a desired cell
population to a desired site
of action. Chemotactic or chemokinetic compositions (e.g. proteins,
antibodies, binding
partners, or modulators of the invention) provide particular advantages in
treatment of wounds
and other trauma to tissues, as well as in treatment of localized infections.
For example,
attraction of lymphocytes, monocytes or neutrophils to tumors or sites of
infection may result
in improved immune responses against the tumor or infecting agent.
A protein or peptide has chemotactic activity for a particular cell population
if it can
stimulate, directly or indirectly, the directed orientation or movement of
such cell population.
Preferably, the protein or peptide has the ability to directly stimulate
directed movement of
cells. Whether a particular protein has chemotactic activity for a population
of cells can be
readily determined by employing such protein or peptide in any known assay for
cell
chemotaxis.
Therapeutic compositions of the invention can be used in the following:
Assays for chemotactic activity (which will identify proteins that induce or
prevent
chemotaxis) consist of assays that measure the ability of a protein to induce
the migration of
cells across a membrane as well as the ability of a protein to induce the
adhesion of one cell
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population to another cell population. Suitable assays for movement and
adhesion include,
without limitation, those described in: Current Protocols in Immunology, Ed by
J. E. Coligan,
A. M. Kruisbeek, D. H. Marguiles, E. M. Shevach, W. Strober, Pub. Greene
Publishing
Associates and Wiley-Interscience (Chapter 6.12, Measurement of alpha and beta
Chemokines
6.12.1-6.12.28; Taub et al. J. Clin. Invest. 95:1370-1376, 1995; Lind et al.
APMIS 103:140-
146, 1995; Muller et al Eur. J. Immunol. 25:1744-1748; Gruber et al. J. of
hnmunol.
152:5860-5867, 1994; Johnston et al. J. of Immunol. 153:1762-1768, 1994.
5.10.10 HEMOSTATIC AND THROMBOLYTIC ACTIVITY
A polypeptide of the invention may also be involved in hemostatis or
thrombolysis or
thrombosis. A polynucleotide of the invention can encode a polypeptide
exhibiting such
attributes. Compositions may be useful in treatment of various coagulation
disorders
(including hereditary disorders, such as hemophilias) or to enhance
coagulation and other
hemostatic events in treating wounds resulting from trauma, surgery or other
causes. A
composition of the invention may also be useful for dissolving or inhibiting
formation of
thromboses and for treatment and prevention of conditions resulting therefrom
(such as, for
example, infarction of cardiac and central nervous system vessels (e.g.,
stroke).
Therapeutic compositions of the invention can be used in the following:
Assay for hemostatic and thrombolytic activity include, without limitation,
those
described in: Linet et al., J. Clin. Pharmacol. 26:131-140, 1986; Burdick et
al., Thrombosis
Res. 45:413-419, 1987; Humphrey et al., Fibrinolysis 5:71-79 (1991); Schaub,
Prostaglandins
35:467-474,1988.
5.10.11 CANCER DIAGNOSIS AND THERAPY
Polypeptides of the invention may be involved in cancer cell generation,
proliferation
or metastasis. Detection of the presence or amount of polynucleotides or
polypeptides of the
invention may be useful for the diagnosis and/or prognosis of one or more
types of cancer.
For example, the presence or increased expression of a
polynucleotide/polypeptide of the
invention may indicate a hereditary risk of cancer, a precancerous condition,
or an ongoing
malignancy. Conversely, a defect in the gene or absence of the polypeptide may
be associated
with a cancer condition. Identification of single nucleotide polymorphisms
associated with
cancer or a predisposition to cancer may also be useful for diagnosis or
prognosis.
Cancer treatments promote tumor regression by inhibiting tumor cell
proliferation,
inhibiting angiogenesis (growth of new blood vessels that is necessary to
support tumor
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growth) and/or prohibiting metastasis by reducing tumor cell motility or
invasiveness.
Therapeutic compositions of the invention may be effective in adult and
pediatric oncology
including in solid phase tumors/malignancies, locally advanced tumors, human
soft tissue
sarcomas, metastatic cancer, including lymphatic metastases, blood cell
malignancies including
multiple myeloma, acute and chronic leukemias, and lymphomas, head and neck
cancers
including mouth cancer, larynx cancer and thyroid cancer, lung cancers
including small cell
carcinoma and non-small cell cancers, breast cancers including small cell
carcinoma and ductal
carcinoma, gastrointestinal cancers including esophageal cancer, stomach
cancer, colon cancer,
colorectal cancer and polyps associated with colorectal neoplasia, pancreatic
cancers, liver
cancer, urologic cancers including bladder cancer and prostate cancer,
malignancies of the
female genital tract including ovarian carcinoma, uterine (including
endometrial) cancers, and
solid tumor in the ovarian follicle, kidney cancers including renal cell
carcinoma, brain cancers
including intrinsic brain tumors, neuroblastoma, astrocytic brain tumors,
gliomas, metastatic
tumor cell invasion in the central nervous system, bone cancers including
osteomas, skin
cancers including malignant melanoma, tumor progression of human skin
keratinocytes,
squamous cell carcinoma, basal cell carcinoma, hemangiopericytoma and
Karposi's sarcoma.
Polypeptides, polynucleotides, or modulators of polypeptides of the invention
(including inhibitors and stimulators of the biological activity of the
polypeptide of the
invention) may be administered to treat cancer. Therapeutic compositions can
be administered
in therapeutically effective dosages alone or in combination with adjuvant
cancer therapy such
as surgery, chemotherapy, radiotherapy, thermotherapy, and laser therapy, and
may provide a
beneficial effect, e.g. reducing tumor size, slowing rate of tumor growth,
inhibiting metastasis,
or otherwise improving overall clinical condition, without necessarily
eradicating the cancer.
The composition can also be administered in therapeutically effective amounts
as a
portion of an anti-cancer cocktail. An anti=cancer cocktail is a mixture of
the polypeptide or
modulator of the invention with one or more anti-cancer drugs in addition to a
pharmaceutically acceptable carrier for delivery. The use of anti-cancer
cocktails as a cancer
treatment is routine. Anti-cancer drugs that are well known in the art and can
be used as a
treatment in combination with the polypeptide or modulator of the invention
include:
Actinomycin D, Aminoglutethimide, Asparaginase, Bleomycin, Busulfan,
Carboplatin,
Carmustine, Chlorambucil, Cisplatin (cis-DDP), Cyclophosphamide, Cytarabine
HCl
(Cytosine arabinoside), Dacarbazine, Dactinomycin, Daunorubicin HCI,
Doxorubicin HCI,
Estramustine phosphate sodium, Etoposide (V16-213), Floxuridine, 5-
Fluorouracil (5-Fu),
Flutamide, Hydroxyurea (hydroxycarbamide), Ifosfamide, Interferon Alpha-2a,
Interferon
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Alpha-2b, Leuprolide acetate (LHRH-releasing factor analog), Lomustine,
Mechlorethamine
HCl (nitrogen mustard), Melphalan, Mercaptopurine, Mesna, Methotrexate (MTX),
Mitomycin, Mitoxantrone HCI, Octreotide, Plicamycin, Procarbazine HCI,
Streptozocin,
Tamoxifen citrate, Thioguanine, Thiotepa, Vinblastine sulfate, Vincristine
sulfate, Amsacrine,
Azacitidine, Hexamethylinelamine, Interleukin-2, Mitoguazone, Pentostatin,
Semustine,
Teniposide, and Vindesine sulfate.
In addition, therapeutic compositions of the invention may be used for
prophylactic
treatment of cancer. There are hereditary conditions and/or environmental
situations (e.g.
exposure to carcinogens) known in the art that predispose an individual to
developing cancers.
Under these circumstances, it may be beneficial to treat these individuals
with therapeutically
effective doses of the polypeptide of the invention to reduce the risk of
developing cancers.
1h vitro models can be used to determine the effective doses of the
polypeptide of the
invention as a potential cancer treatment. These ih vitYO models include
proliferation assays of
cultured tumor cells, growth of cultured tumor cells in soft agar (see
Freshney, (1987) Culture
1 S of Animal Cells: A Manual of Basic Technique, Wily-Liss, New York, NY Ch
18 and Ch 21),
tumor systems in nude mice as described in Giovanella et al. , J. Natl. Can.
Inst. , 52: 921-30
(1974), mobility and invasive potential of tumor cells in Boyden Chamber
assays as described
in Pilkington et al., Anticancer Res., 17: 4107-9 (1997), and angiogenesis
assays such as
induction of vascularization of the chick chorioallantoic membrane or
induction of vascular
endothelial cell migration as described in Ribatta et al., Intl. J. Dev.
Biol., 40: 1189-97 (1999)
and Li et al., Clin. Exp. Metastasis, 17:423-9 (1999), respectively. Suitable
tumor cells lines
are available, e.g. from American Type Tissue Culture Collection catalogs.
5.10.12 RECEPTOR/LIGAND ACTIVITY
A polypeptide of the present invention may also demonstrate activity as
receptor,
receptor ligand or inhibitor or agonist of receptor/ligand interactions. A
polynucleotide of the
invention can encode a polypeptide exhibiting such characteristics. Examples
of such receptors
and ligands include, without limitation, cytokine receptors and their ligands,
receptor kinases
and their ligands, receptor phosphatases and their ligands, receptors involved
in cell-cell
interactions and their ligands (including without limitation, cellular
adhesion molecules (such
as selectins, integrins and their ligands) and receptor/ligand pairs involved
in antigen
presentation, antigen recognition and development of cellular and humoral
immune responses.
Receptors and ligands are also useful for screening of potential peptide or
small molecule
inhibitors of the relevant receptor/ligand interaction. A protein of the
present invention
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(including, without limitation, fragments of receptors and ligands) may
themselves be useful as
inhibitors of receptorlligand interactions.
The activity of a polypeptide of the invention may, among other means, be
measured by
the following methods:
Suitable assays for receptor-ligand activity include without limitation those
described
in: Current Protocols in Immunology, Ed by J. E. Coligan, A. M. Kruisbeek, D.
H.
Margulies, E. M. Shevach, W. Strober, Pub. Greene Publishing Associates and
Wiley-
Interscience (Chapter 7.28, Measurement of Cellular Adhesion under static
conditions 7.28.1-
7.28.22), Takai et al., Proc. Natl. Acad. Sci. USA 84:6864-6868, 1987; Bierer
et al., J. Exp.
Med. 168:1145-1156, 1988; Rosenstein et al., J. Exp. Med. 169:149-160 1989;
Stoltenborg et
al. , J. Immunol. Methods 175:59-68, 1994; Stitt et al. , Cell 80:661-670,
1995.
By way of example, the polypeptides of the invention may be used as a receptor
for a
ligand(s) thereby transmitting the biological activity of that ligand(s).
Ligands may be
identified through binding assays, affinity chromatography, dihybrid screening
assays, BIAcore
assays, gel overlay assays, or other methods known in the art.
Studies characterizing drugs or proteins as agonist or antagonist or partial
agonists or a
partial antagonist require the use of other proteins as competing ligands. The
polypeptides of
the present invention or ligand(s) thereof may be labeled by being coupled to
radioisotopes,
colorimetric molecules or a toxin molecules by conventional methods. ("Guide
to Protein
Purification" Murray P. Deutscher (ed) Methods in Enzymology Vol. 182 (1990)
Academic
Press, Inc. San Diego). Examples of radioisotopes include, but are not limited
to, tritium and
carbon-14 . Examples of colorimetric molecules include, but are not limited
to, fluorescent
molecules such as fluorescamine, or rhodamine or other colorimetric molecules.
Examples of
toxins include, but are not limited, to ricin.
5.10.13 DRUG SCREENING
This invention is particularly useful for screening chemical compounds by
using the
novel polypeptides or binding fragments thereof in any of a variety of drug
screening
techniques. The polypeptides or fragments employed in such a test may either
be free in
solution, affixed to a solid support, borne on a cell surface or located
intracellularly. One
method of drug screening utilizes eukaryotic or prokaryotic host cells which
are stably
transformed with recombinant nucleic acids expressing the polypeptide or a
fragment thereof.
Drugs are screened against such transformed cells in competitive binding
assays. Such cells,
either in viable or fixed form, can be used for standard binding assays. One
may measure, for
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example, the formation of complexes between polypeptides of the invention or
fragments and
the agent being tested or examine the diminution in complex formation between
the novel
polypeptides and an appropriate cell line, which are well known in the art.
Sources for test compounds that may be screened for ability to bind to or
modulate
(i.e., increase or decrease) the activity of polypeptides of the invention
include (1) inorganic
and organic chemical libraries, (2) natural product libraries, and (3)
combinatorial libraries
comprised of either random or mimetic peptides, oligonucleotides or organic
molecules.
Chemical libraries may be readily synthesized or purchased from a number of
commercial sources, and may include structural analogs of known compounds or
compounds
that are identified as "hits" or "leads" via natural product screening.
The sources of natural product libraries are microorganisms (including
bacteria and
fungi), animals, plants or other vegetation, or marine organisms, and
libraries of mixtures for
screening may be created by: (1) fermentation and extraction of broths from
soil, plant or
marine microorganisms or (2) extraction of the organisms themselves. Natural
product
libraries include polyketides, non-ribosomal peptides, and (non-naturally
occurring) variants
thereof. For a review, see Science 282:63-68 (1998).
Combinatorial libraries are composed of large numbers of peptides,
oligonucleotides or
organic compounds and can be readily prepared by traditional automated
synthesis methods,
PCR, cloning or proprietary synthetic methods. Of particular interest are
peptide and
oligonucleotide combinatorial libraries. Still other libraries of interest
include peptide, protein,
peptidomimetic, multiparallel synthetic collection, recombinatorial, and
polypeptide libraries.
For a review of combinatorial chemistry and libraries created therefrom, see
Myers, Curr.
Opir~. Biotechnol. 8:701-707 (1997). For reviews and examples of
peptidomimetic libraries,
see Al-Obeidi et al., Mol. Biotechnol, 9(3):205-23 (1998); Hruby et al., Curr
Opan Chem
Biol, 1(1):114-19 (1997); Dorner et al., Bioorg Med Chem, 4(5):709-15 (1996)
(alkylated
dipeptides).
Identification of modulators through use of the various libraries described
herein
permits modification of the candidate "hit" (or "lead") to optimize the
capacity of the "hit" to
bind a polypeptide of the invention. The molecules identified in the binding
assay are then
tested for antagonist or agonist activity in ih vivo tissue culture or animal
models that are well
known in the art. In brief, the molecules are titrated into a plurality of
cell cultures or animals
and then tested for either celllanimal death or prolonged survival of the
animal/cells.
The binding molecules thus identified may be complexed with toxins, e.g.,
ricin or
cholera, or with other compounds that are toxic to cells such as
radioisotopes. The toxin-
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binding molecule complex is then targeted to a tumor or other cell by the
specificity of the
binding molecule for a polypeptide of the invention. Alternatively, the
binding molecules may
be complexed with imaging agents for targeting and imaging purposes.
5.10.14 ASSAY FOR RECEPTOR ACTIVITY
The invention also provides methods to detect specific binding of a
polypeptide e.g. a
ligand or a receptor. The art provides numerous assays particularly useful for
identifying
previously unknown binding partners for receptor polypeptides of the
invention. For example,
expression cloning using mammalian or bacterial cells, or dihybrid screening
assays can be
used to identify polynucleotides encoding binding partners. As another
example, affinity
chromatography with the appropriate immobilized polypeptide of the invention
can be used to
isolate polypeptides that recognize and bind polypeptides of the invention.
There are a number
of different libraries used for the identification of compounds, and in
particular small
molecules, that modulate (i.e., increase or decrease) biological activity of a
polypeptide of the
invention. Ligands for receptor polypeptides of the invention can also be
identified by adding
exogenous ligands, or cocktails of ligands to two cells populations that are
genetically identical
except for the expression of the receptor of the invention: one cell
population expresses the
receptor of the invention whereas the other does not. The response of the two
cell populations
to the addition of ligands(s) are then compared. Alternatively, an expression
library can be co-
expressed with the polypeptide of the invention in cells and assayed for an
autocrine response
to identify potential ligand(s). As still another example, BIAcore assays, gel
overlay assays, or
other methods known in the art can be used to identify binding partner
polypeptides, including,
(1) organic and inorganic chemical libraries, (2) natural product libraries,
and (3)
combinatorial libraries comprised of random peptides, oligonucleotides or
organic molecules.
The role of downstream intracellular signaling molecules in the signaling
cascade of the
polypeptide of the invention can be determined. For example, a chimeric
protein in which the
cytoplasmic domain of the polypeptide of the invention is fused to the
extracellular portion of a
protein, whose ligand has been identified, is produced in a host cell. The
cell is then incubated
with the ligand specific for the extracellular portion of the chimeric
protein, thereby activating
the chimeric receptor. Known downstream proteins involved in intracellular
signaling can then
be assayed for expected modifications i.e. phosphorylation. Other methods
known to those in
the art can also be used to identify signaling molecules involved in receptor
activity.
5.10.15 ANTI-INFLAMMATORY ACTIVITY
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Compositions of the present invention may also exhibit anti-inflammatory
activity. The
anti-inflammatory activity may be achieved by providing a stimulus to cells
involved in the
inflammatory response, by inhibiting or promoting cell-cell interactions (such
as, for example,
cell adhesion), by inhibiting or promoting chemotaxis of cells involved in the
inflammatory
process, inhibiting or promoting cell extravasation, or by stimulating or
suppressing production
of other factors which more directly inhibit or promote an inflammatory
response.
Compositions with such activities can be used to treat inflammatory conditions
including
chronic or acute conditions, including without limitation intimation
associated with infection
(such as 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 such as TNF or IL-1.
Compositions of
the invention may also be useful to treat anaphylaxis and hypersensitivity to
an antigenic
substance or material. Compositions of this invention may be utilized to
prevent or treat
conditions such as, but not limited to, sepsis, acute pancreatitis, endotoxin
shock, cytokine
induced shock, rheumatoid arthritis, chronic inflammatory arthritis,
pancreatic cell damage
from diabetes mellitus type 1, graft versus host disease, inflammatory bowel
disease,
inflamation associated with pulmonary disease, other autoimmune disease or
inflammatory
disease, an antiproliferative agent such as for acute or chronic mylegenous
leukemia or in the
prevention of premature labor secondary to intrauterine infections.
5.10.16 LEUKEMIAS
Leukemias and related disorders may be treated or prevented by administration
of a
therapeutic that promotes or inhibits function of the polynucleotides and/or
polypeptides of the
invention. Such leukemias and related disorders include but are not limited to
acute leukemia,
acute lymphocytic leukemia, acute myelocytic leukemia, myeloblastic,
promyelocytic,
myelomonocytic, monocytic, erythroleukemia, chronic leukemia, chronic
myelocytic
(granulocytic) leukemia and chronic lymphocytic leukemia (for a review of such
disorders, see
Fishman et al., 1985, Medicine, 2d Ed., J.B. Lippincott Co., Philadelphia).
5.10.17 NERVOUS SYSTEM DISORDERS
Nervous system disorders, involving cell types which can be tested for
efficacy of
intervention with compounds that modulate the activity of the polynucleotides
and/or
polypeptides of the invention, and which can be treated upon thus observing an
indication of
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therapeutic utility, include but are not limited to nervous system injuries,
and diseases or
disorders which result in either a disconnection of axons, a diminution or
degeneration of
neurons, or demyelination. Nervous system lesions which may be treated in a
patient
(including human and non-human mammalian patients) according to the invention
include but
are not limited to the following lesions of either the central (including
spinal cord, brain) or
peripheral nervous systems:
(i) traumatic lesions, including lesions caused by physical injury or
associated with
surgery, for example, lesions which sever a portion of the nervous system, or
compression
injuries;
(ii) ischemic lesions, in which a lack of oxygen in a portion of the nervous
system
results in neuronal injury or death, including cerebral infarction or
ischemia, or spinal cord
infarction or ischemia;
(iii) infectious lesions, in which a portion of the nervous system is
destroyed or
injured as a result of infection, for example, by an abscess or associated
with infection by
human immunodeficiency virus, herpes zoster, or herpes simplex virus or with
Lyme disease,
tuberculosis, syphilis;
(iv) degenerative lesions, in which a portion of the nervous system is
destroyed or
injured as a result of a degenerative process including but not limited to
degeneration
associated with Parkinson's disease, Alzheimer's disease, Huntington's chorea,
or amyotrophic
lateral sclerosis;
(v) lesions associated with nutritional diseases or disorders, in which a
portion of
the nervous system is destroyed or injured by a nutritional disorder or
disorder of metabolism
including but not limited to, vitamin B12 deficiency, folic acid deficiency,
Wernicke disease,
tobacco-alcohol amblyopia, Marchiafava-Bignami disease (primary degeneration
of the corpus
callosum), and alcoholic cerebellar degeneration;
(vi) neurological lesions associated with systemic diseases including but not
limited
to diabetes (diabetic neuropathy, Bell's palsy), systemic lupus erythematosus,
carcinoma, or
sarcoidosis;
(vii) lesions caused by toxic substances including alcohol, lead, or
particular
neurotoxins; and
(viii) demyelinated lesions in which a portion of the nervous system is
destroyed or
injured by a demyelinating disease including but not limited to multiple
sclerosis, human
immunodeficiency virus-associated myelopathy, transverse myelopathy br various
etiologies,
progressive multifocal leukoencephalopathy, and central pontine myelinolysis.
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Therapeutics which are useful according to the invention for treatment of a
nervous
system disorder may be selected by testing for biological activity in
promoting the survival or
differentiation of neurons. For example, and not by way of limitation,
therapeutics which
elicit any of the following effects may be useful according to the invention:
(i) increased survival time of neurons in culture;
(ii) increased sprouting of neurons in culture or in vivo;
(iii) increased production of a neuron-associated molecule in culture or i~
vivo, e. g. ,
choline acetyltransferase or acetylcholinesterase with respect to motor
neurons;
(iv) decreased symptoms of neuron dysfunction in vivo, such as observed during
chronic pain; or
(v) proliferation and differentiation of neural precursors for the treatment
of neural
degenerative diseases, e.g., Parkinson's, Alzheimer's.
