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CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
Nucleic Acids, Proteins, and Antibodies
[001] This application refers to a "Sequence Listing" that is provided only on
electronic media in computer readable form pursuant to Administrative
Instructions
Section 801(a)(i). The Sequence Listing forms a part of this description
pursuant to
Rule 5.2 and Administrative Instructions Sections 801 to 806, and is hereby
incorporated in its entirety.
[002] . The Sequence Listing is provided as an electronic file (PAl l BPCT
seqList.txt,
1,316,195 bytes in size, created on January 12, 2001) on four identical
compact discs
(CD-R), labeled "COPY 1," "COPY 2," "COPY 3," and "CRF.". The Sequence
Listing complies with Annex C of the Administrative Tnstructions, and may be
viewed,
for example, on an IBM-PC machine running the MS-Windows operating system by
using the V viewer software, version 2000 (see World Wide Web URL:
http://www.fileviewer.com).
Field of the Invention
[003] The present invention relates to novel prostate cancer related
polynucleotides,
the polypeptides encoded by these polynucleotides herein collectively referred
to as
"prostate cancer antigens," and antibodies that immunospecifically bind these
polypeptides, and the use of such prostate cancer polynucleotides, antigens,
and
antibodies for detecting, treating, preventing and/or prognosing disorders of
the
reproductive system, particularly disorders of the prostate, including, but
not limited
to, the presence of prostate cancer and prostate cancer metastases. More
specifically,
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isolated prostate cancer nucleic acid molecules are provided encoding novel
prostate
cancer polypeptides. Novel prostate cancer polypeptides and antibodies that
bind to
these polypeptides axe provided. Also provided are vectors, host cells, and
recombinant and synthetic methods for producing human prostate cancer
polynucleotides, polypeptides, and/or antibodies. The invention further
relates to
diagnostic and therapeutic methods useful fox diagnosing, treating, preventing
and/or
prognosing disorders related to the prostate, including prostate cancer, and
therapeutic
methods for treating such disorders. The invention further relates to
screening methods
for identifying agonists and antagonists of polynucleotides and polypeptides
of the
invention. The invention further relates to methods and/or compositions for
inhibiting
or promoting the production and/or function of the polypeptides of the
invention.
Backg~~ouud of the Invention
[004] The normal prostate gland is quite small, weighing only about one ounce,
and
comprised of approximately 30% muscular tissue and 70% glandular tissue. The
prostate wraps around the urethra, through which urine and semen are carried
out to
the tip of the penis. The primary function of the prostate is to produce a
necessary
fluid component of semen; just prior to male orgasm muscular contractions
squeeze
this fluid into the urethra. Disorders of the prostate gland, such as prostate
cancers, are
typically manifested by enlargement of the gland, leading to such symptoms as
impaired urinary flow, infertility, and pain.
[005] About 180,000 new cases of prostate cancer in the United States and
16,000 in
Canada are diagnosed every year. Cancer of the prostate is now the second most
common type of cancer in males, although the causes of prostate cancer are not
well
understood. While men of any age can develop prostate cancer, it is found most
frequently in men over age 50, with risk increasing with age.
[006] Most prostate cancers are adenocarcinomas, cancers that arise in
glandular
cells of the prostate's epithelial tissue. Types of prostate cancers also
include, but are
not limited to, transitional cell carcinomas, ductal carcinomas, and squamous
cell
carcinomas. Prostate cancers usually progress slowly and produce no symptoms
in the
initial stages. Eventually, the tumor may enlarge the prostate gland, pressing
on the
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urethra and causing painful or frequent urination and blood in the urine or
semen.
Sometimes pain in the lower back, pelvis, or upper thighs may signal that
prostate
cancer cells have spread to the ribs, pelvis, and other bones. The prognosis
for prostate
cancer is quite good if it is caught and treated early. The five-year survival
rate for
American men with prostate cancer is almost 93 percent, but this number rises
to
almost 100 percent if the tumor is caught early.
[007] Current therapies include watchful waiting, surgery, radiation therapy,
and
hormone therapy, which may lead to such unpleasant side effects as
incontinence,
impotence, dry orgasm, pubic hair loss, nausea, breast growth, and decreased
libido.
(008] There are a variety of techniques for early detection and
characteristics of
prostate cancers, however, none of them are devoid of problems. Because
prostate
cancer is a notoriously silent disease with few early symptoms, there is an
urgent need
for identification and characterization of factors that modulate activation
and
differentiation of prostate cells, both normally and in disease states. In
particular,
there is a need to isolate and characterize additional molecules that mediate
apoptosis,
DNA repair, tumor-mediated angiogenesis, genetic imprinting, immune responses
to
tumors and tumor antigens, among other things, that can play a role in
detecting,
preventing, ameliorating or correcting dysfunctions or diseases related to the
prostate.
[009] The discovery of new human prostate cancer associated polynucleotides,
the
polypeptides encoded by them, and antibodies that immunospecifically bind
these
polypeptides, satisfies a need in the art by providing new compositions which
are
useful in the diagnosis, treatment, prevention and/or prognosis of disorders
of the
reproductive system, particularly disorders of the prostate, including, but
not limited
to, prostate cancers such as adenocarcinoma, transitional cell carcinomas,
ductal
carcinomas, and squamous cell carcinomas, as well as inflammatory disorders,
such as
chronic prostatitis, granulomatous prostatitis and malacoplakia, prostatic
hyperplasia,
and as described under "Hyperproliferative Disorders" and/or "Reproductive
System
Disorders" below.
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Summary of the Invention
[010] The present invention relates to novel prostate cancer related
polynucleotides, the polypeptides encoded by these polynucleotides herein
collectively
referred to as "prostate cancer antigens," and antibodies that
immunospecifically bind
these polypeptides, and the use of such prostate cancer polynucleotides,
antigens, and
antibodies for detecting, treating, preventing and/or prognosing disorders of
the
reproductive system, particularly disorders of the prostate, including, but
not limited
to, the presence of prostate cancer and prostate cancer metastases. More
specifically,
isolated prostate cancer nucleic acid molecules axe provided encoding novel
prostate
cancer polypeptides. Novel prostate cancer polypeptides and antibodies that
bind to
these polypeptides are provided. Also provided are vectors, host cells, and
recombinant and synthetic methods for producing human pxostate cancer
polynucleotides, polypeptides, and/or antibodies. The invention further
relates to
diagnostic and therapeutic methods useful for diagnosing, treating, preventing
and/or
prognosing disorders related to the prostate, including prostate cancer, and
therapeutic
methods for treating such disorders. The invention further relates to
screening methods
for identifying agonists and antagonists of polynucleotides and polypeptides
of the
invention. The invention further relates to methods and/or compositions for
inhibiting
or promoting the production and/or function of the polypeptides of the
invention.
Detailed Desc~iptio~z
Tables
[011] Table 1A summarizes some of the polynucleotides encompassed by the
invention (including cDNA clones related to the sequences (Clone ID NO:Z),
contig
sequences (contig identifier (Contig ID:) and contig nucleotide sequence
identifier
(SEQ ID NO:X)) and further summarizes certain characteristics of these
polynucleotides and the polypeptides encoded thereby. The first column
provides a
unique clone identifier, "Clone ID NO:Z", for a cDNA plasmid related to each
prostate
cancer associated contig sequence disclosed in Table 1A. The second column
provides a unique contig identifier, "Contig ID:" for each of the contig
sequences
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disclosed in Table 1A. The third column provides the sequence identifier, "SEQ
ID
NO:X", for each of the contig polynucleotide sequences disclosed in Table 1A.
The
fourth column, "ORF (From-To)", provides the location (i.e., nucleotide
position
numbers) within the polynucleotide sequence of SEQ ID NO:X that delineate the
preferred open reading frame (ORF) shown in the sequence listing and
referenced in
Table 1A as SEQ ID NO:Y (column 5). Column 6 lists residues comprising
predicted
epitopes contained in the polypeptides encoded by each of the preferred ORFs
(SEQ
ID NO:Y). Identification of potential immunogenic regions was performed
according
to the method of Jameson and Wolf (CABIOS, 4:181-186 (1988)); specifically,
the
Genetics Computer Group (GCG) implementation of this algorithm, embodied in
the
program PEPTIDESTRUCTURE (Wisconsin Package v10.0, Genetics Computer
Group (GCG), Madison, Wisc.). This method returns a measure of the probability
that
a given residue is found on the surface of the protein. Regions where the
antigenic
index score is greater than 0.9 over at least 6 amino acids are indicated in
Table 1A as
"Predicted Epitopes." In particular embodiments, prostate cancer associated
polypeptides of the invention comprise, or alternatively consist of, one, two,
three,
four, five or more of the predicted epitopes described in Table 1A. It will be
appreciated that depending on the analytical criteria used to predict
antigenic
determinants, the exact address of the determinant may vary slightly. Column
7,
"Tissue Distribution" shows the expression profile of tissue, cells, and/or
cell line
libraries which express the polynucleotides of the invention. The first number
in
column 7 (preceding the colon), represents the tissue/cell source identifier
code
corresponding to the code and description provided in Table 4. Expression of
these
polynucleotides was not observed in the other tissues and/or cell libraries
tested. For
those identifier codes in which the first two letters are not "AR", the second
number in
column 7 (following the colon), represents the number of times a sequence
corresponding to the reference polynucleotide sequence (e.g., SEQ ID NO:X) was
identified in the tissue/cell source. Those tissue/cell source identifier
codes in which
the first two letters are "AR" designate information generated using DNA array
technology. Utilizing this technology, cDNAs were amplified by PCR and then
transferred, in duplicate, onto the array. Gene expression was assayed through
hybridization of first strand cDNA probes to the DNA array. cDNA probes were
CA 02393618 2002-06-03
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generated from total RNA extracted from a variety of different tissues and
cell lines.
Probe synthesis was performed in the presence of 33P dCTP, using oligo(dT) to
prime
reverse transcription. After hybridization, high stringency washing conditions
were
employed to remove non-specific hybrids from the array. The remaining signal,
emanating from each gene target, was measured using a Phosphorimager. Gene
expression was reported as Phosphor Stimulating Luminescence (PSL) which
reflects
the level of phosphor signal generated from the probe hybridized to each of
the gene
targets represented on the array. A local background signal subtraction was
performed
before the total signal generated from each array was used to normalize gene
expression between the different hybridizations. The value presented after
"[array
code]:" represents the mean of the duplicate values, following background
subtraction
and probe normalization. One of slcill in the art could routinely use this
information to
identify normal and/or diseased tissues) which show a predominant expression
pattern
of the corresponding polynucleotide of the invention or to identify
polynucleotides
which show predominant and/or specific tissue and/or cell expression. Column
8,
"Cytologic Band," provides the chromosomal location of polynucleotides
corresponding to SEQ ID NO:X. Chromosomal location was determined by finding
exact matches to EST and cDNA sequences contained in the NCBI (National Center
for Biotechnology Information) UniGene database. Given a presumptive
chromosomal
location, disease locus association was determined by comparison with the
Morbid
Map, derived from Online Mendelian Inheritance in Man (Online Mendelian
Inheritance in Man, OMIMTM. McKusick-Nathans Institute for Genetic Medicine,
Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology
Information, National Library of Medicine (Bethesda, MD) 2000. World Wide Web
URL: http://www.ncbi.nlm.nih.gov/omim/). If the putative chromosomal location
of
the Query overlapped with the chromosomal location of a Morbid Map entry, an
OMIM identification number is provided in column 9 labeled "OMIM Disease
References)". A key to the OMIM reference identification numbers is provided
in
Table 5.
[012] Table 1B summarizes additional polynucleotides encompassed by the
invention (including cDNA clones related to the sequences (Clone ID NO:Z),
contig
sequences (contig identifier (Contig ID:) contig nucleotide sequence
identifiers (SEQ
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ID NO:X)), and genomic sequences (SEQ ID NO:B). The first column provides a
unique clone identifier, "Clone ID NO:Z", for a cDNA clone related to each
contig
sequence. The second column provides the sequence identifier, "SEQ ID NO:X",
for
each contig sequence. The third column provides a unique contig identifier,
"Contig
ID:" for each contig sequence. The fourth column, provides a BAC identifier
"BAC
ID NO:A" for the BAC clone referenced in the corresponding row of the table.
The
fifth column provides the nucleotide sequence identifier, "SEQ ID NO:B" for a
fragment of the BAC clone identified in column four of the corresponding row
of the
table. The sixth column, "Exon From-To", provides the location (i.e.,
nucleotide
position numbers) within the polynucleotide sequence of SEQ ID NO:B which
delineate certain polynucleotides of the invention that are also exemplary
members of
polynucleotide sequences that encode polypeptides of the invention (e.g.,
polypeptides
containing amino acid sequences encoded by the polynucleotide sequences
delineated
in column six, and fragments and variants thereof).
[013] Table 2 summarizes homology and features of some of the polypeptides of
the
invention. The first column provides a unique clone identifier, "Clone ID
NO:Z",
corresponding to a cDNA disclosed in Table 1A. The second column provides the
unique contig identifier, "Contig ID:" corresponding to contigs in Table 1A
and
allowing for correlation with the information in Table 1A. The third column
provides
the sequence identifier, "SEQ ID NO:X", for the contig polynucleotide
sequences.
The fourth column provides the analysis method by which the homology/identity
disclosed in the row was determined. Comparisons were made between
polypeptides
encoded by the polynucleotides of the invention and either a non-redundant
protein
database (herein referred to as "NR"), or a database of protein families
(herein referred
to as "PFAM") as further described below. The fifth column provides a
description of
PFAM/NR hits having significant matches to a polypeptide of the invention.
Column
six provides the accession number of the PFAM/NR hit disclosed in the fifth
column.
Column seven, "Score/Percent Identity", provides a quality score or the
percent
identity, of the hit disclosed in column five. Columns 8 and 9, "NT From" and
"NT
To" respectively, delineate the polynucleotides in "SEQ ID NO:X" that encode a
polypeptide having a significant match to the PFAM/NR database as disclosed in
the
fifth column. In specific embodiments, polypeptides of the invention comprise,
or
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alternatively consist of, an amino acid sequence encoded by the
polynucleotides in
SEQ ID NO:X as delineated in columns 8 and 9, or fragments or variants
thereof.
[014] Table 3 provides polynucleotide sequences that may be disclaimed
according
to certain embodiments of the invention. The first column provides a unique
clone
identifier, "Clone ID NO:Z", for a cDNA clone related to prostate cancer
associated
contig sequences disclosed in Table 1A. The second column provides the
sequence
identifier, "SEQ ID NO:X", for contig polynucleotide sequences disclosed in
Table
1A. The third column provides the unique contig identifier, "Contig ID", for
contigs
disclosed in Table 1A. The fourth column provides a unique integer 'a' where
'a' is
any integer between 1 and the final nucleotide minus 15 of SEQ ID NO:X,
represented as "Range of a", and the fifth column provides a unique integer
'b' where
'b' is any integer between 15 and the anal nucleotide of SEQ ID NO:X,
represented as
"Range of b", where both a and b correspond to the positions of nucleotide
residues
shown in SEQ ID NO:X, and where b is greater than or equal to a + 14: For each
of
the polynucleotides shown as SEQ ID NO:X, the uniquely defined integers can be
substituted into the general formula of a-b, and used to describe
polynucleotides which
may be preferably excluded from the invention. In certain embodiments,
preferably
excluded from the polynucleotides of the invention (including polynucleotide
fragments and variants as described herein and diagnostic and/or therapeutic
uses
based on these polynucleotides) are at least one, two, three, four, five, ten,
or more of
the polynucleotide sequences) having the accession numbers) disclosed in the
sixth
column of this Table (including for example, published sequence in connection
with a
particular BAC clone). In further embodiments, preferably excluded from the
invention are the specific polynucleotide sequences) contained in the clones
corresponding to at least one, two, three, four, five, ten, or more of the
available
material having the accession numbers identified in the sixth column of this
Table
(including for example, the actual sequence contained in an identified BAC
clone).
[015] Table 4 provides a key to the tissue/cell source identifier code
disclosed in
Table 1A, column 7. Column 1 provides the key to the tissue/cell source
identifier
code disclosed in Table 1A, Column 7. Columns 2-5 provide a description of the
tissue
or cell source. Codes corresponding to diseased tissues are indicated in
column 6 with
the word "disease". The use of the word "disease" in column 6 is non-limiting.
The
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tissue or cell source may be specific (e.g. a neoplasm), or may be disease-
associated
(e.g., a tissue sample from a normal portion of a diseased organ).
Furthermore, tissues
and/or cells lacking the "disease" designation may still be derived from
sources
directly or indirectly involved in a disease state or disorder, and therefore
may have a
further utility in that disease state or disorder. In numerous cases where the
tissue/cell
source is a library, column 7 identifies the vector used to generate the
library.
[001] Table 5 provides a key to the OMIMTM reference identification numbers
disclosed in Table 1A, column 9. OMIM reference identification numbers (Column
1)
were derived from Online Mendelian Inheritance in Man (Online Mendelian
Inheritance in Man, OMIMTM. McKusick-Nathans Institute for Genetic Medicine,
Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology
Information, National Library of Medicine, (Bethesda, MD) 2000. World Wide Web
URL: http://www.ncbi.nlm.nih.gov/omim/). Column 2 provides diseases associated
with the cytologic band disclosed in Table 1A, column 8, as determined from
the
Morbid Map database.
[017] Table 6 summarizes ATCC Deposits, Deposit dates, and ATCC designation
numbers of deposits made with the ATCC in connection with the present
application.
[018] Table 7 shows the cDNA libraries sequenced, tissue source description,
vector
information and ATCC designation numbers relating to these cDNA libraries.
[019] Table 8 provides a physical characterization of clones encompassed by
the
invention. The first column provides the unique clone identifier, "Clone ID
NO:Z",
for certain cDNA clones of the invention, as described in Table 1A. The second
column provides the size of the cDNA insert contained in the corresponding
cDNA
clone.
Definitions
[020] The following definitions are provided to facilitate understanding of
certain
terms used throughout this specification.
[021] In the present invention, "isolated" refers to material removed from its
original
environment (e.g., the natural environment if it is naturally occurring), and
thus is
altered "by the hand of man" from its natural state. For example, an isolated
polynucleotide could be part of a vector or a composition of matter, or could
be
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contained within a cell, and still be "isolated" because that vector,
composition of
matter, or particular cell is not the original environment of the
polynucleotide. The
term "isolated" does not refer to genomic or cDNA libraries, whole cell total
or
mRNA preparations, genomic DNA preparations (including those separated by
electrophoresis and transferred onto blots), sheared whole cell genomic DNA
preparations or other compositions where the art demonstrates no
distinguishing
features of the polynucleotide sequences of the present invention.
[022] As used herein, a "polynucleotide" refers to a molecule having a nucleic
acid
sequence encoding SEQ ID NO:Y or a fragment or variant thereof; a nucleic acid
sequence contained in SEQ ID NO:X (as described in column 3 of Table 1A) or
the
complement thereof; a cDNA sequence contained in Clone ID NO:Z (as described
in
column 1 of Table 1A and contained within a library deposited with the ATCC);
a
nucleotide sequence encoding the polypeptide encoded by a nucleotide sequence
in
SEQ TD NO:B as defined in column 6 of Table 1B or a fragment or variant
thereof; or
a nucleotide coding sequence in SEQ ID NO:B as defined in column 6 of Table 1B
or
the complement thereof. For example, the polynucleotide can contain the
nucleotide
sequence of the full length cDNA sequence, including the 5' and 3'
untranslated
sequences, the coding region, as well as fragments, epitopes, domains, and
variants of
the nucleic acid sequence. Moreover, as used herein, a "polypeptide" refers to
a
molecule having an amino acid sequence encoded by a polynucleotide of the
invention
as broadly defined (obviously excluding poly-Phenylalanine or poly-Lysine
peptide
sequences which result from translation of a polyA tail of a sequence
corresponding to
a cDNA).
[023] As used herein, a "prostate cancer antigen" refers collectively to any
polynucleotide disclosed herein (e.g., a nucleic acid sequence contained in
SEQ ID
NO:X or the complement therof, or cDNA sequence contained in Clone ID NO:Z, or
a
nucleotide sequence encoding the polypeptide encoded by a nucleotide sequence
in
SEQ ID NO:B as defined in column 6 of Table 1B, or a nucleotide coding
sequence in
SEQ ID NO:B as defined in column 6 of Table 1B or the complement thereof and
fragments or variants thereof as described herein) or any polypeptide
disclosed herein
(e.g., an amino acid sequence contained in SEQ ID NO:Y, an amino acid sequence
encoded by SEQ ID NO:X, or the complement thereof, an amino acid sequence
CA 02393618 2002-06-03
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encoded by the cDNA sequence contained in Clone ID NO:Z, an amino acid
sequence
encoded by SEQ ID NO:B, or the complement thereof, and fragments or variants
thereof as described herein). These prostate cancer antigens have been
determined to
be predominantly expressed in prostate cancer tissues, including normal or
diseased
tissues (as shown in Table 1A column 7 and Table 4).
[024] In the present invention, "SEQ ID NO:X" was often generated by
overlapping
sequences contained in multiple clones (contig analysis). A representative
clone
containing all or most of the sequence for SEQ ID NO:X is deposited at Human
Genome Sciences, Inc. (HGS) in a catalogued and archived library. As shown,
for
example, in column 1 of Table 1A, each clone is identified by a cDNA Clone ID
(identifier generally referred to herein as Clone ID NO:Z). Eaoh Clone ID is
unique to
an individual clone and the Clone ID is all the information needed to retrieve
a given
clone from the HGS library. Furthermore, certain clones disclosed in this
application
have been deposited with the ATCC on October 5, 2000, having the ATCC
designation numbers PTA 2574 and PTA 2575; and on January 5, 2001, having the
depositor reference numbers TS-1, TS-2, AC-l, and AC-2. In addition to the
individual cDNA clone deposits, most of the cDNA libraries from which the
clones
were derived were deposited at the American Type Culture Collection
(hereinafter
"ATCC"). Table 7 provides a list of the deposited cDNA libraries. One can use
the
Clone ID NO:Z o determine the library source by reference to Tables 6 and 7.
Table
7 lists the deposited cDNA libraries by name and links each library to an ATCC
Deposit. Library names contain four characters, for example, "HTWE." The name
of
a cDNA clone (Clone ID NO:Z) isolated from that library begins with the same
four
characters, for example "HTWEP07". As mentioned below, Table 1A correlates the
Clone ID NO:Z names with SEQ ID NO:X. Thus, starting with an SEQ ID NO:X, one
can use Tables 1A, 6 and 7 to determine the corresponding Clone ID NO:Z, which
library it came from and which ATCC deposit the library is contained in.
Furthermore,
it is possible to retrieve a given cDNA clone from the source library by
techniques
known in the art and described elsewhere herein. The ATCC is located at 10801
University Boulevard, Manassas, Virginia 20110-2209, USA. The ATCC deposits
were made pursuant to the terms of the Budapest Treaty on the international
recognition of the deposit of microorganisms for the purposes of patent
procedure.
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[025] In specific embodiments, the polynucleotides of the invention are at
least 1~5, at
least 30, at least 50, at least 100, at least 125, at least 500, or at least
1000 continuous
nucleotides but are less than or equal to 300 kb, 200 kb, 100 lcb, 50 kb, 15
kb, 10 kb,
7.5 lcb, 5 kb, 2.5 kb, 2.0 kb, or 1 kb, in length. In a further embodiment,
polynucleotides of the invention comprise a portion of the coding sequences,
as
disclosed herein, but do not comprise all or a portion of any intron. In
another
embodiment, the polynucleotides comprising coding sequences do not contain
coding
sequences of a genomic flanking gene (i.e., 5' or 3' to the gene of interest
in the
genome). In other embodiments, the polynucleotides of the invention dd not
contain
the coding sequence of more than 1000, 500, 250, 100, 50, 25, 20, 15, 10, 5,
4, 3, 2, or
1 genomic flanking gene(s).
[026] A "polynucleotide" of the present invention also includes those
polynucleotides
capable of hybridizing, under stringent hybridization conditions, to sequences
contained in SEQ ID NO:X, or the complement thereof (e.g., the complement of
any
one, two, three, four, or more of the polynucleotide fragments described
herein), the
polynucleotide sequence delineated in columns 8 and 9 of Table 2 or the
complement
thereof, and/or cDNA sequences contained in Clone ID NO:Z (e.g., the
complement of
any one, two, three, four, or more of the polynucleotide fragments, or the
cDNA clone
within the pool of cDNA clones deposited with the ATCC, described herein)
andlor
the polynucleotide sequence delineated in column 6 of Table 1B or the
complement
thereof. "Stringent hybridization conditions" refers to an overnight
incubation at 42
degree C in a solution comprising 50% formamide, Sx SSC (750 mM NaCI, 75 mM
trisodium citrate), 50 mM sodium phosphate (pH 7.6), Sx Denhardt's solution,
10%
dextran sulfate, and 20 ~,g/ml denatured, sheared salmon sperm DNA, followed
by
washing the filters in O.lx SSC at about 65 degree C.
[027] Also contemplated are nucleic acid molecules that hybridize to the
polynucleotides of the present invention at lower stringency hybridization
conditions.
Changes in the stringency of hybridization and signal detection are primarily
accomplished through the manipulation of formamide concentration (lower
percentages of formamide result in lowered stringency), salt conditions, or
temperature. For example, lower stringency conditions include an overnight
incubation at 37 degree C in a solution comprising 6X SSPE (20X SSPE = 3M
NaCI;
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0.2M NaHZP04; 0.02M EDTA, pH 7.4), 0.5% SDS, 30% formamide, 100 ug/ml
salmon sperm blocking DNA; followed by washes at 50 degree C with 1XSSPE, 0.1%
SDS. In addition, to achieve even lower stringency, washes performed following
stringent hybridization can be done at higher salt concentrations (e.g. 5X
SSC).
[028] Note that variations in the above conditions may be accomplished through
the
inclusion and/or substitution of alternate blocking reagents used to suppress
background in hybridization experiments. Typical blocking reagents include
Denhardt's reagent, BLOTTO, heparin, denatured salmon sperm DNA, and
commercially available proprietary formulations. The inclusion of specific
blocking
reagents may require modification of the hybridization conditions described
above,
due to problems with compatibility.
[029] Of course, a polynucleotide which hybridizes only to polyA+ sequences
(such
as any 3' terminal polyA+ tract of a cDNA shown in the sequence listing), or
to a
complementary stretch of T (or U) residues, would not be included in the
definition of
"polynucleotide," since such a polynucleotide would hybridize to any nucleic
acid
molecule containing a poly (A) stretch or the complement thereof (e.g.,
practically any
double-stranded cDNA clone generated using oligo dT as a primer).
[030] The polynucleotide of the present invention can be composed of any
polyribonucleotide or polydeoxribonucleotide, which may be unmodified RNA or
DNA or modified RNA or DNA. For example, polynucleotides can be composed of
single- and double-stranded DNA, DNA that is a mixture of single- and double-
stranded regions, single- and double-stranded RNA, and RNA that is mixture of
single- and double-stranded regions, hybrid molecules comprising DNA and RNA
that
may be single-stranded or, more typically, double-stranded or a mixture of
single- and
double-stranded regions. In addition, the polynucleotide can be composed of
triple-
stranded regions comprising RNA or DNA or both RNA and DNA. A polynucleotide
may also contain one or more modified bases or DNA or RNA backbones modified
for
stability or for other reasons. "Modified" bases include, for example,
tritylated bases
and unusual bases such as inosine. A variety of modifications can be made to
DNA
and RNA; thus, "polynucleotide" embraces chemically, enzymatically, or
metabolically modified forms.
13
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
[031] The polypeptide of the present invention can be composed of amino acids
joined to each other by peptide bonds or modified peptide bonds, i.e., peptide
isosteres, and may contain amino acids other than the 20 gene-encoded amino
acids.
The polypeptides may be modified by either natural processes, such as
posttranslational processing, or by chemical modification techniques which are
well
known in the art. Such modifications are well described in basic texts and in
more
detailed monographs, as well as in a voluminous research literature.
Modifications
can occur anywhere in a polypeptide, including the peptide backbone, the amino
acid
side-chains and the amino or carboxyl termini. It will be appreciated that the
same
type of modification may be present in the same or varying degrees at several
sites in a
given polypeptide. Also, a given polypeptide may contain many types of
modifications. Polypeptides may be branched, for example, as a result of
ubiquitination, and they may be cyclic, with or without branching. Cyclic,
branched,
and branched cyclic polypeptides may result from posttranslation natural
processes or
may be made by synthetic methods. Modifications include acetylation,
acylation,
ADP-ribosylation, amidation, covalent attachment of flavin, covalent
attachment of a
heme moiety, covalent attachment of a nucleotide or nucleotide derivative,
covalent
attachment of a lipid or lipid derivative, covalent attachment of
phosphotidylinositol,
cross-linking, cyclization, disulfide bond formation, demethylation, formation
of
covalent cross-links, formation of cysteine, formation of pyroglutamate,
formylation,
gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation,
iodination,
methylation, myristoylation, oxidation, pegylation, proteolytic processing,
phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-
RNA
mediated addition of amino acids to proteins such as arginylation, and
ubiquitination.
(See, for instance, PROTEINS - STRUCTURE AND MOLECULAR PROPERTIES,
2nd Ed., T. E. Creighton, W. H. Freeman and Company, New York (1993);
POSTTRANSLATIONAL COVALENT MODIFICATION OF PROTEINS, B. C.
Johnson, Ed., Academic Press, New York, pgs. 1-12 (1983); Seifter et al.,
Meth.
Enzymol. 182:626-646 (1990); Rattan et al., Ann. N.Y. Acad. Sci. 663:48-62
(1992).)
[032] "SEQ ID NO:X" refers to a polynucleotide sequence described, for
example, in
Tables 1A or 2, while "SEQ ID NO:Y" refers to a polypeptide sequence described
in
column 5 of Table 1A. SEQ ID NO:X is identified by an integer specified in
column 3
14
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
of Table 1A. The polypeptide sequence SEQ ID NO:Y is a translated open reading
frame (ORF) encoded by polynucleotide SEQ ID NO:X. "Clone ID NO:Z" refers to a
cDNA clone described in colurnil 1 of Table 1A.
[033] "A polypeptide having biological activity" refers to a polypeptide
exhibiting
activity similar to, but not necessarily identical to, an activity of a
polypeptide of the
present invention, including mature forms, as measured in a particular
biological
assay, with or without dose dependency. In the case where dose dependency does
exist, it need not be identical to that of the polypeptide, but rather
substantially similar
to the dose-dependence in a given activity as compared to the polypeptide of
the
present invention (i.e., the candidate polypeptide will exhibit greater
activity or not
more than about 25-fold less and, preferably, not more than about tenfold less
activity,
and most preferably, not more than about three-fold less activity relative to
the
polypeptide of the present invention).
[034] Table 1A summarizes some of the polynucleotides encompassed by the
invention (including contig sequences (SEQ ID NO:X) and clones (Clone ID NO:Z)
and further summarizes certain characteristics of these polynucleotides and
the
polypeptides encoded thereby.
Polynucleotides and Polypeutides
TABLE 1A
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
U
G
.r.r
O
O CC
U
1~
O ~ ~""~ O~ O
O O O O
:~ a~
~ o
"~ -~ ~s
.
N N N N ~ N N N N N N N N N
~
a~ ~Q oo O O O ~ ~ O O O O O a ~ l~ 00
'-'
Vi iSr pp ~ ~ ~ O~ M M M M M M lfl~ lfl lD
y '~ O
0 o x x x x x x x x x x x
o
va ~ . .
a
r'' 0 d' M ~p o ~- i
0o ~ ~ N
o
_ N M o ~
~ o
~
P. ~ N
~ s~.,p ~
~, ,
W N ~ ~ ~s p~~.
~ ~ C7 C7
d C'7
00 ~ p o00 00 O O
O
N o N ~ ~M M ~
N N~
~ c o
~ i o
i i i i , b _
i i i ~ 4 N
i ~ ~.
,'~, ~
G v - _ ~ ~ ~
C7 ~ f~ ~
C7 ~
C7
~ ~ E
~
Or ~ N M dw r~~ I~ 0001 O --~N M ~t V1 ~O
A
N N N N N N N N M M M M M M M
N N N N N N N N N N N N N N N
N ~ N
O ~ O N ~ t~ ~ ~ d'~ O
'
M N M V7M ,~ N d M N N N N O d-
M M M N N N
, , , , ,
Q O ~ ~ ~ d. ~ ~ ~ ~ ~ , M
N o~o ~ O M N ~n~ M ~ M
'r
N M d'~n ~O I~00 01O ~ N M d' ~n
Q ~ ~ ~ ~ ~ ~ ~ ~ ~ N N N N N N
z
bA a1 010o h ~ oo l~N ~n~ ~ON oo O .-r
:N ~ ~ ~ M l~ M d-\O N N 0101OW O O
l~ ~Od' l~oo l~ V1V1 ~ l~~ ooN ~ 00
'
p A V V1O ~ l~ V~ V1V1 V1V'7V1l~M V1 O
1
~n V1~O tnin in ~mn M in~n~ N V~ ~O
U ~
~ ~ ~ ~ov ~ ~o~ ~n~ ~000~ ~ o,
,
dl ~O~ M dl ~ M M Vll~~p41
A ~ l~ N d wD Wn M O
O ~. d. opM N .--
N N N ~ ~ ~ ~ ~ ~ ~ W W W
~
z x x x x
v x x x x x x x x x x x
16
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
O O O O O O l~ oo O O ~ O O v'i tn ~i irj tri t~ O O O O O ~ O O O N
O O O~ 01 ~ N V1 tn l~ V1 l0 O ~ O O O O O 01 ~ O O O O ~ ~ V1 O O
M oo N N o0 00 00 0o N N N 01 d' ~ ~D ~O vO ~O N a1 O ~ ~ N v0 t~ in N N
O O N N ON N dN' dN" ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ o0O O ~ N M M ~ ~ V~1 ~ O
M
N
N
Cs.
N
d;
O
d'
M
i
N
N
O O
d'
N
Va r~
M
N
N
N
O
N
due'
N
M
U
w
w
x
17
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
,~ d~. 00 0 o 0 0 0 ~ ~ ~ 0
00 0 ~n 0 0
lfl l0 ~ O~ V1 V~ M M 00 00
~ 00 l~ N d' d' d'
N M d- ~ oo O O O O 01 M oo
N d' O O O
O O ~ ~ ~ N M M d' d' oo N oo
N O O O
O O O O O O O O N N M o0 0o
O Q1 01 d1
cri
C
N
N
O
N N N N N N N N N N N
010101Q~0161 d1~ d1 01 01
O O O O O O O O O O O
x x x x x x x x x x x
0o M N
~ a1
> O d'Q~ N dp N
~
_ _
,
C7 ~ ~na ~ ~ ~, H
C7 a
O G~p O , O p O
p p
00 O 0op V1 0o 00
.~.~ V1
01
'
N N M ~ ,-, '~ ,~ '"i
M M
,
N N N
~
~ ~ ~0 ~ a~ ~ c~
N N N N N N N N N N N
M 01 lp
d100~ M ~ O
~ N ~
, i , i , N ~ N
, ,
~ h ~ ~ M
o ~ ~ N O ,-,
o
M
0oOvO ~ N M d-V1 ~O
N N N M M M M M M M M
~
tn~D ~ d'~ V~l~d'
V1\ON 00~ in InV1V1 O
v7M ~r1~ ooW v~V1N
a1~ ~ ~ ~ d1 a>
d1d-O M ~ d\'~~ ~ N
t~O N d'oo~ ood'oo O O
~ w w rte,w x x ~ ~ z O
U U U U U U U U U U U
w w w w w w w w w w w
x x x x
x x x x x x x
18
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
vo a\
0
0 o
a a
N N N N N M N N N N N d' M N N N N N
d\01O~01 d1d\ 01 01 ~ 01O~ 01 01O~O~d\d101
O ~Ol~l~~ ~O~ ~O ~O ~O~Dl~ ~O ~D~O~O~O~O~
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
~ x x x x x x x x x x x x x x x x x x
' ~ N M ue N ~ O
d ~ ~ ~ ~ ~ d ~ N
N = ~ ' ~
~
d_ ~. ~ ~'
c
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a, p ~ H ~ U a, a
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0 0
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-i M M ~ l0
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N ~ ~ Oi V~ ,-~CVd" ''1 M M Vi ,-,
N ,-~ M ~--~
M ~ N
M ~ N ~ ~ N N
~
ac~ ~ ~ -' ~ ~ N ~ ~ ,~i ~ ~
~ a a c~a ~ U
c~ a
~ w a, ~ a Ha ~ a
O~O ~ N M d- v> ~O t~ooa1 O ~ N M ~ tr1~O
d'~n~n~n ~n~n ~n v~ in~n~W o W o vo ~o~
N N N N N N N N N N N N N N N N N N
~O~ -~~ N M oo O oo~ N
O ~ ~ O
O O ~ oo N ~OM M N ~ ~ N O d'
' '
M ~fd N ~ l!1 ~ ~ N ~ M V~ M M M O \OM
i ~ i ~ i i i ~ ~ ~ ~ ~ ~ N ~ i
l0M O O ~ ~ ~ M ~ N l~~ l~~ ~ ~D
O~~ ~ h ~ ~ v1N ~ d1 ~ N OvN oo~O
N ~ ,-~ ~ M ,.
0001O ~ N M v p I~oo O~ O ~ N M d-V1
M M d'd' d'd' ~ ' ' d'" " i
'
~ d d d V>n V>V1~n~n
O 01~ M M [~ N ~O 00O ~f' O1 N O O1M M M
00d'N M ~OV1 M O 00O O 'd" M ~ 'd"M 'Cf'M
00l~~O~n V1N d' l~ ~nt~l~ N l~~D~nM m
V1V7 V1~f' V1 V1 InO V1 d' M V>V>d'l/~
d\ ~ ~ ~ d\
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~D00e 00 O In lp O w w ~ ~ ~ H
o o x ~ N ~
~ ~
H H H ~ x c
U U U U U U U U U ~ ~1
w w w w w w w
w w w w
x
x x x x x x x x x ~ x x x x x x x
19
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
N
cn
O O ~O
d
N M N N N ~ N M N N N N N N N ~ N N N
~
N
O
O O O O O O p~ O O O
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d
O O O O O O O O O O O O O O O O O O
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x x x x x ~x x x x ~
.
a;
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N N ~ ~ ~ ' ~ ~pm M
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w ~ ~ ''U?; ~7w -. H v~
a ~.Hd~
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0 0 ~ 0 0 0 0 0 o
O 0 0 0 0 0 ~~~ O
.~.~ ~ +~.~-. ,--~
N
O
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d' ~ ~ ~ V1 li M ~--t
00
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x w ~ ~ ~, O o ~,~ ~ .~ ~,
~ O ~, L~l ~ ~ ~ [~
d C~ X1 V~ C'7
I1 C~ H G
h
1 1 ~ ~
I
0001O ~ N M d-tr1~D l~ ooQvO ~ N M d'
vD vo~ ~ t~ ~ t~t~~ ~ ~ t~t~~ 0000 0000
N N N N N N N N N N N N N N N N N N
N M N l~~ ~n M l~O d..d., d. d-~ d. 00a1
r ,~~,M ~ M M N 00M ~ M N N ~ ooN N N
"~
N
N ~ i ~ i M i ' N d' i i
O _
~
N ~ N N N N ~ ~ N ~ N N
~O l~0001O ~ N M d' v> ~O t~ooa\O .--~ N M
O O\M all~ O d'N 01 0o V7 01M l~M ~ O~l~
M \O~ I~~"~I~ ~ I~01 d' 01 ~ I~O ~ 00 r-tV~
V1 v1-~oo~ oo I~M d' I~ ~n d'V1O l~N l~l~
~t'7d'N l~~ l~ V1O Y1 V1 V1 d\U1V1V1d' ~1Y1
~n l~N ~OM ~O V1~ON v7 V~ ~ v1~ V>oo V>in
~ d\d\ ~ ~ d\~
d- ,~O o001 ,-~ O o0N p~ M d1~ O l~l~ 01V1
N ~ ~ w o a a ~ N d H
x x x x x x x x x x x x x x x x x x
~o
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
0 0
0
0 0
N N N N N N N N N N N N N N N N N N N N N N
N N N cViVN N cVcVN N N N N N N iVN N N N N
w n ~n ~n~n~n ow n ~n~n~nv~ ~ntnown ~n~n ~n~nown
O O O O O O O O O O O O O O O O O O O O O O
G7 ~ ~ ~ G7 ~ ~ ~ ~ ~ G7~ ~ ~ ~ G7 G7
00 '-i c~
M V7 ~
~
d-
N N ' ~ oo~ ti
p
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0
0 ~ o 0 0 0
0
ue o N ~ d'N ~ ~ d' M o N
~
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v~ ~ ~ ~ ~ ~ s'-~~, ~ ~ p ~ ~'.~~
cct ~'.~ ~' ~, ~ R.
x i ~ ,- ~ a i v c7 ~ w ~ ~ ~
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W p t~ ooa1O ~ N M dwr1~D I~0001O ~ N M d-tI1~O
0000 00 000od\ O~ O~01d1d1~ a1O~D1O O O O O O O
N N N N N N N N N N N N N N N M M M M M M M
Q ~ ~ O~ ~ N M M M O ~ ~OM d" O M d'M
M 1 M V1M N ~ M M ~ N ~ ~ M N 00M M N ~ N
Y1l~ M M
N ~ N ~ ~ i ~ i ' N ~ i ~ i
--,M ~ M o0od i o00~ , ~ i i i ~ N due' i
~ '~ N ~ N
~, N N ~
,.~
d'~n ~ I~ooO~ O ~ N M d-v'W O N ooa\O ~--~N M d'V1
I~ ~ ~ ~ t~ 00 0000000000 00000000a\a> ala>a1al
h O ~ ~
d'M O M ~ Ol ~ V'7\OO in~ N o ~nO M O ~O o0
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W v1 ~O oot~~ t~ ool~l~l~a1 l~N N d't~~O V100~ ,
V~Um n t~~n~1 ~n N ~n~nv10o m ~ d'O V>V'7tnN d'00
V'1v~ V1 ~ V~in vW ~nv~in~m n N ~O01V1~n ~nN M ~n
~ a\~ ~ ~ a> ~ d1d1~ ~ ~ ~ ~ d1a\
dw 0 N 01v0 N l~~ ~ N oo t~d'O d'~ ~O O M ~D
00 M d1O ~O 0o O ,-, ~ O ~ O ~ 0o~ N l~O'O O
f~Pa U U ~ ~1 ~1 ~ ~ ~ x ~ ~ U ~ rr~~C~C ~ N N d
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~
x x x x x x x x x x x x x x x x x x x x x
21
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
,~ ,-a
O ,~ os ,- ~
':-. ..
'~ o ~',.~ ,.-.
os ~ O ~ ~ O (V N
~
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O O ''~ 000 ~ ~l~
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N N N N N N N ~ N ~ .--~r..,~ ,--i
N N cVN N ,-; N ~ ooM . _; N
(V '-' M N l~
~
W v~W n V~~p v~ ~ ~O~ ~ , v1~ M
V~ O M N ~p ~O "
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O O O .---~~ .--.~ ~ ~ ,~,-i ,--i.-1 ~ N N
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l000~pO l~~O d" V'1 V1~ M O1 00V1
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22
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
.-; ,-i.-i,-i ,--iN
ue O ~ ~
h d ~ ,--i O O
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O
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0
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p ~ ~ ; b4 ~~.,p ~~., ' (V
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M M M M M M M M d'M M M M M M M
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x x ~ x x
23
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
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24
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
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CA 02393618 2002-06-03
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26
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
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27
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
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CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
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29
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
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CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
[035] The first column in Table 1A provides a unique "Clone ID NO:Z" for a
cDNA
clone related to each contig sequence disclosed in Table 1A. This clone ID
references
the cDNA clone which contains at least the 5' most sequence of the assembled
contig,
and at least a portion of SEQ ID NO:X was determined by directly sequencing
the
referenced clone. The reference clone may have more sequence than described in
the
sequence listing or the clone may have less. In the vast majority of cases,
however,
the clone is believed to encode a full-length polypeptide. In the case where a
clone is
not full-length, a full-length cDNA can be obtained by methods ltnown iri the
art
and/or as described elsewhere herein.
[036] The second column in Table 1A provides a unique "Contig ID"
identification
for each contig sequence. The third column provides the "SEQ ID NO:X"
identifier
for each of the prostate cancer associated contig polynucleotide sequences
disclosed in
Table 1A. The fourth column, "ORF (From-To)", provides the location (i.e.,
nucleotide position numbers) within the polynucleotide sequence "SEQ ID NO:X"
that
delineate the preferred open reading frame (ORF) shown in the sequence listing
and
referenced in Table 1A, column 5, as SEQ ID NO:Y. Where the nucleotide
position
number "To" is lower than the nucleotide position number "From", the preferred
ORF
is the reverse complement of the referenced polynucleotide sequence.
[037] The fifth column in Table 1A provides the corresponding SEQ ID NO:Y for
the polypeptide sequence encoded by the preferred ORF delineated in column 4.
In
one embodiment, the invention provides an amino acid sequence comprising, or
alternatively consisting of, a polypeptide encoded by the portion of SEQ ID
NO:X
delineated by "ORF (From-To)". Also provided are polynucleotides encoding such
amino acid sequences and the complementary strand thereto.
[038] Column 6 in Table 1A lists residues comprising epitopes contained in the
polypeptides encoded by the preferred ORF (SEQ ID NO:Y), as predicted using
the
algorithm of Jameson and Wolf, (1988) Comp. Appl. Biosci. 4:181-186. The
Jameson-Wolf antigenic analysis was performed using the computer program
PROTEAN (Version 3.11 for the Power Macintosh, DNASTAR, Inc., 1228 South
Park Street Madison, WI). In specific embodiments, polypeptides of the
invention
comprise, or alternatively consist of, at least one, two, three, four, five or
more of the
31
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
predicted epitopes as described in Table 1A. It will be appreciated that
depending on
the analytical criteria used to predict antigenic determinants, the exact
address of the
determinant may vary slightly.
[039] Column 7 in Table 1A provides an expression profile and library code:
count
for each of the contig sequences (SEQ ID NO:X) disclosed in Table 1A, which
can
routinely be combined with the information provided in Table 4 and used to
determine
the normal or diseased tissues, cells, and/or cell line libraries which
predominantly
express the polynucleotides of the invention. The first number in column 7
(preceding
the colon), represents the tissue/cell source identifier code corresponding to
the code
and descr' iption provided in Table 4. For those identifier codes in which the
first two
letters are not "AR", the second number in column 7 (following the colon)
represents
the number of times a sequence corresponding to the reference polynucleotide
sequence was identified in the tissue/cell source. Those tissue/cell source
identifier
codes in which the first two letters are "AR" designate information generated
using
DNA array technology. TJtilizing this technology, cDNAs were amplified by PCR
and
then transferred, in duplicate, onto the array. Gene expression was assayed
through
hybridization of first strand cDNA probes to the DNA array. cDNA probes were
generated from total RNA extracted from a variety of different tissues and
cell lines.
Probe synthesis was performed in the presence of 33P dCTP, using oligo(dT) to
prime
reverse transcription. After hybridization, high stringency washing conditions
were
employed to remove non-specific hybrids from the array. The remaining signal,
emanating from each gene target, was measured using a Phosphorimager. Gene
expression was reported as Phosphor Stimulating Luminescence (PSL) which
reflects
the level of phosphor signal generated from the probe hybridized to each of
the gene
targets represented on the array. A local background signal subtraction was
performed
before the total signal generated from each array was used to normalize gene
expression between the different hybridizations. The value presented after
"[array
code]:" represents the mean of the duplicate values, following background
subtraction
and probe normalization. One of skill in the art could routinely use this
information to
identify normal and/or diseased tissues) which show a predominant expression
pattern
of the corresponding polynucleotide of the invention or to identify
polynucleotides
which show predominant and/or specific tissue and/or cell expression. The
sequences
32
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
disclosed herein have been determined to be predominantly expressed in
prostate
tissues, including normal and diseased prostate tissues (See Table 1A, column
7 and
Table 4).
[040] Column 8 in Table 1A provides a chromosomal map location for certain
polynucleotides of the invention. Chromosomal location was determined by
ending
exact matches to EST and cDNA sequences contained in the NCBI (National Center
for Biotechnology Information) UniGene database. Each sequence in the UniGene
database is assigned to a "cluster"; all of the ESTs, cDNAs, and STSs in a
cluster are
believed to be derived from a single gene. Chromosomal mapping data is often
available for one or more sequences) in a UniGene cluster; this data (if
consistent) is
then applied to the cluster as a whole. Thus, it is possible to infer the
chromosomal
location of a new polynucleotide sequence by determining its identity with a
mapped
UniGene cluster.
[041] A modified version of the computer program BLASTN (Altshul et al., J.
Mol.
Biol. 215:403-410 (1990), and Gish et al., Nat. Genet. 3:266-272 (1993)) was
used to
search the UniGene database for EST or cDNA sequences that contain exact or
near-
exact matches to a polynucleotide sequence of the invention (the 'Query'). A
sequence
from the UniGene database (the 'Subject') was said to be an exact match if it
contained a segment of 50 nucleotides in length such that 48 of those
nucleotides were
in the same order as found in the Query sequence. If all of the matches that
met this
criteria were in the same UniGene cluster, and mapping data was available for
this
cluster, it is indicated in Table 1A under the heading "Cytologic Band". Where
a
cluster had been further localized to a distinct cytologic band, that band is
disclosed;
where no banding information was available, but the gene had been localized to
a
single chromosome, the chromosome is disclosed.
[001] Once a presumptive chromosomal location was determined for a
polynucleotide of the invention, an associated disease locus was identified by
comparison with a database of diseases which have been experimentally
associated
with genetic loci. The database used was the Morbid Map, derived from OMIMTM
(supra). If the putative chromosomal location of a polynucleotide of the
invention
(Query sequence) was associated with a disease in the Morbid Map database, an
OMIM reference identification number was noted in column 9, Table 1A, labeled
33
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
"OMIM Disease References)". Table 5 is a key to the OMIM reference
identification
numbers (column 1), and provides a description of the associated disease in
Column
2.
