CA2320618A1 - Secreted proteins and polynucleotides encoding them - Google Patents
Secreted proteins and polynucleotides encoding them Download PDFInfo
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Abstract
Novel polynucleotides and the proteins encoded thereby are disclosed.
Description
WO 99!41284 PCTNS99/02898 SECRETED PROTEINS AND P'OLYNUCLEOTIDES ENCODING THEM
This application is a continuation-in-part of provisional application Ser. No.
60/075,118, filed February 11,1998, which is incorporated by reference herein.
The present invention provides novel polynucleotides and proteins encoded by such polynucleotides, along with therapeutic, diagnostic and research utilities for these polynucleotides and proteins.
Technology aimed at the discovery of protein factors (including e.g., cytokines, such as lymphokines, interferons, CSFs and interleukins) has matured rapidly over the 2 0 past decade. The now routine hybridization cloning and expression cloning techniques clone novel polynucleotides "directly" in the sense that they rely on information directly related to the discovered protein (i.e., partial DNA/amino acid sequence of the protein in the case of hybridization cloning; activity of the protein in the case of expression cloning). More recent "indirect" cloning techniques such as signal sequence cloning, which 2 5 isolates DNA sequences based on the presence of a now well-recognized secretory leader sequence motif, as well as various PCR-based or low stringency hybridization cloning techniques, have advanced the state of the art by making available large numbers of DNA/amino acid sequences for proteins that are known to have biological activity by virtue of their secreted nature in the case of leader sequence cloning, or by virtue of the 3 0 cell or tissue source in the case of PCR-based techniques. It is to these proteins and the polynucleotides encoding them that the present invention is directed.
This application is a continuation-in-part of provisional application Ser. No.
60/075,118, filed February 11,1998, which is incorporated by reference herein.
The present invention provides novel polynucleotides and proteins encoded by such polynucleotides, along with therapeutic, diagnostic and research utilities for these polynucleotides and proteins.
Technology aimed at the discovery of protein factors (including e.g., cytokines, such as lymphokines, interferons, CSFs and interleukins) has matured rapidly over the 2 0 past decade. The now routine hybridization cloning and expression cloning techniques clone novel polynucleotides "directly" in the sense that they rely on information directly related to the discovered protein (i.e., partial DNA/amino acid sequence of the protein in the case of hybridization cloning; activity of the protein in the case of expression cloning). More recent "indirect" cloning techniques such as signal sequence cloning, which 2 5 isolates DNA sequences based on the presence of a now well-recognized secretory leader sequence motif, as well as various PCR-based or low stringency hybridization cloning techniques, have advanced the state of the art by making available large numbers of DNA/amino acid sequences for proteins that are known to have biological activity by virtue of their secreted nature in the case of leader sequence cloning, or by virtue of the 3 0 cell or tissue source in the case of PCR-based techniques. It is to these proteins and the polynucleotides encoding them that the present invention is directed.
In one embodiment, the present invention provides a composition comprising an isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:1;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:1 from nucleotide 29 to nucleotide 253;
(c) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone yal5_1 deposited under accession number ATCC 98650;
(d) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone yal5_1 deposited under accession number ATCC 98650;
(e) a polynucleotide comprising the nucleotide sequence of a mature protein coding sequence of clone yal5_1 deposited under accession number ATCC
98650;
(f) a polynucleofide encoding a mature protein encoded by the cDNA
insert of clone yal5_1 deposited under accession number ATCC 98650;
(g) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO~;
2 0 (h) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:2 having biological activity, the fragment comprising eight contiguous amino acids of SEQ ID N0:2;
(i) a polynucleotide which is an allelic variant of a polynucleotide of (a}-(f) above;
2 5 (j) a polynucleotide which encodes a species homologue of the protein of (g) or (h) above ;
(k) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (a~(h); and (1) a polynucleotide that hybridizes under stringent conditions to any 3 0 one of the polynucleotides specified in {a)-(h) and that has a length that is at least 25% of the length of SEQ ID NO:1.
Preferably, such polynucleotide comprises the nucleotide sequence of SEQ ID
N0:1 from nucleotide 29 to nucleotide 253; the nucleotide sequence of the full-length protein coding sequence of clone yal5_1 deposited under accession number ATCC
98650;
or the nucleotide sequence of a mature protein coding sequence of clone yal5_i deposited under accession number ATCC 98650. In other preferred embodiments, the polynucleotide encodes the full-length or a mature protein encoded by the cDNA
insert of clone yal5_1 deposited under accession number ATCC 98650. In further preferred embodiments, the present invention provides a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:2 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:2, or a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:2 having biological activity, the fragment comprising the amino acid sequence from amino acid 32 to amino acid 41 of SEQ ID N0:2.
Other embodiments provide the gene corresponding to the cDNA sequence of SEQ
ID NO:1.
Further embodiments of the invention provide isolated polynucleotides produced according to a process selected from the group consisting of:
(a) a process comprising the steps of:
(i) preparing one or more polynucleotide probes that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
2 0 (aa) SEQ ID NO:1, but excluding the poly(A) tail at the 3' end of SEQ ID N0:1; and (ab) the nucleotide sequence of the cDNA insert of done yal5_1 deposited under accession number ATCC 9$650;
(ii} hybridizing said probes) to human genomic DNA in 2 5 conditions at least as stringent as 4X SSC at 50 degrees C; and (iii) isolating the DNA polynucleotides detected with the probe(s);
and (b) a process comprising the steps of:
3 0 (i) preparing one or more polynucleotide primers that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(ba) SEQ ID NO:1, but excluding the poly(A) tail at the 3' end of SEQ ID N0:1; and (bb) the nucleotide sequence of the cDNA insert of clone yal5_1 deposited under accession number ATCC 98650;
(ii) hybridizing said primers) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C;
(iii) amplifying human DNA sequences; and (iv) isolating the polynucleotide products of step (b)(iii).
Preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID NO:1, and extending contiguously from a nucleotide sequence corresponding to the 5' end of SEQ ID
N0:1 to a nucleotide sequence corresponding to the 3' end of SEQ ID N0:1, but excluding the poly(A) tail at the 3' end of SEQ ID N0:1. Also preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID NO:1 from nucleotide 29 to nucleotide 253, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID N0:1 from nucleotide 29 to nucleotide 253, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID NO:1 from nucleotide 29 to nucleotide 253.
In other embodiments, the present invention provides a composition comprising a protein, wherein said protein comprises an amino acid sequence selected from the group 2 0 consisting of:
(a) the amino acid sequence of SEQ ID N0:2;
(b) a fragment of the amino acid sequence of SEQ ID N0:2, the fragment comprising eight contiguous amino acids of SEQ ID N0:2; and (c) the amino acid sequence encoded by the cDNA insert of clone 2 5 yal5_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins. Preferably such protein comprises the amino acid sequence of SEQ ID N0:2. In further preferred embodiments, the present invention provides a protein comprising a fragment of the amino acid sequence of SEQ ID N0:2 having biological activity, the fragment preferably 3 0 comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:2, or a protein comprising a fragment of the amino acid sequence of SEQ
ID N0:2 having biological activity, the fragment comprising the amino acid sequence from amino acid 32 to amino acid 41 of SEQ ID N0:2.