Such effects may be measured by any method known in the art. In preferred, non-
limiting embodiments, increased survival of neurons may be measured by the
method set forth
in Arakawa et al. (1990, J. Neurosci. 10:3507-3515); increased sprouting of
neurons may be
detected by methods set forth in Pestronk et al. (1980, Exp. Neurol. 70:65-82)
or Brown et al.
(1981, Ann. Rev. Neurosci. 4:17-42); increased production of neuron-associated
molecules
may be measured by bioassay, enzymatic assay, antibody binding, Northern blot
assay, etc.,
depending on the molecule to be measured; and motor neuron dysfunction may be
measured by
assessing the physical manifestation of motor neuron disorder, e. g. ,
weakness, motor neuron
conduction velocity, or functional disability.
In specific embodiments, motor neuron disorders that may be treated according
to the
invention include but are not limited to disorders such as infarction,
infection, exposure to
toxin, trauma, surgical damage, degenerative disease or malignancy that may
affect motor
neurons as well as other components of the nervous system, as well as
disorders that
selectively affect neurons such as amyotrophic lateral sclerosis, and
including but not limited to
progressive spinal muscular atrophy, progressive bulbar palsy, primary lateral
sclerosis,
infantile and juvenile muscular atrophy, progressive bulbar paralysis of
childhood (Fazio-
Londe syndrome), poliomyelitis and the post polio syndrome, and Hereditary
Motorsensory
Neuropathy (Charcot-Marie-Tooth Disease).
5.10.18 OTHER ACTIVITIES
A polypeptide of the invention may also exhibit one or more of the following
additional
activities or effects: inhibiting the growth, infection or function of, or
killing, infectious
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agents, including, without limitation, bacteria, viruses, fungi and other
parasites; effecting
(suppressing or enhancing) bodily characteristics, including, without
limitation, height, weight,
hair color, eye color, skin, fat to lean ratio or other tissue pigmentation,
or organ or body part
size or shape (such as, for example, breast augmentation or diminution, change
in bone form
or shape); effecting biorhythms or circadian cycles or rhythms; effecting the
fertility of male
or female subjects; effecting the metabolism, catabolism, anabolism,
processing, utilization,
storage or elimination of dietary fat, lipid, protein, carbohydrate, vitamins,
minerals, co-
factors or other nutritional factors or component(s); effecting behavioral
characteristics,
including, without limitation, appetite, libido, stress, cognition (including
cognitive disorders),
depression (including depressive disorders) and violent behaviors; providing
analgesic effects
or other pain reducing effects; promoting differentiation and growth of
embryonic stem cells in
lineages other than hematopoietic lineages; hormonal or endocrine activity; in
the case of
enzymes, correcting deficiencies of the enzyme and treating deficiency-related
diseases;
treatment of hyperproliferative disorders (such as, for example, psoriasis);
immunoglobulin-
like activity (such as, for example, the ability to bind antigens or
complement); and the ability
to act as an antigen in a vaccine composition to raise an immune response
against such protein
or another material or entity which is cross-reactive with such protein.
5.10.19 IDENTIFICATION OF POLYMORPHISMS
The demonstration of polymorphisms makes possible the identification of such
polymorphisms in human subjects and the pharmacogenetic use of this
information for
diagnosis and treatment. Such polymorphisms may be associated with, e.g.,
differential
predisposition or susceptibility to various disease states (such as disorders
involving
inflammation or immune response) or a differential response to drug
administration, and this
genetic information can be used to tailor preventive or therapeutic treatment
appropriately. For
example, the existence of a polymorphism associated with a predisposition to
inflammation or
autoimmune disease makes possible the diagnosis of this condition in humans by
identifying the
presence of the polymorphism.
Polymorphisms can be identified in a variety of ways known in the art which
all
generally involve obtaining a sample from a patient, analyzing DNA from the
sample,
optionally involving isolation or amplification of the DNA, and identifying
the presence of the
polymorphism in the DNA. For example, PCR may be used to amplify an
appropriate
fragment of genomic DNA which may then be sequenced. Alternatively, the DNA
may be
subjected to allele-specific oligonucleotide hybridization (in which
appropriate oligonucleotides
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are hybridized to the DNA under conditions permitting detection of a single
base mismatch) or
to a single nucleotide extension assay (in which an oligonucleotide that
hybridizes immediately
adjacent to the position of the polymorphism is extended with one or more
labeled
nucleotides). In addition, traditional restriction fragment length
polymorphism analysis (using
restriction enzymes that provide differential digestion of the genomic DNA
depending on the
presence or absence of the polymorphism) may be performed. Arrays with
nucleotide
sequences of the present invention can be used to detect polymorphisms. The
array can
comprise modified nucleotide sequences of the present invention in order to
detect the
nucleotide sequences of the present invention. In the alternative, any one of
the nucleotide
sequences of the present invention can be placed on the array to detect
changes from those
sequences.
Alternatively a polymorphism resulting in a change in the amino acid sequence
could
also be detected by detecting a corresponding change in amino acid sequence of
the protein,
e.g., by an antibody specific to the variant sequence.
5.10.20 ARTHRITIS AND INFLAMMATION
The immunosuppressive effects of the compositions of the invention against
rheumatoid
arthritis is determined in an experimental animal model system. The
experimental model
system is adjuvant induced arthritis in rats, and the protocol is described by
J. Holoshitz, et
at., 1983, Science, 219:56, or by B. Waksman et al., 1963, Int. Arch. Allergy
Appl.
Immunol., 23:129. Induction of the disease can be caused by a single
injection, generally
intradermally, of a suspension of killed Mycobacterium tuberculosis in
complete Freund's
adjuvant (CFA). The route of injection can vary, but rats may be injected at
the base of the tail
with an adjuvant mixture. The polypeptide is administered in phosphate
buffered solution
(PBS) at a dose of about 1-5 mg/kg. The control consists of administering PBS
only.
The procedure for testing the effects of the test compound would consist of
intradermally injecting killed Mycobacterium tuberculosis in CFA followed by
immediately
administering the test compound and subsequent treatment every other day until
day 24. At 14,
15, 18, 20, 22, and 24 days after injection of Mycobacterium CFA, an overall
arthritis score
may be obtained as described by J. Holoskitz above. An analysis of the data
would reveal that
the test compound would have a dramatic affect on the swelling of the joints
as measured by a
decrease of the arthritis score.
5.11 THERAPEUTIC METHODS
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The compositions (including polypeptide fragments, analogs, variants and
antibodies or
other binding partners or modulators including antisense polynucleotides) of
the invention have
numerous applications in a variety of therapeutic methods. Examples of
therapeutic
applications include, but are not limited to, those exemplified herein.
5.11.1 EXAMPLE
One embodiment of the invention is the administration of an effective amount
of the
metallocarboxypeptidase-like polypeptides or other composition of the
invention to individuals
affected by a disease or disorder that can be modulated by regulating the
peptides of the
invention. While the mode of administration is not particularly important,
parenteral
administration is preferred. An exemplary mode of administration is to deliver
an intravenous
bolus. The dosage of metallocarboxypeptidase-like polypeptides or other
composition of the
invention will normally be determined by the prescribing physician. It is to
be expected that
the dosage will vary according to the age, weight, condition and response of
the individual
patient. Typically, the amount of polypeptide administered per dose will be in
the range of
about 0.01 ~.g/kg to 100 mg/kg of body weight, with the preferred dose being
about 0.1 ~glkg
to 10 mg/kg of patient body weight. For parenteral administration,
rnetallocarboxypeptidase-
like polypeptides of the invention will be formulated in an injectable form
combined with a
pharmaceutically acceptable parenteral vehicle. Such vehicles are well known
in the art and
examples include water, saline, Ringer's solution, dextrose solution, and
solutions consisting
of small amounts of the human serum albumin. The vehicle may contain minor
amounts of
additives that maintain the isotonicity and stability of the polypeptide or
other active ingredient.
The preparation of such solutions is within the skill of the art.
5.12 PHARMACEUTICAL FORMULATIONS AND ROUTES OF
ADMINISTRATION
A protein or other composition of the present invention (from whatever source
derived,
including without limitation from recombinant and non-recombinant sources and
including
antibodies and other binding partners of the polypeptides of the invention)
may be administered
to a patient in need, by itself, or in pharmaceutical compositions where it is
mixed with
suitable carriers or excipient(s) at doses to treat or ameliorate a variety of
disorders. Such a
composition may optionally contain (in addition to protein or other active
ingredient and a
carrier) diluents, fillers, salts, buffers, stabilizers, solubilizers, and
other materials well known
in the art. The term "pharmaceutically acceptable" means a non-toxic material
that does not
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interfere with the effectiveness of the biological activity of the active
ingredient(s). The
characteristics of the carrier will depend on the route of administration. The
pharmaceutical
composition of the invention may also contain cytokines, lymphokines, or other
hematopoietic
factors such as M-CSF, GM-CSF, TNF, IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7,
IL-8, IL-9,
IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IFN, TNFO, TNFl, TNF2, G-CSF, Meg-
CSF,
thrombopoietin, stem cell factor, and erythropoietin. In further compositions,
proteins of the
invention may be combined with other agents beneficial to the treatment of the
disease or
disorder in question. These agents include various growth factors such as
epidermal growth
factor (EGF), platelet-derived growth factor (PDGF), transforming growth
factors (TGF-a and
TGF-(3), insulin-like growth factor (IGF), as well as cytokines described
herein.
The pharmaceutical composition may further contain other agents which either
enhance
the activity of the protein or other active ingredient or complement its
activity or use in
treatment. Such additional factors and/or agents may be included in the
pharmaceutical
composition to produce a synergistic effect with protein or other active
ingredient of the
invention, or to minimize side effects. Conversely, protein or other active
ingredient of the
present invention may be included in formulations of the particular clotting
factor, cytokine,
lymphokine, other hematopoietic factor, thrombolytic or anti-thrombotic
factor, or anti-
inflammatory agent to minimize side effects of the clotting factor, cytokine,
lymphokine, other
hematopoietic factor, thrombolytic or anti-thrombotic factor, or anti-
inflammatory agent (such
as IL-lRa, IL-1 Hyl, IL-1 Hy2, anti-TNF, corticosteroids, immunosuppressive
agents). A
protein of the present invention may be active in multimers (e.g.,
heterodimers or
homodimers) or complexes with itself or other proteins. As a result,
pharmaceutical
compositions of the invention may comprise a protein of the invention in such
multimeric or
complexed form.
As an alternative to being included in a pharmaceutical composition of the
invention
including a first protein, a second protein or a therapeutic agent may be
concurrently
administered with the first protein (e.g., at the same time, or at differing
times provided that
therapeutic concentrations of the combination of agents is achieved at the
treatment site).
Techniques for formulation and administration of the compounds of the instant
application may
be found in "Remington's Pharmaceutical Sciences," Mack Publishing Co.,
Easton, PA, latest
edition. A therapeutically effective dose further refers to that amount of the
compound
sufficient to result in amelioration of symptoms, e. g. , treatment, healing,
prevention or
amelioration of the relevant medical condition, or an increase in rate of
treatment, healing,
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prevention or amelioration of such conditions. When applied to an individual
active
ingredient, administered alone, a therapeutically effective dose refers to
that ingredient alone.
When applied to a combination, a therapeutically effective dose refers to
combined amounts of
the active ingredients that result in the therapeutic effect, whether
administered in combination,
serially or simultaneously.
In practicing the method of treatment or use of the present invention, a
therapeutically
effective amount of protein or other active ingredient of the present
invention is administered
to a mammal having a condition to be treated. Protein or other active
ingredient of the present
invention may be administered in accordance with the method of the invention
either alone or
in combination with other therapies such as treatments employing cytokines,
lymphokines or
other hematopoietic factors. When co- administered with one or more cytokines,
lymphokines
or other hematopoietic factors, protein or other active ingredient of the
present invention may
be administered either simultaneously with the cytokine(s),, lymphokine(s),
other hematopoietic
factor(s), thrombolytic or anti-thrombotic factors, or sequentially. If
administered
sequentially, the attending physician will decide on the appropriate sequence
of administering
protein or other active ingredient of the present invention in combination
with cytokine(s),
lymphokine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic
factors.
5.12.1 ROUTES OF ADMINISTRATION
Suitable routes of administration may, for example, include oral, rectal,
transmucosal,
or intestinal administration; parenteral delivery, including intramuscular,
subcutaneous,
intramedullary injections, as well as intrathecal, direct intraventricular,
intravenous,
intraperitoneal, intranasal, or intraocular injections. Administration of
protein or other active
ingredient of the present invention used in the pharmaceutical composition or
to practice the
method of the present invention can be carried out in a variety of
conventional ways, such as
oral ingestion, inhalation, topical application or cutaneous, subcutaneous,
intraperitoneal,
parenteral or intravenous injection. Intravenous administration to the patient
is preferred.
Alternately, one may administer the compound in a local rather than systemic
manner,
for example, via injection of the compound directly into a arthritic joints or
in fibrotic tissue,
often in a depot or sustained release formulation. In order to prevent the
scarring process
frequently occurring as complication of glaucoma surgery, the compounds may be
administered topically, for example, as eye drops. Furthermore, one may
administer the drug
in a targeted drug delivery system, for example, in a liposome coated with a
specific antibody,
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targeting, for example, arthritic or fibrotic tissue. The liposomes will be
targeted to and taken
up selectively by the afflicted tissue.
The polypeptides of the invention are administered by any route that delivers
an
effective dosage to the desired site of action. The determination of a
suitable route of
administration and an effective dosage for a particular indication is within
the level of skill in
the art. Preferably for wound treatment, one administers the therapeutic
compound directly to
the site. Suitable dosage ranges for the polypeptides of the invention can be
extrapolated from
these dosages or from similar studies in appropriate animal models. Dosages
can then be
adjusted as necessary by the clinician to provide maximal therapeutic benefit.
5.12.2 COMPOSITIONSIFORMULATIONS
Pharmaceutical compositions for use in accordance with the present invention
thus may
be formulated in a conventional manner using one or more physiologically
acceptable carriers
comprising excipients and auxiliaries which facilitate processing of the
active compounds into
preparations which can be used pharmaceutically. These pharmaceutical
compositions may be
manufactured in a manner that is itself known, e.g., by means of conventional
mixing,
dissolving, granulating, dragee-making, levigating, emulsifying,
encapsulating, entrapping or
lyophilizing processes. Proper formulation is dependent upon the route of
administration
chosen. When a therapeutically effective amount of protein or other active
ingredient of the
present invention is administered orally, protein or other active ingredient
of the present
invention will be in the form of a tablet, capsule, powder, solution or
elixir. When
administered in tablet form, the pharmaceutical composition of the invention
may additionally
contain a solid carrier such as a gelatin or an adjuvant. The tablet, capsule,
and powder contain
from about 5 to 95 % protein or other active ingredient of the present
invention, and preferably
from about 25 to 90 % protein or other active ingredient of the present
invention. When
administered in liquid form, a liquid carrier such as water, petroleum, oils
of animal or plant
origin such as peanut oil, mineral oil, soybean oil, or sesame oil, or
synthetic oils may be
added. The liquid form of the pharmaceutical composition may further contain
physiological
saline solution, dextrose or other saccharide solution, or glycols such as
ethylene glycol,
propylene glycol or polyethylene glycol. When administered in liquid form, the
pharmaceutical composition contains from about 0.5 to 90 % by weight of
protein or other
active ingredient of the present invention, and preferably from about 1 to 50
% protein or other
active ingredient of the present invention.
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When a therapeutically effective amount of protein or other active ingredient
of the
present invention is administered by intravenous, cutaneous or subcutaneous
injection, protein
or other active ingredient of the present invention will be in the form of a
pyrogen-free,
parenterally acceptable aqueous solution. The preparation of such parenterally
acceptable
protein or other active ingredient solutions, having due regard to pH,
isotonicity, stability, and
the like, is within the skill in the art. A preferred pharmaceutical
composition for intravenous,
cutaneous, or subcutaneous injection should contain, in addition to protein or
other active
ingredient of the present invention, an isotonic vehicle such as Sodium
Chloride Injection,
Ringer's Injection, Dextrose Injection, Dextrose and Sodium Chloride
Injection, Lactated
Ringer's Injection, or other vehicle as known in the art. The pharmaceutical
composition of
the present invention may also contain stabilizers, preservatives, buffers,
antioxidants, or other
additives known to those of skill in the art. For injection, the agents of the
invention may be
formulated in aqueous solutions, preferably in physiologically compatible
buffers such as
Hanks's solution, Ringer's solution, or physiological saline buffer. For
transmucosal
administration, penetrants appropriate to the barrier to be permeated are used
in the
formulation. Such penetrants are generally known in the art.
For oral administration, the compounds can be formulated readily by combining
the
active compounds with pharmaceutically acceptable carriers well known in the
art. Such
carriers enable the compounds of the invention to be formulated as tablets,
pills, dragees,
capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral
ingestion by a patient
to be treated. Pharmaceutical preparations for oral use can be obtained solid
excipient,
optionally grinding a resulting mixture, and processing the mixture of
granules, after adding
suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable
excipients are, in
particular, fillers such as sugars, including lactose, sucrose, mannitol, or
sorbitol; cellulose
preparations such as, for example, maize starch, wheat starch, rice starch,
potato starch,
gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose,
sodium
carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). If desired,
disintegrating agents
may be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic
acid or a salt
thereof such as sodium alginate. Dragee cores are provided with suitable
coatings. For this
purpose, concentrated sugar solutions may be used, which may optionally
contain gum arabic,
talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or
titanium dioxide, lacquer
solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or
pigments may be
added to the tablets or dragee coatings for identification or to characterize
different
combinations of active compound doses.
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Pharmaceutical preparations which can be used orally include push-fit capsules
made of
gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer,
such as glycerol or
sorbitol. The push-fit capsules can contain the active ingredients in
admixture with filler such
as lactose, binders such as starches, and/or lubricants such as talc or
magnesium stearate and,
optionally, stabilizers. In soft capsules, the active compounds may be
dissolved ~or suspended
in suitable liquids, such as fatty oils, liquid paraffin, or liquid
polyethylene glycols. In
addition, stabilizers may be added. All formulations for oral administration
should be in
dosages suitable for such administration. For buccal administration, the
compositions may
take the form of tablets or lozenges formulated in conventional manner.
For administration by inhalation, the compounds for use according to the
present
invention are conveniently delivered in the form of an aerosol spray
presentation from
pressurized packs or a nebuliser, with the use of a suitable propellant, e. g.
,
dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane,
carbon dioxide or
other suitable gas. In the case of a pressurized aerosol the dosage unit may
be determined by
providing a valve to deliver a metered amount. Capsules and cartridges of, e.
g. , gelatin for
use in an inhaler or insufflator may be formulated containing a powder mix of
the compound
and a suitable powder base such as lactose or starch. The compounds may be
formulated for
parenteral administration by injection, e.g. , by bolus injection or
continuous infusion.
Formulations for injection may be presented in unit dosage form, e. g. , in
ampules or in multi-
dose containers, with an added preservative. The compositions may take such
forms as
suspensions, solutions or emulsions in oily or aqueous vehicles, and may
contain formulatory
agents such as suspending, stabilizing and/or dispersing agents.
Pharmaceutical formulations for parenteral administration include aqueous
solutions of
the active compounds in water-soluble form. Additionally, suspensions of the
active
compounds may be prepared as appropriate oily injection suspensions. Suitable
lipophilic
solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty
acid esters, such as
ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may
contain
substances which increase the viscosity of the suspension, such as sodium
carboxymethyl
cellulose, sorbitol, or dextran. Optionally, the suspension may also contain
suitable stabilizers
or agents which increase the solubility of the compounds to allow for the
preparation of highly
concentrated solutions. Alternatively, the active ingredient may be in powder
form for
constitution with a suitable vehicle, e. g. , sterile pyrogen-free water,
before use.
The compounds may also be formulated in rectal compositions such as
suppositories or
retention enemas, e. g. , containing conventional suppository bases such as
cocoa butter or other
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glycerides. In addition to the formulations described previously, the
compounds may also be
formulated as a depot preparation. Such long acting formulations may be
administered by
implantation (for example subcutaneously or intramuscularly) or by
intramuscular injection.
Thus, for example, the compounds may be formulated with suitable polymeric or
hydrophobic
materials (for example as an emulsion in an acceptable oil) or ion exchange
resins, or as
sparingly soluble derivatives, for example, as a sparingly soluble salt.
A pharmaceutical carrier for the hydrophobic compounds of the invention is a
co-
solvent system comprising benzyl alcohol, a nonpolar surfactant, a water-
miscible organic
polymer, and an aqueous phase. The co-solvent system may be the VPD co-solvent
system.
~ VPD is a solution of 3 % w/v benzyl alcohol, 8 % w/v of the nonpolar
surfactant polysorbate
80, and 65 % w/v polyethylene glycol 300, made up to volume in absolute
ethanol. The VPD
co-solvent system (VPD:SW) consists of VPD diluted 1:1 with a 5 % dextrose in
water
solution. This co-solvent system dissolves hydrophobic compounds well, and
itself produces
low toxicity upon systemic administration. Naturally, the proportions of a co-
solvent system
may be varied considerably without destroying its solubility and toxicity
characteristics.
Furthermore, the identity of the co-solvent components may be varied: for
example, other low-
toxicity nonpolar surfactants may be used instead of polysorbate 80; the
fraction size of
polyethylene glycol may be varied; other biocompatible polymers may replace
polyethylene
glycol, e.g. polyvinyl pyrrolidone; and other sugars or polysaccharides may
substitute for
dextrose. Alternatively, other delivery systems for hydrophobic pharmaceutical
compounds
may be employed. Liposomes and emulsions are well known examples of delivery
vehicles or
carriers for hydrophobic drugs. Certain organic solvents such as
dimethylsulfoxide also may be
employed, 'although usually at the cost of greater toxicity. Additionally, the
compounds may
be delivered using a sustained-release system, such as semipermeable matrices
of solid
hydrophobic polymers containing the therapeutic agent. Various types of
sustained-release
materials have been established and are well known by those skilled in the
art. Sustained-
release capsules may, depending on their chemical nature, release the
compounds for a few
weeks up to over 100 days. Depending on the chemical nature and the biological
stability of
the therapeutic reagent, additional strategies for protein or other active
ingredient stabilization
may be employed.