TABLE 1B
Clone ID SEQ CONTIG BAC ID: SEQ ID EXON
NO:Z ID ID: A NO:B From-To
NO:X
HBZAJ09 11 655769 AC019232 433 1-315
HBZAJ09 11 655769 AC025171 434 1-315
HBZAJ09 11 655769 AC019232 435 1-324
HBZAJ09 11 655769 AC025171 436 1-148
HBZAJ09 11 655769 AC019232 437 1-148
HBZAJ09 11 655769 AC025171 438 1-283
HBZSH16 12 655619 AC069483 439 1-554
HBZSH16 12 655619 AC069483 440 1-920
HBZSH71 13 760418 AC018693 44.1 1-741
HBZSH71 13 760418 AC018693 442 1-252
HBZSI73 14 655737 AC067954 443 1-313
HBZSI73 14 655737 AC067954 444 1-326
HHLAB29 15 557871 AL121813 445 1-173
HHLAB29 15 557871 AL023633 446 1-292
HHLAB29 15 557871 AL160371 447 1-994
HL1AN67 20 655721 AC023247 448 1-245
HL1AN67 20 655721 AC006237 449 1-245
HL1AS26 21 655696 AL157915 450 1-667
HL1AS26 21 655696 AL136294 451 1-667
HPEAF19 22 867892 AC024132 452 1-344
HPEBA51 23 723298 AL353788 453 1-434
HPEBA51 23 723298 AL139184 454 1-434
HPEBA51 23 723298 AL353788 455 1-143
HPEBA51 23 723298 AL139184 456 1-143
HPEBD31 24 655760 AC018761 457 1-538
HPEBD31 24 655760 AC020934 458 1-538
HPEBD31 24 655760 AC018761 459 1-263
HPEBD31 24 655760 AC020934 460 1-736
792-957
1232-1693
1845-2006
2206-2481
2621-3482
3536-3786
3815-4535
4695-5049
HPEBD31 24 655760 AC018761 461 1-736
~
34
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
792-957
1232-1693
1845-2006
2206-2481
2621-3482
3548-3786
3815-4535
4695-5049
HPEBD31 24 655760 AC020934 462 1-263
HPFAA06 25 960801 AC004111 463 1-863
3429-4124
HPFAA06 25 960801 AC010277 464 1-863
3424-4119
HPFAA06 25 960801 AC004111 465 1-667
HPFAA06 25 960801 AC004111 466 1-522
HPFAA06 25 960801 AC010277 467 1-667
HPFAA06 25 960801 AC010277 468 1-401
HPFCA36 26 524720 AC007065 469 1-340
351-738
1335-1773
3 899-4267
14595-14825
18322-18557
19664-20128
20663-20915
22067-22299
HPFCA36 26 524720 AC007065 470 1-495
HPFCA36 26 524720 AC007065 471 1-483
HPFCA71 27 655596 AC018681 472 1-364
HPFCF09 28 536666 AC022417 473 1-174
1973-2115
2563-3003
3442-3591
4140-4231
5955-6389
6564-7100
8645-8708
8978-9101
10914-11290
11985-12297
13345-13410
14962-15695
18991-19133
20469-22756
HPFCF09 28 536666 AC022417 474 1-104
HPFCF24 29 655744 AL160279 475 1-398
HPFCF24 29 655744 AL160279 476 1-313
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
HPFCF83 31 781490 AC036220 477 1-327
HPFCF83 31 781490 AC026273 478 1-327
HPFCF83 31 781490 AC018963 479 1-369
HPFCF83 31 781490 AC023099 480 1-369
627-1264
1708-2248
HPFCF83 31 781490 AC016424 481 1-393
HPFCF83 31 781490 AC008776 482 1-369
HPFCF83 31 781490 AC022264 483 1-369
627-1264
1708-2248
HPFCF83 31 781490 AC024972 484 1-390
HPFCF83 31 781490 AC036220 485 1-1419
HPFCF83 31 781490 AC026273 486 1-1420
HPFCF83 31 781490 AC023099 487 1-1529
HPFCF83 31 781490 AC016424 488 1-612
HPFCF83 31 781490 AC008776 489 1-339
4826-4859
HPFCF83 31 781490 AC018963 490 1-1382
1384-1518
HPFCF83 31 781490 AC023099 491 1-434
HPFCF83 31 781490 AC016424 492 1-1527
HPFCF83 31 781490 AC022264 493 1-1529
HPFCF83 31 781490 AC022264 494 1-434
HPFCF83 31 781490 AC024972 495 1-1524
HPFCF83 31 781490 AC024972 496 1-612
HPFCH15 32 655768 AC068428 497 1-352
HPFCH89 33 655538 AC012589 498 1-227
HPFCH89 33 655538 AC022088 499 1-227
HPFCH89 33 655538 AC012589 500 1-250
HPFCH89 33 655538 AC022088 501 1-250
HPFCM41 34 655736 AC008278 502 1-348
HPFCM41 34 655736 AC008271 503 1-348
HPFCM41 34 655736 AC008278 504 1-471
HPFCM41 34 655736 AC008271 505 1-471
HPFCM87 35 925495 AC004479 506 1-318
HPFCM87 35 925495 AC004480 507 1-318
HPFCM87 35 925495 AC004479 508 1-155
HPFCM87 35 925495 AC004480 509 1-155
HPFC002 37 867871 AC019103 510 1-1224
HPFC067 38 867880 AC024489 511 1-302
HPFCR21 40 655621 AC066603 512 1-448
HPFCR21 40 655621 AC066603 513 1-326
HPFCT53 43 974257 AC078894 514 1-654
HPFCT53 43 974257 AC026815 515 1-654
HPFCT53 43 974257 AC034258 516 1-648
36
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
HPFCT53 43 974257 AC078893 517 1-640
HPFCT53 43 974257 AC068667 518 1-654
HPFCT53 43 974257 AC073166 519 1-640
HPFCT53 43 974257 AC074226 520 1-640
HPFCT53 43 974257 AC027037 521 1-640
HPFCT53 43 974257 AC078898 522 1-640
HPFCT53 43 974257 AC068924 523 1-640
HPFCT62 44 655432 AC016767 524 1-389
HPFCT62 44 655432 AC026369 525 1-389
HPFCT62 44 655432 AL078621 526 1-389
HPFCT62 44 655432 AC016767 527 1-653
HPFCT62 44 655432 AC026369 528 1-104
117-884
890-1137
HPFCT62 44 655432 AL078621 529 1-1121
HPFCX18 46 655588 AC022598 530 1-559
HPFCX18 46 655588 AC024367 531 1-559
HPFCX18 46 655588 AC022598 532 1-484
539-645
HPFCX18 46 655588 AC022598 533 1-421
HPFCX18 46 655588 AC024367 534 1-421
HPFCX18 46 655588 AC024367 535 1-484
539-645
HPFDD06 47 960700 AL359314 536 1-282
HPFDD06 47 960700 AL390239 537 1-418
HPFDD06 47 960700 AL390239 538 1-157
634-1162
HPFDE38 48 655704 AC073616 539 1-615
HPFDE38 48 655704 AC061966 540 1-615
HPFDE38 48 655704 AC061966 541 1-957
HPFDE38 48 655704 AC061966 542 1-396
HPFDF79 50 973732 AL139240 543 1-600
HPFDF79 50 973732 AL139240 544 1-497
HPFDG58 51 655610 AC021557 545 1-358
HPFDG58 51 655610 AC021557 546 1-308
HPFDI23 52 655549 AC044876 547 1-351
HPFDI23 52 655549 AC010983 548 1-351
HPFDI23 52 655549 AC010983 549 1-1694
HPFDL90 53 954333 U73330 550 1-204
HPFDL90 53 954333 AL137143 551 1-204
HPFDL90 53 954333 AL137143 552 1-114
HPFDS59 54 655543 AC004111 553 1-279
HPFDS59 54 655543 AC004111 554 1-429
HPFDT17 55 581133 AC021972 555 1-360
HPFDT17 55 581133 AC023961 556 1-360
~HPFDT17 55 581133 AC023961 557 1-493
37
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
HPFDT54 56 655530 AC078787 558 1-337
HPFDT54 56 655530 AC068844 559 1-337
HPFDT54 56 655530 AC068844 560 1-156
307-357
HPFDT61 57 974569 AC012456 561 1-429
HPFDT61 57 974569 AC012456 562 1-508
HPFDU30 58 522113 AL079301 563 1-353
HPFDU30 58 522113 AL079301 564 1-368
HPFDU30 58 522113 AL079301 565 1-477
HPFDU38 59 867879 AP001816 566 1-357
HPFDU38 59 867879 AC013785 567 1-357
HPFDU38 59 867879 AP001816 568 1-1082
HPFDU38 59 867879 AP001816 569 1-605
HPFDU38 59 867879 AC013785 570 1-1082
HPFDU38 59 867879 AC013785 571 1-605
HPFDV71 61 867870 AC004170 572 1-90
HPFDV71 61 867870 AC004170 573 1-498
742-1013
1596-1878
2017-2131
2550-3098
HPFDZ20 62 655764 AC026262 574 1-320
HPFDZ20 62 655764 AC026262 575 1-145
HPFDZ20 62 655764 AC026262 576 1-394
HPFEA08 63 960372 AL158145 577 1-102
605-988
994-1149
1496-1658
1689-2232
2888-3316
4118-5228
5538-5638
8075-8374
9151-9248
10537-10628
14985-15054
HPFEA08 63 960372 AL158145 578 1-101
HPFEA32 64 925499 AF228661 579 1-296
HPFEA32 64 925499 AF215845 580 1-296
HPIAE79 65 655748 AC011234 581 1-367
HPIAQ49 67 919469 AL161913 582 1-434
HPIAQ49 67 919469 AC007951 583 1-434
HPIAV80 69 615007 AC011747 584 1-316
562-618
724-1313
1814-2395
38
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
HPIAV80 69 615007 AC012495 585 1-316
562-618
724-1313
1814-2395
HPIAV80 69 615007 AC011747 586 1-1776
HPIAV80 69 615007 AC012495 587 1-133
239-638
2245-2345
3320-3556
5015-8143
HPIAZ37 70 655753 AC018613 588 1-357
1494-1815
2463-5309
5330-8041
HPIAZ37 70 655753 AL356099 589 1-357
1495-1816
2464-5308
5330-8041
16792-21577
HPIAZ37 70 655753 AL355474 590 1-357
1494-1815
2463-5308
5329-8041
HPIBT49 72 655719 AC068558 591 1-468
HPJAB 19 74 655540 AC027164 592 1-422
HPJAB19 74 655540 AC024388 593 1-422
HPJAB 19 74 655540 AC027164 594 1-325
HPJAB19 74 655540 AC024388 595 1-325
HPJAB84 75 655531 AC013471 596 1-335
HPJAC36 76 655601 AC073476 597 1-107
2096-2450
3106-3182
3643-3787
4316-4982
5399-5724
6657-7075
7479-7686
9286-9495
9701-9784
10235-10339
HPJAC92 77 867831 AP001374 598 1-441
HPJAC92 77 867831 AP001845 599 1-441
HPJAC92 77 867831 AP001374 600 1-370
HPJAC92 77 867831 AP001845 601 1-370
HPJAD09 78 655712 AL356873 602 1-341
HPJAD09 78 655712 AL080239 603 1-341
HPJAD66 79 ~ 655694 283851 604 1-375
39
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
HPJAD82 80 655765 AC023550 605 1-599
HPJAD82 80 655765 AC078819 606 1-599
HPJAD82 80 655765 AC023550 607 1-262
HPJAD82 80 655765 AC078819 608 1-180
HPJAD82 80 655765 AC023550 609 1-180
HPJAD82 80 655765 AC078819 610 1-262
HPJAV07 81 952852 AC022990 611 1-330
HPJAV07 81 952852 AC022990 612 1-338
HPJBI17 82 655761 AC018493 613 1-433
HPJBI17 82 655761 AC018840 614 1-433
HPJBI17 82 655761 AC011327 615 1-433
HPJBI17 82 655761 AC023514 616 1-433
HPJBI17 82 655761 AC018493 617 1-4779
HPJBI17 82 655761 AC018840 618 1-4959
7250-73
80
HPJBI17 82 655761 AC011327 619 1-4926
7254-73
84
HPJBI17 82 655761 AC023514 620 1-559
HPJBI89 83 655708 AC006071 621 1-97
806-944
2874-2923
3012-3124
4930-5376
7132-7248
8149-8301
11085-11487
12690-12774
13247-13392
HPJBI89 83 655708 AC002092 622 1-50
768-905
2835-2884
2973-3083
4894-5636
7096-7212
8116-8253
HPJBI89 83 655708 AC006071 623 1-676
HPJBK52 84 655751 AC026458 624 1-635
HPJBK52 84 655751 AC026957 625 1-519
HPJBK52 84 655751 AC068974 626 1-638
HPJBK52 84 655751 AC022770 627 1-638
HPJBK52 84 655751 AF271408 628 1-519
HPJBK52 84 655751 AC000378 629 1-636
HPJBK52 84 655751 AF165177 630 1-637
HPJBK52 84 655751 AF284563 631 1-438
HPJBK52 84 655751 AC026957 632 1-1148_
HPJBK52 84 655751 AC068974 633 ~ 1-170
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
HPJBK52 84 655751 AC068974 634 1-674
HPJBK52 84 655751 AC022770 635 1-632
HPJBK52 84 655751 AF271408 636 1-512
HPJBK52 84 655751 AC000378 637 1-336
HPJBK52 84 655751 AF165177 638 1-666
HPJBK52 84 655751 AF284563 639 1-672
HPJBU08 85 958979 AC034223 640 1-365
HPJBU08 85 958979 AC025459 641 1-365
HPJBU08 85 958979 AC034223 642 1-470
HPJBU08 85 958979 AC025459 643 1-470
HPJBV 17 86 655729 AC007394 644 1-300
HPJCC04 87 926787 AC020746 645 1-402
HPJCC04 87 926787 AC020746 646 1-137
996-1100
HPJCC04 87 926787 AC020746 647 1-305
HPJCP10 88 964259 AC010384 648 1-482
HPJCP10 88 964259 AC010471 649 1-482
HPJCP10 88 964259 AL161724 650 1-482
HPJCX26 91 655600 AL354668 651 1-350
HPJCY70 92 655569 AC073576 652 1-378
HPJCY70 92 655569 AL355916 653 1-378
HPJCZ03 93 922850 AC019301 654 1-322
HPJCZ03 93 922850 AC019301 655 1-115
HPJCZ03 93 922850 AC019301 656 1-117
HPJCZ06 94 934170 AC012101 657 1-434
HPJCZ06 94 934170 AC012101 658 1-261
HPJDX94 97 838748 AC027752 659 1-385
HPJDX94 97 838748 AC024033 660 . 1-385
HPJEI55 98 926815 AC012141 661 1-464
HPJEI55 98 926815 AL138843 662 1-464
HPJEI55 98 926815 AL138787 663 1-464
HPJEI55 98 926815 AC012141 664 1-643
HPJEI55 98 926815 AL138843 665 1-206
2313-2650
3456-4431
HPJEI55 98 926815 AC012141 666 1-976
HPJEI55 98 926815 AL138843 667 1-643
HPJEI55 98 926815 AL138787 668 1-206
2313-2650
3456-4433
HPJEI55 98 926815 AL138787 669 1-643
HPJEJ39 99 930988 AL162551 670 1-605
HPJEJ39 99 930988 AL121576 671 1-605
HPJEQ22 100 867725 AC021715 672 1-639
HPJEQ22 100 867725 AL163052 673 1-639
HPJEV06 102 934096 ~ AP000773~ 674 1-769
41
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
HPJEV06 102 934096 AC018708 675 1-768
HPJEV06 102 934096 AC011207 676 1-768
HPJEV06 102 934096 AP000773 677 1-495
909-997
1276-1446
HPJEV06 102 934096 AC018708 678 1-409
HPJEV06 102 934096 AP000773 679 1-409
HPJEV06 102 934096 AC018708 680 1-495
909-997
1276-1446
HPJEV06 102 934096 AC011207 681 1-409
HPJEV06 102 934096 AC011207 682 1-495
909-997
1276-1446
HPZAB38 104 655591 AC008954 683 1-263
HPZAB38 104 655591 AC026707 684 1-263
HPZAB38 104 655591 AC008971 685 1-263
HPZAB38 104 655591 AC026707 686 1-186
HPZAB38 104 655591 AC008971 687 1-180
HPJFA10 106 963322 AC009299 688 1-607
HPJFA10 106 963322 AC009299 689 1-465
HPJFA10 106 963322 AC009299 690 1-475
HPJEV95 107 929723 AL359456 691 1-711
HPJEV95 107 929723 AL390724 692 1-633
HPJEV95 107 929723 AL390724 693 1-368
HPJEV95 107 929723 AL359456 694 1-1365
HPJET11 109 965894 AP001270 695 1-961
HPJET 11 109 965894 AP001270 696 1-344
HPJET11 109 965894 AP001270 697 1-427
HPJES 17 110 859867 AP001857 698 1-444
HPJES 17 110 859867 AC015703 699 1-444
HPJES 17 110 859867 AP001857 700 1-54
1030-1290
HPJEL02 111 918315 AC025014 701 1-1195
1827-2531
4783-5133
5139-5379
5902-6081
6463-7267
7466-7724
8041-8216
8269-9037
9310-10364
10545-10988
11353-12100
HPJEL02 111 918315 AC011850 702 ~ 1-416
42
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
1048-1381
4025-4374
4380-4621
5927-6305
HPJEL02 111 918315 AC011850 703 1-334
HPJEL02 111 918315 AC020590 704 1-397
HPJEL02 111 918315 AL162451 705 1-416
1052-1446
2106-2304
4264-4614
4620-4861
5947-6495
HPJEL02 111 918315 AC012661 706 1-396
HPJEL02 111 918315 AC011850 707 1-660
HPJEL02 111 918315 AC025014 708 1-1181
HPJEL02 111 918315 AC011850 709 1-247
HPJEL02 111 918315 AL162451 710 1-249
HPJEL02 111 918315 AC020590 711 1-659
HPJEL02 111 918315 AC012661 712 1-486
HPJEG53 112 974074 AC006137 713 1-508
HPJEG53 112 974074 AL050328 714 1-508
HPJEG53 112 974074 AC006137 715 1-266
1353-1457
1654-1954
HPJEG53 112 974074 AL050328 716 1-323
1647-1959
HPJDT03 114 922815 AC009143 717 1-459
HPJDT03 114 922815 AC009123 718 1-459
3173-3221
5754-6155
HPJDP54 115 949149 AC022608 719 1-531
HPJDP54 115 949149 AC021472 720 1-531
HPJDP54 115 949149 AC069078 721 1-531
HPJDP54 115 949149 AC022608 722 1-301
HPJDP54 115 949149 AC022608 723 1-537
HPJDP54 115 949149 AC021472 724 1-1124
HPJDP54 115 949149 AC021472 725 1-301
HPJDP54 115 949149 AC069078 726 1-1124
HPJDP54 115 949149 AC069078 727 1-301
HPJDCO1 117 915056 AL357517 728 1-607
HPJDC01 117 915056 AL356792 729 1-607
HPJDCO1 117 915056 AL357517 730 1-532
HPJDCO1 117 915056 AL357517 731 1-221
HPJDCO1 117 915056 AL356792 732 1-532
HPJDCOl _117 915056 AL356792 733 1-221
_
HPJCT81 ~ 120 494874 AC068243 734 1-652
43
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
HPJCT81 120 494874 AC068243 735 1-119
HPJCT81 120 494874 AC068243 736 1-420
HPJCT26 121 559949 AC022064 737 1-130
781-1384
3527-3569
HPJCT26 121 559949 AC022064 738 1-198
HPJCS73 122 975087 AC008013 739 1-751
869-128
8
1741-2134
3713-4192
4219-4525
5032-5188
6221-6459
7627-7887
8458-9081
9227-9966
10464-10713
11232-11320
11620-11777
11791-12453
12643-13059
14536-14632
15693-16508
16536-17099
17433-17823
18365-18520
19494-19542
19895-20386
20452-21075
21128-21475
22370-22928
22994-23030
HPJCS73 122 975087 AC009533 740 1-221
367-759
1212-1606
3182-3992
4509-4666
4820-4982
5711-5948
7122-7382
7953-8576
8722-9484
9977-10227
10746-10834
11133-11288
11304-11966
12156-12572
44
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
14044-14140
14735-15547
15575-16138
16472-16862
17405-17560
18541-18589
18938-19448
20178-20525
21420-21971
22037-22073
22331-22434
22548-22685
22842-23316
23334-23726
25414-26133
26228-26338
26375-26622
26657-26756
27017-27239
27287-27340
27456-27676
27850-28149
28593-28639
28670-29013
29189-29345
29359-30420
HPJCS73 122 975087 AC008013 741 1-294
HPJCS73 122 975087 AC008013 742 1-106
220-357
575-1050
1060-1459
3153-3870
3965-4359
4392-4496
4756-4977
5025-5078
5198-5418
5593-5895
6301-6763
6941-8173
8913-9547
9927-10355
10651-11058
11461-11749
HPJCS73 122 975087 AC009533 743 1-636
HPJCS32 124 699046 AC024922 744 1-274
HPJCS32 124 699046 AC024922 745 1-274
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
HPJCL55 126 670083 AC068280 746 1-895
HPJBS35 131 867818 AC016276 747 1-431
HPJBS35 131 867818 AC015557 748 1-436
HPJBS35 131 867818 AC015557 749 1-495
HPJBL76 132 769889 AC007066 750 1-1543
HPJBL76 132 769889 AC018466 751 1-1543
HPJBL76 132 769889 AC007066 752 1-785'
HPJBL76 132 769889 AC007066 753 1-1761
HPJBL76 132 769889 AC018466 754 1-1761
HPJBL76 132 769889 AC018466 755 1-785
HPJBK25 134 974606 AC005077 756 1-540
HPJBK25 134 974606 AC005077 757 1-124
HPJBK14 135 974593 AC005202 758 1-604
HPJBK14 135 974593 AC005202 759 1-98
HPJBH45 136 717088 AC073089 760 1-681
HPJBH45 136 717088 AC006480 761 1-681
HPJBH45 136 717088 AC073089 762 1-238
HPJBH45 136 717088 AC006480 763 1-218
HPJBH45 136 717088 AC006480 764 1-493
HPJAU73 138 806718 AC011689 765 1-1216
HPJAU73 138 806718 AC078939 766 1-1496
HPJAU73 138 806718 AC011043 767 1-712
904-1867
1874-1906
2000-2124
2337-3891
HPJAU73 138 806718 AC011841 768 1-710
902-1864
1997-2121
2334-3824
4232-5905
HPJAU73 138 806718 AC078939 769 1-646
837-1797
1804-1836
1930-3820
4161-5834
HPJAU73 138 806718 AC078939 770 1-1358
HPJAU73 138 806718 AC011043 771 1-105
HPJAU73 138 806718 AC078939 772 1-906
HPJAU73 138 806718 AC011841 773 1-541
HPJAU73 138 806718 AC011841 774 1-105
HPJAU73 138 806718 AC078939 775 1-564
HPJAU73 138 806718 AC078939 776 1-105
HPJAP92 139 887830 AL353687 777 1-430
HPJAP92 139 887830 297832 778 1-430
HPJAP92 139 887830 AL353687 779 1-262
46
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
HPJAP92 139 887830 297832 780 1-262
HPJAN69 141 754858 AC025957 781 1-345
HPJAN67 142 751384 AL139244 782 1-161
1052-1592
3665-4095
4361-4549
HPJAN67 142 751384 AC004962 783 1-83
719-835
1648-1811
2702-3242
5315-5745
6011-6199
HPJAN67 142 751384 AL139244 784 1-506
HPJAN67 142 751384 AC004962 785 1-1876
HPJAN57 143 734503 AC007747 786 1-433
HPJAN57 143 734503 AL158136 787 ~ 1-433
HPJAN57 143 734503 AC007747 788 1-623
HPJAN57 143 734503 AL158136 789 1-623
HPJAJ20 144 669000 AP000584 790 1-564
648-2086
3513-3644
HPJAJ20 144 669000 AC011256 791 1-564
648-2086
3514-3645
HPJAJ20 144 669000 AP000588 792 1-564
648-2086
3513-3644
HPJAJ20 144 669000 AP000584 793 1-386
HPJAJ20 144 669000 AC011256 794 1-386
HPJAJ20 144 669000 AP000588 795 1-386
HPJAE51 145 725761 AL353654 796 1-392
842-1387
HPJAE51 145 725761 AC004842 797 1-392
842-1387
HPJAE51 145 725761 AL035696 798 1-392
842-1387
HPJAE51 145 725761 AL353654 799 1-169
179-295
HPJAE51 145 725761 AC004842 800 1-168
178-294
HPJAE51 145 725761 AL035696 801 1-162
HPJAA27 146 419786 AC074007 802 1-531
HPJAA27 146 419786 AL356953 803 1-531
HPJAA27 146 419786 AC018896 804 1-531
HPICG93 147 887817 AL356975 805 1-447
HPICG93 147 887817 AL357812 806 1-423
47
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
HPICE06 148 935095 AC007506 807 1-133
HPICE06 148 935095 AC007506 808 1-623
HPIBT62 150 743135 AC068150 809 1-62
2884-2997
3285-3503
4212-4325
5273-5353
7542-7640
7721-8853
HPIBT62 150 743135 AC068150 810 1-766
HPIB089 151 786741 AL355102 811 1-98
763-882
1106-1289
1883-2041
2351-2629
3424-3590
4426-4726
5712-8082
HPIB089 151 786741 AL355102 812 1-101
1847-2078
HPIB089 151 786741 AL355102 813 1-2260
HPIBI89 152 867845 AC009696 814 1-149
511-650
806-1203
1520-2566
2570-2737
3468-3611
3880-4009
4098-4206
HPIBC93 154 785971 297630 815 1-418
2009-2216
2619-2865
3398-3578
4946-5048
5089-5669
7182-7343
7476-7560
7718-7895
7913-8163
8257-8378
8422-8957
HPIBC93 154 785971 297630 816 1-2182
HPIBB45 155 867850 AL110504 817 1-5312
HPIBB32 157 698901 AC040962 818 1-323
HPIBB32 157 698901 AL161903 819 1-415
HPIBB32 157 698901 AL021366 820 1-415
HPIBB32 157 698901 ~ AL050332~ 821 1-415
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HPIBB32 157 698901 AL161903 822 1-183
HPIBB32 157 698901 AC040962 823 1-111
HPIBB32 157 698901 AL161903 824 1-111
HPIBB32 157 698901 AL021366 825 1-194
HPIBB32 157 698901 AL021366 826 1-111
HPIBB32 157 698901 AL050332 827 ~ 1-111
HPIBB32 157 698901 AL050332 828 1-194
HPIAW91 159 790033 AC004200 829 1-719
HPIAW91 159 790033 AC011858 830 1-719
HPIAW91 159 790033 AB023056 831 1-719
HPIAV06 160 935111 AC008542 832 1-41
499-841
945-1795
1847-2073
2214-2453
3031-3131
3396-4444
4470-5202
5863-6644
7027-7181
7474-7771
7857-8016
8110-8448
HPIAV06 160 935111 AC023788 833 1-71
998-1207
4649-5094
5184-5215
5490-5821
6192-6604
6708-6745
6917-7852
7993-8232
8809-8909
9174-10222
10248-10976
11637-12418
12801-12955
13248-13545
13631-13790
13884-14221
HPIAV06 160 935111 AC008404 834 1-446
537-568
843-1166
1553-1961
2065-2915
2967-3193
3334-3573
49
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4515-5563
5589-6320
6980-7761
8144-8298
8591-8888
8974-9133
9227-9566
HPIAV06 160 935111 AC008404 835 1-393
HPIAV06 160 935111 AC023788 836 1-393
HPIAQ70 161 973604 AC008751 837 1-930
HPFDX38 164 709302 AC023631 838 1-2429
HPFDX38 164 709302 AC011962 839 1-2428
HPFCZ82 165 780198 AC048350 840 1-900
HPFCZ82 165 780198 AC037193 841 1-876
HPFCZ82 165 780198 AC008042 842 1-688
1078-1977
HPFCZ82 165 780198 AC037193 843 1-128
961-991
4864-5402
HPFCZ82 165 780198 AC037193 844 1-688
HPFCZ60 166 430125 AC010611 845 1-694
HPFCZ60 166 430125 AC010255 846 1-694
HPFCZ60 166 430125 AC010611 847 1-190
HPFCZ60 166 430125 AC010255 848 1-190
HPFCZ10 167 968360 AC024493 849 1-337
HPFCZ10 167 968360 AL359983 850 1-337
HPFCZ10 167 968360 AL357555 851 1-337
HPFCP53 170 526574 AC023329 852 1-101
HPFCP53 170 526574 AC069380 853 1-238
HPFCP53 170 526574 AL162583 854 1-130
HPFCL56 173 732601 AC027270 855 1-154
744-867
1696-1817
1958-2117
2143-2244
3812-3907
4266-4379
4520-4734
4822-4936
5686-5748
5 820-5952
6060-6191
7271-8847
9423-9518
10087-10163
10751-10891
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12158-12252
12330-12717
13997-14286
14515-14846
14946-15228
16306-16744
16881-17380
18392-18826
19323-19437
19503-20654
20746-21268
21327-21815
22145-22695
22742-23675
23977-24173
HPFCL56 173 732601 AP002748 856 1-551
598-1452
HPFCL56 173 732601 AC027270 857 1-154
HPFCL56 173 732601 AP002748 858 1-196
HPFCL56 173 732601 AC027270 859 1-282
HPFCA01 176 928672 AC005531 860 1-873
HPFCA01 176 928672 AC073184 861 1-873
HPFCA01 176 928672 AC005531 862 1-934
HPFCA01 176 928672 AC073184 863 1-934
HPEBT82 177 524246 AC018865 864 1-466
HPEBT82 177 524246 AC018865 865 1-128
HPEBT49 181 530021 AC046171 866 1-373
HPEBT49 181 530021 AC046171 867 1-209
1274-1611
HPEBT49 181 530021 AC046171 868 1-208
HPEBT34 182 706836 AC009677 869 1-360
HPEBT14 183 535061 AL358573 870 1-245
HPEBT14 183 535061 AL139113 871 1-246
HPEBT14 183 535061 AL358573 872 1-576
HPEBT14 183 535061 AL139113 873 1-576
~
HPEBL08 186 960240 AC007684 874 1-38
2047-2188
2599-2984
3134-4018
4336-4377
4685-4800
6534-6618
8404-8480
8739-8851
12237-12815
14345-14412
14489-14605
51
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15097-15445
15469-15664
16908-17608
18139-18250
19641-19696
HPEBL08 186 960240 AC007684 875 1-1190
HPEBL08 186 960240 AC007684 876 1-394
429-990
1194-1451
HPEBG10 189 867888 AL356133 877 1-293
HPEBG10 189 867888. AL356133 878 1-503
HPEBA61 191 742251 AC007036 879 1-78
HPEBA61 191 742251 AC007036 880 1-225
HPEBA05 192 928027 AC026647 881 1-379
HPEBA05 192 928027 AL359754 882 1-374
1483-1516
HPEBA05 192 928027 AL159175 883 1-374
1483-1516
HPEBA05 192 928027 AL359754 884 1-673
HPEBA05 192 928027 AC026647 885 1-672
HPEBA05 192 928027 AL159175 886 1-673
HPEAA57 196 514231 AC018662 887 1-784
890-1375
1837-2156
2324-2766
3080-3286
4028-4155
4903-5424
5721-6302
6782-7063
7153-7571
7923-8053
11271-11598
HPEAA57 196 514231 AC008039 888 1-784
890-1375
1837-2156
2324-2766
3080-3286
4028-4155
4905-5426
5723-6304
6784-7065
7155-7573
7925-8055
11273-11600
HPEAA57 196 514231 AC018662 889 1-419
_
~HPEAA57 96 514231 AC008039 890 ~1-418
~ ~
52
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HL2AD32 201 699746 AL390235 891 1-1176
HL2AD32 201 699746 AL359742 892 1-672
HL2AD32 201 699746 AL096773 893 1-3033
HL2AD32 201 699746 AL390235 894 1-73
1953-2544
2759-2870
3020-3482
4843-6352
HL2AD32 201 699746 AL096773 895 1-518
1341-1514
3365-3956
4169-4282
4430-4892
6254-7763
HLlAN46 204 522981 AL137060 896 1-555
HLlAN46 204 522981 AC069475 897 1-555
HL1AN46 204 522981 AL137060 898 1-826
HL1AN46 204 522981 AL137060 899 1-522
590-2392
HL1AN46 204 522981 AC069475 900 1-826
HL1AN46 204 522981 AC069475 901 1-519
592-970
1168-2400
HBZSG02 206 920249 AC008053 902 1-996
HBZSG02 206 920249 AC008053 903 ' 1-112
HBZSD32 207 699335 AC011235 904 1-354
HBZSD32 207 699335 AC011235 905 1-151
HBZAJ73 208 764479 AC073594 906 1-729
1248-1374
HBZAJ73 208 764479 AC068986 907 1-729
1248-1375
HBZAJ73 208 764479 AC010892 908 1-729
1248-1375
HBZAJ73 208 764479 AC073594 909 1-555
HBZAJ73 208 764479 AC068986 910 1-554
HBZAJ73 208 764479 AC010892 911 1-554
HBZAJ26 209 681879 AC036116 912 1-682
HBZAJ26 209 681879 AL358976 913 1-682
HBZAJ26 209 681879 AC036116 914 1-245
1588-2237
HBZAJ26 209 681879 AL358976 915 1-689
HBZAJ26 209 681879 AC036116 916 1-689
HBZAJ26 209 681879 AL358976 917 1-245
1588-2237
HBZAI39 210 847621 AC009036 918 1-1337
HBZAI39 210 847621 AC012320 919 1-1338
53
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HBZAI39 210 847621 AC009036 920 1-126
HBZAI39 210 847621 AC009036 921 1-104
HBZAI14 211 847620 AC073635 922 1-466
HBZAI14 211 847620 AC073635 923 1-676
HBZAB 15 212 660348 AC019190 924 1-894
941-2689
HBZAB 15 212 660348 AC025171 925 1-894
941-2485
HBZAB08 213 959560 AP002448 926 1-235
HBZAB08 213 959560 AP002448 927 1-272
[043] Table 1B summarizes additional polynucleotides encompassed by the
invention (including cDNA clones related to the sequences (Clone ID NO:Z),
contig
sequences (contig identifier (Contig ID:) contig nucleotide sequence
identifiers (SEQ ID
NO:X)), and genomic sequences (SEQ ID NO:B). The first column provides a
unique
clone identifier, "Clone ID NO:Z", for a cDNA clone related to each contig
sequence.
The second column provides the sequence identifier, "SEQ ID NO:X", for each
contig
sequence. The third column provides a unique contig identifier, "Contig ID:"
for each
contig sequence. The fourth column, provides a BAC identifier "BAC ID NO:A"
for the
BAC clone referenced in the corresponding row of the table. The fifth column
provides
the nucleotide sequence identifier, "SEQ ID NO:B" for a fragment of the BAC
clone
identified in column four of the corresponding row of the table. The sixth
column, "Exon
From-To", provides the location (i.e., nucleotide position numbers) within the
polynucleotide sequence of SEQ ID NO:B which delineate certain polynucleotides
of the
invention that are also exemplary members of polynucleotide sequences that
encode
polypeptides of the invention (e.g., polypeptides containing amino acid
sequences encoded
by the polynucleotide sequences delineated in column six, and fragments and
variants
thereof).
TABLE 2
54
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WO 01/55316 PCT/USO1/01328
00 00 ~ ~n O ~n .~ ~ h N V~ M
M ~
M ~ co d' h h v~ O ~O d1 h
Ei ~ N N d ,-~ oo
~ d' N M
~
O M M M M M
zH
00 0o CT ~ ~n O~ N ~ d- 01 h 01 d'
~ cT
~O ~ d- 00 d' O~ ~ N in V~ ~O O~
0o ,~ ~O
O ~ M cal ~ M d' ~ N
N ~
z
w
0 0 0 ~ ~: 0 0 o so
wi . O d- d- ov O O O O oo
~t-
+~ ~ O DO 01 M ~ O O O ~ O 01
~.O
it
C~
V G~
P~1
H
O ,--m n ~ M
I
'_~
V h
O "_'
~ ~ ~
bA bJJ "d
V~
N w ~ h
~
O ~ '~ ~~ ~~ ~ 1 M ~ 01
I ~
_ M 0 _ _
O O O ~,- o Mh O ~oO O O
- 0~
O O O h ~ ,--~~ O ,-, \p O O
w w w .fl .~ 00 w .~ O w w
~ l0 .,~
M
~ z ~, ~ ~, ,
0
0 0
--, .~ v
~
,.fl O V ~ , O 'TJ ~ ~ ~
0, 4-i
~ U ~ ,
, 7~ ,'~,~ O ~, v~
, ,-, O
O
O _ ~
O H ~ M d' -~ ~ ~ ~ H
~ i~ i-~ ~i
-,_.,
r-~ ~ r-~ h
v n
O ~ ~ ~ y..,
v
cd ~ ~' cCi ~ cd
~ '~
~
O , O ~r , O ~
~
~
P~1 ~ P-iW ~ ~ ~ U N ~ U M P~ P-i
~ U ''O ~ ~ "t~ U
00 00 00 00
ri
d
--s
~ ~ ~ ~
N N
r
h d-
~
W ~ M O ~ h ~f1 O O O
~ ,..,~o h h o0 0~ .--.~ ,--.
z
h N O N N
o o
o o
O ~ N ~ n ~ ~ h N
O
d o O
- o 1
h M d' ~ O O V7 M
H
w .--.a
..
v x
z x x x x x x x x
ss
CA 02393618 2002-06-03
WO 01/55316 PCT/USO1/01328
0o t~ o0 0o
N
0o a1 a1 a1
N
d- N d'
M
-W 1 ~O N d'
01 ~ O N d1
N N N M
0 0 ~ o
c~ l~ ~ C~
O
l~ oo ~ C~
O
M
d' '
_b17 '_
O
., O O N
-,
O
~
W d1
~
by by p~ b4
v~ ~
U U
o ;~ ;~
' '
'
F.rS~ ~ ~ U
~ ~
~
" ~ ~ 'D ~ '
~
S.-i~ ~ , .,-
, , -i
, ~;
o
N ~ ~ ~ ~
N U
~ ~ u
. ~
O ~ ~ ~ ~.~ ,..~r
V ~ w .~'
~ a
a
'' ~ Q)
r ''
~O r
n n
l~ l~
~ N N
'~h~ d'
~
~
~ w w ~ ,-a _~
~ o
o
O W ~
W
d- ~ d'
_
cd CC3 c~
_ _ _
00 d-
N
d' d-
00 0o O
N N ~o
.-i ~ M
O
N
a
x x
56
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[044] Table 2 further characterizes certain encoded polypeptides of the
invention, by
providing the results of comparisons to protein and protein family databases.
The first
column provides a unique clone identifier, "Clone ID NO:", corresponding to a
cDNA
clone disclosed in Table 1A. The second column provides the unique contig
indentifier, "Contig ID:" which allows correlation with the information in
Table 1A.
The third column provides. the sequence identifier, "SEQ ID NO:X", for the
contig
polynucleotide sequences. The fourth column provides the analysis method by
which
the homology/identity disclosed in the row was determined. The fifth column
provides a description of PFam/NR hits having significant matches identified
by each
analysis. Column six provides the accession number of the PFam/NR hit
disclosed in
the fifth column. Column seven, "Score/Percent Identity", provides a quality
score or
the percent identity, of the hit disclosed in column five. Comparisons were
made
between polypeptides encoded by polynucleotides of the invention and a non-
redundant protein database (herein referred to as "NR"), or a database of
protein
families (herein referred to as "PFam"), as described below.
[045] The NR database, which comprises the NBRF PIR database, the NCBI
GenPept database, and the SIB SwissProt and TrEMBL databases, was made non-
redundant using the computer program nrdb2 (Warren Gish, Washington University
in
Saint Louis). Each of the polynucleotides shown in Table 1A, column 3 (e.g.,
SEQ ID
NO:X or the 'Query' sequence) was used to search against the NR database. The
computer program BLASTX was used to compare a 6-frame translation of the Query
sequence to the NR database (for information about the BLASTX algorithm please
see
Altshul et al., J. Mol.. Biol. 215:403-410 (1990), and Gish et al., Nat.
Genet. 3:266-
272 (1993)). A description of the sequence that is most similar to the Query
sequence
(the highest scoring 'Subject') is shown in column five of Table 2 and the
database
accession number fox that sequence is provided in column six. The highest
scoring
'Subject' is reported in Table 2 if (a) the estimated probability that the
match occurred
by chance alone is less than 1.0e-07, and (b) the match was not to a lcnown
repetitive
element. BLASTX returns alignments of short polypeptide segments of the Query
and
Subject sequences which share a high degree of similarity; these segments are
known
as High-Scoring Segment Pairs or HSPs. Table 2 reports the degree of
similarity
57
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between the Query and the Subject for each,HSP as a percent identity in Column
7.
The percent identity is determined by dividing the number of exact matches
between
the two aligned sequences in the HSP, dividing by the number of Query amino
acids in
the HSP and multiplying by 100. The polynucleotides of SEQ ID NO:X which
encode
the polypeptide sequence that generates an HSP are delineated by columns 8 and
9 of
Table 2.
[046] The PFam database, PFam version 5.2, (Sonnhammer et al., Nucl. Acids
Res.,
26:320-322, (1998)) consists of a series of multiple sequence alignments; one
alignment for each protein family. Each multiple sequence alignment is
converted into
a probability model called a Hidden Markov Model, or HMM, that represents the
position-specific variation among the sequences that make up the multiple
sequence
alignment (see, e.g., R. Durbin et al., Biological sequeJ2ce analysis:
probabilistic
models of proteins afad nucleic acids, Cambridge University Press, 1998 for
the theory
of HMMs). The program HMMER version 1.8 (Sean Eddy, Washington University in
Saint Louis) was used to compare the predicted protein sequence for each Query
sequence (SEQ ID NO:Y in Table 1A) to each of the HMMs derived from PFam
version 5.2. A HMM derived from PFam version 5.2 was said to be a significant
match to a polypeptide of the invention if.the score returned by HMMER 1.8 was
greater than 0.8 times the HMMER 1.8 score obtained with the most distantly
related
known member of that protein family. The description of the PFam family which
shares a significant match with a polypeptide of the invention is listed in
column 5 of
Table 2, and the database accession number of the PFam hit is provided in
column 6.
Column 7 provides the score returned by HMMER version 1.8 for the alignment.
Columns 8 and 9 delineate the polynucleotides of SEQ ID NO:X which encode the
polypeptide sequence which shows a significant match to a PFam protein family.
[047] As mentioned, columns 8 and 9 in Table 2, "NT From" and "NT To",
delineate
the polynucleotides of "SEQ ID NO:X" that encode a polypeptide having a
significant
match to the PFam/NR database as disclosed in the fifth column of Table 2. In
one
embodiment, the invention provides a protein comprising, or alternatively
consisting
of, a polypeptide encoded by the polynucleotides of SEQ ID NO:X delineated in
58
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columns 8 and 9 of Table 2. Also provided are polynucleotides encoding such
proteins, and the complementary strand thereto.
(048] The nucleotide sequence SEQ ID NO:X and the translated SEQ ID NO:Y are
sufficiently accurate and otherwise suitable for a variety of uses well known
in the art
and described further below. For instance, the nucleotide sequences of SEQ ID
NO:X
are useful for designing nucleic acid hybridization probes that will detect
nucleic acid
sequences contained in SEQ ID NO:X or the cDNA contained in Clone ID NO:Z.
These probes will also hybridize to nucleic acid molecules in biological
samples,
thereby enabling immediate applications in chromosome mapping, linkage
analysis,
tissue identification and/or typing, and a variety of forensic and diagnostic
methods of
the invention. Similarly, polypeptides identified from SEQ ID NO:Y may be used
to
generate antibodies which bind specifically to these polypeptides, or
fragments
thereof, and/or to the polypeptides encoded by the cDNA clones identified in,
for
example, Table 1A.
[049] Nevertheless, DNA sequences generated by sequencing reactions can
contain
sequencing errors. The errors exist as misidentified nucleotides, or as
insertions or
deletions of nucleotides in the generated DNA sequence. The erroneously
inserted or
deleted nucleotides cause frame shifts in the reading frames of the predicted
amino
acid sequence. In these cases, the predicted amino acid sequence diverges from
the
actual amino acid sequence, even though the generated DNA sequence may be
greater
than 99.9% identical to the actual DNA sequence (for example, one base
insertion or
deletion in an open reading frame of over 1000 bases).
[050] Accordingly, for those applications requiring precision in the
nucleotide
sequence or the amino acid sequence, the present invention provides not only
the
generated nucleotide sequence identified as SEQ ID NO:X, and a predicted
translated
amino acid sequence identified as SEQ ID NO:Y, but also a sample of plasmid
DNA
containing cDNA Clone ID NO:Z (deposited with the ATCC on October 5, 2000, and
receiving ATCC designation numbers PTA 2574 and PTA 2575; deposited with the
ATCC on January 5, 2001, having the depositor reference numbers TS-1, TS-2, AC-
1,
and AC-2; and/or as set forth, for example, in Table 1A, 6 and 7). The
nucleotide
sequence of each deposited clone can readily be determined by sequencing the
59
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deposited clone in accordance with known methods. Further, techniques known in
the
art can be used to verify the nucleotide sequences of SEQ ID NO:X.
[051] The predicted amino acid sequence can then be verified from such
deposits.
Moreover, the amino acid sequence of the protein encoded by a particular clone
can
also be directly determined by peptide sequencing or by expressing the protein
in a
suitable host cell containing the deposited human cDNA, collecting the
protein, and
determining its sequence.
RACE Protocol For Recovery of Full-Length Genes
[052] Partial cDNA clones can be made full-length by utilizing the rapid
amplification of cDNA ends (RACE) procedure described in Frohman, M.A., et
al.,
Proc. Nat'l. Acad. Sci. USA, 85:8998-9002 (1988). A cDNA clone missing either
the
5' or 3' end can be reconstructed to include the absent base pairs extending
to the
translational start or stop codon, respectively. In some cases, cDNAs are
missing the
start codon of translation. The following briefly describes a modification of
this
original 5' RACE procedure. Poly A+ or total RNA is reverse transcribed with
Superscript II (GibcoBRL) and an antisense or complementary primer specific to
the
cDNA sequence. The primer is removed from the reaction with a Microcon
Concentrator (Amicon). The first-strand cDNA is then tailed with dATP and
terminal
deoxynucleotide transferase (Gibco/BRL). Thus, an anchor sequence is produced
which is needed for PCR amplification. The second strand is synthesized from
the
dA-tail in PCR buffer, Taq DNA polymerase (Perkin-Elmer Cetus), an oligo-dT
primer containing three adjacent restriction sites (XhoI, SaII and CIaI) at
the 5' end and
a primer containing just these restriction sites. This double-stranded cDNA is
PCR
amplified for 40 cycles with the same primers as well as a nested cDNA-
specific
antisense primer. The PCR products are size-separated on an ethidium bromide-
agarose gel and the region of gel containing cDNA products the predicted size
of
missing protein-coding DNA is removed. cDNA is purified from the agarose with
the
Magic PCR Prep kit (Promega), restriction digested with XhoI or SalI, and
ligated to a
plasmid such as pBluescript SKII (Stratagene) at XhoI and EcoRV sites. This
DNA is
transformed into bacteria and the plasmid clones sequenced to identify the
correct
CA 02393618 2002-06-03
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protein-coding inserts. Correct 5' ends are confirmed by comparing this
sequence with
the putatively identified homologue and overlap with the partial cDNA clone.
Similar
methods known in the art andlor commercial kits are used to amplify and
recover 3'
ends.
[053] Several quality-controlled kits are commercially available for purchase.
Similar.reagents and methods to those above are supplied in kit form from
Gibco/BRL
for both 5' and 3' RACE for recovery of full length genes. A second kit is
available
from Clontech which is a modification of a related technique, SLIC (single-
stranded
ligation to single-stranded cDNA), developed by Dumas et al., Nucleic Acids
Res.,
19:5227-32 (1991). The major differences in procedure are that the RNA is
alkaline
hydrolyzed after reverse transcription and RNA ligase is used to join a
restriction site-
containing anchor primer to the first-strand cDNA. This obviates the necessity
for the
dA-tailing reaction which results in a polyT stretch that is difficult to
sequence past.
[054] An alternative to generating 5' or 3' cDNA from RNA is to use cDNA
library
double-stranded DNA. An asymmetric PCR-amplified antisense cDNA strand is
synthesized with an antisense cDNA-specific primer and a plasmid-anchored
primer.
These primers are removed.and a symmetric PCR reaction is performed with a
nested
cDNA-specific antisense primer and the plasmid-anchored primer.
RNA Ligase Protocol For Gefze~ating The 5' or 3' End Sequences To Obtain Full
Length
Genes
[055] Once a gene of interest is identified, several methods are available for
the
identification of the 5' or 3' portions of the gene which may not be present
in the
original cDNA plasmid. These methods include, but are not limited to, filter
probing,
clone enrichment using specific probes and protocols similar and identical to
5' and 3'
RACE. While the full length gene may be present in the library and can be
identified
by probing, a useful method for generating the 5' or 3' end is to use the
existing
sequence information from the original cDNA to generate the missing
information. A
method similar to 5' RACE is available for generating the missing 5' end of a
desired
full-length gene. (This method was published by Fromont-Racine et al., Nucleic
Acids
Res., 21(7):1683-1684 (1993)). Briefly, a specific RNA oligonucleotide is
ligated to
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the 5' ends of a population of RNA presumably containing full-length gene RNA
transcript. A primer set containing a primer specific to the ligated RNA
oligonucleotide and a primer specific to a known sequence of the gene of
interest, is
used to PCR amplify the 5' portion of the desired full length gene which may
then be
sequenced and used to generate the full length gene. This method starts with
total
RNA isolated from the desired source, poly A RNA may be used but is not a
prerequisite for this procedure. The RNA preparation may then be treated With
phosphatase if necessary to eliminate 5' phosphate groups on degraded or
damaged
RNA, which may interfere with the later RNA ligase step. The phosphatase, if
used, is
then inactivated and the RNA is treated with tobacco acid pyrophosphatase in
order to
remove the cap structure present at the 5' ends of messenger RNAs. This
reaction
leaves a 5' phosphate group at the 5' end of the cap cleaved RNA which can
then be
ligated to an RNA oligonucleotide using T4 RNA ligase. This modified RNA
preparation can then be used as a template for first strand cDNA synthesis
using a
gene specific oligonucleotide. The first strand synthesis reaction can then be
used as a
template for PCR amplification of the desired 5' end using a primer specific
to the
ligated RNA oligonucleotide and a primer specific to the known sequence of the
prostate cancer antigen of interest. The resultant product is then sequenced
and
analyzed to confirm that the 5' end sequence belongs to the relevant prostate
cancer
antigen.
[056] The present invention also relates to vectors or plasmids, which include
such
DNA sequences, as well as the use of the DNA sequences. The material deposited
with the ATCC (deposited with the ATCC on October 5, 2000, and receiving ATCC
designation numbers PTA 2574 and PTA 2575; deposited with the ATCC on January
5, 2001, having the depositor reference numbers TS-1, TS-2, AC-l, and AC-2;
and/or
as set forth, for example, in Tables 1A, 6 and 7) is a mixture of cDNA clones
derived
from a variety of human tissue and cloned in either a plasmid vector or a
phage vector,
as shown, for example, in Table 7. These deposits are referred to as "the
deposits"
herein. The tissues from which some of the clones were derived are listed in
Table 7,
and the vector in which the corresponding cDNA is contained is also indicated
in
Table 7. The deposited material includes cDNA clones corresponding to SEQ ID
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NO:X described, for example, in Table 1A (Clone ID NO:Z). A clone which is
isolatable from the ATCC Deposits by use of a sequence listed as SEQ TD NO:X,
may
include the entire coding region of a human gene or in other cases such clone
may
include a substantial portion of the coding region of a human gene.
Furthermore,
although the sequence listing may in some instances list only a portion of the
DNA
sequence in a clone included in the ATCC Deposits, it is well within the
ability of one
skilled in the art to sequence the DNA included in a clone contained in the
ATCC
Deposits by use of a sequence (or portion thereof) described in, for example
Tables 1A
or 2 by procedures hereinafter further described, and others apparent to those
skilled in
the art.
[057] Also provided in Table 7 is the name of the vector which contains the
cDNA
clone. Each vector is routinely used in the art. The following additional
information
is provided for convenience.
[058] Vectors Lambda Zap (U.S. Patent Nos. 5,128,256 and 5,286,636), Uni-Zap
XR
(U.S. Patent Nos. 5,128,256 and 5,286,636), Zap Express (U.S. Patent Nos.
5,128,256
and 5,286,636), pBhuescript (pBS) (Short, J. M. et al., Nucleic Acids Res.
16:7583-
7600 (1988); Alting-Mees, M. A. and Short, J. M., Nucleic Acids Res. 17.9494
(1989))
and pBK (Ahting-Mees, M. A. et al., Strategies 5:58-61 (1992)) are
commercially
available from Stratagene Cloning Systems, Inc., 11011 N. Torrey Pines Road,
La
Jolla, CA, 92037. pBS contains an ampicillin resistance gene and pBK contains
a
neomycin resistance gene. Phagemid pBS may be excised from the Lambda Zap and
Uni-Zap XR vectors, and phagemid pBK may be excised from the Zap Express
vector.
Both phagemids may be transformed into E. coli strain XL-1 Blue, also
available from
Stratagene.
[059] Vectors pSportl, pCMVSport 1.0, pCMVSport 2.0 and pCMVSport 3.0, were
obtained from Life Technologies, Inc., P. O. Box 6009, Gaithersburg, MD 20897.
All
Sport vectors contain an ampicillin resistance gene and may be transformed
into E.
coli strain DHlOB, also available from Life Technologies. See, for instance,
Gruber,
C. E., et al., Focus 15:59- (1993). Vector lafmid BA (Bento Soares, Columbia
University, New York, NY) contains an ampicihhin resistance gene and can be
transformed into E. coli strain XL-1 Blue. Vector pCR~2.1, which is available
from
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Invitrogen, 1600 Faraday Avenue, Carlsbad, CA 92008, contains an ampicillin
resistance gene and may be transformed into E. coli strain DHlOB, available
from Life
Technologies. See, for instance, Clark, J. M., Nuc. Acids Res. 16:9677-9686
(1988)
and Mead, D. et al., Bio/Technology 9: (1991).
[060] The present invention also relates to the genes corresponding to SEQ ID
NO:X,
SEQ ID NO:Y, and/or the deposited clone (Clone ID NO:Z). The corresponding
gene
can be isolated in accordance with known methods using the sequence
information
disclosed herein. Such methods include preparing probes or primers from the
disclosed sequence and identifying or amplifying the corresponding gene from
appropriate sources of genomic material.
(061] Also provided in the present invention are allelic variants, orthologs,
and/or
species homologs. Procedures known in the art can be used to obtain full-
length genes,
allelic variants, splice variants, full-length coding portions, orthologs,
andlor species
homologs of prostate cancer associated genes corresponding to SEQ ID NO:X or
the
complement thereof, polypeptides encoded by SEQ ID NO:X or the complement
thereof, and/or the cDNA contained in Clone ID NO:Z, using information from
the
sequences disclosed herein or the clones deposited with the ATCC. For example,
allelic variants and/or species homologs may be isolated and identified by
making
suitable probes or primers from the sequences provided herein and screening a
suitable
nucleic acid source for allelic variants and/or the desired homologue.
[062] The polypeptides of the invention can be prepared in any suitable
manner.
Such polypeptides include isolated naturally occurring polypeptides,
recombinantly
produced polypeptides, synthetically produced polypeptides, or polypeptides
produced
by a combination of these methods. Means for preparing such polypeptides are
well
understood in the art.
[063] The polypeptides may be in the form of the secreted protein, including
the
mature form, or may be a part of a larger protein, such as a fusion protein
(see below).
It is often advantageous to include an additional amino acid sequence which
contains
secretory or leader sequences, pro-sequences, sequences which aid in
purification,
such as multiple histidine residues, or an additional sequence for stability
during
recombinant production.
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[064] The polypeptides of the present invention are preferably provided in an
isolated
form, and preferably are substantially purified. A recombinantly produced
version of
a polypeptide, including the secreted polypeptide, can be substantially
purified using
techniques described herein or otherwise known in the art, such as, for
example, by the
one-step method described in Smith and Johnson, Gene 67:31-40 (1988).
Polypeptides of the invention also can be purified from natural, synthetic or
recombinant sources using techniques described herein or otherwise known in
the art,
such as, for example, antibodies of the invention raised against the prostate
cancer
polypeptides of the present invention in methods which are well known in the
art.
[065] The present invention provides a polynucleotide comprising, or
alternatively
consisting of, the nucleic acid sequence of SEQ ID NO:X, and/or the cDNA
sequence
contained in Clone ID NO:Z. The present invention also provides a polypeptide
comprising, or alternatively, consisting of, the polypeptide sequence of SEQ
ID NO:Y,
a polypeptide encoded by SEQ ID NO:X or a complement thereof, a polypeptide
encoded by the cDNA contained in Clone ID NO:Z, and/or the polypeptide
sequence
encoded by a nucleotide sequence in SEQ ID NO:B as defined in column 6 of
Table
1B. Polynucleotides encoding a polypeptide comprising, or alternatively
consisting of
the polypeptide sequence of SEQ ID NO:Y, a polypeptide encoded by SEQ ID NO:X,
-
a polypeptide encoded by the cDNA contained in Clone ID NO:Z and/or a
polypeptide
sequence encoded by a nucleotide sequence in SEQ ID NO:B as defined in column
6
of Table 1B are also encompassed by the invention. The present invention
further
encompasses a polynucleotide comprising, or alternatively consisting of, the
complement of the nucleic acid sequence of SEQ ID NO:X, a nucleic acid
sequence
encoding a polypeptide encoded by the complement of the nucleic acid sequence
of
SEQ ID NO:X, and/or the cDNA contained in Clone ID NO:Z.
[066] Moreover, representative examples of polynucleotides of the invention
comprise, or alternatively consist of, one, two, three, four, five, six,
seven, eight, nine,
ten, or more of the sequences delineated in Table 1B column 6, or any
combination
thereof. Additional, representative examples of polynucleotides of the
invention
comprise, or alternatively consist of, one, two, three, four, five, six,
seven, eight, nine,
ten, or more of the complementary strands) of the sequences delineated in
Table 1B
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column 6, or any combination thereof. In further embodiments, the above-
described
polynucleotides of the invention comprise, or alternatively consist of,
sequences
delineated in Table 1B, column 6, and have a nucleic acid sequence which is
different
from that of the BAC fragment having the sequence disclosed in SEQ ID NO:B
(see
Table 1B, column 5). In additional embodiments; the above-described
polynucleotides
of the invention comprise, or alternatively consist of, sequences delineated
in Table
1B, column 6, and have a nucleic acid sequence which is different from that
published
for the BAC clone identified as BAC ID NO:A (see Table 1B, column 4). In
additional embodiments, the above-described polynucleotides of the invention
comprise, or alternatively consist of, sequences delineated in Table 1B,
column 6, and
have a nucleic acid sequence which is different from that contained in the BAC
clone
identified as BAC ID NO:A (see Table 1B, column 4). Polypeptides encoded by
these
polynucleotides, other polynucleotides that encode these polypeptides, and
antibodies
that bind these polypeptides are also encompassed by the invention.
Additionally,
fragments and variants of the above-described polynucleotides and polypeptides
are
also encompassed by the invention.
[067] Further, representative examples of polynucleotides of the invention
comprise,
or alternatively consist of, one, two, three, four, five, six, seven, eight,
nine, ten, or
more of the sequences delineated in column 6 of Table 1B which correspond to
the
same Clone ID NO:Z (see Table 1B, column 1), or any combination thereof.
Additional, representative examples of polynucleotides of the invention
comprise, or
alternatively consist of, one, two, three, four, five, six, seven, eight,
nine, ten, or more
of the complementary strands) of the sequences delineated in column 6 of Table
1B
which correspond to the same Clone ID NO:Z (see Table 1B, column 1), or any
combination thereof. In further embodiments, the above-described
polynucleotides of
the invention comprise, or alternatively consist of, sequences delineated in
column 6
of Table 1B which correspond to the same Clone ID NO:Z (see Table 1B, column
1)
and have a nucleic acid sequence which is different from that of the BAC
fragment
having the sequence disclosed in SEQ ID NO:B (see Table 1B, column 5). In
additional embodiments, the above-described polynucleotides of the invention
comprise, or alternatively consist of, sequences delineated in column 6 of
Table 1B
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which correspond to the same Clone ID NO:Z (see Table 1B, column 1) and have a
nucleic acid sequence which is different from that published for the BAC clone
identified as BAC ID NO:A (see Table 1B, column 4). In additional embodiments,
the above-described polynucleotides of the invention comprise, or
alternatively consist
of, sequences delineated in column 6 of Table 1B which correspond to the same
Clone
ID NO:Z (see Table 1B, column 1) and have a nucleic acid sequence which is
different
from that contained in the BAC clone identified as BAC ID NO:A (see Table 1B,
column 4). Polypeptides encoded by these polynucleotides, other
polynucleotides that
encode these polypeptides, and antibodies that bind these polypeptides are
also
encompassed by the invention. Additionally, fragments and variants of the
above-
described polynucleotides and polypeptides are also encompassed by the
invention.
[068] Further, representative examples of polynucleotides of the invention
comprise,
or alternatively consist of, one, two, three, four, five, six, seven, eight,
nine, ten, or
more of the sequences delineated in column 6 of Table 1B which correspond to
the
same contig sequence identifer SEQ ID NO:X (see Table 1B, column 2), or any
combination thereof. Additional, representative examples of polynucleotides of
the
invention comprise, or alternatively consist of, one, two, three, four, five,
six, seven,
eight, nine, ten, or more of the complementary strands) of the sequences
delineated in
column 6 of Table 1B which correspond to the same contig sequence identifer
SEQ ID
NO:X (see Table 1B, column 2), or any combination thereof. In further
embodiments,
the above-described polynucleotides of the invention comprise, or
alternatively consist
of, sequences delineated in column 6 of Table 1B which correspond to the same
contig
sequence identifer SEQ ID NO:X (see Table 1B, column 2) and have a nucleic
acid
sequence which is different from that of the BAC fragment having the sequence
disclosed in SEQ ID NO:B (see Table 1B, column 5). In additional embodiments,
the
above-described polynucleotides of the invention comprise, or alternatively
consist of,
sequences delineated in column 6 of Table 1B which correspond to the same
contig
sequence identifer SEQ ID NO:X (see Table 1B, column 2) and have a nucleic
acid
sequence which is different from that published for the BAC clone identified
as BAG
ID NO:A (see Table 1B, column 4). In additional embodiments, the above-
described
polynucleotides of the invention comprise, or alternatively consist of,
sequences
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delineated in column 6 of Table 1B which correspond to the same contig
sequence
identifer SEQ ID NO:X (see Table 1B, column 2) and have a nucleic acid
sequence
which is different from that contained in the BAC clone identified as BAC ID
NO:A
(See Table 1B, column 4). Polypeptides encoded by these polynucleotides, other
polynucleotides that encode these polypeptides, and antibodies that bind these
polypeptides are also encompassed by the invention. Additionally, fragments
and
variants of the above-described polynucleotides and polypeptides are also
encompassed by the invention.
[069] Moreover, representative examples of polynucleotides of the invention
comprise, or alternatively consist of, one, two, three, four, five, six,
seven, eight, nine,
ten, or more of the sequences delineated in the same row of Table 1B column 6,
or any
combination thereof. Additional, representative examples of polynucleotides of
the
invention comprise, or alternatively consist of, one, two, three, four, five,
six, seven,
eight, nine, ten, or more of the complementary strands) of the sequences
delineated in
the same row of Table 1B column 6, or any combination thereof. In preferred
embodiments, the polynucleotides of the invention comprise, or alternatively
consist
of, one, two, three, four, five, six, seven, eight, nine, ten, or more of the
complementary strands) of the sequences delineated in the same row of Table 1B
column 6, wherein sequentially delineated sequences in the table (i.e.
corresponding to
those exons located closest to each other) are directly contiguous in a 5' to
3'
orientation. In further embodiments, above-described polynucleotides of the
invention
comprise, or alternatively consist of, sequences delineated in the same row of
Table
1B, column 6, and have a nucleic acid sequence which is different from that of
the
BAC fragment having the sequence disclosed in SEQ ID NO:B (see Table 1B,
column
5). In additional embodiments, the above-described polynucleotides of the
invention
comprise, or alternatively consist of, sequences delineated in the same row of
Table
1B, column 6, and have a nucleic acid sequence which is different from that
published
for the BAC clone identified as BAC ID NO:A (see Table 1B, column 4). In
additional embodiments, the above-described polynucleotides of the invention
comprise, or alternatively consist of, sequences delineated in the same row of
Table
1B, column 6, and have a nucleic acid sequence which is different from that
contained
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in the BAC clone identified as BAC ID NO:A (see Table 1B, column 4).
Polypeptides
encoded by these polynucleotides, other polynucleotides that encode these
polypeptides, and antibodies that bind these polypeptides are also encompassed
by the
invention.
[070] In additional specific embodiments, polynucleotides of the invention
comprise,
or alternatively consist of, one, two; three, four, five, six, seven, eight,
nine, ten, or
more of the sequences delineated in column 6 of Table 1B, and the
polynucleotide
sequence of SEQ ID NO:X (e.g., as defined in Table 1B, column 2) or fragments
or
variants thereof. Polypeptides encoded by these polynucleotides, other
polynucleotides that encode these polypeptides, and antibodies that bind these
polypeptides are also encompassed by the invention.
[071] In additional specific embodiments, polynucleotides of the invention
comprise,
or alternatively consist of, one, two, three, four, five, six, seven, eight,
nine, ten, or
more of the sequences delineated in column 6 of Table 1B which correspond to
the
same Clone ID NO:Z (see Table 1B, column 1), and the polynucleotide sequence
of
SEQ ID NO:X (e.g., as defined in Table 1A or 1B) or fragments or variants
thereof. In
preferred embodiments, the delineated sequences) and polynucleotide sequence
of
SEQ ID NO:X correspond to the same Clone ID NO:Z. Polypeptides encoded by
these polynucleotides, other polynucleotides that encode these polypeptides,
and
antibodies that bind these polypeptides are also encompassed by the invention.
[072] In further specific embodiments, polynucleotides of the invention
comprise, or
alternatively consist of, one, two, three, four, five, six, seven, eight,
nine, ten, or more
of the sequences delineated in the same row of column 6 of Table 1B, and the
polynucleotide sequence of SEQ ID NO:X (e.g., as defined in Table 1A or 1B) or
fragments or variants thereof. In preferred embodiments, the delineated
sequences)
and polynucleotide sequence of SEQ ID NO:X correspond to the same row of
column
6 of Table 1B. Polypeptides encoded by these polynucleotides, other
polynucleotides
that encode these polypeptides, and antibodies that bind these polypeptides
are also
encompassed by the invention.
[073] In additional specific embodiments, polynucleotides of the invention
comprise,
or alternatively consist of a polynucleotide sequence in which the 3' 10
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polynucleotides of one of the sequences delineated in column 6 of Table 1B and
the 5'
polynucleotides of the sequence of SEQ ID NO:X are directly contiguous.
Nucleic
acids which hybridize to the complement of these 20 contiguous polynucleotides
under
stringent hybridization conditions or alternatively, under lower stringency
conditions,
are also encompassed by the invention. Polypeptides encoded by these
polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic
acids that
encode these polypeptides, and antibodies that bind these polypeptides are
also
encompassed by the invention. Additionally, fragments and variants of the
above-
described polynucleotides, nucleic acids, and polypeptides are also
encompassed by
the invention.
[074] In additional specific embodiments, polynucleotides of the invention
comprise,
or alternatively consist of, a polynucleotide sequence in which the 3' 10
polynucleotides of one of the sequences delineated in column 6 of Table 1B and
the 5'
10 polynucleotides of a fragment or variant of the sequence of SEQ ID NO:X are
directly contiguous Nucleic acids which hybridize to the complement of these
20
contiguous polynucleotides under stringent hybridization conditions or
alternatively,
under lower stringency conditions, are also encompassed by the invention.
Polypeptides encoded by these polynucleotides and/or nucleic acids, other
polynucleotides and/or nucleic acids encoding these polypeptides, and
antibodies that
bind these polypeptides are also encompassed by the invention. Additionally,
fragments and variants of the above-described polynucleotides, nucleic acids,
and
polypeptides are also encompassed by the invention.
[075] In specific embodiments, polynucleotides of the invention comprise, or
alternatively consist of, a polynucleotide sequence in which the 3' 10
polynucleotides
of the sequence of SEQ ID NO:X and the 5' 10 polynucleotides of the sequence
of one
of the sequences delineated in column 6 of Table 1B are directly contiguous.