In one embodiment, the present invention provides a composition comprising an isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:3;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:3 from nucleotide 151 to nucleotide 288;
{c) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:3 from nucleotide 196 to nucleotide 288;
(d) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone ya24_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone ya24_1 deposited under accession number ATCC 98650;
(f) a polynucleotide comprising the nucleotide sequence of a mature protein coding sequence of clone ya24_1 deposited under accession number ATCC
98650;
(g) a polynucleotide encoding a mature protein encoded by the cDNA
insert of clone ya24_1 deposited under accession number ATCC 98650;
(h) a polynucleotide encoding a protein comprising the amino acid 2 0 sequence of SEQ ID N0:4;
(i) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:4 having biological activity, the fragment comprising eight contiguous amino acids of SEQ ID N0:4;
(j) a polynucleotide which is an allelic variant of a polynucleotide of 2 5 (a)-(g) above;
(k) a polynucleotide which encodes a species homologue of the protein of (h) or (i) above ;
(1) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (a)-(i); and 3 0 (m) a polynucleotide that hybridizes under stringent rnnditions to any one of the polynucleotides specified in (a~(i) and that has a length that is at least 25% of the length of SEQ ID N0:3.
Preferably, such polynucleotide comprises the nucleotide sequence of SEQ ID
N0:3 from nucleotide 151 to nucleotide 288; the nucleotide sequence of SEQ ID
N0:3 from nucleotide 196 to nucleotide 288; the nucleotide sequence of the full-length protein coding sequence of clone ya24_1 deposited under accession number ATCC 98650; or the nucleotide sequence of a mature protein coding sequence of clone ya24_1 deposited under accession number ATCC 98650. In other preferred embodiments, the polynucleotide encodes the full length or a mature protein encoded by the cDNA insert of clone ya24_1 deposited under accession number ATCC 98650. In further preferred embodiments, the present invention provides a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:4 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:4, or a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:4 having biological activity, the fragment comprising the amino acid sequence from amino acid 18 to amino acid 27 of SEQ
ID N0:4.
Other embodiments provide the gene corresponding to the cDNA sequence of SEQ
ID N0:3.
Further embodiments of the invention provide isolated polynucleotides produced according to a process selected from the group consisting of:
(a) a process comprising the steps of:
(i) preparing one or more polynudeotide probes that hybridize 2 0 in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(aa) SEQ ID N0:3, but excluding the poly(A) tail at the 3' end of SEQ ID N0:3; and (ab) the nucleotide sequence of the cDNA insert of clone 2 5 ya24_i deposited under accession number ATCC 98650;
(ii) hybridizing said probes) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C; and (iii) isolating the DNA polynucleotides detected with the probe(s);
3 0 and (b) a process comprising the steps of:
(i) preparing one or more polynucleotide primers that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:1;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:1 from nucleotide 29 to nucleotide 253;
(c) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone yal5_1 deposited under accession number ATCC 98650;
(d) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone yal5_1 deposited under accession number ATCC 98650;
(e) a polynucleotide comprising the nucleotide sequence of a mature protein coding sequence of clone yal5_1 deposited under accession number ATCC
98650;
(f) a polynucleofide encoding a mature protein encoded by the cDNA
insert of clone yal5_1 deposited under accession number ATCC 98650;
(g) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO~;
2 0 (h) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:2 having biological activity, the fragment comprising eight contiguous amino acids of SEQ ID N0:2;
(i) a polynucleotide which is an allelic variant of a polynucleotide of (a}-(f) above;
2 5 (j) a polynucleotide which encodes a species homologue of the protein of (g) or (h) above ;
(k) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (a~(h); and (1) a polynucleotide that hybridizes under stringent conditions to any 3 0 one of the polynucleotides specified in {a)-(h) and that has a length that is at least 25% of the length of SEQ ID NO:1.
Preferably, such polynucleotide comprises the nucleotide sequence of SEQ ID
N0:1 from nucleotide 29 to nucleotide 253; the nucleotide sequence of the full-length protein coding sequence of clone yal5_1 deposited under accession number ATCC
98650;
or the nucleotide sequence of a mature protein coding sequence of clone yal5_i deposited under accession number ATCC 98650. In other preferred embodiments, the polynucleotide encodes the full-length or a mature protein encoded by the cDNA
insert of clone yal5_1 deposited under accession number ATCC 98650. In further preferred embodiments, the present invention provides a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:2 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:2, or a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:2 having biological activity, the fragment comprising the amino acid sequence from amino acid 32 to amino acid 41 of SEQ ID N0:2.
Other embodiments provide the gene corresponding to the cDNA sequence of SEQ
ID NO:1.
Further embodiments of the invention provide isolated polynucleotides produced according to a process selected from the group consisting of:
(a) a process comprising the steps of:
(i) preparing one or more polynucleotide probes that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
2 0 (aa) SEQ ID NO:1, but excluding the poly(A) tail at the 3' end of SEQ ID N0:1; and (ab) the nucleotide sequence of the cDNA insert of done yal5_1 deposited under accession number ATCC 9$650;
(ii} hybridizing said probes) to human genomic DNA in 2 5 conditions at least as stringent as 4X SSC at 50 degrees C; and (iii) isolating the DNA polynucleotides detected with the probe(s);
and (b) a process comprising the steps of:
3 0 (i) preparing one or more polynucleotide primers that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(ba) SEQ ID NO:1, but excluding the poly(A) tail at the 3' end of SEQ ID N0:1; and (bb) the nucleotide sequence of the cDNA insert of clone yal5_1 deposited under accession number ATCC 98650;
(ii) hybridizing said primers) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C;
(iii) amplifying human DNA sequences; and (iv) isolating the polynucleotide products of step (b)(iii).
Preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID NO:1, and extending contiguously from a nucleotide sequence corresponding to the 5' end of SEQ ID
N0:1 to a nucleotide sequence corresponding to the 3' end of SEQ ID N0:1, but excluding the poly(A) tail at the 3' end of SEQ ID N0:1. Also preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID NO:1 from nucleotide 29 to nucleotide 253, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID N0:1 from nucleotide 29 to nucleotide 253, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID NO:1 from nucleotide 29 to nucleotide 253.
In other embodiments, the present invention provides a composition comprising a protein, wherein said protein comprises an amino acid sequence selected from the group 2 0 consisting of:
(a) the amino acid sequence of SEQ ID N0:2;
(b) a fragment of the amino acid sequence of SEQ ID N0:2, the fragment comprising eight contiguous amino acids of SEQ ID N0:2; and (c) the amino acid sequence encoded by the cDNA insert of clone 2 5 yal5_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins. Preferably such protein comprises the amino acid sequence of SEQ ID N0:2. In further preferred embodiments, the present invention provides a protein comprising a fragment of the amino acid sequence of SEQ ID N0:2 having biological activity, the fragment preferably 3 0 comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:2, or a protein comprising a fragment of the amino acid sequence of SEQ
ID N0:2 having biological activity, the fragment comprising the amino acid sequence from amino acid 32 to amino acid 41 of SEQ ID N0:2.
In one embodiment, the present invention provides a composition comprising an isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:3;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:3 from nucleotide 151 to nucleotide 288;
{c) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:3 from nucleotide 196 to nucleotide 288;
(d) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone ya24_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone ya24_1 deposited under accession number ATCC 98650;
(f) a polynucleotide comprising the nucleotide sequence of a mature protein coding sequence of clone ya24_1 deposited under accession number ATCC
98650;
(g) a polynucleotide encoding a mature protein encoded by the cDNA
insert of clone ya24_1 deposited under accession number ATCC 98650;
(h) a polynucleotide encoding a protein comprising the amino acid 2 0 sequence of SEQ ID N0:4;
(i) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:4 having biological activity, the fragment comprising eight contiguous amino acids of SEQ ID N0:4;
(j) a polynucleotide which is an allelic variant of a polynucleotide of 2 5 (a)-(g) above;
(k) a polynucleotide which encodes a species homologue of the protein of (h) or (i) above ;
(1) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (a)-(i); and 3 0 (m) a polynucleotide that hybridizes under stringent rnnditions to any one of the polynucleotides specified in (a~(i) and that has a length that is at least 25% of the length of SEQ ID N0:3.