The pharmaceutical compositions also may comprise suitable solid or gel phase
carriers
or excipients. Examples of such carriers or excipients include but are not
limited to calcium
carbonate, calcium phosphate, various sugars, starches, cellulose derivatives,
gelatin, and
polymers such as polyethylene glycols. Many of the active ingredients of the
invention may be
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provided as salts with pharmaceutically compatible counter ions. Such
pharmaceutically
acceptable base addition salts are those salts which retain the biological
effectiveness and
properties of the free acids and which are obtained by reaction with inorganic
or organic bases
such as sodium hydroxide, magnesium hydroxide, ammonia, trialkylamine,
dialkylamine,
monoalkylamine, dibasic amino acids, sodium acetate, potassium benzoate,
triethanol amine
and the like.
The pharmaceutical composition of the invention may be in the form of a
complex of
the proteins) or other active ingredient of present invention along with
protein or peptide
antigens. The protein and/or peptide antigen will deliver a stimulatory signal
to both B and T
lymphocytes. B lymphocytes will respond to antigen through their surface
immunoglobulin
receptor. T lymphocytes will respond to antigen through the T cell receptor
(TCR) following
presentation of the antigen by MHC proteins. MHC and structurally related
proteins including
those encoded by class I and class II MHC genes on host cells will serve to
present the peptide
antigens) to T lymphocytes. The antigen components could also be supplied as
purified
MHC-peptide complexes alone or with co-stimulatory molecules that can directly
signal T
cells. Alternatively antibodies able to bind surface immunoglobulin and other
molecules on B
cells as well as antibodies able to bind the TCR and other molecules on T
cells can be
combined with the pharmaceutical composition of the invention.
The pharmaceutical composition of the invention may be in the form of a
liposome in
which protein of the present invention is combined, in addition to other
pharmaceutically
acceptable carriers, with amphipathic agents such as lipids which exist in
aggregated form as
micelles, insoluble monolayers, liquid crystals, or lamellar layers in aqueous
solution.
Suitable lipids for liposomal formulation include, without limitation,
monoglycerides,
diglycerides, sulfatides, lysolecithins, phospholipids, saponin, bile acids,
and the like.
Preparation of such liposomal formulations is within the level of skill in the
art, as disclosed,
for example, in U.S. Patent Nos. 4,235,871; 4,501,728; 4,837,028; and
4,737,323, all of .
which are incorporated herein by reference.
The amount of protein or other active ingredient of the present invention in
the
pharmaceutical composition of the present invention will depend upon the
nature and severity
of the condition being treated, and on the nature of prior treatments which
the patient has
undergone. Ultimately, the attending physician will decide the amount of
protein or other
active ingredient of the present invention with which to treat each individual
patient. Initially,
the attending physician will administer low doses of protein or other active
ingredient of the
present invention and observe the patient's response. Larger doses of protein
or other active
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ingredient of the present invention may be administered unfit the optimal
therapeutic effect is
obtained for the patient, and at that point the dosage is not increased
further. It is
contemplated that the various pharmaceutical compositions used to practice the
method of the
present invention should contain about 0.01 ~,g to about 100 mg (preferably
about 0.1 ,ug to
about 10 mg, more preferably about 0.1 ~,g to about 1 mg) of protein or other
active ingredient
of the present invention per kg body weight. For compositions of the present
invention which
are useful for bone, cartilage, tendon or ligament regeneration, the
therapeutic method includes
administering the composition topically, systematically, or locally as an
implant or device.
When administered, the therapeutic composition for use in this invention is,
of course, in a
pyrogen-free, physiologically acceptable form. Further, the composition may
desirably be
encapsulated or injected in a viscous form for delivery to the site of bone,
cartilage or tissue
damage. Topical administration may be suitable for wound healing and tissue
repair.
Therapeutically useful agents other than a protein or other active ingredient
of the invention
which may also optionally be included in the composition as described above,
may
alternatively or additionally, be administered simultaneously or sequentially
with the
composition in the methods of the invention. Preferably for bone and/or
cartilage formation,
the composition would include a matrix capable of delivering the protein-
containing or other
active ingredient-containing composition to the site of bone and/or cartilage
damage, providing
a structure for the developing bone and cartilage and optimally capable of
being resorbed into
the body. Such matrices may be formed of materials presently in use for other
implanted
medical applications.
The choice of matrix material is based on biocompatibility, biodegradability,
mechanical properties, cosmetic appearance and interface properties. The
particular
application of the compositions will define the appropriate formulation.
Potential matrices for
the compositions may be biodegradable and chemically defined calcium sulfate,
tricalcium
phosphate, hydroxyapatite, polylactic acid, polyglycolic acid and
polyanhydrides. Other
potential materials are biodegradable and biologically well-defined, such as
bone or dermal
collagen. Further matrices are comprised of pure proteins or extracellular
matrix components.
Other potential matrices are nonbiodegradable and chemically defined, such as
sintered
hydroxyapatite, bioglass, aluminates, or other ceramics. Matrices may be
comprised of
combinations of any ~of the above mentioned types of material, such as
polylactic acid and
hydroxyapatite or collagen and tricalcium phosphate. The bioceramics may be
altered in
composition, such as in calcium-aluminate-phosphate and processing to alter
pore size, particle
size, particle shape, and biodegradability. Presently preferred is a 50:50
(mole weight)
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copolymer of lactic acid and glycolic acid in the form of porous particles
having diameters
ranging from 150 to 800 microns. In some applications, it will be useful to
utilize a
sequestering agent, such as carboxymethyl cellulose or autologous blood clot,
to prevent the
protein compositions from disassociating from the matrix.
A preferred family of sequestering agents is cellulosic° materials such
as alkylcelluloses
(including hydroxyalkylcelluloses), including methylcellulose, ethylcellulose,
hydroxyethylcellulose, hydroxypropylcellulose, hydroxypropyl-methylcellulose,
and
carboxymethylcellulose, the most preferred being cationic salts of
carboxymethylcellulose
(CMC). Other preferred sequestering agents include hyaluronic acid, sodium
alginate,
IO poly(ethylene glycol), polyoxyethylene oxide, carboxyvinyl polymer and
polyvinyl alcohol).
The amount of sequestering agent useful herein is 0.5-20 wt % , preferably 1-
10 wt % based on
total formulation weight, which represents the amount necessary to prevent
desorption of the
protein from the polymer matrix and to provide appropriate handling of the
composition, yet
not so much that the progenitor cells are prevented from infiltrating the
matrix, thereby
15 providing the protein the opportunity to assist the osteogenic activity of
the progenitor cells. In
further compositions, proteins or other active ingredient of the invention may
be combined
with other agents beneficial fo the treatment of the bone and/or cartilage
defect, wound, or
tissue in question. These agents include various growth factors such as
epidermal growth
factor (EGF), platelet derived growth factor (PDGF), transforming growth
factors (TGF-a and
20 TGF-(3), and insulin-like growth factor (IGF).
The therapeutic compositions are also presently valuable for veterinary
applications.
Particularly domestic animals and thoroughbred horses, in addition to humans,
are desired
patients for such treatment with proteins or other active ingredient of the
present invention.
The dosage regimen of a protein-containing pharmaceutical composition to be
used in tissue
25 regeneration will be determined by the attending physician-considering
various factors which
modify the action of the proteins, e.g., amount of tissue weight desired to be
formed, the site
of damage, the condition of the damaged tissue, the size of a wound, type of
damaged tissue
(e. g. , bone), the patient's age, sex, and diet, the severity of any
infection, time of
administration and other clinical factors. The dosage may vary with the type
of matrix used in
30 the reconstitution and with inclusion of other proteins in the
pharmaceutical composition. For
example, the addition of other known growth factors, such as IGF I (insulin
like growth factor
I), to the final composition, may also effect the dosage. Progress can be
monitored by periodic
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assessment of tissue/bone growth andlor repair, for example, X-rays,
histomorphometric
determinations and tetracycline labeling.
Polynucleotides of the present invention can also be used for gene therapy.
Such
polynucleotides can be introduced either in vivo or ex vivo into cells for
expression in a
mammalian subject. Polynucleotides of the invention may also be administered
by other known
methods for introduction of nucleic acid into a cell or organism (including,
without limitation,
in the form of viral vectors or naked DNA). Cells may also be cultured ex vivo
in the presence
of proteins of the present invention in order to proliferate or to produce a
desired effect on or
activity in such cells. Treated cells can then be introduced in vivo for
therapeutic purposes.
5.12.3 EFFECTIVE DOSAGE
Pharmaceutical compositions suitable for use in the present invention include
compositions wherein the active ingredients are contained in an effective
amount to achieve its
intended purpose. More specifically, a therapeutically effective amount means
an amount
effective to prevent development of or to alleviate the existing symptoms of
the subject being
treated. Determination of the effective amount is well within the capability
of those skilled in
the art, especially in light of the detailed disclosure provided herein. For
any compound used
in the method of the invention, the therapeutically effective dose can be
estimated initially from
appropriate in vitro assays. For example, a dose can be formulated in animal
models to achieve
a circulating concentration range that can be used to more accurately
determine useful doses in
humans. For example, a dose can be formulated in animal models to achieve a
circulating
concentration range that includes the ICso as determined in cell culture (i.
e. , the concentration
of the test compound which achieves a half maximal inhibition of the protein's
biological
activity). Such information can be used to more accurately determine useful
doses in humans.
A therapeutically effective dose refers to that amount of the compound that
results in
amelioration of symptoms or a prolongation of survival in a patient. Toxicity
and therapeutic
efficacy of such compounds can be determined by standard pharmaceutical
procedures in cell
cultures or experimental animals, e. g. , for determining the LDso (the dose
lethal to 50 % of the
population) and the EDso (the dose therapeutically effective in 50% of the
population). The
dose ratio between toxic and therapeutic effects is the therapeutic index and
it can be expressed
as the ratio between LDso and EDso. Compounds which exhibit high therapeutic
indices are
preferred. The data obtained from these cell culture assays and animal studies
can be used in
formulating a range of dosage for use in human. The dosage of such compounds
lies
preferably within a range of circulating concentrations that include the EDso
with little or no
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toxicity. The dosage may vary within this range depending upon the dosage form
employed
and the route of administration utilized. The exact formulation, route of
administration and
dosage can be chosen by the individual physician in view of the patient's
condition. See, e.g. ,
Fingl et al., 1975, in "The Pharmacological Basis of Therapeutics", Ch. 1 p.1.
Dosage
amount and interval may be adjusted individually to provide plasma levels of
the active moiety
which are sufficient to maintain the desired effects, or minimal effective
concentration (MEC).
The MEC will vary for each compound but can be estimated from in vitro data.
Dosages
necessary to achieve the MEC will depend on individual characteristics and
route of
administration. However, HPLC assays or bioassays can be used to determine
plasma
concentrations .
Dosage intervals can also be determined using MEC value. Compounds should be
administered using a regimen which maintains plasma levels above the MEC for
10-90 % of the
time, preferably between 30-90 % and most preferably between 50-90 % . In
cases of local
administration or selective uptake, the effective local concentration of the
drug may not be
related to plasma concentration.
An exemplary dosage regimen for polypeptides or other compositions of the
invention
will be in the range of about 0.01 p,g/kg to 100 mg/kg of body weight daily,
with the preferred
dose being about 0.1 p,g/kg to 25 mg/kg of patient body weight daily, varying
in adults and
children. Dosing may be once daily, or equivalent doses may be delivered at
longer or shorter
intervals.
The amount of composition administered will, of course, be dependent on the
subject
being treated, on the subject's age and weight, the severity of the
affliction, the manner of
administration and the judgment of the prescribing physician.
5.12.4 PACKAGING '
The compositions may, if desired, be presented in a pack or dispenser device
which
may contain one or more unit dosage forms containing the active ingredient.
The pack may,
for example, comprise metal or plastic foil, such as a blister pack. The pack
or dispenser
device may be accompanied by instructions for administration. Compositions
comprising a
compound of the invention formulated in a compatible pharmaceutical carrier
may also be
prepared, placed in an appropriate container, and labeled for treatment of an
indicated
condition.
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5.13 ANTIBODIES
Also included in the invention are antibodies to proteins, or fragments of
proteins of the
invention. The term "antibody" as used herein refers to irnmunoglobulin
molecules and
immunologically active portions of immunoglobulin (Ig) molecules, i.e.,
molecules that contain
an antigen-binding site that specifically binds (immunoreacts with) an
antigen. Such antibodies
include, but are not limited to, polyclonal, monoclonal, chimeric, single
chain, Fab, Fab~ and
Ftab~>z fragments, and an Fab expression library. In general, an antibody
molecule obtained from
humans relates to any of the classes IgG, IgM, IgA, IgE and IgD, which differ
from one
another by the nature of the heavy chain present in the molecule. Certain
classes have
subclasses as well, such as IgG~, IgGz, and others. Furthermore, in humans,
the light chain
may be a kappa chain or a lambda chain. Reference herein to antibodies
includes a reference
to all such classes, subclasses and types of human antibody species.
An isolated related protein of the invention may be intended to serve as an
antigen, or a
portion or fragment thereof, and additionally can be used as an immunogen to
generate
antibodies that immunospecifically bind the antigen, using standard techniques
for polyclonal
and monoclonal antibody preparation. The full-length protein can be used or,
alternatively, the
invention provides antigenic peptide fragments of the antigen for use as
immunogens. An
antigenic peptide fragment comprises at least 6 amino acid residues of the
amino acid sequence
of the full length protein, such as an amino acid sequence shown in SEQ ID NO:
4, 6 - 19, 24
- 25, or 27, and encompasses an epitope thereof such that an antibody raised
against the
peptide forms a specific immune complex with the full length protein or with
any fragment that
contains the epitope. Preferably, the antigenic peptide comprises at least 10
amino acid
residues, or at least 15 amino acid residues, or at least 20 amino acid
residues, or at least 30
amino acid residues. Preferred epitopes encompassed by the antigenic peptide
are regions of
the protein that are located on its surface; commonly these are hydrophilic
regions.
In certain embodiments of the invention, at least one epitope encompassed by
the
antigenic peptide is a region of metallocarboxypeptidase-like protein that is
located on the
surface of the protein, e.g., a hydrophilic region. A hydrophobicity analysis
of the human
related protein sequence will indicate which regions of a related protein are
particularly
hydrophilic and, therefore, are likely to encode surface residues useful for
targeting antibody
production. As a means for targeting antibody production, hydropathy plots
showing regions
of hydrophilicity and hydrophobicity may be generated by any method well known
in the art,
including, for example, the Kyte Doolittle or the Hopp Woods methods, either
with or without
Fourier transformation. See, e.g., Hopp and Woods, 1981, Proc. Nat. Acad. Sci.
USA 78:
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3824-3828; Kyte and Doolittle 1982, J. Mol. Biol. 157: 105-142., each of which
is
incorporated herein by reference in its entirety. Antibodies that are specific
for one or more
domains within an antigenic protein, or derivatives, fragments, analogs or
homologs thereof,
are also provided herein.
A protein of the invention, or a derivative, fragment, analog, homolog or
ortholog
thereof, mayabe utilized as an immunogen in the generation of antibodies that
immunospecifically bind these protein components.
The term "specific for" indicates that the variable regions of the antibodies
of the
invention recognize and bind polypeptides of the invention exclusively (r. e.
, able to distinguish
the polypeptide of the invention from other similar polypeptides despite
sequence identity,
homology, or similarity found in the family of polypeptides), but may also
interact with other
proteins (for example, S. aureus protein A or other antibodies in ELISA
techniques) through
interactions with sequences outside the variable region of the antibodies, and
in particular, in
the constant region of the molecule. Screening assays to determine binding
specificity of an
antibody of the invention are well known and routinely practiced in the art.
For a
comprehensive discussion of such assays, see Harlow et al. (Eds), Antibodies A
Laboratory
Manual; Cold Spring Harbor Laboratory; Cold Spring Harbor, NY (1988), Chapter
6.
Antibodies that recognize and bind fragments of the polypeptides of the
invention are also
contemplated, provided that the antibodies are first and foremost specific
for, as defined above,
full-length polypeptides of the invention. As with antibodies that are
specific for full length
polypeptides of the invention, antibodies of the invention that recognize
fragments are those
which can distinguish polypeptides from the same family of polypeptides
despite inherent
sequence identity, homology, or similarity found in the family of proteins.
Antibodies of the invention are useful for, for example, therapeutic purposes
(by
modulating activity of a polypeptide of the invention), diagnostic purposes to
detect or
quantitate a polypeptide of the invention, as well as purification of a
polypeptide of the
invention. Kits comprising an antibody of the invention for any of the
purposes described
herein are also comprehended. In general, a kit of the invention also includes
a control antigen
for which the antibody is immunospecific. The invention further provides a
hybridoma that
produces an antibody according to the invention. Antibodies of the invention
are useful for
detection and/or purification of the polypeptides of the invention.
Monoclonal antibodies binding to the protein of the invention may be useful
diagnostic
agents for the immunodetection of the protein. Neutralizing monoclonal
antibodies binding to
the protein may also be useful therapeutics for both conditions associated
with the protein and
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also in the treatment of some forms of cancer where abnormal expression of the
protein is
involved. In the case of cancerous cells or leukemic cells, neutralizing
monoclonal antibodies
against the protein may be useful in detecting and preventing the metastatic
spread of the
cancerous cells, which may be mediated by the protein.
The labeled antibodies of the present invention can be used for iu vitro, in
vivo, and in
situ assays to identify cells or tissues in which a fragment of the
polypeptide of interest is
expressed. The antibodies may also be used directly in therapies or other
diagnostics. The
present invention further provides the above-described antibodies immobilized
on a solid
support. Examples of such solid supports include plastics such as
polycarbonate, complex
carbohydrates such as agarose and Sepharose~, acrylic resins and such as
polyacrylamide and
latex beads. Techniques for coupling antibodies to such solid supports are
well known in the
art (Weir, D.M. et al., "Handbook of Experimental Immunology" 4th Ed.,
Blackwell
Scientific Publications, Oxford, England, Chapter 10 (1986); Jacoby, W.D. et
al., Meth.
Enzym. 34 Academic Press, N.Y. (1974)). The immobilized antibodies of the
present
invention can be used for in vitro, in vivo, and in situ assays as well as for
immuno-affinity
purification of the proteins of the present invention.
Various procedures known within the art may be used for the production of
polyclonal
or monoclonal antibodies directed against a protein of the invention, or
against derivatives,
fragments, analogs homologs or orthologs thereof (see, for example,
Antibodies: A Laboratory
Manual, Harlow E, and Lane D, 1988, Cold Spring Harbor Laboratory Press, Cold
Spring
Harbor, NY, incorporated herein by reference). Some of these antibodies are
discussed
below.
5.13.1 POLYCLONAL ANTIBODIES
For the production of polyclonal antibodies, various suitable host animals
(e.g., rabbit,
goat, mouse or other mammal) may be immunized by one or more injections with
the native
protein, a synthetic variant thereof, or a derivative of the foregoing. An
appropriate
immunogenic preparation can contain, for example, the naturally occurring
immunogenic
protein, a chemically synthesized polypeptide representing the irnmunogenic
protein, or a
recombinantly expressed immunogenic protein. Furthermore, the protein may be
conjugated
to a second protein known to be immunogenic in the mammal being immunized.
Examples of
such immunogenic proteins include but are not limited to keyhole limpet
hemocyanin, serum
albumin, bovine thyroglobulin, and soybean trypsin inhibitor. The preparation
can further
include an adjuvant. Various adjuvants used to increase the immunological
response include,
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but are not limited to, Freund's (complete and incomplete), mineral gels
(e.g., aluminum
hydroxide), surface-active substances (e.g., lysolecithin, pluronic polyols,
polyanions,
peptides, oil emulsions, dinitrophenol, etc.), adjuvants usable in humans such
as Bacille
Calmette-Guerin and Corynebacterium parvum, or similar immunostimulatory
agents.
Additional examples of adjuvants that can be employed include MPL-TDM adjuvant
(monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).
The polyclonal antibody molecules directed against the immunogenic protein can
be
isolated from the mammal (e.g., from the blood) and further purified by well
known
techniques, such as affinity chromatography using protein A or protein G,
which provide
primarily the IgG fraction of immune serum. Subsequently, or alternatively,
the specific
antigen which is the target of the immunoglobulin sought, or an epitope
thereof, may be
immobilized on a column to purify the immune specific antibody by
immunoaffinity
chromatography. Purification of immunoglobulins is discussed, for example, by
D. Wilkinson
(The Scientist, published by The Scientist, Inc., Philadelphia PA, Vol. 14,
No. 8 (April 17,
2000), pp. 25-28).
5.13.2 MONOCLONAL ANTI$ODIES
The term "monoclonal antibody" (MAb) or "monoclonal antibody composition", as
used herein, refers to a population of antibody molecules that contain only
one molecular
species of antibody molecule consisting of a unique light chain gene product
and a unique
heavy chain gene product. In particular, the complementarity determining
regions (CDRs) of
the monoclonal antibody are identical in all the molecules of the population.
MAbs thus
contain an antigen-binding site capable of immunoreacting with a particular
epitope of the
antigen characterized by a unique binding affinity for it.
Monoclonal antibodies can be prepared using hybridoma methods, such as those
described by Kohler and Milstein, Nature, 256:495 (1975). In a hybridoma
method, a mouse,
hamster, or other appropriate host animal, is typically immunized with an
immunizing agent to
elicit lymphocytes that produce or are capable of producing antibodies that
will specifically
bind to the immunizing agent. Alternatively, the lymphocytes can be immunized
in vitro.