Nucleic
acids which hybridize to the complement of these 20 contiguous polynucleotides
under
stringent hybridization conditions or alternatively, under lower stringency
conditions,
are also encompassed 'by the invention. Polypeptides encoded by these
polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic
acids
encoding these polypeptides, and antibodies that bind these polypeptides are
also
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encompassed by the invention. Additionally, fragments and variants of the
above-
described polynucleotides, nucleic acids, and polypeptides are also
encompassed by
the invention.
[076] In specific embodiments, polynucleotides of the invention comprise, or
alternatively consist of, a polynucleotide sequence in which the 3' 10
polynucleotides
of a fragment or variant of the sequence of SEQ ID NO:X and the 5' 10
polynucleotides of the sequence of one of the sequences delineated in column 6
of
Table 1B are directly contiguous. Nucleic acids which hybridize to the
complement of
these 20 contiguous polynucleotides under stringent hybridization conditions
or
alternatively, under lower stringency conditions, are also encompassed by the
invention. Polypeptides encoded by these polynucleotides and/or nucleic acids,
other
polynucleotides and/or nucleic acids encoding these polypeptides, and
antibodies that
bind these polypeptides are also encompassed by the invention. Additionally,
fragments and variants of the above-described polynucleotides, nucleic acids,
and
polypeptides, are also encompassed by the invention.
[077] In further specific embodiments, polynucleotides of the invention
comprise, or
alternatively consist of, a polynucleotide sequence in which the 3' 10
polynucleotides
of one of the sequences delineated in column 6 of Table 1B and the 5' 10
polynucleotides of another sequence in column 6 are directly contiguous.
Nucleic
acids which hybridize to the complement of these 20 contiguous polynucleotides
under
stringent hybridization conditions or alternatively, under lower stringency
conditions,
are also encompassed by the invention. Polypeptides encoded by these
polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic
acids
encoding these polypeptides, and antibodies that bind these polypeptides are
also
encompassed by the invention. Additionally, fragments and variants of the
above-
described polynucleotides, nucleic acids, and polypeptides are also
encompassed by
the invention.
[078] In specific embodiments, polynucleotides of the invention comprise, or
alternatively consist of, a polynucleotide sequence in which the 3' 10
polynucleotides
of one of the sequences delineated in column 6 of Table 1B and the 5' 10
polynucleotides of another sequence in column 6 corresponding to the same
Clone ID
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NO:Z (see Table 1B, column 1) are directly contiguous. Nucleic acids which
hybridize to the complement of these 20 lower stringency conditions, are also
encompassed by the invention. Polypeptides encoded by these polynucleotides
and/or
nucleic acids, other polynucleotides and/or nucleic acids encoding these
polypeptides,
and antibodies that bind these polypeptides are also encompassed by the
invention.
Additionally, fragments and variants of the above-described polynucleotides,
nucleic
acids, and polypeptides are also encompassed by the invention.
[079] In specific embodiments, polynucleotides of the invention comprise, or
alternatively consist of, a polynucleotide sequence in which the 3' 10
polynucleotides
of one sequence in column 6 corresponding to the same contig sequence
identifer
SEQ ID NO:X (see Table 1B, column 2) are directly contiguous. Nucleic acids
which
hybridize to the complement of these 20 contiguous polynucleotides under
stringent
hybridization conditions or alternatively, under lower stringency conditions,
are also
encompassed by the invention. Polypeptides encoded by these polynucleotides
and/or
nucleic acids, other polynucleotides andlor nucleic acids encoding these
polypeptides,
and antibodies that bind these polypeptides are also encompassed by the
invention.
Additionally, fragments and variants of the above-described polynucleotides,
nucleic
acids, and polypeptides are also encompassed by the invention.
[080] In specific embodiments, polynucleotides of the invention comprise, or
alternatively consist of a polynucleotide sequence in which the 3' 10
polynucleotides
of one of the sequences delineated in column 6 of Table 1B and the 5' 10
polynucleotides of another sequence in column 6 corresponding to the same row
are
directly contiguous. In preferred embodiments, the 3' 10 polynucleotides of
one of the
sequences delineated in column 5 of Table 1B is directly contiguous with the
5' 10
polynucleotides of the next sequential exon delineated in Table 1B, column 6.
Nucleic
acids which hybridize to the complement of these 20 contiguous polynucleotides
under
stringent hybridization conditions or alternatively, under lower stringency
conditions,
are also encompassed by the invention. Polypeptides encoded by these
polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic
acids
encoding these polypeptides, and antibodies that bind these polypeptides are
also
encompassed by the invention. Additionally, fragments and variants of the
above-
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described polynucleotides, nucleic acids, and polypeptides are also
encompassed by
the invention.
[081] Many polynucleotide sequences, such as EST sequences, are publicly
available
and accessible through sequence databases and may have been publicly available
prior
to conception of the present invention. Preferably, such related
polynucleotides are
specifically excluded from the scope of the present invention. Accordingly,
for each
contig sequence (SEQ ID NO:X) listed in the third column of Table 1A,
preferably
excluded are one or more polynucleotides comprising a nucleotide sequence
described
by the general formula of a-b, where a is any integer between 1 and the final
nucleotide minus 15 of SEQ ID NO:X, b is an integer of 15 to the final
nucleotide of
SEQ ID NO:X, where both a and b correspond to the positions of nucleotide
residues
shown in SEQ ID NO:X, and where b is greater than or equal to a + 14. More
specifically, preferably excluded are one or more polynucleotides comprising a
nucleotide sequence described by the general formula of a-b, where a and b are
integers as defined in columns 4 and 5, respectively, of Table 3. In specific
embodiments, the polynucleotides of the invention do not consist of at least
one, two,
three, four, five, ten, or more of the specific polynucleotide sequences
referenced by
the Genbank Accession No. as disclosed in column 6 of Table 3 (including for
example, published sequence in connection with a particular BAC clone). In
further
embodiments, preferably excluded from the invention are the specific
polynucleotide
sequences) contained in the clones corresponding to at least one, two, three,
four,
five, ten, or more of the available material having the accession numbers
identified in
the sixth column of this Table (including for example, the actual sequence
contained in
an identified BAC clone). In no way is this listing meant to encompass all of
the
sequences which may be excluded by the general formula, it is just a
representative
example. All references available through these accessions are hereby
incorporated by
reference in their entirety.
TABLE 3
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o ~ o'n, os
,~ No ~, ~ o, t~ t°~ t~
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d~ N t~ ~O l~ l~ ~ d~ d= N wi ~
~O ~ l~ p O M ~ 01 00 ~ (v ~ ~ l~ 00
O ~ ~ 00 ~' 00 O
~
~ o M ~ I~ 00 v0 N ~n O o0 t~ o O W '~1'~O
M N O ~D ~W n v~
N M
N
dW0 00 ~ '~h V7 ~Wn ~ O
~t W d' tn 00 ~n ~n O d' N O O
tW0 00 O p
O O O
O O O O N O O O O O O O O O O ~ O O
O O
N ~
dd~~~d~aN~~~~~'~~~~~N~Qa~ ~
~Ol~M
N N ~D
~nd wY
i ~
N M O~
~nd'~t'
i i
O o0O
N d W7
~OM
h O O~
~tvo~n
--~N M
N N N
O
~ N
N
104
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TABLE 4
Code Description Tissue Organ Cell DiseaseVector
Line
AR022 a_Heart a_Heart
AR023 a_Liver a_Liver
AR024 a_mammar land a_mammar
land
AR025 a_Prostate a_Prostate
AR026 a_small intestinea_small intestine
AR027 a_Stomach a_Stomach
AR028 Blood B cells Blood B cells
AR029 Blood B cells Blood B cells
activated activated
AR030 Blood B cells Blood B cells
resting restin
AR031 Blood T cells Blood T cells
activated activated
AR032 Blood T cells Blood T cells
restin restin
AR033 brain brain
AR034 breast breast
AR035 breast cancer breast cancer
AR036 Cell Line CAOV3Cell Line
CAOV3
AR037 cell line PA-1 cell line
PA-1
AR038 cell line transformedcell line
transformed
AR039 colon colon
AR040 colon (9808co65R)colon (9808co65R)
AR041 colon (9809co15)colon (9809co15)
AR042 colon cancer colon cancer
AR043 colon cancer colon cancer
(9808co64R) (9808co64R)
AR044.colon cancer colon cancer
9809co14 9809co14
AR045 com clone 5 com clone
5
AR046 corn clone 6 corn clone
6
AR047 corn clone2 corn clone2
AR048 corn clone3 corn clone3
AR049 Corn Clone4 Corn Clone4
ARO50 Donor II B CellsDonor II
24hrs B Cells
24hrs
AR051 Donor II B CellsDonor II
72hrs B Cells
72hrs
AR052 Donor II B-CellsDonor II
24 hrs. B-Cells
24
hrs.
AR053 Donor II B-CellsDonor II
72hrs B-Cells
72hrs
AR054 Donor II RestingDonor II
B Cells Resting
B
Cells
ARO55 Heart Heart
AR056 Human Lung (clonetech)Human Lung
(clonetech)
AR057 Human Mammary Human Mammary
(clontech) (clontech)
AR058 Human Thymus Human Thymus
(clonetech) (clonetech)
AR059 Jurkat (unstimulated)Jurkat
(unstimulated)
AR060 Kidne Kidney
AR061 Liver Liver
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AR062 Liver (Clontech)Liver (Clontech)
AR063 Lymphocytes Lymphocytes
chronic
lymphocytic chronic lymphocytic
leukaemia
leukaemia
AR064 Lymphocytes Lymphocytes
diffuse large
B cell lymphomadiffuse large
B cell
I m homa
AR065 Lymphocytes Lymphocytes
follicular
lym homa follicular
1 m homa
AR066 normal breast normal breast
AR067 Normal Ovarian Normal Ovarian
(4004901) (4004901)
AR068 Normal Ovary Normal Ovary
95086045
95086045
AR069 Normal Ovary Normal Ovary
97016208
97016208
AR070 Normal Ovary Normal Ovary.
98066005
98066005
AR071 Ovarian Cancer Ovarian Cancer
AR072 Ovarian Cancer Ovarian Cancer
(97026001) (97026001)
AR073 Ovarian Cancer Ovarian Cancer
(97076029) (97076029)
AR074 Ovarian Cancer Ovarian Cancer
(98046011 ) (98046011
)
AR075 Ovarian Cancer Ovarian Cancer
(98066019) (98066019)
AR076 Ovarian Cancer Ovarian Cancer
(98076017) (98076017)
AR077 Ovarian Cancer Ovarian Cancer
(98096001 ) (98096001
)
AR078 ovarian cancer ovarian cancer
15799
15799
AR079 Ovarian Cancer Ovarian Cancer
.
17717AID 17717AID
AR080 Ovarian Cancer Ovarian Cancer
400466481 400466481
AR081 Ovarian Cancer Ovarian Cancer
4005315A 1 4005315A
1
AR082 ovarian cancer ovarian cancer
94127303
94127303
AR083 Ovarian Cancer Ovarian Cancer
96069304
96069304
AR084 Ovarian Cancer Ovarian Cancer
97076029
97076029
AR085 Ovarian Cancer Ovarian Cancer
98076045
98076045
AR086 ovarian cancer ovarian cancer
98096001
98096001
AR087 Ovarian Cancer Ovarian Cancer
9905C032RC 9905C032RC
AR088 Ovarian cancer Ovarian cancer
9907 C00 9907
3rd C00 3rd
AR089 Prostate Prostate
AR090 Prostate (clonetech)Prostate
(clonetech)
AR091 rostate cancer rostate cancer
AR092 prostate cancerprostate
#15176 cancer
#15176
AR093 prostate cancerprostate
#15509 cancer
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#15509
AR094 prostate cancerprostate
#15673 cancer
#15673
AR095 5ma11 IntestineSmall Intestine
(Clontech)
(Clontech)
AR096 S leen S Teen
AR097 Thymus T cells Thymus T
activated cells
activated
AR098 Thymus T cells Thymus T
resting cells
restin
AR099 Tonsil Tonsil
AR100 Tonsil geminal Tonsil geminal
center
centroblast center centroblast
AR101 Tonsil germinalTonsil germinal
center B
cell center B
cell
AR102 Tonsil lymph Tonsil lymph
node node
AR103 Tonsil memory Tonsil memory
B cell B
cell
AR104 Whole Brain Whole Brain
AR105 Xeno raft ES-2 Xeno raft
ES-2
AR106 Xenograft SW626Xenograft
SW626
H0130 LNCAP untreatedLNCAP Cell ProstateCell Uni-ZAP
. Line Line
XR
H0131 LNCAP + o.3nM LNCAP Cell ProstateCell Uni-ZAP
81881 Line Line
XR
H0132 LNCAP + 30nM LNCAP Cell ProstateCell Uni-ZAP
81881 Line Line
XR
H0165 Human Prostate Human ProstateProstate diseaseUni-ZAP
Cancer,
Stage B2 Cancer, stage XR
B2
H0166 Human Prostate Human ProstateProstate diseaseUni-ZAP
Cancer,
Sta a B2 fractionCancer, sta XR
a B2
H0168 Human Prostate Human ProstateProstate diseaseUni-ZAP
Cancer,
Sta a C Cancer, stage XR
C
H0169 Human Prostate Human ProstateProstate diseaseUni-ZAP
Cancer,
Sta a C fractionCancer, sta XR
a C
H0207 LNCAP, differentialLNCAP Cell ProstateCell pBluescript
Line Line
ex ression
H0383 Human Prostate Human Prostate Uni-ZAP
BPH, re-
excision BPH XR
50136 PERM TF274 stromal cellBone Cell Lambda
Line
marrow ZAP II
SO150 LNCAP prostate LNCAP Cell ProstateCell Uni-ZAP
cell line Line Line
XR
50152 PC3 Prostate PC3 prostate Uni-ZAP
cell line cell
line XR
S0168 Prostate/LNCAP,PC3 prostate pBluescript
cell
subtraction line
I
S0188 Prostate,BPH, Human Prostate diseasepSportl
Lib 2
BPH
S0190 Prostate BPH,LibHuman Prostate pSportl
2,
subtracted BPH
T0091 Liver, hepatocellular pBluescript
carcinoma SK-
L0070 Selected chromosome
21
cDNA librar
L0365 NCI_CGAP_Phel pheochromocytoma Bluescript
SK-
L0435 Infant brain, lafmid
LLNL array BA
of Dr. M. Soares
1NIB
1~7
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L0438 normalized infanttotal brain brain lafmid
brain BA
cDNA
L0439 Snares infant whole Lafmid
brain 1NIB brain BA
L0519 NCI CGAP_Pr3 AMP10
L0526 NCI_CGAP_Prl2 metastatic pAMPlO
prostate
bone lesion
L0532 NCI CGAP_Thyl thyroid AMP10
L0542 NCI_CGAP_Prl normal prostaticprostate pAMPlO
l
a ithelial
cells
L0586 HTCDLl pBluescript
SK(-)
L0587 Stratagene colon pBluescript
HT29
(#937221)
SK-
L0589 Stratagene fetal pBluescript
retina
937202 SK-
L0592 Stratagene hNT pBluescript
neuron
01937233)
SK-
L0598 Morton Fetal cochlea ear pBluescript
Cochlea
SK-
L0599 Stratagenelung(#937210) lung , pBluescript
SK-
L0601 Stratagene pancreas pancreas pBluescript
(#937208)
SK-
L0604 Stratagene musclemuscle skeletal pBluescript
937209
muscle SK-
L0605 Stratagene fetalfetal spleenspleen pBluescript
spleen
(#937205)
SK-
L0665 NCI_CGAP_Ut4 serous papillaryuterus pCMV-
carcinoma, SPORT6
high
grade, 2
pooled t
L0667 NCI_CGAP_CMLI myeloid cells,whole pCMV-
18 blood
pooled CML SPORT6
cases,
BCR/ABL rearra
L0717 Gessler Wilms SPORT1
tumor
L0731 Soares_pregnant uterus pTTT3-Pac
uterus_
NbHPU
L0740 Snares melanocytemelanocyte pT7T3D
2NbHM (Pharmacia)
with
a
modified
of linker
L0741 Snares adult brain pT7T3D
brain
N2b4HB55Y (Pharmacia)
with
a
modified
of linker
L0743 5oares breast breast pT7T3D
2NbHBst
(Pharmacia)
with
a
modified
olylinker
L0744 Snares breast breast pT7T3D
3NbHBst
(Pharmacia)
with
a
modified
of linker
L0745 Snares retina retina eye pT7T3D
N2b4HR
(Pharmacia)
with
a
10g
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modified
olylinker
L0747 Soares fetal_heart heart pTTT3D
NbHH
19W (Pharmacia)
with
a
modified
of linker
L0748 Soares fetal Liver pT7T3D
liver spleen and
1NFLS Spleen (Pharmacia)
with
a
modified
polylinker
L0749 Soares fetal Liver pT7T3D
liver_spleen and
1NFLS S1 Spleen (Pharmacia)
with
a
modified
of linker
L0750 Soares fetal lung pT7T3D
lung NbHLl
9W (Pharmacia)
with
a
modified
olylinker
L0751 Soares ovary ovarian tumorovary pT7T3D
tumor
NbHOT (Pharmacia)
with
a
modified
of linker
L0752 Soares_parathyroid_tumorparathyroid parathyroid pT7T3D
tumor
NbHPA gland (Pharmacia)
with
a
modified
of linker
L0754 Soares placenta placenta pT7T3D
Nb2HP
(Pharmacia)
with
a
modified
of linker
L0756 Soares multiplemultiple pT7T3D
sclerosis sclerosis
2NbHMSP lesions (Pharmacia)
with
a
modified
polylinker
V_TYPE
L0758 5oares_testis pT7T3D-Pac
NHT
(Pharmacia)
with
a
modified
olylinker
L0759 Soares_total_fetus_Nb2H pT7T3D-Pac
F8_9w (Pharmacia)
with
a
modified
of linker
L0763 NCI_CGAP_Br2 breast ' pT7T3D-Pac
(Pharmacia)
with
a
modified
olylinker
L0766 NCI_CGAP_GCB germinal pT7T3D-Pac
1 center B
cell (Pharmacia)
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with
a
modified
polylinker
L0769 NCI_CGAP_Brn25 anaplastic brain pT7T3D-Pac
oligodendroglioma (Pharmacia)
with
a
modified
olylinker
L0770 NCI_CGAP_Brn23 glioblastomabrain pT7T3D-Pac
(pooled) (Pharmacia)
with
a
modified
olylinker
L0771 NCI_CGAP_Co8 adenocarcinomacolon pT7T3D-Pac
(Pharmacia)
with
a
modified
of linker
L0774 NCI_CGAP_Kid3 kidney pT7T3D-Pac
(Pharmacia)
with
a
modified
of linker
L0775 NCI_CGAP_KidS 2 pooled kidney pTTT3D-Pac
tumors
(clear cell (Pharmacia)
type)
with
a
modified
olylinker
L0776 NCI_CGAP_Lu5 carcinoid lung pTTT3D-Pac
(Pharmacia)
with
a
modified
of linker
L0777 Soares NhHMPu_S1Pooled humanmixed pT7T3D-Pac
(see
melanocyte, below) (Pharmacia)
fetal
heart, and with
pregnant a
modified
of linker
L0779 Soares_NFL T pooled pTTT3D-Pac
GBC_S1
(Pharmacia)
with
a
modified
olylinker
L0780 Soares_NSF_F8_9W_OT pooled pT7T3D-Pac
PA_P_S 1 (Pharmacia)
with
a
modified
olylinker
L0783 NCI CGAP_Pr22 normal prostateprostate pT7T3D-Pac
(Pharmacia)
with
a
modified
olylinker
L0790 NCI_CGAP_Sub4 pT7T3D-Pac
(Pharmacia)
with
a
modified
of linker
L0794 NCI_CGAP_GC6 pooled germ ~ pT7T3D-Pac
~ ~ cell
tumors (Pharmacia)
110
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with
a
modified
polylinker
L0809NCI_CGAP_Pr28 prostate pT7T3D-Pac
(Pharmacia)
with
a
modified
polylinker
TABLE 5
OMIM Description
Reference
103050 Autism, succin 1 urinemic
103050 Aden losuccinase deficienc
106300 Ai losin s and litis
108800 Atrial se tal defect, secundum ty a
120290 OSMED s ndrome, 215150
120290 Stickler s drome, a II, 184840
120435 Muir-Torre s ndrome, 158320
120435 Colorectal cancer, heredita , non of osis, a
1 Ovarian cancer
120810 C4 deficienc
120820 C4 deficienc
124030 Parkinsonism, susce tibili to
124030 Debrisoquine sensitivi
126600 Drusen, radial, autosomal dominant
134580 Factor XIIIB deficienc
135300 Fibromatosis, in ival
136435 Ovarian dysgenesis, hypergonadotropic, with normal
karyotype,
233300
138981 Pulmona alveolar roteinosis, 265120
142857 Pem hi oid, susce tibili to
142858 Be llium disease, chronic, susce tibili to
145260 Pseudoh oaldosteronism, a II
150270 La n eal adductor aral sis
152790 Precocious ubert , male, 176410
152790 Le di cell h o lasia
157170 Holoprosencephaly-2
167250 Pa et disease of bone
170261 Bare 1 m hoc to s ndrome, a I, due to TAP2 deficienc
177900 Psoriasis susce tibili -1
179450 Ra weed sensitivi
179605 Retinitis i mentosa, di enic
179605 Retinitis i mentosa-7, eri herin-related
179605 Retinitis punctata albescens
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179605 Butterfl d stro h , retinal
179605 Macular d stro h
180297 Anemia, hemol tic, Rh-null, su ressor e, 268150
182380 Glucose/ alactose malabso tion
182601 Spastic para legia-4
188826 Sorsb fundus d stro h , 136900
190040 Dermatofibrosarcoma rotuberans
190040 Giant-cell fibroblastoma
190040 Menin ioma, SIS-related
201910 Adrenal h a lasia, con enital, due to 21-h drox
lase deficient
217000 C2 deficient
222100 Diabetes mellitus, insulin-de endent-1
233100 [Renal lucosuria]
235200 Hemochromatosis
248611 Ma 1e s ru urine disease, a Ib
256550 Sialidosis, a I
256550 Sialidosis, a II
263200 Pol c stic kidne disease, autosomal recessive
278300 Xanthinuria, a I
600105 Retinitis i mentosa-12, autosomal recessive
600202 Dyslexia, specific, 2
600261 Ehlers-Danlos-like s ndrome
600364 Cone d stro h -3, 602093
600759 Alzheimer disease-4
601071 Deafness, autosomal recessive 9
601498 Peroxisomal biogenesis disorder, complementation
grou 4
601690 Platelet-activatin factor ace 1h drolase deficient
601771 Glaucoma 3A, rima infantile, 231300
601868 Deafness, autosomal dominant 13
601975 Ectodermal d s lasia/skin fra ilit s ndrome
602134 Tremor, familial essential, 2
602280 Retinitis i mentosa-14, 600132
_ Ossification of osterior lon itudinal 1i ament
602475 of s ine
Polynucleotide and Polypeptide llariarats
[082] The present invention is also directed to variants of the prostate
cancer
associated polynucleotide sequence disclosed in SEQ ID NO:X or the
complementary
strand thereto, nucleotide sequences encoding the polypeptide of SEQ ID NO:Y,
the
nucleotide sequence of SEQ ID NO:X encoding the polypeptide sequence as
defined
in column 6 of Table 1A, nucleotide sequences encoding the polypeptide as
defined in
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column 6 of Table 1A, the nucleotide sequence as defined in columns 8 and 9 of
Table 2, nucleotide sequences encoding the polypeptide encoded by the
nucleotide
sequence as defined in columns 8 and 9 of Table 2, the nucleotide sequence as
defined
in column 6 of Table 1B, nucleotide sequences encoding the polypeptide encoded
by
the nucleotide sequence as defined in column 6 of Table 1B, the cDNA sequence
.
contained in Clone ID NO:Z, and/or nucleotide'sequences .encoding a
polypeptide
encoded by the cDNA sequence contained in Clone ID NO:Z:
[083] The present invention also encompasses variants of the polypeptide
sequence
disclosed in SEQ ID NO:Y, a polypeptide sequence as defined in column 6 of
Table
1A, a polypeptide sequence encoded by the polynucleotide sequence in SEQ ID
NO:X, a polypeptide sequence encoded by the nucleotide sequence as defined in
columns 8 and 9 of Table 2, a polypeptide sequence encoded by the nucleotide
sequence as defined in column 6 of Table 1B, a polypeptide sequence encoded by
the
complement of the polynucleotide sequence in SEQ ID NO:X, and/or a polypeptide
sequence encoded by the cDNA sequence contained in Clone ID NO:Z.
[084] "Variant" refers to a polynucleotide or polypeptide differing from the
polynucleotide or polypeptide of the present invention, but retaining
essential
properties thereof. Generally, variants are overall closely similar, and,' in
many
regions, identical to the polynucleotide or polypeptide of the present
invention.
[085] Thus, one aspect of the invention provides an isolated nucleic acid
molecule
comprising, or alternatively consisting of, a polynucleotide having a
nucleotide
sequence selected from the group consisting of: (a) a nucleotide sequence
described in
SEQ ID NO:X or contained in the cDNA sequence of Clone ID NO:Z; (b) a
nucleotide sequence in SEQ ID NO:X or the cDNA in Clone ID NO:Z which encodes
a mature prostate cancer associated polypeptide; (c) a nucleotide sequence in
SEQ ID
NO:X or the cDNA sequence of Clone ID NO:Z, which encodes a biologically
active
fragment of a prostate cancer associated polypeptide; (d) a nucleotide
sequence in
SEQ ID NO:X or the cDNA sequence of Clone ID NO:Z, which encodes an antigenic
fragment of a prostate cancer associated polypeptide; (e) a nucleotide
sequence
encoding a prostate cancer associated polypeptide having the complete amino
acid
sequence of SEQ ID NO:Y or the complete amino acid sequence encoded by the
113
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cDNA in Clone ID NO:Z; (f) a nucleotide sequence encoding a mature prostate
cancer
associated polypeptide of the amino acid sequence of SEQ ID NO:Y or the amino
acid
sequence encoded by the cDNA in Clone ID NO:Z; (g) a nucleotide sequence
encoding a biologically active fragment of a prostate cancer associated
polypeptide
having the complete amino acid sequence of SEQ ID NO:Y or the complete amino
acid sequence encoded by the cDNA in Clone ID NO:Z; (h) a nucleotide sequence
encoding an antigenic fragment of a prostate cancer associated polypeptide
having the
complete amino acid sequence of SEQ ID NO:Y or the complete amino acid
sequence
encoded by the cDNA in Clone ID NO:Z; and (i) a nucleotide sequence
complementary to any of the nucleotide sequences in (a), (b), (c), (d), (e),
(f), (g), or
(h), above.
[086] The present invention is also directed to nucleic acid molecules which
comprise, or alternatively consist of, a nucleotide sequence which is at least
80%,
85%, 90%, 95%, 96%, 97%, 98%, 99% or 100%, identical to, for example, any of
the
nucleotide sequences in (a), (b), (c), (d), (e), (f), (g), (h), or (i) above,
the nucleotide
coding sequence in SEQ ID NO:X or the complementary strand thereto, the
nucleotide
coding sequence of the cDNA contained in Clone ID NO:Z or the complementary
strand thereto, a nucleotide sequence encoding the polypeptide of SEQ ID NO:Y,
a
nucleotide sequence encoding a. polypeptide sequence encoded by the nucleotide
sequence in SEQ ID NO:X, a polypeptide sequence encoded by the complement of
the
polynucleotide sequence in SEQ ID NO:X, a nucleotide sequence encoding the
polypeptide encoded by the cDNA contained in Clone ID NO:Z, the nucleotide
coding
sequence in SEQ ID NO:X as defined in columns 8 and 9 of Table 2 or the
complementary strand thereto, a nucleotide sequence encoding the polypeptide
encoded by the nucleotide sequence in SEQ ID NO:X as defined in columns 8 and
9 of
Table 2 or the complementary strand thereto, the nucleotide coding sequence in
SEQ
ID NO:B as defined in column 6 of Table 1B or the complementary strand
thereto, a
nucleotide sequence encoding the polypeptide encoded by the nucleotide
sequence in
SEQ ID NO:B as defined in column 6 of Table 1B or the complementary strand
thereto, the nucleotide sequence in SEQ ID NO:X encoding the polypeptide
sequence
as defined in column 6 of Table 1A or the complementary strand thereto,
nucleotide
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sequences encoding a polypeptide as defined in column 6 of Table 1A or the
complementary strand thereto, and/or polynucleotide fragments of any of these
nucleic
acid molecules (e.g., those fragments described herein). Polynucleotides which
hybridize to the complement of these nucleic acid molecules under stringent
hybridization conditions or alternatively, under lower stringency conditions,
are also
encompassed by, the invention, as are polypeptides encoded by these
polynucleotides
and nucleic acids.
[087] In a preferred embodiment, the invention encompasses nucleic acid
molecules
which comprise, or alternatively, consist of a polynucleotide which hybridizes
under
stringent hybridization conditions, or alternatively, under lower stringency
conditions,
to a polynucleotide in (a), (b), (c), (d), (e), (f), (g), (h), or (i) above,
as are polypeptides
encoded by these polynucleotides. In another preferred embodiment,
polynucleotides
which hybridize to the complement of these nucleic acid molecules under
stringent
hybridization conditions or alternatively, under lower stringency conditions,
are also
encompassed by the invention, as are polypeptides encoded by these
polynucleotides.
[088] In another embodiment, the invention provides a purified protein
comprising,
or alternatively consisting of, ,a polypeptide having an amino acid sequence
selected
from the group consisting of: (a) the complete amino acid sequence of SEQ ID
NO:Y
or the complete amino;acid sequence encoded by~the cDNA in Clone ID NO:Z; (b)
the
amino acid sequence of a mature prostate cancer associated polypeptide having
the
amino acid sequence of SEQ ID NO:Y or the amino acid sequence encoded by the
cDNA in Clone ID NO:Z; (c) the amino acid sequence of a biologically active
fragment of a prostate cancer associated polypeptide having the complete amino
acid
sequence of SEQ ID NO:Y or the complete amino acid sequence encoded by the
cDNA in Clone ID NO:Z; and (d) the amino acid sequence of an antigenic
fragment of
a prostate cancer associated polypeptide having the complete amino acid
sequence of
SEQ ID NO:Y or the complete amino acid sequence encoded by the cDNA in Clone
ID NO:Z.
[089] The present invention is also directed to proteins which comprise, or
alternatively consist of, an amino acid sequence which is at least 80%, 85%,
90%,
95%, 96%, 97%, 98%, 99% or 100%, identical to, for example, any of the amino
acid
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sequences in (a), (b), (c), or (d), above, the amino acid sequence shown in
SEQ ID
NO:Y, the amino acid sequence encoded by the cDNA contained in Clone ID NO:Z,
the amino acid sequence of the polypeptide encoded by the nucleotide sequence
in
SEQ ID NO:X as defined in columns 8 and 9 of Table 2, the amino acid sequence
of
the polypeptide encoded by the nucleotide sequence in :SEQ ID NO:B as defined
in
column 6 of Table 1B, the amino acid sequence as defined in column 6 of Table
1A,
an amino acid sequence encoded by the nucleotide sequence in SEQ ID NO:X, and
an
amino acid sequence encoded by the complement of the polynucleotide sequence
in
SEQ ID NO:X. Fragments of these polypeptides are also provided (e.g., those
fragments described herein). Further proteins encoded by polynucleotides which
hybridize to the complement of the nucleic acid molecules encoding these amino
acid
sequences under stringent hybridization conditions or alternatively, under
lower
stringency conditions, are also encompassed by the invention, as are the
polynucleotides encoding these proteins.
[090] By a nucleic acid having a nucleotide sequence at least, for example,
95%
"identical" to a reference nucleotide sequence of the present invention, it is
intended
that the nucleotide sequence of the nucleic acid is identical to the reference
sequence
except that the nucleotide sequence may include up to five point mutations per
each
100 nucleotides of the reference nucleotide sequence encoding the polypeptide.
In
other words, to obtain a nucleic acid having a nucleotide sequence at least
95%
identical to a reference nucleotide sequence, up to 5% of the nucleotides in
the
reference sequence may be deleted or substituted with another nucleotide, or a
number
of nucleotides up to 5% of the total nucleotides in the reference sequence may
be
inserted into the reference sequence. The query sequence may be an entire
sequence
referred to in Table 1A or 2 as the ORF (open reading frame), or any fragment
specified, as described herein.
[091] As a practical matter, whether any particular nucleic acid molecule or
polypeptide is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to
a
nucleotide sequence of the present invention can be determined conventionally
using
known computer programs. A preferred method for determining the best overall
match between a query sequence (a sequence of the present invention) and a
subject
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sequence, also referred to as a global sequence alignment, can be determined
using the
FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App.
Biosci. 6:237-245 (1990)). In a sequence alignment the query and subject
sequences
axe both DNA sequences. An RNA sequence can be compared by converting U's to
T's. The result of said global sequence alignment is expressed as percent
identity.
Preferred parameters used in a FASTDB alignment of DNA sequences to calculate
percent identity are: Matrix=Unitary, k-tuple=4, Mismatch Penalty=1; Joining
Penalty=30, Randomization Group Length=0, Cutoff Score=1, Gap Penalty=5, Gap
Size Penalty 0.05, Window Size=500 or the length of the subject nucleotide
sequence,
whichever is shorter.
[092] If the subject sequence is shorter than the query sequence because of 5'
or 3'
deletions, not because of internal deletions, a manual correction must be made
to the
results. This is because the FASTDB program does not account for 5' and 3'
truncations of the subject sequence when calculating percent identity. For
subject
sequences truncated at the 5' or 3' ends, relative to the query sequence, the
percent
identity is corrected by calculating the number of bases of the query sequence
that are
5' and 3' of the subject sequence, which are not matched/aligned, as a percent
of the
total bases of the query sequence. Whether a nucleotide is, matched/aligned is
determined by results of the FASTDB sequence alignment. This percentage is
then
subtracted from the percent identity, calculated by the above FASTDB program
using
the specified parameters, to arrive at a final percent identity score. This
corrected
score is what is used for the purposes of the present invention. Only bases
outside the
5' and 3' bases of the subject sequence, as displayed by the FASTDB alignment,
which are not matched/aligned with the query sequence, are calculated for the
purposes of manually adjusting the percent identity score.
[093] For example, a 90 base subject sequence is aligned to a 100 base query
sequence to determine percent identity. The deletions occur at the 5' end of
the
subject sequence and therefore, the FASTDB alignment does not show a
matched/alignment of the first 10 bases at 5' end. The 10 unpaired bases
represent
10% of the sequence (number of bases at the 5' and 3' ends not matched/total
number
of bases in the query sequence) so 10% is subtracted from the percent identity
score
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calculated by the FASTDB program. If the remaining 90 bases were perfectly
matched the final percent identity would be 90%. In another example, a 90 base
subject sequence is compared with a 100 base query sequence. This time the
deletions
are internal deletions so that there are no bases on the 5' or 3' of the
subject sequence
which are not matched/aligned with the query. In this case the percent
identity
calculated by FASTDB is not manually corrected. Once again, only bases 5' and
3' of
the subject sequence which° are not matched/aligned with the query
sequence are
manually corrected for. No other manual corrections are to be made for the
purposes
of the present invention.
[094] By a polypeptide having an amino acid sequence at least, for example,
95%
"identical" to a query amino acid sequence of the present invention, it is
intended that
the amino acid sequence of the subject polypeptide is identical to the query
sequence
except that the subject polypeptide sequence may include up to five amino acid
alterations per each 100 amino acids of the query amino acid sequence. In
other
words, to obtain a polypeptide having an amino acid sequence at least 95%
identical to
a query amino acid sequence, up to 5% of the amino acid residues in the
subject
sequence may be inserted, deleted, (indels) or substituted with another amino
acid.
These alterations of the reference sequence may occur at the amino or carboxy
terminal positions of the reference:amino acid sequence or anywhere between
those
terminal positions, interspersed either individually among residues in the
reference
sequence or in one or more contiguous groups within the reference sequence.
[095] As a practical matter, whether any particular polypeptide is at least
80%, 85%,
90%, 95%, 96%, 97%, 98% or 99% identical to, for instance, the amino acid
sequence
of a polypeptide referred to in Table 1A (e.g., an amino acid sequence
identified in
columns 5 or 6) or Table 2 (e.g., the amino acid sequence of the polypeptide
encoded
by the polynucleotide sequence defined in columns 8 and 9 of Table 2) or a
fragment
thereof, the amino acid sequence of the polypeptide encoded by the
polynucleotide
sequence in SEQ ID NO:B as defined in column 6 of Table 1B or a fragment
thereof,
the amino acid sequence of the polypeptide encoded by the nucleotide sequence
in
SEQ ID NO:X or a fragment thereof, or an amino acid sequence of the
polypeptide
encoded by cDNA contained in Clone ID NO:Z, or a fragment thereof, can be
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determined conventionally using known computer programs. A preferred method
for
determining the best overall match between a query sequence (a sequence of the
present invention) and a subject sequence, also referred to as a global
sequence
alignment, can be determined using the FASTDB computer program based on the
algorithm of Brutlag et al. (Comp. App. Biosci.6:237-245 (1990)). In a
sequence
alignment the query and subject sequences are either both nucleotide sequences
or
both amino acid sequences. The result of said global sequence alignment is
expressed
as percent identity. Preferred parameters used in a FASTDB amino acid
alignment
are: Matrix=PAM 0, k-tuple=2, Mismatch Penalty=l, Joining Penalty=20,
Randomization Group Length=0, Cutoff Score=1, Window Size=sequence length, Gap
Penalty=5, Gap Size Penalty=0.05, Window Size=500 or the length of the subject
amino acid sequence, whichever is shorter.
[096] If the subject sequence is shorter than the query sequence due to N- or
C-
terminal deletions, not because of internal deletions, a manual correction
must be
made to the results. This is because the FASTDB program does not account for N-
and C-terminal truncations of the subject sequence when calculating global
percent
identity. For subject sequences truncated at the N- and C-termini, relative to
the query
sequence, the percent identity is corrected by calculating the number of
residues of the
query sequence that are N- and C-terminal of the subject sequence, which are
not
matched/aligned with a corresponding subject residue, as a percent of the
total bases of
the query sequence. Whether a residue is matched/aligned is determined by
results of
the FASTDB sequence alignment. This percentage is then subtracted from the
percent
identity, calculated by the above FASTDB program using the specified
parameters, to
arrive at a final percent identity score. This final percent identity score is
what is used
for the purposes of the present invention. Only residues to the N- and C-
termini of the
subject sequence, which are not matched/aligned with the query sequence, are
considered for the purposes of manually adjusting the percent identity score.
That is,
only query residue positions outside the farthest N- and C- terminal residues
of the
subject sequence.
[097] For example, a 90 amino acid residue subject sequence is aligned with a
100
residue query sequence to determine percent identity. The deletion occurs at
the N-
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terminus of the subject sequence and therefore, the FASTDB alignment does not
show
a matching/alignment of the first 10 residues at the N-terminus. The 10
unpaired
residues represent 10% of the sequence (number of residues at the N- and C-
termini
not matched/total number of residues in the query sequence) so 10% is
subtracted from
the percent identity score calculated by the FASTDB program. If the remaining
90
residues were perfectly matched the final percent identity would be 90%. In
another'
example, a 90 residue subject sequence is compared with a 100 residue query'
sequence. This time the deletions are internal deletions so there are no
residues at the
N- or C-termini of the subject sequence which are not matched/aligned with the
query.
In this case the percent identity calculated by FASTDB is not manually
corrected.
Once again, only residue positions outside the N- and C-terminal ends of the
subject
sequence, as displayed in the FASTDB alignment, which are not matched/aligned
with
the query sequence are manually corrected for. No other manual corrections are
to be
made for the purposes of the present invention.
[098] The polynucleotide variants of the invention may contain alterations in
the
coding regions, non-coding regions, or both. Especially preferred are
polynucleotide
variants containing alterations, which produce silent substitutions,
additions, or
deletions, but do not alter the properties or activities of the encoded
polypeptide.
Nucleotide variants produced by silent substitutions due to the degeneracy of
the
genetic code are preferred. Moreover, polypeptide variants in which less than
50, less
than 40, less than 30, less than 20, less than 10, or 5-50, 5-25, 5-10, 1-5,
or 1-2 amino
acids are substituted, deleted, or added in any combination are also
preferred.
Polynucleotide variants can be produced for a variety of reasons, e.g., to
optimize
codon expression for a particular host (change codons in the human mRNA to
those
preferred by a bacterial host such as E. coli).
[099] Naturally occurring variants are called "allelic variants," and refer to
one of
several alternate forms of a gene occupying a given locus on a chromosome of
an
organism. (Genes II, Lewin, B., ed., John Wiley & Sons, New York (1985).)
These
allelic variants can vary at either the polynucleotide and/or polypeptide
level and are
included in the present invention. Alternatively, non-naturally occurring
variants may
be produced by mutagenesis techniques or by direct synthesis.
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[0100] Using known methods of protein engineering and recombinant DNA
technology, variants may be generated to improve or alter the characteristics
of the
polypeptides of the present invention. For instance, one or more amino acids
can be
deleted from the N-terminus or C-terminus of the polypeptides of the present
invention
without substantial loss of biological function. As an example, the authors of
Ron et
al., J. Biol. Chem..268: 2984-2988 (19.93), reported variant KGF proteins
having
heparin binding activity even after deleting 3, 8, or 27 amino-terminal amino
acid
residues. Similarly, Interferon gamma exhibited up to ten times higher
activity after
deleting 8-10 amino acid residues from the carboxy terminus of this protein.
(Dobeli
et al., J. Biotechnology 7:199-216 (1988).)
[0101] Moreover, ample evidence demonstrates that variants often retain a
biological activity similar to that of the naturally occurring protein. For
example,
Gayle and coworkers (J. Biol. Chem. 268:22105-22111 (1993)) conducted
extensive
mutational analysis of human cytokine IL-1 a. They used random mutagenesis to
generate over 3,500 individual IL-la mutants that averaged 2.5 amino acid
changes
per variant over the entire length of the molecule. Multiple mutations were
examined
at every possible amino acid position.. The investigators found that "[m]ost
of the
molecule could.be.altered with little effect on either [binding or biological
activity]."
In fact, only 23 unique amino acid sequences, out of more than 3,500
nucleotide
sequences examined, produced a protein that significantly differed in activity
from
wild-type.
[0102] Furthermore, even if deleting one or more amino acids from the N-
terminus
or C-terminus of a polypeptide results in modification or loss of one or more
biological functions, other biological activities may still be retained. For
example, the
ability of a deletion variant to induce and/or to bind antibodies which
recognize the
secreted form will likely be retained when less than the majority of the
residues of the
secreted form are removed from the N-terminus or C-terminus. Whether a
particular
polypeptide lacking N- or C-terminal residues of a protein retains such
immunogenic
activities can readily be determined by routine methods described herein and
otherwise
known in the art.
[0103] Thus, the invention further includes polypeptide variants which show a
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functional activity (e.g., biological activity) of the polypeptides of the
invention. Such
variants include deletions, insertions, inversions, repeats, and substitutions
selected
according to general rules known in the art so as have little effect on
activity.
[0104] The present application is directed to nucleic acid molecules at least
80%,
85%, 90%, 95%, 96%; 97%, 98%, 99% or 100% identical to .the nucleic acid
sequences disclosed herein, (e.g., encoding a polypeptide having the amino
acid
sequence of an N and/or C terminal deletion), irrespective of whether they
encode a
polypeptide having functional activity. This is because even where a
particular nucleic
acid molecule does not encode a polypeptide having functional activity, one of
skill in
the art would still know how to use the nucleic acid molecule, for instance,
as a
hybridization probe or a polymerase chain reaction (PCR) primer. Uses of the
nucleic
acid molecules of the present invention that do not encode a polypeptide
having
functional activity include, ifzte~ alia, (1) isolating a gene or allelic or
splice variants
thereof in a cDNA library; (2) in situ hybridization (e.g., "FISH") to
metaphase
chromosomal spreads to provide precise chromosomal location of the gene, as
described in Verma et al., Human Chromosomes: A Manual of Basic Techniques,
Pergamon Press, New York (1988); (3) Northern Blot analysis for detecting mRNA
expression in specific tissues (e.g., normal prostate or diseased prostate
tissues); and
(4) iya situ hybridization (e.g., histochemistry) for detecting.mRNA
expression in
specific tissues (e.g., normal prostate or diseased prostate tissues).
[0105] Preferred, however, are nucleic acid molecules having sequences at
least
80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the nucleic acid
sequences disclosed herein, which do, in fact, encode a polypeptide having
functional
activity. By a polypeptide having "functional activity" is meant, a
polypeptide capable
of displaying one or more known functional activities associated with a full-
length
(complete) protein of the invention. Such functional activities include, but
are not
limited to, biological activity, antigenicity [ability to bind (or compete
with a
polypeptide of the invention for binding) to an anti-polypeptide of the
invention
antibody], immunogenicity (ability to generate antibody which binds to a
specific
polypeptide of the invention), ability to form multimers with polypeptides of
the
invention, and ability to bind to a receptor or ligand for a polypeptide of
the invention.
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[0106] The functional activity of the polypeptides, and fragments, variants
and
derivatives of the invention, can be assayed by various methods.
[0107] For example, in one embodiment where one is assaying for the ability to
bind or compete with full-length polypeptide of the present invention for
binding to an
anti-polypeptide of the invention antibody, various immunoassays known in the
art
can be used, including but not limited to, competitive and non-competitive
assay
systems using techniques such as radioimmunoassays, ELISA (enzyme linked
immunosorbent assay), "sandwich" immunoassays, immunoradiometric assays, gel
diffusion precipitation reactions, immunodiffusion assays, in situ
immunoassays
(using colloidal gold, enzyme or radioisotope labels, for example), western
blots,
precipitation reactions, agglutination assays (e.g., gel agglutination assays,
hemagglutination assays), complement fixation assays, immunofluorescence
assays,
protein A assays, and immunoelectrophoresis assays, etc. In one embodiment,
antibody binding is detected by detecting a label on the primary antibody. In
another
embodiment, the primary antibody is detected by detecting binding of a
secondary
antibody or reagent to the primary antibody. In a further embodiment, the
secondary
antibody is labeled. Many means are known in the art for detecting binding in
an
immunoassay and are within the scope of the present invention.
[0108] In another embodiment, where a ligand is identified, or the ability of
a
polypeptide fragment, variant or derivative of the invention to multimerize is
being
evaluated, binding can be assayed, e.g., by means well-known in the art, such
as, for
example, reducing and non-reducing gel chromatography, protein affinity
chromatography, and affinity blotting. See generally, Phizicky et al.,
Microbiol. Rev.
59:94-123 (1995). In another embodiment, the ability of physiological
correlates of a
polypeptide of the present invention to bind to a substrates) of the
polypeptide of the
invention can be routinely assayed using techniques known in the art.
[0109] In addition, assays described herein (see Examples) and otherwise known
in the art may routinely be applied to measure the ability of polypeptides of
the present
invention and fragments, variants and derivatives thereof to elicit
polypeptide related
biological activity (either in vit>~o or izz vivo). Other methods will be
known to the
skilled artisan and are within the scope of the invention.
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[0110] Of course, due to the degeneracy of the genetic code, one of ordinary
skill
in the art will immediately recognize that a large number of the nucleic acid
molecules
having a sequence at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100%
identical to, for example, the nucleic acid sequence of the cDNA contained in
Clone
ID NO:Z, a nucleic acid sequence referred to in Table 1A (e.g., SEQ ID NO:X),
a
nucleic acid sequence disclosed in Table 2 (e.g., the nucleic acid sequence
delineated
in columns 8 and 9) or fragments thereof; will encode polypeptides "having
functional
activity." In fact, since degenerate variants of any of these nucleotide
sequences all
encode the same polypeptide, in many instances, this will be clear to the
skilled artisan
even without performing the above described comparison assay. It will be
further
recognized in the art that, for such nucleic acid molecules that are not
degenerate
variants, a reasonable number will also encode a polypeptide having functional
activity. This is because the skilled artisan is fully aware of amino acid
substitutions
that are either less likely or not likely to significantly effect protein
function (e.g.,
replacing one aliphatic amino acid with a second aliphatic amino acid), as
further
described below.
[0111] For example, guidance concerning how to make phenotypically silent
amino acid substitutions is provided in Bowie et al.; "Deciphering the Message
in
Protein Sequences: Tolerance to Amino Acid. Substitutions," Science 247:1306-
1310
(1990), wherein the authors indicate that there are two main strategies for
studying the
tolerance of an amino acid sequence to change.
[0112] The first strategy exploits the tolerance of amino acid substitutions
by
natural selection during the process of evolution. 'By comparing amino acid
sequences
in different species, conserved amino acids can be identified. These conserved
amino
acids are likely important for protein function. In contrast, the amino acid
positions
where substitutions have been tolerated by natural selection indicates that
these
positions are not critical for protein function. Thus, positions tolerating
amino acid
substitution could be modified while still maintaining biological activity of
the protein.
[0113] The second strategy uses genetic engineering to introduce amino acid
changes at specific positions of a cloned gene to identify regions critical
for protein
function. For example, site directed mutagenesis or alanine-scanning
mutagenesis
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(introduction of single alanine mutations at every residue in the molecule)
can be used.
See Cunningham et al., Science 244:1081-1085 (1989). The resulting mutant
molecules can then be tested for biological activity.
[0114] As the authors state, these two strategies have revealed that proteins
are
surprisingly. tolerant of amino. acid substitutions: The authors further
indicate which
amino acid changes are likely to be permissive at certain amino acid positions
~in the
protein. For example, most buried (within the tertiary structure of the
protein) amino
acid residues require nonpolar side chains, whereas few features of surface
side chains
are generally conserved. Moreover, tolerated conservative amino acid
substitutions
involve replacement of the aliphatic or hydrophobic amino acids Ala, Val, Leu
and Ile;
replacement of the hydroxyl residues Ser and Thr; replacement of the acidic
residues
Asp and Glu; replacement of the amide residues Asn and Gln, replacement of the
basic
residues Lys, Arg, and His; replacement of the aromatic residues Phe, Tyr, and
Trp,
and replacement of the small-sized amino acids Ala, Ser, Thr, Met, and Gly.
Besides
conservative amino acid substitutions, variants of the present invention
include (i)
substitutions with one or more of the non-conserved amino acid residues, where
the
substituted amino acid residues may or may not be one encoded by the genetic
code,
or (ii) substitutions with one or more of the amino acid residues having a
substituent
group, or (iii) fusion of the mature polypeptide with another compound, such
as a
compound to increase the stability and/or solubility of the polypeptide (for
example,
polyethylene glycol), or (iv) fusion of the polypeptide with additional amino
acids,
such as, for example, an IgG Fc fusion region peptide, serum albumin
(preferably
human serum albumin) or a fragment or variant thereof, or leader or secretory
sequence, or a sequence facilitating purification. Such variant polypeptides
are
deemed to be within the scope of those skilled in the art from the teachings
herein.
[0115] For example, polypeptide variants containing amino acid substitutions
of
charged amino acids with other charged or neutral amino acids may produce
proteins
with improved characteristics, such as less aggregation. Aggregation of
pharmaceutical formulations both reduces activity and increases clearance due
to the
aggregate's immunogenic activity. See Pinckard et al., Clin. Exp. Immunol.
2:331-
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340 (1967); Robbins et al., Diabetes 36: 838-845 (1987); Cleland et al., Crit.
Rev.
Therapeutic Drug Carrier Systems 10:307-377 (1993).
[0116] A further embodiment of the invention relates to polypeptides which
comprise the amino acid sequence of a polypeptide having an amino acid
sequence
which contains at least one amino acid substitution, but notmore than 50 amino
acid
substitutions, even more preferably, not more than 40 amino acid
substitutions, still
more preferably, not more than 30 amino acid substitutions, and still even
more
preferably, not more than 20 amino acid substitutions from a polypeptide
sequence
disclosed herein. Of course it is highly preferable for a polypeptide to have
an amino
acid sequence which comprises the amino acid sequence of a polypeptide of SEQ
ID
NO:Y, an amino acid sequence encoded by SEQ ID NO:X, an amino acid sequence
encoded by the portion of SEQ ID NO:X as defined in columns 8 and 9 of Table
2, an
amino acid sequence encoded by the complement of SEQ ID NO:X, and/or the amino
acid sequence encoded by cDNA contained in Clone ID NO:Z which contains, in
order of ever-increasing preference, at least one, but not more than 10, 9, 8,
7, 6, 5, 4,
3, 2 or 1 amino acid substitutions.
[0117] In specific embodiments, the polypeptides of the invention comprise, or
alternatively, consist of, fragments or variants of a reference amino acid
sequence
selected from: (a) the amino acid sequence of SEQ ID NO:Y or fragments thereof
(e.g., the mature form and/or other fragments described herein); (b) the amino
acid
sequence encoded by SEQ ID NO:X or fragments thereof; (c) the amino acid
sequence
encoded by the complement of SEQ ID NO:X or fragments thereof; (d) the amino
acid
sequence encoded by the portion of SEQ ID NO:X as defined in columns 8 and 9
of
Table 2 or fragments thereof; and (e) the amino acid sequence encoded by cDNA
contained in Clone ID NO:Z or fragments thereof; wherein the fragments or
variants
have 1-5, 5-10, 5-25, 5-50, 10-50 or 50-150, amino acid residue additions,
substitutions, and/or deletions when compared to the reference amino acid
sequence.
In preferred embodiments, the amino acid substitutions are conservative.
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
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Polyraucleotide ahd Polypeptide Fr-agrnerats
[0118] The present invention is also directed to polynucleotide fragments of
the
polynucleotides (nucleic acids) of the invention. In the present invention, a
"polynucleotide fragment" refers to a polynucleotide having a nucleic acid
sequence
which, for example:; is a portion of the cDNA .contained in Clone ID NO:Z or
the
complementary strand thereto; is a portion of the polynucleotide sequence
encoding
the polypeptide encoded by the cDNA contained ~ in Clone ID NO:Z or the
complementary strand thereto; is a portion of a polynucleotide sequence
encoding the
amino acid sequence encoded by the region of SEQ ID NO:X as defined in columns
8
and 9 of Table 2 or the complementary strand thereto; is a portion of the
polynucleotide sequence of SEQ ID NO:X as defined in columns 8 and 9 of Table
2 or
the complementary strand thereto; is a portion of the polynucleotide sequence
in SEQ
ID NO:X or the complementary strand thereto; is a polynucleotide sequence
encoding
a portion of the polypeptide of SEQ ID NO:Y; is a polynucleotide sequence
encoding
a portion of a polypeptide encoded by SEQ ID NO:X; is a polynucleotide
sequence
encoding a portion of a polypeptide encoded by the complement of the
polynucleotide
sequence in SEQ ID NO:X; is a portion of a polynucleotide sequence encoding
the
amino acid sequence encoded by the region of SEQ ID NO:B as defined in column
6
of Table 1B or the complementary strand thereto; or is a portion of the
polynucleotide
sequence of SEQ ID NO:B as defined in column 6 of Table 1B or the
complementary
strand thereto.
[0119] The polynucleotide fragments of the invention are preferably at least
about
15 nt, and more preferably at least about 20 nt, still more preferably at
least about 30
nt, and even more preferably, at least about 40 nt, at least about 50 nt, at
least about 75
nt, or at least about 150 nt in length. A fragment "at least 20 nt in length,"
for
example, is intended to include 20 or more contiguous bases from the cDNA
sequence
contained in Clone ID NO:Z, or the nucleotide sequence shown in SEQ ID NO:X or
the complementary stand thereto. In this context "about" includes the
particularly
recited value or a value larger or smaller by several (5, 4, 3, 2, or 1)
nucleotides, at
either terminus or at both termini. These nucleotide fragments have uses that
include,
but are not limited to, as diagnostic probes and primers as discussed herein.
Of course,
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larger fragments (e.g., at least 160, 170, 180, 190, 200, 250, 500, 600, 1000,
or 2000
nucleotides in length) are also encompassed by the invention.
[0120] Moreover, representative examples of polynucleotide fragments of the
invention, comprise, or alternatively consist of, a sequence from about
nucleotide
number 1-50, 51-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-
450, 451-500, 501-550, 551-600, 651-700, 701-750, 751-800, 800-850, 851-900,
901-
950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-
1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-
1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-
2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-
2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-2650, 2651-
2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-
3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-
3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-
3750, 3751-3800, 3801-3850, 3851-3900, 3901-3950, 3951-4000, 4001-4050, 4051-
4100, 4101-4150, 4151-4200, 4201-4250, 4251-4300, 4301-4350, 4351-4400, 4401-
4450, 4451-4500, 4501-4550, 4551-4600, 4601-4650, 4651-4700, 4701-4750, 4751-
4800, 4801-4850, 4851-4900, 4901-4950, 4951-5000, 5001-5050, 5051-5100, 5101-
5150, 5151-5200, 5201-5250, 5251-5300, 5301-5350, 5351-5400, 5401-5450; 5451-
5500, 5501-5550, 5551-5600, 5601-5650, 5651-5700, 5701-5750, 5751-5800, 5801-
5850, 5851-5900, 5901-5950, 5951-6000, 6001-6050, 6051-6100, 6101-6150, 6151-
6200, 6201-6250, 6251-6300, 6301-6350, 6351-6400, 6401-6450, 6451-6500, 6501-
6550, 6551-6600, 6601-6650, 6651-6700, 6701-6750, 6751-6800, 6801-6850, 6851-
6900, 6901-6950, 6951-7000, 7001-7050, 7051-7100, 7101-7150, 7151-7200, 7201-
7250, 7251-7300 or 7301 to the end of SEQ ID NO:X, or the complementary strand
thereto. In this context "about" includes the particularly recited range or a
range larger
or smaller by several (5, 4, 3, 2, or 1) nucleotides, at either terminus or at
both termini.
Preferably, these fragments encode a polypeptide, which has a functional
activity (e.g.,
biological activity). More preferably, these polynucleotides can be used as
probes or
primers as discussed herein. Polynucleotides which hybridize to one or more of
these
polynucleotides under stringent hybridization conditions or alternatively,
under lower
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stringency conditions axe also encompassed by the invention, as are
polypeptides
encoded by these polynucleotides.
[0121] Further representative examples of polynucleotide fragments of the
invention, comprise, or alternatively consist of, a sequence from about
nucleotide
number 1-50, 51-100;101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-
450, 451-500, 501-550, 551-600, 651-700, 701-750, 751-800, 800-850, 851-900,
901-
950, 951-1000, 1001-1050, 1051-1100, 1101-1150, 1151-1200, 1201-1250, 1251-
1300, 1301-1350, 1351-1400, 1401-1450, 1451-1500, 1501-1550, 1551-1600, 1601-
1650, 1651-1700, 1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-
2000, 2001-2050, 2051-2100, 2101-2150, 2151-2200, 2201-2250, 2251-2300, 2301-
2350, 2351-2400, 2401-2450, 2451-2500, 2501-2550, 2551-2600, 2601-2650, 2651-
2700, 2701-2750, 2751-2800, 2801-2850, 2851-2900, 2901-2950, 2951-3000, 3001-
3050, 3051-3100, 3101-3150, 3151-3200, 3201-3250, 3251-3300, 3301-3350, 3351-
3400, 3401-3450, 3451-3500, 3501-3550, 3551-3600, 3601-3650, 3651-3700, 3701-
3750, 3751-3800, 3801-3850, 3851-3900, 3901-3950, 3951-4000, 4001-4050, 4051-
4100, 4101-4150, 4151-4200, 4201-4250, 4251-4300, 4301-4350, 4351-4400, 4401-
4450, 4451-4500, 4501-4550, 4551-4600, 4601-4650, 4651-4700, 4701-4750, 4751-
4800, 4801-4850, 4851-4900, 4901-4950, 4951-5000; 5001-5050, 5051-5100, 5101-
5150, .5151-5200, 5201-5250, 5251-5300, 5301-5350, 5351-5400, 5401-5450, 5451-
5500, 5501-5550, 5551-5600, 5601-5650, 5651-5700, 5701-5750, 5751-5800, 5801-
5850, 5851-5900, 5901-5950, 5951-6000, 6001-6050, 6051-6100, 6101-6150, 6151-
6200, 6201-6250, 6251-6300, 6301-6350, 6351-6400, 6401-6450, 6451-6500, 6501-
6550, 6551-6600, 6601-6650, 6651-6700, 6701-6750, 6751-6800, 6801-6850, 6851-
6900, 6901-6950, 6951-7000, 7001-7050, 7051-7100, 7101-7150, 7151-7200, 7201-
7250, 7251-7300 or 7301 to the end of the cDNA sequence contained in Clone ID
NO:Z, or the complementary strand thereto. In this context "about" includes
the
particularly recited range or a range larger or smaller by several (5, 4, 3,
2, or 1)
nucleotides, at either terminus or at both termini. Preferably, these
fragments encode a
polypeptide, which has a functional activity (e.g., biological activity). More
preferably, these polynucleotides can be used as probes or primers as
discussed herein.