Preferably, such polynucleotide comprises the nucleotide sequence of SEQ ID
N0:3 from nucleotide 151 to nucleotide 288; the nucleotide sequence of SEQ ID
N0:3 from nucleotide 196 to nucleotide 288; the nucleotide sequence of the full-length protein coding sequence of clone ya24_1 deposited under accession number ATCC 98650; or the nucleotide sequence of a mature protein coding sequence of clone ya24_1 deposited under accession number ATCC 98650. In other preferred embodiments, the polynucleotide encodes the full length or a mature protein encoded by the cDNA insert of clone ya24_1 deposited under accession number ATCC 98650. In further preferred embodiments, the present invention provides a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:4 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:4, or a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:4 having biological activity, the fragment comprising the amino acid sequence from amino acid 18 to amino acid 27 of SEQ
ID N0:4.
Other embodiments provide the gene corresponding to the cDNA sequence of SEQ
ID N0:3.
Further embodiments of the invention provide isolated polynucleotides produced according to a process selected from the group consisting of:
(a) a process comprising the steps of:
(i) preparing one or more polynudeotide probes that hybridize 2 0 in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(aa) SEQ ID N0:3, but excluding the poly(A) tail at the 3' end of SEQ ID N0:3; and (ab) the nucleotide sequence of the cDNA insert of clone 2 5 ya24_i deposited under accession number ATCC 98650;
(ii) hybridizing said probes) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C; and (iii) isolating the DNA polynucleotides detected with the probe(s);
3 0 and (b) a process comprising the steps of:
(i) preparing one or more polynucleotide primers that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(ba) SEQ ID N0:3, but excluding the poly(A) tail at the 3' end of SEQ ID N0:3; and (bb) the nucleotide sequence of the cDNA insert of clone ya24_i deposited under accession number ATCC 98650;
(ii) hybridizing said primers) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C;
(iii) amplifying human DNA sequences; and (iv) isolating the polynucleotide products of step (b)(iii).
Preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:3, and extending contiguously from a nucleotide sequence corresponding to the 5' end of SEQ ID
N0:3 to a nucleotide sequence corresponding to the 3' end of SEQ ID N0:3 , but excluding the poly(A) tail at the 3' end of SEQ ID N0:3. Also preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:3 from nucleotide 151 to nucleotide 288, and extending contiguously from a nucleotide sequence rnnresponding to the 5' end of said sequence of SEQ ID N0:3 from nucleotide 151 to nucleotide 288, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID N0:3 from nucleotide 151 to nucleotide 288. Also preferably the polynucleotide isolated according to the above 2 0 process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID
N0:3 from nucleotide 196 to nucleotide 288, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID
N0:3 from nucleotide 196 to nucleotide 288, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID N0:3 from nucleotide 196 to nucleotide 288.
2 5 In other embodiments, the present invention provides a composition comprising a protein, wherein said protein comprises an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID N0:4;
(b) a fragment of the amino acid sequence of SEQ ID N0:4, the 3 0 fragment comprising eight contiguous amino aclds of SEQ ID N0:4; and (c) the amino acid sequence encoded by the cDNA insert of clone ya24_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins. Preferably such protein comprises the amino acid sequence of SEQ ID N0:4. In further preferred WO 99/41284 PCT/US99/p2898 embodiments, the present invention provides a protein comprising a fragment of the amino acid sequence of SEQ ID N0:4 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:4, or a protein comprising a fragment of the amino acid sequence of SEQ
ID N0:4 having biological activity, the fragment comprising the amino acid sequence from amino acid 18 to amino acid 27 of SEQ ID N0:4.
In one embodiment, the, present invention provides a composition comprising an isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:5;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:5 from nucleotide 615 to nucleotide 908;
(c) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:5 from nucleotide 774 to nucleotide 908;
{d) a polynucleotide comprising the nucleotide sequence of the full-~g'~ Pmt Wing sequence of clone yb42_i deposited under accession number ATCC 98650;
(e) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone yb42_1 deposited under accession number ATCC 98650;
2 0 (f) a polynucleotide comprising the nucleotide sequence of a mature protein coding sequence of clone yb42_1 deposited under accession number ATCC
98650;
(g) a polynucleotide encoding a mature protein encoded by the cDNA
insert of clone yb42_1 deposited under accession number ATCC 98650;
2 5 (h) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID N0:6;
(i) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:6 having biological activity, the fragment comprising eight contiguous amino acids of SEQ ID N0:6;
3 0 (j) a polynucleotide which is an allelic variant of a polynucleotide of (ar(g) above;
(k) a polynucleotide which encodes a species homologue of the protein of (h) or {i) above ;
(ii) hybridizing said primers) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C;
(iii) amplifying human DNA sequences; and (iv) isolating the polynucleotide products of step (b)(iii).
Preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:3, and extending contiguously from a nucleotide sequence corresponding to the 5' end of SEQ ID
N0:3 to a nucleotide sequence corresponding to the 3' end of SEQ ID N0:3 , but excluding the poly(A) tail at the 3' end of SEQ ID N0:3. Also preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:3 from nucleotide 151 to nucleotide 288, and extending contiguously from a nucleotide sequence rnnresponding to the 5' end of said sequence of SEQ ID N0:3 from nucleotide 151 to nucleotide 288, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID N0:3 from nucleotide 151 to nucleotide 288. Also preferably the polynucleotide isolated according to the above 2 0 process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID
N0:3 from nucleotide 196 to nucleotide 288, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID
N0:3 from nucleotide 196 to nucleotide 288, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID N0:3 from nucleotide 196 to nucleotide 288.
2 5 In other embodiments, the present invention provides a composition comprising a protein, wherein said protein comprises an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID N0:4;
(b) a fragment of the amino acid sequence of SEQ ID N0:4, the 3 0 fragment comprising eight contiguous amino aclds of SEQ ID N0:4; and (c) the amino acid sequence encoded by the cDNA insert of clone ya24_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins. Preferably such protein comprises the amino acid sequence of SEQ ID N0:4. In further preferred WO 99/41284 PCT/US99/p2898 embodiments, the present invention provides a protein comprising a fragment of the amino acid sequence of SEQ ID N0:4 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:4, or a protein comprising a fragment of the amino acid sequence of SEQ
ID N0:4 having biological activity, the fragment comprising the amino acid sequence from amino acid 18 to amino acid 27 of SEQ ID N0:4.
In one embodiment, the, present invention provides a composition comprising an isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:5;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:5 from nucleotide 615 to nucleotide 908;
(c) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:5 from nucleotide 774 to nucleotide 908;
{d) a polynucleotide comprising the nucleotide sequence of the full-~g'~ Pmt Wing sequence of clone yb42_i deposited under accession number ATCC 98650;
(e) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone yb42_1 deposited under accession number ATCC 98650;
2 0 (f) a polynucleotide comprising the nucleotide sequence of a mature protein coding sequence of clone yb42_1 deposited under accession number ATCC
98650;
(g) a polynucleotide encoding a mature protein encoded by the cDNA
insert of clone yb42_1 deposited under accession number ATCC 98650;
2 5 (h) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID N0:6;
(i) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:6 having biological activity, the fragment comprising eight contiguous amino acids of SEQ ID N0:6;
3 0 (j) a polynucleotide which is an allelic variant of a polynucleotide of (ar(g) above;
(k) a polynucleotide which encodes a species homologue of the protein of (h) or {i) above ;
(1) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (a~(i); and (m) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (a)-(i) and that has a length that is at least 25% of the length of SEQ ID N0:5.