The immunizing agent will typically include the protein antigen, a fragment
thereof or a
fusion protein thereof. Generally, either peripheral blood lymphocytes are
used if cells of
human origin are desired, or spleen cells or lymph node cells are used if non-
human
mammalian sources are desired. The lymphocytes.are then fused with an
immortalized cell
line using a suitable fusing agent, such as polyethylene glycol, to form a
hybridoma cell
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(Goding, Monoclonal Antibodies: Principles and Practice, Academic Press,
(1986) pp. 59-
103). Immortalized cell lines are usually transformed mammalian cells,
particularly myeloma
cells of rodent, bovine and human origin. Usually, rat or mouse myeloma cell
lines are
employed. The hybridoma cells can be cultured in a suitable culture medium
that preferably
contains one or more substances that inhibit the growth or survival of the
unfused,
immortalized cells. For example, if the parental cells lack the enzyme
hypoxanthine guanine
phosphoribosyl transferase (HGPRT or HPRT), the culture medium for the
hybridomas
typically will include hypoxanthine, aminopterin, and thymidine ("HAT
medium"), which
substances prevent the growth of HGPRT-deficient cells.
Preferred immortalized cell lines are those that fuse efficiently, support
stable high
level expression of antibody by the selected antibody-producing cells, and are
sensitive to a
medium such as HAT medium. More preferred immortalized cell lines are murine
myeloma
lines, which can be obtained, for instance, from the Salk Institute Cell
Distribution Center, San
Diego, California and the American Type Culture Collection, Manassas,
Virginia. Human
myeloma and mouse-human heteromyeloma cell lines also have been described for
the
production of human monoclonal antibodies (Kozbor, J. Immunol., 133:3001
(1984); Brodeur
et al., Monoclonal Antibody Production Technigues and Applications, Marcel
Dekker, Inc.,
New York, (1987) pp. 51-63).
The culture medium in which the hybridoma cells are cultured can then be
assayed for
the presence of monoclonal antibodies directed against the antigen.
Preferably, the binding
specificity of monoclonal antibodies produced by the hybridoma cells is
determined by
immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay
(RIA) or
enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are
known in the
art. The binding affinity of the monoclonal antibody can, for example, be
determined by the
Scatchard analysis of Munson and Pollard, Anal. Biochem., 107:220 (1980).
Preferably,
antibodies having a high degree of specificity and a high binding affinity for
the target antigen
are isolated.
After the desired hybridoma cells are identified, the clones can be subcloned
by limiting
dilution procedures and grown by standard methods. Suitable culture media for
this purpose
include, for example, Dulbecco's Modified Eagle's Medium and RPMI-1640 medium.
Alternatively, the hybridoma cells can be grown in vivo as ascites in a
mammal.
The monoclonal antibodies secreted by the subclones can be isolated or
purified from
the culture medium or ascites fluid by conventional immunoglobulin
purification procedures
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such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel
electrophoresis, dialysis, or affinity chromatography.
The monoclonal antibodies can also be made by recombinant DNA methods, such as
those described in U.S. Patent No. 4,816,567. DNA encoding the monoclonal
antibodies of
the invention can be readily isolated and sequenced using conventional
procedures (e.g., by
using oligonucleotide probes that are capable of binding specifically to genes
encoding the
heavy and light chains of marine antibodies). The hybridoma cells of the
invention serve as a
preferred source of such DNA. Once isolated, the DNA can be placed into
expression vectors,
which are then transfected into host cells such as simian COS cells, Chinese
hamster ovary
(CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin
protein, to
obtain the synthesis of monoclonal antibodies in the recombinant host cells.
The DNA also can
be modified, for example, by substituting the coding sequence for human heavy
and light chain
constant domains in place of the homologous marine sequences (U.S. Patent No.
4,816,567;
Morrison, Nature 368, 812-13 (1994)) or by covalently joining to the
immunoglobulin coding
sequence all or part of the coding sequence for a non-immunoglobulin
polypeptide. Such a
non-immunoglobulin polypeptide can be substituted for the constant domains of
an antibody of
the invention, or can be substituted for the variable domains of one antigen-
combining site of
an antibody of the invention to create a chimeric bivalent antibody.
5.13.3 HUMANIZED ANTIBODIES
The antibodies directed against the protein antigens of the invention can
further
comprise humanized antibodies or human antibodies. These antibodies are
suitable for
administration to humans without engendering an immune response by the human
against the
administered immunoglobulin. Humanized forms of antibodies are chimeric
immunoglobulins,
immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab')a or
other antigen-
binding subsequences of antibodies) that are principally comprised of the
sequence of a human
immunoglobulin, and contain minimal sequence derived from a non-human
immunoglobulin.
Humanization can be performed following the method of Winter and co-workers
(Jones et al.,
Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988);
Verhoeyen et al.,
Science, 239:1534-1536 (1988)), by substituting rodent CDRs or CDR sequences
for the
corresponding sequences of a human antibody. (See also U.S. Patent No.
5,225,539). In
some instances, Fv framework residues of the human immunoglobulin are replaced
by
corresponding non-human residues. Humanized antibodies can also comprise
residues that are
found neither in the recipient antibody nor in the imported CDR or framework
sequences. In
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general, the humanized antibody will comprise substantially all of at least
one, and typically
two, variable domains, in which all or substantially all of the CDR regions
correspond to those
of a non-human immunoglobulin and all or substantially all of the framework
regions are those
of a human immunoglobulin consensus sequence. The humanized antibody optimally
also will
S comprise at least a portion of an immunoglobulin constant region (Fc),
typically that of a
human immunoglobulin (Jones et ~1., 1986; Riechmann et al., 1988; and Presta,
Curr. On.
Struct. Biol., 2:593-S96 (1992)).
5.13.4 HUMAN ANTIBODIES
Fully human antibodies relate to antibody molecules in which essentially the
entire
sequences of both the light chain and the heavy chain, including the CDRs,
arise from human
genes. Such antibodies are termed "human antibodies", or "fully human
antibodies" herein.
Human monoclonal antibodies can be prepared by the trioma technique; the human
B-cell
hybridoma technique (see Kozbor, et al., 1983 Immunol Today 4: 72) and the EBV
hybridoma
1S technique to produce human monoclonal antibodies (see Cole, et al., 1985
In: MONOCLONAL
ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp. 77-96). Human
monoclonal
antibodies may be utilized in the practice of the present invention and may be
produced by
using human hybridomas (see Cote, et al., 1983. Proc Natl Acad Sci USA 80:
2026-2030) or .
by transforming human B-cells with Epstein Barr Virus in vitro (see Cole, et
al., 1985 In:
MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc., pp. 77-96).
In addition, human antibodies can also be produced using additional
techniques,
including phage display libraries (Hoogenboom and Winter, J. Mol. Biol.,
227:381 (1991);
Marks et al., J. Mol. Biol., 222:581 (1991)). Similarly, human antibodies can
be made by
introducing human immunoglobulin loci into transgenic animals, e.g., mice in
which the
2S endogenous immunoglobulin genes have been partially or completely
inactivated. Upon
challenge, human antibody production is observed, which closely resembles that
seen in
humans in all respects, including gene rearrangement, assembly, and antibody
repertoire. This
approach is described, for example, in U.S. Patent Nos. S,S4S,807; S,S4S,806;
S,S69,825;
S,62S,126; 5,633,425; 5,661,016, and in Marks et al. Bio/Technolo~y 10, 779-
783 (1992));
Lonberg et al. Nature 368 8S6-8S9 (1994)); Morrison (Nature 368, 812-13
(1994)); Fishwild
et al, (Nature Biotechnolo~y 14, 845-51 (1996)); Neuberger (Nature
Biotechnology 14, 826
(1996)); and Lonberg and Huszar (Intern. Rev. Immunol. 13 6S-93 (1995)).
Human antibodies may additionally be produced using transgenic nonhuman
animals
that are modified so as to produce fully human antibodies rather than the
animal's endogenous
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antibodies in response to challenge by an antigen. (See PCT publication
W094/02602). The
endogenous genes encoding the heavy and light immunoglobulin chains in the
nonhuman host
have been incapacitated, and active loci encoding human heavy and light chain
immunoglobulins are inserted into the host's genome. The human genes are
incorporated, for
example, using yeast artificial chromosomes containing the requisite human DNA
segments.
An animal which provides all the desired modifications is then obtained as
progeny by
crossbreeding intermediate transgenic animals containing fewer than the full
complement of the
modifications. The preferred embodiment of such a nonhuman animal is a mouse,
and is
termed the XenomouseTM as disclosed in PCT publications WO 96/33735 and WO
96J34096.
This animal produces B cells that secrete fully human immunoglobulins. The
antibodies can be
obtained directly from the animal after immunization with an immunogen of
interest, as, for
example, a preparation of a polyclonal antibody, or alternatively from
immortalized B cells
derived from the animal, such as hybridomas producing monoclonal antibodies.
Additionally,
the genes encoding the immunoglobulins with human variable regions can be
recovered and
expressed to obtain the antibodies directly, or can be further modified to
obtain analogs of
antibodies such as, for example, single chain Fv molecules.
An example of a method of producing a nonhuman host, exemplified as a mouse,
lacking expression of an endogenous immunoglobulin heavy chain is disclosed in
U.S. Patent
No. 5,939,598. It can be obtained by a method including deleting the J segment
genes from at
Ieast one endogenous heavy chain locus in an embryonic stem cell to prevent
rearrangement of
the locus and to prevent formation of a transcript of a rearranged
immunoglobulin heavy chain
locus, the deletion being effected by a targeting vector containing a gene
encoding a selectable
marker; and producing from the embryonic stem cell a transgenic mouse whose
somatic and
germ cells contain the gene encoding the selectable marker.
A method for producing an antibody of interest, such as a human antibody, is
disclosed
in U.S. Patent No. 5,916,771. It includes introducing an expression vector
that contains a
nucleotide sequence encoding a heavy chain into one mammalian host cell in
culture,
introducing an expression vector containing a nucleotide sequence encoding a
light chain into
another mammalian host cell, and fusing the two cells to form a hybrid cell.
The hybrid cell
expresses an antibody containing the heavy chain and the light chain.
In a further improvement on this procedure, a method for identifying a
clinically
relevant epitope on an immunogen, and a correlative method for selecting an
antibody that
binds immunospecifically to the relevant epitope with high affinity, are
disclosed in PCT
publication WO 99/53049.
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5.13.5 FAB FRAGMENTS AND SINGLE CHAIN ANTIBODIES
According. to the invention, techniques can be adapted for the production of
single-chain antibodies specific to an antigenic protein of the invention (see
e.g., U.S. Patent
No. 4,946,778). In addition, methods can be adapted for the construction of
Fab expression
libraries (see e.g., Huse, et al., 1989 Science 246: 1275-1281) to allow rapid
and effective
identification of monoclonal Fab fragments with the desired specificity for a
protein or
derivatives, fragments, analogs or homologs thereof. Antibody fragments that
contain the
idiotypes to a protein antigen may be produced by techniques known in the art
including, but
not limited to: (i) an F~aboz fragment produced by pepsin digestion of an
antibody molecule; (ii)
an Fan fragment generated by reducing the disulfide bridges of an F~ab~>z
fragment; (iii) an Fab
fragment generated by the treatment of the antibody molecule with papain and a
reducing agent
and (iv) F~ fragments.
5.13.6 BISPECIFIC ANTIBODIES
Bispecific antibodies are monoclonal, preferably human or humanized,
antibodies that
have binding specificities for at least two different antigens. In the present
case, one of the
binding specificities is for an antigenic protein of the invention. The second
binding target is
any other antigen, and advantageously is a cell-surface protein or receptor or
receptor subunit.
Methods for making bispecific antibodies are known in the art. Traditionally,
the
recombinant production of bispecific antibodies is based on the co-expression
of two
immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have
different
specificities (Milstein and Cuello, Nature, 305:537-539 (1983)). Because of
the random
assortment of immunoglobulin heavy and light chains, these hybridomas
(quadromas) produce
a potential mixture of ten different antibody molecules, of which only one has
the correct
bispecific structure. The purification of the correct molecule is usually
accomplished by
affinity chromatography steps. Similar procedures are disclosed in WO
93/08829, published
13 May 1993, and in Traunecker et al., 1991 EMBO J., 10:3655-3659.
Antibody variable domains with the desired binding specificities (antibody-
antigen
combining sites) can be fused to immunoglobulin constant domain sequences. The
fusion
preferably is with an immunoglobulin heavy-chain constant domain, comprising
at least part of
the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain
constant region
(CH1) containing the site necessary for light-chain binding present in at
least one of the
fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired,
the
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immunoglobulin light chain, are inserted into separate expression vectors, and
are co-
transfected into a suitable host organism. For further details of generating
bispecific antibodies
see, for example, Suresh et al., Methods in Enzymology,, 121:210 (1986).
According to another approach described in WO 96!27011, the interface between
a pair
of antibody molecules can be engineered to maximize the percentage of
heterodimers that are
recovered from recombinant cell culture. The preferred interface comprises at
least a part of
the CH3 region of an antibody constant domain. In this method, one or more
small amino acid
side chains from the interface of the first antibody molecule are replaced
with larger side
chains (e.g. tyrosine or tryptophan). Compensatory "cavities" of identical or
sinular size to
the large side chains) are created on the interface of the second antibody
molecule by
replacing large amino acid side chains with smaller ones (e.g. alanine or
threonine). This
provides a mechanism for increasing the yield of the heterodimer over other
unwanted
end-products such as homodimers.
Bispecific antibodies can be prepared as full length antibodies or antibody
fragments
(e.g. F(ab')z bispecific antibodies). Techniques for generating bispecific
antibodies from
antibody fragments have been described in the literature. For example,
bispecific antibodies
can be prepared using chemical linkage. Brennan et al., Science 229:81 (1985)
describe a
procedure wherein intact antibodies are proteolytically cleaved to generate
F(ab')a fragments.
These fragments are reduced in the presence of the dithiol complexing agent
sodium arsenite to
stabilize vicinal dithiols and prevent intermolecular disulfide formation. The
Fab' fragments
generated are then converted to thionitrobenzoate (TNB) derivatives. One of
the Fab'-TNB
derivatives is then reconverted to the Fab'-thiol by reduction with
mercaptoethylamine and is
mixed with an equimolar amount of the other Fab'-TNB derivative to form the
bispecific
antibody. The bispecific antibodies produced can be used as agents for the
selective
irnrnobilization of enzymes.
' Additionally, Fab' fragments can be directly recovered from E. coli and
chemically
coupled to form bispecific antibodies. Shalaby et al., J. Exp. Med. 175:217-
225 (1992)
describe the production of a fully humanized bispecific antibody F(ab')a
molecule. Each Fab'
fragment was separately secreted from E. coli and subjected to directed
chemical coupling in
vitro to form the bispecific antibody. The bispecific antibody thus formed was
able to bind to
cells overexpressing the ErbB2 receptor and normal human T cells, as well as
trigger the lytic
activity of human cytotoxic lymphocytes against human breast tumor targets.
Various techniques for making and isolating bispecific antibody fragments
directly from
recombinant cell culture have also been described. For example, bispecific
antibodies have
CA 02399672 2002-08-02
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been produced using leucine zippers. Kostelny et al., J. Immunol. 148(5):1547-
1553 (1992).
The leucine zipper peptides from the Fos and Jun proteins were linked to the
Fab' portions of
two different antibodies by gene fusion. The antibody homodimers were reduced
at the hinge
region to form monomers and then re-oxidized to form the antibody
heterodimers. This
method can also be utilized for the production of antibody homodimers. The
"diabody"
technology described by Hollinger et al., Proc. Natl. Acad. Sci. USA 90:6444-
6448 (1993)
has provided an alternative mechanism for making bispecific antibody
fragments. The
fragments comprise a heavy-chain variable domain (VH) connected to a light-
chain variable
domain (VL) by a linker which is too short to allow pairing between the two
domains on the
same chain. Accordingly, the VH and VL domains of one fragment are forced to
pair with the
complementary V~ and VH domains of another fragment, thereby forming two
antigen-binding
sites. Another strategy for making bispecific antibody fragments by the use of
single-chain Fv
(sFv) dimers has also been reported. See, Gruber et al., J. Immunol. 152:5368
(1994).
Antibodies with more than two valencies are contemplated. For example,
trispecific
antibodies can be prepared. Tutt et al., J. Imrnunol. 147:60 (1991).
Exemplary bispecific antibodies can bind to two different epitopes, at least
one of
which originates in the protein antigen of the invention. Alternatively, an
anti-antigenic arm of
an immunoglobulin molecule can be combined with an arm which binds to a
triggering
molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD2, CD3,
CD28, or B7), or
Fc receptors for IgG (Fc R), such as Fc RI (CD64), Fc RII (CD32) and Fc RIII
(CD16) so as
to focus cellular defense mechanisms to the cell expressing the particular
antigen. Bispecific
antibodies can also be used to direct cytotoxic agents to cells which express
a particular
antigen. These antibodies possess an antigen-binding arm and an arm which
binds a cytotoxic
agent or a radionuclide chelator, such as EOTUBE, DPTA, DOTA, or TETA. Another
bispecific antibody of interest binds the protein antigen described herein and
further binds
tissue factor (TF).
5.13.7 HETEROCONJUGATE ANTIBODIES
Heteroconjugate antibodies are also within the scope of the present invention.
Heteroconjugate antibodies are composed of two covalently joined antibodies.
Such antibodies
have, for example, been proposed to target immune system cells to unwanted
cells (U.S.
Patent No. 4,676,980), and for treatment of HIV infection (WO 91/00360; WO
92/200373; EP
03089). It is contemplated that the antibodies can be prepared in vitro using
known methods in
synthetic protein chemistry, including those involving crosslinking agents.
For example,
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immunotoxins can be constructed using a disulfide exchange reaction or by
forming a thioether
bond. Examples of suitable reagents for this purpose include iminothiolate and
methyl-4-
mercaptobutyrimidate and those disclosed, for example, in LT.S. Patent No.
4,676,980.
5.13.8 EFFECTOR FUNCTION ENGINEERING
It can be desirable to modify the antibody of the invention with respect to
effector
function, so as to enhance, e.g., the effectiveness of the antibody in
treating cancer. For
example, cysteine residues) can be introduced into the Fc region, thereby
allowing interchain
disulfide bond formation in this region. The homodimeric antibody thus
generated can have
improved internalization capability and/or increased complement-mediated cell
killing and
antibody-dependent cellular cytotoxicity (ADCC). See Caron et al., J. Exp
Med., 176: 1191-
1195 (1992) and Shopes, J. Immunol., 148: 2918-2922 (1992). Homodimeric
antibodies with
enhanced anti-tumor activity can also be prepared using heterobifunctional
cross-linkers as
described in Wolff et al. Cancer Research, 53: 2560-2565 (1993).
Alternatively, an antibody
can be engineered that has dual Fc regions and can thereby have enhanced
complement lysis
and ADCC capabilities. See Stevenson et al., Anti-Cancer Drug Design, 3: 219-
230 (1989).
5.13.9 IMMUNOCONJUGATES
The invention also pertains to immunoconjugates comprising an antibody
conjugated to
a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an
enzymatically active toxin
of bacterial, fungal, plant, or animal origin, or fragments thereof), or a
radioactive isotope
(i.e., a radioconjugate).
Chemotherapeutic agents useful in the generation of such immunoconjugates have
been
described above. Enzymatically active toxins and fragments thereof that can be
used include
diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin
A chain (from
Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-
sarcin,
Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins
(PAPI, PAPA, and
PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis
inhibitor,
gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the
tricothecenes. A variety of
radionuclides are available for the production of radioconjugated antibodies.
Examples include
zizBi~ isil~ isiln~ 9oY~ and laeRe.
Conjugates of the antibody and cytotoxic agent are made using a variety of
bifunctional
protein-coupling agents such as N-succinimidyl-3-(2-pyridyldithiol) propionate
(SPDP),
iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl
adipimidate
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HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as
glutareldehyde), bis-
azido compounds (such as bis (p-azidobenzoyl} hexanediamine), bis-diazonium
derivatives
(such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as
tolyene 2,6-
diisocyanate), and bis-active fluorine compounds (such as 1,5-difluoro-2,4-
dinitrobenzene).
For example, a ricin immunotoxin can be prepared as described in Vitetta et
al., Science, 238:
1098 (1987). Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylene
triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for
conjugation of
radionucleotide to the antibody. See W094/11026.
In another embodiment, the antibody can be conjugated to a "receptor" (such
streptavidin) for utilization in tumor pretargeting wherein the antibody-
receptor conjugate is
administered to the patient, followed by removal of unbound conjugate from the
circulation
using a clearing agent and then administration of a "ligand" (e.g., avidin)
that is in turn
conjugated to a cytotoxic agent.
5.14 COMPUTER READABLE SEQUENCES
In one application of this embodiment, a nucleotide sequence of the present
invention
can be recorded on computer readable media. As used herein, "computer readable
media"
refers to any medium which can be read and accessed directly by a computer.
Such media
include, but are not limited to: magnetic storage media, such as floppy discs,
hard disc storage
medium, and magnetic tape; optical storage media such as CD-ROM; electrical
storage media
such as RAM and ROM; and hybrids of these categories such as magnetic/optical
storage
media. A skilled artisan can readily appreciate how any of the presently known
computer
readable mediums can be used to create a manufacture comprising computer
readable medium
having recorded thereon a nucleotide sequence of the present invention. As
used herein,
"recorded" refers to a process for storing information on computer readable
medium. A
skilled artisan can readily adopt any of the presently known methods for
recording information
on computer readable medium to generate manufactures comprising the nucleotide
sequence
information of the present invention.
A variety of data storage structures are, available to a skilled artisan for
creating a
computer readable medium having recorded thereon a nucleotide sequence of the
present
invention. The choice of the data storage structure will generally be based on
the means
chosen to access the stored information. In addition, a variety of data
processor programs and
formats can be used to store the nucleotide sequence information of the
present invention on
computer readable medium. The sequence information can be represented in a
word
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processing text file, formatted in commercially-available software such as
WordPerfect and
Microsoft Word, or represented in the form of an ASCII file, stored in a
database application,
such as DB2, Sybase, Oracle, or the like. A skilled artisan can readily adapt
any number of
data processor structuring formats (e. g. text file or database) in order to
obtain computer
readable medium having recorded thereon the nucleotide sequence information of
the present
invention.