Polynucleotides which hybridize to one or more of these polynucleotides under
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stringent hybridization conditions or alternatively, under lower stringency
conditions
are also encompassed by the invention, as are polypeptides encoded by these
polynucleotides.
[0122] Moreover, representative examples of polynucleotide fragments of the
invention comprise, or alternatively consist of, a nucleic acid sequence
comprising
one, two, three, four, five, six, seven, eight, nine, ten, or more of the
above described
polynucleotide fragments of the invention in combination with a polynucleotide
sequence delineated in Table 1B column 6. Additional, representative examples
of
polynucleotide fragments of the invention comprise, or alternatively consist
of, a
nucleic acid sequence comprising one, two, three, four, five, six, seven,
eight, nine,
ten, or more of the above described polynucleotide fragments of the invention
in
combination with a polynucleotide sequence that is the complementary strand of
a
sequence delineated in column 6 of Table 1B. In further embodiments, the above-
described polynucleotide fragments of the invention comprise, or alternatively
consist
of, sequences delineated in Table 1B, column 6, and have a nucleic acid
sequence
which is different from that of the BAC fragment having the sequence disclosed
in
SEQ ID NO:B (see Table 1B, column 5). In additional embodiments, the above-
described polynucleotide fragments of the invention comprise, or alternatively
consist
of, sequences delineated in Table 1B, column. 6, and have a nucleic acid
sequence .
which is different from that published for the BAC clone identified as BAC ID
NO:A
(see Table IB, column 4). In additional embodiments, the above-described
polynucleotides of the invention comprise, or alternatively consist of,
sequences
delineated Table 1B, column 6, and have a nucleic acid sequence which is
different
from that contained in the BAC clone identified as BAC ID NO:A (see Table 1B,
column 4). Polypeptides encoded by these polynucleotides, other
polynucleotides that
encode these polypeptides, and antibodies that bind these polypeptides are
also
encompassed by the invention. Additionally, fragments and variants of the
above-
described polynucleotides and polypeptides are also encompassed by the
invention.
[0123] In additional specific embodiments, polynucleotides of the invention
comprise, or alternatively consist of, one, two, three, four, five, six,
seven, eight, nine,
ten, or more fragments of the sequences delineated in column 6 of Table 1B,
and the
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polynucleotide sequence of SEQ ID NO:X (e.g., as defined in Table 1B, column
2) or
fragments or variants thereof. Polypeptides encoded by these polynucleotides,
other
polynucleotides that encode these polypeptides, and antibodies that bind these
polypeptides are also encompassed by the invention.
[0124] In additional specific embodiments, polynucleotides of the invention
comprise, or alternatively consist of, one, two, three, four, five, six;
seven, eight; nine,
ten, or more fragments of the sequences delineated in column 6 of Table 1B
which
correspond to the same Clone ID NO:Z (see Table 1B, column 1), and the
polynucleotide sequence of SEQ ID NO:X (e.g., as defined in Table 1A or 1B) or
fragments or variants thereof. Polypeptides encoded by these polynucleotides,
other
polynucleotides that encode these polypeptides, and antibodies that bind these
polypeptides are also encompassed by the invention.
[0125] In further specific embodiments, polynucleotides of the invention
comprise, or alternatively consist of, one, two, three, four, five, six,
seven, eight, nine,
ten, or more fragments of the sequences delineated in the same row of column 6
of
Table 1B, and the polynucleotide sequence of SEQ ID NO:X (e.g., as defined in
Table
1A or 1B) or fragments or variants thereof. Polypeptides encoded by these
polynucleQtides, other polynucleotides that encode these polypeptides, and
antibodies
that bind these polypeptides are also encompassed by the invention.
[0126] In additional specific embodiments, polynucleotides of the invention
comprise, or alternatively consist of a polynucleotide sequence in which the
3' 10
polynucleotides of one of the sequences delineated in column 6 of Table 1B and
the 5'
polynucleotides of the sequence of SEQ ID NO:X are directly contiguous.
Nucleic
acids which hybridize to the complement of these 20 contiguous polynucleotides
under
stringent hybridization conditions or alternatively, under lower stringency
conditions,
are also encompassed by the invention. Polypeptides encoded by these
polynucleotides and/or nucleic acids, other polynucleotides and/or nucleic
acids that
encode these polypeptides, and antibodies that bind these polypeptides are
also
encompassed by the invention. Additionally, fragments and variants of the
above-
described polynucleotides, nucleic acids, and polypeptides are also
encompassed by
the invention.
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[0127] In additional specific embodiments, polynucleotides of the invention
comprise, or alternatively consist of a polynucleotide sequence in which the
3' 10
polynucleotides of one of the sequences delineated in column 6 of Table 1B and
the 5'
polynucleotides of a fragment or variant of the sequence of SEQ ID NO:X (e.g.,
as
described herein) are directly contiguous Nucleic acids which hybridize to the
complement of these 20 contiguous polynucleotides under stringent
hybridization
conditions or alternatively, under lower stringency conditions, are also
encompassed
by the invention. Polypeptides encoded by these polynucleotides and/or nucleic
acids,
other polynucleotides and/or nucleic acids encoding these polypeptides, and
antibodies
that bind these polypeptides are also encompassed by the invention.
Additionally,
fragments and variants of the above-described polynucleotides, nucleic acids,
and
polypeptides are also encompassed by the invention.
[0128] In further specific embodiments, polynucleotides of the invention
comprise, or alternatively consist of a polynucleotide sequence in which the
3' 10
polynucleotides of a fragment or variant of the sequence of SEQ ID NO:X and
the 5'
10 polynucleotides of the sequence of one of the sequences delineated in
column 6 of
Table 1B are directly contiguous. Nucleic acids which hybridize to the
complement of
these 20 contiguous polynucleotides under stringent hybridization conditions
or
alternatively, under lower stringency conditions, are also encompassed by the
invention. Polypeptides encoded by these polynucleotides and/or nucleic acids,
other
polynucleotides and/or nucleic acids encoding these polypeptides, and
antibodies that
bind these polypeptides are also encompassed by the invention. Additionally,
fragments and variants of the above-described polynucleotides, nucleic acids,
and
polypeptides are also encompassed by the invention.
[0129] In specific embodiments, polynucleotides of the invention comprise, or
alternatively consist of a polynucleotide sequence in which the 3' 10
polynucleotides
of one of the sequences delineated in column 6 of Table 1B and the 5' 10
polynucleotides of another sequence in column 6 are directly contiguous. In
preferred
embodiments, the 3' 10 polynucleotides of one of the sequences delineated in
column
6 of Table 1B is directly contiguous with the 5' 10 polynucleotides of the
next
sequential exon delineated in Table 1B, column 6. Nucleic acids which
hybridize to
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the complement of these 20 contiguous polynucleotides under stringent
hybridization
conditions or alternatively, under lower stringency conditions, are also
encompassed
by the invention. Polypeptides encoded by these polynucleotides and/or nucleic
acids,
other polynucleotides and/or nucleic acids encoding these polypeptides, and
antibodies
that bind these polypeptides are also encompassed by the invention.
Additionally,
fragments and variants of the above-described polynucleotides; nucleic acids,
and
polypeptides are also encompassed by the invention.
(0130] In the present invention, a "polypeptide fragment" refers to an amino
acid
sequence which is a portion of that contained in SEQ ID NO:Y, a portion of an
amino
acid sequence encoded by the portion of SEQ ID NO:X as defined in columns 8
and 9
of Table 2, a portion of an amino acid sequence encoded by the polynucleotide
sequence of SEQ ID NO:X, a portion of an amino acid sequence encoded by the
complement of the polynucleotide sequence in SEQ ID NO:X, and/or a portion of
an
amino acid sequence encoded by the cDNA contained in Clone ID NO:Z. Protein
(polypeptide) fragments may be "free-standing," or comprised within a larger
polypeptide of which the fragment forms a part or region, most preferably as a
single
continuous region. Representative examples of polypeptide fragments of the
invention, include, for. example, fragments comprising, or alternatively
consisting of,
from about amino acid number 1-20, 21-40, 4I-60, 61-80, 8I-100, 102-120, 121-
140,
141-160, 161-180, 181-200, 201-220, 221-240, 241-260, 261-280, 281-300, 301-
320,
321-340, 341-360, 361-380, 381-400, 401-420, 421-440, 441-460, 461-480, 481-
500,
501-520, 521-540, 541-560, 561-580, 581-600, 601-620, 621-640, 641-660, 661-
680,
681-700, 701-720, 721-740, 741-760, 761-780, 781-800, 801-820, 821-840, 841-
860,
861-880, 881-900, 901-920, 921-940, 941-960, 961-980, 981-1000, 1001-1020,
1021-
1040, 1041-1060, 1061-1080, 1081-1100, 1101-1120, 1121-1140, 1141-1160, 1161-
1180, 1181-1200, 1201-1220, 1221-1240, 1241-1260, 1261-1280, 1281-1300, 1301-
1320, 1321-1340, 1341-1360, 1361-1380, 1381-1400, 1401-1420, 1421-1440, or
1441
to the end of the coding region. In a preferred embodiment, polypeptide
fragments of
the invention include, for example, fragments comprising, or alternatively
consisting
of, from about amino acid number 1-20, 21-40, 41-60, 61-80, 81-100, 102-120,
121-
140, 141-160, 161-180, 181-200, 201-220, 221-240, 241-260, 261-280, 281-300,
301-
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320, 321-340, 341-360, 361-380, 381-400, 401-420, 421-440, 441-460, 461-480,
481-
500, 501-520, 521-540, 541-560, 561-580, 581-600, 601-620, 621-640, 641-660,
661-
680, 681-700, 701-720, 721-740, 741-760, 761-780, 781-800, 801-820, 821-840,
841-
860, 861-880, 881-900, 901-920, 921-940, 941-960, 961-980, 981-1000, 1001-
1020,
1021-1040, .1041-1060, 1061-1080, 1081-1100, 1101-1120, 1121-1140, 1141-1160,
1161-1180, 1181-1200, 1201-1220, 1221-1240, 1241-1260, 1261-1280, 1281-1300,
1301-1320, 1321-1340, 1341-1360, 1361-1380, 1381-1400, 1401-1420, 1421-1440,
or
1441 to the end of the coding region of SEQ ID NO:Y. Moreover, polypeptide
fragments of the invention may be at least about 10, 15, 20, 25, 30, 35, 40,
45, 50, 55,
60, 65, 70, 75, 80, 85, 90, 100, 110, 120, 130, 140, or 150 amino acids in
length. In
this context "about" includes the particularly recited ranges or values, or
ranges or
values larger or smaller by several (5, 4, 3, 2, or 1) amino acids, at either
extreme or at
both extremes. Polynucleotides encoding these polypeptide fragments are also
encompassed by the invention.
[0131] Even if deletion of one or more amino acids from the N-terminus of a
protein results in modification of loss of one or more biological functions of
the
protein, other functional activities (e.g., biological activities, ability to
multimerize,
ability to bind a ligand) may still be retained. For example, the ability of
shortened
muteins to induce and/or bind to antibodies which recognize the complete or
mature
forms of the polypeptides generally will be retained when less than the
majority of the
residues of the complete or mature polypeptide are removed from the N-
terminus.
Whether a particular polypeptide lacking N-terminal residues of a complete
polypeptide retains such immunologic activities can readily be determined by
routine
methods described herein and otherwise known in the art. It is not unlikely
that a
mutein with a large number of deleted N-terminal amino acid residues may
retain
some biological or immunogenic activities. In fact, peptides composed of as
few as
six amino acid residues may often evoke an immune response.
[0132] Accordingly, polypeptide fragments include the secreted protein as well
as
the mature form. Further preferred polypeptide fragments include the secreted
protein
or the mature form having a continuous series of deleted residues from the
amino or
the carboxy terminus, or both. For example, any number of amino acids, ranging
from
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1-60, can be deleted from the amino terminus of either the secreted
polypeptide or the
mature form. Similarly, any number of amino acids, ranging from 1-30, can be
deleted from the carboxy terminus of the secreted protein or mature form.
Furthermore, any combination of the above amino and carboxy terminus deletions
is
preferred. Similarly, polynucleotides encoding these polypeptide. fragments -
are also
preferred.
[0133] The present invention further provides polypeptides having one or more
residues deleted from the amino terminus of the amino acid sequence of a
polypeptide
disclosed herein (e.g., a polypeptide of SEQ ID NO:Y, a polypeptide encoded by
the
polynucleotide sequence contained in SEQ ID NO:X or the complement thereof, a
polypeptide encoded by the portion of SEQ ID NO:X as defined in columns 8 and
9 of
Table 2, and/or a polypeptide encoded by the cDNA contained in Clone ID NO:Z).
In
particular, N-terminal deletions may be described by the general formula m-q,
where q
is a whole integer representing the total number of amino acid residues in a
polypeptide of the invention (e.g., the polypeptide disclosed in SEQ ID NO:Y,
or the
polypeptide encoded by the portion of SEQ ID NO:X as defined in columns 8 and
9 of
Table 2), and m is defined as any integer ranging from 2 to q-6.
Polynucleotides
encoding these polypeptides are also encompassed by the invention.
[0134] The present invention further provides polypeptides having one or more
residues from the carboxy terminus of the amino acid sequence of a polypeptide
disclosed herein (e.g., a polypeptide of SEQ ID NO:Y, a polypeptide encoded by
the
polynucleotide sequence contained in SEQ ID NO:X, a polypeptide encoded by the
portion of SEQ ID NO:X as defined in columns 8 and 9 of Table 2, and/or a
polypeptide encoded by the cDNA contained in Clone ID NO:Z). In particular, C-
terminal deletions may be described by the general formula 1-n, where n is any
whole
integer ranging from 6 to q-1, and where n corresponds to the position of
amino acid
residue in a polypeptide of the invention. Polynucleotides encoding these
polypeptides
are also encompassed by the invention.
[0135] In addition, any of the above described N- or C-terminal deletions can
be
combined to produce a N- and C-terminal deleted polypeptide. The invention
also
provides polypeptides having one or more amino acids deleted from both the
amino
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and the carboxyl termini, which may be described generally as having residues
m-n of
a polypeptide encoded by SEQ ID NO:X (e.g., including, but not limited to, the
preferred polypeptide disclosed as SEQ ID NO:Y and the polypeptide encoded by
the
portion of SEQ ID NO:X as defined in columns 8 and 9 of Table 2), the cDNA
contained in Clone ID NO:Z, and/or the complement thereof, where n and m are
integers as described above. Polynucleotides encoding these polypeptides are
also
encompassed by the invention.
[0136] Also as mentioned above, even if deletion of one or more amino acids
from
the C-terminus of a protein results in modification of loss of one or more
biological
functions of the protein, other functional activities (e.g., biological
activities, ability to
multimerize, ability to bind a ligand) may still be retained. Fox example the
ability of
the shortened mutein to induce andlor bind to antibodies which recognize the
complete
or mature forms of the polypeptide generally will be retained when less than
the
majority of the residues of the complete or mature polypeptide are removed
from the
C-terminus. Whether a particular polypeptide lacking C-terminal residues of a
complete polypeptide retains such immunologic activities can readily be
determined
by routine methods described herein and otherwise known in the art. It is not
unlikely
that a mutein with a large number of deleted C-terminal amino acid residues
may
retain some biological or immunogenic activities. In fact, peptides composed
of as
few as six amino acid residues may often evoke an immune response.
[0137] The present application is also directed to proteins containing
polypeptides
at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a polypeptide
sequence set forth herein. In preferred embodiments, the application is
directed to
proteins containing polypeptides at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or
99% identical to polypeptides having the amino acid sequence of the specific N-
and
C-terminal deletions. Polynucleotides encoding these polypeptides are also
encompassed by the invention.
[0138] Any polypeptide sequence encoded by, for example, the polynucleotide
sequences set forth as SEQ ID NO:X or the complement thereof, (presented, for
example, in Tables 1A and 2), the cDNA contained in Clone ID NO:Z, or the
polynucleotide sequence as defined in column 6 of Table 1B, may be analyzed to
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determine certain preferred regions of the polypeptide. For example, the amino
acid
sequence of a polypeptide encoded by a polynucleotide sequence of SEQ ID NO:X
(e.g., the polypeptide of SEQ ID NO:Y and the polypeptide encoded by the
portion of
SEQ ID NO:X as defined in columns 8 and 9 of Table 2) or the cDNA contained in
Clone ID NO:Z may be analyzed using the default parameters of the DNASTAR
computer algorithm (DNASTAR, Inc:, 1228 S. Park St., Madison, WI 53715 USA;
http://www.dnastar.com~.
[0139] Polypeptide regions that may be routinely obtained using the DNASTAR
computer algorithm include, but are not limited to, Gamier-Robson alpha-
regions,
beta-regions, turn-regions, and coil-regions; Chou-Fasman alpha-regions, beta-
regions,
and turn-regions; Kyte-Doolittle hydrophilic regions and hydrophobic regions;
Eisenberg alpha- and beta-amphipathic regions; Karplus-Schulz flexible
regions;
Emini surface-forming regions; and Jameson-Wolf regions of high antigenic
index.
Among highly preferred polynucleotides of the invention in this regard are
those that
encode polypeptides comprising regions that combine several~structural
features, such
as several (e.g., 1, 2, 3 or 4) of the features set out above.
[0140] Additionally, Kyte-Doolittle hydrophilic regions and hydrophobic
regions,
Emini surface-forming regions and Jameson-Wolf regions of high antigenic index
(i.e., containing four or more contiguous amino acids having an antigenic
index of
greater than or equal to 1.5, as identified using the default parameters of
the Jameson-
Wolf program) can routinely be used to determine polypeptide regions that
exhibit a
high degree of potential for antigenicity. Regions of high antigenicity are
determined
from data by DNASTAR analysis by choosing values which represent regions of
the
polypeptide which are likely to be exposed on the surface of the polypeptide
in an
environment in which antigen recognition may occur in the process of
initiation of an
immune response.
[0141] Preferred polypeptide fragments of the invention are fragments
comprising,
or alternatively, consisting of, an amino acid sequence that displays a
functional
activity (e.g. biological activity) of the polypeptide sequence of which the
amino acid
sequence is a fragment. By a polypeptide displaying a "functional activity" is
meant a
polypeptide capable of one or more lcnown functional activities associated
with a full-
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length protein, such as, for example, biological activity, antigenicity,
immunogenicity,
and/or multimerization, as described herein.
[0142] Other preferred polypeptide fragments are biologically active
fragments.
Biologically active fragments are those exhibiting activity similar, but not
necessarily
identical, to an activity of the polypeptide of the present invention. The
biological
activity of the fragments may include an improved desired activity, or a
decreased
undesirable activity.
[0143] In preferred embodiments, polypeptides of the invention comprise, or
alternatively consist of, one, two, three, four, five or more of the antigenic
fragments
of the polypeptide of SEQ ID NO:Y, or portions thereof. Polynucleotides
encoding
these polypeptides are also encompassed by the invention.
[0144] The present invention encompasses polypeptides comprising, or
alternatively consisting of, an epitope of: the polypeptide sequence shown in
SEQ ID
NO:Y; a polypeptide sequence encoded by SEQ ID NO:X or the complementary
strand thereto; the polypeptide sequence encoded by the portion of SEQ ID NO:X
as
defined in columns 8 and 9 of Table 2; the polypeptide sequence encoded by the
portion of SEQ ID NO:B as defined in column 6 of Table 1B or the complement
thereto; the polypeptide sequence encoded by the cDNA contained in Clone-ID
NO:Z;
or the polypeptide sequence encoded by a polynucleotide that hybridizes to the
sequence of SEQ ID NO:X, the complement of the sequence of SEQ ID NO:X, the
complement of a portion of SEQ ID NO:X as defined in columns 8 and 9 of Table
2,
or the cDNA sequence contained in Clone ID NO:Z under stringent hybridization
conditions or alternatively, under lower stringency hybridization as defined
supra. The
present invention further encompasses polynucleotide sequences encoding an
epitope
of a polypeptide sequence of the invention (such as, for example, the sequence
disclosed in SEQ ID NO:X, or a fragment thereof), polynucleotide sequences of
the
complementary strand of a polynucleotide sequence encoding an epitope of the
invention, and polynucleotide sequences which hybridize to the complementary
strand
under stringent hybridization conditions or alternatively, under lower
stringency
hybridization conditions defined supra.
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[0145] The term "epitopes," as used herein, refers to portions of a
polypeptide
having antigenic or immunogenic activity in an animal, preferably a mammal,
and
most preferably in a human. In a preferred embodiment, the present invention
encompasses a polypeptide comprising an epitope, as well as the polynucleotide
encoding this polypeptide. An "immunogenic epitope;" as used herein, is
defined as a
portion of a protein that elicits an antibody response in an animal, as
determined by
any method known in the art, fox example, by the methods for generating
antibodies
described infra. (See, for example, Geysen et al., Proc. Natl. Acad. Sci. USA
81:3998- 4002 (1983)). The term "antigenic epitope," as used herein, is
defined as a
portion of a protein to which an antibody can immunospecifically bind its
antigen as
determined by any method well known in the art, for example, by the
immunoassays
described herein. Immunospecific binding excludes non-specific binding but
does not
necessarily exclude cross- reactivity with other antigens. Antigenic epitopes
need not
necessarily be immunogenic.
[0146] Fragments, which function as epitopes may be produced by any
conventional means. (See, e.g., Houghten, R. A., Proc. Natl. Acad. Sci. USA
82:5131-
5135 (1985) further described in U.S. Patent No. 4,631,211.)
[0147] In the present invention, antigenic epitopes preferably contain a
sequence
of at least 4, at least 5, at least 6, at least 7, more preferably at least 8,
at least 9, at
least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at
least 20, at least
25, at least 30, at least 40, at least 50, and, most preferably, between about
15 to about
30 amino acids. Preferred polypeptides comprising immunogenic or antigenic
epitopes are at least 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,
80, 85, 90, 95,
or 100 amino acid residues in length. Additional non-exclusive preferred
antigenic
epitopes include the antigenic epitopes disclosed herein, as well as portions
thereof.
Antigenic epitopes are useful, fox example, to raise antibodies, including
monoclonal
antibodies, that specifically bind the epitope. Preferred antigenic epitopes
include the
antigenic epitopes disclosed herein, as well as any combination of two, three,
four, five
or more of these antigenic epitopes. Antigenic epitopes can be used as the
target
molecules in immunoassays. (See, for instance, Wilson et al., Cell 37:767-778
(1984); Sutcliffe et al., Science 219:660-666 (1983)).
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[0148] Non-limiting examples of epitopes of polypeptides that can be used to
generate antibodies of the invention include a polypeptide comprising, or
alternatively
consisting of, at least one, two, three, four, five, six or more of the
portions) of SEQ
ID NO:Y specified in column 6 of Table 1A. These polypeptide fragments have
been
determined to bear antigenic epitopes of the proteins of the invention by the
analysis
of the Jameson-Wolf antigenic index, which is included in the-DNAStar suite of
computer programs. By "comprise" it is intended that a polypeptide contains at
least
one, two, three, four, Fme, six or more of the portions) of SEQ ID NO:Y shown
in
column 6 of Table 1A, but it may contain additional flanking residues on
either the
amino or carboxyl termini of the recited portion. Such additional flanking
sequences
are preferably sequences naturally found adjacent to the portion; i.e.,
contiguous
sequence shown in SEQ ID NO:Y. The flanking sequence may, however, be
sequences from a heterolgous polypeptide, such as from another protein
described
herein or from a heterologous polypeptide not described herein. In particular
embodiments, epitope portions of a polypeptide of the invention comprise one,
two,
three, or more of the portions of SEQ ID NO:Y shown in column 6 of Table 1A.
Polynucleotides encoding these polypeptides are also encompassed by the
invention.
[0149] Similarly, immunogenic epitopes can be used, for example, to induce
antibodies according to methods well known in the art. See, for instance,
Sutcliffe et
al., supra; Wilson et al., supra; Chow et al., Proc. Natl. Acad. Sci. USA
82:910-914;
and Bittle et al., J. Gen. Virol. 66:2347-2354 (1985). Preferred immunogenic
epitopes include the immunogenic epitopes disclosed herein, as well as any
combination of two, three, four, five or more of these immunogenic epitopes.
The
polypeptides comprising one or more immunogenic epitopes may be presented for
eliciting an antibody response together with a carrier protein, such as an
albumin, to an
animal system (such as rabbit or mouse), or, if the polypeptide is of
sufficient length
(at least about 25 amino acids), the polypeptide may be presented without a
carrier.
However, immunogenic epitopes comprising as few as 8 to 10 amino acids have
been
shown to be sufficient to raise antibodies capable of binding to, at the very
least, linear
epitopes in a denatured polypeptide (e.g., in Western blotting).
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[0150] Epitope-bearing polypeptides of the present invention may be used to
induce antibodies according to methods well known in the art including, but
not
limited to, in vivo immunization, iya vitro immunization, and phage display
methods.
See, e.g., Sutcliffe et al., supra; Wilson et al., supra, and Bittle et al.,
J. Gen. Virol.,
66:2347-2354 (1985). If io vivo immunization is used, animals may be immunized
with free peptide; however, anti-peptide antibody titer may be boosted by
coupling the
peptide to a macromolecular carrier, such as keyhole limpet hemacyanin (KLH)
or
tetanus toxoid. For instance, peptides containing cysteine residues may be
coupled to
a carrier using a linker such as maleimidobenzoyl- N-hydroxysuccinimide ester
(MBS), while other peptides may be coupled to carriers using a more general
linking
agent such as glutaraldehyde. Animals such as rabbits, rats and mice are
immunized
with either free or carrier- coupled peptides, for instance, by
intraperitoneal and/or
intradermal injection of emulsions containing about 100 ~g of peptide or
carrier
protein and Freund's adjuvant or any other adjuvant known for stimulating an
immune
response. Several booster injections may be needed, for instance, at intervals
of about
two weeks, to provide a useful titer of anti-peptide antibody which can be
detected, for
example, by ELISA assay using free peptide adsorbed to a solid surface. The
titer of
anti-peptide antibodies in serum from an immunized animal may be increased by
selection of anti-peptide antibodies, for instance, by adsorption to the
peptide on a
solid support and elution of the selected antibodies according to methods well
known
in the art.
[0151] As one of skill in the art will appreciate, and as discussed above, the
polypeptides of the present invention (e.g., those comprising an immunogenic
or
antigenic epitope) can be fused to heterologous polypeptide sequences. For
example,
polypeptides of the present invention (including fragments or variants
thereof), may be
fused with the constant domain of immunoglobulins (IgA, IgE, IgG, IgM), or
portions
thereof (CH1, CH2, CH3, or any combination thereof and portions thereof,
resulting in
chimeric polypeptides. By way of another non-limiting example, polypeptides
and/or
antibodies of the present invention (including fragments or variants thereof)
may be
fused with albumin (including but not limited to recombinant human serum
albumin or
fragments or variants thereof (see, e.g., U.S. Patent No. 5,876,969, issued
March 2,
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1999, EP Patent 0 413 622, and U.S. Patent No. 5,766,883, issued June 16,
1998,
herein incorporated by reference in their entirety)). In a preferred
embodiment,
polypeptides and/or antibodies of the present invention (including fragments
or
variants thereof) are fused with the mature form of human serum albumin (i.e.,
amino
acids 1 - 585 of human serum albumin as shown in Figures 1 and 2 of EP Patent
0.322
094) which is herein incorporated by reference in its entirety. In another
preferred
embodiment, polypeptides and/or antibodies of the present invention (including
fragments or variants thereof) are fused with polypeptide fragments
comprising, or
alternatively consisting of, amino acid residues 1-z of human serum albumin,
where z
is an integer from 369 to 419, as described in U.S. Patent 5,766,883 herein
incorporated by reference in its entirety. Polypeptides and/or antibodies of
the present
invention (including fragments or variants thereof) may be fused to either the
N- or C-
tenninal end of the heterologous protein (e.g., immunoglobulin Fc polypeptide
or
hmnan serum albumin polypeptide). Polynucleotides encoding fusion proteins of
the
invention are also encompassed by the invention.
[0152] Such fusion proteins as those described above may facilitate
purification
and may increase half life in vivo. This has been shown for chimeric proteins
consisting of the first two domains of the human CD4-polypeptide and various
domains of the constant regions of the heavy or light chains of mammalian
immunoglobulins. See, e.g., EP 394,827; Traunecker et al., Nature, 331:84-86
(1988).
Enhanced delivery of an antigen across the epithelial barrier to the immune
system has
been demonstrated for antigens (e.g., insulin) conjugated to an FcRn binding
partner
such as IgG or Fc fragments (see, e.g., PCT Publications WO 96/22024 and WO
99/04813). IgG Fusion proteins that have a disulfide-linked dimeric structure
due to
the IgG portion desulfide bonds have also been found to be more efficient in
binding
and neutralizing other molecules than monomeric polypeptides or fragments
thereof
alone. See, e.g., Fountoulakis et al., J. Biochem., 270:3958-3964 (1995).
Nucleic
acids encoding the above epitopes can also be recombined with a gene of
interest as an
epitope tag (e.g., the hemagglutinin (HA) tag or flag tag) to aid in detection
and
purification of the expressed polypeptide. For example, a system described by
Janknecht et al. allows for the ready purification of non-denatured fusion
proteins
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expressed in human cell lines (Janknecht et al., 1991, Proc. Natl. Acad. Sci.
USA
88:8972- 897). In this system, the gene of interest is subcloned into a
vaccinia
recombination plasmid such that the open reading frame of the gene is
translationally
fused to an amino-terminal tag consisting of six histidine residues. The tag
serves as a
matrix binding domain fox the fusion protein. Extracts from cells infected
with the.
recombinant vaccinia virus are loaded onto Ni2+ nitriloacetic acid-agarose
column and
histidine-tagged proteins can be selectively eluted with imidazole-containing
buffers.
Fusioiz Proteins
[0153] Any polypeptide of the present invention can be used to generate fusion
proteins. For example, the polypeptide of the present invention, when fused to
a
second protein, can be used as an antigenic tag. Antibodies raised against the
polypeptide of the present invention can be used to indirectly detect the
second protein
by binding to the polypeptide. Moreover, because secreted proteins target
cellular
locations based on trafficking signals, polypeptides of the present invention
which are
shown to be secreted can be used as targeting molecules once fused to other
proteins.
[0154] Examples of domains that can be fused to polypeptides of the present
invention include not only heterologous signal sequences, but also other
heterologous
functional regions. The fusion does not necessarily need ~to be direct, but
may occur
through linker sequences.
[0155] In certain preferred embodiments, proteins of the invention are fusion
proteins comprising an amino acid sequence that is an N and/or C- terminal
deletion of
a polypeptide of the invention. In preferred embodiments, the invention is
directed to
a fusion protein comprising an amino acid sequence that is at least 80%, 85%,
90%,
95%, 96%, 97%, 98% or 99% identical to a polypeptide sequence of the
invention.
Polynucleotides encoding these proteins are also encompassed by the invention.
[0156] Moreover, fusion proteins may also be engineered to improve
characteristics of the polypeptide of the present invention. For instance, a
region of
additional amino acids, particularly charged amino acids, may be added to the
N-
terminus of the polypeptide to improve stability and persistence during
purification
from the host cell or subsequent handling and storage. Also, peptide moieties
may be
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added to the polypeptide to facilitate purification. Such regions may be
removed prior
to final preparation of the polypeptide. The addition of peptide moieties to
facilitate
handling of polypeptides is familiar and routine techniques in the art.
[0157] As one of skill in the art will appreciate that, as discussed above,
polypeptides of the present invention, and epitope-bearing fragments .thereof,
can be
combined with heterologous polypeptide sequences. For example, the
polypeptides of
the present invention may be fused with heterologous polypeptide sequences,
for
example, the polypeptides of the present invention may be fused with the
constant
domain of immunoglobulins (IgA, IgE, IgG, IgM) or portions thereof (CHl, CH2,
CH3, and any combination thereof, including both entire domains and portions
thereof), or albumin (including, but not limited to, native or recombinant
human
albumin or fragments or variants thereof (see, e.g., U.S. Patent No.
5,876,969, issued
March 2, 1999, EP Patent 0 413 622, and U.S. Patent No. 5,766,883, issued June
I6,
1998, herein incorporated by reference in their entirety)), resulting in
chimeric
polypeptides. For example, EP-A-O 464 533 (Canadian counterpart 2045869)
discloses fusion proteins comprising various portions of constant region of
immunoglobulin molecules together with another human protein or part thereof.
In
many cases, the Fc part in a fusion protein is beneficial in therapy and
diagnosis, and .
thus can result in, for example, improved pharmacokinetic properties (EP-A
0232
262). Alternatively, deleting the Fc part after the fusion protein has been
expressed,
detected, and purified, would be desired. For example, the Fc portion may
hinder
therapy and diagnosis if the fusion protein is used as an antigen for
immunizations. In
drug discovery, for example, human proteins, such as hIL-5, have been fused
with Fc
portions for the purpose of high-throughput screening assays to identify
antagonists of
hIL-5. See, D. Bennett et al., J. Molecular Recognition 8:52-58 (1995); I~.
Johanson et
al., J. Biol. Chem. 270:9459-9471 (1995).
[0158] Moreover, the polypeptides of the present invention can be fused to
marker
sequences, such as a polypeptide, which facilitates purification of the fused
polypeptide. In preferred embodiments, the marker amino acid sequence is a
hexa-
histidine peptide, such as the tag provided in a pQE vector (QIAGEN, Inc.,
9259 Eton
Avenue, Chatsworth, CA, 91311), among others, many of which are commercially
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available. As described in Gentz et al., Proc. Natl. Acad. Sci. USA 86:821-824
(1989), for instance, hexa-histidine provides for convenient purification of
the fusion
protein. Another peptide tag useful for purification, the "HA" tag,
corresponds to an
epitope derived from the influenza hemagglutinin protein (Wilson et al., Cell
37:767
(1984).)
[0159] Additional fusion proteins of the invention may be generated through
the
techniques of gene-shuffling, motif shuffling, exon-shuffling, and/or codon-
shuffling
(collectively referred to as "DNA shuffling"), briefly described below, and
further
described herein. DNA shuffling may be employed to modulate the activities of
polypeptides of the invention, such methods can be used to generate
polypeptides with
altered activity, as well as agonists and antagonists of the polypeptides.
See,
generally, U.S. Patent Nos. 5,605,793; 5,811,238; 5,830,721; 5,834,252; and
5,837,458, and Patten et al., Curr. Opinion Biotechnol. 8:724-33 (1997);
Harayama,
Trends Biotechnol. 16(2):76-82 (1998); Hansson et al., J. Mol. Biol. 287:265-
76
(1999); and Lorenzo and Blasco, Biotechniques 24(2):308-13 (1998); each of
these
patents and publications are hereby incorporated by reference in its
entirety). In a
preferred embodiment, one or more components, motifs, sections, parts,
domains,
fragments, etc., of a polynucleotide encoding a polypeptide of the invention
may be
recombined with one or more components, motifs, sections, parts, domains,.
fragments, etc., of one or more heterologous molecules encoding a heterologous
polypeptide.
[0160] Thus, any of these above fusions can be engineered using the
polynucleotides or the polypeptides of the present invention.
Recombinant and Synthetic Production of Polypeptides of the Invention
[0161] The present invention also relates to vectors containing the
polynucleotide
of the present invention, host cells, and the production of polypeptides by
synthetic
and recombinant techniques. The vector may be, for example, a phage, plasmid,
viral,
or retroviral vector. Retroviral vectors may be replication competent or
replication
defective. In the latter case, viral propagation generally will occur only in
complementing host cells.
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[0162] The polynucleotides of the invention may be joined to a vector
containing a
selectable marker for propagation in a host. Generally, a plasmid vector is
introduced
in a precipitate, such as a calcium phosphate precipitate, or in a complex
with a
charged lipid. If the vector is a virus, it may be packaged iyi vitro using an
appropriate
packaging cell line and then transduced into host cells.
[0163] The polynucleotide insert should be operatively linked to an
appropriate
promoter, such as the phage lambda PL promoter, the E. coli lac, tip, phoA and
tac
promoters, the SV40 early and late promoters and promoters of retroviral LTRs,
to
name a few. Other suitable promoters will be known to the skilled artisan. The
expression constructs will further contain sites for transcription initiation,
termination,
and, in the transcribed region, a ribosome binding site for translation. The
coding
portion of the transcripts expressed by the constructs will preferably include
a
translation initiating codon at the beginning and a termination codon (UAA,
UGA or
UAG) appropriately positioned at the end of the polypeptide to be translated.
[0164] As indicated, the expression vectors will preferably include at least
one
selectable marker. Such markers include dihydrofolate reductase, 6418 or
neomycin
resistance, glutamine synthase, for eukaryotic cell culture and tetracycline,
kanamycin
or ampicillin resistance genes for culturing in E. coli and other bacteria.
Representative examples of appropriate hosts include, but are not limited to,
bacterial
cells, such as E. coli, Streptomyces and SalmofZella typhimu~ium cells; fungal
cells,
such as yeast cells (e.g., Saccha~omyces cerevisiae or Piclaia pastoris (ATCC
Accession No. 201178)); insect cells such as Drosophila S2 and Spodopte~a Sf9
cells;
animal cells such as CHO, COS, 293, NSO and Bowes melanoma cells; and plant
cells. Appropriate culture mediums and conditions for the above-described host
cells
are known in the art.
[0165] Among vectors preferred for use in bacteria include pQE70, pQE60 and
pQE-9, available from QIAGEN, Inc.; pBluescript vectors, Phagescript vectors,
pNHBA, pNHl6a, pNHl8A, pNH46A, available from Stratagene Cloning Systems,
Inc.; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRITS available from Pharmaci~
Biotech, Inc. Among preferred eulcaryotic vectors are pWLNEO, pSV2CAT, pOG44,
pXTl and pSG available from Stratagene; and pSVK3, pBPV, pMSG and pSVL
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available from Pharmacia. Preferred expression vectors for use in yeast
systems
include, but are not limited to pYES2, pYDI, pTEFl/Zeo, pYES2/GS, pPICZ,
pGAPZ, pGAPZaIph, pPIC9, pPIC3.5, pHIL-D2, pHIL-Sl, pPIC3.5K, pPIC9K, and
PA0815 (all available from Invitrogen, Carlsbad, CA). Other suitable vectors
will be
readily apparent to the skilled artisan.
[0166] Vectors which use glutamine synthase (GS) or DHFR as the selectable
marlcers can be amplified in the presence of the drugs methionine sulphoximine
or
methotrexate, respectively. An advantage of glutamine synthase based vectors
is the
availabilty of cell lines (e.g., the murine myeloma cell line, NSO) which are
glutamine
synthase negative. Glutamine synthase expression systems can also function in
glutamine synthase expressing cells (e.g., Chinese Hamster Ovary (CHO) cells)
by
providing additional inhibitor to prevent the functioning of the endogenous
gene. A
glutamine synthase expression system and components thereof are detailed in
PCT
publications: W087/04462; W086/05807; W089/01036; W089/10404; and
W091/06657 which are hereby incorporated in their entireties by reference
herein.
Additionally, glutamine synthase expression vectors can be obtained from Lonza
Biologics, Inc. (Portsmouth, NH). Expression and production of monoclonal
antibodies using a GS expression system in murine myeloma cells is described
in
Bebbington et al., Bioltechr~ology 10:169(1992) and in Biblia and Robinson
Bioteclznol. Prog. 11:1 (1995) which are herein incorporated by reference.
[0167] The present invention also relates to host cells containing the above-
described vector constructs described herein, and additionally encompasses
host cells
containing nucleotide sequences of the invention that are operably associated
with one
or more heterologous control regions (e.g., promoter and/or enhancer) using
techniques known of in the art. The host cell can be a higher eulcaryotic
cell, such as
a mammalian cell (e.g., a human derived cell), or a lower eukaryotic cell,
such as a
yeast cell, or the host cell can be a prokaryotic cell, such as a bacterial
cell. A host
strain may be chosen, which modulates the expression of the inserted gene
sequences,
or modifies and processes the gene product in the specific fashion desired.
Expression
from certain promoters can be elevated in the presence of certain inducers;
thus
expression of the genetically engineered polypeptide may be controlled.
Furthermore,
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different host cells have characteristics and specific mechanisms for the
translational
and post-translational processing and modification (e.g., phosphorylation,
cleavage) of
proteins. Appropriate cell lines can be chosen to ensure the desired modif
cations and
processing of the foreign protein expressed.
[0168] Introduction of the nucleic acids and nucleic acid constructs of the
invention into the host cell can be effected by calcium phosphate
transfection, DEAE-
dextran mediated transfection, cationic lipid-mediated transfection,
electroporation,
transduction, infection, or other methods. Such methods are described in many
standard laboratory manuals, such as Davis et al., Basic Methods In Molecular
Biology (1986). It is specifically contemplated that the polypeptides of the
present
invention may in fact be expressed by a host cell lacking a recombinant
vector.
[0169] In addition to encompassing host cells containing the vector constructs
discussed herein, the invention also encompasses primary, secondary, and
immortalized host cells of vertebrate origin, particularly mammalian origin,
that have
been engineered to delete or replace endogenous genetic material (e.g.,
prostate cancer
antigen coding sequence), and/or to include genetic material (e.g.,
heterologous
polynucleotide sequences) that is operably associated with prostate cancer
associated
polynucleotides of the invention and which activates, alters, and/or amplifies
endogenous prostate cancer associated polynucleotides. For example, techniques
known in the art may be used to operably associate heterologous control
regions (e.g.,
promoter and/or enhancer) and endogenous prostate cancer associated
polynucleotide
sequences via homologous recombination (see, e.g., US Patent Number 5,641,670,
issued June 24, 1997; International Publication Number WO 96/29411;
International
Publication Number WO 94/12650; Koller et al., Proc. Natl. Acad. Sci. USA
86:8932-
8935 (1989); and Zijlstra et al., Nature 342:435-438 (1989), the disclosures
of each of
which are incorporated by reference in their entireties).
[0170] Polypeptides of the present invention can also be recovered from:
products
purified from natural sources, including bodily fluids, tissues and cells,
whether
directly isolated or cultured; products of chemical synthetic procedures; and
products
produced by recombinant techniques from a prokaryotic or eukaryotic host,
including,
for example, bacterial, yeast, higher plant, insect, and mammalian cells.
Depending
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upon the host employed in a recombinant production procedure, the polypeptides
of
the present invention may be glycosylated or may be non-glycosylated. In
addition,
polypeptides of the invention may also include an initial modified methionine
residue,
in some cases as a result of host-mediated processes. Thus, it is well known
in the art
that the N-terminal methionine encoded by the translation initiation codon
generally is
removed with high efftciency from any protein after translation in all
eukaryotic cells.
While the N-terminal.methionine on most proteins also is efficiently removed
in most
prokaryotes, for some proteins, this prokaryotic removal process is
inefficient,
depending on the nature of the amino acid to which the N-terminal methionine
is
covalently linked.
[0171] In one embodiment, the yeast Pichia pastoris is used to express
polypeptides of the invention in a eukaryotic system. Piclaia pastoris is a
methylotrophic yeast which can metabolize methanol as its sole carbon source.
A
main step in the methanol metabolization pathway is the oxidation of methanol
to
formaldehyde using O2. This reaction is catalyzed by the enzyme alcohol
oxidase. In
order to metabolize methanol as its sole carbon source, Pichia pasto~is must
generate
high levels of alcohol oxidase due, in part, to the relatively low affinity of
alcohol
oxidase for 02. Consequently, in a growth medium depending on methanol as a
main
carbon source, the promoter region of one of the two alcohol oxidase genes
(AOXI ) is
highly active. In the presence of methanol, alcohol oxidase produced from the
AOXI
gene comprises up to approximately 30% of the total soluble protein in Pichia
pastoris. See, Ellis, S.B., et al., Mol. Cell. Biol. 5:1111-21 (1985); I~outz,
P.J, et al.,
Yeast 5:167-77 (1989); Tschopp, J.F., et al., Nucl. Acids Res. 15:3859-76
(1987).
Thus, a heterologous coding sequence, such as, for example, a polynucleotide
of the
present invention, under the transcriptional regulation of all or part of the
AOXI
regulatory sequence is expressed at exceptionally high levels in Pichia yeast
grown in
the presence of methanol.
[0172] In one example, the plasmid vector pPIC9K is used to express DNA
encoding a polypeptide of the invention, as set forth herein, in a Pichea
yeast system
essentially as described in "Piclaia Protocols: Methods in Molecular Biology,"
D.R.
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Higgins and J. Cregg, eds. The Humana Press, Totowa, NJ, 1998. This expression
vector allows expression and secretion of a polypeptide of the invention by
virtue of
the strong AOXI promoter linked to the Pichia pastoJ°is alkaline
phosphatase (PHO)
secretory signal peptide (i.e., leader) located upstream of a multiple cloning
site.
[0173] Many other yeast vectors could be used in place of pPIC9K, such as,
pYES2, pYDl, pTEFl/Zeo, pYES2/GS, pPICZ, pGAPZ, pGAPZalpha, pPIC9,
pPIC3.5, pHIL-D2, PHIL-S1, pPIC3.5K, and PA0815, as one skilled in the art
would
readily appreciate, as long as the proposed expression construct provides
appropriately
located signals for transcription, translation, secretion (if desired), and
the like,
including an in-frame AUG as required.
[0174] In another embodiment, high-level expression of a heterologous coding
sequence, such as, for example, a polynucleotide of the present invention, may
be
achieved by cloning the heterologous polynucleotide of the invention into an
expression vector such as, for example, pGAPZ or pGAPZalpha, and growing the
yeast culture in the absence of methanol.
[0175] In addition to encompassing host cells containing the vector constructs
discussed herein, the invention also encompasses primary, secondary, and
immortalized host cells of vertebrate origin, particularly mammalian origin,
that have
been engineered to delete or replace endogenous genetic material (e.g., coding
sequence), and/or to include genetic material (e.g., heterologous
polynucleotide
sequences) that is operably associated with polynucleotides of the invention,
and
which activates, alters, and/or amplifies endogenous polynucleotides. For
example,
techniques known in the art may be used to operably associate heterologous
control
regions (e.g., promoter and/or enhancer) and endogenous polynucleotide
sequences
via homologous recombination (see, e.g., U.S. Patent No. 5,641,670, issued
June 24,
1997; International Publication No. WO 96/29411, published September 26, 1996;
International Publication No. WO 94/12650, published August 4, 1994; Koller et
al.,
Proc. Natl. Acad. Sci. USA 86:8932-8935 (1989); and Zijlstra et al., Nature
342:435-
438 (1989), the disclosures of each of which are incorporated by reference in
their
entireties).
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[0176] In addition, polypeptides of the invention can be chemically
synthesized
using techniques lalown in the art (e.g., see Creighton, 1983, Proteins:
Structures and
Molecular Principles, W.H. Freeman & Co., N.Y., and Hunkapiller et al.,
Natuf°e,
310:105-111 (1984)). For example, a polypeptide corresponding to a fragment of
a
polypeptide can be synthesized by use of a peptide synthesizer. Furthermore,
if
desired, nonclassical amino acids or chemical amino acid analogs can be
introduced as
a .substitution or addition into the polypeptide sequence. Non-classical amino
acids
include, but are not limited to, to the D-isomers of the common amino acids,
2,4-
diaminobutyric acid, a-amino isobutyric acid, 4-aminobutyric acid, Abu, 2-
amino
butyric acid, g-Abu, e-Ahx, 6-amino hexanoic acid, Aib, 2-amino isobutyric
acid,
3-amino propionic acid, ornithine, norleucine, norvaline, hydroxyproline,
sarcosine,
citrulline, homocitrulline, cysteic acid, t-butylglycine, t-butylalanine,
phenylglycine,
cyclohexylalanine, b-alanine, fluoro-amino acids, designer amino acids such as
b-
methyl amino acids, Ca-methyl amino acids, Na-methyl amino acids, and amino
acid
analogs in general. Furthermore, the amino acid can be D (dextrorotary) or L
(levorotary).
[0177] The invention encompasses polypeptides of the present invention which
are
differentially modified during or after translation, e.g., by glycosylation,
acetylation,
phosphorylation, amidation, derivatization by known protecting/blocking
groups,
proteolytic cleavage, linkage to an antibody molecule or other cellular
ligand, etc.
Any of numerous chemical modifications may be carried out by known techniques,
including but not limited, to specific chemical cleavage by cyanogen bromide,
trypsin,
chymotrypsin, papain, V8 protease, NaBH4; acetylation, formylation, oxidation,
reduction; metabolic synthesis in the presence of tunicamycin; etc.
[0178] Additional post-translational modifications encompassed by the
invention
include, for example, e.g., N-linked or O-linked carbohydrate chains,
processing of
N-terminal or C-terminal ends), attachment of chemical moieties to the amino
acid
backbone, chemical modifications of N-linked or O-linked carbohydrate chains,
and
addition or deletion of an N-terminal methionine residue as a result of
procaryotic host
cell expression. The polypeptides may also be modified with a detectable
label, such
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as an enzymatic, fluorescent, isotopic or affinity label to allow for
detection and
isolation of the protein.
[0179] Examples of suitable enzymes include horseradish peroxidase, alkaline
phosphatase, beta-galactosidase, or acetylcholinesterase; examples of suitable
prosthetic group complexes include streptavidin/biotin and avidin/biotin;
examples of
suitable fluorescent materials include umbelliferone, fluorescein, fluorescein
isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein; dansyl chloride
or
phycoerythrin; an example of a luminescent material includes luminol; examples
of
bioluminescent materials include luciferase, luciferin, and aequorin; and
examples of
suitable radioactive material include iodine (lzlh lzsh lzsh 131I)~. carbon
(14C), sulfur
(3sS), tritium (3H), indium (111In' 112In' 113mIn' 115mIn), technetium
(99TC,99mTC),
thallium (zolTi), gallium (68Ga, 6~Ga), palladium (lo3Pd), molybdenum (99Mo),
xenon
(133xe) fluorine (18F) ls3sm l~~Lu ls9Gd 149P1n 140La 17s~ 166H~ 90Y 47SC
186Re
> > > > > > > > > > > >
lssRe~ l4zPr~ lose and g~Ru.
[0180] In specific embodiments, a polypeptide of the present invention or
fragment or variant thereof is attached to macrocyclic chelators that
associate with
radiometal ions, including but not limited to, l~~Lu, 9oY, 166Ho, and lsssm,
to
polypeptides. In a preferred embodiment, the radiometal ion associated with
the
macrocyclic chelators is 111In. In another preferred embodiment, the
radiometal ion
associated with the macrocyclic chelator is 9°Y. In specific
embodiments, the
macrocyclic chelator is 1,4,7,10-tetraazacyclododecane-N,N',N",N"'-tetraacetic
acid
(DOTA). In other specific embodiments, DOTA is attached to an antibody of the
invention or fragment thereof via a linker molecule. Examples of linker
molecules
useful for conjugating DOTA to a polypeptide are commonly known in the art -
see,
for example, DeNardo et al., Clin Cancer Res. 4(10):2483-90 (1998); Peterson
et al.,
Bioconjug. Chem. 10(4):553-7 (1999); and Zimmerman et al, Nucl. Med. Biol.
26(8):943-50 (1999); which are hereby incorporated by reference in their
entirety.
[0181] As mentioned, the prostate cancer associated proteins of the invention
may
be modified by either natural processes, such as posttranslational processing,
or by
chemical modification techniques which are well known in the art. It will be
appreciated that the same type of modification may be present in the same or
varying
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degrees at several sites in a given prostate cancer associated polypeptide.
Prostate
cancer associated polypeptides may be branched, for example, as a result of
ubiquitination, and they may be cyclic, with or without branching. Cyclic,
branched,
and branched cyclic prostate cancer associated polypeptides may result from
posttranslation natural processes or may be made by synthetic methods.
Modifications
include acetylation, acylation, ADP-ribosylation, amidation, covalent
attachment of
flavin, covalent attachment of a heme moiety, covalent attachment of a
nucleotide or
nucleotide derivative, covalent attachment of a lipid or lipid derivative,
covalent
attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond
formation, demethylation, formation of covalent cross-links, formation of
cysteine,
formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation,
GPI
anchor formation, hydroxylation, iodination, methylation, myristoylation,
oxidation,
pegylation, proteolytic processing, phosphorylation, prenylation,
racemization,
selenoylation, sulfation, transfer-RNA mediated addition of amino acids to
proteins
such as arginylation, and ubiquitination. (See, for instance, PROTEINS -
STRUCTURE AND MOLECULAR PROPERTIES, 2nd Ed., T. E. Creighton, W.
H. Freeman and Company, New York (1993); POSTTRANSLATIONAL
COVALENT MODIFICATION OF PROTEINS, B. C. Johnson, Ed., Academic
Press, New York, pgs. 1-12 (1983); Seifter et al., Meth. Enzymol. 182:626-646
(1990);
Rattan et al., Ann. N.Y. Acad. Sci. 663:48-62 (1992)).
[0182] Also provided by the invention are chemically modified derivatives of
the
polypeptides of the invention which may provide additional advantages such as
increased solubility, stability and circulating time of the polypeptide, or
decreased
immunogenicity (see U.S. Patent No. 4,179,337). The chemical moieties for
derivitization may be selected from water soluble polymers such as
polyethylene
glycol, ethylene glycol/propylene glycol copolymers, carboxymethylcellulose,
dextran, polyvinyl alcohol and the like. The polypeptides may be modified at
random
positions within the molecule, or at predetermined positions within the
molecule and
may include one, two, three or more attached chemical moieties.
[0183] The polymer may be of any molecular weight, and may be branched or
unbranched. For polyethylene glycol, the preferred molecular weight is between
about
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1 lcDa and about 100 kDa (the term "about" indicating that in preparations of
polyethylene glycol, some molecules will weigh more, some less, than the
stated
molecular weight) for ease in handling and manufacturing. Other sizes may be
used,
depending on the desired therapeutic profile (e.g., the duration of sustained
release
desired, the effects, if any on biological activity, the ease in handling, the
degree or
lack of antigenicity and other known effects of the polyethylene glycol to a
therapeutic
protein or analog). For example, the polyethylene glycol may have an average
molecular weight of about 200, 500, 1000, 1500, 2000, 2500, 3000, 3500, 4000,
4500,
5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000, 9500, 10,000, 10,500,
11,000,
11,500, 12,000, 12,500, 13,000, 13,500, 14,000, 14,500, 15,000, 15,500,
16,000,
16,500, 17,000, 17,500, 18,000, 18,500, 19,000, 19,500, 20,000, 25,000,
30,000,
35,000, 40,000, 50,000, 55,000, 60,000, 65,000, 70,000, 75,000, 80,000,
85,000,
90,000, 95,000, or 100,000 kDa.
[0184] As noted above, the polyethylene glycol may have a branched structure.
Branched polyethylene glycols are described, for example, in U.S. Patent No.
5,643,575; Morpurgo et al., Appl. Biochem. Biotechnol. 56:59-72 (1996);
Vorobjev et
al., Nucleosides Nucleotides 18:2745-2750 (1999); and Caliceti et al.,
Bioconjug.
Chem. 10:638-646 (1999), the disclosures of each of which are incorporated
herein by
reference.
[0185] The polyethylene glycol molecules (or other chemical moieties) should
be
attached to the protein with consideration of effects on functional or
antigenic domains
of the protein. There are a number of attachment methods available to those
skilled in
the art, such as, for example, the method disclosed in EP 0 401 384 (coupling
PEG to
G-CSF), herein incorporated by reference; see also Malik et al., Exp. Hematol.
20:1028-1035 (1992), reporting pegylation of GM-CSF using tresyl chloride. For
example, polyethylene glycol may be covalently bound through amino acid
residues
via a reactive group, such as a free amino or carboxyl group. Reactive groups
are
those to which an activated polyethylene glycol molecule may be bound. The
amino
acid residues having a free amino group may include lysine residues and the
N-terminal amino acid residues; those having a free carboxyl group may include
aspartic acid residues glutamic acid residues and the C-terminal amino acid
residue.
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Sulfllydryl groups may also be used as a reactive group for attaching the
polyethylene
glycol molecules. Preferred for therapeutic purposes is attachment at an amino
group,
such as attachment at the N-terminus or lysine group.
[0186] As suggested above, polyethylene glycol may be attached to proteins
via linkage to any of a number of amino acid residues. For example;
polyethylene
glycol can be linked to proteins via covalent bonds to .lysine, histidine,
aspartic acid,
glutamic acid, or cysteine residues. One or more reaction chemistries may be
employed to attach polyethylene glycol to specific amino acid residues (e.g.,
lysine,
histidine, aspartic acid, glutamic acid, or cysteine) of the protein or to
more than one
type of amino acid residue (e.g., lysine, histidine, aspartic acid, glutamic
acid, cysteine
and combinations thereof) of the protein.
[0187] One may specifically desire proteins chemically modified at the
N-terminus. Using polyethylene glycol as an illustration of the present
composition,
one may select from a variety of polyethylene glycol molecules (by molecular
weight,
branching, etc.), the proportion of polyethylene glycol molecules to protein
(polypeptide) molecules in the reaction mix, the type of pegylation reaction
to be
performed, and the method of obtaining the selected N-terminally pegylated
protein.
The method of obtaining the N-terminally pegylated preparation (i.e.,
separating this
moiety from other monopegylated moieties if necessary) maybe by purification
of the
N-terminally pegylated material from a population of pegylated protein
molecules.
Selective proteins chemically modified at the N-terminus modification may be
accomplished by reductive alkylation which exploits differential reactivity of
different
types of primary amino groups (lysine versus the N-terminal) available for
derivatization in a particular protein. Under the appropriate reaction
conditions,
substantially selective derivatization of the protein at the N-terminus with a
carbonyl
group containing polymer is achieved.
[0188] As indicated above, pegylation of the proteins of the invention may be
accomplished by any number of means. For example, polyethylene glycol may be
attached to the protein either directly or by an intervening linker.
Linlcerless systems
for attaching polyethylene glycol to proteins are described in Delgado et al.,
Crit. Rev.
Thera. Drug Carrier Sys. 9:249-304 (1992); Francis et al., Intern. J. of
Hematol. 68:1-
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18 (1998); U.S. Patent No. 4,002,531; U.S. Patent No. 5,349,052; WO 95/06058;
and
WO 98/32466, the disclosures of each of which are incorporated herein by
reference.