Preferably, such polynucleotide comprises the nucleotide sequence of SEQ ID
N0:5 from nucleotide 615 to nucleotide 908; the nucleotide sequence of SEQ ID
N0:5 from nucleotide 774 to nucleotide 908; the nucleotide sequence of the full-length protein coding sequence of clone yb42_1 deposited under accession number ATCC 98650; or the nucleotide sequence of a mature protein coding sequence of clone yb42_1 deposited under accession number ATCC 98650. In other preferred embodiments, the polynucleotide encodes the full-length or a mature protein encoded by the cDNA insert of clone yb42_1 deposited under accession number ATCC 9$650. In further preferred embodiments, the present invention provides a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:6 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:6, or a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:6 having biological activity, the fragment comprising the amino acid sequence from amino acid 44 to amino acid 53 of SEQ
2 0 ID N0:6.
Other embodiments provide the gene corresponding to the cDNA sequence of SEQ
ID N0:5.
Further embodiments of the invention provide isolated polynucleotides produced according to a process selected from the group consisting of:
2 5 (a) a process comprising the steps of:
(i) preparing one or more polynucleotide probes that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(aa) SEQ ID N0:5, but excluding the poly(A) tail at the 3 0 3' end of SEQ ID N0:5; and (ab) the nucleotide sequence of the cDNA insert of clone yb42_i deposited under accession number ATCC 98650;
(ii) hybridizing said probes) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C; and {iii) isolating the DNA polynucleotides detected with the probe(s);
and (b) a process comprising the steps of:
(i) preparing one or more polynucleotide primers that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(ba) SEQ ID N0:5, but excluding the poly(A) tail at the 3' end of SEQ ID N0:5; and _ (bb) the nucleotide sequence of the cDNA insert of clone yb42_1 deposited under accession number ATCC 98650;
(ii) hybridizing said primers) to human genomic DNA in conditions at least as stringent as 4X S5C at 50 degrees C;
(iii) amplifying human DNA sequences; and 25 (iv) isolating the polynucleotide products of step {b)(iii).
Preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:5, and extending contiguously from a nucleotide sequence corresponding to the 5' end of SEQ ID
IV0:5 to a nucleotide sequence corresponding to the 3' end of SEQ ID N0:5 , but excluding the 2 0 poly(A) tail at the 3' end of SEQ ID N0:5. Also preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:5 from nucleotide 615 to nucleotide 908, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID N0:5 from nucleotide 615 to nucleotide 908, to a nucleotide sequence 2 5 corresponding to the 3' end of said sequence of SEQ ID N0:5 from nucleotide 615 to nucleotide 908. Also preferably the polynucleotide isolated according to the above process comprises a nucleotide sequenre corresponding to the cDNA sequence of SEQ ID
N0:5 from nucleotide 774 to nucleotide 908, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID
N0:5 from 3 0 nucleotide 774 to nucleotide 908, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID N0:5 from nucleotide 774 to nucleotide 908.
In other embodiments, the present invention provides a composition comprising a protein, whex~itt said protein comprises an amino acid sequence selected from the group consisting of:
WO 99/41284 PCT/US99l02898 (a) the amino acid sequence of SEQ ID N4:6;
(b) a fragment of the amino acid sequence of SEQ ID N0:6, the fragment comprising eight contiguous amino acids of SEQ ID N0:6; and (c) the amino acid sequence encoded by the cDNA insert of clone yb42_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins. Preferably such protein comprises the amino acid sequence of SEQ ID N0:6. In further preferred embodiments, the present invention provides a protein comprising a fragment of the amino acid sequence of SEQ ID N0:6 having biological activity, the fragment preferably comprising Wight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:6, or a protein comprising a fragment of the amino acid sequence of SEQ
ID N0:6 having biological activity, the fragment comprising the amino acid sequence from amino acid 44 to amino acid 53 of SEQ ID N0:6.
In one embodiment, the present invention provides a composition comprising an isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:7;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:7 from nucleotide 1203 to nucleotide 2327;
2 0 (c) a polynudeotide comprising the nucleotide sequence of the full-length protein coding sequence of clone yc9 1 deposited under accession number ATCC 98650;
(d) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone y~ 1 deposited under accession number ATCC 98650;
2 5 (e) a polynucleotide comprising the nucleotide sequence of a mature protein coding sequence of clone y~ 1 deposited under accession number ATCC
98650;
(f) a polynudeotide encoding a mature protein encoded by the cDNA
insert of clone y~ 1 deposited under accession number ATCC 98650;
3 0 (g) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:8;
(h) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:8 having biological activity, the fragment comprising eight contiguous amino acids of SEQ ID N0:8;
(i) a polynucleotide which is an allelic variant of a polynucleotide of {a)-(f) above;
(j) a polynudeotide which encodes a speaes homologue of the protein of (g) or (h) above ;
(k) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (ar(h); and {1) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (ar(h) and that has a length that is at least 25% of the length of SEQ ID N0:7.
Preferably, such polynucleotide comprises the nucleotide sequence of SEQ ID
N0:7 from nucleotide 1203 to nucleotide 2327; the nucleotide sequence of the full-length protein coding sequence of clone y~ 1 deposited under accession number ATCC
98650;
or the nucleotide sequence of a mature prntein coding sequence of clone y~ 1 deposited under accession number ATCC 98650. In other preferred embodiments, the polynucleotide encodes the full-length or a mature protein encoded by the cDNA
insert of clone y~ 1 deposited under accession number ATCC 98650. In further preferred embodiments, the present invention provides a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:8 having biological activity, the fragment preferably comprising eight (more preferably twenty, most 2 0 preferably thirty) contiguous amino ands of SEQ ID N0:8, or a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:8 having biological activity, the fragment rnmprising the amino acid sequence from amino acid 182 to amino acid 191 of SEQ ID N0:8.
Other embodiments provide the gene corresponding to the cDNA sequence of SEQ
2 5 ID N0:7.
Further embodiments of the invention provide isolated polynucleotides produced according to a process selected from the group consisting of:
(a) a process comprising the steps of:
(i) preparing one or more polynucleotide probes that hybridize 3 0 in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(aa) SEQ ID N0:7, but excluding the poly(A) tail at the 3' end of SEQ ID N0:7; and (ab) the nucleotide sequence of the cDNA insert of clone yc9_1 deposited under accession number ATCC 98650;
(ii) hybridizing said probes) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C; and (iii) isolating the DNA polynucleotides detected with the probe(s);
and (b) a process comprising the steps of:
(i) preparing one or more polynucleotide primers that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(ba) SEQ ID N0:7, but excluding the poly(A) tail at the 3' end of SEQ ID N0:7; and (bb) the nucleotide sequence of the cDNA insert of clone y~ 1 deposited under accession number ATCC 98650;
(ii) hybridizing said primers) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C;
(iii) amplifying human DNA sequences; and (iv) isolating the polynucleotide products of step (b)(iii).