By providing any of the nucleotide sequences SEQ ID NO: 1-3, 5, 23, or 26 or a
representative fragment thereof; or a nucleotide sequence at least 95 %
identical to any of the
nucleotide sequences of the SEQ ID NO: 1-3, 5, 23, or 26 in computer readable
form, a
skilled artisan can routinely access the sequence information for a variety of
purposes.
Computer software is publicly available which allows a skilled artisan to
access sequence
information provided in a computer readable medium. The examples which follow
demonstrate how software which implements the BLAST (Altschul et aL, J. Mol.
Biol.
215:403-410 (1990)) and BLAZE (Brutlag et al., Comp. Chem. 17:203-207 (1993))
search
algorithms on a Sybase system is used to identify open reading frames (ORFs)
within a nucleic
acid sequence. Such ORFs may be protein encoding fragments and may be useful
in producing
commercially important proteins such as enzymes used in fermentation reactions
and in the
production of commercially useful metabolites.
As used herein, "a computer-based system" refers to the hardware means,
software
means, and data storage means used to analyze the nucleotide sequence
information of the
present invention. The minimum hardware means of the computer-based systems of
the
present invention comprises a central processing unit (CPU), input means,
output means, and
data storage means. A skilled artisan can readily appreciate that any one of
the currently
available computer-based systems are suitable for use in the present
invention. As stated
above, the computer-based systems of the present invention comprise a data
storage means
having stored therein a nucleotide sequence of the present invention and the
necessary
hardware means and software means for supporting and implementing a search
means. As
used herein, "data storage means" refers to memory which can store nucleotide
sequence
information of the present invention, or a memory access means which can
access
manufactures having recorded thereon the nucleotide sequence information of
the present
invention.
As used herein, "search means" refers to one or more programs which are
implemented
on the computer-based system to compare a target sequence or target structural
motif with the
sequence information stored within the data storage means. Search means are
used to identify
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fragments or regions of a known sequence which match a particular target
sequence or target
motif. A variety of known algorithms are disclosed publicly and a variety of
commercially
available software for conducting search means are and can be used in the
computer-based
systems of the present invention. Examples of such software includes, but is
not limited to,
Smith-Waterman, MacPattern (EMBL), BLASTN and BLASTA (NPOLYPEPTIDEIA). A
skilled artisan can readily recognize that any one of the available algorithms
or implementing
software packages for conducting homology searches can be adapted for use in
the present
computer-based systems. As used herein, a "target sequence" can be any nucleic
acid or
amino acid sequence of six or more nucleotides or two or more amino acids. A
skilled artisan
can readily recognize that the longer a target sequence is, the less likely a
target sequence will
be present as a random occurrence in the database. The most preferred sequence
length of a
target sequence is from about 10 to 100 amino acids, or from about 30 to 300
nucleotide
residues. However, it is well recognized that searches for commercially
important fragments,
such as sequence fragments involved in gene expression and protein processing,
may be of
shorter length.
As used herein, "a target structural motif, " or "target motif, " refers to
any rationally
selected sequence or combination of sequences in which the sequences) are
chosen based on a
three-dimensional configuration which is formed upon the folding of the target
motif. There
are a variety of target motifs known in the art. Protein target motifs
include, but are not
limited to, enzyme active sites and signal sequences. Nucleic acid target
motifs include, but
are not limited to, promoter sequences, hairpin structures and inducible
expression elements
(protein binding sequences).
5.15 TRIPLE HELIX FORMATION
In addition, the fragments of the present invention, as broadly described, can
be used to
control gene expression through triple helix formation or antisense DNA or
RNA, both of
which methods are based on the binding of a polynucleotide sequence to DNA or
RNA.
Polynucleotides suitable for use in these methods are usually 20 to 40 bases
in length and are
designed to be complementary to a region of the gene involved in transcription
(triple helix -
see Lee et al., Nucl. Acids Res. 6:3073 (1979); Cooney et al., Science
15241:456 (1988); and
Dervan et al., Science 251:1360 (1991)) or to the mRNA itself (antisense -
Olmno, J.
Neurochem. 56:560 (1991); Oligodeoxynucleotides 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
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translation of an mRNA molecule into polypeptide. Both techniques have been
demonstrated
to be effective in model systems. Information contained in the sequences of
the present
invention is necessary for the design of an antisense or triple helix
oligonucleotide.
5.16 DIAGNOSTIC ASSAYS AND KITS
The present invention further provides methods to identify the presence or
expression
of one of the ORFs of the present invention, or homolog thereof, in a test
sample, using a
nucleic acid probe or antibodies of the present invention, optionally
conjugated or otherwise
associated with a suitable label.
In general, methods for detecting a polynucleotide of the invention can
comprise
contacting a sample with a compound that binds to and forms a complex with the
polynucleotide for a period sufficient to form the complex, and detecting the
complex, so that
if a complex is detected, a polynucleotide of the invention is detected in the
sample. Such
methods can also comprise contacting a sample under stringent hybridization
conditions with
nucleic acid primers that anneal to a polynucleotide of the invention under
such conditions, and
amplifying annealed polynucleotides, so that if a polynucleotide is amplified,
a polynucleotide
of the invention is detected in the sample.
In general, methods for detecting a polypeptide of the invention can comprise
contacting a sample with a compound that binds to and forms a complex with the
polypeptide
for a period sufficient to form the complex, and detecting the complex, so
that if a complex is
detected, a polypeptide of the invention is detected in the sample.
In detail, such methods comprise incubating a test sample with one or more of
the
antibodies or one or more of the nucleic acid probes of the present invention
and assaying for
binding of the nucleic acid probes or antibodies to components within the test
sample.
Conditions for incubating a nucleic acid probe or antibody with a test sample
vary.
Incubation conditions depend on the format employed in the assay, the
detection methods
employed, and the type and nature of the nucleic acid probe or antibody used
in the assay.
One skilled in the art will recognize that any one of the commonly available
hybridization,
amplification or irnrnunological assay formats can readily be adapted to
employ the nucleic
acid probes or antibodies of the present invention. Examples of such assays
can be found in
Chard, T., An Introduction to Radioimmunoassay and Related Techniques,
Elsevier Science
Publishers, Amsterdam, The Netherlands (1986); Bullock, G.R. et al.,
Techniques in
Immunocytochemistry, Academic Press, Orlando, FL Vol. 1 (1982), Vol. 2 (1983),
Vol. 3
(1985); Tijssen, P., Practice and Theory of immunoassays: Laboratory
Techniques in
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Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam,
The
Netherlands (1985). The test samples of the present invention include cells,
protein or
membrane extracts of cells, or biological fluids such as sputum, blood, serum,
plasma, or
urine. The test sample used in the above-described method will vary based on
the assay
format, nature of the detection method and the tissues, cells or extracts used
as the sample to
be assayed. Methods for preparing protein extracts or membrane extracts of
cells are well
known in the art and can be readily be adapted in order to obtain a sample
which is compatible
with the system utilized.
In another embodiment of the present invention, kits are provided which
contain the
necessary reagents to carry out the assays of the present invention.
Specifically, the invention
provides a compartment kit to receive, in close confinement, one or more
containers which
comprises: (a) a first container comprising one of the probes or antibodies of
the present
invention; and (b) one or more other containers comprising one or more of the
following: wash
reagents, reagents capable of detecting presence of a bound probe or antibody.
In detail, a compartment kit includes any kit in which reagents are contained
in separate
containers. Such containers include small glass containers, plastic containers
or strips of
plastic or paper. Such containers allows one to efficiently transfer reagents
from one
compartment to another compartment such that the samples and reagents are not
cross-
contaminated, and the agents or solutions of each container can be added in a
quantitative
fashion from one compartment to another. Such containers will include a
container which will
accept the test sample, a container which contains the antibodies used in the
assay, containers
which contain wash reagents (such as phosphate buffered saline, Tris-buffers,
etc.), and
containers which contain the reagents used to detect the bound antibody or
probe. Types of
detection reagents include labeled nucleic acid probes, labeled secondary
antibodies, or in the
alternative, if the primary antibody is labeled, the enzymatic, or antibody
binding,reagents
which are capable of reacting with the labeled antibody. One skilled in the
art will readily
recognize that the disclosed probes and antibodies of the present invention
can be readily
incorporated into one of the established kit formats which are well known in
the art.
5.17 MEDICAL IMAGING
The novel polypeptides and binding partners of the invention are useful in
medical
imaging of sites expressing the molecules of the invention (e.g., where the
polypeptide of the
invention is involved in the immune response, for imaging sites of
inflammation or infection).
See, e.g., Kunkel et al., U.S. Pat. NO. 5,413,778. Such methods involve
chemical attachment
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of a labeling or imaging agent, administration of the labeled polypeptide to a
subject in a
pharmaceutically acceptable carrier, and imaging the labeled polypeptide i~
vivo at the target
site.
S.1S SCREENING ASSAYS
Using the isolated proteins and polynucleotides of the invention, the present
invention
further provides methods of obtaining and identifying agents which bind to a
polypeptide
encoded by an ORF corresponding to any of the nucleotide sequences set forth
in the SEQ ID
NO: 1-3, 5, 23, or 26, or bind to a specific domain of the polypeptide encoded
by the nucleic
acid. In detail, said method comprises the steps of:
(a) contacting an agent with an isolated protein encoded by an ORF of the
present
invention, or nucleic acid of the invention; and
(b) determining whether the agent binds to said protein or said nucleic acid.
In general, therefore, such methods for identifying compounds that bind to a
polynucleotide of the invention can comprise contacting a compound with a
polynucleotide of
the invention for a time sufficient to form a polynucleotide/compound complex,
and detecting
the complex, so that if a polynucleotide/compound complex is detected, a
compound that binds
to a polynucleotide of the invention is identified.
Likewise, in general, therefore, such methods for identifying compounds that
bind to a
polypeptide of the invention can comprise contacting a compound with a
polypeptide of the
invention for a time sufficient to form a polypeptide/compound complex, and
detecting the
complex, so that if a polypeptidelcompound complex is detected, a compound
that binds to a
polynucleotide of the invention is identified.
Methods for identifying compounds that bind to a polypeptide of the invention
can also
comprise contacting a compound with a polypeptide of the invention in a cell
for a time
sufficient to form a polypeptide/compound complex, wherein the complex drives
expression of
a receptor gene sequence in the cell, and detecting the complex by detecting
reporter gene
sequence expression, so that if a polypeptide/compound complex is detected, a
compound that
binds a polypeptide of the invention is identified.
Compounds identified via such methods can include compounds which modulate the
activity of a polypeptide of the invention (that is, increase or decrease its
activity, relative to
activity observed in the absence of the compound). Alternatively, compounds
identified via
such methods can include compounds which modulate the expression of a
polynucleotide of the
invention (that is, increase or decrease expression relative to expression
levels observed in the
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absence of the compound). Compounds, such as compounds identified via the
methods of the
invention, can be tested using standard assays well known to those of skill in
the art for their
ability to modulate activity/expression.
The agents screened in the above assay can be, but are not limited to,
peptides,
carbohydrates, vitamin derivatives, or other pharmaceutical agents. The agents
can be selected
and screened at random or rationally selected or designed using protein
modeling techniques.
For random screening, agents such as peptides, carbohydrates, pharmaceutical
agents
and the like are selected at random and are assayed for their ability to bind
to the protein
encoded by the ORF of the present invention. Alternatively, agents may be
rationally selected
or designed. As used herein, an agent is said to be "rationally selected or
designed" when the
agent is chosen based on the configuration of the particular protein. For
example, one skilled
in the art can readily adapt currently available procedures to generate
peptides, pharmaceutical
agents and the like, capable of binding to a specific peptide sequence, in
order to generate
rationally designed antipeptide peptides, for example see Hurby et al. ,
Application of Synthetic
Peptides: Antisense Peptides," In Synthetic Peptides, A User's Guide, W.H.
Freeman, NY
(1992), pp. 289-307, and Kaspczak et al., Biochemistry 28:9230-8 (1989), or
pharmaceutical
agents, or the like.
In addition to the foregoing, one class of agents of the present invention, as
broadly
described, can be used to control gene expression through binding to one of
the ORFs or
EMFs of the present invention. As described above, such agents can be randomly
screened or
rationally designed/selected. Targeting the ORF or EMF allows a skilled
artisan to design
sequence specific or element specific agents, modulating the expression of
either a single ORF
or multiple ORFs which rely on the same EMF for expression control. One class
of DNA
binding agents are agents which contain base residues which hybridize or form
a triple helix
formation by binding to DNA or RNA. Such agents can be based on the classic
phosphodiester, ribonucleic acid backbone, or can be a variety of sulfhydryl
or polymeric
derivatives which have base attachment capacity.
Agents suitable for use in these methods usually contain 20 to 40 bases and
are
designed to be complementary to a 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); Oligodeoxynucleotides 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
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translation of an mRNA molecule into polypeptide. Both techniques have been
demonstrated
to be effective in model systems. Information contained in the sequences of
the present
invention is necessary for the design of an antisense or triple helix
oligonucleotide and other
DNA binding agents.
Agents which bind to a protein encoded by one of the ORFs of the present
invention
can be used as a diagnostic agent. Agents which bind to a protein encoded by
one of the ORFs
of the present invention can be formulated using known techniques to generate
a
pharmaceutical composition.
5.19 USE OF NUCLEIC ACIDS AS PROBES
Another aspect of the subject invention is to provide for polypeptide-specific
nucleic
acid hybridization probes capable of hybridizing with naturally occurring
nucleotide sequences.
The hybridization probes of the subject invention may be derived from any of
the nucleotide
sequences SEQ ID NO: 1-3, 5, 23, or 26. Because the corresponding gene is only
expressed
in a limited number of tissues, a hybridization probe derived from of any of
the nucleotide
sequences SEQ ID NO: 1-3, 5, 23, or 26 can be used as an indicator of the
presence of RNA
of cell type of such a tissue in a sample.
Any suitable hybridization technique can be employed, such as, for example, in
situ
hybridization. PCR as described in US Patents Nos. 4,683,195 and 4,965,188
provides
additional uses for oligonucleotides based upon the nucleotide sequences. Such
probes used in
PCR may be of recombinant origin, may be chemically synthesized, or a mixture
of both. The
probe will comprise a discrete nucleotide sequence for the detection of
identical sequences or a
degenerate pool of possible sequences for identification of closely related
genomic sequences.
Other means for producing specific hybridization probes for nucleic acids
include the
cloning of nucleic acid sequences into vectors for the production of mRNA
probes. Such
vectors are known in the art and are commercially available and may be used to
synthesize
RNA probes ih vitro by means of the addition of the appropriate RNA polymerase
as T7 or
SP6 RNA polymerase and the appropriate radioactively labeled nucleotides. The
nucleotide
sequences may be used to construct hybridization probes for mapping their
respective genomic
sequences. The nucleotide sequence provided herein may be mapped to a
chromosome or
specific regions of a chromosome using well known genetic and/or chromosomal
mapping
techniques. These techniques include in situ hybridization, linkage analysis
against known
chromosomal markers, hybridization screening with libraries or flow-sorted
chromosomal
preparations specific to known chromosomes, and the like. The technique of
fluorescent in
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situ hybridization of chromosome spreads has been described, among other
places, in Verma et
al (1988) Human Chromosomes: A Manual of Basic Techniques, Pergamon Press, New
York
NY.
Fluorescent in ,ritu hybridization of chromosomal preparations and other
physical
chromosome mapping techniques may be correlated with additional genetic map
data.
Examples of genetic map data can be found in the 1994 Genome Issue of Science
(265:1981f).
Correlation between the location of a nucleic acid on a physical chromosomal
map and a
specific disease (or predisposition to a specific disease) may help delimit
the region of DNA
associated with that genetic disease. The nucleotide sequences of the subject
invention may be
used to detect differences in gene sequences between normal, carrier or
affected individuals.
5.20 PREPARATION OF SUPPORT BOUND OLIGONUCLEOTIDES
Oligonucleotides, i.e., small nucleic acid segments, may be readily prepared
by, for
example, directly synthesizing the oligonucleotide by chemical means, as is
commonly practiced
using an automated oligonucleotide synthesizer.
Support bound oligonucleotides may be prepared by any of the methods known to
those of
skill in the art using any suitable support such as glass, polystyrene or
Teflon. One strategy is to
precisely spot oligonucleotides synthesized by standard synthesizers.
Immobilization can be
achieved using passive adsorption (Inouye & Hondo, 1990 J. Clin Microbiol
28(6) 1462-72);
using UV light (Nagata et al., 1985; Dahlen et al., 1987; Morrissey & Collins,
Mol. Cell Probes
1989 3(2) 189-.207) or by covalent binding of base modified DNA (Kelleret al.,
1988; 1989); all
references being specifically incorporated herein.
Another strategy that may be employed is the use of the strong biotin-
streptavidin
interaction as a linker. For example, Broude et al. (1994) Proc. Natl. Acad.
Sci USA 91(8)
3072-6 describe the use of biotinylated probes, although these are duplex
probes, that are
immobilized on streptavidin-coated magnetic beads. Streptavidin-coated beads
may be purchased
from Dynal, Oslo. Of course, this same linking chemistry is applicable to
coating any surface
with streptavidin. Biotinylated probes may be purchased from various sources,
such as, e.g.,
Operon Technologies (Alameda, CA).
Nunc Laboratories (Naperville, IL) is also selling suitable material that
could be used.
Nunc Laboratories have developed a method by which DNA can be covalently bound
to the
microwell surface termed Covalink NH. CovaLink NH is a polystyrene surface
grafted with
secondary amino groups ( > NH) that serve as bridge-heads for further covalent
coupling.
CovaLink Modules may be purchased from Nunc Laboratories. DNA molecules may be
bound
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to CovaLink exclusively at the 5'-end by a phosphoramidate bond, allowing
immobilization of
more than 1 pmol of DNA (Rasmussenet al., (1991) Anal Biochem 198(1) 138-42.
The use of CovaLink NH strips for covalent binding of DNA molecules at the 5'-
end has
been described (Rasmussen et al., 1991). In this technology, a phosphoramidate
bond is
employed (Chu et al., 1983 Nucleic Acids 11(18) 6513-29). This is beneficial
as immobilization
using only a single covalent bond is preferred. The phosphoramidate bond joins
the DNA to the
CovaLink NH secondary amino groups that are positioned at the end of
spacer~arms covalently
grafted onto the polystyrene surface through a 2 nm long spacer arm. To link
an oligonucleotide
to CovaLink NH via an phosphoramidate bond, the oligonucleotide terminus must
have a 5'-end
phosphate group. It is, perhaps, even possible for biotin to be covalently
bound to CovaLink and
then streptavidinused to bind the probes.
More specifically, the linkage method includes dissolving DNA in water (7.5
ng/ul) and
denaturing for 10 min. at 95°C and cooling on ice for 10 min. Ice-cold
0.1 M 1-methylimidazole,
pH 7.0 (1-MeIrn~), is then added to a final concentration of 10 mM 1-Mehrv. A
ss DNA solution
is then dispensed into CovaLink NH strips (75 ul/well) standing on ice.
Carbodiimide 0.2 M 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide(EDC),
dissolved in
10 mM 1-MeIm~, is made fresh and 25 u1 added per well. The strips are
incubated for 5 hours at
50°C. After incubation the strips are washed using, e.g., Nunc-Immuno
Wash; first the wells are
washed 3 times, then they are soaked with washing solution for 5 min., and
finally they are
washed 3 times (where in the washing solution is 0.4 N NaOH, 0.25 % SDS heated
to S~C).
It is contemplated that a further suitable method for use with the present
invention is that
described in PCT Patent Application WO 90103382 (Southern & Maskos),
incorporated herein by
reference. This method of preparing an oligonucleotide bound to a support
involves attaching a
nucleoside 3'-reagent through the phosphate group by a covalent phosphodiester
link to aliphatic
hydroxyl groups carried by the support. The oligonucleotide is then
synthesized on the supported
nucleoside and protecting groups removed from the synthetic oligonucleotide
chain under standard
conditions that do not cleave the oligonucleotide from the support. Suitable
reagents include
nucleoside phosphoramidite and nucleoside hydrogen phosphorate.
An on-chip strategy for the preparation of DNA probe for the preparation of
DNA probe
arrays may be employed. For example, addressable laser-activated
photodeprotection may be
employed in the chemical synthesis of oligonucleotides directly on a glass
surface, as described by
Fodor et al. (1991) Science 251(4995) 767-73, incorporated herein by
reference. Probes may
also be immobilized on nylon supports as described by Van Ness et al. (1991)
Nucleic Acids Res.
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19(12) 3345-50; or linked to Teflon using the method of Duncan & Cavalier
(1988) Anal
Biochem 169(1) 104-8; all references being specifically incorporated herein.
To link an oligonucleotide to a nylon support, as described by Van Ness et al.
(1991),
requires activation of the nylon surface via alkylation and selective
activation of the 5'-amine of
oligonucleotides with cyanuric chloride.
One particular way to prepare support bound oligonucleotides is to utilize the
light-
generated synthesis described by Pease et al., (1994) Proc. Natl. Acad. Sci
USA 91(11) 5022-6.
These authors used current photolithographic techniques to generate arrays of
immobilized
oligonucleotide probes (DNA chips). These methods, in which light is used to
direct the synthesis
of oligonucleotide probes in high-density, miniaturized arrays, utilize
photolabile 5'-protectedN
acyl-deoxynucleosidephosphoramidites, surface linker chemistry and versatile
combinatorial
synthesis strategies. A matrix of 256 spatially defined oligonucleotide probes
may be generated in
this manner.
5.21 PREPARATION OF NUCLEIC ACII? FRAGMENTS
The nucleic acids may be obtained from any appropriate source, such as cDNAs,
genomic
DNA, chromosomal DNA, microdissected chromosome bands, cosmid or YAC inserts,
and
RNA, including mRNA without any amplification steps. For example, Sambrooket
al. (I989)
describes three protocols for the isolation of high molecular weight DNA from
mammalian cells
(p. 9. I4-9.23).