[0189] One system for attaching polyethylene glycol directly to amino acid
residues of proteins without an intervening linker employs tresylated MPEG,
which is
produced by the modification of monmethoxy polyethylene glycol (MPEG) using
tresylchloride (C1SOZCH2CF3). Upon reaction of protein with tresylated MPEG,
polyethylene glycol is directly attached to amine groups of the protein. Thus,
the
invention includes protein-polyethylene glycol conjugates produced by reacting
proteins of the invention with a polyethylene glycol molecule having a
2,2,2-trifluoreothane sulphonyl group.
[0190] Polyethylene glycol can also be attached to proteins using a number of
different intervening linkers. For example, U.S. Patent No. 5,612,460, the
entire
disclosure of which is incorporated herein by reference, discloses urethane
linkers for
connecting polyethylene glycol to proteins. Protein-polyethylene glycol
conjugates
wherein the polyethylene glycol is attached to the protein by a linker can
also be
produced by reaction of proteins with compounds such as MPEG-
succinimidylsuccinate, MPEG activated with 1,1'-carbonyldiimidazole, MPEG-
2,4,5-trichloropenylcarbonate, MPEG-p-nitrophenolcarbonate, and .various MPEG-
succinate derivatives. A number of additional polyethylene glycol derivatives
and
reaction chemistries for attaching polyethylene glycol to proteins are
described in
International Publication No. WO 98/32466, the entire disclosure of which is
incorporated herein by reference. Pegylated protein products produced using
the
reaction chemistries set out herein are included within the scope of the
invention.
(0191] The number of polyethylene glycol moieties attached to each protein of
the
invention (i.e., the degree of substitution) may also vary. For example, the
pegylated
proteins of the invention may be linked, on average, to 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 12,
15, 17, 20, or more polyethylene glycol molecules. Similarly, the average
degree of
substitution within ranges such as 1-3, 2-4, 3-5, 4-6, 5-7, 6-8, 7-9, 8-10, 9-
11, 10-12,
11-13, 12-14, 13-15, 14-16, 15-17, 16-18, 17-19, or 18-20 polyethylene glycol
moieties per protein molecule. Methods for determining the degree of
substitution are
discussed, for example, in Delgado et al., Crit. Rev. Thera. Drug Carrier Sys.
9:249-
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304 (1992).
[0192] The prostate cancer associated polypeptides of the invention can be
recovered and purified from chemical synthesis and recombinant cell cultures
by
standard methods which include, but are not limited to, ammonium sulfate or
ethanol
precipitation, acid extraction, anion or canon- exchange chromatography,
phosphocellulose chromatography, hydrophobic interaction chromatography,
affinity
chromatography, hydroxylapatite chromatography and lectin chromatography. Most
preferably, high performance liquid chromatography ("HPLC") is employed for
purification. Well known techniques for refolding protein may be employed to
regenerate active conformation when the polypeptide is denatured during
isolation
and/or purification.
[0193] Prostate cancer associated polynucleotides and polypeptides may be used
in
accordance with the present invention for a variety of applications,
particularly those
that make use of the chemical and biological properties of prostate cancer
associated
antigens. Among these are applications in the detection, prevention, diagnosis
and/or
treatment of diseases associated with the prostate, such as e.g., prostate
cancers such as
adenocarcinoma, transitional cell carcinomas, ductal carcinomas, and squamous
cell
carcinomas, and as described under "Hyperproliferative Disorders" and/or
"Reproductive System Disorders" below. Additional applications relate to
diagnosis
and to treatment of disorders of cells, tissues and organisms. These aspects
of the
invention are discussed further below.
[0194] In a preferred embodiment, polynucleotides expressed in a particular
tissue
type are used to detect, diagnose, treat, prevent and/or prognose disorders
associated
with the tissue type.
[0195] The polypeptides of the invention may be in monomers or multimers
(i.e.,
dimers, trimers, tetramers and higher multimers). Accordingly, the present
invention
relates to monomers and multimers of the polypeptides of the invention, their
preparation, and compositions (preferably, Therapeutics) containing them. In
specific
embodiments, the polypeptides of the invention are monomers, dimers, trimers
or
tetramers. In additional embodiments, the multimers of the invention are at
least
dimers, at least trimers, or at least tetramers.
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[0196] Multimers encompassed by the invention may be homomers or heteromers.
As used herein, the term homomer refers to a multimer containing only
polypeptides
corresponding to a protein of the invention (e.g., the amino acid sequence of
SEQ ID
NO:Y, an amino acid sequence encoded by SEQ ID NO:X or the complement of SEQ
ID NO:X, the amino acid sequence encoded by the portion of SEQ ID NO:X as.
defined in columns 8 and 9 of Table 2, and/or an amino acid sequence encoded
by
cDNA contained in Clone ID NO:Z (including fragments, variants, splice
variants, and
fusion proteins, corresponding to these as described herein)). These homomers
may
contain polypeptides having identical or different amino acid sequences. In a
specific
embodiment, a homomer of the invention is a multimer containing only
polypeptides
having an identical amino acid sequence. In another specific embodiment, a
homomer
of the invention is a multimer containing polypeptides having different amino
acid
sequences. In specific embodiments, the multimer of the invention is a
homodimer
(e.g., containing two polypeptides having identical or different amino acid
sequences)
or a homotrimer (e.g., containing three polypeptides having identical and/or
different
amino acid sequences). In additional embodiments, the homomeric multimer of
the
invention is at least a homodimer, at least a homotrimer, or at least a
homotetramer.
[0197] As used herein, the term heteromer refers to a multimer containing two
or
more heterologous polypeptides (i.e., polypeptides of different proteins) in
addition to
the polypeptides of the invention. In a specific embodiment, the multimer of
the
invention is a heterodimer, a heterotrimer, or a heterotetramer. In additional
embodiments, the heteromeric multimer of the invention is at least a
heterodimer, at
least a heterotrimer, or at least a heterotetramer.
[0198] Multimers of the invention may be the result of hydrophobic,
hydrophilic,
ionic and/or covalent associations and/or may be indirectly linked by, for
example,
liposome formation. Thus, in one embodiment, multimers of the invention, such
as,
for example, homodimers or homotrimers, are formed when polypeptides of the
invention contact one another in solution. In another embodiment,
heteromultimers of
the invention, such as, for example, heterotrimers or heterotetramers, are
formed when
polypeptides of the invention contact antibodies to the polypeptides of the
invention
(including antibodies to the heterologous polypeptide sequence in a fusion
protein of
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the invention) in solution. In other embodiments, multimers of the invention
are
formed by covalent associations with and/or between the polypeptides of the
invention. Such covalent associations may involve one or more amino acid
residues
contained in the polypeptide sequence (e.g., that recited in SEQ ID NO:Y,
encoded by
the portion of SEQ ID NO:X as defined in columns 8 and 9 of Table 2, andlor
encoded
by the cDNA contained in Clone ID NO:Z). In one instance, the covalent
associations
are cross-linking between cysteine residues located within the polypeptide
sequences
which interact in the native (i.e., naturally occurring) polypeptide. In
another instance,
the covalent associations are the consequence of chemical or recombinant
manipulation. Alternatively, such covalent associations may involve one or
more
amino acid residues contained in the heterologous polypeptide sequence in a
fusion
protein. In one example, covalent associations are between the heterologous
sequence
contained in a fusion protein of the invention (see, e.g., U.S. Patent Number
5,478,925). In a specific example, the covalent associations are between the
heterologous sequence contained in a Fc fusion protein of the invention (as
described
herein). In another specific example, covalent associations of fusion proteins
of the
invention are between heterologous polypeptide sequence from another protein
that is
capable of forming covalently associated multimers, such as for example,
osteoprotegerin (see, e.g., International, Publication NO: WO 98/49305, the
contents of
which are herein incorporated by reference in its entirety). In another
embodiment,
two or more polypeptides of the invention are joined through peptide Linkers.
Examples include those peptide linkers described in U.S. Pat. No. 5,073,627
(hereby
incorporated by reference). Proteins comprising multiple polypeptides of the
invention
separated by peptide linkers may be produced using conventional recombinant
DNA
technology.
[0199] Another method for preparing multimer polypeptides of the invention
involves use of polypeptides of the invention fused to a leucine zipper or
isoleucine
zipper polypeptide sequence. Leucine zipper and isoleucine zipper domains are
polypeptides that promote multimerization of the proteins in which they are
found.
Leucine zippers were originally identified in several DNA-binding proteins
(Landschulz et al., Science 240:1759, (1988)), and have since been found in a
variety
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of different proteins. Among the known leucine zippers axe naturally occurring
peptides and derivatives thereof that dimerize or trimerize. Examples of
leucine zipper
domains suitable for producing soluble multimeric proteins of the invention
are those
described in PCT application WO 94/10308, hereby incorporated by reference.
Recombinant fusion proteins comprising a polypeptide of the invention fused to
a
polypeptide sequence that dimerizes or trimerizes in solution are expressed in
suitable
host cells, and the resulting soluble multimeric fusion protein is recovered
from the
culture supernatant using techniques known in the art.
[0200] Trimeric polypeptides of the invention may offer the advantage of
enhanced biological activity. Preferred leucine zipper moieties and isoleucine
moieties are those that preferentially form trimers. One example is a leucine
zipper
derived from lung surfactant protein D (SPD), as described in Hoppe et al.
(FEBS
Letters 344:191, (1994)) and in U.S. patent application Ser. No. 08/446,922,
hereby
incorporated by reference. Other peptides derived from naturally occurring
trimeric
proteins may be employed in preparing trimeric polypeptides of the invention.
[0201] In another example, proteins of the invention are associated by
interactions
between Flag~ polypeptide sequence contained in fusion proteins of the
invention
containing Flag~ polypeptide sequence: In a further embodiment, proteins of
the
invention are associated by interactions between heterologous polypeptide
sequence
contained in Flag~ fusion proteins of the invention and anti-Flag~ antibody.
[0202j The multimers of the invention may be generated using chemical
techniques known in the art. For example, polypeptides desired to be contained
in the
multimers of the invention may be chemically cross-linked using linker
molecules and
linker molecule length optimization techniques known in the art (see, e.g.,
U.S. Patent
Number 5,478,925, which is herein incorporated by reference in its entirety).
Additionally, multimers of the invention may be generated using techniques
known in
the art to form one or more inter-molecule cross-links between the cysteine
residues
located within the sequence of the polypeptides desired to be contained in the
multimer (see, e.g., U.S. Patent Number 5,478,925, which is herein
incorporated by
reference in its entirety). Further, polypeptides of the invention may be
routinely
modif ed by the addition of cysteine or biotin to the C-terminus or N-terminus
of the
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polypeptide and techniques known in the art may be applied to generate
multimers
containing one or more of these modified polypeptides (see, e.g., U.S. Patent
Number
5,478,925, which is herein incorporated by reference in its entirety).
Additionally,
techniques known in the art may be applied to generate liposomes containing
the
polypeptide components desired to be contained in the multimer of the
invention (seep
e.g., U.S. Patent Number 5,478,925, which is herein incorporated by reference
in its
entirety).
[0203] Alfiernatively, multimers of the invention may be generated using
genetic
engineering techniques known in the art. In one embodiment, polypeptides
contained
in multimers of the invention are produced recombinantly using fusion protein
technology described herein or otherwise known in the art (see, e.g., U.S.
Patent
Number 5,478,925, which is herein incorporated by reference in its entirety).
In a
specific embodiment, polynucleotides coding for a homodimer of the invention
are
generated by ligating a polynucleotide sequence encoding a polypeptide of the
invention to a sequence encoding a linker polypeptide and then further to a
synthetic
polynucleotide encoding the translated product of the polypeptide in the
reverse
orientation from the original C-terminus to the N-terminus (laclcing the
leader
sequence) (see, e.g., .U..S Patent Number 5,478,925, which is herein
incorporated by
reference in its entirety). In another embodiment, recombinant techniques
described
herein or otherwise known in the art are applied to generate recombinant
polypeptides
of the invention which contain a transmembrane domain (or hydrophobic or
signal
peptide) and which can be incorporated by membrane reconstitution techniques
into
liposomes (see, e.g., U.S. Patent Number 5,478,925, which is herein
incorporated by
reference in its entirety).
Antibodies
[0204] Further polypeptides of the invention relate to antibodies and T-cell
antigen
receptors (TCR) which immunospecifically bind a polypeptide, polypeptide
fragment,
or variant of the invention (e.g., a polypeptide or fragment or variant of the
amino acid
sequence of SEQ ID NO:Y or a polypeptide encoded by the cDNA contained in
Clone
ID NO:Z, and/or an epitope, of the present invention) as determined by
immunoassays
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well known in the art for assaying specific antibody-antigen binding.
Antibodies of
the invention include, but are not limited to, polyclonal, monoclonal,
multispecific,
human, humanized or chimeric antibodies, single chain antibodies, Fab
fragments,
F(ab') fragments, fragments produced by a Fab expression library, anti-
idiotypic
(anti-Id) antibodies (including, e.g., anti-Id antibodies to antibodies of the
invention),
intracellularly-made antibodies (i.e., intrabodies), and epitope-binding
fragments of
any of the above. The term "antibody," as used herein, refers to
immunoglobulin
molecules and immunologically active portions of immunoglobulin molecules,
i.e.,
molecules that contain an antigen binding site that immunospecifically binds
an
antigen. The immunoglobulin molecules of the invention can be of any type
(e.g.,
IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., IgGl, IgG2, IgG3, IgG4, IgA1
and
IgA2) or subclass of immunoglobulin molecule. In preferred embodiments, the
immunoglobulin molecules of the invention are IgGl. In other preferred
embodiments, the immunoglobulin molecules of the invention are IgG4.
[0205] Most preferably the antibodies are human antigen-binding antibody
fragments of the present invention and include, but are not limited to, Fab,
Fab' and
F(ab')2, Fd, single-chain Fvs (scFv), single-chain antibodies, disulfide-
linked Fvs
(sdFv) and fragments comprising either a VL or VH domain. Antigen-binding
antibody fragments, including single-chain antibodies, may comprise the
variable
regions) alone or in combination with the entirety or a portion of the
following: hinge
region, CH1, CH2, and CH3 domains. Also included in the invention are antigen-
binding fragments also comprising any combination of variable regions) with a
hinge
region, CH1, CH2, and CH3 domains. The antibodies of the invention may be from
any animal origin including birds and mammals. Preferably, the antibodies are
human,
marine (e.g., mouse and rat), donkey, ship rabbit, goat, guinea pig, camel,
horse, or
chicken. As used herein, "human" antibodies include antibodies having the
amino
acid sequence of a human immunoglobulin and include antibodies isolated from
human immunoglobulin libraries or from animals transgenic for one or more
human
immunoglobulin and that do not express endogenous immunoglobulins, as
described
infra and, for example in, U.S. Patent No. 5,939,598 by Kucherlapati et al.
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[0206] The antibodies of the present invention may be monospecific,
bispecific,
trispecific or of greater multispecificity. Multispecific antibodies may be
specific for
different epitopes of a polypeptide of the present invention or may be
specific for both
a polypeptide of the present invention as well as for a heterologous epitope,
such as a
heterologouspolypeptide or solid support material. See, e.g.; PCT publications
WO
93/17715; WO 92/08802; WO 91/00360; WO 92/05793; Tutt, et al:; J. Immunol.
147:60-69 (1991); U.S. Patent Nos. 4,474,893; 4,714,681; 4,925,648; 5,573,920;
5,601,819; I~.ostelny et al., J. Immunol. 148:1547-1553 (1992).
[0207] Antibodies of the present invention may be described or specified in
terms
of the epitope(s) or portions) of a polypeptide of the present invention which
they
recognize or specifically bind. The epitope(s) or polypeptide portions) may be
specified as described herein, e.g., by N-terminal and C-terminal positions,
or by size
in contiguous amino acid residues, or listed in the Tables and Figures.
Preferred
epitopes of the invention include those shown in column 6 of Table 1A, as well
as
polynucleotides that encode these epitopes. Antibodies, which specifically
bind any
epitope or polypeptide of the present invention may also be excluded.
Therefore, the
present invention includes antibodies that specifically bind polypeptides of
the present
invention, and allows for the exclusion of the same.
[0208] Antibodies of the present invention may also be described or specified
in
terms of their cross-reactivity. Antibodies that do not bind any other analog,
ortholog,
or homolog of a polypeptide of the present invention are included. Antibodies
that
bind polypeptides with at least 95%, at least 90%, at least 85%, at least 80%,
at least
75%, at least 70%, at least 65%, at least 60%, at least 55%, and at least 50%
identity
(as calculated using methods known in the art and described herein) to a
polypeptide
of the present invention are also included in the present invention. In
specific
embodiments, antibodies of the present invention cross-react with marine, rat
and/or
rabbit homologs of human proteins and the corresponding epitopes thereof.
Antibodies
that do not bind polypeptides with less than 95%, less than 90%, less than
85%, less
than 80%, less than 75%, less than 70%, less than 65%, less than 60%, less
than 55%,
and less than 50% identity (as calculated using methods known in the art and
described herein) to a polypeptide of the present invention are also included
in the
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present invention. In a specific embodiment, the above-described cross-
reactivity is
with respect to any single specific antigenic or immunogenic polypeptide, or
combinations) of 2, 3, 4, 5, or more of the specific antigenic and/or
immunogenic
polypeptides disclosed herein. Further included in the present invention are
antibodies
which bind polypeptides encoded by polynucleotides which hybridize to a
polynucleotide of the present invention under stringent hybridization
conditions (as
described herein). Antibodies of the present invention may also be described
or
specified in terms of their binding affinity to a polypeptide of the
invention. Preferred
binding affinities include those with a dissociation constant or I~d less than
5 X 10-2
M, 10-2 M, 5 X 10-3 M, 10-3 M, 5 X 104 M, 10-4 M, 5 X 10-5 M, 10-5 M, 5 X 10-6
M,
10-6M, 5 X 10-~ M, 10' M, 5 X 10-g M, 10-8 M, 5 X 10-9 M, 10-9 M, 5 X 10-
1° M, 10-10
M, 5 X IO-11 M, IO-11 M, 5 X 10-12 M, I0~12 M, 5 X IO-13 M, 1O-13 M, 5 X 10-14
M, 10-
14 M, 5 X 10-15 M, or 10-15 M.
[0209] The invention also provides antibodies that competitively inhibit
binding of
an antibody to an epitope of the invention as determined by any method known
in the
art for determining competitive binding, for example, the immunoassays
described
herei-n. In preferred embodiments, the antibody competitively inhibits binding
to the
epitope by at least 95%, at least 90%, at least 85 %, at least 80%, at least
75%, at least
70%, at least 60%, or at least 50%.
[0210] Antibodies of the present invention may act as agonists or antagonists
of
the polypeptides of the present invention. For example, the present invention
includes
antibodies which disrupt the receptor/ligand interactions with the
polypeptides of the
invention either partially or fully. Preferably, antibodies of the present
invention bind
an antigenic epitope disclosed herein, or a portion thereof. The invention
features both
receptor-specific antibodies and ligand-specific antibodies. The invention
also
features receptor-specific antibodies, which do not prevent ligand binding but
prevent
receptor activation. Receptor activation (i.e., signaling) may be determined
by
techniques described herein or otherwise known in the art. For example,
receptor
activation can be determined by detecting the phosphorylation (e.g., tyrosine
or
serine/threonine) of the receptor or its substrate by immunoprecipitation
followed by
western blot analysis (for example, as described supf°a). In specific
embodiments,
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antibodies are provided that inhibit ligand activity or receptor activity by
at least 95%,
at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least
60%, or at
least 50% of the activity in absence of the antibody.
[0211] The invention also features receptor-specific antibodies which both
prevent
ligand binding and receptor activation as well as antibodies that recognize
the .
receptor-ligand complex, and, preferably, do not specifically recognize the
unbound
receptor or the unbound ligand. Likewise, included in the invention are
neutralizing
antibodies which bind the ligand and prevent binding of the ligand to the
receptor, as
well as antibodies which bind the ligand, thereby preventing receptor
activation, but
do not prevent the ligand from binding the receptor. Further included in the
invention
are antibodies, which activate the receptor. These antibodies may act as
receptor
agonists, i.e., potentiate or activate either all or a subset of the
biological activities of
the ligand-mediated receptor activation, for example, by inducing dimerization
of the
receptor. The antibodies may be specified as agonists, antagonists or inverse
agonists
for biological activities comprising the specific biological activities of the
peptides of
the invention disclosed herein. The above antibody agonists can be made using
methods known in the art. See, e.g., PCT publication WO 96/40281; U.S. Patent
No.
5,811;097; Deng et al., Blood 92(6):1981-1988 (1998); Chen et al., Cancer Res.
58(16):3668-3678 (1998); Harrop et al.,.J. Immunol. 161(4):1786-1794 (1998);
Zhu et
al., Cancer Res. 58(15):3209-3214 (1998); Yoon et al., J. Immunol. 160(7):3170-
3179
(1998); Prat et al., J. Cell. Sci. 111(Pt2):237-247 (1998); Pitard et al., J.
Immunol.
Methods 205(2):177-190 (1997); Liautard et al., Cytokine 9(4):233-241 (1997);
Carlson et al., J. Biol. Chem. 272(17):11295-11301 (1997); Taryman et al.,
Neuron
14(4):755-762 (1995); Muller et al., Structure 6(9):1153-1167 (1998); Bartunek
et al.,
Cytolcine 8(1):14-20 (1996) (which are all incorporated by reference herein in
their
entireties).
[0212] Antibodies of the present invention may be used, for example, to
purify,
detect, and target the polypeptides of the present invention, including both
in vitro and
ifz vivo diagnostic and therapeutic methods. For example, the antibodies have
utility in
immunoassays for qualitatively and quantitatively measuring levels of the
polypeptides of the present invention in biological samples. See, e.g., Harlow
et al.,
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Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2nd ed.
1988); incorporated by reference herein in its entirety.
[0213] As discussed in more detail below, the antibodies of the present
invention
may be used either alone or in combination with other compositions. The
antibodies
may further be recombinantly fused to a heterologous polypeptide at the N- or
C-
terminus or chemically conjugated (including covalent and non-covalent
conjugations) to polypeptides or other compositions. For example, antibodies
of the
present invention may be recombinantly fused or conjugated to molecules useful
as
labels in detection assays and effector molecules such as heterologous
polypeptides,
drugs, radionuclides, or toxins. See, e.g., PCT publications WO 92/08495; WO
91/14438; WO 89/12624; U.S. Patent No. 5,314,995; and EP 396,387; the
disclosures
of which are incorporated herein by reference in their entireties.
[0214] The antibodies of the invention include derivatives that are modified,
i.e.,
by the covalent attachment of any type of molecule to the antibody such that
covalent
attachment does not prevent the antibody from generating an anti-idiotypic
response.
For example, but not by way of limitation, the antibody derivatives include
antibodies
that have been modified, e.g., by glycosylation, acetylation, pegylation,
phosphylation,
amidation, derivatization, by known protectinglblocking groups, proteolytic
cleavage,
linkage to a cellular ligand or other protein, etc. Any of numerous chemical
modifications may be carried out by known techniques, including, but not
limited to
specific chemical cleavage, acetylation, formylation, metabolic synthesis of
tunicamycin, etc. Additionally, the derivative may contain one or more non-
classical
amino acids.
[0215] The antibodies of the present invention may be generated by any
suitable
method known in the art. Polyclonal antibodies to an antigen-of interest can
be
produced by various procedures well known in the art. For example, a
polypeptide of
the invention can be administered to various host animals including, but not
limited to,
rabbits, mice, rats, etc. to induce the production of sera containing
polyclonal
antibodies specific for the antigen. Various adjuvants may be used to increase
the
immunological response, depending on the host species, and include but are not
limited to, Freund's (complete and incomplete), mineral gels such as aluminum
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hydroxide, surface active substances such as lysolecithin, pluronic polyols,
polyanions,
peptides, oil emulsions, keyhole limpet hemocyanins, dinitrophenol, and
potentially
useful human adjuvants such as BCG (bacille Calmette-Guerin) and
corynebacterium
parvum. Such adjuvants are also well known in the art.
[0216] Monoclonal antibodies can be prepared using a wide variety of
techniques
lcnown in the art including the use of hybridoma, recombinant, and phage
display
technologies, or a combination thereof. For example, monoclonal antibodies can
be
produced using hybridoma techniques including those known in the art and
taught, for
example, in Harlow et al., Antibodies: A Laboratory Manual, (Cold Spring
Harbor
Laboratory Press, 2nd ed. 1988); Hammerling, et al., in: Monoclonal Antibodies
and
T-Cell Hybridomas 563-681 (Elsevier, N.Y., 1981) (said references incorporated
by
reference in their entireties). The term "monoclonal antibody" as used herein
is not
limited to antibodies produced through hybridoma technology. The term
"monoclonal
antibody" refers to an antibody that is derived from a single clone, including
any
eukaryotic, prokaryotic, or phage clone, and not the method by which it is
produced.
[0217] Methods for producing and screening for specific antibodies using
hybridoma technology are routine and well known in the art and are discussed
in detail
in the Examples. In a non-limiting example, mice can be immunized with a
polypeptide of the invention or a cell expressing such peptide. Once an immune
response is detected, e.g., antibodies specific for the antigen are detected
in the mouse
serum, the mouse spleen is harvested and splenocytes isolated. The splenocytes
are
then fused by well known techniques to any suitable myeloma cells, for example
cells
from cell line SP20 available from the ATCC. Hybridomas are selected and
cloned by
limited dilution. The hybridoma clones are then assayed by methods known in
the art
for cells that secrete antibodies capable of binding a polypeptide of the
invention.
Ascites fluid, which generally contains high levels of antibodies, can be
generated by
immunizing mice with positive hybridoma clones.
[0218] Accordingly, the present invention provides methods of generating
monoclonal antibodies as well as antibodies produced by the method comprising
culturing a hybridoma cell secreting an antibody of the invention wherein,
preferably,
the hybridoma is generated by fusing splenocytes isolated from a mouse
immunized
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with an antigen of the invention with myeloma cells and then screening the
hybridomas resulting from the fusion for hybridoma clones that secrete an
antibody
able to bind a polypeptide of the invention.
[0219] Another well known method for producing both polyclonal and monoclonal
human B cell lines is transformation using Epstein Barr Virus (EBV). Protocols
for
generating EBV-transformed B cell lines are commonly known in the art, such
as, for
example, the protocol outlined in Chapter 7.22 of Current Protocols in
Immunology;
Coligan et al., Eds., 1994, John Wiley & Sons, NY, which is hereby
incorporated in its
entirety by reference herein. The source of B cells for transformation is
commonly
human peripheral blood, but B cells for transformation may also be derived
from other
sources including, but not limited to, lymph nodes, tonsil, spleen, tumor
tissue, and
infected tissues. Tissues are generally made into single cell suspensions
prior to EBV
transformation. Additionally, steps may be taken to either physically remove
or
inactivate T cells (e.g., by treatment with cyclosporin A) in B cell-
containing samples,
because T cells from individuals seropositive for anti-EBV antibodies can
suppress B
cell immortalization by EBV.
[0220] In general, the sample containing human B cells is innoculated with
EBV,
and cultured for 3-4 weeks. A typical source of EBV is the culture supernatant
of the
B95-8 cell line (ATCC #VR-1492). Physical signs of EBV transformation can
generally be seen towards the end of the 3-4 week culture period. By phase-
contrast
microscopy, transformed cells may appear large, clear, hairy and tend to
aggregate in
tight clusters of cells. Initially, EBV lines are generally polyclonal.
However, over
prolonged periods of cell cultures, EBV lines may become monoclonal or
polyclonal
as a result of the selective outgrowth of particular B cell clones.
Alternatively,
polyclonal EBV transformed lines may be subcloned (e.g., by limiting dilution
culture)
or fused with a suitable fusion partner and plated at limiting dilution to
obtain
monoclonal B cell lines. Suitable fusion partners for EBV transformed cell
lines
include mouse myeloma cell lines (e.g., SP2/0, X63-Ag8.653), heteromyeloma
cell
lines (human x mouse; e.g, SPAM-8, SBC-H20, and CB-F7), and human cell lines
(e.g., GM 1500, SKO-007, RPMI 8226, and KR-4). Thus, the present invention
also
provides a method of generating polyclonal or monoclonal human antibodies
against
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polypeptides of the invention or fragments thereof, comprising EBV-
transformation of
human B cells.
[0221] Antibody fragments, which recognize specific epitopes may be generated
by known techniques. For example, Fab and F(ab')2 fragments of the invention
may
be produced by proteolytic cleavage of immunoglobulin molecules, using enzymes
such as papain (to produce Fab fragments) or pepsin (to produce F(ab')2
fragments).
F(ab')2 fragments contain the variable region, the light chain constant region
and the
CHl domain of the heavy chain. For example, the antibodies of the present
invention can also be generated using various phage display methods known in
the art
and as discussed in detail in the Examples (e.g., Example 10). In phage
display
methods, functional antibody domains are displayed on the surface of phage
particles,
which carry the polynucleotide sequences encoding them. In a particular
embodiment,
such phage can be utilized to display antigen binding domains expressed from a
repertoire or combinatorial antibody library (e.g.,- human or murine). Phage
expressing an antigen binding domain that binds the antigen of interest can be
selected
or identified with antigen, e.g., using labeled antigen or antigen bound or
captured to a
solid surface or bead. Phage used in these methods are typically filamentous
phage
including fd and Ml3 binding domains expressed from phage with Fab, Fv or
disulfide
stabilized Fv antibody domains recombinantly fused to either the phage gene
III or
gene VIII protein. Examples of phage display methods that can be used to make
the
antibodies of the present invention include those disclosed in Brinkman et
al., J.
Immunol. Methods 182:41-50 (1995); Ames et al., J. Immunol. Methods 184:177-
186
(1995); Kettleborough et al., Eur. J. Immunol. 24:952-958 (1994); Persic et
al., Gene
187 9-18 (1997); Burton et al., Advances in Immunology 57:191-280 (1994); PCT
application No. PCT/GB91/OI134; PCT publications WO 90/02809; WO 91/10737;
WO 92/01047; WO 92/18619; WO 93/11236; WO 95/15982; WO 95/20401; and U.S.
Patent Nos. 5,698,426; 5,223,409; 5,403,484; 5,580,717; 5,427,908; 5,750,753;
5,821,047; 5,571,698; 5,427,908; 5,516,637; 5,780,225; 5,658,727; 5,733,743
and
5,969,108; each of which is incorporated herein by reference in its entirety.
[0222] As described in the above references, after phage selection, the
antibody
coding regions from the phage can be isolated and used to generate whole
antibodies,
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including human antibodies, or any other desired antigen binding fragment, and
expressed in any desired host, including mammalian cells, insect cells, plant
cells,
yeast, and bacteria, e.g., as described in detail below. For example,
techniques to
recombinantly produce Fab, Fab' and F(ab')2 fragments can also be employed
using
methods known in the art such as those disclosed in PGT publication WO
92/22324;
Mullinax et al., BioTechniques 12(6):864-869 (1992); and Sawai et al., AJRI
34:26-
34 (1995); and Better et al., Science 240:1041-1043 (1988) (said references
incorporated by reference in their entireties).
[0223] Examples of techniques which can be used to produce single-chain Fvs
and
antibodies include those described in U.S. Patents 4,946,778 and 5,258,498;
Huston et
al., Methods in Enzymology 203:46-88 (1991); Shu et al., PNAS 90:7995-7999
(1993); and Skerra et al., Science 240:1038-1040 (1988). For some uses,
including in
vivo use of antibodies in humans and in vitro detection assays, it may be
preferable to
use chimeric, humanized, or human antibodies. A chimeric antibody is a
molecule in
which different portions of the antibody are derived from different animal
species,
such as antibodies having a variable region derived from a murine monoclonal
antibody and a human immunoglobulin constant region. Methods for producing
chimeric antibodies are known in the art. See e.g., Morrison, Science 229:1202
(1985); Oi et al., BioTechniques 4:214 (1986); Gillies et al., (1989) J.
Immunol.
Methods 125:191-202; U.S. Patent Nos. 5,807,715; 4,816,567; and 4,816397,
which
are incorporated herein by reference in their entirety. Humanized antibodies
are
antibody molecules from non-human species antibody that binds the desired
antigen
having one or more complementarity determining regions (CDRs) from the non-
human species and a framework regions from a human immunoglobulin molecule.
Often, framework residues in the human framework regions will be substituted
with
the corresponding residue from the CDR donor antibody to alter, preferably
improve,
antigen binding. These framework substitutions are identified by methods well
known
in the art, e.g., by modeling of the interactions of the CDR and framework
residues to
identify framework residues important for antigen binding and sequence
comparison
to identify unusual framework residues at particular positions. (See, e.g.,
Queen et al.,
U.S. Patent No. 5,585,089; Riechmann et al., Nature 332:323 (1988), which are
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incorporated herein by reference in their entireties.) Antibodies can be
humanized
using a variety of techniques known in the art including, for example, CDR-
grafting
(EP 239,400; PCT publication WO 91/09967; U.S. Patent Nos. 5,225,539;
5,530,101;
and 5,585,089), veneering or resurfacing (EP 592,106; EP 519,596; Padlan,
Molecular
Immunology 28(4/5):489-498 (1991); Studnicka et al., Protein Engineering
7(6):805-
814 (1994); Roguska. et al., PNAS 91:969-973 (1994)), and chain shuffling
(U.5.
Patent No. 5,565,332).
[0224] Completely human antibodies are particularly desirable fox therapeutic
treatment of human patients. Human antibodies can be made by a variety of
methods
known in the art including phage display methods described above using
antibody
libraries derived from human immunoglobulin sequences. See also, U.S. Patent
Nos.
4,444,887 and 4,716,111; and PCT publications WO 98/46645, WO 98/50433, WO
98/24893, WO 98/16654, WO 96/34096, WO 96/33735, and WO 91/10741; each of
which is incorporated herein by reference in its entirety.
[0225] Human antibodies can also be produced using transgenic mice which are
incapable of expressing functional endogenous immunoglobulins, but which can
express human immunoglobulin genes. For example, the human heavy and light
chain
immunoglobulin gene complexes may be introduced randomly or by homologous
recombination into mouse embryonic stem cells. Alternatively, the human
variable
region, constant region, and diversity region may be introduced into mouse
embryonic
stem cells in addition to the human heavy and light chain genes. The mouse
heavy and
light chain immunoglobulin genes may be rendered non-functional separately or
simultaneously with the introduction of human immunoglobulin loci by
homologous
recombination. In particular, homozygous deletion of the JH region prevents
endogenous antibody production. The modified embryonic stem cells are expanded
and microinjected into blastocysts to produce chimeric mice. The chimeric mice
are
then bred to produce homozygous offspring, which express human antibodies. The
transgenic mice are immunized in the normal fashion with a selected antigen,
e.g., all
or a portion of a polypeptide of the invention. Monoclonal antibodies directed
against
the antigen can be obtained from the immunized, transgenic mice using
conventional
hybridoma technology. The human immunoglobulin transgenes harbored by the
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transgenic mice rearrange during B cell differentiation, and subsequently
undergo
class switching and somatic mutation. Thus, using such a technique, it is
possible to
produce therapeutically useful IgG, IgA, IgM and IgE antibodies. For an
overview of
this technology for producing human antibodies, see Lonberg and Huszar, Int.
Rev.
Immunol. 13:65-93 (1995). For a detailed discussion of this technology for
producing
human antibodies and human monoclonal antibodies and protocols for producing
such
antibodies, see, e.g., PCT publications WO 98/24893; WO 92/01047; WO 96/34096;
WO 96/33735; European Patent No. 0 598 877; U.S. Patent Nos. 5,413,923;
5,625,126; 5,633,425; 5,569,825; 5,661,016; 5,545,806; 5,814,318; 5,885,793;
5,916,771; 5,939,598; 6,075,181 and 6,114,598, which are incorporated by
reference
herein in their entirety. In addition, companies such as Abgenix, Inc.
(Freemont, CA)
and Genpharm (San Jose, CA) can be engaged to provide human antibodies
directed
against a selected antigen using technology similar to that described above.
[0226] Completely human antibodies which recognize a selected epitope can be
generated using a technique referred to as "guided selection." In this
approach a
selected non-human monoclonal antibody, e.g., a mouse antibody, is used to
guide the
selection of a completely human antibody recognizing the same epitope.
(Jespers et
al., Biotechnology 12:899-903 (1988)).
[0227] Further, antibodies to the polypeptides of the invention can, in turn,
be
utilized to generate anti-idiotype antibodies that "mimic" polypeptides of the
invention
using techniques well known to those skilled in the art. (See, e.g., Greenspan
& Bona,
FASEB J. 7(5):437-444; (1989) and Nissinoff, J. Immunoh. 147(8):2429-2438
(1991)). For example, antibodies which bind to and competitively inhibit
polypeptide
multimerization and/or binding of a polypeptide of the invention to a ligand
can be
used to generate anti-idiotypes that "mimic" the polypeptide multimerization
and/or
binding domain and, as a consequence, bind to and neutralize polypeptide
and/or its
ligand. Such neutralizing anti-idiotypes or Fab fragments of such anti-
idiotypes can be
used in therapeutic regimens to neutralize polypeptide ligand/receptor. For
example,
such anti-idiotypic antibodies can be used to bind a polypeptide of the
invention and/or
to bind its ligand(s)/receptor(s), and thereby block its biological activity.
Alternatively, antibodies which bind to and enhance polypeptide
multimerization
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and/or binding, and/or receptor/ligand multimerization, binding and/or
signaling can
be used to generate anti-idiotypes that function as agonists of a polypeptide
of the
invention and/or its ligand/receptor. Such agonistic anti-idiotypes or Fab
fragments of
such anti-idiotypes can be used in therapeutic regimens as agonists of the
polypeptides
of the invention or its ligand(s)/receptor(s). For example, such anti-
idiotypic
antibodies can be used to bind a polypeptide of the invention and/or to bind
its
ligand(s)/receptor{s), and thereby promote or enhance its biological activity.
[0228] Intrabodies of the invention can be produced using methods known in the
art, such as those disclosed and reviewed in Chen et al., Hum. Gene Ther.
5:595-601
(1994); Marasco, W.A., Gene Ther. 4:11-15 (I997); Rondon and Marasco, Annu.
Rev.
Microbiol. 51:257-283 (1997); Proba et al., J. Mol. Biol. 275:245-253 (1998);
Cohen
et al., Oncogene 17:2445-2456 (1998); Ohage and Steipe, J. Mol. Biol. 291:1119-
1128
(1999); Ohage et al., J. Mol. Biol. 291:1129-1134 (1999); Wirtz and Steipe,
Protein
Sci. 8:2245-2250 (1999); Zhu et al., J. Imrnunol. Methods 231:207-222 (1999);
and
references cited therein.
Polynucleotides Encoding Antibodies
[0229] The invention further provides polynucleotides comprising a nucleotide
sequence encoding an antibody of the invention and fragments thereof. The
invention
also encompasses polynucleotides that hybridize under stringent or
alternatively, under
lower stringency hybridization conditions, e.g., as defined supra, to
polynucleotides
that encode an antibody, preferably, that specifically binds to a polypeptide
of the
invention, preferably, an antibody that binds to a polypeptide having the
amino acid
sequence of SEQ ID NO:Y, to a polypeptide encoded by a portion of SEQ ID NO:X
as
defined in columns 8 and 9 of Table 2, and/or to a polypeptide encoded by the
cDNA
contained in Clone ID NO:Z.
[0230] The polynucleotides may be obtained, and the nucleotide sequence of the
polynucleotides determined, by any method known in the art. For example, if
the
nucleotide sequence of the antibody is known, a polynucleotide encoding the
antibody
may be assembled from chemically synthesized oligonucleotides (e.g., as
described in
Kutmeier et al., BioTechniques 17:242 (1994)), which, briefly, involves the
synthesis
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of overlapping oligonucleotides containing portions of the sequence encoding
the
antibody, annealing and ligating of those oligonucleotides, and then
amplification of
the ligated oligonucleotides by PCR.
[023I] Alternatively, a polynucleotide encoding an antibody may be generated
from nucleic acid from a suitable source. If a clone containing a nucleic acid
encoding
a particular antibody is not available, but the sequence of the antibody
molecule is
known, a nucleic acid encoding the immunoglobulin may be chemically
synthesized
or obtained from a suitable source (e.g., an antibody cDNA library, or a cDNA
library
generated from, or nucleic acid, preferably poly A+ RNA, isolated from, any
tissue or
cells expressing the antibody, such as hybridoma cells selected to express an
antibody
of the invention) by PCR amplification using synthetic primers hybridizable to
the 3'
and 5' ends of the sequence or by cloning using an oligonucleotide probe
specific fox
the particular gene sequence to identify, e.g., a cDNA clone from a cDNA
library that
encodes the antibody. Amplified nucleic acids generated by PCR may then be
cloned
into replicable cloning vectors using any method well known in the art.
[0232] Once the nucleotide sequence and corresponding amino acid sequence of
the antibody is determined, the nucleotide sequence of the antibody may be
manipulated using methods well known in the art for the manipulation of
nucleotide
sequences, e.g.; recombinant DNA techniques, site directed mutagenesis, PCR,
etc.
(see, for example, the techniques described in Sambrook et al., 1990,
Molecular
Cloning, A Laboratory Manual, 2d Ed., Cold Spring Harbor Laboratory, Cold
Spring
Harbor, NY and Ausubel et al., eds., 1998, Current Protocols in Molecular
Biology,
John Wiley & Sons, NY, which are both incorporated by reference herein in
their
entireties ), to generate antibodies having a different amino acid sequence,
for example
to create amino acid substitutions, deletions, and/or insertions.
[0233] In a specific embodiment, the amino acid sequence of the heavy and/or
light chain variable domains may be inspected to identify the sequences of the
complementarily determining regions (CDRs) by methods that are well know in
the
art, e.g., by comparison to known amino acid sequences of other heavy and
light chain
variable regions to determine the regions of sequence hypervariability. Using
routine
recombinant DNA techniques, one or more of the CDRs may be inserted within
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framework regions, e.g., into human framework regions to humanize a non-human
antibody, as described supra. The framework regions may be naturally occurring
or
consensus framework regions, and preferably human framework regions (see,
e.g.,
Chothia et al., J. Mol. Biol. 278: 457-479 (1998) for a listing of human
framework
regions). Preferably, the polynucleotide generated by the combination . of the
framework - regions and CDRs encodes an antibody that specifically binds ' a
polypeptide of the invention. Preferably, as discussed supr°a, one or
more amino acid
substitutions may be made within the framework regions, and, preferably, the
amino
acid substitutions improve binding of the antibody to its antigen.
Additionally, such
methods may be used to make amino acid substitutions or deletions of one or
more
variable region cysteine residues participating in an intrachain disulfide
bond to
generate antibody molecules lacking one or more intrachain disulfide bonds.
Other
alterations to the polynucleotide are encompassed by the present invention and
within
the skill of the art.
[0234] In addition, techniques developed for the production of "chimeric
antibodies" (Morrison et al., Proc. Natl. Acad. Sci. 81:851-855 (1984);
Neuberger et
al., Nature 312:604-608 (1984); Takeda et al., Nature 314:452-454 (1985)) by
splicing genes from a mouse antibody molecule of appropriate antigen
specificity
together with genes from a human antibody molecule of appropriate~biological
activity
can be used. As described sacpr~a, a chimeric antibody is a molecule in which
different
portions are derived from different animal species, such as those having a
variable
region derived from a murine mAb and a human immunoglobulin constant region,
e.g., humanized antibodies.
[0235] Alternatively, techniques descxibed for the production of single chain
antibodies (U.S. Patent No. 4,946,778; Bird, Science 242:423- 42 (1988);
Huston et
al., Proc. Natl. Acad. Sci. USA 85:5879-5883 (1988); and Ward et al., Nature
334:544-54 (1989)) can be adapted to produce single chain antibodies. Single
chain
antibodies are formed by linking the heavy and light chain fragments of the Fv
region
via an amino acid bridge, resulting in a single chain polypeptide. Techniques
for the
assembly of :functional Fv fragments in E. coli may also be used (Skerra et
al., Science
242:1038- 1041 (I988)).
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Methods of P~oducirTg Antibodies
[0236] The antibodies of the invention can be produced by any method known in
the art for the synthesis of antibodies, in particular, by chemical synthesis
or
preferably, by recombinant expression techniques. Methods of producing
antibodies
include, but are not limited to, hybridoma technology; EBV transformation, and
other
methods discussed herein as well as through the use recombinant DNA
technology, as
discussed below.
[0237] Recombinant expression of an antibody of the invention, or fragment,
derivative or analog thereof, (e.g., a heavy or light chain of an antibody of
the
invention or a single chain antibody of the invention), requires construction
of an
expression vector containing a polynucleotide that encodes the antibody. Once
a
polynucleotide encoding an antibody molecule or a heavy or light chain of an
antibody, or portion thereof (preferably containing the heavy or light chain
variable
domain), of the invention has been obtained, the vector for the production of
the
antibody molecule may be produced by recombinant DNA technology using
techniques well known in the art. Thus, methods for preparing a protein by
expressing
a polynucleotide containing an antibody encoding nucleotide sequence are
described
herein. Methods. which are well known to those skilled in the art can be used
to
construct expression vectors containing antibody coding sequences and
appropriate
transcriptional and translational control signals. These methods include, for
example,
iu. vitro recombinant DNA techniques, synthetic techniques, and iu vivo
genetic
recombination. The invention, thus, provides replicable vectors comprising a
nucleotide sequence encoding an antibody molecule of the invention, or a heavy
or
light chain thereof, or a heavy or light chain variable domain, operably
linked to a
promoter. Such vectors may include the nucleotide sequence encoding the
constant
region of the antibody molecule (see, e.g., PCT Publication WO 86/05807; PCT
Publication WO 89/01036; and U.S. Patent No. 5,122,464) and the variable
domain of
the antibody may be cloned into such a vector for expression of the entire
heavy or
light chain.
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[0238] The expression vector is transferred to a host cell by conventional
techniques and the transfected cells are then cultured by conventional
techniques to
produce an antibody of the invention. Thus, the invention includes host cells
containing a polynucleotide encoding an antibody of the invention, or a heavy
or light
chain thereof, or a single chain antibody of the invention, operably linked to
a
heterologous promoter. In preferred embodiments for the expression of double-
chained antibodies, vectors encoding both the heavy and light chains may be co-
expressed in the host cell for expression of the entire immunoglobulin
molecule, as
detailed below.
[0239] A variety of host-expression vector systems may be utilized to express
the
antibody molecules of the invention. Such host-expression systems represent
vehicles
by which the coding sequences of interest may be produced and subsequently
purified,
but also represent cells which may, when transformed or transfected with the
appropriate nucleotide coding sequences, express an antibody molecule of the
invention in situ. These include but are not limited to microorganisms such as
bacteria
(e.g., E. coli, B. subtilis) transformed with recombinant bacteriophage DNA,
plasmid
DNA or cosmid DNA expression vectors containing antibody coding sequences;
yeast
(e.g., Saccharomyces, Pichia) transformed with recombinant yeast expression
vectors
containing antibody coding sequences; insect cell systems infected with
recombinant
virus expression vectors (e.g., baculovirus) containing antibody coding
sequences;
plant cell systems infected with recombinant virus expression vectors (e.g.,
cauliflower
mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant
plasmid expression vectors (e.g., Ti plasmid) containing antibody coding
sequences; or
mammalian cell systems (e.g., COS, CHO, BHI~, 293, 3T3 cells) harboring
recombinant expression constructs containing promoters derived from the genome
of
mammalian cells (e.g., metallothionein promoter) or from mammalian viruses
(e.g.,
the adenovirus late promoter; the vaccinia virus 7.5K promoter). Preferably,
bacterial
cells such as Escherichia coli, and more preferably, eukaryotic cells,
especially for the
expression of whole recombinant antibody molecule, are used for the expression
of a
recombinant antibody molecule. For. example, mammalian cells such as Chinese
hamster ovary cells (CHO), in conjunction with a vector such as the major
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intermediate early gene promoter element from human cytomegalovirus is an
effective
expression system for antibodies (Foecking et al., Gene 45:101 (1986); Cockett
et al.,
Bio/Technology 8:2 (1990)).
[0240] In bacterial systems, a number of expression vectors may be
advantageously selected depending upon the use intended for the antibody
molecule
being expressed. For example, when a large quantity of such a protein is to be
produced, for the generation of pharmaceutical compositions of an antibody
molecule,
vectors which direct the expression of high levels of fusion protein products
that are
readily purified may be desirable. Such vectors include, but are not limited,
to the E.
coli expression vector pUR278 (Ruther et al., EMBO J. 2:1791 (1983)), in which
the
antibody coding sequence may be ligated individually into the vector in frame
with the
Iac Z coding region so that a fusion protein is produced; pIN vectors (Inouye
&
Inouye, Nucleic Acids Res. 13:3101-3109 (1985); Van Heeke & Schuster, J. Biol.
Chem. 24:5503-5509 (1989)); and the like. pGEX vectors may also be used to
express
foreign polypeptides as fusion proteins with glutathione S-transferase (GST).
In
general, such fusion proteins are soluble and can easily be purified from
lysed cells by
adsorption and binding to matrix glutathione-agarose beads followed by elution
in the
presence of free glutathione. The pGEX vectors are designed to include
thrombin or
factor Xa protease cleavage sites so that the cloned target gene product can
be released
fr om the GST moiety.
[0241] In an insect system, Autographa californica nuclear polyhedrosis virus
(AcNPV) is used as a vector to express foreign genes. The virus grows in
S~odopte~°a
frugi~e~da cells. The antibody coding sequence may be cloned individually into
non-
essential regions (for example the polyhedrin gene) of the virus and placed
under
control of an AcNPV promoter (for example the polyhedrin promoter).
[0242] In mammalian host cells, a number of viral-based expression systems may
be utilized. In cases where an adenovirus is used as an expression vector, the
antibody
coding sequence of interest may be ligated to an adenovirus
transcription/translation
control complex, e.g., the late promoter and tripartite leader sequence. This
chimeric
gene may then be inserted in the adenovirus genome by ira vitro or ih vivo
recombination. Insertion in a non- essential region of the viral genome (e.g.,
region
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E1 or E3) will result in a recombinant virus that is viable and capable of
expressing the
antibody molecule in infected hosts. (e.g., see Logan & Shenk, Proc. Natl.
Acad. Sci.
USA 81:355-359 (1984)). Specific initiation signals may also be required for
efficient
translation of inserted antibody coding sequences. These signals include the
ATG
initiation codon and adjacent sequences. Furthermore, the initiation codon
must be in
phase with the reading frame of the desired coding sequence to ensure
translation of
the entire insert. These exogenous translational control signals and
initiation codons
can be of a variety of origins, both natural and synthetic. The efficiency of
expression
may be enhanced by the inclusion of appropriate transcription enhancer
elements,
transcription terminators, etc. (see Bittner et al., Methods in Enzymol.
153:51-544
(1987)).
[0243] In addition, a host cell strain may be chosen which modulates the
expression of the inserted sequences, or modifies and processes the gene
product in
the specific fashion desired. Such modifications (e.g., glycosylation) and
processing
(e.g., cleavage) of protein products may be important for the function of the
protein.
Different host cells have characteristic and specific mechanisms for the post-
translational processing and modification of proteins and gene products.
Appropriate
cell lines or host systems can be chosen to ensure the correct modification
and
processing of the foreign protein expressed. To this end, eukaryotic host
cells which
possess the cellular machinery for proper processing of the primary
transcript,
glycosylation, and phosphorylation of the gene product may be used. Such
mammalian host cells include but are not limited to CHO, VERY, BHK, Hela, COS,
MDCK, 293, 3T3, WI38, and in particular, breast cancer cell lines such as, for
example, BT483, Hs578T, HTB2, BT20 and T47D, and normal mammary gland cell
line such as, for example, CRL7030 and Hs578Bst.
[0244] For long-term, high-yield production of recombinant proteins, stable
expression is preferred. For example, cell lines, which stably express the
antibody
molecule may be engineered. Rather than using expression vectors which contain
viral origins of replication, host cells can be transformed with DNA
controlled by
appropriate expression control elements (e.g., promoter, enhancer, sequences,
transcription terminators, polyadenylation sites, etc.), and a selectable
marker.
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Following the introduction of the foreign DNA, engineered cells may be allowed
to
grow for 1-2 days in an enriched media, and then are switched to a selective
media.
The selectable marker in the recombinant plasmid confers resistance to the
selection
and allows cells to stably integrate the plasmid into their chromosomes and
grow to
form foci which in turn can be cloned and expanded into cell lines. This
method may
advantageously be used to engineer cell lines, which express the antibody
molecule.
Such engineered cell lines may be particularly useful in screening and
evaluation of
compounds that interact directly or indirectly with the antibody molecule.
[0245] A number of selection systems may be used, including but not limited to
the herpes simplex virus thymidine kinase (Wigler et al., Cell 11:223 (1977)),
hypoxanthine-guanine phosphoribosyltransferase (Szybalska & Szybalski, Proc.
Natl.
Acad. Sci. USA 48:202 (1992)), and adenine phosphoribosyltransferase (Lowy et
al.,
Cell 22:817 (1980)) genes can be employed in tk-, hgprt- or aprt- cells,
respectively.
Also, antimetabolite resistance can be used as the basis of selection for the
following
genes: dhfr, which confers resistance to methotrexate (Wigler et al., Natl.
Acad. Sci.
USA 77:357 (1980); O'Hare et al., Proc. Natl. Acad. Sci. USA 78:1527 (1981));
gpt,
which confers resistance to mycophenolic acid (Mulligan & Berg, Proc. Natl.
Acad.
Sci. USA 78:2072 (1981)); neo, which confers resistance to the aminoglycoside
G-418
Clinical Pharmacy 12:488-505; Wu and Wu, Biotherapy 3:87-95 (1991);
Tolstoshev,
Ann. Rev. Pharmacol. Toxicol. 32:573-596 (1993); Mulligan, Science 260:926-932
(1993); and Morgan and Anderson, Ann. Rev. Biochem. 62:191-217 (1993); TIB
TECH 11(5):155-215 (1993)); and hygro, which confers resistance to hygromycin
(Santerre et al., Gene 30:147 (1984)). Methods commonly known in the art of
recombinant DNA technology may be routinely applied to select the desired
recombinant clone, and such methods are described, for example, in Ausubel et
al.
(eds.), Current Protocols in Molecular Biology, John Wiley & Sons, NY (1993);
Kriegler, Gene Transfer and Expression, A Laboratory Manual, Stockton Press,
NY
(1990); and in Chapters 12 and 13, Dracopoli et al. (eds), Current Protocols
in Human
Genetics, John Wiley & Sons, NY (1994); Colberre-Garapin et al., J. Mol. Biol.
150:1
(1981), which are incorporated by reference herein in their entireties.
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[0246] The expression levels of an antibody molecule can be increased by
vector
amplification (for a review, see Bebbington and Hentschel, The use of vectors
based
on gene amplification for the expression of cloned genes in mammalian cells in
DNA
cloning, Vol.3. (Academic Press, New York, 1987)). When a marker in the vector
system expressing antibody is amplifiable, .increase in the level of inhibitor
present in
culture of host cell will increase the number of copies of the marker gene.
Since the
amplified region is associated with the antibody gene, production of the
antibody will
also increase (Grouse et al., Mol. Cell. Biol. 3:257 (1983)).
[0247] Vectors, which use glutamine synthase (GS) or DHFR as the selectable
markers can be amplified in the presence of the drugs methionine sulphoximine
or
methotrexate, respectively. An advantage of glutamine synthase based vectors
are the
availabilty of cell lines (e.g., the murine myeloma cell line, NSO) which are
glutamine
synthase negative. Glutamine synthase expression systems can also function in
glutamine synthase expressing cells (e.g., Chinese Hamster Ovary (CHO) cells)
by
providing additional inhibitor to prevent the functioning of the endogenous
gene. A
glutamine synthase expression system and components thereof are detailed in
PCT
publications: W087/04462; W086/05807; W089/01036; W089/10404; and
W091/06657, which are incorporated in their entireties by reference herein.
Additionally, glutamine synthase expression vectors that may be used according
to the
present invention are commercially available from suplliers, including, for
example
Lonza Biologics, Inc. (Portsmouth, NH). Expression and production of
monoclonal
antibodies using a GS expression system in murine myeloma cells is described
in
Bebbington et al., Biotechnology 10:169(1992) and in Biblia and Robinson
Biotechnol. Prog. 11:1 (1995) which are incorporated in their entireties by
reference
herein.
[0248] The host cell may be co-transfected with two expression vectors of the
invention, the first vector encoding a heavy chain derived polypeptide and the
second
vector encoding a light chain derived polypeptide. The two vectors may contain
identical selectable markers, which enable equal expression of heavy and light
chain
polypeptides. Alternatively, a single vector may be used which encodes, and is
capable of expressing, both heavy and light chain polypeptides. In such
situations, the
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light chain should be placed before the heavy chain to avoid an excess of
toxic free
heavy chain (Proudfoot, Nature 322:52 (1986); Kohler, Proc. Natl. Acad. Sci.
USA
77:2197 (1980)). The coding sequences for the heavy and light chains may
comprise
cDNA or genomic DNA.
[0249] Once an antibody molecule of the invention has been produced by an
animal, chemically synthesized, or recombinantly expressed, it may be purified
by any
method known in the art for purification of an immunoglobulin molecule, for
example,
by chromatography (e.g., ion exchange, affinity, particularly by affinity for
the
specific antigen after Protein A, and sizing column chromatography),
centrifugation,
differential solubility, or by any other standard technique for the
purification of
proteins. In addition, the antibodies of the present invention or fragments
thereof can
be fused to heterologous polypeptide sequences described herein or otherwise
known
in the art, to facilitate purification.
[0250] The present invention encompasses antibodies recombinantly fused or
chemically conjugated (including both c0valently and non-covalently
conjugations) to
a polypeptide (or portion thereof, preferably at least 10, 20, 30, 40, 50, 60,
70, 80, 90
or 100 amino acids of the polypeptide) of the present invention to generate
fusion
proteins. The fusion does not necessarily need to be direct, but may occur
through
linker sequences. The antibodies may be specific for antigens other than
polypeptides
(or portion thereof, preferably at least 10, 20, 30, 40, 50, 60, 70, 80, 90 or
100 amino
acids of the polypeptide) of the present invention. For example, antibodies
may be
used to target the polypeptides of the present invention to particular cell
types, either
in vitro or ifa vivo, by fusing or conjugating the polypeptides of the present
invention to
antibodies specific for particular cell surface receptors. Antibodies fused or
conjugated to the polypeptides of the present invention may also be used in iu
vitro
immunoassays and purification methods using methods known in the art. See
e.g.,
Harbor et al., supra, and PCT publication WO 93/21232; EP 439,095; Naramura et
al.,
Immunol. Lett. 39:91-99 (1994); U.S. Patent 5,474,981; Gillies et al., PNAS
89:1428-
1432 (1992); Fell et al., J. Immunol. 146:2446-2452 (1991), which are
incorporated
by reference in their entireties.
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[0251] The present invention further includes compositions comprising the
polypeptides of the present invention fused or conjugated to antibody domains
other
than the variable regions. For example, the polypeptides of the present
invention may
be fused or conjugated to an antibody Fc region, or portion thereof. The
antibody
portion fused to a polypeptide of the present invention may comprise the
constant
region, hinge region; CH1 domain, CH2 domain, and CH3 domain or any
combination
of whole domains or portions thereof. The polypeptides may also be fused or
conjugated to the above antibody portions to form multimers. For example, Fc
portions fused to the polypeptides of the present invention can form dimers
through
disulfide bonding between the Fc portions. Higher multimeric forms can be made
by
fusing the polypeptides to portions of IgA and IgM. Methods for fusing or
conjugating the polypeptides of the present invention to antibody portions are
known
in the art. See, e.g., U.S. Patent Nos. 5,336,603; 5,622,929; 5,359,046;
5,349,053;
5,447,851; 5,112,946; EP 307,434; EP 367,166; PCT publications WO 96/04388; WO
91106570; Ashkenazi et al., Proc. Natl. Acad. Sci. USA 88:10535-10539 (1991);
Zheng et al., J. Immunol. 154:5590-5600 (1995); and Vil et al., Proc. Natl.