2 0 Preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:7, and exfiending contiguously from a nucleotide sequence corresponding to the 5' end of SEQ ID
N0:7 to a nucleotide sequence corresponding to the 3' end of SEQ ID N0:7 , but excluding the poly(A) tail at the 3' end of SEQ ID N0:7. Also preferably the polynucleotide isolated 2 5 according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:7 from nucleotide 1203 to nucleotide 2327, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID N0:7 from nucleotide 1203 to nucleotide 2327, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID N0:7 from nucleotide 1203 to 3 0 nucleotide 2327.
In other embodiments, the present invention provides a composition comprising a protein, wherein said protein comprises an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID N0:8;
WO 99/41284 PCf/US99/OZ898 (b) a fragment of the amino acid sequence of SEQ ID N0:8, the fragment comprising eight contiguous amino acids of SEQ ID N0:8; and (c) the amino acid sequence encoded by the cDNA insert of clone y~ 1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins. Preferably such protein comprises the amino acid sequence of SEQ ID N0:8. In further preferred embodiments, the present invention provides a protein comprising a fragment of the amino acid sequence of SEQ ID N0:8 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:8, or a protein comprising a fragment of the amino acid sequence of SEQ
ID NO:B having biological activity, the fragment comprising the amino acid sequence from amino acid 182 to amino acid 191 of SEQ ID N0:8.
In one embodiment, the present invention provides a composition comprising an isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:9;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:9 from nucleotide 230 to nucleotide 823;
(c) a polynucleotide comprising the nucleotide sequence of SEQ ID
2 0 N0:9 from nucleotide 584 to nucleotide 823;
(d) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone ycl9_i deposited under accession number ATCC 98650;
(e) a polynucleotide encoding the full-length protein encoded by the 2 5 cDNA insert of clone ycl9_1 deposited under accession number ATCC 98650;
(f) a polynucleotide comprising the nucleotide sequence of a mature protein coding sequence of clone ycl9_1 deposited under accession number ATCC
98650;
(g) a polynucleotide encoding a mature protein encoded by the cDNA
3 0 insert of clone ycl9_1 deposited under accession number ATCC 98650;
(h) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:10;
(i) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:10 having biological activity, the fragment comprising eight contiguous amino acids of SEQ ID NO:10;
(j) a polynucleotide which is an allelic variant of a polynucleotide of (a)-(g) above;
(k) a polynucleotide which encodes a species homologue of the protein of (h) or (i) above ;
(1) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (a)-(i); and (m) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (a~(i) and that has a length that is at least 25% of the length of SEQ ID N0:9.
Preferably, such polynucleotide comprises the nucleotide sequence of SEQ ID
N0:9 from nucleotide 230 to nucleotide 823; the nucleotide sequence of SEQ ID
N0:9 from nucleotide 584 to nucleotide 823; the nucleotide sequence of the full-length protein coding sequence of clone ycl9_1 deposited under accession number ATCC 98650; or the nucleotide sequence of a mature protein coding sequence of clone ycl9_1 deposited under accession number ATCC 98650. In other preferred embodiments, the polynucleotide encodes the full length or a mature protein encoded by the cDNA insert of clone ycl9_1 2 0 deposited under accession number ATCC 98650. In further preferred embodiments, the present invention provides a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:10 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:10, or a polynucleotide encoding a protein comprising a 2 5 fragment of the amino acid sequence of SEQ ID NO:10 having biological activity, the fragment comprising the amino acid sequence from amino acid 94 to amino acid 103 of SEQ ID NO:10.
Other embodiments provide the gene corresponding to the cDNA sequenre of SEQ
ID N0:9.
3 0 Further embodiments of the invention provide isolated polynucleotides produced according to a process selected from the group consisting of:
(a) a process comprising the steps of:
(i) preparing one or more polynucleotide probes that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(aa) SEQ ID N0:9, but excluding the poly(A) tail at the 3' end of SEQ ID N0:9; and (ab) the nucleotide sequence of the cDNA insert of clone ycl9_1 deposited under accession number ATCC 98650;
(ii) hybridizing said probes) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C; and (iii) isolating the DNA polynudeotides detected with the probe(s);
and (b) a process comprising the steps of:
(i) preparing one or more polynucleotide primers that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(ba) SEQ ID N0:9, but excluding the poly(A) tail at the 3' end of SEQ ID N0:9; and (bb) the nucleotide sequence of the cDNA insert of clone 2 0 ycl9_i deposited under accession number ATCC 98650;
(ii) hybridizing said primers) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C;
(iii) amplifying human DNA sequences; and (iv) isolating the polynudeotide products of step (b)(iii).
2 5 Preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence co~p~g to the cDNA sequence of SEQ ID N0:9, and extending contiguously from a nucleotide sequence corresponding to the 5' end of SEQ ID
N0:9 to a nucleotide sequence corresponding to the 3' end of SEQ ID N0:9 , but excluding the poly(A) tail at the 3' end of SEQ ID N0:9. Also preferably the polynucleotide isolated 3 0 according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:9 from nucleotide 230 to nucleotide 823, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID N0:9 from nucleotide 230 to nucleotide 823, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID N0:9 from nucleotide 230 to nucleotide 823. Also preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID
N0:9 from nucleotide 584 to nucleotide 823, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID
N0:9 from nucleotide 584 to nucleotide 823, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID N0:9 from nucleotide 584 to nucleotide 823.
In other embodiments, the present invention provides a composition comprising a protein, wherein said protein comprises an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID N0:10;
(b) a fragment of the amino acid sequence of SEQ ID NO:10, the fragment comprising eight contiguous amino acids of SEQ ID N0:10; and (c) the amino acid sequence encoded by the cDNA insert of clone ycl9_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins. Preferably such protein comprises the amino acid sequence of SEQ ID N0:10. In further preferred embodiments, the present invention provides a protein comprising a fragment of the amino acid sequence of SEQ ID N0:10 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids 2 0 of SEQ ID NO:10, or a protein comprising a fragment of the amino acid sequence of SEQ
ID N0:10 having biological activity, the fragment comprising the amino acid sequence from amino acid 94 to. amino acid 103 of SEQ ID NO:10.
In one embodiment, the present invention provides a composition comprising an isolated polynucleotide selected from the group consisting of:
2 5 (a) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:11;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:11 from nucleotide 292 to nucleotide 534;
(c) a polynucleotide comprising the nucleotide sequence of the full-3 0 length protein coding sequence of clone yc20_1 deposited under accession number ATCC 98650;
(d) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone yc20_1 deposited under accession number ATCC 98650;
(e) a polynudeotide comprising the nucleotide sequence of a mature protein coding sequence of clone yc20_1 deposited under accession number ATCC
98650;
(f) a polynucleotide encoding a mature protein encoded by the cDNA
insert of clone yc20_1 deposited under accession number ATCC 98650;
(g) a polynudeotide encoding a protein comprising the amino acid sequence of SEQ ID N0:12;
(h) a polynudeotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:12 having biological activity, the fragment comprising eight contiguous amino acids of SEQ ID N0:12;
(i) a polynudeotide which is an allelic variant of a polynudeotide of (a)-(f) above;
(j) a polynudeotide which encodes a species homologue of the protein of (g) or (h) above ;
(k) a polynucleotide that hybridizes under stringent conditions to any one of the polynudeotides specified in (ar(h); and (I) a polynucleotide that hybridizes under stringent conditions to any one of the polynudeotides specified in (a~(h) and that has a length that is at least 25% of the length of SEQ ID N0:11.