DNA fragments may be prepared as clones in M13, plasmid or lambda vectors
andlor
prepared directly from genomic DNA or cDNA by PCR or other amplification
methods. Samples
may be prepared or dispensed in multiwell plates. About 100-1000 ng of DNA
samples may be
prepared in 2-500 ml of final volume.
The nucleic acids would then be fragmented by any of the methods known to
those of skill
in the art including, for example, using restriction enzymes as described at
9.24-9.28 of
Sambrook et al. (1989), shearing by ultrasound and NaOH treatment.
Low pressure shearing is also appropriate, as described by Schrieferet al.
(1990) Nucleic
Acids Res. 18(24) 7455-6. In this method, DNA samples are passed through a
small French
pressure cell at a variety of low to intermediate pressures. A lever device
allows controlled
application of low to intermediate pressures to the cell. The results of these
studies indicate that
low-pressure shearing is a useful alternative to~ sonic and enzymatic DNA
fragmentation methods.
One particularly suitable way for fragmenting DNA is contemplated to be that
using the
two base recognition endonuclease, CviJI, described by Fitzgerald et al.
(1992) Nucleic Acids
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Res. 20(14) 3753-62. These authors described an approach for the rapid
fragmentation and
fractionation of DNA into particular sizes that they contemplated to be
suitable for shotgun
cloning and sequencing.
The restriction endonuclease CviJI normally cleaves the recognition sequence
PuGCPy
S between the G and C to leave blunt ends. Atypical reaction conditions, which
alter the specificity
of this enzyme (CviJI**), yield a quasi-random distribution of DNA fragments
form the small
molecule pUCl9 (2688 base pairs). Fitzgerald et al. (1992) quantitatively
evaluated the
randomness of this fragmentation strategy, using a CviJI** digest of pUCl9
that was size
fractionated by a rapid gel filtration method and directly ligated, without
end repair, to a lac Z
minus M13 cloning vector. Sequence analysis of 76 clones showed that CviJI**
restricts pyGCPy
and PuGCPu, in addition to PuGCPy sites, and that new sequence data is
accumulated at a rate
consistent with random fragmentation.
As reported in the literature, advantages of this approach compared to
sonication and
agarose gel fractionation include: smaller amounts of DNA are required (0.2-
0.5 ug instead of 2-
1 S 5 ug); and fewer steps are involved (no preligation, end repair, chemical
extraction, or agarose
gel electrophoresis and elution are needed).
Irrespective of the manner in which the nucleic acid fragments are obtained or
prepared, it
is important to denature the DNA to give single stranded pieces available for
hybridization. This
is achieved by incubating the DNA solution for 2-5 minutes at 80-90PC. The
solution is then
cooled quickly to 2°C to prevent renaturation of the DNA fragments
before they are contacted
with the chip. Phosphate groups must also be removed from genornic DNA by
methods known in
the art.
5.22 PREPARATION OF DNA ARRAYS
Arrays may be prepared by spotting DNA samples on a support such as a nylon
2S membrane. Spotting may be performed by using arrays of metal pins (the
positions of which
correspond to an array of wells in a microtiter plate) to repeated by transfer
of about 20 n1 of a
DNA solution to a nylon membrane. By offset printing, a density of dots higher
than the density
of the wells is achieved. One to 2S dots may be accommodated in 1 mrr~,
depending on the type
of label used. By avoiding spotting in some preselected number of rows and
columns, separate
subsets (subarrays) may be formed. Samples in one subarray may be the same
genomic segment
of DNA (or the same gene) from different individuals, or may be different,
overlapped genomic
clones. Each of the subarrays may represent replica spotting of the same
samples. In one
example, a selected gene segment may be amplified from 64 patients. For each
patient, the
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amplified gene segment may be in one 96-well plate (all 96 wells containing
the same sample). A
plate fox each of the 64 patients is prepared. By using a 96-pin device, all
samples may be spotted
on one 8 x 12 cm membrane. Subarrays may contain 64 samples, one from each
patient. Where
the 96 subarrays are identical, the dot span may be 1 mn~ and there may be a 1
mm space
between subarrays.
Another approach is to use membranes or plates (available from NUNC,
Naperville,
Illinois) which may be partitioned by physical spacers e.g. a plastic grid
molded over the
membrane, the grid being similar to the sort of membrane applied to the bottom
of multiwell
plates, or hydrophobic strips. A fixed physical spacer is not preferred for
imaging by exposure to
flat phosphor-storage screens or x-ray films.
The present invention is illustrated in the following examples. Upon
consideration of the
present disclosure, one of skill in the art will appreciate that many other
embodiments and
variations may be made in the scope of the present invention. Accordingly, it
is intended that the
broader aspects of the present invention not be limited to the disclosure of
the following
examples. The present invention is not to be limited in scope by the
exemplifiedembodiments
which are intended as illustrations of single aspects of the invention, and
compositions and
methods which are functionally equivalent are within the scope of the
invention. Indeed,
numerous modifications and variations in the practice of the invention are
expected to occur to
those skilled in the art upon consideration of the present preferred
embodiments. Consequently,
the only limitations which should be placed upon the scope of the invention
are those which
appear in the appended claims.
All references cited within the body of the instant specification are hereby
incorporated by
reference in their entirety.
6.0 EXAMPLES
EXAMPLE 1
Isolation of SEO ID NO: 1 from a cDNA Library of Small Intestine
A plurality of novel nucleic acids were obtained from a cDNA library prepared
from
small intestine (Hyseq clone identification numbers 11732488 (SEQ ID NO: 1))
using standard
PCR, sequencing by hybridization sequence signature analysis, arid Sanger
sequencing
techniques. The inserts of the library were amplified with PCR using primers
specific for
vector sequences flanking the inserts. These samples were spotted onto nylon
membranes and
interrogated with oligonucleotide probes to give sequence signatures. The
clones were
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clustered into groups of similar or identical sequences, and single
representative clones were
selected from each group for gel sequencing. The 5' sequence of the amplified
inserts was
then deduced using the reverse M13 sequencing primer in a typical Sanger
sequencing
protocol. PCR products were purified and subjected to fluorescent dye
terminator cycle
sequencing. Single-pass gel sequencing was done using a 377 Applied Biosystems
(ABI)
sequencer. The insert was identified as a novel sequence not previously
obtained from this
library and not previously reported in public databases. The sequence was
designated as SEQ
ID NO: 1.
I0 EXAMPLE 2
ASSEMBLAGE OF SEO ID NO: 2
The nucleic acid of the present invention, designated as SEQ ID NO: 2 was
assembled
using SEQ ID N0:1 as a seed. Then a recursive algorithm was used to extend the
seed into an
extended assemblage, by pulling additional sequences from different databases
(i.e., Hyseq's
database containing EST sequences, dbEST version 114, gb pri 114, and UniGene
version 101)
that belong to this assemblage. The algorithm terminated when there was no
additional sequences
from the above databases that would extend the assemblage. Inclusion of
component sequences
into the assemblage was based on a BLASTN hit to the extending assemblage with
BLAST score
greater than 300 and percent identity greater than 95 % .
The nearest neighbor result for the assembled contigs were obtained by a FASTA
version
3 search against Genpept release 114, using FASTXY algorithm. FASTXY is an
improved
version of FASTA alignment which allows in-codon frame shifts. The nearest
neighbor result
showed the closest homologue for each assemblage from Genpept (and contains
the translated
amino acid sequences for which the assemblage encodes). The nearest neighbor
results is set
forth below:
SEQ ID AccessionDescription Smith- % Identity
NO: No. Waterman
Score
1611 AJ224866Homo sapiens 632 55.769
procarboxypeptidase
B
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A polypeptide was predicted to be encoded by SEQ ID NO: 2 as set forth below.
The
polypeptide was predicted using a software program called FASTY (available
from
http://fasta.bioch.vir ig nia.edu) which selects a polypeptide based on a
comparison of translated
novel polynucleotide to known polypeptides (W.R. Pearson, Methods in
Enzymology, 183: 63-98
(1990), herein incorporated by reference).
PredictedPredictedAMINO ACID ENCODED BY SEQ ID NO: 2
beginningend (A=Alanine, C=Cysteine, D=Aspartic Acid,
E=
nucleotidenucleotideGlutamic Acid, F=Phenylalanine, G=Glycine,
location location H=Histidine, I=Isoleucine, K=Lysine,
L=Leucine,
correspond-correspond-M=Methionine, N=Asparagine, P=Proline,
ing to ing to Q=Glutamine, R=Arginine, S=Serine, T=Threonine,
first last
amino amino V=Valine, W=Tryptophan, Y=Tyrosine,
acid acid
residue residue X=Unknown, *=Stop Codon, /=possible
of of nucleotide
amino amino deletion, \=possible nucleotide insertion)
acid acid
segment segment
3 497 KEV VTQHFL*VTYETHPIYYLKISQPSGNPKKIIW
DCGIHAREWIAPAFCQWFVKEILQNHKDNSRIRK
LMNLDFYVLPVLNIDGYIYTWTTDRLWRKSRSPH
NGTCFGTDLNRNFNASWCSIGASRNCQDQTFCGT
PVSEPETKAVASFIESKNDDFCA (SEQ ID NO:
19)
EXAMPLE 3
ASSEMBLAGE OF SEO ID NOs: 3, 4, 23, and 24
Assembly of the novel nucleotide sequences of SEQ ID NO: 3 and 23 were
accomplished by using the EST sequence SEQ ID NO: 1 as a seed. The seed was
extended by
gel sequencing (377 Applied Biosystems (ABI) sequencer) using primers to
extend the 3' end
(primer extension). The 5' end was extended using RACE in part, as disclosed
in Marathon-
ReadyTM cDNA User Manual (PT1156-1) (Clontech) herein incorporated by
reference. The
RACE was also done by using primers and using reverse transcribed cDNA from
mixed
mRNA obtained from Clontech, Invitrogen and Biochain.
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A polypeptide (SEQ ID NO: 4) was predicted to be encoded by SEQ ID N0:3 as set
forth below. The polypeptide was predicted using a software program called
BLASTX which
selects a polypeptide based on a comparison of translated novel
polynucleotides to known
polypeptides. The initial methionine starts at position 94 of SEQ ID NO: 3 and
the putative
stop codon, TAA, begins at position 1216 of the nucleotide sequence.
A polypeptide (SEQ ID NO: 24) was predicted to be encoded by SEQ ID NO: 23
based
on the polypeptide sequence derived from SEQ ID NO: 3. The initial methionine
starts at
position 94 of SEQ ID NO: 23 and the putative stop codon, TAA, begins at
position 1216 of
the nucleotide sequence. SEQ ID NO: 23 is a variant of SEQ ID NO: 3, where a
single
nucleotide substitution at position 348 results in a single amino acid change.
Figure 1 shows the BLASTP amino acid sequence alignment between the protein
encoded by SEQ ID NO: 3 (i.e. SEQ ID NO: 4) and the Bothops jararaca
carboxypeptidase
homolog protein (SEQ ID NO: 20) indicating that the two sequences share 67 %
similarity over
326 amino acid residues of SEQ ID NO: 4 and 46% identity over the same 326
amino acid
residues of SEQ ID NO: 4.
Figure 2 shows the BLASTP amino acid sequence alignment between the protein
encoded by SEQ ID NO: 3 (i.e. SEQ ID NO: 4) and the human carboxypeptidase B
mutant
protein (SEQ ID NO: 21) indicating that the two sequences share 66 %
similarity over 312
amino acid residues of SEQ ID NO: 4 and 48 % identity over the same 312 amino
acid residues
of SEQ ID NO: 4.
A predicted approximately twenty-residue signal peptide is encoded from
approximately
residue 1 to residue 20 inclusive of SEQ ID NO: 4 (SEQ ID NO: 16). The signal
peptide
region was predicted using the Kyte-Doolittle hydrophobicity prediction
algorithm (J. Mol
Biol, 157, pp. 105-31 (1982), incorporated herein by reference).
A predicted approximately fifteen-residue GPI anchor is encoded from
approximately
residue 360 to residue 374 inclusive of SEQ ID NO: 4 (SEQ ID NO: 17). The GPI
anchor
was predicted using the Kyte-Doolittle hydrophobicity prediction algorithm (J.
Mol Biol, 157,
pp. 105-31 (1982), incorporated herein by reference).
Using the eMATRIX software package (Stanford University, Stanford, CA) (Wu, et
al., J. Comp. Biol., vol. 6, pp. 219-235 (1999), herein incorporated by
reference), zinc
carboxypeptidase, zinc-binding region 1 protein signature sequences are
predicted. These
include regions encoded from approximately residue I29 to residuel69 inclusive
of SEQ ID
NO: 4 (SEQ ID N0:6), approximately residue 99 to 112 inclusive of SEQ ID NO: 4
(SEQ ID
NO: 7), approximately residue 50 to residue 90 inclusive of SEQ ID NO: 4 (SEQ
ID NO: 9),
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approximately residue 228 to residue 249 inclusive of SEQ ID NO: 4 (SEQ ID NO:
10),
approximately residue I73 to residue 187 inclusive of SEQ ID NO 4: (SEQ ID NO:
11),
approximately residue 199 to residue 225 inclusive of SEQ ID NO 4: (SEQ ID NO:
12), and
approximately residue 285 to residue 302 inclusive of SEQ ID NO 4: (SEQ TD
NO:15). The
eMATRIX software package (Stanford University, Stanford, CA) (Wu, et al., J.
Comp. Biol.,
vol. 6, pp. 219-235 (1999), herein incorporated by reference), has also
predicted
carboxypeptidase A metalloprotease (M14) family signature sequences encoded
from
approximately residue 99 to residue 113 inclusive of SEQ ID N0:4 (SEQ ID NO:
8),
approximately residue 233 to residue 246 inclusive of SEQ ID NO: 4 (SEQ ID NO:
13), and
approximately residue 179 to residue 187 inclusive of SEQ ID NO: 4 (SEQ ID NO:
14). The
domains corresponding to SEQ ID NO: 6 through and including SEQ ID NO: 15 are
as
follows wherein A=Alanine, C=Cysteine, D=Aspartic Acid, E= Glutamic Acid,
F=Phenylalanine, G=Glycine, H=Histidine, I=Isoleucine, K=Lysine, L=Leucine,
M=Methionine, N=Asparagine, P=Proline, Q=Glutarnine, R=Arginine, S=Serine,
T=Threonine, V=Valine, W=Tryptophan, Y=Tyrosine:
Zinc carboxypeptidases, zinc-binding region 1 domain
HKDNSRIRKLLRNLDFYVLPVLNIDGYIYTWTTDRLWRKSR
designated as SEQ ID NO: 6, p-value of 3.308e-28, BL00132C (identification
number
correlating to signature); located at residues 129-169 of SEQ ID NO: 4 and
Zinc carboxypeptidases, zinc-binding region 1 domain
KIIWMDCGIHAREW
designated as SEQ ID NO: 7, p-value of 1.871e-16, BL00132B (identification
number
correlating to signature); located at residues 99-112 of SEQ ID NO: 4 and
Zinc carboxypeptidases, zinc-binding region 1 domain
YHPMGEIYEWMREISEKYKEVVTQHFLGVTYETHPIYYLKI
designated as SEQ ID NO: 9, p-value of 1.682e-14, BL00132A (identification
number
correlating to signature); located at residues 50-90 of SEQ ID NO: 4 and
Zinc carboxypeptidases, zinc-binding region 1 domain
DILCFLTMHSYGQLILTPYGYT
designated as SEQ ID NO: 10, p-value of 7.254e-14, BL00132F (identification
number
correlating to signature); located at residues 228-249 of SEQ ID NO: 4 and
Zinc carboxypeptidases, zinc-binding region 1 domain
NNGTCFGTDLNRNFN
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designated as SEQ ID NO: 11, p-value of 2.875e-12, BL00132D (identification
number
correlating to signature); located at residues 173-187 of SEQ ID NO: 4 and
Zinc carboxypeptidases, zinc-binding region 1 domain
CQDQTFCGTGPVSEPETKAVASFIESK
designated as SEQ ID NO: 12, p-value of 3.552e-12, BL00132E (identification
number
correlating to signature); located at residues 199-225 of SEQ ID NO: 4 and
Zinc carboxypeptidases, zinc-binding region I domain DILYASSGSSRDWARDIG
designated as SEQ ID NO: 15, p-value of 4.541e-10, BL00132G (identification
number
correlating to signature); located at residues 285-302 of SEQ ID NO: 4 and
Carboxypeptidase A metalloprotease (M14) family signature domain
KIIWMDCGIHAREWI
designated as SEQ ID NO: 8, p-value of 7.857e-16, PR00765B (identification
number
correlating to signature); located at residues 99-113 of SEQ ID NO: 4 and
Carboxypeptidase A metalloprotease (M14) family signature domain
LTMHSYGQLILTPY
designated as SEQ ID NO: 13, p-value of S.SOOe-11, PR00765D (identification
number
correlating to signature); located at residues 233-246 of SEQ ID NO: 4 and
Carboxypeptidase A metalloprotease (M14) family signature domain GTDLNRNFN
designated as SEQ ID NO: 14, p-value of 1.290e-10, PR00765C (identification
number
correlating to signature); located at residues 179-187 of SEQ ID NO: 4.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA), several regions of the metallocarboxypeptidase-like polypeptide,
SEQ ID NO: 4,
were determined to have procarboxypeptidase characteristic motifs. A region at
residues 7
through 347 was found to have characteristic motifs of the porcine
procarboxypeptidase B,
with PSI BLAST e-value of 0.0, protein database identification number entry =
lnsa
(Research collaboratory for Structural Bioinformatics
http:/lwww.rcsb.org/pbd), verify score
= 0.93, located at residues 7 -347 of SEQ ID NO: 4.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc. , San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 4 was
also predicted
to have a region at residues 2 - 349 with characteristic motifs to the human
procarboxypeptidase A2, with PSI BLAST e-value 0.0, protein database
identification number
entry = laye (Research collaboratory for Structural Bioinformatics
http://www.rcsb.org/pbd),
verify score = 0.78, located at residues 2 - 349 of SEQ ID NO: 4.
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Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc. , San
Diego., CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 4 was
also predicted
to have a region at residues 2 - 347 with characteristic motifs to the porcine
pancreatic
procarboxypeptidase A, with PSI BLAST e-value 0.0, protein database
identification number
entry = lpca (Research collaboratory for Structural Bioinformatics
http://www.rcsb.org/pbd),
verify score = 0.68, located at residues 2 - 347 of SEQ ID NO: 4.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 4 was
also predicted
to have a region at residues 42 - 347 with characteristic motifs to the bovine
pancreatic
carboxypeptidase B, with PSI BLAST e-value 0.0, protein database
identification number entry
= lcpb (Research collaboratory for Structural Bioinforrnatics
http:/Iwww.rcsb.org/pbd),
verify score = 0.39, located at residues 42 - 347 of SEQ ID NO: 4.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 4 was
also predicted
to have a region at residues 40 - 347 with characteristic motifs to the bovine
pancreatic
procarboxypeptidase A, with PSI BLAST e-value 0.0, protein database
identification number
entry = 2ctc (Research collaboratory for Structural Bioinformatics
http://www.rcsb.org/pbd),
verify score = 0.86, located at residues 40 - 347 of SEQ ID NO: 4.
The metallocarboxypeptidase-like polypeptide of SEQ ID NO: 24 is also an
approximately 374-amino acid secreted, glycosylphosphatidylinositol (GPI)-
linked protein with
a predicted molecular mass of approximately 41 kDa unglycosylated. It is a
variant of the
metallocarboxypeptidase-like polypeptide of SEQ ID NO: 4 that contains a
single nucleotide
base substitution, resulting one amino acid change in the polypeptide. The
metallocarboxypeptidase-like polypeptide of SEQ ID N0: 24 has an identical
signal peptide,
GPI anchor, carboxypeptidase A metalloprotease (M14) family signatures, and
zinc
carboxypeptidases zinc-binding region 1 domains as the peptide of SEQ ID NO:
4, with the
exception of the zinc binding region-1 signature located at residues 50 - 90.
This is the region
of the polypeptides that contains the amino acid change. For SEQ ID NO: 24
this domain is as
follows:
Zinc carboxypeptidases, zinc-binding region 1 domain
YHPMGEIYEWMREISEKYKEVVTQHFLGVTYETHPMYYLKI
designated as SEQ ID NO: 27, p-value of 8.286e-15, BL00132A (identification
number
correlating to signature); located at residues 50-90 of SEQ ID NO: 24.
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Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA), several regions of the metallocarboxypeptidase-like polypeptide,
SEQ ID NO: 24,
were determined to have procarboxypeptidase characteristic motifs. A region at
residues 7
through 347 was found to have characteristic motifs of the porcine
procarboxypeptidase B,
with PSI BLAST e-value of 0.0, protein database identification number entry =
lnsa
(Research collaboratory for Structural Bioinformatics
http://www.rcsb.org/pbd), verify score
= 0.75, located at residues 7 -347 of SEQ ID NO: 24.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the rnetallocarboxypeptidase-like polypeptide of SEQ ID NO: 24 was
also
predicted to have a region at residues 2 - 349 with characteristic motifs to
the human
procarboxypeptidase A2, with PSI BLAST e-value 0.0, protein database
identification number
entry = laye (Research collaboratory for Structural Bioinformatics
http://www.rcsb.org/pbd),
verify score = 0.71, located at residues 2 - 349 of SEQ ID NO: 24.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 24 was
also
predicted to have a region at residues 2 - 347 with characteristic motifs to
the porcine
pancreatic procarboxypeptidase A, with PSI BLAST e-value 0.0, protein database
identification number entry = lpca (Research collaboratory for Structural
Bioinformatics
http://www.rcsb.org/pbd), verify score = 0.77, located at residues 2 - 347 of
SEQ ID NO:
24.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 24 was
also
predicted to have a region at residues 42 - 347 with characteristic motifs to
the bovine
pancreatic carboxypeptidase B, with PST BLAST e-value 0.0, protein database
identification
number entry = lcpb (Research collaboratory for Structural Bioinformatics
http://www.rcsb.org/pbd), verify score = 0.39, located at residues 42 - 347 of
SEQ ID NO:
24.