Acad. Sci.
USA 89:11337- 11341 (1992) (said references incorporated by reference in their
entireties). .
[0252] As discussed, ,supy~a, the polypeptides corresponding to a polypeptide,
polypeptide fragment, or a variant of SEQ ID NO:Y may be fused or conjugated
to the
above antibody portions to increase the in vivo half life of the polypeptides
or for use
in immunoassays using methods known in the art. Further, the polypeptides
corresponding to SEQ ID NO:Y may be fused or conjugated to the above antibody
portions to facilitate purification. One reported example describes chimeric
proteins
consisting of the first two domains of the human CD4-polypeptide and various
domains of the constant regions of the heavy or light chains of mammalian
immunoglobulins. See EP 394,827; Traunecker et al., Nature 331:84-86 (1988).
The
polypeptides of the present invention fused or conjugated to an antibody
having
disulfide- linked dimeric structures (due to the IgG) may also be more
efficient in
binding and neutralizing other molecules, than the monomeric secreted protein
or
protein fragment alone. See, for example, Fountoulalcis et al., J. Biochem.
270:3958-
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3964 (1995). In many cases, the Fc part in a fusion protein is beneficial in
therapy and
diagnosis, and thus can result in, for example, improved pharmacokinetic
properties.
See, for example, EP A 232,262. Alternatively, deleting the Fc part after the
fusion
protein has been expressed, detected, and purified, would be desired. For
example, the
Fc portion may hinder therapy and diagnosis if the fusion protein is used as
an antigen
for immunizations. In drug discovery, for example, human proteins; such as hIL-
5,
have been fused with Fc portions for the purpose of high-throughput screening
assays
to identify antagonists of hIL-5. (See, Bennett et al., J. Molecular
Recognition 8:52-58
(1995); Johanson et al., J. Biol. Chem. 270:9459-9471 (1995)).
[0253] Moreover, the antibodies or fragments thereof of the present invention
can
be fused to marlcer sequences, such as a peptide to facilitate purification.
In preferred
embodiments, the marker amino acid sequence is a hexa-histidine peptide, such
as the
tag provided in a pQE vector (QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, CA,
91311), among others, many of which are commercially available. As described
in
Gentz et al., Proc. Natl. Acad. Sci. USA 86:821-824 (1989), for instance, hexa-
histidine provides for convenient purification of the fusion protein. Other
peptide tags
useful for purification include, but are not limited to, the "HA" tag, which
corresponds
to an epitope derived from the influenza hemagglutinin protein (Wilson et al.,
Cell
37:767 (1984)) and the "flag" tag.
[0254] The present invention further encompasses antibodies or fragments
thereof
conjugated to a diagnostic or therapeutic agent. The antibodies can be used
diagnostically to, for example, monitor the development or progression of a
tumor as
part of a clinical testing procedure to, e.g., determine the efftcacy of a
given treatment
regimen. Detection can be facilitated by coupling the antibody to a detectable
substance. Examples of detectable substances include various enzymes,
prosthetic
groups, fluorescent materials, luminescent materials, bioluminescent
materials,
radioactive materials, positron emitting metals using various positron
emission
tomographies, and nonradioactive paramagnetic metal ions. The detectable
substance
may be coupled or conjugated either directly to the antibody (or fragment
thereof) or
indirectly, through an intermediate (such as, for example, a linker known in
the art)
using techniques known in the art. See, for example, U.S. Patent No. 4,741,900
for
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metal ions which can be conjugated to antibodies for use as diagnostics
according to
the present invention.
[0255] Further, an antibody or fragment thereof may be conjugated to a
therapeutic moiety such as a cytotoxin, e.g., a cytostatic or cytocidal agent,
a
therapeutic agent or a radioactive metal ion, e.g., alpha-emitters such as,
for example,
213Bi. A cytotoxin or cytotoxic agent includes any agent that is detrimental
to cells.
Examples include paclitaxol, cytochalasin B, gramicidin D, ethidium bromide,
emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine,
colchicin,
doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone,
mithramycin,
actinomycin D, 1-dehydrotestosterone, glucocorticoids, procaine, tetracaine,
lidocaine, propranolol, and puromycin and analogs or homologs thereof.
Therapeutic
agents include, but are not limited to, antimetabolites (e.g., methotrexate, 6-
mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil decarbazine),
alkylating
agents (e.g., mechlorethamine, thioepa chlorambucil, melphalan, carmustine
(BSNU)
and lomustine (CCNU), cyclothosphamide, busulfan, dibromomannitol,
streptozotocin, mitomycin C, and cis- dichlorodiamine platinum (II) (DDP)
cisplatin),
anthracyclines (e.g., daunorubicin (formerly daunomycin) and doxorubicin),
antibiotics (e.g., dactin0mycin (formerly actinomycin), bleomycin,
mithramycin, and
anthramycin (AMC)), and anti-mitotic agents (e.g., vincristine and
vinblastine).
[0256] The conjugates of the invention can be used for modifying a given
biological response, the therapeutic agent or drug moiety is not to be
construed as
limited to classical chemical therapeutic agents. For example, the drug moiety
may be
a protein or polypeptide possessing a desired biological activity. Such
proteins may
include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or
diphtheria toxin; a protein such as tumor necrosis factor, a-interferon, 13-
interferon,
nerve growth factor, platelet derived growth factor, tissue plasminogen
activator, an
apoptotic agent, e.g., TNF-alpha, TNF-beta, AIM I (See, International
Publication No.
WO 97/33899), AIM II (See, International Publication No. WO 97/34911), Fas
Ligand
('Takahashi et al., Irzt. Ifnn2urZOl., 6:1567-1574 (1994)), VEGI (See,
International
Publication No. WO 99/23105), a thrombotic agent or an anti- angiogenic agent,
e.g.,
angiostatin or endostatin; or, biological response modifiers such as, for
example,
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lymphokines, interleukin-1 ("IL-1 "), interleukin-2 ("IL-2"), interleukin-6
("IL-6"),
granulocyte macrophage colony stimulating factor ("GM-CSF"), granulocyte
colony
stimulating factor ("G-CSF"), or other growth factors.
[0257] Antibodies may also be attached to solid supports, which are
particularly
useful for immunoassays or purification of the target antigen. Such solid
supports
include, but are not limited to, glass, cellulose, polyacrylamide, nylon,
polystyrene,
polyvinyl chloride or polypropylene.
[0258] Techniques for conjugating such therapeutic moiety to antibodies are
well
known. See, for example, Arnon et al., "Monoclonal Antibodies For
Immunotargeting
Of Drugs In Cancer Therapy", in Monoclonal Antibodies And Cancer Therapy,
Reisfeld et al. (eds.), pp. 243-56 (Alan R. Liss, Inc. 1985); Hellstrom et
al.,
"Antibodies For Drug Delivery", in Controlled Drug Delivery (2nd Ed.),
Robinson et
al. (eds.), pp. 623-53 (Marcel Dekker, Inc. 1987); Thorpe, "Antibody Carriers
Of
Cytotoxic Agents In Cancer Therapy: A Review", in Monoclonal Antibodies '84:
Biological And Clinical Applications, Pinchera et al. (eds.), pp. 475-506
(1985);
"Analysis, Results, And Future Prospective Of The Therapeutic Use Of
Radiolabeled
Antibody In Cancer Therapy", in Monoclonal Antibodies For Cancer Detection And
Therapy, Baldwin et al. (eds.), pp: 303-16 (Academic Press 1985), and Thorpe
et al.,
"The Preparation And Cytotoxic Properties Of Antibody-Toxin Conjugates",
hnmunol. Rev. 62:119-58 (1982).
[0259] Alternatively, an antibody can be conjugated to a second antibody to
form
an antibody heteroconjugate as described by Segal in U.S. Patent No.
4,676,980,
which is incorporated herein by reference in its entirety.
[0260] An antibody, with or without a therapeutic moiety conjugated to it,
administered alone or in combination with cytotoxic factors) andlor
cytolcine(s) can
be used as a therapeutic.
Inzmunopheyaotypi~g
[0261] The antibodies of the invention may be utilized for immunophenotyping
of
cell lines and biological samples. Translation products of the genes of the
present
invention may be useful as cell specific markers, or more specifically as
cellular
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markers that are differentially expressed at various stages of differentiation
and/or
maturation of particular cell types. Monoclonal antibodies directed against a
specific
epitope, or combination of epitopes, will allow for the screening of cellular
populations expressing the marker. Various techniques can be utilized using
monoclonal antibodies to screen for cellular populations expressing the
marker(s), and
include magnetic separation using antibody-coated magnetic beads, "panning"
with
antibody attached to a solid matrix (i.e., plate), and flow cytometry (See,
e.g., U.S.
Patent 5,985,660; and Morrison et al., Cell, 96:737-49 (1999)).
[0262] These techniques allow for the screening of particular populations of
cells,
such as might be found with hematological malignancies (i.e. minimal residual
disease
(MRD) in acute leukemic patients) and "non-self' cells in transplantations to
prevent
Graft-versus-Host Disease (GVHD). Alternatively, these techniques allow for
the
screening of hematopoietic stem and progenitor cells capable of undergoing
proliferation and/or differentiation, as might be found in human umbilical
cord blood.
Assays For Antibody Bifzdirag
[0263] The antibodies of the invention may be assayed for immunospecific
binding by any method known in the art. The immunoassays which can be used
include but are not limited to competitive and non-competitive assay systems
using
techniques such as western blots, radioimmunoassays, ELISA (enzyme linked
immunosorbent assay), "sandwich" immunoassays, immunoprecipitation assays,
precipitin reactions, gel diffusion precipitin reactions, immunodiffusion
assays,
agglutination assays, complement-fixation assays, immunoradiometric assays,
fluorescent immunoassays, and protein A immunoassays, to name but a few. Such
assays are routine and well known in the art (see, e.g., Ausubel et al, eds,
1994,
Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New
Yorlc,
which is incorporated by reference herein in its entirety). Exemplary
immunoassays
are described briefly below (but are not intended by way of limitation).
[0264] Immunoprecipitation protocols generally comprise lysing a population of
cells in a lysis buffer such as RIPA buffer (1% NP-40 or Triton X- 100, 1%
sodium
deoxycholate, 0.1 % SDS, 0.15 M NaCI, 0.01 M sodium phosphate at pH 7.2, 1
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Trasylol) supplemented with protein phosphatase and/or protease inhibitors
(e.g.,
EDTA, PMSF, aprotinin, sodium vanadate), adding the antibody of interest to
the cell
lysate, incubating for a period of time (e.g., 1-4 hours) at 4° C,
adding protein A
and/or protein G sepharose beads to the cell lysate, incubating for about an
hour or
more at 4° C, washing the beads in lysis buffer and resuspending the
beads in
SDS/sample buffer. The ability of the antibody of interest to
immunoprecipitate a
particular antigen can be assessed by, e.g., western blot analysis: One of
skill in the art
would be knowledgeable as to the parameters that can be modified to increase
the
binding of the antibody to an antigen and decrease the background (e.g., pre-
clearing
the cell lysate with sepharose beads). For further discussion regarding
immunoprecipitation protocols see, e.g., Ausubel et al., eds., (1994), Current
Protocols
in Molecular Biology, Vol. l, John Wiley & Sons, Inc., New York, section
10.16.1.
[0265] Western blot analysis generally comprises preparing protein samples,
electrophoresis of the protein samples in a polyacrylamide gel (e.g., 8%- 20%
SDS-
PAGE depending on the molecular weight of the antigen), transferring the
protein
sample from the polyacrylamide gel to a membrane such as nitrocellulose, PVDF
or
nylon, blocking the membrane in blocking solution (e.g., PBS with 3% BSA or
non-fat
milk), washing the membrane in washing buffer (e.g., PBS-Tween 20), blocking
the
membrane with primary antibody (the antibody of interest) diluted in blocking
buffer,
washing the membrane in washing buffer, blocking the membrane with a secondary
antibody (which recognizes the primary antibody, e.g., an anti-human antibody)
conjugated to an enzymatic substrate (e.g., horseradish peroxidase or alkaline
phosphatase) or radioactive molecule (e.g., 32P or 125I) diluted in blocking
buffer,
washing the membrane in wash buffer, and detecting the presence of the
antigen. One
of skill in the art would be knowledgeable as to the parameters that can be
modified to
increase the signal detected and to reduce the background noise. For further
discussion regarding western blot protocols see, e.g., Ausubel et al., eds.,
(1994),
Current Protocols in Molecular Biology, Vol. 1, John Wiley & Sons, Inc., New
York,
section 10.8.1.
[0266] ELISAs comprise preparing antigen, coating the well of a 96 well
microtiter plate with the antigen, adding the antibody of interest conjugated
to a
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detectable compound such as an enzymatic substrate (e.g., horseradish
peroxidase or
alkaline phosphatase) to the well and incubating for a period of time, and
detecting the
presence of the antigen. In ELISAs the antibody of interest does not have to
be
conjugated to a detectable compound; instead, a second antibody (which
recognizes
the antibody of interest) conjugated to a detectable compound may be added to
the
well: Further, instead of coating the well with the antigen, the antibody may
be coated
to the well: In this case, a second antibody conjugated to a detectable
compound may
be added following the addition of the antigen of interest to the coated well.
One of
skill in the art would be knowledgeable as to the parameters that can be
modified to
increase the signal detected as well as other variations of ELISAs known in
the art.
For further discussion regarding ELISAs see, e.g., Ausubel et al., eds,
(1994), Current
Protocols in Molecular Biology, Vol. l, John Wiley & Sons, Inc., New York,
section
11.2.1.
[0267] The binding affinity of an antibody to an antigen and the off rate of
an
antibody-antigen interaction can be determined by competitive binding assays.
One
example of a competitive binding assay is a radioimmunoassay comprising the
incubation .of labeled antigen (e.g., 3H or 125I) with the antibody of
interest in the
presence of increasing amounts of unlabeled antigen, and the detection of the
antibody
bound to the labeled antigen. The affinity of the antibody of interest for a
particular
antigen and the binding off rates can be determined from the data by scatchard
plot
analysis. Competition with a second antibody can also be determined using
radioimmunoassays. In this case, the antigen is incubated with antibody of
interest
conjugated to a labeled compound (e.g., 3H or 125I) in the presence of
increasing
amounts of an unlabeled second antibody.
[0268] Antibodies of the invention may be characterized using
immunocytochemisty methods on cells (e.g., mammalian cells, such as CHO cells)
transfected with a vector enabling the expression of a prostate cancer antigen
or with
vector alone using techniques commonly known in the art. Antibodies that bind
prostate cancer antigen transfected cells, but not vector-only transfected
cells, are
prostate cancer antigen specific.
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Therapeutic Uses
[0269] The present invention is further directed to antibody-based therapies
which
involve administering antibodies of the invention to an animal, preferably a
mammal,
and most preferably a human, patient for treating one or more of the disclosed
diseases, disorders, or conditions. Therapeutic compounds of the invention
include,
but are not limited to, antibodies of the invention (including fragments,
analogs and
derivatives thereof as described herein) and nucleic acids encoding antibodies
of the
invention (including fragments, analogs and derivatives thereof and anti-
idiotypic
antibodies as described herein). The antibodies of the invention can be used
to treat,
inhibit or prevent diseases, disorders or conditions associated with aberrant
expression
and/or activity of a polypeptide of the invention, including, but not limited
to, any one
or more of the diseases, disorders, or conditions described herein. The
treatment
and/or prevention of diseases, disorders, or conditions associated with
aberrant
expression and/or activity of a polypeptide of the invention includes, but is
not limited
to, alleviating symptoms associated with those diseases, disorders or
conditions.
Antibodies of the invention may be provided in pharmaceutically acceptable
compositions as known in the art or as described herein.
[0270] In a specific and preferred embodiment, the present invention is
directed to
antibody-based therapies which involve administering antibodies of the
invention to an
animal, preferably a mammal, and most preferably a human, patient for treating
one or
more of the diseases, disorders, or conditions of the prostate, including, but
not limited
to, prostate cancers such as adenocarcinoma, transitional cell carcinomas,
ductal
carcinomas, and squamous cell carcinomas, and as described under
"Hyperproliferative Disorders" and/or "Reproductive System Disorders" below.
Therapeutic compounds of the invention include, but are not limited to,
antibodies of
the invention (e.g., antibodies directed to the full length protein expressed
on the cell
surface of a mammalian cell; antibodies directed to an epitope of a prostate
cancer
associated polypeptide of the invention (such as, a linear epitope (shown in
Table 1A,
column 6) or a conformational epitope), including fragments, analogs and
derivatives
thereof as described herein) and nucleic acids encoding antibodies of the
invention
(including fragments, analogs and derivatives thereof and anti-idiotypic
antibodies as
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described herein). The antibodies of the invention can be used to treat,
inhibit or
prevent diseases, disorders or conditions associated with aberrant expression
and/or
activity of a polypeptide of the invention, including, but not limited to, any
one or
more of the diseases, disorders, or conditions of the prostate described
herein. The
treatment and/or prevention of diseases, disorders, or conditions of the
prostate cancer
associated with aberrant expression and/or activity of a polypeptide of the
invention
includes, but is not limited to, alleviating symptoms associated with those
diseases,
disorders or conditions. Antibodies of the invention may be provided in
pharmaceutically acceptable compositions as known in the art or as described
herein.
[0271] A summary of the ways in which the antibodies of the present invention
may be used therapeutically includes binding polynucleotides or polypeptides
of the
present invention locally or systemically in the body or by direct
cytotoxicity of the
antibody, e.g. as mediated by complement (CDC) or by effector cells (ADCC).
Some
of these approaches are described in more detail below. Armed with the
teachings
provided herein, one of ordinary skill in the art will know how to use the
antibodies of
the present invention for diagnostic, monitoring or therapeutic purposes
without undue
experimentation.
[0272] The antibodies of this invention may be advantageously utilized in
combination with other. monoclonal or chimeric antibodies, or with lymphokines
or
hematopoietic growth factors (such as, e.g., IL-2, IL-3 and IL-7), for
example, which
serve to increase the number or activity of effector cells which interact with
the
antibodies.
[0273] The antibodies of the invention may be administered alone or in
combination with other types of treatments (e.g., radiation therapy,
chemotherapy,
hormonal therapy, immunotherapy and anti-tumor agents). Generally,
administration
of products of a species origin or species reactivity (in the case of
antibodies) that is
the same species as that of the patient is preferred. Thus, in a preferred
embodiment,
human antibodies, fragments derivatives, analogs, or nucleic acids, are
administered
to a human patient for therapy or prophylaxis.
[0274] It is preferred to use high affinity and/or potent i~2 vivo inhibiting
and/or
neutralizing antibodies against polypeptides or polynucleotides of the present
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invention, fragments or regions thereof, for both immunoassays directed to and
therapy of disorders related to polynucleotides or polypeptides, including
fragments
thereof, of the present invention. Such antibodies, fragments, or regions,
will
preferably have an affinity for polynucleotides or polypeptides of the
invention,
including fragments thereof. Preferred binding affinities include those with a
dissociation constant or I~d less than 5 X 10-2 M, 10-2 M, 5 X 10-3 M, 10-3 M,
5 X 10-4
M, 10-4 M, 5 X 10-5 M, 10-5 M, 5 X 10-6 M, 10-6 M, 5 X 10-~ M, 10-~ M, 5 X 10-
8 M,
10-8 M, 5 X 10-9 M, 10-9 M, 5 X 10-1° M, 10-1° M, 5 X 10-11 M,
10-1' M, 5 X 10-12 M,
10-12 M, 5 X 10-13 M, 10-13 M, 5 X 10-14 M, 10-14 M, 5 X 10-15 M, and 10-15 M.
Gene Thef°apy
[0275] In a specific embodiment, nucleic acids comprising sequences encoding
antibodies or functional derivatives thereof, are administered to treat,
inhibit or
prevent a disease or disorder associated with aberrant expression and/or
activity of a
polypeptide of the invention, by way of gene therapy. Gene therapy refers to
therapy
performed by the administration to a subject of an expressed or expressible
nucleic
acid. In this embodiment of the invention, the nucleic acids produce their
encoded
protein that mediates a therapeutic effect.
[0276] Any of the methods for gene therapy available in the art can be used
according to the present invention. Exemplary methods are described below.
[0277] For general reviews of the methods of gene therapy, see Goldspiel et
al.,
Clinical Pharmacy 12:488-505 (1993); Wu and Wu, Biotherapy 3:87-95 (1991);
Tolstoshev, Ann. Rev. Pharmacol. Toxicol. 32:573-596 (1993); Mulligan, Science
260:926-932 (1993); and Morgan and Anderson, Ann. Rev. Biochem. 62:191-217
(1993); May, TIBTECH 11(5):155-215 (1993). Methods commonly known in the art
of recombinant DNA technology which can be used are described in Ausubel et
al.
(eds.), Current Protocols in Molecular Biology, John Wiley & Sons, NY (1993);
and
Kriegler, Gene Transfer and Expression, A Laboratory Manual, Stockton Press,
NY
(1990).
[0278] In a preferred embodiment, the compound comprises nucleic acid
sequences encoding an antibody, said nucleic acid sequences being part of
expression
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vectors that express the antibody or fragments or chimeric proteins or heavy
or light
chains thereof in a suitable host. In particular, such nucleic acid sequences
have
promoters operably linked to the antibody coding region, said promoter being
inducible or constitutive, and, optionally, tissue-specific. In another
particular
embodiment, nucleic acid molecules are used in which the antibody coding
sequences
and any other desired sequences are flanked by regions that promote homologous
recombination at a desired site in the genome, thus providing for
intrachromosomal
expression of the antibody encoding nucleic acids (Roller and Smithies, Proc.
Natl.
Acad. Sci. USA 86:8932-8935 (1989); Zijlstra et al., Nature 342:435-438
(1989). In
specific embodiments, the expressed antibody molecule is a single chain
antibody;
alternatively, the nucleic acid sequences include sequences encoding both the
heavy
and light chains, or fragments thereof, of the antibody.
[0279] Delivery of the nucleic acids into a patient may be either direct, in
which
case the patient is directly exposed to the nucleic acid or nucleic acid-
carrying
vectors, or indirect, in which case, cells are first transformed with the
nucleic acids i~c
vitro, then transplanted into the patient. These two approaches are known,
respectively, as i~ vivo or ex vivo gene therapy.
[0280] In a specific embodiment, the nucleic acid sequences are directly
administered ih vivo, where it is expressed to produce the encoded product.
This can .
be accomplished by any of numerous methods known in the art, e.g., by
constructing
them as part of an appropriate nucleic acid expression vector and
administering it so
that they become intracellular, e.g., by infection using defective or
attenuated
retrovirals or other viral vectors (see U.S. Patent No. 4,980,286), or by
direct injection
of naked DNA, or by use of microparticle bombardment (e.g., a gene gun;
Biolistic,
Dupont), or coating with lipids or cell-surface receptors or transfecting
agents,
encapsulation in liposomes, microparticles, or microcapsules, or by
administering
them in linkage to a peptide which is known to enter the nucleus, by
administering it
in linlcage to a ligand subject to receptor-mediated endocytosis (see, e.g.,
Wu and Wu,
J. Biol. Chem. 262:4429-4432 (1987)) (which can be used to target cell types
specifically expressing the receptors), etc. In another embodiment, nucleic
acid-ligand
complexes can be formed in which the ligand comprises a fusogenic viral
peptide to
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disrupt endosomes, allowing the nucleic acid to avoid lysosomal degradation.
In yet
another embodiment, the nucleic acid can be targeted ira vivo for cell
specific uptake
and expression, by targeting a specific receptor (see, e.g., PCT Publications
WO
92/06180; WO 92/22635; W092/20316; W093/14188, WO 93/20221).
Alternatively, the nucleic acid can be introduced. intracellularly and
incorporated
within host cell DNA for expression, by homologous recombination (Koller and
Smithies, Proc. Natl. Acad. Sci. USA 86:8932-8935 (1989); Zijlstra et al.,
Nature
342:435-438 (1989)).
[0281] In a specific embodiment, viral vectors that contains nucleic acid
sequences
encoding an antibody of the invention are used. For example, a retroviral
vector can
be used (see Miller et al., Meth. Enzymol. 217:581-599 (1993)). These
retroviral
vectors contain the components necessary for the correct packaging of the
viral
genome and integration into the host cell DNA. The nucleic acid sequences
encoding
the antibody to be used in gene therapy axe cloned into one or more vectors,
which
facilitates delivery of the gene into a patient. More detail about retroviral
vectors can
be found in Boesen et al., Biotherapy 6:291-302 (1994), which describes the
use of a
retroviral vector to deliver the mdrl gene to hematopoietic stem cells in
order to make
the stem cells more resistant to chemotherapy. Other references illustrating
the use of
retroviral vectors in gene therapy are: Clowes et al., J. Clin. Invest. 93:644-
651
(1994); Kiem et al., Blood 83:1467-1473 (1994); Salmons and Gunzberg, Human
Gene Therapy 4:129-141 (1993); and Grossman and Wilson, Curr. Opin. in
Genetics
and Devel. 3:110-114 (1993).
[0282] Adenoviruses are other viral vectors that can be used in gene therapy.
Adenoviruses are especially attractive vehicles for delivering genes to
respiratory
epithelia. Adenoviruses naturally infect respiratory epithelia where they
cause a mild
disease. Other targets for adenovirus-based delivery systems axe liver, the
central
nervous system, endothelial cells, and muscle. Adenoviruses have the advantage
of
being capable of infecting non-dividing cells. Kozarsky and Wilson, Current
Opinion
in Genetics and Development 3:499-503 (1993) present a review of adenovirus-
based
gene therapy. Bout et al., Human Gene Therapy 5:3-10 (1994) demonstrated the
use
of adenovirus vectors to transfer genes to the respiratory epithelia of rhesus
monkeys.
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Other instances of the use of adenoviruses in gene therapy can be found in
Rosenfeld
et al., Science 252:431-434 (1991); Rosenfeld et al., Cell 68:143- 155 (1992);
Mastrangeli et al., J. Clin. Invest. 91:225-234 (1993); PCT Publication
W094/12649;
and Wang, et al., Gene Therapy 2:775-783 (1995). In a preferred embodiment,
adenovirus vectors are used.
[0283] Adeno-associated~virus (AAV) has also been proposed for use in gene
therapy (Walsh et al., Proc. Soc. Exp. Biol. Med. 204:289-300 (1993); U.S.
Patent
No. 5,436,146).
[0284] Another approach to gene therapy involves transferring a gene to cells
in
tissue culture by such methods as electroporation, lipofection, calcium
phosphate
mediated transfection, or viral infection. Usually, the method of transfer
includes the
transfer of a selectable marker to the cells. The cells are then placed under
selection
to isolate those cells that have taken up and are expressing the transferred
gene. Those
cells are then delivered to a patient.
[0285] In this embodiment, the nucleic acid is introduced into a cell prior to
administration in vivo of the resulting recombinant cell. Such introduction
can be
carried out by any method known in the art, including but not limited to
transfection,
electroporation, microinjection, infection with a viral or bacteriophage
vector
containing the nucleic acid sequences, cell fusion, chromosome-mediated gene
transfer, microcell-mediated gene transfer, spheroplast fusion, etc. Numerous
techniques are known in the art for the introduction of foreign genes into
cells (see,
e.g., Loeffler and Behr, Meth. Enzymol. 217:599-618 (1993); Cohen et al.,
Meth.
Enzymol. 217:618-644 (1993); Cline, Pharmac. Ther. 29:69-92m (1985) and may be
used in accordance with the present invention, provided that the necessary
developmental and physiological functions of the recipient cells are not
disrupted. The
technique should provide for the stable transfer of the nucleic acid to the
cell, so that
the nucleic acid is expressible by the cell and preferably heritable and
expressible by
its cell progeny.
[0286] The resulting recombinant cells can be delivered to a patient by
various
methods known in the art. Recombinant blood cells (e.g., hematopoietic stem or
progenitor cells) are preferably administered intravenously. The amount of
cells
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envisioned fox use depends on the desired effect, patient state, etc., and can
be
determined by one skilled in the art.
[0287] Cells into which a nucleic acid can be introduced for purposes of gene
therapy encompass any desired, available cell type, and include but are not
limited to
epithelial cells, endothelial cells, keratinocytes, fibroblasts, muscle cells,
hepatocytes;
blood cells such as T lymphocytes, B lymphocytes, monocytes, macrophages,
neutrophils, eosinophils, megakaryocytes, granulocytes; various stem or
progenitor
cells, in particular hematopoietic stem or progenitor cells, e.g., as obtained
from bone
marrow, umbilical cord blood, peripheral blood, fetal liver, etc.
[0288j In a preferred embodiment, the cell used for gene therapy is autologous
to
the patient.
[0289] In an embodiment in which recombinant cells are used in gene therapy,
nucleic acid sequences encoding an antibody are introduced into the cells such
that
they are expressible by the cells or their progeny, and the recombinant cells
are then
administered in vivo for therapeutic effect. In a specific embodiment, stem or
progenitor cells are used. Any stem and/or progenitor cells which can be
isolated and
maintained izz vitro can potentially be used in accordance with this
embodiment of the
present invention (see e.g. PCT Publication WO 94/08598; Stemple and Anderson,
Cell 71:973-985 (1992); Rheinwald, Meth. Cell Bio. 21A:229 (1980); and
Pittelkow
and Scott, Mayo Clinic Proc. 61:771 (1986)).
[0290] In a specific embodiment, the nucleic acid to be introduced for
purposes of
gene therapy comprises an inducible promoter operably linked to the coding
region,
such that expression of the nucleic acid is controllable by the presence or
absence of
an appropriate inducer of transcription.
Demonstration of Thef°apeutic or' ProplZylactic Activity
[0291] The compounds or pharmaceutical compositions of the invention are
preferably tested i~r. vitro, and then in vivo for the desired therapeutic or
prophylactic
activity, prior to use in humans. For example, irz vitro assays to demonstrate
the
therapeutic or prophylactic utility of a compound or pharmaceutical
composition
include, the effect of a compound on a cell line or a patient tissue sample.
The effect
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of the compound or composition on the cell line and/or tissue sample can be
determined utilizing techniques known to those of skill in the art including,
but not
limited to, rosette formation assays and cell lysis assays. In accordance with
the
invention, i~ vitf~o assays which can be used to determine whether
administration of a
specific compound is indicated; include if2 vitro cell culture assays in.which
a patient
tissue sample is~ grown in culture, and exposed to or otherwise administered a
compound, and the effect of such compound upon the tissue sample is observed.
TherapeuticlP~oplaylactic Admifaistration ayad Composition
[0292] The invention provides methods of treatment, inhibition and prophylaxis
by
administration to a subject of an effective amount of a compound or
pharmaceutical
composition of the invention, preferably a polypeptide or antibody of the
invention. In
a preferred embodiment, the compound is substantially purified (e.g.,
substantially
free from substances that limit its effect or produce undesired side-effects).
The
subject is preferably an animal, including but not limited to animals such as
cows,
pigs, horses, chiclcens, cats, dogs, etc., and is preferably a mammal, and
most
preferably human.
[0293] Formulations and methods of administration that can be employed when
the compound comprises .a nucleic acid or an immunoglobulin are described
above;
additional appropriate formulations and routes of administration can be
selected from
among those described herein below.
[0294] Various delivery systems are known and can be used to administer a
compound of the invention, e.g., encapsulation in liposomes, microparticles,
microcapsules, recombinant cells capable of expressing the compound, receptor-
mediated endocytosis (see, e.g., Wu and Wu, J. Biol. Chem. 262:4429-4432
(1987)),
construction of a nucleic acid as part of a retroviral or other vector, etc.
Methods of
introduction include but are not limited to intradermal, intramuscular,
intraperitoneal,
intravenous, subcutaneous, intranasal, epidural, and oral routes. The
compounds or
compositions may be administered by any convenient route, for example by
infusion
or bolus injection, by absorption through epithelial or mucocutaneous linings
(e.g.,
oral mucosa, rectal and intestinal mucosa, etc.) and may be administered
together with
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other biologically active agents. Administration can be systemic or local. Tn
addition,
it may be desirable to introduce the pharmaceutical compounds or compositions
of the
invention into the central nervous system by any suitable route, including
intraventricular and intrathecal injection; intraventricular injection may be
facilitated
by an intraventricular catheter, for example, attached to a reservoir, such as
. an
Ommaya reservoir. Pulmonary administration can also be employed, e.g., by use
of an
inhaler or nebulizer, and formulation with an aerosolizing agent.
[0295] In a specific embodiment, it may be desirable to administer the
pharmaceutical compounds or compositions of the invention locally to the area
in need
of treatment; this may be achieved by, for example, and not by way of
limitation, local
infusion during surgery, topical application, e.g., in conjunction with a
wound dressing
after surgery, by injection, by means of a catheter, by means of a
suppository, or by
means of an implant, said implant being of a porous, non-porous, or gelatinous
material, including membranes, such as sialastic membranes, or fibers.
Preferably,
when administering a protein, including an antibody, of the invention, care
must be
taken to use materials to which the protein does not absorb.
[0296] In another embodiment, the compound or composition can be delivered in
a
vesicle, in particular a liposome (see Langer, Science 249:1527-1533 (1990);
Treat et
al., in Liposomes in the Therapy of Infectious Disease and Cancer, Lopez-
Berestein
and Fidler (eds.), Liss, New York, pp. 353- 365 (1989); Lopez-Berestein,
ibid., pp.
317-327; see generally ibid.)
[0297] In yet another embodiment, the compound or composition can be delivered
in a controlled release system. In one embodiment, a pump may be used (see
Langer,
sups°a; Sefton, CRC Crit. Ref. Biomed. Eng. 14:201 (1987); Buchwald et
al., Surgery
88:507 (1980); Saudek et al., N. Engl. J. Med. 321:574 (1989)). In another
embodiment, polymeric materials can be used (see Medical Applications of
Controlled
Release, Langer and Wise (eds.), CRC Pres., Boca Raton, Florida (1974);
Controlled
Drug Bioavailability, Drug Product Design and Performance, Smolen and Ball
(eds.),
Wiley, New Yorlc (1984); Ranger and Peppas, J., Macromol. Sci. Rev. Macromol.
Chem. 23:61 (1983); see also Levy et al., Science 228:190 (1985); During et
al., Ann.
Neurol. 25:351 (1989); Howard et al., J.Neurosurg. 71:105 (1989)). In yet
another
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embodiment, a controlled release system can be placed in proximity of the
therapeutic
target, e.g., the brain, thus requiring only a fraction of the systemic dose
(see, e.g.,
Goodson, in Medical Applications of Controlled Release, supra, vol. 2, pp. 115-
138
(1984)).
[0298] Other controlled release systems are discussed in the review by Langer
(Science 249:1527-1533 (1990)).'
[0299] In a specific embodiment where the compound of the invention is a
nucleic
acid encoding a protein, the nucleic acid can be administered in vivo to
promote
expression of its encoded protein, by constructing it as part of an
appropriate nucleic
acid expression vector and administering it so that it becomes intracellular,
e.g., by use
of a retroviral vector (see U.S. Patent No. 4,980,286), or by direct
injection, or by use
of microparticle bombardment (e.g., a gene gun; Biolistic, Dupont), or coating
with
lipids or cell-surface receptors or transfecting agents, or by administering
it in linkage
to a homeobox- like peptide which is known to enter the nucleus (see e.g.,
Joliot et al.,
Proc. Natl. Acad. Sci. USA 88:1864-1868 (1991)), etc. Alternatively, a nucleic
acid
can be introduced intracellularly and incorporated within host cell DNA for
expression, by homologous recombination.
[0300] The present invention also provides pharmaceutical compositions. Such
compositions comprise a therapeutically effective amount of a compound, and a
pharmaceutically acceptable carrier. In a specific embodiment, the term
"pharmaceutically acceptable" means approved by a regulatory agency of the
Federal
or a state government or listed in the U.S. Pharmacopeia or other generally
recognized
pharmacopeia for use in animals, and more particularly in humans. The term
"carrier"
refers to a diluent, adjuvant, excipient, or vehicle with which the
therapeutic is
administered. Such pharmaceutical carriers can be sterile liquids, such as
water and
oils, including those of petroleum, animal, vegetable or synthetic origin,
such as
peanut oil, soybean oil, mineral oil, sesame oil and the like. Water is a
preferred
carrier when the pharmaceutical composition is administered intravenously.
Saline
solutions and aqueous dextrose and glycerol solutions can also be employed as
liquid
carriers, particularly for injectable solutions. Suitable pharmaceutical
excipients
include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk,
silica gel,
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sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim
milk,
glycerol, propylene, glycol, water, ethanol and the like. The composition, if
desired,
can also contain minor amounts of wetting or emulsifying agents, or pH
buffering
agents. These compositions can take the form of solutions, suspensions,
emulsion,
tablets, pills, capsules, powders, sustained-release formulations and the
like. The
composition can be formulated as a suppository, with traditional binders and
carriers
such as triglycerides. Oral formulation can include standard carriers such as
pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium
saccharine, cellulose, magnesium carbonate, etc. Examples of suitable
pharmaceutical
carriers are described in "Remington's Pharmaceutical Sciences" by E.W.
Martin.
Such compositions will contain a therapeutically effective amount of the
compound,
preferably in purified form, together with a suitable amount of carrier so as
to provide
the form for proper administration to the patient. The formulation should suit
the
mode of administration.
[0301] In a preferred embodiment, the composition is formulated in accordance
with routine procedures as a pharmaceutical composition adapted for
intravenous
administration to human beings. Typically, compositions for intravenous
administration are solutions in sterile isotonic aqueous buffer. Where
necessary, the
composition may also include a solubilizing agent and a local anesthetic such
as
lignocaine to ease pain at the site of the injection. Generally, the
ingredients are
supplied either separately or mixed together in unit dosage form, for example,
as a dry
lyophilized powder or water free concentrate in a hermetically sealed
container such as
an ampoule or sachette indicating the quantity of active agent. Where the
composition
is to be administered by infusion, it can be dispensed with an infusion bottle
containing sterile pharmaceutical grade water or saline. Where the composition
is
administered by injection, an ampoule of sterile water for injection or saline
can be
provided so that the ingredients may be mixed prior to administration.
[0302] The compounds of the invention can be formulated as neutral or salt
forms.
Pharmaceutically acceptable salts include those formed with anions such as
those
derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc.,
and those
formed with cations such as those derived from sodium, potassium, ammonium,
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calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino
ethanol,
histidine, procaine, etc.
[0303] The amount of the compound of the invention, which will be effective in
the treatment, inhibition and prevention of a disease or disorder associated
with
aberrant expression and/or activity of a polypeptide of the invention cambe
determined
by standard clinical techniques. In addition, ifa vitro assays may optionally
be
employed to help ,identify optimal dosage ranges. The precise dose to be
employed in
the formulation will also depend on the route of administration, and the
seriousness of
the disease or disorder, and should be decided according to the judgment of
the
practitioner and each patient's circumstances. Effective doses may be
extrapolated
from dose-response curves derived from iri vitro or animal model test systems.
[0304] For antibodies, the dosage administered to a patient is typically 0.1
mg/kg
to 100 mg/lcg of the patient's body weight. Preferably, the dosage
administered to a
patient is between 0.1 mg/kg and 20 mg/kg of the patient's body weight, more
preferably 1 mg/kg to 10 mg/kg of the patient's body weight. Generally, human
antibodies have a longer half life within the human body than antibodies from
other
species due to the immune response to the foreign polypeptides. Thus, lower
dosages
of human antibodies and less .frequent administration is often possible.
Further, the
dosage and frequency of administration of antibodies of the invention may be
reduced
by enhancing uptake and tissue penetration (e.g., into the brain) of the
antibodies by
modifications such as, for example, lipidation.
[0305] The invention also provides a pharmaceutical pack or kit comprising one
or
more containers filled with one or more of the ingredients of the
pharmaceutical
compositions of the invention. Optionally associated with such containers) can
be a
notice in the form prescribed by a governmental agency regulating the
manufacture,
use or sale of pharmaceuticals or biological products, which notice reflects
approval
by the agency of manufacture, use or sale for human administration.
Diagyzosis and Inaaging
[0306] Labeled antibodies, and derivatives and analogs thereof, which
specifically
bind to a polypeptide of interest can be used for diagnostic purposes to
detect,
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diagnose, or monitor diseases, disorders, and/or conditions associated with
the aberrant
expression and/or activity of a polypeptide of the invention. The invention
provides
for the detection of aberrant expression of a polypeptide of interest,
comprising (a)
assaying the expression of the polypeptide of interest in cells or body fluid
of an
individual using one or more antibodies.specific to the polypeptide interest
and.(b)
comparing the level of gene expression with a standard gene expression level,
whereby
an increase or decrease in the assayed polypeptide gene expression level
compared to
the standard expression level is indicative of aberrant expression.
[0307] The invention provides a diagnostic assay for diagnosing a prostate
disorder, comprising (a) assaying the expression of the polypeptide of
interest in cells
or body fluid of an individual using one or more antibodies specific to the
polypeptide
interest and (b) comparing the level of gene expression with a standard gene
expression level, whereby an increase or decrease in the assayed polypeptide
gene
expression level compared to the standard expression level is indicative of a
particular
disorder. With respect to cancer, the presence of a relatively high amount of
transcript
in biopsied tissue from an individual may indicate a predisposition for the
development of the disease, or may provide a means for detecting the disease
prior to
the appearance of actual clinical, symptoms. A more definitive diagnosis of
this type
may allow health professionals to employ preventative measures , or aggressive
treatment earlier thereby preventing the development or further progression of
the
cancer.
[0308] Antibodies of the invention can be used to assay protein levels in a
biological sample using classical immunohistological methods known to those of
skill
in the art (e.g., see Jalkanen et al., J. Cell. Biol. 101:976-985 (1985);
Jalkanen et al., J.
Cell . Biol. 105:3087-3096 (1987)). Other antibody-based methods useful for
detecting protein gene expression include immunoassays, such as the enzyme
linked
immunosorbent assay (ELISA) and the radioimmunoassay (RIA). Suitable antibody
assay labels are known in the art and include enzyme labels, such as, glucose
oxidase;
radioisotopes, such as iodine (125I, 121I), carbon (14C), sulfur (35S),
tritium (3H),
indium (112In), and technetium (99Tc); luminescent labels, such as luminol;
and
fluorescent labels, such as fluorescein and rhodamine, and biotin.
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(0309] One facet of the invention is the detection and diagnosis of a disease
or
disorder associated with aberrant expression of a polypeptide of interest in
an animal,
preferably a mammal and most preferably a human. A preferred embodiment of the
invention is the detection and diagnosis of a disease or disorder of the
prostate
associated with aberrant ,expression of a prostate cancer antigen in an
animal,
preferably a mammal and most preferably a human, In one embodiment, diagnosis
comprises: a) administering (for example, parenterally, subcutaneously, or '
intraperitoneally) to a subject an effective amount of a labeled molecule
which
specifically binds to the polypeptide of interest; b) waiting for a time
interval
following the administering for permitting the labeled molecule to
preferentially
concentrate at sites in the subject where the polypeptide is expressed (and
for
unbound labeled molecule to be cleared to background level); c) determining
background level; and d) detecting the labeled molecule in the subject, such
that
detection of labeled molecule above the background level indicates that the
subject has
a particular disease or disorder associated with aberrant expression of the
polypeptide
of interest. Background level can be determined by various methods including,
comparing the amount of labeled molecule .detected to a standard value
previously
determined for a particular system.
(0310]. It will be understood in the art that the size of the subject and the
imaging
system used will determine the quantity of imaging moiety needed to produce
diagnostic images. In the case of a radioisotope moiety, for a human subject,
the
quantity of radioactivity injected will normally range from about 5 to 20
millicuries of
99mTc. The labeled antibody or antibody fragment will then preferentially
accumulate at the location of cells which contain the specific protein. IrT
vivo tumor
imaging is described in S.W. Burchiel et al., "Immunopharmacokinetics of
Radiolabeled Antibodies and Their Fragments." (Chapter 13 in Tumor Imaging:
The
Radiochemical Detection of Cancer, S.W. Burchiel and B. A. Rhodes, eds.,
Masson
Publishing Inc. (1982)).
[0311] Depending on several variables, including the type of label used and
the
mode of administration, the time interval following the administration for
permitting
the labeled molecule to preferentially concentrate at sites in the subject and
for
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unbound labeled molecule to be cleared to background level is 6 to 48 hours or
6 to 24
hours or 6 to 12 hours. In another embodiment the time interval following
administration is 5 to 20 days or 5 to 10 days.
[0312] In an embodiment, monitoring of the disease or disorder is carried out
by
repeating the method for diagnosing the disease or disorder, for example, one
month
after initial diagnosis, six months after initial diagnosis, one year after
initial diagnosis,
etc.
[0313] Presence of the labeled molecule can be detected in the patient using
methods known in the art for ih vivo scanning. These methods depend upon the
type
of label used. Skilled artisans will be able to determine the appropriate
method for
detecting a particular label. Methods and devices that may be used in the
diagnostic
methods of the invention include, but are not limited to, computed tomography
(CT),
whole body scan such as position emission tomography (PET), magnetic resonance
imaging (MRI), and sonography.
[0314] In a specific embodiment, the molecule is labeled with a radioisotope
and is
detected in the patient using a radiation responsive surgical instrument
(Thurston et al.,
U.S. Patent No. 5,441,050). In another embodiment, the molecule is labeled
with a
fluorescent compound and is 'detected in the patient: using a~ fluorescence
responsive
scanning instrument: :.In another embodiment, the. molecule is labeled with a
positron
emitting metal and is detected in the patent using positron emission-
tomography. In
yet another embodiment, the molecule is labeled with a paramagnetic label and
is
detected in a patient using magnetic resonance imaging (MRI).
Kits
[0315] The present invention provides kits that can be used in the above
methods.
In one embodiment, a kit comprises an antibody of the invention, preferably a
purified
antibody, in one or more containers. In a specific embodiment, the kits of the
present
invention contain a substantially isolated polypeptide comprising an epitope
which is
specifically immunoreactive with an antibody included in the kit. Preferably,
the kits
of the present invention further comprise a control antibody which does not
react with
the polypeptide of interest. In another specific embodiment, the kits of the
present
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invention contain a means for detecting the binding of an antibody to a
polypeptide of
interest (e.g., the antibody may be conjugated to a detectable substrate such
as a
fluorescent compound, an enzymatic substrate, a radioactive compound or a
luminescent compound, or a second antibody which recognizes the first antibody
may
be conjugated~to a detectable substrate): .
[0316] In another specific embodiment ,of the present invention; the' kit is a
diagnostic kit for' use in screening serum ° containing antibodies
specific against
proliferative and/or cancerous polynucleotides and polypeptides. Such a kit
may
include a control antibody that does not react with the polypeptide of
interest. Such a
kit may include a substantially isolated polypeptide antigen comprising an
epitope,
which is specifically immunoreactive with at least one anti-polypeptide
antigen
antibody. Further, such a kit includes means for detecting the binding of said
antibody
to the antigen (e.g., the antibody may be conjugated to a fluorescent compound
such as
fluorescein or rhodamine, which can be detected by flow cytometry). In
specific
embodiments, the kit may include a recombinantly produced or chemically
synthesized polypeptide antigen. The polypeptide antigen of the kit may also
be
attached to a solid support.
[0317] In a more specific embodiment the detecting means of the above-
described
kit includes a solid support to which said polypeptide antigen is attached.
Such a kit
may also include a non-attached reporter-labeled anti-human antibody. In this
embodiment, binding of the antibody to the polypeptide antigen can be detected
by
binding of the said reporter-labeled antibody.
[0318] In an additional embodiment, the invention includes a diagnostic kit
for use
in screening serum containing antigens of the polypeptide of the invention.
The
diagnostic kit includes a substantially isolated antibody specifically
immunoreactive
with polypeptide or polynucleotide antigens, and means for detecting the
binding of
the polynucleotide or polypeptide antigen to the antibody. In one embodiment,
the
antibody is attached to a solid support. In a specific embodiment, the
antibody may be
a monoclonal antibody. The detecting means of the kit may include a second,
labeled
monoclonal antibody. Alternatively, or in addition, the detecting means may
include a
labeled, competing antigen.
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[0319] In one diagnostic configuration, test serum is reacted with a solid
phase
reagent having a surface-bound antigen obtained by the methods of the present
invention. After binding with specific antigen antibody to the reagent and
removing
unbound serum components by washing, the reagent is reacted with reporter-
labeled
anti-human antibody to bind~reporter to the reagent.in proportion to the
amount of .
bound anti-antigen antibody on the solid support. The. reagent is again
.washed to
remove unbound labeled antibody, and .the amount ~of reporter associated with
the
reagent is determined. Typically, the reporter is an enzyme, which is detected
by
incubating the solid phase in the presence of a suitable fluorometric,
luminescent or
colorimetric substrate (Sigma, St. Louis, MO).
[0320] The solid surface reagent in the above assay is prepared by known
techniques for attaching protein material to solid support material, such as
polymeric
beads, dip sticks, 96-well plate or filter material. These attachment methods
generally
include non-specific adsorption of the protein to the support or covalent
attachment of
the protein, typically through a free amine group, to a chemically reactive
group on the
solid support, such as an activated carboxyl, hydroxyl, or aldehyde group.
Alternatively, streptavidin coated plates can be used in conjunction with
biotinylated
antigen(s)..
[0321] . Thus; the invention provides an assay system or kit for carrying out
this
diagnostic method. The kit generally includes a support with surface- bound
recombinant antigens, and a reporter-labeled anti-human antibody for detecting
surface-bound anti-antigen antibody.
Uses of the Polynucleotides
[0322] Each of the polynucleotides identified herein can be used in numerous
ways as reagents. The following description should be considered exemplary and
utilizes lcnown techniques.
[0323] The polynucleotides of the present invention are useful for chromosome
identification. There exists an ongoing need to identify new chromosome
markers,
since few chromosome marking reagents, based on actual sequence data (repeat
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polymorphisms), are presently available. Each sequence is specifically
targeted to and
can hybridize with a particular location on an individual human chromosome,
thus
each polynucleotide of the present invention can routinely be used as a
chromosome
marker using techniques known in the art. Table 1 A, column 8 provides the
chromosome location of some.of the polynucleotides of the invention. .
[0324] Briefly, sequences can' be mapped to chromosomes by preparing PCR
primers (preferably at least 15 by (e.g., 15-25 bp) from the sequences shown
in SEQ
ID NO:X. Primers can optionally be selected using computer analysis so that
primers
do not span more than one predicted exon in the genomic DNA. These primers are
then used for PCR screening of somatic cell hybrids containing individual
human
chromosomes. Only those hybrids containing the human gene corresponding to SEQ
ID NO:X will yield an amplified fragment.
[0325] Similarly, somatic hybrids provide a rapid method of PCR mapping the
polynucleotides to particular chromosomes. Three or more clones can be
assigned per
day using a single thermal cycler. Moreover, sublocalization of the
polynucleotides
can be achieved with panels of specific chromosome fragments. Other gene
mapping
strategies that can be used include in situ hybridization, prescreening with
labeled
flow-sorted chromosomes, preselection by hybridization to construct chromosome
specific-cDNA libraries, and computer mapping techniques (See, e.g.; Shuler,
Trends
Biotechnol 16:456-459 (1998) which is hereby incorporated by reference in its
entirety).
[0326] Precise chromosomal location of the polynucleotides can also be
achieved
using fluorescence in situ hybridization (FISH) of a metaphase chromosomal
spread.
This technique uses polynucleotides as short as 500 or 600 bases; however,
polynucleotides 2,000-4,000 by are preferred. For a review of this technique,
see
Verma et al., "Human Chromosomes: a Manual of Basic Techniques," Pergamon
Press, New Yorlc (1988).
[0327] For chromosome mapping, the polynucleotides can be used individually
(to
marls a single chromosome or a single site on that chromosome) or in panels
(for
marking multiple sites and/or multiple chromosomes).
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[0328] Thus, the present invention also provides a method fox chromosomal
localization which involves (a) preparing PCR primers from the polynucleotide
sequences in Table 1A and/or Table 2 and SEQ ID NO:X and (b) screening somatic
cell hybrids containing individual chromosomes.
[0329] The polynucleotides of the present invention would likewise be
useful.for
radiation hybrid mapping,. HAPPY.mapping; and long range restriction
mapping~'For a'.
review of these techniquesvand others' lcnown in the art; see, e.g. Dear;
"Genome
Mapping: A Practical Approach," IRL Press at Oxford University Press, London
(1997); Aydin, J. Mol. Med. 77:691-694 (1999); Hacia et al., Mol. Psychiatry
3:483-
492 (1998); Herrick et al., Chromosome Res. 7:409-423 (1999); Hamilton et al.,
Methods Cell Biol. 62:265-280 (2000); and/or Ott, J. Hered. 90:68-70 (1999),
each of
which is hereby incorporated by reference in its entirety.
[0330] Once a polynucleotide has been mapped to a precise chromosomal
location,
the physical position of the polynucleotide can be used in linkage analysis.
Linkage
analysis establishes coinheritance between a chromosomal location and
presentation of
a particular disease. (Disease mapping data are found, for example, in V.
McKusick,
Mendelian Inheritance in Man (available on line through Johns Hoplcins
University
Welch Medical Library).) , Column 9 of 'Table 1A provides an OMIM reference
identification number of diseases associated with the cytologic band disclosed
in
column 8 of Table 1A, as determined using techniques described herein and by
reference to Table 5. Assuming 1 megabase mapping resolution and one gene per
20
kb, a cDNA precisely localized to a chromosomal region associated with the
disease
could be one of 50-500 potential causative genes.
[0331] Thus, once coinheritance is established, differences in a
polynucleotide of
the invention and the corresponding gene between affected and unaffected
individuals
can be examined. First, visible structural alterations in the chromosomes,
such as
deletions or translocations, are examined in chromosome spreads or by PCR. If
no
structural alterations exist, the presence of point mutations are ascertained.
Mutations
observed in some or all affected individuals, but not in normal individuals,
indicate
that the mutation may cause the disease. However, complete sequencing of the
polypeptide and the corresponding gene from several normal individuals is
required to
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distinguish the mutation from a polymorphism. If a new polymorphism is
identified,
this polymorphic polypeptide can be used for further linkage analysis.
[0332] Furthermore, increased or decreased expression of the gene in affected
individuals as compared to unaffected individuals can be assessed using the
polynucleotides of the invention. : Any of these alterations (altered
expression,
chromosomal rearrangement; ormutation) can be used as a diagnostic or
prognostics
marker. Diagnostic and prognostic methods, kits and reagents encompassed by
the
present invention are briefly described below and more thoroughly elsewhere
herein
(see e.g., the sections labeled "Antibodies", "Diagnostic Assays", and
"Methods for
Detecting Prostate Diseases, Including Cancer").
[0333] Thus, the invention also provides a diagnostic method useful during
diagnosis of a disorder, involving measuring the expression level of
polynucleotides of
the present invention in cells or body fluid from an individual and comparing
the
measured gene expression level with a standard level of polynucleotide
expression
level, whereby an increase or decrease in the gene expression level compared
to the
standard is indicative of a disorder. Additional non-limiting examples of
diagnostic
methods encompassed by the present invention are more thoroughly. described
elsewhere herein (see, e.g., Example 12).
j0334] In still another embodiment, the invention includes a kit for analyzing
samples for the presence of proliferative and/or cancerous polynucleotides
derived
from a test subject, as further described herein. In a general embodiment, the
kit
includes at least one polynucleotide probe containing a nucleotide sequence
that will
specifically hybridize with a polynucleotide of the invention and a suitable
container.
In a specific embodiment, the kit includes two polynucleotide probes defining
an
internal region of the polynucleotide of the invention, where each probe has
one strand
containing a 31'mer-end internal to the region. In a further embodiment, the
probes
may be useful as primers for polymerase chain reaction amplification.
[0335] Where a diagnosis of a related disorder, including, for example,
diagnosis
of a tumor, has already been made according to conventional methods, the
present
invention is useful as a prognostic indicator, whereby patients exhibiting
enhanced or
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depressed polynucleotide of the invention expression will experience a worse
clinical
outcome relative to patients expressing the gene at a level nearer the
standard level.
[0336] By "measuring the expression level of polynucleotides of the invention"
is
intended qualitatively or quantitatively measuring or estimating the level of
the
polypeptide of the invention or the level of the mRNA encoding the polypeptide
of the
invention in a first biological sample either directly (e.g., by determining
or estimating
absolute protein level or mRNA level) or relatively (e.g., by comparing to the
polypeptide level or mRNA level in a second biological sample). Preferably,
the
polypeptide level or mRNA level in the first biological sample is measured or
estimated and compared to a standard polypeptide level or mRNA level, the
standard
being taken from a second biological sample obtained from an individual not
having
the related disorder or being determined by averaging levels from a population
of
individuals not having a related disorder. As will be appreciated in the art,
once a
standard polypeptide level or mRNA level is known, it can be used repeatedly
as a
standard for comparison.
[0337] By "biological sample" is intended any biological sample obtained from
an
individual, body fluid, cell line, tissue culture, or other source which
contains
polypeptide of the present invention or the corresponding mRNA. As indicated,
biological samples include body fluids (such as semen, lymph, vaginal pool,
sera,
plasma, urine, synovial fluid and spinal fluid) which contain the polypeptide
of the
present invention, and tissue sources found to express the polypeptide of the
present
invention. Methods for obtaining tissue biopsies and body fluids from mammals
are
well known in the art. Where the biological sample is to include mRNA, a
tissue
biopsy is the preferred source.
[0338] The methods) provided above may preferably be applied in a diagnostic
method and/or kits in which polynucleotides and/or polypeptides of the
invention are
attached to a solid support. In one exemplary method, the support may be a
"gene
chip" or a "biological chip" as described in U.S. Patents 5,837,832,
5,874,219, and
5,856,174. Further, such a gene chip with polynucleotides of the invention
attached
may be used to identify polymorphisms between the isolated polynucleotide
sequences
of the invention, with polynucleotides isolated from a test subject. The
knowledge of
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such polymorphisms (i.e., their location, as well as, their existence) would
be
beneficial in identifying disease loci for many disorders, such as for
example, in neural
disorders, immune system disorders, muscular disorders, reproductive
disorders,
gastrointestinal disorders, pulmonary disorders, digestive disorders,
cardiovascular
disorders, renal disorders, proliferative disorders, and/or cancerous diseases
and
conditions. Such a method is described inU.S. Patents 5,858,659 and 5856;104.'
The
U.S. Patents referenced supra are hereby incorporated by reference in their
entirety
herein.
[0339] The present invention encompasses polynucleotides of the present
invention that are chemically synthesized, or reproduced as peptide nucleic
acids
(PNA), or according to other methods known in the art. The use of PNAs would
serve
as the preferred form if the polynucleotides of the invention are incorporated
onto a
solid support, or gene chip. For the purposes of the present invention, a
peptide nucleic
acid (PNA) is a polyamide type of DNA analog and the monomeric units for
adenine,
guanine, thymine and cytosine are available commercially (Perceptive
Biosystems).
Certain components of DNA, such as phosphorus, phosphorus oxides, or
deoxyribose
derivatives, are not present in PNAs. As disclosed by Nielsen et al.; Science
254:1497
(1991); and Egholm et al.,.Nature 365:666 (1993), PNAs bind specifically and
tightly
to complementary DNA strands and are not degraded by nucleases. In fact, PNA
binds
more strongly to DNA than DNA itself does. This is probably because there is
no
electrostatic repulsion between the two strands, and also the polyamide
backbone is
more flexible. Because of this, PNA/DNA duplexes bind under a wider range of
stringency conditions than DNA/DNA duplexes, making it easier to perform
multiplex
hybridization. Smaller probes can be used than with DNA due to the strong
binding. In
addition, it is more likely that single base mismatches can be determined with
PNA/DNA hybridization because a single mismatch in a PNA/DNA 15-mer lowers the
melting point (Tm) by 8°-20° C, vs. 4°-16° C
for the DNA/DNA 15-mer duplex.