2 0 Preferably, such polynudeotide comprises the nucleotide sequ~ce of SEQ ID
NO:11 from nucleotide 292 to nucleotide 534; the nucleotide sequence of the full-length protein coding sequence of clone yc20_1 deposited under accession number ATCC
98650;
or the nucleotide sequence of a mature protein coding sequence of clone yc20_1 deposited under accession number ATCC 98650. In other preferred embodiments, the 2 5 polynudeotide encodes the full-length or a mature protein encoded by the cDNA insert of done yc20_1 deposited under accession number ATCC 98650. In further preferred embodiments, the present invention provides a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:12 having biological activity, the fragment preferably comprising eight (more preferably twenty, most 3 0 preferably thirty) contiguous amino acids of SEQ ID N0:12, or a polynudeotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:12 having biological activity, the fragment comprising the amino acid sequence from amino acid 35 to amino acid 44 of SEQ ID N0:12.
Other embodiments provide the gene corresponding to the cDNA sequeruce of SEQ
ID N0:11.
Further embodiments of the invention provide isolated polynucleotides produced according to a process selected from the group consisting of:
(a) a process comprising the steps of:
(i) preparing one or more polynucleotide probes that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(aa) SEQ ID N0:11, but excluding the poly(A) tail at the 3' end of SEQ ID N0:11; and (ab) the nucleotide sequence of the cDNA insert of clone yc20_1 deposited under accession number-ATCC 98650;
(ii) hybridizing said probes) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C; and (iii) isolating the DNA polynucleotides detected with the probe(s);
and (b) a process comprising the steps of:
(i) preparing one or more polynucleotide primers that 2 0 hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(ba) SEQ ID N0:11, but excluding the poly(A) tail at the 3' end of SEQ ID NO:11; and (bb) the nucleotide sequence of the cDNA insert of clone 2 5 yc20_1 deposited under accession number ATCC 98650;
(ii) hybridizing said primers) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C;
(iii) amplifying human DNA sequences; and (iv) isolating the polynucleotide products of step (b)(iii).
3 0 Fieferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:11, and extending contiguously from a nucleotide sequence corresponding to the 5' end of SEQ
ID N0:11 to a nucleotide sequence corresponding to the 3' end of SEQ ID NO:11 , but excluding the poly(A) tail at the 3' end of SEQ ID NO:11. Also preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:11 from nucleotide 292 to nucleotide 534, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID N0:11 from nucleotide 292 to nucleotide 534, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID NO:11 from nucleotide 292 to nucleotide 534.
In other embodiments, the present invention provides a composition comprising a protein, wherein said protein comprises an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID N0:12;
(b) a fragment of the amino acid sequence of SEQ ID N0:12, the fragment comprising eight contiguous amino acids of SEQ ID N0:12; and (c) the amino acid sequence encoded by the cDNA insert of clone yc20_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins. Preferably such protein comprises the amino acid sequence of SEQ ID N0:12. In further preferred embodiments, the present invention provides a protein comprising a fragment of the amino acid sequence of SEQ ID N0:12 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids 2 0 of SEQ ID N0:12, or a protein comprising a fragment of the amino acid sequence of SEQ
ID N0:12 having biological activity, the fragment comprising the amino acid sequence from amino acid 35 to amino acid 44 of SEQ ID N0:12.
In certain preferred embodiments, the polynucleotide is operably linked to an expression control sequence. The invention also provides a host cell, including bacterial, 2 5 yeast, insect and mannmalian cells, transformed with such polynucleotide compositions.
Also provided by the present invention are organisms that have enhanced, reduced, or modified expression of the genes) corresponding to the polynucleotide sequences disclosed herein.
Processes are also provided for producing a protein, which comprise:
3 0 (a) growing a culture of the host cell transformed with such polynucleotide compositions in a suitable culture medium; and (b) purifying the protein from the culture.
The protein produced according to such methods is also provided by the present invention.
Protein compositions of the present invention may further comprise a pharmaceutically acceptable carrier. Compositions comprising an antibody which specifically reacts with such protein are also provided by the present invention.
Methods are also provided for preventing, treating or ameliorating a medical condition which comprises administering to a mammalian subject a therapeutically effective amount of a composition comprising a protein of the present invention and a pharmaceutically acceptable carrier.
Figures 1A and 1B are schematic representations of the pED6 and pNOTs vectors, respectively, used for deposit of clones disclosed herein.
DETAILED g ~S('RTPTTC~Iu Nucleotide and amino acid sequences, as presently determined, are reported belqw for each clone and protein disclosed in the present application. The nucleotide sequence of each clone can readily be determined by sequencing of the deposited clone in accordance with known methods. The predicted amino acid sequence (both full length and mature forms) can then be determined from such nucleotide sequence. The amino 2 0 acid sequence of the protein encoded by a particular clone can also be determined by expression of the clone in a suitable host cell, collecting the protein and determining its sequence. For each disclosed protein applicants have identified what they have determined to be the reading frame best identifiable with sequence information available at the time of filing.
2 5 As used herein a "secreted" protein is one which, when expressed in a suitable host cell, is transported across or through a membrane, including transport as a result of signal sequences in its amino acid sequence. "Secreted" proteins include without limitation profieins secreted wholly (e.g., soluble profieins) or partially (e.g. , receptors) from the cell in which they are expressed. "Secreted" proteins also include without limitation proteins 3 0 which are transported across the membrane of the endoplasmic reticulum.
Clone ",L 1"
A polynucleotide of the preset invention has been identified as clone "yal5_1".
yal5_1 was isolated from a human adult testes cDNA library and was identified as encoding a seaeted or transmembrane protein on the basis of computer analysis of the amino acid sequence of the encoded protein. yal5_1 is a full-length clone, including the entire coding sequence of a secreted protein (also referred to herein as "yal5_1 protein").
The nucleotide sequence of yal5_1 as presently determined is reported in SEQ
ID
NO:1, and includes a poly(A) tail. What applicants presently believe to be the proper reading frame and the predicted amino acid sequence of the yal5_1 protein corresponding to the foregoing nucleotide sequence is reported in SEQ ID N0:2. Amino acids 8 to 20 of SEQ ID N0:2 are a possible leader/signal sequence, with the predicted mature amino acid sequence beginning at amino acid 21. Due to the hydrophobic nature of the predicted leader/signal sequence, it is likely to act as a transmembrane domain should the predicfied leader/signal sequence not be separated from the remainder of the yal5_1 protein.
The EcoRI/NotI restriction fragment obtainable from the deposit containing clone yal5_1 should be approximately 1100 bp.
The nucleotide sequence disclosed herein for yal5_1 was searched against the GenBank and GeneSeq nucleotide sequence databases using BLASTN/BLASTX and FASTA search protocols. yal5_1 demonstrated at least some sianilarity with sequences identified as 294056 (Human DNA sequence from PAC 436M11 on chromosome Xp22.11-22.2; contains a serine threonine protein phosphatase gene, ESTs and STSs).
Based upon sequence similarity, yal5_1 proteins and each similar protein or peptide may 2 0 share at least some activity. The TopPredII computer program predicts a potential transmembrane domain within the yal5_1 protein sequence centered around amino acid 40 of SEQ ID N0:2. The nucleotide sequence of yal5_1 indicates that it may contain an Alu repetitive element.
2 5 Clone "3ra24 1"
A polynucleotide of the present invention has been identified as clone "ya24_1 ".
ya24_i was isolated from a human adult testes cDNA library and was identified as encoding a secreted or transmembrane protein on the basis of rnmputer analysis of the amino acid sequence of the encoded protein. ya24_1 is a full-length clone, including the 3 0 entire coding sequence of a secreted protein (also referred to herein as "ya24_1 protein").