Using Molecular Simulations Inc. GeneAtlas software (Molecular Simulations
Inc., San
Diego, CA) the metallocarboxypeptidase-like polypeptide of SEQ ID NO: 24 was
also
predicted to have a region at residues 40 - 347 with characteristic motifs to
the bovine
pancreatic procarboxypeptidase A, with PSI BLAST e-value 0.0, protein database
identification number entry = 2ctc (Research collaboratory for Structural
Bioinformatics
http://www.rcsb.org/pbd), verify score = 0.91, located at residues 40 - 347 of
SEQ ID NO:
24.
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SEQ ID NO: 3 and 23 were determined to be present in the following tissues:
mammary gland (Invitrogen) (Hyseq library name MMG001), small intestine
(Clontech)
(Hyseq library name SIN001), and skeletal muscle (Clontech) (Hyseq library
name SKM001).
The tissue expression information was determined using the tissue source of
the ESTs that
comprise SEQ ID NO: 3 and 23 and the tissue sources of the other ESTs of the
cluster to
which those ESTs belong. Clusters were made depending on the sequence
signature of each
sequence as described in Example 1.
EXAMPLE 4
A. Expression of SEO ID NO: 4 or 24 in cells
Chinese Hamster Ovary (CHO) cells or other suitable cell types are grown in
DMEM
(ATCC) and IO % fetal bovine serum (FBS) (Gibco) to 70 % confluence. Prior to
transfection
the media is changed to DMEM and 0.5 % FCS. Cells are transfected with cDNAs
for SEQ
ID NO: 3, 5, 23, or 26, or with pBGal vector by the FuGENE-6 transfection
reagent
(Boehringer). In summary, 4 p1 of FuGENE-6 is diluted in 100 ~,l of DMEM and
incubated
for 5 minutes. Then, this is added to 1 ~,g of DNA and incubated for 15
minutes before adding
it to a 35 mm dish of CHO cells. The CHO cells are incubated at 37°C
with 5% COz. After
24 hours, media and cell lysates are collected, centrifuged and dialyzed
against assay buffer
(15 mM Tris pH 7.6, 134 mM NaCI, 5 mM glucose, 3 mM CaClz and MgClz.
B. Expression Study Using SEO ID NO: 1-3, 5, 23, or 26
The expression of SEQ ID NO: 1-3, 5, 23, or 26 in various tissues is analyzed
using a
semi-quantitative polymerase chain reaction-based technique. Human cDNA
libraries are used
as sources of expressed genes from tissues of interest (adult bladder, adult
brain, adult heart,
adult kidney, adult lymph node, adult liver, adult lung, adult ovary, adult
placenta, adult
rectum, adult spleen, adult testis, bone marrow, thymus, thyroid gland, fetal
kidney, fetal
liver, fetal liver-spleen, fetal skin, fetal brain, fetal leukocyte and
macrophage). Gene-specific
primers are used to amplify portions of the SEQ ID NO: 1-3, 5, 23, or 26
sequence from the
samples. Amplified products are separated on an agarose gel, transferred and
chemically
linked to a nylon filter. The filter is then hybridized with a radioactively
labeled (33P-dCTP)
double-stranded probe generated from SEQ ID NO: 1-3, 5, 23, or 26 using a
Klenow
polymerase, random-prime method. The filters are washed (high stringency) and
used to
expose a phosphorimaging screen for several hours. Bands indicate the presence
of cDNA
118
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including SEQ ID NO: 1-3, 5, 23, or 26 sequences in a specific library, and
thus mRNA
expression in the corresponding cell type or tissue.
119
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SEQ'ITENCE LISTING
<110> Fiyseq, Inc.
Boyle, Brian J.
Mize, Nancy K.
Arterburn, Matthew C.
Yeung, George
Tang, Y. Tom
Liu, Chenghua
Drmanac, Radoje T.
Wang, Menq-Yun
Chen, Lichuan
Yang, Yea-Huey
<120> METHODS AND MATERTALS RELATING TO METALLOCARBOXYPEPTIDASE-LIKE
POLYPEPTIDES AND POLYNUCLEOTIDES
<130> HYS-28/ 21272-034
<140> NOT YET ASSIGNED
<141> 2001-02-05
<150> 09/676,135
<151> 2000-09-29
<150> 09/560,875
<151> 2000-04-27
<150> 09/496,914
<151> 2000-02-03
<160>
27
<170>
PatentIn
version
3.0
<210>
1
<211>
498
<212>
DNA
<213>
homo
Sapiens
<400>
1
agtacaaggaagtggtgacacagcatttcctatgagtgacctatgagacccaccccatat60
attatctgaagatcagccaaccatctggtaatcccaagaaaatcatttggatggactgtg120
gaattcacgccagagaatggattgctcctgctttttgccaatggttcgtcaaagaaattc180
tacaaaaccataaagacaactcaaggatacgcaagctccttatgaacctggacttctatg240
tccttccagttcttaacatagatggttatatctacacttggacaactgatcgtctttgga300
ggaaatcccgttcaccccataataatggcacatgttttgggacggatctcaatcgaaatt360
tcaatgcttcttggtgtagtattggtgcctctagaaactgccaagatcaaacattctgtg420
ggacagggccagtgtctgaaccagagactaaagctgttgccagcttcatagagagcaaga480
atgatgatttttgtgctt 498
<210> 2
<211> 498
<212> DNA
<213> homo Sapiens
1
CA 02399672 2002-08-02
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<400>
2
agtacaaggaagtggtgacacagcatttcctactagtgacctatgagacccaccccatat60
attatctgaagatcagccaaccatctggtaatcccaagaaaatcatttggatggactgtg120
gaattcacgccagagaatggattgetcctgctttttgccaatggttcgtcaaagaaattc180
tacaaaaccataaagacaactcaaggatacgcaagctccttatgaacctggacttctatg240
tccttccagttcttaacatagatggttatatctacacttggacaactgatcgtctttgga300
ggaaatcccgttcaccccataataatggcacatgttttgggacggatctcaatcgaaatt360
tcaatgcttcttggtgtagtattggtgcctctagaaactgccaagatcaaacattctgtg420
ggacagggccagtgtctgaaccagagactaaagetgttgccagcttcatagagagcaaga480
atgatgatttttgtgctt 498
<210>
3
<211>
1342
<212> .
DNA
<213> sapiens
homo
<220>
<221>
CDS
<222> ..(1218)
(94)
<400>
3
agtggtaacaacgcagagta tctcaaggacacttgatccactgccagaga60
acgcggggat
ggcccagaattttctaactt aga atg t gaa acc 114
actgtgtggc aag cct
ctg ct
Met Lys
Pro Leu
Leu Glu
Thr
Z 5
ctt tat ttg atg ctg cct gga ctg gga gat aga 162
ctt ggg gtt ggg tat
Leu Tyr Leu Met Leu Pro Gly Leu Gly Asp Arg
Leu Gly Val Gly Tyr
15 20
tcc tta caa aga caa att gtg aag tca agt cca 210
gcc cac gag gac gtg
Ser Leu Gln Arg Gln Ile Val Lys Ser Ser Pro
AIa His Glu Asp Val
25 30 35
tgg agc ctg gag acg tat tcc tat aac ata tac cac ccc atg gga gag 258
Trp Ser Leu Glu Thr Tyr Ser Tyr Asn Ile Tyr His Pro Met Gly Glu
40 45 50 55
atc tat gag tgg atg aga gag atc agt gag aag tac aag gaa gtg gtg 306
Ile Tyr Glu Trp Met Arg Glu Ile Ser Glu Lys Tyr Lys Glu Val Val
60 65 70
aca cag cat ttc cta gga gtg acc tat gag acc cac ccc ata tat tat 354
Thr Gln His Phe Leu Gly Val Thr Tyr Glu Thr His Pro Ile Tyr Tyr
75 80 85
ctg aag atc agc caa cca tct ggt aat ccc aag aaa atc att tgg atg 402
Leu Lys Ile Ser Gln Pro Ser Gly Asn Pro Lys Lys Ile Ile Trp Met
90 95 100
gac tgt gga att cac gcc aga gaa tgg att get cct get ttt tgc caa 450
Asp Cys Gly Ile His AIa Arg Glu Trp Ile AIa Pro Ala Phe Cys Gln
105 110 115
2
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tggttcgtcaaa gaaattctacaaaac cataaagacaactca aggata 498
TrpPheVaILys GluIleLeuGlnAsn HisLysAspAsnSer ArgIle
120 125 130 135
cgcaagctcctt aggaacctggacttc tatgtcCttccagtt cttaac 546
ArgLysLeuLeu ArgAsnLeuAspPhe TyrValLeuProVal LeuAsn
140 145 150
atagatggttat atctacacttggaca actgatcgtctttgg aggaaa 594
IleAspGlyTyr TleTyrThrTrpThr ThrAspArgLeuTrp ArgLys
155 160 165
tcccgttcaccc cataataatggcaca tgttttgggacggat ctcaat 642
SerArgSerPro HisAsnAsnGlyThr CysPheGlyThrAsp LeuAsn
170 175 180
cgaaatttcaat gettcttggtgtagt attggtgcctctaga aactgc 690
ArgAsnPheAsn AlaSerTrpCysSer IleGlyAlaSerArg AsnCys
185 190 195
caagatcaaaca ttctgtgggacaggg ccagtgtctgaacca gagact 738
GlnAspGlnThr PheCysGlyThrGly ProValSerGluPro GluThr
200 205 210 215
aaagetgttgcc agcttcatagagagc aagaaggatgatatt ttgtgc 786
LysAlaValAla SerPheIleGluSer LysLysAspAspIle LeuCys
220 225 230
ttcctgaccatg cactcttatgggcag ttaattctcacacct tacggc 834
PheLeuThrMet HisSerTyrGlyGln LeuIleLeuThrPro TyrGly
235 240 245
tacaccaaaaat aaatcaagtaaccac ccagaaatgattcaa gttgga 882
TyrThrLysAsn LysSerSerAsnHis ProGluMetIleGln ValGly
250 255 260
cagaaggcagca aatgcattgaaagca aagtatggaaccaat tataga 930
GlnLysAlaAla AsnAlaLeuLysAla LysTyrGlyThrAsn TyrArg
265 270 275
gttggatcgagt gcagatattttatat gcctcatcagggtat tcaaga 978
ValGlySerSer AlaAspIleLeuTyr AlaSerSerGlySer SerArg
2B0 285 290 295
gattgggcccga gacattgggattccc ttctcatatacgttt gagctg 1026
AspTrpAlaArg AspIleGlyIlePro PheSerTyrThrPhe GluLeu
300 305 31D
agggacagtgga acatatgggtttgtt ctgccagaagetcag atccag 1074
ArgAspSerGly ThrTyrGlyPheVal LeuProGluAlaGln IleGln
315 320 325
cccacctgtgag gagaccatggagget gtgctgtcagtcctg gatgat 1122
ProThrCysGlu GluThrMetGluAla ValLeuSerValLeu AspAsp
330 335 340
gtgtatgcgaaa cactggcactcggac agtgetggaagggtg acatct 1170
ValTyrAlaLys HisTrpHisSerAsp SerAlaGlyArgVal ThrSer
345 350 355
gccactatgctg ctgggcctgctggtg tcctgcatgtctctt ctctaa 1218
AlaThrMetLeu LeuGlyLeuLeuVal SerCysMetSerLeu Leu
360 365 370
3
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gtgcattctg cccaggcctg ctcaacccca gtggcatgag tgtggctgga ggaacggtgt 1278
gttatggttg taaagaaacc aaataattta actaaaaata attcctattt caaaaaaaaa 1338
aaaa 1342
<210> 4
<211> 374
<212> P12T
<213> homo Sapiens
<400> 4
Met Lys Pro Leu Leu Glu Thr Leu Tyr Leu Leu Gly Met Leu Val Pro
1 5 10 15
Gly Gly Leu Gly Tyr Asp Arg Ser Leu Ala Gln His Arg Gln Glu Ile
20 25 30
Val Asp Lys Ser Val Ser Pro Trp Ser Leu Glu Thr Tyr Ser Tyr Asn
35 40 45
Ile Tyr His Pro Met Gly Glu Ile Tyr Glu Trp Met Arg G1u Ile Sex
50 55 60
Glu Lys Tyr Lys Glu Val Val Thr Gln His Phe Leu Gly Val Thr Tyr
65 70 75 80
Glu Thr His Pro Ile Tyr Tyr Leu Lys Ile Ser Gln Pro Ser Gly Asn
85 90 95
Pro Lys Lys Ile Ile Trp Met Asp Cys Gly Ile His Ala Arg Glu Trp
100 105 110
Ile Ala Pro Ala Phe Cys Gln Trp Phe Val Lys Glu Ile Leu Gln Asn
115 120 125
His Lys Asp Asn Ser Arg Ile Arg Lys Leu Leu Arg Asn Leu Asp Phe
130 135 140
Tyr Val Leu Pro Val Leu Asn Ile Asp Gly Tyr Ile Tyr Thr Trp Thr
145 150 155 160
Thr Asp Arg Leu Trp Arg Lys Ser Arg Ser Pro His Asn Asn Gly Thr
165 ' 170 175
Cys Phe Gly Thr Asp Leu Asn Arg Asn Phe Asn Ala Ser Trp Cys Ser
180 185 190
Ile Gly Ala Ser Arg Asn Cys Gln Asp Gln Thr Phe Cys Gly Thr Gly
CA 02399672 2002-08-02
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195 200 205
Pro Val Ser Glu Pro Glu Thr Lys Ala Val Ala Ser Phe Ile Glu Ser
210 215 220
Lys Lys Asp Asp Ile Leu Cys Phe Leu Thr Met His Ser Tyr Gly Gln
225 230 235 240
Leu Ile Leu Thr Pro Tyr Gly Tyr Thr Lys Asn Lys Ser Ser Asn His
245 250 255
Pro Glu Met Tle Gln Val Gly Gln Lys Ala Ala Asn Ala Leu Lys Ala
260 265 270
Lys Tyr Gly Thr Asn Tyr Arg Va1 Gly Ser Ser Ala Asp Ile Leu Tyr
275 280 285
Ala Ser Ser Gly Ser Ser Arg Asp Trp Ala Arg Asp Ile Gly Ile Pro
290 295 300
Phe Ser Tyr Thr Phe Glu Leu Arg Asp Ser Gly Thr Tyr Gly Phe Val
305 310 315 320
Leu Pro Glu Ala Gln Ile Gln Pro Thr Cys Glu G1u Thr Met Glu Ala
325 330 335
Val Leu Ser Val Leu Asp Asp Va1 Tyr Ala Lys His Trp His Ser Asp
340 345 350
Ser Ala Gly Arg Val Thr Ser Ala Thr Met Leu Leu Gly Leu Leu Val
355 360 365
Ser Cys Met Ser Leu Leu
370
<210> 5
<211> 1125
<212> DNA
<213> homo sapiens
<400>
atgaagcctctgcttgaaaccctttatcttttggggatgctggttcctggagggctggga60
tatgatagatccttagcccaacacagacaagagattgtggacaagtcagtgagtccatgg120
agcctggagacgtattcctataacatataccaccccatgggagagatctatgagtggatg180
agagagatcagtgagaagtacaaggaagtggtgacacagcatttcctaggagtgacctat240
gagacccaccccatatattatctgaagatcagccaaccatctggtaatcccaagaaaatc300
atttggatggactgtggaattcacgccagagaatggattgctcctgctttttgccaatgg360
5
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ttcgtcaaagaaattctacaaaaccataaagacaactcaaggatacgcaagctccttagg420
aacctggacttctatgtccttccagttcttaacatagatggttatatctacacttggaca480
actgatcgtctttggaggaaatcccgttcaccccataataatggcacatgttttgggacg540
gatctcaatcgaaatttcaatgcttcttggtgtagtattggtgcctctagaaactgccaa600
gatcaaacattctgtgggacagggccagtgtctgaaccagagactaaagctgttgccagc660
ttcatagagagcaagaaggatgatattttgtgcttcetgaccatgcactcttatgggcag720
ttaattctcacacettacggctacaccaaaaataaatcaagtaaccacccagaaatgatt780
caagttggacagaaggcagcaaatgcattgaaagcaaagtatggaaccaattatagagtt840
ggatcgagtgcagatattttatatgcctcatcagggtcttcaagagattgggcccgagac900
attgggattcccttctcatatacgtttgagctgagggacagtggaacatatgggtttgtt960
ctgccagaagctcagatccagcccacctgtgaggagaccatggaggctgtgctgtcagtc1020
ctggatgatgtgtatgcgaaacactggcactcggacagtgctggaagggtgacatctgcc1080
actatgctgctgggcctgctggtgtcctgcatgtctcttctctaa 1125
<210> 6
<211> 41
<212> PRT
<213> homo Sapiens
<400> 6
His Lys Asp Asn Ser Arg Ile Arg Lys Leu Leu Arg Asn Leu Asp Phe
1 5 10 15
Tyr Val Leu Pro Val Leu Asn Ile Asp Gly Tyr Ile Tyr Thr Trp Thr
20 25 30
Thr Asp Arg Leu Trp Arg Lys Ser Arg
35 40
<210> 7
<211> 14
<212> PRT
<213> homo Sapiens
<400> 7
Lys Ile Ile Trp Met Asp Cys Gly Ile His Ala Arg Glu Trp
1 5 10
<210> 8
<211> 15
<212> PRT
<213> homo Sapiens
<400> 8
Lys Ile Ile Trp Met Asp Cys Gly Ile His Ala Arg Glu Trp Ile
1 5 10 15
6
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<210> 9
<211> 41
<212> PRT
<213> homo Sapiens
0
<400> 9
Tyr His Pro Met Gly Glu Ile Tyr Glu Trp Met Arg Glu Ile Ser Glu
1 5 10 15
Lys Tyr Lys Glu Val Val Thr Gln His Phe Leu Gly Val Thr Tyr Glu
20 25 30
Thr His Pro Ile Tyr Tyr Leu Lys Ile
35 40
<210> 10
<211> 22
<212> PRT
<213> homo Sapiens
<400> 10
Asp Ile Leu Cys Phe Leu Thr Met His Ser Tyr Gly Gln Leu Ile Leu
1 5 10 Z5
Thr Pro Tyr Gly Tyr Thr
<210> 11
<211> 15
<212> PRT
<213> homo Sapiens
<400> 11
Asn Asn Gly Thr Cys Phe Gly Thr Asp Leu Asn Arg Asn Phe Asn
1 5 10 15
<210> 12
<211> 27
<212> PRT
<213> homo Sapiens
<400> 12
Cys Gln Asp Gln Thr Phe Cys Gly Thr Gly Pro Val Ser Glu Pro Glu
1 5 10 15
Thr Lys A1a Val A1a Ser Phe Ile Glu Ser Lys
20 25
<210> 13
<211> 14
<212> PRT
<213> homo Sapiens
<400> 13
Leu Thr Met His Ser Tyr Gly G1n Leu Ile Leu Thr Pro Tyr
1 5 10
<210> 14
<211> 9
7
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<212> PRT
<213> homo sapiens
<400> 14
Gly Thr Asp Leu Asn Arg Asn Phe Asn
1 5
<210> 15
<211> 18
<212> PRT
<213> homo Sapiens
<400> 15
Asp Ile Leu Tyr Ala Ser Ser G1y Ser Ser Arg Asp Trp Ala Arg Asp
1 5 ~ 10 15
T1e Gly
<210> 16
<211> 20
<212> PRT
<213> homo Sapiens
<400> 16
Met Lys Pro Leu Leu Glu Thr Leu Tyr Leu Leu GIy Met Leu Va1 Pro
1 5 10 15
Gly Gly Leu G1y
<210> 17
<211> 15
<212> PRT
<213> homo Sapiens
<400> 17
Ala Thr Met Leu Leu Gly Leu Leu Val Ser Cys Met Ser Leu Leu
l 5 l0 15
<2l0> 18
<211> 354
<212> PRT
<213> homo Sapiens
<400> 18
Tyr Asp Arg Ser Leu Ala Gln His Arg Gln Glu Ile Val~ASp Lys Ser
1 5 10 15
Val Ser Pro Trp Sex Leu Glu Thr Tyr Ser Tyr Asn Tle Tyr His Pro
20 25 30
Met Gly Glu Ile Tyr Glu Trp Met Arg Glu Tle Ser Glu Lys Tyr Lys
35 40 45
Glu Val Val Thr Gln His Phe Leu Gly Val Thr Tyr Glu Thr His Pro
50 55 60
Ile Tyr Tyr Leu Lys Ile Ser Gln Pro Ser Gly Asn Pro Lys Lys Ile
g
CA 02399672 2002-08-02
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65 70 75 80