Also, the absence of charge groups in PNA means that hybridization can be done
at
low ionic strengths and reduce possible interference by salt during the
analysis.
[0340] The compounds of the present invention have uses which include, but are
not limited to, detecting cancer in mammals. In particular the invention is
useful
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during diagnosis of pathological cell proliferative neoplasias which include,
but are
not limited to: acute myelogenous leukemias including acute monocytic
leukemia,
acute myeloblastic leukemia, acute promyelocytic leukemia, acute
myelomonocytic
leukemia, acute erythroleukemia, acute megakaryocytic leukemia, and acute
undifferentiated leukemia etc.; and chronic myelogenous leukemias
including:chronic
myelomonocytic leukemia, chronic granulocytic leukemia, etc. , Preferred
mammals
include monkeys, apes, cats, dogs, cows, pigs, horses, rabbits and humans.
Particularly preferred are humans.
[0341] The compounds of the present invention have preferred uses which
include,
but are not limited to, detecting prostate cancer in mammals. In particular
the
invention is useful during diagnosis of pathological cell proliferative
neoplasias, which
include, but are not limited to: prostate cancers such as adenocarcinoma,
transitional
cell carcinomas, ductal carcinomas, and squamous cell carcinomas, and as
described
under "Hyperproliferative Disorders" and/or "Reproductive System Disorders"
below.
Preferred mammals include monkeys, apes, cats, dogs, cows, pigs, horses,
rabbits and
humans. Particularly preferred are humans.
[0342] Pathological cell proliferative disorders are. often associated with
inappropriate activation of proto-oncogenes. (Gelmann, E. P. et al., "The
Etiology of
Acute Leukemia: Molecular~Genetics and Viral Oncology," in Neoplastic Diseases
of
the Blood, Vol 1., Wiernik, P. H. et al. eds., 161-182 (1985)). Neoplasias are
now
believed to result from the qualitative alteration of a normal cellular gene
product, or
from the quantitative modification of gene expression by insertion into the
chromosome of a viral sequence, by chromosomal translocation of a gene to a
more
actively transcribed region, or by some other mechanism. (Gelmann et al.,
,rup~°a) It is
lilcely that mutated or altered expression of specific genes is involved in
the
pathogenesis of some leukemias, among other tissues and cell types. (Gelmann
et al.,
supoa) Indeed, the human counterparts of the oncogenes involved in some animal
neoplasias have been amplified or translocated in some cases of human leukemia
and
carcinoma. (Gelmann et al., supra)
[0343] For example, c-myc expression is highly amplified in the non-
lymphocytic
leukemia cell line HL-60. When HL-60 cells are chemically induced to stop
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proliferation, the level of c-myc is found to be downregulated. (International
Publication Number WO 91/15580). However, it has been shown that exposure of
HL-
60 cells to a DNA construct that is complementary to the 5' end of c-myc or c-
myb
blocks translation of the corresponding mRNAs which downregulates expression
of
the c-myc or c-myb proteins and causes arrest of cell proliferation
and.differentiation
of the treated cells. . (International Publication Number WO 91/15580;
'Wickstrom et
al., Proc. Natl. Acad. Sci. 85:1028 (1988); Anfossi et al:, Proc. Natl. Acad:
Sci.
86:3379 (1989)). However, the skilled artisan would appreciate the present
invention's
usefulness is not be limited to treatment, prevention, diagnosis and/or
prognosis, of
proliferative disorders of cells and tissues of hematopoietic origin, in light
of the
numerous cells and cell types of varying origins which are known to exhibit
proliferative phenotypes. In preferred embodiments, the compounds and/or
methods
of the invention are used to treat, prevent, diagnose, and/or prognose,
proliferative
disorders of prostate cells and tissues.
[0344] In addition to the foregoing, a polynucleotide of the present invention
can
be used to control gene expression through triple helix formation or through
antisense
DNA or RNA. Antisense techniques are discussed, for example, in Okano, J.
Neurochem. 56: 560 (1991); "Oligodeoxynucleotides as Antisense Inhibitors of
Gene
Expression,, CRC Press; Boca Raton, FL (1988). Triple helix formation is
discussed in,
for instance Lee et al., Nucleic Acids Research 6: 3073 (1979); Cooney et al.,
Science
fl
241: 456 (1988); and Dervan et al., Science 251: 1360 (1991). Both methods
rely on
binding of the polynucleotide to a complementary DNA or RNA. For these
techniques, preferred polynucleotides are usually oligonucleotides 20 to 40
bases in
length and complementary to either the region of the gene involved in
transcription
(triple helix - see Lee et al., Nucl. Acids Res. 6:3073 (1979); Cooney et al.,
Science
241:456 (1988); and Dervan et al., Science 251:1360 (1991)) or to the mRNA
itself
(antisense - Okano, J. Neurochem. 56:560 (1991); Oligodeoxy-nucleotides as
Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, FL (1988).)
Triple
helix formation optimally results in a shut-off of RNA transcription from DNA,
while
antisense RNA hybridization blocks translation of an mRNA molecule into
polypeptide. The oligonucleotide described above can also be delivered to
cells such
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that the antisense RNA or DNA may be expressed in vivo to inhibit production
of
polypeptide of the present invention antigens. Both techniques are effective
in model
systems, and the information disclosed herein can be used to design antisense
or triple
helix polynucleotides in an effort to treat disease, and in particular, for
the treatment of
proliferative diseases : and/or conditions. Non-limiting antisense,: and
triple helix
methods encompassed by the present 'invention are more thoroughly described .
elsewhere herein (see;, e.g.; the section labeled "Antisense and Ribozyme
(Antagonists)").
[0345] Polynucleotides of the present invention are also useful in gene
therapy.
One goal of gene therapy is to insert a normal gene into an organism having a
defective gene, in an effort to correct the genetic defect. The
polynucleotides
disclosed in the present invention offer a means of targeting such genetic
defects in a
highly accurate manner. Another goal is to insert a new gene that was not
present in
the host genome, thereby producing a new trait in the host cell. Additional
non-
limiting examples of gene therapy methods encompassed by the present invention
are
more thoroughly described elsewhere herein (see, e.g., the sections labeled
"Gene
Therapy Methods" and Examples .16,.17. and 1 ~).
[0346] The polynucleotides are also useful for identifying individuals from
minute
biological samples: The United States military, for example, is considering
the use of.
restriction fragment length polymorphism (RFLP) for identification of its
personnel.
In this technique, an individual's genomic DNA is digested with one or more
restriction enzymes, and probed on a Southern blot 'to yield unique bands for
identifying personnel. This method does not suffer from the current
limitations of
"Dog Tags" which can be lost, switched, or stolen, making positive
identification
difficult. The polynucleotides of the present invention can be used as
additional DNA
markers for RFLP.
[0347] The polynucleotides of the present invention can also be used as an
alternative to RFLP, by determining the actual base-by-base DNA sequence of
selected portions of an individual's genome. These sequences can be used to
prepare
PCR primers for amplifying and isolating such selected DNA, which can then be
sequenced. Using this technique, individuals can be identified because each
individual
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will have a unique set of DNA sequences. Once an unique ID database is
established
for an individual, positive identification of that individual, living or dead,
can be made
from extremely small tissue samples.
[0348] Forensic biology also benefits from using DNA-based identification
techniques as disclosed.herein. DNA sequences .taken from very. small
biological
samples such as tissues, e.g., hair- or skin, or body fluids, e.g., bloody
saliva,-semen,
synovial fluid, amniotic fluid, , breast milk, lymph, pulmonary sputum or
surfactant,
urine, fecal matter, etc., can be amplified using PCR. In one prior art
technique, gene
sequences amplified from polymorphic loci, such as DQa class II HLA gene, are
used
in forensic biology to identify individuals. (Erlich, H., PCR Technology,
Freeman and
Co. (1992).) Once these specific polymorphic loci are amplified, they are
digested
with one or more restriction enzymes, yielding an identifying set of bands on
a
Southern blot probed with DNA corresponding to the DQa class II HLA gene.
Similarly, polynucleotides of the present invention can be used as polymorphic
markers for forensic purposes.
[0349] There is also a need for reagents capable of identifying the source of
a
particular tissue. Such need arises, for example, in forensics when presented
with
tissue of unknown origin: Appropriate reagents can . comprise, for. example,
DNA.
probes or primers prepared from. the sequences of the present invention,
specific to '
tissues, including but not limited to, those sequences referred to in Table
1A. Panels
of such reagents can identify tissue by species and/or by organ type. In a
similar
fashion, these reagents can be used to screen tissue cultures for
contamination.
Additional non-limiting examples of such uses are further described herein.
[0350] Because prostate cancer antigens are found expressed in the prostate,
the
polynucleotides of the present invention are also useful as hybridization
probes for
differential identification of the tissues) or cell types) present in a
biological sample.
Similarly, polypeptides and antibodies directed to polypeptides of the present
invention are useful to provide immunological probes for differential
identification of
the tissues) (e.g., immunohistochemistry assays) or cell types) (e.g.,
immunocytochemistry assays). In a specific embodiment, the polynucleotides of
the
present invention are also useful as hybridization probes for differential
identification
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of prostate cancer tissues) or cell types) present in a biological sample.
Similarly,
polypeptides and antibodies directed to polypeptides of the present invention
are
useful to provide immunological probes for differential identification of
prostate
cancer tissues) (e.g., immunohistochemistry assays) or cell types) (e.g.,
immunocytochemistry assays). In addition, for.,a.number of disorders of the
above
tissues or cells, significantly higher or lower levels of gene expression of
the
polynucleotides/polypeptides. of the present invention may be detected in
certain
tissues (e.g., tissues expressing polypeptides and/or polynucleotides of the
present
invention, for example, normal prostate or diseased prostate tissues, and/or
those
tissues/cells corresponding to the library source relating to a polynucleotide
sequence
of the invention as disclosed in column 7 of Table 1A, and/or cancerous and/or
wounded tissues) or bodily fluids (e.g., semen, lymph, vaginal pool, serum,
plasma,
urine, synovial fluid or spinal fluid) taken from an individual having such a
disorder,
relative to a "standard" gene expression level, i.e., the expression level in
healthy
tissue from an individual not having the disorder.
[0351] Thus, the invention provides a diagnostic method of a disorder, which
involves: (a) assaying gene expression level in cells or body fluid of an
individual; (b)
comparing the gene expression level witha standard gene:expression level,
whereby
an.increase or decrease in he assayed gene. expression level compared to the
standard '.
expression level is indicative of a disorder.
[0352] In the very least, the polynucleotides of the present invention can be
used
as molecular weight markers on Southern gels, as diagnostic probes for the
presence of
a specific mRNA in a particular cell type, as a probe to "subtract-out" known
sequences in the process of discovering novel polynucleotides, for selecting
and
making oligomers for attachment to a "gene chip" or other support, to raise
anti-DNA
antibodies using DNA immunization techniques, and as an antigen to elicit an
immune
response.
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Uses of the Polypentides
[0353] Each of the polypeptides identified herein can be used in numerous
ways.
The following description should be considered exemplary and utilizes known
techniques.
[0354] Polypeptides and antibodies directed to polypeptides of .the present
invention are useful to provide immunological probes for differential
identification of
the tissues) (e:g.; immunohistochemistry assays such as, for example; ABC
immunoperoxidase (Hsu et al., J. Histochem. Cytochem. 29:577-580 (1981)) or
cell
types) (e.g., immunocytochemistry assays).
[0355] Antibodies can be used to assay levels of polypeptides encoded by
polynucleotides of the invention in 'a biological sample using classical
immunohistological methods known to those of skill in the art (see, e.g.,
Jalkanen, et
al., J. Cell. Biol. 101:976-985 (1985); Jalkanen, et al., J. Cell. Biol.
105:3087-3096
(1987)). Other antibody-based methods useful for detecting protein gene
expression
include immunoassays, such as the enzyme linked immunosorbent assay (ELISA)
and
the radioimmunoassay (RIA). Suitable antibody assay labels are known in the
art and
include enzyme labels, such as, glucose oxidase; radioisotopes, such as iodine
(l3il,
izsh 123I' lzil)~ carbon (14C), sulfur (3sS), tritium (3H), indium (ltsmln,
llsmln, lzIn,
nlln), and technetium (99Tc, 99mTc), thallium. (2°1Ti), gallium (68Ga,
6~Ga), palladium
(io3Pd), molybdenum (99Mo), xenon (l3sXe), fluorine (18F), ls3Sm, l~~Lu,
ls~Gd, la9Pm,
iaoLa msYb 166H~ 90Y 47SC 186Re 188Re 142Pr 105 9~Ru. luminescent labels such
> > > > > > > > > > >
as luminol; and fluorescent labels, such as fluorescein and rhodamine, and
biotin.
[0356] In addition to assaying levels of polypeptide of the present invention
in a
biological sample, proteins can also be detected ih vivo by imaging. Antibody
labels
or markers for iya vivo imaging of protein include those detectable by X-
radiography,
NMR or ESR. For X-radiography, suitable labels include radioisotopes such as
barium or cesium, which emit detectable radiation but are not overtly harmful
to the
subject. Suitable markers for NMR and ESR include those with a detectable
characteristic spin, such as deuterium, which may be incorporated into the
antibody by
labeling of nutrients for the relevant hybridoma.
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[0357] A prostate cancer antigen-specific antibody or antibody fragment which
has
been labeled with an appropriate detectable imaging moiety, such as a
radioisotope
for exam 1e lsll llzln 99mTc (1311 lzsl 1231 lzll) carbon (14C) sulfur (3sS)
tritium
( p > > > > > > > > > >
(3H), indium (lls"'In, 113mIn, llzln, 111In), and technetium (99Tc, 99mTc),
thallium (zolTi),
gallium (68Ga, 6~Ga), palladium (losPd), molybdenum.(99Mo), xenon (133Xe),
fluorine
(18F 153sm 177Lu 159Gd . 149Pm 140La 175Yb 166H~ 90Y 4~Sc ls6Re 188Re l4zPr
> > . > > > > > > > > > > >
lose 9~Ru), a radio-opaque substance, or a material detectable by nuclear
magnetic
resonance, is introduced (for example, parenterally, subcutaneously or
intraperitoneally) into the mammal to be examined for a prostate disorder. It
will be
understood in the art that the size of the subject and the imaging system used
will
determine the quantity of imaging moiety needed to produce diagnostic images.
In the
case of a radioisotope moiety, for a human subject, the quantity of
radioactivity
injected will normally range from about 5 to 20 millicuries of 99mTc. The
labeled
antibody or antibody fragment will then preferentially accumulate at the
location of
cells which express the polypeptide encoded by a polynucleotide of the
invention. In
vivo tumor imaging is described in S.W. Burchiel et al.,
"Immunopharmacokinetics of
Radiolabeled Antibodies and Their Fragments" (Chapter 13 in Tumoy~ Imaging:
The
Radiochemical Detection of Cayace~, S.W. Burchiel and B. A. Rhodes, eds.,
Masson
Publishing Inca (1982)).
[0358] In one embodiment, the invention provides a method for the specific
delivery of compositions of the invention to cells by administering
polypeptides of the
invention (e.g., polypeptides encoded by polynucleotides of the invention
and/or
antibodies) that are associated with heterologous polypeptides or nucleic
acids. In one
example, the invention provides a method for delivering a therapeutic protein
into the
targeted cell. In another example, the invention provides a method for
delivering a
single stranded nucleic acid (e.g., antisense or ribozymes) or double stranded
nucleic
acid (e.g., DNA that can integrate into the cell's genome or replicate
episomally and
that can be transcribed) into the targeted cell.
[0359] In another embodiment, the invention provides a method for the specific
destruction of cells (e.g., the destruction of tumor cells) by administering
polypeptides
of the invention in association with toxins or cytotoxic prodrugs.
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[0360] In a preferred embodiment, the invention provides a method for the
specific
destruction of prostate cells (e.g., aberrant prostate cells, prostate
neoplasm) by
administering polypeptides of the invention (e.g., polypeptides encoded by
polynucleotides of the invention and/or antibodies) in association with toxins
or
cytotoxic prodrugs. In another preferred embodiment the invention provides a
method
for the specific destruction of tissues/cells corresponding .to the library
source relating
to a polynucleotide sequence of the invention as disclosed in column 7 of
Table 1A by
administering polypeptides of the invention in association with toxins or
cytotoxic
prodrugs.
[0361] By "toxin" is meant one or more compounds that bind and activate
endogenous cytotoxic effector systems, radioisotopes, holotoxins, modified
toxins,
catalytic subunits of toxins, or any molecules or enzymes not normally present
in or on
the surface of a cell that under defined conditions cause the cell's death.
Toxins that
may be used according to the methods of the invention include, but are not
limited to,
radioisotopes known in the art, compounds such as, for example, antibodies (or
complement fixing containing portions thereof) that bind an inherent or
induced
endogenous cytotoxic effector system, hymidinekinase, endonuclease, RNAse,
alpha
toxin, ricin, abrin, Pseudomonas exotoxin A, diphtheria toxin, saporin,
momordin,
gelonin, polceweed antiviral protein, alpha-sarcin and cholera toxin. "Toxin"
also
includes a cytostatic or cytocidal agent, a therapeutic agent or a radioactive
metal ion,
e.g., alpha-emitters such as, for example, zl3Bi, or other radioisotopes such
as, for
exam 1e 103Pd 133Xe 1311 111In 68CTe S~Co 65Zn 85Sr 32P 35S 90y 153Sm 153Gd
p > > > > > > > > > > > > > >
ls9Yb slCr s4Mn ~SSe 113Sn g°Yttrium ll~Tin lg6Rhenium 166Holmium and
> > > > > > > > >
188Rhenium; luminescent labels, such as luminol; and fluorescent labels, such
as
fluorescein and rhodamine, and biotin.
[0362] In a specific embodiment, the invention provides a method for the
specific
destruction of cells (e.g., the destruction of tumor cells) by administering
polypeptides
of the invention or antibodies of the invention in association with the
radioisotope 9°Y.
In another specific embodiment, the invention provides a method for the
specific
destruction of cells (e.g., the destruction of tumor cells) by administering
polypeptides
of the invention or antibodies of the invention in association with the
radioisotope
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mln. In a further specific embodiment, the invention provides a method for the
specific destruction of cells (e.g., the destruction of tumor cells) by
administering
polypeptides of the invention or antibodies of the invention in association
with the
radioisotope 13i1.
[0363] Techniques l~nown in the art may be applied to label polypeptides of
the
invention (including antibodies), -.Such techniques include, but are not
limited to, the
use of bifunctional conjugating agents (see e.g., U.S. Patent Nos. 5,756,065;
5,714,631; 5,696,239; 5,652,361; 5,505,931; 5,489,425; 5,435,990; 5,428,139;
5,342,604; 5,274,119; 4,994,560; and 5,808,003; the contents of each of which
are
hereby incorporated by reference in its entirety).
[0364] Thus, the invention provides a diagnostic method of a disorder, which
involves (a) assaying the expression level of a polypeptide of the present
invention in
cells or body fluid of an individual; and (b) comparing the assayed
polypeptide
expression level with a standard polypeptide expression level, whereby an
increase or
decrease in the assayed polypeptide expression level compared to the standard
expression level is indicative of a disorder. With respect to cancer, the
presence of a
relatively high amount of transcript in biopsied tissue from an individual may
indicate
a predisposition. for the .development of the. disease,' or may -provide . a
means for
detecting the disease prior to the -appearance of actual clinical symptoms. A
more
definitive diagnosis of this type may allow health professionals to employ
preventative
measures or aggressive treatment earlier thereby preventing the development or
further
progression of the cancer.
[0365] Moreover, polypeptides of the present invention can be used to treat or
prevent diseases or conditions of the prostate such as, for example, prostate
cancers
such as adenocarcinoma, transitional cell carcinomas, ductal carcinomas, and
squamous cell carcinomas, and as described under "Hyperproliferative
Disorders"
and/or "Reproductive System Disorders" below. In preferred embodiments,
polynucleotides expressed in a particular tissue type (see, e.g., Table 1A,
column 7)
are used to diagnose, detect, prevent, treat and/or prognose disorders
associated with
the tissue type. For example, patients can be administered a polypeptide of
the present
invention in an effort to replace absent or decreased levels of the
polypeptide (e.g.,
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insulin), to supplement absent or decreased levels of a different polypeptide
(e.g.,
hemoglobin S for hemoglobin B, SOD, catalase, DNA repair proteins), to inhibit
the
activity of a polypeptide (e.g., an oncogene or tumor supressor), to activate
the activity
of a polypeptide (e.g., by binding to a receptor), to reduce the activity of a
membrane
bound receptor. by competing with it for free ligand~(e.g., soluble TNF
receptors used
in reducing inflammation), or to bring about a desired response (e.g., blood
vessel
growth inhibition, enhancement of the immune response to proliferative cells
or
tissues).
[0366] Similarly, antibodies directed to a polypeptide of the present
invention can
also be used to treat disease (as described supra, and elsewhere herein). For
example,
administration of an antibody directed to a polypeptide of the present
invention can
bind, and/or neutralize the polypeptide, and/or reduce overproduction of the
polypeptide. Similarly, administration of an antibody can activate the
polypeptide,
such as by binding to a polypeptide bound to a membrane (receptor).
[0367] At the very least, the polypeptides of the present invention can be
used as
molecular weight markers on SDS-PAGE gels or on molecular sieve gel filtration
columns using methods well known to those of skill in the art. Polypeptides
can also
be used to raise antibodies, which in turn are used to measure protein
expression from
a recombinant cell, as a way of assessing transformation of the host cell.
Moreover,
the polypeptides of the present invention can be used to test the biological
activities
described herein.
Diagnostic Asssays
[0368] The compounds of the present invention are useful for diagnosis,
treatment,
prevention and/or prognosis of various prostate-related disorders in mammals,
preferably humans. Such disorders include, but are not limited to, prostate
cancers
such as adenocarcinoma, transitional cell carcinomas, ductal carcinomas, and
squamous cell carcinomas, and as described under "Hyperproliferative
Disorders"
and/or "Reproductive System Disorders" below. In preferred embodiments,
polynucleotides expressed in a particular tissue type (see, e.g., Table 1A,
column 7)
are used to diagnose, detect, prevent, treat and/or prognose disorders
associated with
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the tissue type.
[0369] Prostate cancer antigens are expressed in the prostate. For a number of
prostate-related disorders, substantially altered (increased or decreased)
levels of
prostate cancer antigen gene expression can be detected in prostate cancer
tissue or
other cells or bodily fluids (e.g., sera, plasma, urine, semen,.synovial
fluid~or spinal
fluid) taken from an individual having such a disorder; relative to a
'.'standard" prostate
cancer antigen gene expression level, that is, the prostate cancer antigen
expression
level in prostate tissues or bodily fluids from an individual not having the
prostate
disorder. Thus, the invention provides a diagnostic method useful during
diagnosis of
a prostate disorder, which involves measuring the expression level of the gene
encoding the prostate cancer associated polypeptide in prostate tissue or
other cells or
body fluid from an individual and comparing the measured gene expression level
with
a standard prostate cancer antigens gene expression level, whereby an increase
or
decrease in the gene expression levels) compared to the standard is indicative
of an
prostate disorder.
[0370] In specific embodiments, the invention provides a diagnostic method
useful
during diagnosis of a disorder of a normal or diseased tissue/cell source
corresponding .
to column 7 of Table 1A; which involves measuring the expression level of the:
coding
sequence of a polynucleotide sequence associated with this tissue/cell source
as
disclosed in Table 1A in the tissue/cell source or other cells or body fluid
from an
individual and comparing the expression level of the coding sequence with a
standard
expression level of the coding sequence of a polynucleotide sequence, whereby
an
increase or decrease in the gene expression levels) compared to the standard
is
indicative of a disorder of a normal or diseased tissue/cell source
corresponding to
column 7 of Table 1A.
[0371] In particular, it is believed that certain tissues in mammals with
cancer of
cells or tissue of the prostate express significantly enhanced or reduced
levels of
normal or altered prostate cancer antigen expression and mRNA encoding the
prostate
cancer associated polypeptide when compared to a corresponding "standard"
level.
Further, it is believed that enhanced or depressed levels of the prostate
cancer
associated polypeptide can be detected in certain body fluids (e.g., sera,
plasma, urine,
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and spinal fluid) or cells or tissue from mammals with such a cancer when
compared
to sera from mammals of the same species not having the cancer.
[0372] For example, as disclosed herein, prostate cancer associated
polypeptides
of the invention are expressed in the prostate. Accordingly, polynucleotides
of the
invention (e.g., polynucleotide sequences complementary to all or a portion of
a
prostate cancer antigen mRNA nucleotide sequence of SEQ ID NO:X, nucleotide
sequence encoding SEQ ID NO:Y, nucleotide sequence encoding a polypeptide
encoded by SEQ ID NO:X and/or a nucleotide sequence delineated by columns 8
and
9 of Table 2) and antibodies (and antibody fragments) directed against the
polypeptides of the invention may be used to quantitate or qualitate
concentrations of
cells of the prostate cancer expressing prostate cancer antigens, preferrably
on their
cell surfaces. These polynucleotides and antibodies additionally have
diagnostic
applications in detecting abnormalities in the level of prostate cancer
antigens gene
expression, or abnormalities in the structure and/or temporal, tissue,
cellular, or
subcellular location of prostate cancer antigens. These diagnostic assays may
be
performed in vivo or in vitro, such as, for example, on blood samples, biopsy
tissue or
autopsy tissue.. In specific embodiments, polynucleotides and antibodies of
the
invention are used to quantitate or qualitate tissues/cells corresponding to
the library
source disclosed in column 7 of Table 1A expressing the corresponding prostate
cancer sequence disclosed in the same row of Table 1A, preferrably on their
cell
surface.
[0373] Thus, the invention provides a diagnostic method useful during
diagnosis
of a prostate disorder, including cancers, which involves measuring the
expression
level of the gene encoding the prostate cancer antigen polypeptide in prostate
tissue or
other cells or body fluid from an individual and comparing the measured gene
expression level with a standard prostate cancer antigen gene expression
level,
whereby an increase or decrease in the gene expression level compared to the
standard
is indicative of a prostate disorder. In specific embodiments, polynucleotides
and
antibodies of the invention are used to quantitate or qualitate tissues/cells
corresponding to the library source disclosed in column 7 of Table 1A
expressing the
corresponding prostate cancer sequence disclosed in the same row of Table 1A,
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preferrably on their cell surface.
[0374] Where a diagnosis of a disorder in the prostate, including diagnosis of
a
tumor, has already been made according to conventional methods, the present
invention is useful as a prognostic indicator, whereby patients exhibiting
enhanced or
depressed prostate cancer antigen gene expression will experience a worse
clinical
outcome relative to patients expressing the gene at a level nearer the
standard level.
[0375] By "assaying the expression level of the gene encoding the prostate
cancer
associated polypeptide" is intended qualitatively or quantitatively measuring
or
estimating the level of the prostate cancer antigen polypeptide or the level
of the
mRNA encoding the prostate cancer antigen polypeptide in a first biological
sample
either directly (e.g., by determining or estimating absolute protein level or
mRNA
level) or relatively (e.g., by comparing to the prostate cancer associated
polypeptide
level or mRNA level in a second biological sample). Preferably, the prostate
cancer
antigen polypeptide expression level or mRNA level in the first biological
sample is
measured or estimated and compared to a standard prostate cancer antigen
polypeptide
level or mRNA level, the standard being talcen from a second biological sample
obtained from an individual not having the disorder or being determined by
averaging
levels from a population of individuals not having a disorder of the prostate.
As will
be appreciated in the art, once a standard prostate cancer antigen polypeptide
level or
mRNA level is known, it can be used repeatedly as a standard for comparison.
[0376] By "biological sample" is intended any biological sample obtained from
an
individual, cell line, tissue culture, or other source containing prostate
cancer antigen
polypeptides (including portions thereof) or mRNA. As indicated, biological
samples
include body fluids (such as sera, plasma, urine, synovial fluid and spinal
fluid) which
contain cells expressing prostate cancer antigen polypeptides, prostate
tissue, and other
tissue sources found to express the full length or fragments thereof of a
prostate cancer
antigen. Methods for obtaining tissue biopsies and body fluids from mammals
are
well known in the art. Where the biological sample is to include mRNA, a
tissue
biopsy is the preferred source.
[0377] Total cellular RNA can be isolated from a biological sample using any
suitable technique such as the single-step guanidinium-thiocyanate-phenol-
chloroform
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method described in Chomczynski and Sacchi, Anal. Biochem. 162:156-159 (1987).
Levels of mRNA encoding the prostate cancer antigen polypeptides are then
assayed
using any appropriate method. These include Northern blot analysis, S1
nuclease
mapping, the polymerase chain reaction (PCR), reverse transcription in
combination
with the polymerase chain reaction (RT-PCR),. and reverse transcription in
combination with the ligase chain reaction (RT-LCR).
[0378] The present invention also relates to diagnostic assays such as
quantitative
and diagnostic assays fox detecting levels of prostate cancer antigen
polypeptides, in a
biological sample (e.g., cells and tissues), including determination of normal
and
abnormal levels of polypeptides. Thus, for instance, a diagnostic assay in
accordance
with the invention for detecting over-expression of prostate cancer antigens
compared
to normal control tissue samples may be used to detect the presence of tumors.
Assay
techniques that can be used to determine levels of a polypeptide, such as a
prostate
cancer antigen polypeptide of the present invention in a sample derived from a
host are
well-known to those of skill in the art. Such assay methods include
radioimmunoassays, competitive-binding assays, Western Blot analysis and ELISA
assays. Assaying prostate cancer antigen polypeptide levels in a biological
sample can
occur using any art-known method..
[0379] Assaying prostate cancer antigen polypeptide levels in a biological
sample
can occur using antibody-based techniques. For example, prostate cancer
antigen
polypeptide expression in tissues can be studied with classical
immunohistological
methods (Jallcanen et al., J. Cell. Biol. 101:976-985 (1985); Jallcanen, M.,
et al., J.
Cell . Biol. 105:3087-3096 (1987)). Other antibody-based methods useful for
detecting prostate cancer antigen polypeptide gene expression include
immunoassays,
such as the enzyme linked immunosorbent assay (ELISA) and the radioimmunoassay
(RIA). Suitable antibody assay labels are known in the art and include enzyme
labels,
such as, glucose oxidase, and radioisotopes, such as iodine (lash 121I),
carbon (14C),
sulfur (35S), tritium (3H), indium (lzIn), and technetium (9~"'Tc), and
fluorescent
labels, such as fluorescein and rhodamine, and biotin.
[0380] The tissue or cell type to be analyzed will generally include those
which are
known, or suspected, to express the prostate cancer antigen gene (such as, for
example,
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cells of the prostate or prostate cancer). The protein isolation methods
employed
herein may, for example, be such as those described in Harlow and Lane
(Harlow, E.
and Lane, D., 1988, "Antibodies: A Laboratory Manual", Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, New York), which is incorporated herein
by
reference in its entirety: The isolated cells can be derived from cell culture
or from a
patient. The analysis of cells taken from culture may be a necessary step in
the
assessment of cells that could be used as part of a cell-based gene therapy
technique
or, alternatively, to test the effect of compounds on the expression of the
prostate
cancer antigen gene.
[0381] For example, antibodies, or fragments of antibodies, such as those
described herein, may be used to quantitatively or qualitatively detect the
presence of
prostate cancer antigen gene products or conserved variants or peptide
fragments
thereof. This can be accomplished, for example, by immunofluorescence
techniques
employing a fluorescently labeled antibody coupled with light microscopic,
flow
cytometric, or fluorimetric detection.
[0382] In a preferred embodiment, antibodies, or fragments of antibodies
directed
to any one or all of the predicted epitope domains of the prostate cancer
antigen
polypeptides (Shown in Table 1A, column 6) may be used to quantitatively or
qualitatively detect the presence of prostate cancer antigen gene products or
conserved
variants or peptide fragments thereof. This can be accomplished, for example,
by
immunofluorescence techniques employing a fluorescently labeled antibody
coupled
with light microscopic, flow cytometric, or fluorimetric detection.
[0383] In an additional preferred embodiment, antibodies, or fragments of
antibodies directed to a conformational epitope of a prostate cancer antigen
may be
used to quantitatively or qualitatively detect the presence of prostate cancer
antigen
gene products or conserved variants or peptide fragments thereof. This can be
accomplished, for example, by immunofluorescence techniques employing a
fluorescently labeled antibody coupled with light microscopic, flow
cytometric, or
fluorimetric detection.
[0384] The antibodies (or fragments thereof), and/or prostate cancer antigen
polypeptides of the present invention may, additionally, be employed
histologically, as
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in immunofluorescence, immunoelectron microscopy or non-immunological assays,
for in situ detection of prostate cancer antigen gene products or conserved
variants or
peptide fragments thereof. In situ detection may be accomplished by removing a
histological specimen from a patient, and applying thereto a labeled antibody
or
prostate cancer antigen.polypeptide of the present invention. The antibody (or
fragment thereof) or prostate cancer antigen polypeptide is preferably applied
by
overlaying the labeled antibody (or fragment) onto a biological sample.
Through the
use of such a procedure, it is possible to determine not only the presence of
the
prostate cancer antigen gene product, or conserved variants or peptide
fragments, or
prostate cancer antigen polypeptide binding, but also its distribution in the
examined
tissue. Using the present invention, those of ordinary skill will readily
perceive that
any of a wide variety of histological methods (such as staining procedures)
can be
modified in order to achieve such in situ detection.
[0385] Immunoassays and non-immunoassays for prostate cancer antigen gene
products or conserved variants or peptide fragments thereof will typically
comprise
incubating a sample, such as a biological fluid, a tissue extract, freshly
harvested cells,
or lysates of cells which have been incubated in cell culture, in the presence
of a
detectably labeled antibody capable of binding prostate cancer antigen gene
products
or conserved variants or peptide fragments thereof, and detecting the bound
antibody
by any of a number of techniques well-known in the art.
[0386] The biological sample may be brought in contact with and immobilized
onto a solid phase support or carrier such as nitrocellulose, or other solid
support
which is capable of immobilizing cells, cell particles or soluble proteins.
The support
may then be washed with suitable buffers followed by treatment with the
detectably
labeled anti- prostate cancer antigen antibody or detectable prostate cancer
antigen
polypeptide. The solid phase support may then be washed with the buffer a
second
time to remove unbound antibody or polypeptide. Optionally the antibody is
subsequently labeled. The amount of bound label on solid support may then be
detected by conventional means.
[0387] By "solid phase support or carrier" is intended any support capable of
binding an antigen or an antibody. Well-known supports or carriers include
glass,
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polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural
and
modified celluloses, polyacrylamides, gabbros, and magnetite. The nature of
the
carrier can be either soluble to some extent or insoluble for the purposes of
the present
invention. The support material may have virtually any possible structural
configuration so long as. the coupled molecule is capable of binding to an
antigen or
antibody. Thus, the support configuration may be spherical; as in a bead, or
cylindrical, as in the inside surface of a test tube, or the external surface
of a rod.
Alternatively, the surface may be flat such as a sheet, test strip, etc.
Preferred supports
include polystyrene beads. Those skilled in the art will know many other
suitable
carriers for binding antibody or antigen, or will be able to ascertain the
same by use of
routine experimentation.
[0388] The binding activity of a given lot of anti- prostate cancer antigen
antibody
or prostate cancer antigen polypeptide may be determined according to well
known
methods. Those skilled in the art will be able to determine operative and
optimal
assay conditions for each determination by employing routine experimentation.
[0389] In addition to assaying prostate cancer antigen polypeptide levels or
polynucleotide levels in a biological sample obtained from an individual,
prostate
cancer antigen polypeptide or polynucleotide can also be detected ifz vivo by
imaging.
For example, in one embodiment of the invention, prostate cancer antigen
polypeptide
and/or anti- prostate cancer antigen antibodies are used to image prostate
diseased
cells, such as neoplasms. In another embodiment, prostate cancer antigen
polynucleotides of the invention (e.g., polynucleotides complementary to all
or a
portion of prostate cancer antigen mRNA) and/or anti- prostate cancer antigen
antibodies (e.g., antibodies directed to any one or a combination of the
epitopes of
prostate cancer antigens, antibodies directed to a conformational epitope of
prostate
cancer antigens, antibodies directed to the full length polypeptide expressed
on the cell
surface of a mammalian cell) are used to image diseased or neoplastic cells of
the
prostate.
[0390] Antibody labels or markers for ira vivo imaging of prostate cancer
antigen
polypeptides include those detectable by X-radiography, NMR, MRI, CAT-scans or
ESR. For X-radiography, suitable labels include radioisotopes such as barium
or
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cesium, which emit detectable radiation but are not overtly harmful to the
subject.
Suitable marl~ers for NMR and.ESR include those with a detectable
characteristic spin,
such as deuterium, which may be incorporated into the antibody by labeling of
nutrients for the relevant hybridoma. Where if2 vivo imaging is used to detect
enhanced
levels of prostate cancer antigen polypeptides for diagnosis in humans, it may
be -
preferable to use human antibodies or "humanized" chimeric monoclonal
antibodies.
Such antibodies can be produced using techniques described herein or otherwise
known in the art. For example methods for producing chimeric antibodies are
known
in the art. See, for review, Morrison, Scieface 229:1202 (1985); Oi et al.,
BioTechfZiques 4:214 (1986); Cabilly et al., IJ.S. Patent No. 4,816,567;
Taniguchi et
al., EP 171496; Morrison et al., EP 173494; Neuberger et al., WO 8601533;
Robinson
et al., WO 8702671; Boulianne et al., Nature 312:643 (1984); Neuberger et al.,
Nature
314:268 (1985).
[0391] Additionally, any prostate cancer antigen polypeptides whose presence
can
be detected, can be administered. For example, prostate cancer antigen
polypeptides
labeled with a radio-opaque or other appropriate compound can be administered
and
visualized in vivo; as discussed, above for labeled antibodies. Further such
prostate
cancer antigen polypeptides can be utilized for in vity-o diagnostic
procedures.
[0392] A prostate cancer antigen polypeptide-specific antibody or antibody
fragment which has been labeled with an appropriate detectable imaging moiety,
such
as a radioisotope (for example, 1311, 112In, 99mTc), a radio-opaque substance,
or a
material detectable by nuclear magnetic resonance, is introduced (for example,
parenterally, subcutaneously or intraperitoneally) into the mammal to be
examined for
a prostate disorder. It will be understood in the art that the size of the
subject and the
imaging system used will determine the quantity of imaging moiety needed to
produce
diagnostic images. In the case of a radioisotope moiety, for a human subject,
the
quantity of radioactivity injected will normally range from about 5 to 20
millicuries of
99mTc. The labeled antibody or antibody fragment will then preferentially
accumulate
at the location of cells which contain prostate cancer antigen protein. I~r
vivo tumor
imaging is described in S.W. Burchiel et al., "Immunopharmacokinetics of
Radiolabeled Antibodies and Their Fragments" (Chapter 13 in Tumor Imagirzg:
The
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Radiochemical DetectioyZ of Cancer°, S.W. Burchiel and B. A. Rhodes,
eds., Masson
Publishing Ins. (1982)).
[0393] With respect to antibodies, one of the ways in which the anti- prostate
cancer antigen antibody can be detestably labeled is by linking the same to an
enzyme
and using the linked product in an enzyme immunoassay (EIA) (Voller, A., "The
Enzyme Linked Immunosorbent Assay (ELISA)", 1978, Diagnostic Horizons 2:1-7,
Microbiological Associates Quarterly Publication, Walkersville, MD); Voller et
al., J.
Clin. Pathol. 31:507-520 (1978); Butler, J.E., Meth. E~rzymol. 73:482-523
(1981);
Maggio, E. (ed.), 1980, Enzyme Immunoassay, CRC Press, Boca Raton, FL,;
Ishilcawa, E. et al., (eds.), 1981, Enzyme Immunoassay, I~gaku Shoin, Tokyo).
The
enzyme, which is bound to the antibody will react with an appropriate
substrate,
preferably a chromogenic substrate, in such a manner as to produce a chemical
moiety
which can be detected, for example, by spectrophotometric, fluorimetric or by
visual
means. Enzymes which can be used to detestably label the antibody include, but
are
not limited to, malate dehydrogenase, staphylococcal nuclease, delta-5-steroid
isomerase, yeast alcohol dehydrogenase, alpha-glycerophosphate, dehydrogenase,
triose phosphate isomerase, horseradish peroxidase, alkaline phosphatase,
asparaginase, glucose oxidase, beta-galactosidase, ribonuclease, urease,
catalase,
glucose-6-phosphate dehydrogenase, glucoamylase and acetylcholinesterase.
Additionally, the detection can be accomplished by colorimetric methods which
employ a chromogenic substrate for the enzyme. Detection may also be
accomplished
by visual comparison of the extent of enzymatic reaction of a substrate in
comparison
with similarly prepared standards.
[0394] Detection may also be accomplished using any of a variety of other
immunoassays. For example, by radioactively labeling the antibodies or
antibody
fragments, it is possible to detect prostate cancer antigens through the use
of a
radioimmunoassay (RIA) (see, for example, Weintraub, B., Principles of
Radioimmunoassays, Seventh Training Course on Radioligand Assay Techniques,
The
Endocrine Society, March, 1986, which is incorporated by reference herein).
The
radioactive isotope can be detected by means including, but not limited to, a
gamma
counter, a scintillation counter, or autoradiography.
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[0395] It is also possible to label the antibody with a fluorescent compound.
When the fluorescently labeled antibody is exposed to light of the proper wave
length,
its presence can then be detected due to fluorescence. Among the most commonly
used fluorescent labeling compounds are fluorescein isothiocyanate, rhodamine,
phycoerythrin, phycocyanin, allophycocyanin, ophthaldehyde and fluorescamine.
.
[0396] The antibody can also be detectably labeled using fluorescence emitting
metals such as ls2Eu, or others of the lanthanide series. These metals can be
attached
to the antibody using such metal chelating groups as
diethylenetriaminepentacetic acid
(DTPA) or ethylenediaminetetraacetic acid (EDTA).
[0397] The antibody also can be detectably labeled by coupling it to a
chemiluminescent compound. The presence of the chemiluminescent-tagged
antibody
is then determined by detecting the presence of luminescence that arises
during the
course of a chemical reaction. Examples of particularly useful
chemiluminescent
labeling compounds are luminol, isoluminol, theromatic acridinium ester,
imidazole,
acridinium salt and oxalate ester.
[0398] Likewise, a bioluminescent compound may be used to label the antibody
of
the present invention. Bioluminescence is a type of chemiluminescence found in
biological systems. in, which a catalytic protein increases the efficiency of
the
chemiluminescent reaction.. The presence of a bioluminescent protein is
determined
by detecting the presence of luminescence. Important bioluminescent compounds
for
purposes of labeling are luciferin, luciferase and aequorin.
Methods for Detecting Prostate Disease, Including Cancer
[0399] In general, a prostate disease or cancer may be detected in a patient
based
on the presence of one or more prostate cancer antigen proteins of the
invention and/or
polynucleotides encoding such proteins in a biological sample (for example,
blood,
sera, urine, and/or tumor biopsies) obtained from the patient. In other words,
such
proteins and/or polynucleotides may be used as markers to indicate the
presence or
absence of a prostate disease or disorder, including cancer. Cancers that may
be
diagnosed, and/or prognosed using the compositions of the invention include
but are
not limited to, prostate cancer. In addition, such proteins and/or
polynucleotides may
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be useful for the detection of other diseases and cancers, including cancers
of
tissues/cells corresponding to the library source disclosed in column 7 of
Table 1A
expressing the corresponding prostate cancer sequence disclosed in the same
row of
Table 1A. The binding agents provided herein generally permit detection of the
level
of antigen that binds to the agent in the biological sample. Polynucleotide
primers and
probes may be used to detect the level of mRNA encoding prostate cancer
antigen
polypeptides, which is also indicative of the presence or absence of a
prostate disease
or disorder, including cancer. In general, prostate cancer antigen
polypeptides should
be present at a level that is at least three fold higher in diseased tissue
than in normal
tissue.
[0400] There are a variety of assay formats known to those of ordinary skill
in the
art for using a binding agent to detect polypeptide marlcers in a sample. See,
e.g.,
Harlow and Lane, su~~a. In general, the presence or absence of a prostate
disease in a
patient may be determined by (a) contacting a biological sample obtained from
a
patient with a binding agent; (b) detecting in the sample a level of
polypeptide that
binds to the binding agent; and (c) comparing the level of polypeptide with a
predetermined cut-off value.
[0401] In a preferred embodiment, the assay involves the wse of binding agent
immobilized on a solid support to bind to and remove the prostate cancer
antigen
polypeptide of the invention from the remainder of the sample. The bound
polypeptide
may then be detected using a detection reagent that contains a reporter group
and
specifically binds to the binding agent/polypeptide complex. Such detection
reagents
may comprise, for example, a binding agent that specifically binds to the
polypeptide
or an antibody or other agent that specifically binds to the binding agent,
such as an
anti-immunoglobulin, protein G, protein A or a lectin. Alternatively, a
competitive
assay may be utilized, in which a polypeptide is labeled with a reporter group
and
allowed to bind to the immobilized binding agent after incubation of the
binding agent
with the sample. The extent to which components of the sample inhibit the
binding of
the labeled polypeptide to the binding agent is indicative of the reactivity
of the
sample with the immobilized binding agent. Suitable polypeptides for use
within such
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assays include prostate cancer antigen polypeptides and portions thereof, or
antibodies,
to which the binding agent binds, as described above.
[0402] The solid support may be any material known to those of skill in the
art to
which prostate cancer antigen polypeptides of the invention may be attached.
For
example, the solid support may be a test well in a microtiter plate or a
nitrocellulose or
other suitable membrane. Alternatively, the support may be a bead or disc,
such as
glass fiberglass, latex or a plastic material such as polystyrene or
polyvinylchloride.
The support may also be a magnetic particle or a fiber optic sensor, such as
those
disclosed, for example, in U.S. Patent No. 5,359,681. The binding agent may be
immobilized on the solid support using a variety of techniques known to those
of skill
in the art, which are amply described in the patent and scientific literature.
In the
context of the present invention, the term "immobilization" refers to both
noncovahent
association, such as adsorption, and covalent attachment (which may be a
direct
linkage between the agent and functional groups on the support or may be a
linkage by
way of a cross-hinking agent). Immobilization by adsorption to a well in a
microtiter
plate or to a membrane is preferred. In such cases, adsorption may be achieved
by
contacting the binding agent, in a suitable buffer, with the solid support for
the suitable
amount of time. The contact time varies with temperature, but is typically
between
about 1 hour and about 1 day: In general, contacting a well of plastic
microtiter plate
(such as polystyrene or polyvinyhchloride) with an amount of binding agent
ranging
from about 10 ng to about 10 ug, and preferably about 100 ng to about 1 ug, is
sufficient to immobilize an adequate amount of binding agent.
[0403] Covalent attachment of binding agent to a solid support may generally
be
achieved by first reacting the support with a bifunctional reagent that will
react with
both the support and a functional group, such as a hydroxyh or amino group, on
the
binding agent. For example, the binding agent may be covalently attached to
supports
having an appropriate polymer coating using benzoquinone or by condensation of
an
aldehyde group on the support with an amine and an active hydrogen on the
binding
partner (see, e.g., Pierce Immunotechnology Catalog and Handbook, 1991, at A12-
A13).
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Gene Therapy Methods
[0404] Also encompassed by the present invention are gene therapy methods for
treating or preventing disorders, diseases and conditions. The gene therapy
methods
relate to the introduction of nucleic acid (DNA, RNA and antisense DNA or RNA)
sequences into an animal to achieve expression of a prostate cancer antigen of
the
present invention. This method requires a polynucleotide which codes for a
polypeptide of the present invention operatively linked to a promoter and any
other
genetic elements necessary for the expression of the polypeptide by the target
tissue.
Such gene therapy and delivery techniques are known in the art, see, for
example,
W090/11092, which is herein incorporated by reference.
[0405] Thus, for example, cells from a patient may be engineered with a
polynucleotide (DNA or RNA) comprising a promoter operably linked to a
polynucleotide of the present invention ex vivo, with the engineered cells
then being
provided to a patient to be treated with the polypeptide of the present
invention. Such
methods are well-known in the art. For example, see Belldegrun, A., et al., J.
Natl.
Cancer Inst. 85: 207-216 (1993); Ferrantini, M. et al., Cancer Research 53:
1107-1112
(1993); Ferrantini, M. et al., J. Immunology 153: 4604-4615 (1994); Kaido, T.,
et al.,
Int. J. Cancer 60: 221-229 (1995); Ogura, H., et al.; Cancer Research 50: 5102-
5106
(1990); Santodonato, L., et al., Human Gene Therapy 7:1-10 (1996);
Santodonato, L.,
et al., Gene Therapy 4:1246-1255 (1997); and Zhang, J.-F. et al., Cancer Gene
Therapy 3: 31-38 (1996)), which are herein incorporated by reference. In one
embodiment, the cells, which are engineered are arterial cells. The arterial
cells may
be reintroduced into the patient through direct injection to the artery, the
tissues
surrounding the artery, or through catheter injection.
[0406] As discussed in more detail below, the polynucleotide constructs can be
delivered by any method that delivers injectable materials to the cells of an
animal,
such as, injection into the interstitial space of tissues (heart, muscle,
skin, lung, liver,
and the like). The polynucleotide constructs may be delivered in a
pharmaceutically
acceptable liquid or aqueous carrier.
[0407] In one embodiment, the polynucleotide of the present invention is
delivered
as a naked polynucleotide. The term "naked" polynucleotide, DNA or RNA refers
to
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sequences that are free from any delivery vehicle that acts to assist, promote
or
facilitate entry into the cell, including viral sequences, viral particles,
liposome
formulations, lipofectin or precipitating agents and the like. However, the
polynucleotide of the present invention can also be delivered in liposome
formulations
and lipofectin formulations and the.like can be:prepared by methods well known
to
those skilled in the art. Such methods are described, for example, in U.S.
Patent Nos.
5,593,972, 5,589,466, and 5,580,859, which are herein incorporated by
reference.
[0408] The polynucleotide vector constructs used in the gene therapy method
are
preferably constructs that will not integrate into the host genome nor will
they contain
sequences that allow for replication. Appropriate vectors include pWLNEO,
pSV2CAT, pOG44, pXTl and pSG available from Stratagene; pSVK3, pBPV, pMSG
and pSVL available from Pharmacia; and pEF1/V5, pcDNA3.1, and pRc/CMV2
available from Invitrogen. Other suitable vectors will be readily apparent to
the
skilled artisan.
[0409] Any strong promoter known to those skilled in the art can be used for
driving the expression of the polynucleotide sequence. Suitable promoters
include
adenoviral promoters, such as the adenoviral major late promoter; or
heterologous
promoters, such as the cytomegalovirus (CMV) promoter; the respiratory
syncytial
virus (RSV) promoter; inducible promoters, such as the MMT promoter, the
metallothionein promoter; heat shock promoters; the albumin promoter; the
ApoAI
promoter; human globin promoters; viral thymidine kinase promoters, such as
the
Herpes Simplex thymidine lcinase promoter; retroviral LTRs; the b-actin
promoter;
and human growth hormone promoters. The promoter also may be the native
promoter for the polynucleotide of the present invention.
[0410] Unlilce other gene therapy techniques, one major advantage of
introducing
naked nucleic acid sequences into target cells is the transitory nature of the
polynucleotide synthesis in the cells. Studies have shown that non-replicating
DNA
sequences can be introduced into cells to provide production of the desired
polypeptide for periods of up to six months.
[0411] The polynucleotide construct can be delivered to the interstitial space
of
tissues within the an animal, including of muscle, skin, brain, lung, liver,
spleen, bone
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marrow, thymus, heart, lymph, blood, bone, cartilage, pancreas, kidney, gall
bladder,
stomach, intestine, testis, ovary, uterus, rectum, nervous system, eye, gland,
and
connective tissue. Interstitial space of the tissues comprises the
intercellular, fluid,
mucopolysaccharide matrix among the reticular fibers of organ tissues, elastic
fibers in
the walls of vessels or chambers, collagen fibers of fibrous tissues, or that
same matrix
within connective tissue ensheathing muscle cells or in the lacunae of bone.
It is
similarly the space occupied by the plasma of the circulation and the lymph
fluid of the
lymphatic channels. Delivery to the interstitial space of muscle tissue is
preferred for
the reasons discussed below. They may be conveniently delivered by injection
into the
tissues comprising these cells. They are preferably delivered to and expressed
in
persistent, non-dividing cells which are differentiated, although delivery and
expression
may be achieved in non-differentiated or less completely differentiated cells,
such as,
for example, stem cells of blood or skin fibroblasts. Iyi vivo muscle cells
are
particularly competent in their ability to take up and express
polynucleotides.
[0412] For the naked nucleic acid sequence injection, an effective dosage
amount
of DNA or RNA will be in the range of from about 0.05 mg/kg body weight to
about 50
mg/kg body weight. Preferably the dosage will be from about 0.005 mg/kg to
about 20
mg/kg and more preferably from about 0.05 mg/kg to about 5 mg/kg. Of course,
as the
artisan of ordinary skill will appreciate, this dosage will vary according to
the tissue site
of injection. The appropriate and effective dosage of nucleic acid sequence
can readily
be determined by those of ordinary skill in the art and may depend on the
condition
being treated and the route of administration.
[0413] The preferred route of administration is by the parenteral route of
injection
into the interstitial space of tissues. However, other parenteral routes may
also be
used, such as, inhalation of an aerosol formulation particularly for delivery
to lungs or
bronchial tissues, throat or mucous membranes of the nose. In addition, naked
DNA
constructs can be delivered to arteries during angioplasty by the catheter
used in the
procedure.
[0414] The naked polynucleotides are delivered by any method known in the art,
including, but not limited to, direct needle injection at the delivery site,
intravenous
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injection, topical administration, catheter infusion, and so-called "gene
guns". These
delivery methods are known in the art.
[0415] The constructs may also be delivered with delivery vehicles such as
viral
sequences, viral particles, liposome formulations, lipofectin, precipitating
agents, etc.
Such methods of delivery are known in the art.
[0416] In certain embodiments, the polynucleotide constructs are complexed in
a
liposome preparation. Liposomal preparations for use in the instant invention
include
cationic (positively charged), anionic (negatively charged) and neutral
preparations.
However, cationic liposomes are particularly preferred because a tight charge
complex
can be formed between the cationic liposome and the polyanionic nucleic acid.
Cationic liposomes have been shown to mediate intracellular delivery of
plasmid DNA
(Felgner et al., Proc. Natl. Acad. Sci. USA (1987) 84:7413-7416, which is
herein
incorporated by reference); mRNA (Malone et al., Proc. Natl. Acad. Sci. USA
(1989)
86:6077-6081, which is herein incorporated by reference); and purified
transcription
factors (Debs et al., J. Biol. Chem. (1990) 265:10189-10192, which is herein
incorporated by reference), in functional form.
[0417] Cationic liposomes are readily available. For example,
N[1-2,3-dioleyloxy)propyl]-N,N,N-triethylammonium .(DOTMA) liposomes are
particularly useful and are available under the trademark Lipofectin, from
GIBCO
BRL, Grand Island, N.Y., (see, also, Felgner et al., Proc. Natl Acad. Sci. USA
(1987)
84:7413-7416, which is herein incorporated by reference). Other commercially
available liposomes include transfectace (DDAB/DOPE) and DOTAPIDOPE
(Boehringer).
(0418] Other cationic Iiposomes can be prepared from readily available
materials
using techniques well known in the art. See, e.g. PCT Publication No. WO
90/11092
(which is herein incorporated by reference) for a description of the synthesis
of
DOTAP (1,2-bis(oleoyloxy)-3-(trimethylammonio)propane) liposomes. Preparation
of
DOTMA liposomes is explained in the literature, see, e.g., P. Felgner et al.,
Proc. Natl.
Acad. Sci. USA 84:7413-7417, which is herein incorporated by reference.
Similar
methods can be used to prepare liposomes from other cationic lipid materials.
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[0419] Similarly, anionic and neutral liposomes are readily available, such as
from
Avanti Polar Lipids (Birmingham, Ala.), or can be easily prepared using
readily
available materials. Such materials include phosphatidyl choline, cholesterol,
phosphatidyl ethanolamine, dioleoylphosphatidyl choline (DOPC),
dioleoylphosphatidyl glycerol (DOPG), dioleoylphoshatidyl ethanolamine (DOPE),
among others. These materials can also be mixed with the DOTMA and DOTAP
starting materials in appropriate ratios. Methods for making liposomes using
these
materials are well known in the art.
[0420] For example, commercially dioleoylphosphatidyl choline (DOPC),
dioleoylphosphatidyl glycerol (DOPG), and dioleoylphosphatidyl ethanolamine
(DOPE) can be used in various combinations to make conventional liposomes,
with or
without the addition of cholesterol. Thus, for example, DOPG/DOPC vesicles can
be
prepared by drying 50 mg each of DOPG and DOPC under a stream of nitrogen gas
into a sonication vial. The sample is placed under a vacuum pump overnight and
is
hydrated the following day with deionized water. The sample is then sonicated
for 2
hours in a capped vial, using a Heat Systems model 350 sonicator equipped with
an
inverted cup (bath type) probe at the maximum setting while the bath is
circulated at
15EC. Alternatively, negatively charged vesicles can be prepared without
sonication to
produce multilamellar vesicles or by extrusion through nucleopore membranes to
produce unilamellar vesicles of discrete size. Other methods are known and
available
to those of skill in the art.
[0421] The liposomes can comprise multilamellar vesicles (MLVs), small
unilamellar vesicles (SUVs), or large unilamellar vesicles (LUVs), with SUVs
being
preferred. The various liposome-nucleic acid complexes are prepared using
methods
well known in the art. See, e.g., Straubinger et al., Methods of Immunology
(1983),
101:512-527, which is herein incorporated by reference. For example, MLVs
containing nucleic acid can be prepared by depositing a thin film of
phospholipid on
the walls of a glass tube and subsequently hydrating with a solution of the
material to
be encapsulated. SUVs are prepared by extended sonication of MLVs to produce a
homogeneous population of unilamellar liposomes. The material to be entrapped
is
added to a suspension of preformed MLVs and then sonicated. When using
liposomes
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containing cationic lipids, the dried lipid film is resuspended in an
appropriate solution
such as sterile water or an isotonic buffer solution such as 10 mM Tris/NaCl,
sonicated, and then the preformed liposomes are mixed directly with the DNA.
The
liposome and DNA form a very stable complex due to binding of the positively
charged liposomes to the cationic DNA. SUVs find use with small nucleic acid
fragments. LUVs are prepared by a number of methods, well known in the art.
Commonly used methods include Caz+-EDTA chelation (Papahadjopoulos et al.,
Biochim. Biophys. Acta (1975) 394:483; Wilson et al., Cell 17:77 (1979); ether
.
injection (Deamer, D. and Bangham, A., Biochim. Biophys. Acta 443:629 (1976);
Ostro et al., Biochem. Biophys. Res. Commun. 76:836 (1977); Fraley et al.,
Proc. Natl.
Acad. Sci. USA 76:3348 (1979)); detergent dialysis (Enoch, H, and
Strittmatter, P.,
Proc. Natl. Acad. Sci. USA 76:145 (1979)); and reverse-phase evaporation (REV)
(Fraley et al., J. Biol. Chem. 255:10431 (1980); Szoka et al., Proc. Natl.
Acad. Sci.