The nucleotide sequence of ya24_1 as presently determined is reported in SEQ
ID
N0:3, and includes a poly(A) tail. What applicants presently believe to be the proper reading frame and the predicted amino acid sequence of the ya24_1 protein corresponding to the foregoing nucleotide sequence is reported in SEQ ID N0:4. Amino acids 3 to 15 of SEQ ID N0:4 are a predicted leader/signal sequence, with the predicted mature amino aced sequence beginning at amino acid 16. Due to the hydrophobic nature of the predicted leader/signal sequence, it is likely to act as a transmembrane domain should the predicted leader/signal sequence not be separated from the remainder of the ya24_1 protein.
The EcoRI/NotI restriction fragment obtainable from the deposit containing clone ya24_1 should be approximately 750 bp.
The nucleotide sequence disclosed herein for ya24_1 was searched against the GenBank and GeneSeq nucleotide sequence databases using BLAST1V/BLAST?C and FASTA search protocols. ya24_1 demonstrated at least some similarity with sequences identified as AA537299 (vk46d03.r1 Soares mouse mammary gland NbMMG Mus musculus cDNA clone 949637 5'). Based upon sequence similarity, ya24_1 proteins and each similar protein or peptide may share at least some activity.
Clone "; 1"
A polynucleotide of the present invention has been identified as clone "yb42_1".
yb42_1 was isolated from a human fetal brain cDNA library and was identified as encoding a secreted or transmembrane protein on the basis of computer analysis of the amino acid sequence of the encoded protein. yb42_1 is a full-length clone, including the entire coding sequence of a secreted protein (also referred to herein as "yb42_1 protein").
2 0 The nucleotide sequence of yb42_1 as presently determined is reported in SEQ ID
N0:5, and includes a poly(A) tail. What applicants presently believe to be the proper reading frame and the predicted amino acid sequence of the yb42_1 protein corresponding to the foregoing nucleotide sequence is reported in SEQ ID N0:6.
Amino acids 41 to 53 of SEQ ID N0:6 are a predicted leader/signal sequence, with the predicted 2 5 mature amino acid sequence beginning at amino acid 54. Due to the hydrophobic nature of the predicted leader/signal sequence, it is likely to act as a transmembrane domain should the predicted leader/signal sequence not be separated from the remainder of the yb42_1 protein.
Another potential yb42_i reading frame and predicted amino acid sequence is 3 0 encoded by basepairs 1879 to 2220 of SEQ ID N0:5 and is reported in SEQ ID
N0:19;
amino acids 54 to 66 of SEQ ID N0:19 are a predicted leader/signal sequence, with the predicted mature amino acid sequence beginning at amino acid 67 of SEQ ID
N0:19. Due to the hydrophobic nature of this predicted leader/signal sequence, it is likely to act as a transmembrane domain should the predicted leader/signal sequence not be separated from the remainder of the protein of SEQ ID N0:19.
The EcoRI/NotI restriction fragment obtainable from the deposit containing clone yb42_1 should be approximately 3900 bp.
The nucleotide sequence disclosed herein for yb42_1 was searched against the GenBank and GeneSeq nucleotide sequence databases using BLASTN/BLASTX and FASTA search protocols. yb42_1 demonstrated at least some similarity with sequences identified as AA213992 (zn58d08.s1 Stratagene muscle 937209 Homo sapiens cDNA
clone 562383 3'). Based upon sequence similarity, yb42_1 proteins and each similar protein or peptide may share at least some activity. The nucleotide sequence of yb42_1 indicates that it may contain at least one MIR repeat sequence.
Clone ",yes 1"
A poiynucleotide of the present invention has been identified as clone "yes 1".
y~ 1 was isolated from a human fetal kidney (293 cell line) cDNA library and was identified as encoding a secreted or transmembrane protein on the basis of computer analysis of the amino acid sequence of the encoded protein. y~ 1 is a full-length clone, including the entire coding sequence of a secreted protein (also referred to herein as "yes 1 protein").
2 0 The nucleotide sequence of yc9_1 as presently defiermined is reported in SEQ ID
N0:7, and includes a poly(A) tail. What applicants presently believe to be the proper reading frame and the predicted amino acid sequence of the y~ 1 protein corresponding to the foregoing nucleotide sequence is reported in SEQ ID N0:8.
The EcoRI/NotI restriction fragment obtainable from the deposit rnntaining clone 2 5 yc9_1 should be approximately 3300 bp.
The nucleotide sequence disclosed herein for y~ 1 was searched against the GenBank and GeneSeq nucleotide sequence databases using BLASTN/BLASTX and FASTA search protocols. y~ 1 demonstrated at least some similarity with sequences identified as AA588539 (nm94a07.s1 NCI_CGAP_Co9 Homo sapiens cDNA clone 3 0 IMAGE:10~5860) and N47418 (yy88e12.r1 Homo Sapiens cDNA clone 280654 5').
The predicted amino acid sequence disclosed herein for yc9_1 was searched against the GenPept and GeneSeq amino acid sequence databases using the BLASTx search protocol.
The predicted y~ 1 protein demonstrated at least some similarity to sequences identified as X97196 (D. melanogaster X gene). Based upon sequence similarity, y~ 1 profieins and WO 99/d1284 PCT/US99102898 each similar protein or peptide may share at least some activity. The TopPredil rnmputer program predicts two potential transmembrane domains within the yc9_1 protein sequence, centered around amino acids 80 and 200 of SEQ ID N0:8, respectively.
Clone"ycl9 1"
A polynucleotide of the present invention has been identified as clone "ycl9_1".
ycl9_1 was isolated from a human fetal kidney (293 cell line) cDNA library and was identified as encoding a secreted or transmembrane protein on the basis of computer analysis of the amino acid sequence of the encoded protein. ycl9_1 is a full-length clone, including the entire coding sequence of a secreted protein (also referred to herein as "ycl9_1 protein").
The nucleotide sequence of ycl9_1 as presently determined is reported in SEQ
ID
N0:9, and includes a poly(A) tail. What applicants presently believe to be the proper reading frame and the predicted amino acid sequence of the ycl9_1 protein corresponding to the foregoing nucleotide sequence is reported in SEQ ID N0:10. Amino acids 106 to 118 of SEQ ID N0:10 are a predicted leader/signal sequence, with the predicted mature amino acid sequence beginning at amino acid 119. Due to the hydrophobic nature of the predicted leader/signal sequence, it is likely to act as a transmembrane domain should the predicted leader/signal sequence not be separated from the remainder of the ycl9_1 2 0 protein.
The EcoRI/NotI restriction fragment obtainable from the deposit containing clone ycl9_1 should be approximately 1400 bp.