I1e Trp Met Asp Cys Gly Ile His Ala Arg Glu Trp Ile A1a Pro Ala
85 90 95
Phe Cys Gln Trp Phe Val Lys Glu Ile Leu Gln Asn His Lys Asp Asn
100 105 110
Ser Arg Tle Arg Lys Leu Leu Arg Asn Leu Asp Phe Tyr Val Leu Pro
115 120 125
Val Leu Asn Ile Asp Gly Tyr Ile Tyr Thr Trp Thr Thr Asp Arg Leu
130 135 140
Trp Arg Lys Ser Arg Ser Pro His Asn Asn Gly Thr Cys Phe Gly Thr
145 150 155 160
Asp Leu Asn Arg Asn Phe Asn Ala Ser Trp Cys Ser Ile G1y A1a Ser
165 170 175
Arg Asn Cys Gln Asp Gln Thr Phe Cys Gly Thr Gly Pro Val Ser Glu
180 185 190
Pro Glu Thr Lys Ala Val Ala Ser Phe Ile Glu Ser Lys Lys Asp Asp
195 200 205
I1e Leu Cys Phe Leu Thr Met His Ser Tyr Gly Gln Leu Ile Leu Thr
210 215 220
Pro Tyr Gly Tyr Thr Lys Asn Lys Ser Ser Asn His Pro Glu Met Ile
225 230 235 240
Gln Val Gly Gln Lys Ala Ala Asn Ala Leu Lys Ala Lys Tyr Gly Thr
245 250 255
Asn Tyr Arg Val Gly Ser Ser Ala Asp Ile Leu Tyr A1a Ser Ser G1y
260 265 270
Ser Ser Arg Asp Trp Ala Arg Asp Ile Gly Ile Pro Phe Ser Tyr Thr
275 280 285
Phe Glu Leu Arg Asp Ser Gly Thr Tyr Gly Phe Val Leu Pro Glu Ala
290 295 300
Gln Ile Gln Pro Thr Cys Glu Glu Thr Met Glu Ala Val Leu Ser Val
305 310 315 320
Leu Asp Asp Val Tyr Ala Lys His Trp His Ser Asp Ser Ala Gly Arg
325 330 335
Val Thr Ser Ala Thr Met Leu Leu Gly Leu Leu Val Ser Cys Met Ser
340 345 350
Leu Leu
<210> Z9
<211> 165
<212> PRT
<213> homo Sapiens
<400> 19
Tyr Lys Glu Val Val Thr Gln His Phe Leu Leu Val Thr Tyr Glu Thr
9
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1 5 10 15
His Pro Ile Tyr Tyr Leu Lys Ile Ser Gln Pro Ser Gly Asn Pro Lys
20 25 30
Lys Ile I1e Trp Met Asp Cys Gly Ile His Ala Arg Glu Trp Ile Ala
35 40 45
Pro Ala Phe Cys Gln Trp Phe Val Lys Glu Ile Leu Gln Asn His Lys
5D 55 60
Asp Asn Ser Arg Ile Arg Lys Leu Leu Met Asn Leu Asp Phe Tyr Val
65 70 ~ 75 80
Leu Pro VaI Leu Asn Ile Asp Gly Tyr Ile Tyr Thr Trp Thr Thr Asp
85 90 95
Arg Leu Trp Arg Lys Ser Arg Ser Pro His Asn Asn Gly Thr Cys Phe
100 105 110
Gly Thr Asp Leu Asn Arg Asn Phe Asn Ala Ser Trp Cys Ser Ile Gly
l15 120 125
A1a Ser Arg Asn Cys Gln Asp Gln Thr Phe Cys Gly Thr Gly Pro Val
130 135 140
Ser Glu Pro Glu Thr Lys Ala Val Ala Ser Phe Ile Glu Ser Lys Asn
145 150 155 160
Asp Asp Phe Cys Ala
165
c2I0> 20
<211> 324
<212> PRT
<213> bothrops jararaca
<400> 20
Ile Leu Gln G1n Ser Gly Leu Asn Tyr Glu Ile Leu Ile Asp Asn Leu
1 5 10 15
Gln Ala Val Leu Asp Arg Gln Leu Asp Asn His Ala Arg Thr Ala Gly
20 25 30
Tyr Asn Tyr Glu Lys Tyr Asn Ser Trp Glu Lys Ile Asp Ala Trp Thr
35 40 45
A1a Asp Ile A1a Asn Glu Asn Pro Ser Leu Val Ser Arg Leu Gln Ile
50 55 60
Gly Thr Thr Phe Glu Gly Arg Pro Met Pro Leu Leu Lys Val Gly Lys
65 70 75 . 80
Pro Gly Val Asn Lys Lys Ala Ile Phe Ile Asp Cys Gly Phe His Ala
85 90 95
Arg Glu Trp Ile Ser Pro Ala Phe Cys Gln Trp Phe Val Arg Glu Ala
100 105 110
Val Arg Thr Tyr Gly Lys Glu Thr Ile Met Thr Gln Leu Leu Asn Lys
115 120 125
Leu Asp Phe Tyr Ile Leu Pro Val Leu Asn Ile Asp Gly Tyr Val Tyr
CA 02399672 2002-08-02
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130 l35 140
Ser Trp Lys Gln Ser Arg Met Trp Arg Lys Thr Arg Ser Val Asn A1a
145 150 155 160
Gly Ser Thr Cys Ile Gly Thr Asp Pro Asn Arg Asn Phe Asp A1a Ala
165 170 175
Trp Cys Ser Val Gly Ala Ser Arg Asn Pro Cys Ser Glu Thr Tyr Cys
180 185 190
Gly Ser Lys Pro Glu Ser Glu Lys Glu Thr Lys Ala Leu Ala Asp Phe
195 200 205
Ile Arg Arg Asn Arg Ser IIe Ile Gln AIa Tyr Leu Thr Ile His Ser
210 215 220
Tyr Ser Gln Met Leu Leu Tyr Pro Tyr Ser Tyr Thr Tyr Asp Leu Thr
225 230 235 240
Ser Asn Asn Lys Lys Leu Asn Ser Ile Ala Lys Glu Ala Ile Arg Glu
245 250 255
Leu Lys Val Leu Phe Gly Thr Glu Tyr Thr Tyr Gly Pro Gly Ala Ala
260 265 270
Thr Ile Tyr Pro Ala Ala Gly Gly Ser Asp Asp Trp Ala Tyr Asp Gln
275 280 285
Gly Ile Lys Tyr Ala Phe Thr Phe Glu Leu Arg Asp Lys Gly Arg Tyr
290 295 300
Gly Phe Ala Leu Pro Glu Ser Gln Ile Lys Pro Thr Cys Glu Glu Thr
305 310 315 320
Met Ile Ala Val
<210> 21
<211> 311
<212> PRT
<213> homo sapiens
<400> 21
His Ser Tyr Glu Lys Tyr Asn Lys Trp Glu Thr Ile Glu Ala Trp Thr
1 5 10 15
Gln G1n Val Ala Thr Glu Asn Pro Ala Leu Ile Ser Arg Ser Val Ile
20 25 30
Gly Thr Thr Phe Glu G1y Arg Ala Ile Tyr Leu Leu Lys Val Gly Lys
35 40 45
Ala Gly Gln Asn Lys Pro A1a Ile Phe Met Asp Cys Gly Phe His Ala
50 55 60
Arg G1u Trp Ile Ser Pro Ala Phe Cys Gln Trp Phe Val Arg Glu Ala
65 70 75 80
Val Arg Thr Tyr Gly Arg Glu Ile Gln Val Thr Glu Leu Leu Asp Lys
85 90 95
Leu Asp Phe Tyr Val Leu Pro Val Leu Asn Ile Asp Gly Tyr Ile Tyr
I1
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100 105 110
Thr Trp Thr Lys Ser Arg Phe Trp Arg Lys Thr Arg Ser Thr His Thr
115 120 125
Gly Ser Ser Cys Ile Gly Thr Asp Pro Asn Arg Asn Phe Asp Ala Gly
130 135 140
Trp Cys Glu Ile Gly Ala Ser Arg Asn Pro Cys Asp Glu Thr Tyr Cys
145 150 155 160
Gly Pro Ala Ala Glu Ser Glu Lys Glu Thr Lys Ala Leu Ala Asp Phe
165 170 175
Ile Arg Asn Lys Leu Ser Ser Ile Lys Ala Tyr Leu Thr Ile His Ser
180 185 190
Tyr Ser Gln Met Met Ile Tyr Pro Tyr Ser Tyr Ala Tyr Lys Leu G1y
195 200 205
Glu Asn Asn Ala Glu Leu Asn Ala Leu Ala Lys Ala Thr Val Lys Glu
210 215 220
Leu AIa Ser Leu His Gly Thr Lys Tyr Thr Tyr Gly Pro Gly Ala Thr
225 230 235 240
Thr Ile Tyr Pro Ala Ala Gly Asn Ser Arg Asp Trp Ala Tyr Asp Gln
245 250 255
Gly Ile Arg Tyr Ser Phe Thr Phe Glu Leu Arg Asp Thr Gly Arg Tyr
260 265 270
Gly Phe Leu Leu Pro Glu Ser Gln Ile Arg Ala Thr Cys Glu Glu Thr
275 280 285
Phe Leu A1a Ile Lys Tyr Val Ala Ser Tyr Val Leu Glu His Leu Tyr
290 295 300
His His His His His His Glu
305 310
<210> 22
<211> 6
<212> PRT
<213> homo Sapiens
<220>
<221> X
<222> (1)..(6)
<223> X=any amino acid
<400> 22
His Xaa Xaa Glu Xaa His
1 5
<210>23
<211>1342
<212>DNA
<213>homo Sapiens
<220>
<221>CDS
12
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<222> (94)..(1218)
<400> 23
agtggtaaca acgcagagta acgcggggat tctcaaggac acttgatcca ctgccagaga 60
ggcccagaat aga ctg gaa 114
tttctaactt atg ctt acc
actgtgtggc aag
cct
Met Pro Leu
Lys Leu
Glu
Thr
1 5
ctttatcttttg gggatgctggtt cctggagggctg ggatat gataga 162
LeuTyrLeuLeu GlyMetLeuVal ProGlyGlyLeu GlyTyr AspArg
10 15 20
tccttagcccaa cacagacaagag attgtggacaag tcagtg agtcca 210
SerLeuAlaGln HisArgGlnGlu IleValAspLys SerVal SerPro
25 30 35
tggagactggag acgtattcctat aacatataccac cccatg ggagag 258
TrpSerLeuGlu ThrTyrSerTyr AsnIleTyrHis ProMet GlyGlu
40 45 50 55
atctatgagtgg atgagagagatc agtgagaagtac aaggaa gtggtg 306
IleTyrGluTrp MetArgGluIle SerGluLysTyr LysGlu ValVal
60 65 70
aoacagcatttc ctaggagtgacc tatgagaoccac ccaatg tattat 354
ThrGlnHisPhe LeuGlyValThr TyrGluThrHis ProMet TyrTyr
75 80 85
ctgaagatcagc caaccatctggtaat cccaagaaaatcatt tggatg 402
LeuLysIleSer GlnProSerGlyAsn ProLysLysIleIle TrpMet
90 95 100
gactgtggaatt cacgccagagaatgg attgetcetgetttt tgccaa 450
AspCysGlyIle HisAlaArgGluTrp IleAlaProAlaPhe CysGln
105 110 115
tggttcgtcaaa gaaattctacaaaac cataaagacaactca aggata 498
TrpPheValLys GluIleLeuGlnAsn HisLysAspAsnSer ArgIle
120 125 130 135
egcaagctcctt aggaaoctggacttc tatgtccttecagtt cttaac 546
ArgLysLeuLeu ArgAsnLeuAspPhe TyrVa1LeuProVal LeuAsn
140 145 150
atagatggttat atctacacttggaca actgatcgtctttgg aggaaa 594
IleAspGlyTyr IleTyrThrTrpThr ThrAspArgLeuTrp ArgLys
155 160 165
tCCCgttCaCCC Cataataatggcaca tgttttgggacggat ctaaat 642
SerArgSerPro HisAsnAsnGlyThr CysPheGlyThrAsp LeuAsn
170 175 180
cgaaatttcaat gettcttggtgtagt attggtgcctctaga aactgc 690
ArgAsnPheAsn AlaSerTrpCysSer IleGlyAlaSerArg AsnCys
185 190 195
caagatcaaaca ttctgtgggacaggg ccagtgtctgaacca gagact 738
GlnAspGlnThr PheCysGlyThrGly ProValSerGluPro GluThr
200 205 210 215
aaagetgttgcc agcttcatagagagc aagaaggatgatatt ttgtgc 786
LysAlaValAla SerPheIleGIuSer LysLysAspAspIle LeuCys
220 225 230
13
CA 02399672 2002-08-02
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ttcctgaccatg cactcttatgggcag ttaattctcacaccttac ggc 834
PheLeuThrMet HisSerTyrGlyGln LeuIleLeuThrProTyr Gly
235 240 245
tacaccaaaaat aaatcaagtaaccac ccagaaatgattcaagtt gga 882
TyrThrLysAsn LysSerSexAsnHis ProGluMetIleGlnVal Gly
250 255 260
cagaaggcagca aatgcattgaaagca aagtatggaaccaattat aga 930
GlnLysA1aAla AsnAlaLeuLys~Ala LysTyrGlyThrAsnTyr Arg
265 270 275
gttggatcgagt gcagatattttatat gccteatcagggtcttca aga 978
ValGlySerSer AlaAspIleLeuTyr AlaSerSerGlySerSer Arg
280 285 290 295
gattgggcccga gacattgggattCCC ttctaatatacgtttgag ctg 1026
AspTrpA1aArg AspIleGlyIlePro PheSerTyrThrPheGlu Leu
300 305 310
agggacagtgga acatatgggtttgtt etgccagaagct,cagatc cag 1074
ArgAspSerGly ThrTyrGlyPheVal LeuProGluAlaGlnIle Gln
315 320 325
cccacctgtgag gagaccatggagget gtgctgtcagtcctggat gat 1122
ProThrCysGlu GluThrMetGluAla ValLeuSerValLeuAsp Asp
330 335 340
gtgtatgcgaaa cactggcactcggac agtgetggaagggtgaca tct 1170
ValTyrAlaLys HisTrpHisSerAsp SerAlaGlyArgValThr Ser
345 350 355
gccactatgctg ctgggcctgctggtg tcctgcatgtctcttctc taa 1218
AlaThrMetLeu LeuGlyLeuLeuVa1 SerCysMetSerLeuLeu
360 365 370
gtgcattctg cccaggcctg ctcaacccca gtggcatgag tgtggctgga ggaacggtgt 1278
gttatggttg taaagaaacc aaataattta actaaaaata cttcctattt caaaaaaaaa 1338
aaaa 1342
<210> 24
<211> 374
<212> PRT
<213> homo Sapiens
<400> 24
Met Lys Pro Leu Leu Glu Thr Leu Tyr Leu Leu Gly Met Leu Val Pro
1 5 10 15
Gly Gly Leu Gly Tyr Asp Arg Ser Leu Ala Gln His Arg Gln Glu Ile
20 25 30
Val Asp Lys Ser Val Ser Pro Trp Ser Leu Glu Thr Tyr Ser Tyr Asn
35 40 45
Ile Tyr His Pro Met Gly Glu Ile Tyr Glu Trp Met Arg Glu Ile Ser
14
CA 02399672 2002-08-02
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50 55 60
Glu Lys Tyr Lys Glu Val Val Thr Gln His Phe Leu Gly Va1 Thr Tyr
65 70 75 80
Glu Thr His Pro Met Tyr Tyr Leu Lys Ile Ser Gln Pro Ser Gly Asn
85 90 95
Pro Lys Lys Ile Ile Trp Met Asp Cys Gly Tle His A1a Arg G1u Trp
100 105 110
Ile Ala Pro Ala Phe Cys Gln Trp Phe Val Lys Glu Ile Leu Gln Asn
115 120 125
His Lys Asp Asn Ser Arg Ile Arg Lys Leu Leu Arg Asn Leu Asp Phe
130 135 140
Tyr Val Leu Pro Val Leu Asn Ile Asp Gly Tyr Ile Tyr Thr Trp Thr
145 150 155 160
Thr Asp Arg Leu Trp Arg Lys Ser Arg Ser Pro His Asn Asn Gly Thr
165 170 175
Cys Phe Gly Thr Asp Leu Asn Arg Asn Phe Asn Ala Ser Trp Cys Ser
180 185 190
Ile Gly Ala Ser Arg Asn Cys Gln Asp Gln Thr Phe Cys Gly Thr Gly
195 200 205
Pro Val Ser G1u Pro Glu Thr Lys Ala Val Ala Ser Phe Ile Glu Ser
210 215 220
Lys Lys Asp Asp Ile Leu Cys Phe Leu Thr Met His Ser Tyr Gly Gln
225 230 235 240
Leu Ile Leu Thr Pro Tyr Gly Tyr Thr Lys Asn Lys Ser Ser Asn Ais
245 250 255
Pro Glu Met Ile Gln Val Gly Gln Lys Ala Ala Asn Ala Leu Lys Ala
260 265 270
Lys Tyr Gly Thr Asn Tyr Arg Val. Gly Ser Ser Ala Asp Ile Leu Tyr
275 280 285
Ala Ser Ser Gly Ser Sex Arg Asp Trp Ala Arg Asp Ile Gly Ile Pro
290 295 300
Phe Ser Tyr Thr Phe Glu Leu Arg Asp Ser Gly Thr Tyr Gly Phe Val
CA 02399672 2002-08-02
WO 01/57265 PCT/USO1/03783
305 310 315 320
Leu Pro Glu Ala Gln I1e Gln Pro Thr Cys G1u Glu Thr Met Glu Ala
325 330 335
Val Leu Ser Val Leu Asp Asp Val Tyr Ala Lys His Trp His Sex Asp
340 345 350
Ser Ala Gly Arg Val Thr Ser AIa Thr Met Leu Leu Gly Leu Leu Val
355 360 365
Ser Cys Met Ser Leu Leu
370
<210> 25
<211> 354
<212> PRT
<213> homo sapiens
<400> 25
Tyr Asp Arg Ser Leu Ala Gln His Arg Gln Glu Ile Val Asp Lys Ser
1 5 10 15
Val Ser Pro Trp Ser Leu Glu Thr Tyr Ser Tyr Asn IIe Tyr His Pro
20 25 30
Met Gly Glu Ile Tyr Glu Trp Met Arg Glu Ile Ser Glu Lys Tyr Lys
35 40 45
Glu Val Val Thr Gln His Phe Leu Gly Val Thr Tyr Glu Thr His Pro
50 55 60
Met Tyr Tyr Leu Lys Ile Ser Gln Pro Ser Gly Asn Pro Lys Lys I1e
65 70 75 80
Ile Trp Met Asp Cys Gly Ile His Ala Arg Glu Trp Ile Ala Pro Ala
85 90 95
Phe Cys Gln Trp Phe Val Lys Glu IIe Leu GIn Asn His Lys Asp Asn
100 105 110
Ser Arg Ile Arg Lys Leu Leu Arg Asn Leu Asp Phe Tyr Val Leu Pro
115 120 125
Val Leu Asn Tle Asp Gly Tyr Ile Tyr Thr Trp Thr Thr Asp Arg Leu
l30 135 140
Trp Arg Lys Ser Arg Ser Pro His Asn Asn Gly Thr Cys Phe Gly Thr
145 150 155 160
Asp Leu Asn Arg Asn Phe Asn Ala Ser Trp Cys Ser Ile Gly Ala Ser
165 170 175
Arg Asn Cys Gln Asp Gln Thr Phe Cys Gly Thr Gly Pro Val Ser Glu
180 185 190
Pro Glu Thr Lys Ala Val Ala Ser Phe Ile Glu Ser Lys Lys Asp Asp
195 200 205
16
CA 02399672 2002-08-02
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Ile Leu Cys Phe Leu Thr Met His Ser Tyr Gly Gln Leu Ile Leu Thr
210 21S 220
Pro Tyr Gly Tyr Thr Lys Asn Lys Ser Ser Asn His Pro Glu Met Ile
225 230 235 240
Gln Val Gly Gln Lys Ala Ala Asn Ala Leu Lys Ala Lys Tyr Gly Thr
245 250 255
Asn Tyr Arg Val Gly Ser Ser Ala Asp Ile Leu Tyr Ala Ser Ser Gly
260 265 ' 270
Ser Ser Arg Asp Trp Ala Arg Asp Ile Gly Ile Pro Phe Ser Tyr Thr
275 280 285
Phe Glu Leu Arg Asp Ser Gly Thr Tyr Gly Phe Val Leu Pro Glu Ala
290 295 300
Gln Ile Gln Pro Thr Cys Glu Glu Thr Met,Glu Ala Val Leu Ser Val
305 310 315 320
Leu Asp Asp Val Tyr Ala Lys His Trp His Ser Asp Ser Ala Gly Arg
325 330 335
Val Thr Ser Ala Thr Met Leu Leu Gly Leu Leu Val Ser Cys Met Ser
340 345 350
Leu Leu
<210> 26
<211> 1125
<212 > DNA
<213> homo Sapiens
<400>
26
atgaagcctctgcttgaaaccctttatcttttggggatgctggttcctggagggctggga60
tatgatagatccttagcccaacacagacaagagattgtggacaagtcagtgagtccatgg120
agcctggagacgtattcctataacatataccaccccatgggagagatctatgagtggatg180
agagagatcagtgagaagtacaaggaagtggtgacacagcatttcctaggagtgacctat240
gagacccaccccatgtattatctgaagatcagccaaccatctggtaatcccaagaaaatc300
atttggatggactgtggaattcacgccagagaatggattgctcctgctttttgccaatgg360
ttcgtcaaagaaattetacaaaaccataaagacaactcaaggatacgcaagctccttagg420
aacctggacttctatgtccttccagttcttaacatagatggttatatctacacttggaca480
actgatcgtctttggaggaaatcccgttcaccccataataatggcacatgttttgggacg540
gatctcaatcgaaatttcaatgcttcttggtgtagtattggtgcctctagaaactgccaa600
gatcaaacattctgtgggacagggccagtgtctgaaccagagactaaagctgttgccagc660
ttcatagagagcaagaaggatgatattttgtgcttcctgaccatgcactcttatgggcag720
ttaattctcacaccttacggctacaccaaaaataaatcaagtaaccacccagaaatgatt780
caagttggacagaaggcagcaaatgcattgaaagcaaagtatggaaccaattatagagtt840
17
CA 02399672 2002-08-02
WO 01/57265 PCT/USO1/03783
ggatcgagtgcagatattttatatgcctcatcagggtcttcaagagattgggcccgagac900
attgggattcccttctcatatacgtttgagctgagggacagtggaacatatgggtttgtt960
ctgccagaagctcagatccagcccacctgtgaggagaccatggaggctgtgctgtcagtc1020
ctggatgatgtgtatgcgaaacactggcactcggacagtgctggaagggtgacatctgcc1080
actatgctgctgggcctgctggtgtcctgcatgtctcttctctaa 1125
<210> 27
<211> 41
<212> PRT
<213> homo sapiens
<400> 27
Tyr His Pro Met Gly Glu Ile Tyr Glu Trp Met Arg G1u Ile Ser Glu
1 5 10- 15
Lys Tyr Lys Glu Val Val Thr GlnIHis Phe Leu Gly Val Thr Tyr Glu
20 25 30
Thr His Pro Met Tyr Tyr Leu Lys Ile
35 40
18