USA 75:145 (1978); Schaefer-Ridder et al., Science 215:166 (1982)), which are
herein incorporated by reference.
[0422] Generally, the ratio of DNA to liposomes will be from about 10:1 to
about
1:10. Preferably, the ration will be from about 5:1 to about 1:5. More
preferably, the
ration will be about 3:1 to about 1:3. Still more preferably, the ratio will
be about 1:1.
[0423] U.S. Patent No. 5,676,954 (which is herein incorporated by reference)
reports on the injection of genetic material, complexed with cationic
liposomes
carriers, into mice. U.S. Patent Nos. 4,897,355, 4,946,787, 5,049,386,
5,459,127,
5,589,466, 5,693,622, 5,580,859, 5,703,055, and international publication no.
WO
94/9469 (which are herein incorporated by reference) provide cationic lipids
for use in
transfecting DNA into cells and mammals. U.S. Patent Nos. 5,589,466,
5,693,622,
5,580,859, 5,703,055, and International Publication No. WO 94/9469 provide
methods
for delivering DNA-cationic lipid complexes to mammals.
[0424] In certain embodiments, cells are engineered, ex vivo or if2 vivo,
using a
retroviral particle containing RNA, which comprises a sequence encoding a
polypeptide of the present invention. Retroviruses from which the retroviral
plasmid
vectors may be derived include, but are not limited to, Moloney Murine
Leukemia
Virus, spleen necrosis virus, Rous sarcoma Virus, Harvey Sarcoma Virus, avian
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leukosis virus, gibbon ape leukemia virus, human immunodeficiency virus,
Myeloproliferative Sarcoma Virus, and mammary tumor virus.
[0425] The retroviral plasmid vector is employed to transduce packaging cell
lines
to form producer cell lines. Examples of packaging cells which may be
transfected
include, but are not limited to, the PE501, PA317, R-2, R-AM, PA12, T19-14X,
VT-
19-17-H2, RCRE, RCRIP, GP+E-86, GP+envAml2, and DAN cell lines as described
in Miller, Human Gene Therapy 1:5-14 (1990), which is incorporated herein by
reference in its entirety. The vector may transduce the packaging cells
through any
means known in the art. Such means include, but are not limited to,
electroporation,
the use of liposomes, and CaP04 precipitation. In one alternative, the
retroviral
plasmid vector may be encapsulated into a liposome, or coupled to a lipid, and
then
administered to a host.
[0426] The producer cell line generates infectious retroviral vector
particles, which
include polynucleotide encoding a polypeptide of the present invention. Such
retroviral vector particles then may be employed, to transduce eukaryotic
cells, either
iya vitro or ira vivo. The transduced eukaryotic cells will express a
polypeptide of the
present invention.
[0427] In certain other embodiments, cells are engineered, ex vivo or in vivo,
with
polynucleotide contained in an adenovirus vector. Adenovirus can be
manipulated
such that it encodes and expresses a polypeptide of the present invention, and
at the
same time is inactivated in terms of its ability to replicate in a normal
lytic viral life
cycle. Adenovirus expression is achieved without integration of the viral DNA
into the
host cell chromosome, thereby alleviating concerns about insertional
mutagenesis.
Furthermore, adenoviruses have been used as live enteric vaccines for many
years with
an excellent safety profile (Schwartz, et al., Am. Rev. Respir. Dis.109:233-
238
(1974)). Finally, adenovirus mediated gene transfer has been demonstrated in a
number of instances including transfer of alpha-1-antitrypsin and CFTR to the
lungs of
cotton rats (Rosenfeld et al., Science 252:431-434 (1991); Rosenfeld et al.,
Cell
68:143-155 (I991)). Furthermore, extensive studies to attempt to establish
adenovirus
as a causative agent in human cancer were uniformly negative (Green et al.,
Proc.
Natl. Acad. Sci. LTSA 76:6606 (1979)).
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[0428] Suitable adenoviral vectors useful in the present invention are
described,
for example, in I~ozarsky and Wilson, Curr. Opin. Genet. Devel. 3:499-503
(1993);
Rosenfeld et al., Cell 68:143-155 (1992); Engelhardt et al., Human Genet.
Ther.
4:759-769 (1993); Yang et al., Nature Genet. 7:362-369 (1994); Wilson et al.,
Nature
365:691-692 (1993); and U.S. Patent No. 5,652,224, which are herein
incorporated by
references For example; the adenovirus vector Ad2 is useful and can be grown
in
human 293 cells. These cells contain the El region of adenovirus and
constitutively
express Ela and Elb, which complement the defective adenoviruses by providing
the
products of the genes deleted from the vector. In addition to Ad2, other
varieties of
adenovirus (e.g., Ad3, AdS, and Ad7) are also useful in the present invention.
[0429] Preferably, the adenoviruses used in the present invention are
replication
deficient. Replication deficient adenoviruses require the aid of a helper
virus and/or
packaging cell line to form infectious particles. The resulting virus is
capable of
infecting cells and can express a polynucleotide of interest which is operably
linked to
a promoter, but cannot replicate in most cells. Replication deficient
adenoviruses may
be deleted in one or more of all or a portion of the following genes: Ela,
Elb, E3, E4,
E2a, or L1 through L5.
[0430] In certain other embodiments, the cells are engineered, ex vivo or in
vivo,
using an adeno-associated virus (AAV). AAVs are naturally occurring defective
viruses that require helper viruses to produce infectious particles (Muzyczka,
N., Curr.
Topics in Microbiol. Immunol. 158:97 (1992)). It is also one of the few
viruses that
may integrate its DNA into non-dividing cells. Vectors containing as little as
300 base
pairs of AAV can be paclcaged and can integrate, but space for exogenous DNA
is
limited to about 4.5 kb. Methods for producing and using such AAVs are known
in
the art. See, for example, U.S. Patent Nos. 5,139,941, 5,173,414, 5,354,678,
5,436,146, 5,474,935, 5,478,745, and 5,589,377.
[0431] For example, an appropriate AAV vector for use in the present invention
will include all the sequences necessary for DNA replication, encapsidation,
and host-
cell integration. The polynucleotide construct is inserted into the AAV vector
using
standard cloning methods, such as those found in Sambrook et al., Molecular
Cloning:
A Laboratory Manual, Cold Spring Harbor Press (1989). The recombinant AAV
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vector is then transfected into packaging cells which are infected with a
helper virus,
using any standard technique, including lipofection, electroporation, calcium
phosphate precipitation, etc. Appropriate helper viruses include adenoviruses,
cytomegaloviruses, vaccinia viruses, or herpes viruses. Once the packaging
cells are
transfected and infected, they will produce infectious AAV viral particles,
which
contain the polynucleotide construct. These viral particles are then used to
transduce
eukaryotic cells, either'ex vivo or in vivo. The transduced cells will contain
the
polynucleotide construct integrated into its genome, and will express a
polypeptide of
the invention.
[0432] Another method of gene therapy involves operably associating
heterologous control regions and endogenous prostate cancer antigen
polynucleotide
sequences (e.g., encoding a prostate cancer antigen polypeptide of the present
invention) via homologous recombination (see, e.g., U.S. Patent No. 5,641,670,
issued
June 24, 1997; International Publication No. WO 96/2941 l, published September
26,
1996; International Publication No. WO 94/12650, published August 4, 1994;
Koller
et al., Proc. Natl. Acad. Sci. USA 86:8932-8935 (1989); and Zijlstra et al.,
Nature
342:435-438 (1989), which are herein incorporated by reference. This method
involves the activation of a gene which is present in the target cells, but
which is not
normally expressed in the cells, or is expressed at a lower level than
desired:
[0433] Polynucleotide constructs are made, using standard techniques known in
the art, which contain the promoter with targeting sequences flanking the
promoter.
Suitable promoters are described herein. The targeting sequence is
sufficiently
complementary to an endogenous sequence to permit homologous recombination of
the promoter-targeting sequence with the endogenous sequence. The targeting
sequence will be sufficiently near the 5' end of the desired endogenous
polynucleotide
sequence so the promoter will be operably linked to the endogenous sequence
upon
homologous recombination.
[0434] The promoter and the targeting sequences can be amplified using PCR.
Preferably, the amplified promoter contains distinct restriction enzyme sites
on the 5'
and 3' ends. Preferably, the 3' end of the first targeting sequence contains
the same
restriction enzyme site as the 5' end of the amplified promoter and the 5' end
of the
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second targeting sequence contains the same restriction site as the 3' end of
the
amplified promoter. The amplified promoter and targeting sequences are
digested and
ligated together.
[0435] The promoter-targeting sequence construct is delivered to the cells,
either
as naked polynucleotide, or in conjunction with transfection-facilitating
agents, such
as liposomes, viral sequences; viral particles, whole viruses, lipofection,
precipitating
agents; etc., described in more detail above. The P promoter-targeting
sequence can
be delivered by any method, included direct needle injection, intravenous
injection,
topical administration, catheter infusion, particle accelerators, etc. The
methods are
described in more detail below.
[0436] The promoter-targeting sequence construct is taken up by cells.
Homologous recombination between the construct and the endogenous sequence
takes
place, such that an endogenous sequence is placed under the control of the
promoter.
The promoter then drives the expression of the endogenous sequence.
[0437] The polynucleotide encoding a polypeptide of the present invention may
contain a secretory signal sequence that facilitates secretion of the protein.
Typically,
the signal sequence is positioned in the coding region of the polynucleotide
to be
expressed towards or at the 5' end of the coding region. The signal sequence
may be
homologous or heterologous to the prostate cancer antigen polynucleotide of
interest
and may be homologous or heterologous to the cells to be transfected.
Additionally,
the signal sequence may be chemically synthesized using methods known in the
art.
[0438] Any mode of administration of any of the above-described
polynucleotides
constructs can be used so long as the mode results in the expression of one or
more
molecules in an amount sufficient to provide a therapeutic effect. This
includes direct
needle injection, systemic injection, catheter infusion, biolistic injectors,
particle
accelerators (i.e., "gene guns"), gelfoam sponge depots, other commercially
available
depot materials, osmotic pumps (e.g., Alza minipumps), oral or suppositorial
solid
(tablet or pill) pharmaceutical formulations, and decanting or topical
applications
during surgery. For example, direct injection of naked calcium phosphate-
precipitated
plasmid into rat liver and rat spleen or a protein-coated plasmid into the
portal vein has
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resulted in gene expression of the foreign gene in the rat livers (Kaneda et
al., Science
243:375 (1989)).
[0439] A preferred method of local administration is by direct injection.
Preferably, a recombinant molecule of the present invention complexed with a
delivery vehicle is administered by direct injection into or locally within
the area of
arteries. Administration of a composition locally within the area of arteries
refers to
injecting the composition centimeters and preferably, millimeters within
arteries.
[0440] Another method of local administration is to contact a polynucleotide
construct of the present invention in or around a surgical wound. For example,
a
patient can undergo surgery and the polynucleotide construct can be coated on
the
surface of tissue inside the wound or the construct can be injected into areas
of tissue
inside the wound.
[0441] Therapeutic compositions useful in systemic administration, include
recombinant molecules of the present invention complexed to a targeted
delivery
vehicle of the present invention. Suitable delivery vehicles for use with
systemic
administration comprise liposomes comprising ligands for targeting the vehicle
to a
particular site. In specific embodiments, suitable delivery vehicles for use
with
systemic administration comprise liposomes comprising polypeptides of the
invention
for targeting the vehicle to a particular site.
[0442] Preferred methods of systemic administration, include intravenous
injection, aerosol, oral and percutaneous (topical) delivery. Intravenous
injections can
be performed using methods standard in the art. Aerosol delivery can also be
performed using methods standard in the art (see, for example, Stribling et
al., Proc.
Natl. Acad. Sci. USA 189:11277-11281, 1992, which is incorporated herein by
reference). Oral delivery can be performed by complexing a polynucleotide
construct
of the present invention to a carrier capable of withstanding degradation by
digestive
enzymes in the gut of an animal. Examples of such carriers, include plastic
capsules or
tablets, such as those known in the art. Topical delivery can be performed by
mixing a
polynucleotide construct of the present invention with a lipophilic reagent
(e.g.,
DMSO) that is capable of passing into the skin.
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[0443] Determining an effective amount of substance to be delivered can depend
upon a number of factors including, for example, the chemical structure and
biological
activity of the substance, the age and weight of the animal, the precise
condition
requiring treatment and its severity, and the route of administration. The
frequency of
treatments depends upon a number of factors, such as the amount of
polynucleotide
constructs administered per dose, as well as the health and history of the
subject. The
precise amount, number of doses, and timing of doses will be determined by the
attending physician or veterinarian.
[0444] Therapeutic compositions of the present invention can be administered
to
any animal, preferably to mammals and birds. Preferred mammals include humans,
dogs, cats, mice, rats, rabbits sheep, cattle, horses and pigs, with humans
being
particularly preferred.
Biological Activities
[0445] Polynucleotides or polypeptides, or agonists or antagonists of the
present
invention, can be used in assays to test for one or more biological
activities. If these
polynucleotides or polypeptides, or agonists or antagonists of the present
invention, do
exhibit activity in a particular assay, it is likely that these molecules may
be involved
in the diseases associated with the biological activity. Thus, the
polynucleotides and
polypeptides, and agonists or antagonists could be used to treat, prevent
diagnose
and/or prognose the associated disease.
[0446] The prostate cancer antigen polynucleotides and polypeptides of the
invention are predicted to have predominant expression in prostate tissues.
[0447] Thus, the prostate cancer antigens of the invention may be useful as
therapeutic molecules. Each would be useful for diagnosis, detection,
treatment andlor
prevention of diseases or disorders of the prostate, including but not limited
to prostate
cancers such as adenocarcinoma, transitional cell carcinomas, ductal
carcinomas, and
squamous cell carcinomas.
[0448] In a preferred embodiment, polynucleotides of the invention (e.g., a
nucleic
acid sequence of SEQ ID NO:X or the complement thereof; or the cDNA sequence
contained in Clone ID NO:Z, or fragments or variants thereof) and/or
polypeptides of
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the invention (e.g., an amino acid sequence contained in SEQ ID NO:Y, an amino
acid
sequence encoded by SEQ ID NO:X, or the complement threof, an amino acid
sequence encoded by the cDNA sequence contained in Clone ID NO:Z and fragments
or variants thereof as described herein) are useful for the diagnosis,
detection,
treatement, and/or prevention of diseases or disorders of the tissues/cells
corresponding to the library source disclosed in column 7 of Table 1A
expressing the
corresponding prostate cancer sequence disclosed in the same row of Table 1A.
In
certain embodiments, a polypeptide of the invention, or polynucleotides,
antibodies,
agonists, or antagonists corresponding to that polypeptide, may be used to
diagnose
and/or prognose diseases and/or disorders associated with the tissues) in
which the
polypeptide of the invention is expressed, including one, two, three, four,
five, or more
tissues disclosed in Table 1A, column 7 (Tissue Distribution Library Code).
[0449] Particularly, the prostate cancer antigens may be a useful therapeutic
for
prostate cancer. Treatment, diagnosis, detection, and/or prevention of
prostate
disorders could be carried out using a prostate cancer antigen or soluble form
of a
prostate cancer antigen, a prostate cancer antigen ligand, gene therapy, or ex
vivo
applications. Moreover, inhibitors of a prostate cancer antigen, either
blocking
antibodies or mutant forms,. could modulate .the expression of the prostate
cancer
antigen. These inhibitors may be useful to treat, diagnose, detect, and/or
prevent .
diseases associated with the misregulation of a prostate cancer antigen.
[0450] In one embodiment, the invention provides a method for the specific
delivery of compositions of the invention to cells (e.g., normal or diseased
prostate
cells) by administering polypeptides of the invention (e.g., prostate cancer
antigen
polypeptides or anti- prostate cancer antigen antibodies) that are associated
with
heterologous polypeptides or nucleic acids. In one example, the invention
provides a
method for delivering a therapeutic protein into the targeted cell (e.g., an
aberrant
prostate cell or prostate cancer cell). In another example, the invention
provides a
method for delivering a single stranded nucleic acid (e.g., antisense or
ribozymes) or
double stranded nucleic acid (e.g., DNA that can integrate into the cell's
genome or
replicate episomally and that can be transcribed) into the targeted cell.
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[0451] In another embodiment, the invention provides a method for the specific
destruction of cells (e.g., the destruction of aberrant prostate cells,
including, but not
limited to, prostate tumor cells) by administering polypeptides of the
invention (e.g.,
prostate cancer antigen polypeptides or fragments thereof, or anti- prostate
cancer
antigen antibodies) in association with toxins or cytotoxic prodrugs.
[0452] By "toxin" is meant compounds that bind and activate endogenous
cytotoxic effector systems, radioisotopes, holotoxins, modified toxins,
catalytic
subunits of toxins, cytotoxins (cytotoxic agents), or any molecules or enzymes
not
normally present in or on the surface of a cell that under defined conditions
cause the
cell's death. Toxins that may be used according to the methods of the
invention
include, but are not limited to, radioisotopes known in the art, compounds
such as, for
example, antibodies (or complement fixing containing portions thereof) that
bind an
inherent or induced endogenous cytotoxic effector system, thymidine kinase,
endonuclease, RNAse, alpha toxin, ricin, abrin, Pseudomonas exotoxin A,
diphtheria
toxin, saporin, momordin, gelonin, pokeweed antiviral protein, alpha-sarcin
and
cholera toxin. "Toxin" also includes a cytostatic or cytocidal agent, a
therapeutic agent
or a radioactive metal ion, e.g., alpha-emitters such as, for example, 2isBi,
or other
radioisoto es such as for exam 1e . iosPd is3Xe i3il ssGe S~Co 65Zn sSSr 32P
ssS
p ~ p > > > > > > > > > >
Soy 153Sm 153Gd is9yb siCr s4Mn ~sse u3Sn goyttrium lmTin lssRhenium
> > > > > > > > > > >
i6sHolmium, and lssRhenium; luminescent labels, such as luminol; and
fluorescent
labels, such as fluorescein and rhodamine, and biotin.
[0453] Techniques known in the art may be applied to label antibodies of the
invention. Such techniques include, but are not limited to, the use of
bifunctional
conjugating agents (see e.g., U.S. Patent Nos. 5,756,065; 5,714,631;
5,696,239;
5,652,361; 5,505,931; 5,489,425; 5,435,990; 5,428,139; 5,342,604; 5,274,119;
4,994,560; and 5,808,003; the contents of each of which are hereby
incorporated by
reference in its entirety). A cytotoxin or cytotoxic agent includes any agent
that is
detrimental to cells. Examples include paclitaxol, cytochalasin B, gramicidin
D,
ethidium bromide, emetine, mitomycin, etoposide, tenoposide, vincristine,
vinblastine,
colchicin, doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone,
mithramycin, actinomycin D, 1-dehydrotestosterone, glucocorticoids, procaine,
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tetracaine, lidocaine, propranolol, and puromycin and analogs or homologs
thereof.
Therapeutic agents include, but are not limited to, antimetabolites (e.g.,
methotrexate,
6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil decarbazine),
alkylating
agents (e.g., mechlorethamine, thioepa chlorambucil, melphalan, cannustine
(BSNU)
and lomustine (CCNU), cyclothosphamide, busulfan, dibromomannitol,
streptozotocin, mitomycin C, and cis- dichlorodiamine platinum (II) (DDP)
cisplatin),
anthracyclines (e.g., daunorubicin (formerly ~daunomycin) and doxorubicin),
antibiotics (e.g., dactinomycin (formerly actinomycin), bleomycin,
mithramycin, and
anthramycin (AMC)), and anti-mitotic agents (e.g., vincristine and
vinblastine).
[0454] By "cytotoxic prodrug" is meant a non-toxic compound that is converted
by
an enzyme, normally present in the cell, into a cytotoxic compound. Cytotoxic
prodrugs that may be used according to the methods of the invention include,
but are
not limited to, glutamyl derivatives of benzoic acid mustard alkylating agent,
phosphate derivatives of etoposide or mitomycin C, cytosine arabinoside,
daunorubisin, and phenoxyacetamide derivatives of doxorubicin.
[0455] It will be appreciated that conditions caused by a decrease in the
standard
or normal level of a prostate cancer antigen activity in an individual,
particularly
disorders of the prostate, can be treated by administration of a prostate
cancer antigen
polypeptide (e.g., such as, for example, the complete prostate cancer antigen
polypeptide, the soluble form of the extracellular domain of a prostate cancer
antigen
polypeptide, or cells expressing the complete protein) or agonist. Thus, the
invention
also provides a method of treatment of an individual in need of an increased
level of
prostate cancer antigen activity comprising administering to such an
individual a
pharmaceutical composition comprising an amount of an isolated prostate cancer
antigen polypeptide of the invention, or agonist thereof (e.g., an agonistic
anti-
prostate cancer antigen antibody), effective to increase the prostate cancer
antigen
activity Ievel in such an individual.
[0456] It will also be appreciated that conditions caused by a increase in the
standard or normal level of prostate cancer antigen activity in an individual,
particularly disorders of the prostate, can be treated by administration of
prostate
cancer antigen polypeptides (e.g., such as, for example, the complete prostate
cancer
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antigen polypeptide, the soluble form of the extracellular domain of a
prostate cancer
. antigen polypeptide, or cells expressing the complete protein) or antagonist
(e.g., an
antagonistic prostate cancer antigen antibody). Thus, the invention also
provides a
method of treatment of an individual in need of an decreased level of prostate
cancer
antigen activity comprising administering to such an individual a
pharmaceutical
composition comprising an amount of an isolated prostate cancer antigen
polypeptide.
of the invention, or antagonist thereof (e:g., an antagonistic anti-prostate
cancer
antigen antibody), effective to decrease the prostate cancer antigen activity
level in
such an individual.
[0457] More generally, polynucleotides, translation products and antibodies
corresponding to this gene may be useful for the diagnosis, prognosis,
prevention,
and/or treatment of diseases and/or disorders associated with the following
systems.
Reproductive System Disorders
[0458] The polynucleotides or polypeptides, or agonists or antagonists of the
invention may be used for the diagnosis, treatment, or prevention of diseases
and/or
disorders of the reproductive system. Reproductive system disorders that can
be
treated by the compositions of the invention, include, but are not limited to,
reproductive system injuries, infections, neoplastic disorders, congenital
defects, and
diseases or disorders which result in infertility, complications with
pregnancy, labor,
or parturition, and postpartum difficulties.
[0459] Reproductive system disorders and/or diseases include diseases and/or
disorders of the testes, including, but not limited to, testicular atrophy,
testicular
feminization, cryptorchism (unilateral and bilateral), anorchia, ectopic
testis,
epididymitis and orchitis (typically resulting from infections such as, for
example,
gonorrhea, mumps, tuberculosis, and syphilis), testicular torsion, vasitis
nodosa, germ
cell tumors (e.g., seminomas, embryonal cell carcinomas, teratocarcinomas,
choriocarcinomas, yolk sac tumors, and teratomas), stromal tumors (e.g.,
Leydig cell
tumors), hydrocele, hematocele, varicocele, spermatocele, inguinal hernia, and
disorders of sperm production (e.g., immotile cilia syndrome, aspermia,
asthenozoospennia, azoospermia, oligospermia, and teratozoospermia).
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[0460] Reproductive system disorders also include, but are not limited to,
disorders of the prostate gland, such as acute non-bacterial prostatitis,
chronic non-
bacterial prostatitis, acute bacterial prostatitis, chronic bacterial
prostatitis,
prostatodystonia, prostatosis, granulomatous prostatitis, malacoplakia, benign
prostatic
hypertrophy or hyperplasia, and prostate neoplastic . disorders, including
adenocarcinomas, transitional cell carcinomas, ductal carcinomas, and squamous
cell
carcinomas.
[0461] Additionally, the compositions of the invention may be useful in the
diagnosis, treatment, and/or prevention of disorders or diseases of the penis
and
urethra, including, but not limited to, inflammatory disorders, such as
balanoposthitis,
balanitis xerotica obliterans, phimosis, paraphimosis, syphilis, herpes
simplex virus,
gonorrhea, non-gonococcal urethritis, chlamydia, mycoplasma, trichomonas, HIV,
AIDS, Reiter's syndrome, condyloma acuminatum, condyloma latum, and pearly
penile papules; urethral abnormalities, such as hypospadias, epispadias, and
phimosis;
premalignant lesions, including Erythroplasia of Queyrat, Bowen's disease,
Bowenoid
paplosis, giant condyloma of Buscke-Lowenstein, and varrucous carcinoma;
penile
cancers, including squamous cell carcinomas, carcinoma in situ, verrucous
carcinoma,
and disseminated penile carcinoma; urethral neoplastic disorders, including
penile
urethral carcinoma, bulbomembranous urethral carcinoma, and prostatic urethral
carcinoma; and erectile disorders, such as priapism, Peyronie's disease,
erectile
dysfunction, and impotence.
[0462] Moreover, diseases and/or disorders of the vas deferens include, but
are not
limited to, vasculititis and CBAVD (congenital bilateral absence of the vas
deferens);
additionally, the polynucleotides, polypeptides, and agonists or antagonists
of the
present invention may be used in the diagnosis, treatment, andlor prevention
of
diseases and/or disorders of the seminal vesicles, including but not limited
to, hydatid
disease, congenital chloride diarrhea, and polycystic kidney disease.
[0463] Other disorders and/or diseases of the male reproductive system that
may
be diagnosed, treated, and/or prevented with the compositions of the invention
include,
but are not limited to, Klinefelter's syndrome, Young's syndrome, premature
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ejaculation, diabetes mellitus, cystic fibrosis, Kartagener's syndrome, high
fever,
multiple sclerosis, and gynecomastia.
[0464] Further, the polynucleotides, polypeptides, and agonists or antagonists
of
the present invention may be used in the diagnosis, treatment, and/or
prevention of
diseases and/or disorders of the vagina and vulva, including, but not limited
to,
bacterial vaginosis, candida vaginitis, herpes simplex virus, chancroid,
granuloma
inguinale, lymphogranuloma venereum, scabies, human papillomavirus, vaginal
trauma, vulvar trauma, adenosis, chlamydia vaginitis, gonorrhea, trichomonas
vaginitis, condyloma acuminatum, syphilis, molluscum contagiosum, atrophic
vaginitis, Paget's disease, lichen sclerosus, lichen planus, vulvodynia, toxic
shock
syndrome, vaginismus, vulvovaginitis, vulvar vestibulitis, and neoplastic
disorders,
such as squamous cell hyperplasia, clear cell carcinoma, basal cell carcinoma,
melanomas, cancer of Bartholin's gland, and vulvar intraepithelial neoplasia.
[0465] Disorders and/or diseases of the uterus that may be diagnosed, treated,
and/or prevented with the compositions of the invention include, but are not
limited to,
dysmenorrhea, retroverted uterus, endometriosis, fibroids, adenomyosis,
anovulatory
bleeding, amenorrhea, Cushing's syndrome, hydatidiform moles, Asherman's
syndrome, premature menopause, precocious puberty, uterine polyps,
dysfunctional
uterine bleeding (e.g., due to aberrant hormonal signals), and neoplastic
disorders,
such as adenocarcinomas, keiomyosarcomas, and sarcomas. Additionally, the
polypeptides, polynucleotides, or agonists or antagonists of the invention may
be
useful as a marker or detector of, as well as in the diagnosis, treatment,
and/or
prevention of congenital uterine abnormalities, such as bicornuate uterus,
septate
uterus, simple unicornuate uterus, unicornuate uterus with a noncavitary
rudimentary
horn, unicornuate uterus with a non-communicating cavitary rudimentary horn,
unicornuate uterus with a communicating cavitary horn, arcuate uterus, uterine
didelfus, and T-shaped uterus.
[0466] Ovarian diseases and/or disorders that may be diagnosed, treated,
and/or
prevented with the compositions of the invention include, but are not limited
to,
anovulation, polycystic ovary syndrome (Stein-Leventhal syndrome), ovarian
cysts,
ovarian hypofunction, ovarian insensitivity to gonadotropins, ovarian
overproduction
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of androgens, right ovarian vein syndrome, amenorrhea, hirutism, and ovarian
cancer
(including, but not limited to, primary and secondary cancerous growth,
Sertoli-Leydig
tumors, endometriod carcinoma of the ovary, ovarian papillary serous
adenocarcinoma, ovarian mucinous adenocarcinoma, and Ovarian I~rukenberg
tumors).
[0467] Cervical diseases and/or disorders that may be diagnosed, treated,
and/or
prevented with the compositions of the invention include, but are not limited
to,
cervicitis, chronic cervicitis, mucopurulent cervicitis, cervical dysplasia,
cervical
polyps, Nabothian cysts, cervical erosion, cervical incompetence, and cervical
neoplasms (including, for example, cervical carcinoma, squamous metaplasia,
squamous cell carcinoma, adenosquamous cell neoplasia, and columnar cell
neoplasia).
[0468] Additionally, diseases and/or disorders of the reproductive system that
may
be diagnosed, treated, and/or prevented with the compositions of the invention
include,
but are not limited to, disorders and/or diseases of pregnancy, including
miscarriage
and stillbirth, such as early abortion, late abortion, spontaneous abortion,
induced
abortion, therapeutic abortion, threatened abortion, missed abortion,
incomplete
abortion, complete abortion, habitual abortion, missed abortion, and septic
abortion;
ectopic pregnancy, anemia, Rh incompatibility, vaginal bleeding during
pregnancy,
gestational diabetes, intrauterine growth retardation, polyhydramnios, HELLP
syndrome, abruptio placentae, placenta previa, hyperemesis, preeclampsia,
eclampsia,
herpes gestationis, and urticaria of pregnancy. Additionally, the
polynucleotides,
polypeptides, and agonists or antagonists of the present invention may be used
in the
diagnosis, treatment, and/or prevention of diseases that can complicate
pregnancy,
including heart disease, heart failure, rheumatic heart disease, congenital
heart disease,
mitral valve prolapse, high blood pressure, anemia, kidney disease, infectious
disease
(e.g., rubella, cytomegalovirus, toxoplasmosis, infectious hepatitis,
chlamydia, HIV,
AIDS, and genital herpes), diabetes mellitus, Graves' disease, thyroiditis,
hypothyroidism, Hashimoto's thyroiditis, chronic active hepatitis, cirrhosis
of the
liver, primary biliary cirrhosis, asthma, systemic lupus eryematosis,
rheumatoid
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arthritis, myasthenia gravis, idiopathic thrombocytopenic purpura,
appendicitis,
ovarian cysts, gallbladder disorders,and obstruction of the intestine.
[0469] Complications associated with labor and parturition that may be
diagnosed,
treated, and/or prevented with the compositions of the invention include, but
are not
limited to, premature rupture of the membranes, pre-term labor, post-term
pregnancy,
postmaturity, labor that progresses too slowly, fetal distress (e.g., abnormal
heart rate
(fetal or maternal), breathing problems, and abnormal fetal position),
shoulder
dystocia, prolapsed umbilical cord, amniotic fluid embolism, and aberrant
uterine
bleeding.
[0470] Further, diseases and/or disorders of the postdelivery period, that may
be
diagnosed, treated, and/or prevented with the compositions of the invention,
include,
but are not limited to, endometritis, myometritis, parametritis, peritonitis,
pelvic
thrombophlebitis, pulmonary embolism, endotoxemia, pyelonephritis, saphenous
thrombophlebitis, mastitis, cystitis, postpartum hemorrhage, and inverted
uterus.
[0471] Other disorders and/or diseases of the female reproductive system that
may
be diagnosed, treated, and/or prevented by the polynucleotides, polypeptides,
and
agonists or antagonists of the present invention include, but are not limited
to, Turner's
syndrome, pseudohermaphroditism, premenstrual syndrome, pelvic inflammatory
disease, pelvic congestion (vascular engorgement); frigidity, anorgasmia,
dyspareunia,
ruptured fallopian tube, and Mittelschmerz.
Immune Activity
[0472] Polynucleotides, polypeptides, antibodies, and/or agonists or
antagonists of
the present invention may be useful in treating, preventing, diagnosing and/or
prognosing diseases, disorders, and/or conditions of the immune system, by,
for
example, activating or inhibiting the proliferation, differentiation, or
mobilization
(chemotaxis) of immune cells. Immune cells develop through a process called
hematopoiesis, producing myeloid (platelets, red blood cells, neutrophils, and
macrophages) and lymphoid (B and T lymphocytes) cells from pluripotent stem
cells.
The etiology of these immune diseases, disorders, andlor conditions may be
genetic,
somatic, such as cancer and some autoimmune diseases, acquired (e.g., by
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chemotherapy or toxins), or infectious. Moreover, polynucleotides,
polypeptides,
antibodies, and/or agonists or antagonists of the present invention can be
used as a
marker or detector of a particular immune system disease or disorder.
[0473] In another embodiment, a polypeptide of the invention, or
polynucleotides,
antibodies, agonists, or antagonists corresponding to that polypeptide, may be
used to
treat diseases and disorders of the immune system and/or to inhibit or enhance
an
immune response generated by cells associated with the tissues) in which the
polypeptide of the invention is expressed, including one, two, three, four,
five, or more
tissues disclosed in Table 1A, column 7 (Tissue Distribution Library Code).
[0474] Polynucleotides, polypeptides, antibodies, and/or agonists or
antagonists of
the present invention may be useful in treating, preventing, diagnosing,
and/or
prognosing immunodeficiencies, including both congenital and acquired
immunodeficiencies. Examples of B cell immunodeficiencies in which
immunoglobulin levels B cell function and/or B cell numbers are decreased
include:
X-linked agammaglobulinemia (Bruton's disease), X-linked infantile
agammaglobulinemia, X-linked immunodeficiency with hyper IgM, non X-linked
immunodeficiency with hyper IgM, X-linked lymphoproliferative syndrome (XLP),
agammaglobulinemia including congenital and acquired agammaglobulinemia, adult
onset agammaglobulinemia; late-onset agammaglobulinemia, dysgammaglobulinemia,
hypogammaglobulinemia, unspecified hypogammaglobulinemia, recessive
agammaglobulinemia (Swiss type), Selective IgM deficiency, selective IgA
deficiency, selective IgG subclass deficiencies, IgG subclass deficiency (with
or
without IgA deficiency), Ig deficiency with increased IgM, IgG and IgA
deficiency
with increased IgM, antibody deficiency with normal or elevated Igs, Ig heavy
chain
deletions, kappa chain deficiency, B cell lymphoproliferative disorder (BLPD),
common variable immunodeficiency (CVID), common variable immunodeficiency
(CVI) (acquired), and transient hypogammaglobulinemia of infancy.
[0475] In specific embodiments, ataxia-telangiectasia or conditions associated
with ataxia-telangiectasia are treated, prevented, diagnosed, and/or
prognosing using
the polypeptides or polynucleotides of the invention, and/or agonists or
antagonists
thereof.
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[0476] Examples of congenital immunodeficiencies in which T cell and/or B cell
function and/or number is decreased include, but are not limited to: DiGeorge
anomaly, severe combined immunodeficiencies (SCID) (including, but not limited
to,
X-linked SCID, autosomal recessive SLID, adenosine deaminase deficiency,
purine
nucleoside phosphorylase (PNP) deficiency, Class II MHC deficiency (Bare
lymphocyte syndrome), Wiskott-Aldrich syndrome, and ataxia telangiectasia),
thymic
hypoplasia, third and fourth pharyngeal pouch syndrome, 22q11.2 deletion,
chronic
mucocutaneous candidiasis, natural killer cell deficiency (NK), idiopathic
CD4+ T-
lymphocytopenia, immunodeficiency with predominant T cell defect
(unspecified),
and unspecified immunodeficiency of cell mediated immunity.
[0477] In specific embodiments, DiGeorge anomaly or conditions associated with
DiGeorge anomaly are treated, prevented, diagnosed, and/or prognosed using
polypeptides or polynucleotides of the invention, or antagonists or agonists
thereof.
[0478] Other immunodeficiencies that may be treated, prevented, diagnosed,
and/or prognosed using polypeptides or polynucleotides of the invention,
and/or
agonists or antagonists thereof, include, but are not limited to, chronic
granulomatous
disease, Chediak-Higashi syndrome, myeloperoxidase deficiency, leukocyte
glucose-
6-phosphate dehydrogenase 'deficiency, X-linked lymphoproliferative syndrome
(XLP), leukocyte adhesion deficiency, complement component deficiencies
(including
C1, C2, C3, C4, C5, C6, C7, C8 and/or C9 deficiencies), reticular dysgenesis,
thymic
alymphoplasia-aplasia, immunodeficiency with thymoma, severe congenital
leukopenia, dysplasia with immunodeficiency, neonatal neutropenia, short
limbed
dwarfism, and Nezelof syndrome-combined immunodeficiency with Igs.
[0479] In a preferred embodiment, the immunodeficiencies and/or conditions
associated with the immunodeficiencies recited above are treated, prevented,
diagnosed and/or prognosed using polynucleotides, polypeptides, antibodies,
and/or
agonists or antagonists of the present invention.
[0480] In a preferred embodiment polynucleotides, polypeptides, antibodies,
and/or agonists or antagonists of the present invention could be used as an
agent to
boost immunoresponsiveness among immunodeficient individuals. In specific
embodiments, polynucleotides, polypeptides, antibodies, and/or agonists or
antagonists
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of the present invention could be used as an agent to boost
immunoresponsiveness
among B cell and/or T cell immunodeficient individuals.
[0481] The polynucleotides, polypeptides, antibodies, and/or agonists or
antagonists of the present invention may be useful in treating, preventing,
diagnosing
and/or prognosing autoimmune disorders. Many autoimmune disorders result from
inappropriate recognition of self as foreign material by immune cells. This
inappropriate recognition results in an immune response leading to the
destruction of
the host tissue. Therefore, the administration of polynucleotides and
polypeptides of
the invention that can inhibit an immune response, particularly the
proliferation,
differentiation, or chemotaxis of T-cells, may be an effective therapy in
preventing
autoimmune disorders.
[0482] Autoimmune diseases or disorders that may be treated, prevented,
diagnosed and/or prognosed by polynucleotides, polypeptides, antibodies,
and/or
agonists or antagonists of the present invention include, but are not limited
to, one or
more of the following: systemic lupus erythematosus, rheumatoid arthritis,
ankylosing
spondylitis, multiple sclerosis, autoimmune thyroiditis, Hashimoto's
thyroiditis,
autoimmune hemolytic anemia, hemolytic anemia, thrombocytopenia, autoimmune
thrombocytopenia purpura, ~ autoimmune neonatal thrombocytopenia, idiopathic
thrombocytopenia purpura, purpura (e.g., Henloch-Scoenlein purpura),
autoimmunocytopenia, Goodpasture's syndrome, Pemphigus vulgaris, myasthenia
gravis, Grave's disease (hyperthyroidism), and insulin-resistant diabetes
mellitus.
[0483] Additional disorders that are likely to have an autoimmune component
that
may be treated, prevented, and/or diagnosed with the compositions of the
invention
include, but are not limited to, type II collagen-induced arthritis,
antiphospholipid
syndrome, dermatitis, allergic encephalomyelitis, myocarditis, relapsing
polychondritis, rheumatic heart disease, neuritis, uveitis ophthalmia,
polyendocrinopathies, Reiter's Disease, Stiff Man Syndrome, autoimmune
pulmonary
inflammation, autism, GuiIIain-Barre Syndrome, insulin dependent diabetes
mellitus,
and autoimmune inflammatory eye disorders.
[0484] Additional disorders that are likely to have an autoimmune component
that
may be treated, prevented, diagnosed and/or prognosed with the compositions of
the
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invention include, but are not limited to, scleroderma with anti-collagen
antibodies
(often characterized, e.g., by nucleolar and other nuclear antibodies), mixed
connective
tissue disease (often characterized, e.g., by antibodies to extractable
nuclear antigens
(e.g., ribonucleoprotein)), polymyositis (often characterized, e.g., by
nonhistone
ANA), pernicious anemia (often characterized, e.g., by antiparietal cell,
microsomes,
and intrinsic factor antibodies), idiopathic Addison's disease (often
characterized, e.g.,
by humoral and cell-mediated adrenal cytotoxicity, infertility (often
characterized,
e.g., by antispermatozoal antibodies), glomerulonephritis (often
characterized, e.g., by
glomerular basement membrane antibodies or immune complexes), bullous
pemphigoid (often characterized, e.g., by IgG and complement in basement
membrane), Sjogren's syndrome (often characterized, e.g., by multiple tissue
antibodies, and/or a specific nonhistone ANA (SS-B)), diabetes mellitus (often
characterized, e.g., by cell-mediated and humoral islet cell antibodies), and
adrenergic
drug resistance (including adrenergic drug resistance with asthma or cystic
fibrosis)
(often characterized, e.g., by beta-adrenergic receptor antibodies).
[0485] Additional disorders that may have an autoimmune component that may be
treated, prevented, diagnosed and/or prognosed with the compositions of the
invention
include, but are not limited to, chronic active hepatitis (often
characterized, e.g., by
smooth muscle antibodies), primary biliary cirrhosis (often characterized,
e.g., by
mitochondria antibodies), other endocrine gland failure (often characterized,
e.g., by
specific tissue antibodies in some cases), vitiligo (often characterized,
e.g., by
melanocyte antibodies), vasculitis (often characterized, e.g., by Ig and
complement in
vessel walls and/or low serum complement), post-MI (often characterized, e.g.,
by
myocardial antibodies), cardiotomy syndrome (often characterized, e.g., by
myocardial
antibodies), urticaria (often characterized, e.g., by IgG and IgM antibodies
to IgE),
atopic dermatitis (often characterized, e.g., by IgG and IgM antibodies to
IgE), asthma
(often characterized, e.g., by IgG and IgM antibodies to IgE), and many other
inflammatory, granulomatous, degenerative, and atrophic disorders.
[0486] In a preferred embodiment, the autoimmtme diseases and disorders and/or
conditions associated with the diseases and disorders recited above are
treated,
prevented, diagnosed and/or prognosed using for example, antagonists or
agonists,
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polypeptides or polynucleotides, or antibodies of the present invention. In a
specific
preferred embodiment, rheumatoid arthritis is treated, prevented, and/or
diagnosed
using polynucleotides, polypeptides, antibodies, and/or agonists or
antagonists of the
present invention.
[0487] In another specific preferred embodiment, systemic lupus erythematosus
is
treated, prevented, and/or diagnosed using polynucleotides, polypeptides,
antibodies,
and/or agonists or antagonists of the present invention. In another specific
preferred
embodiment, idiopathic thrombocytopenia purpura is treated, prevented, and/or
diagnosed using polynucleotides, polypeptides, antibodies, and/or agonists or
antagonists of the present invention.
[0488] In another specific preferred embodiment IgA nephropathy is treated,
prevented, and/or diagnosed using polynucleotides, polypeptides, antibodies,
and/or
agonists or antagonists of the present invention.
[0489] In a preferred embodiment, the autoimmune diseases and disorders and/or
conditions associated with the diseases and disorders recited above are
treated,
prevented, diagnosed andlor prognosed using polynucleotides, polypeptides,
antibodies, and/or agonists or antagonists of the present invention.
[0490] In preferred embodiments polypeptides; antibodies, polynucleotides
and/or
agonists or antagonists of the present invention are used as a
immunosuppressive
agent(s).
[0491] Polynucleotides, polypeptides, antibodies, and/or agonists or
antagonists of
the present invention may be useful in treating, preventing, prognosing,
and/or
diagnosing diseases, disorders, and/or conditions of hematopoietic cells.
Polynucleotides, polypeptides, antibodies, and/or agonists or antagonists of
the present
invention could be used to increase differentiation and proliferation of
hematopoietic
cells, including the pluripotent stem cells, in an effort to treat or prevent
those
diseases, disorders, and/or conditions associated with a decrease in certain
(or many)
types hematopoietic cells, including but not limited to, leukopenia,
neutropenia,
anemia, and thrombocytopenia. Alternatively, Polynucleotides, polypeptides,
antibodies, and/or agonists or antagonists of the present invention could be
used to
increase differentiation and proliferation of hematopoietic cells, including
the
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pluripotent stem cells, in an effort to treat or prevent those.diseases,
disorders, and/or
conditions associated with an increase in certain (or many) types of
hematopoietic
cells, including but not limited to, histiocytosis.
[0492] Allergic reactions and conditions, such as asthma (particularly
allergic
asthma) or other respiratory problems, may also be treated, prevented,
diagnosed
and/or prognosed using polypeptides, antibodies, or polynucleotides of the
invention,
and/or agonists or antagonists thereof. Moreover, these molecules can be used
to treat,
prevent, prognose, and/or diagnose anaphylaxis, hypersensitivity to an
antigenic
molecule, or blood group incompatibility.
[0493] Additionally, polypeptides or polynucleotides of the invention, and/or
agonists or antagonists thereof, may be used to treat, prevent, diagnose
and/or
prognose IgE-mediated allergic reactions. Such allergic reactions include, but
are not
limited to, asthma, rhinitis, and eczema. In specific embodiments,
polynucleotides,
polypeptides, antibodies, and/or agonists or antagonists of the present
invention may
be used to modulate IgE concentrations in vitro or in vivo.
[0494] Moreover, polynucleotides, polypeptides, antibodies, and/or agonists or
antagonists of the present invention have uses in the diagnosis, prognosis,
prevention,
and/or treatment of inflammatory conditions.. For. example, since
polypeptides,
antibodies, or polynucleotides of the invention, and/or agonists or
antagonists of the
invention may inhibit the activation, proliferation and/or differentiation of
cells
involved in an inflammatory response, these molecules can be used to prevent
and/or
treat chronic and acute inflammatory conditions. Such inflammatory conditions
include, but are not limited to, for example, inflammation associated with
infection
(e.g., septic shock, sepsis, or systemic inflammatory response syndrome),
ischemia-
reperfusion injury, endotoxin lethality, complement-mediated. hyperacute
rejection,
nephritis, cytokine or chemokine induced lung injury, inflammatory bowel
disease,
Crohn's disease, over production of cytokines (e.g., TNF or IL-1.),
respiratory
disorders (e.g., asthma and allergy); gastrointestinal disorders (e.g.,
inflammatory
bowel disease); cancers (e.g., gastric, ovarian, lung, bladder, liver, and
breast); CNS
disorders (e.g., multiple sclerosis; ischemic brain injury andlor stroke,
traumatic brain
injury, neurodegenerative disorders (e.g., Parkinson's disease and Alzheimer's
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disease); AIDS-related dementia; and prion disease); cardiovascular disorders
(e.g.,
atherosclerosis, myocarditis, cardiovascular disease, and cardiopulmonary
bypass
complications); as well as many additional diseases, conditions, and disorders
that are
characterized by inflammation (e.g., hepatitis, rheumatoid arthritis, gout,
trauma,
pancreatitis, sarcoidosis, dermatitis, renal ischemia-reperfusion injury,
Grave's
disease, systemic lupus erythematosus, diabetes mellitus, and allogenic
transplant
rejection).
[0495] Because inflammation is a fundamental defense mechanism, inflammatory
disorders can effect virtually any tissue of the body. Accordingly,
polynucleotides,
polypeptides, and antibodies of the invention, as well as agonists or
antagonists
thereof, have uses in the treatment of tissue-specific inflammatory disorders,
including, but not limited to, adrenalitis, alveolitis, angiocholecystitis,
appendicitis,
balanitis, blepharitis, bronchitis, bursitis, carditis, cellulitis,
cervicitis, cholecystitis,
chorditis, cochlitis, colitis, conjunctivitis, cystitis, dermatitis,
diverticulitis,
encephalitis, endocarditis, esophagitis, eustachitis, fibrositis,
folliculitis, gastritis,
gastroenteritis, gingivitis, glossitis, hepatosplenitis, lceratitis,
labyrinthitis, laryngitis,
lymphangitis, mastitis, media otitis, meningitis, metritis, mucitis,
myocarditis,
myosititis, myringitis, nephritis, neuritis, orchitis, osteochondritis,
otitis, pericarditis,
peritendonitis, peritonitis, pharyngitis, phlebitis, poliomyelitis,
prostatitis, pulpitis,
retinitis, rhinitis, salpingitis, scleritis, sclerochoroiditis, scrotitis,
sinusitis, spondylitis,
steatites, stomatitis, synovitis, syringitis, tendonitis, tonsillitis,
urethritis, and vaginitis.
[0496] In specific embodiments, polypeptides, antibodies, or polynucleotides
of
the invention, and/or agonists or antagonists thereof, are useful to diagnose,
prognose,
prevent, and/or treat organ transplant rejections and graft-versus-host
disease. Organ
rejection occurs by host immune cell destruction of the transplanted tissue
through an
immune response. Similarly, an immune response is also involved in GVHD, but,
in
this case, the foreign transplanted immune cells destroy the host tissues.
Polypeptides,
antibodies, or polynucleotides of the invention, and/or agonists or
antagonists thereof,
that inhibit an immune response, particularly the activation, proliferation,
differentiation, or chemotaxis of T-cells, may be an effective therapy in
preventing
organ rejection or GVHD. In specific embodiments, polypeptides, antibodies, or
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polynucleotides of the invention, and/or agonists or antagonists thereof, that
inhibit an
immune response, particularly the activation, proliferation, differentiation,
or
chemotaxis of T-cells, may be an effective therapy in preventing experimental
allergic
and hyperacute xenograft rejection.
[0497] In other embodiments, polypeptides, antibodies, or polynucleotides of
the
invention, and/or agonists or antagonists thereof, are useful to diagnose,
prognose,
prevent, and/or treat immune complex diseases, including, but not limited to,
serum
sickness, post streptococcal glomerulonephritis, polyarteritis nodosa, and
immune
complex-induced vasculitis.
[0498] Polypeptides, antibodies, polynucleotides and/or agonists or
antagonists of
the invention can be used to treat, detect, and/or prevent infectious agents.
For
example, by increasing the immune response, particularly increasing the
proliferation
activation and/or differentiation of B and/or T cells, infectious diseases may
be treated,
detected, and/or prevented. The immune response may be increased by either
enhancing an existing immune response, or by initiating a new immune response.
Alternatively, polynucleotides, polypeptides, antibodies, and/or agonists or
antagonists
of the present invention may also directly inhibit the infectious agent (refer
to section
of application listing infectious agents, etc), without necessarily eliciting-
an immune
response.
[0499] In another embodiment, polypeptides, antibodies, polynucleotides and/or
agonists or antagonists of the present invention are used as a vaccine
adjuvant that
enhances immune responsiveness to an antigen. In a specific embodiment,
polypeptides, antibodies, polynucleotides and/or agonists or antagonists of
the present
invention are used as an adjuvant to enhance tumor-specific immune responses.
[0500] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an
adjuvant to
enhance anti-viral immune responses. Anti-viral immune responses that may be
enhanced using the compositions of the invention as an adjuvant, include virus
and
virus associated diseases or symptoms described herein or otherwise known in
the art.
In specific embodiments, the compositions of the invention are used as an
adjuvant to
enhance an immune response to a virus, disease, or symptom selected from the
group
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consisting of: AIDS, meningitis, Dengue, EBV, and hepatitis (e.g., hepatitis
B). In
another specific embodiment, the compositions of the invention are used as an
adjuvant to enhance an immune response to a virus, disease, or symptom
selected from
the group consisting of: HIV/AIDS, respiratory syncytial virus, Dengue,
rotavirus,
Japanese B encephalitis, influenza A and.B, parainfluenza, measles,
cytomegalovirus,
rabies, Junin, Chikungunya, Rift Valley Fever, herpes simplex, and yellow
fever.
[0501] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an
adjuvant to
enhance anti-bacterial or anti-fungal immune responses. Anti-bacterial or anti-
fungal
immune responses that may be enhanced using the compositions of the invention
as an
adjuvant, include bacteria or fungus and bacteria or fungus associated
diseases or
symptoms described herein or dtherwise known in the art. In specific
embodiments,
the compositions of the invention are used as an adjuvant to enhance an immune
response to a bacteria or fungus, disease, or symptom selected from the group
consisting of: tetanus, Diphtheria, botulism, and meningitis type B.
[0502] In another specific embodiment, the compositions of the invention are
used
as an adjuvant to enhance an immune response to a bacteria or fungus, disease,
or
symptom selected from the group. consisting of: Vibrio chole~ae, Mycobacterium
lep~ae, Salmonella t~phi, Salmonella paratyphi, Meisse~ia meningitidis,
Streptococcus
pneumoniae, Group B streptococcus, Shigella spp., Enterotoxigenic Escherichia
coli,
Enterohemorrhagic E. coli, and Bof~~elia bu~gdo~fe~°i.
[0503] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an
adjuvant to
enhance anti-parasitic immune responses. Anti-parasitic immune responses that
may
be enhanced using the compositions of the invention as an adjuvant, include
parasite
and parasite associated diseases or symptoms described herein or otherwise
known in
the art. In specific embodiments, the compositions of the invention are used
as an
adjuvant to enhance an immune response to a parasite. In another specific
embodiment, the compositions of the invention are used as an adjuvant to
enhance an
immune response to Plasmodium (malaria) or Leishmania.
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[0504] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention may also be employed
to treat
infectious diseases including silicosis, sarcoidosis, and idiopathic pulmonary
fibrosis;
for example, by preventing the recruitment and activation of mononuclear
phagocytes.
[0505] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present~invention are used as an antigen
for the
generation of antibodies to inhibit or enhance immune mediated responses
against
polypeptides of the invention.
[0506] In one embodiment, polypeptides, antibodies, polynucleotides and/or
agonists or antagonists of the present invention are administered to an animal
(e.g.,
mouse, rat, rabbit, hamster, guinea pig, pigs, micro-pig, chicken, camel,
goat, horse,
cow, sheep, dog, cat, non-human primate, and human, most preferably human) to
boost the immune system to produce increased quantities of one or more
antibodies
(e.g., IgG, IgA, IgM, and IgE), to induce higher affinity antibody production
and
immunoglobulin class switching (e.g., IgG, IgA, IgM, and IgE), and/or to
increase an
immune response.
[0507] In another specific embodiment,. polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as a
stimulator of B
cell responsiveness to pathogens.
[0508] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an
activator of T
cells.
[0509] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an agent
that
elevates the immune status of an individual prior to their receipt of
immunosuppressive therapies.
[0510] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an agent
to induce
higher affinity antibodies.
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[0511] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an agent
to increase
serum immunoglobulin concentrations.
[0512] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an agent
to
accelerate recovery of immunocompromised individuals.
[0513] In another specific embodiment, polypeptides; antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an agent
to boost
immunoresponsiveness among aged populations and/or neonates.
(0514] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an immune
system
enhancer prior to, during, or after bone marrow transplant and/or other
transplants
(e.g., allogeneic or xenogeneic organ transplantation). With respect to
transplantation,
compositions of the invention may be administered prior to, concomitant with,
and/or
after transplantation. In a specific embodiment, compositions of the invention
are
administered after transplantation, prior to the beginning of recovery of T-
cell
populations. In another specific embodiment, compositions of the invention are
first
administered after transplantation after the beginning of recovery of T cell
populations, but prior to full recovery of B cell populations.
[0515] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an agent
to boost
immunoresponsiveness among individuals having an acquired loss of B cell
function.
Conditions resulting in an acquired loss of B cell function that may be
ameliorated or
treated by administering the polypeptides, antibodies, polynucleotides and/or
agonists
or antagonists thereof, include, but are not limited to, HIV Infection, AIDS,
bone
marrow transplant, and B cell chronic lymphocytic leulcemia (CLL).
[0516] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an agent
to boost
immunoresponsiveness among individuals having a temporary immune deficiency.
Conditions resulting in a temporary immune deficiency that may be ameliorated
or
treated by administering the polypeptides, antibodies, polynucleotides and/or
agonists
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or antagonists thereof, include, but are not limited to, recovery from viral
infections
(e.g., influenza), conditions associated with malnutrition, recovery from
infectious
mononucleosis, or conditions associated with stress, recovery from measles,
recovery
from blood transfusion, and recovery from surgery.
[0517] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists. of the present invention are used as a
regulator of
antigen presentation by monocytes, dendritic cells, and/or B-cells. In one
embodiment, polynucleotides, polypeptides, antibodies, and/or agonists or
antagonists
of the present invention enhance antigen presentation or antagonizes antigen
presentation in vitro or in vivo. Moreover, in related embodiments, said
enhancement
or antagonism of antigen presentation may be useful as an anti-tumor treatment
or to
modulate the immune system.
[0518] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as an agent
to direct an
individual's immune system towards development of a humoral response (i.e.
TH2) as
opposed to a TH1 cellular response.
[0519] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as a means
.to. induce
tumor proliferation and thus make it more susceptible to anti-neoplastic
agents. For
example, multiple myeloma is a slowly dividing disease and is thus refractory
to
virtually all anti-neoplastic regimens. If these cells were forced to
proliferate more
rapidly their susceptibility profile would likely change.
[0520] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as a
stimulator of B
cell production in pathologies such as AIDS, chronic lymphocyte disorder
and/or
Common Variable Immunodificiency.
[0521] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as a therapy
for
generation and/or regeneration of lymphoid tissues following surgery, trauma
or
genetic defect. In another specific embodiment, polypeptides, antibodies,
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polynucleotides and/or agonists or antagonists of the present invention are
used in the
pretreatment of bone marrow samples prior to transplant.
[0522] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as a gene-
based
therapy for genetically inherited disorders resulting in immuno-
incompetence/immunodeficiency.such as observed among SCID patients.
[0523] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as a means of
activating monocytes/macrophages to defend against parasitic diseases that
effect
monocytes such as Leishmania.
[0524] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as a means of
regulating secreted cytolcines that are elicited by polypeptides of the
invention.
[0525] In another embodiment, polypeptides, antibodies, polynucleotides andlor
agonists or antagonists of the present invention are used in one or more of
the
applications decribed herein, as they may apply to veterinary medicine.
[0526] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as a means of
blocking
various aspects of immune responses to foreign agents or self. Examples of
diseases
or conditions in which blocking of certain aspects of immune responses may be
desired include autoimmune disorders such as lupus, and arthritis, as well as
immunoresponsiveness to skin allergies, inflammation, bowel disease, injury
and
diseases/disorders associated with pathogens.
[0527] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as a therapy
for
preventing the B cell proliferation and Ig secretion associated with
autoimmune
diseases such as idiopathic thrombocytopenic purpura, systemic lupus
erythematosus
and multiple sclerosis.
[0528] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as a
inhibitor of B
and/or T cell migration in endothelial cells. This activity disrupts tissue
architecture or
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cognate responses and is useful, for example in disrupting immune responses,
and
blocking sepsis.
[0529] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used as a therapy
for
chronic hypergammaglobulinemia evident in such diseases as monoclonal
gammopathy of undetermined significance (MGUS), Waldenstrom's disease, related
idiopathic monoclonal gammopathies, and plasmacytomas.
[0530] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention may be employed for
instance
to inhibit polypeptide chemotaxis and activation of macrophages and their
precursors,
and of neutrophils, basophils, B lymphocytes and some T-cell subsets, e.g.,
activated
and CD8 cytotoxic T cells and natural killer cells, in certain autoimmune and
chronic
inflammatory and infective diseases. Examples of autoimmune diseases are
described
herein and include multiple sclerosis, and insulin-dependent diabetes.
[0531] The polypeptides, antibodies, polynucleotides and/or agonists or
antagonists of the present invention may also be employed to treat idiopathic
hyper-
eosinophilic syndrome by, for example, preventing eosinophil production and
migration.
[0532] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used to enhance or
inhibit
complement mediated cell lysis.
[0533] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention are used to enhance or
inhibit
antibody dependent cellular cytotoxicity.
[0534] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention may also be employed
for
treating atherosclerosis, for example, by preventing monocyte infiltration in
the artery
wall.
[0535] In another specific embodiment, polypeptides, antibodies,
polynucleotides
and/or agonists or antagonists of the present invention may be employed to
treat adult
respiratory distress syndrome CARDS).
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