The nucleotide sequence disclosed herein for ycl9_1 was searched against the GenBank and GeneSeq nucleotide sequence databases using BLASTN/BLASTX and 2 5 FASTA search protocols. ycl9_l demonstrated at least some similarity with sequences identified as AA126002 (z185a08.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 511382 3') and AA3070~ (EST177917 Colon carcinoma (HCC) cell line Homo Sapiens cDNA 5' end). The predicted amino acid sequence disclosed herein for ycl9_1 was searched against the GenPept and GeneSeq amino acid sequence databases using the 3 0 BLASTX search protocol. The predicted ycl9_1 protein demonstrated at least some similarity to sequences identified as X83742 (MAP kinase phosphotase [Xenopus laevis]), and to several tyrosine phosphatases from other species. Based upon sequence similarity, ycl9_1 proteins and each similar protein or peptide may share at least some activity. The TopPredII computer program predicts an additional potential transmembrane domain within the ycl9_1 protein sequence centered around amino acid 43 of SEQ ID
NO:10; this region (amino acids 30 to 42 of SEQ ID N0:10) may also be a leader/signal sequence, with the predicted mature amino acid sequence beginning at amino acid 43.
ycl9_i protein was expressed in a COS cell expression system, and an expressed protein band of approximately 23 kDa was detected in conditioned medium and membrane fractions using SDS polyacrylamide gel electrophoresis.
one "3rc20 1"
A polynucleotide of the present invention has been identified as clone "yc20_1".
yc20_1 was isolated from a human fetal kidney (293 cell line) cDNA library and was identified as encoding a secreted or transmembrane protein on the basis of computer analysis of the amino acid sequence of the encoded protein. yc20_1 is a full-length clone, including the entire coding sequence of a secreted protein (also referred to herein as "yc20_1 protein").
The nucleotide sequence of yc20_1 as presently determined is reported in SEQ
ID
NO:11, and includes a poly(A) tail. What applicants presently believe to be the proper reading frame and the predicted amino acid sequence of the yc20_1 protein corresponding to the foregoing nucleotide sequence is reported in SEQ ID N0:12.
The EcoRI/NotI restriction fragment obtainable from the deposit containing clone 2 0 yc20_1 should be approximately 1450 bp.
The nucleotide sequence disclosed herein for yc20_1 was searched against the GenBank and GeneSeq nucleotide sequence databases using BIrASTN/BLASTX and FASTA search protocols. yc20_1 demonstrated at least some similarity with sequences identified as AA447839 (aa18c12.r1 Soares NhHM1'u Sl Homo Sapiens cDNA clone 2 5 813622 5'), N33405 (yy41e10.s1 Homo Sapiens cDNA clone 273834 3'), and T19519 (Human gene signature HLTMGS00580). Based upon sequence similarity, yc20_1 proteins and each similar protein or peptide may share at least some activity.
3 0 Clones yal5_l, ya24_l, yb42_l, y~ 1, ycl9_l, and yc20_1 were deposited on February 11, 1998 with the American Type Culture Collection (10801 University Boulevard, Mantissas, Virginia 20110-2209 U.S.A.) as an original deposit under the Budapest Treaty and were given the accession number ATCC 98650, from which each clone comprising a particular polynucleotide is obtainable. All restrictions on the availability to the public of the deposited material will be irrevocably removed upon the granting of the patent, except for the requirements specified in 37 C.F.R. ~
1.$OS(b), and the term of the deposit will complywith 37 C.F.R. ~ 1.806.
Each clone has been transfected into separate bacterial cells (E. co&~ in this composite deposit. Each clone can be removed kom the vector in which it was deposited bY Pe~o~g an EcoRI/NotI digestion (5' site, EcoRI; 3' site, NotI) to produce the appropriate fragment for such clone. Each clone was deposited in either the pED6 or pNOTs vector depicted in Figures lA and 1B, respectively. The pED6dpc2 vector ("pED6") was derived kom pED6dpc1 by insertion of a new polylinker to facilitate cDNA cloning (Kaufman et al.,1991, Nucleic Acids Res.19: 44g5-4490); the pNOTs vector was derived from pMT2 (Kaufman et al.,1989, Mol. Cell. Biol. 9: 946-958) by deletion of the DHFR sequences, insertion of a new polylinker, and i~mon of the M13 origin of replication in the CIaI site. In some instances, the deposited clone can become "flipped"
(i.e., in the reverse orientation) in the deposited isolate. In such instances, the cDNA insert can still be isolated by digestion with EcoRI and NotI. However, NotI will then produce the 5' site and EcoRI will produce the 3' site for placement of the cDNA in proper orientation for expression in a suitable vector. The cDNA may also be expressed kom the vectors in which they were deposited.
Ba~~ re~ c°ng a P~~ clone can be obtained from the composite 2 0 deposit as follows:
An oligonucleotide probe or probes should be designed to the sequence that is known for that particular clone, This sequence can be derived kom the sequences provided herein, or kom a combination of those sequences. The sequence of an oligonudeotide probe that was used to isolate or to sequence each full-length clone is 2 5 identified below, and should be most reliable in isolating the clone of interest.
Probe SeauencP
yal5_1 _ SEQ ID N0:13 ya24_1 SEQ ID N0:14 3 0 yb42_1 SEQ ID N0:15 Y~'1 SEQ ID N0:16 ycl9_1 SEQ ID N0:17 yc20_1 SEQ ID N0:18 In the sequences listed above which include an N at position 2, that position is occupied in preferred probes/primers by a biotinylated phosphoaramidite residue rather than a nucleotide (such as, for example, that produced by use of biotin phosphoramidite (1-dimethoxytrityloxy-2-(N-biotinyl-4-aminobutyl)-propyl-3-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramadite) (Glen Research, cat. no.10-1953)).
The design of the oligonucleotide probe should preferably follow these parameters:
(a) It should be designed to an area of the sequence which has the fewest ambiguous bases ("N's"), if any;
(b) It should be designed to have a T°, of approx. 80 ° C
(assuming 2° for each A or T and 4 degrees for each G or C).
The oligonucleotide should preferably be labeled with y ~P ATP (specific activity 6000 Ci/mmole) and T4 polynucleotide kinase using commonly employed techniques for labeling oligonudeotides. Other labeling techniques can also be used.
Unincorporated label should preferably be removed by gel filtration duomatography or other established methods. The amount of radioactivity incorporated into the probe should be quantitated by measurement in a scintillation counter.. Preferably, specific activity of the resulting probe should be approximately 4e+6 dpm/pmole.
The bacterial culture containing the pool of full length clones should preferably 2 0 be thawed and 100 Nl of the stock used to inoculate a sterile culture flask containing 25 ml of sterile L-broth containing ampicillin at 100 ug/ml. The culture should preferably be grown to saturation at 37°C, and the saturated culture should preferably be diluted in fresh L-broth. Aliquots of these dilutions should preferably be plated to determine the dilution and volume which will yield approximately 5000 distinct and well-separated 2 5 colonies on solid bacteriological media containing L-broth containing ampicillin at 100 pg/ml and agar at 1.5~° in a 150 mm petri dish when grown overnight at 37°C. Other known methods of obtaining distinct, well-separated colonies can also be employed.
Standard colony hybridization procedures should then be used to transfer the colonies to nitrocellulose filters and lyre, denature and bake them.
3 0 The filter is then preferably incubated at 65°C for 1 hour with gentle agitation in 6X SSC (20X stock is 175.3 g NaCI/liter, 88.2 g Na citrate/liter, adjusted to pH 7.0 with NaOH) containing 0.5% SDS,100 ug/ml of yeast RNA, and 10 mM 1,DTA
(approximately 10 mL per 150 mm filter). Preferably, the probe is then added to the hybridization mix at a concentration greater than or equal to le+6 dpm/mL. The filter is then preferably wo ~iaizsa rrrivs~roz898 incubated at 65°C with gentle agitation overnight. The filter is then preferably washed in 500 mL of 2X SSC/0.5% SDS at room temperature without agitation, preferably followed by 500 mL of 2X SSC/0.1% SDS at room temperature with gentle shaking for 15 minutes.
A third wash with O.1X SSC/0.5% SDS at 65°C for 30 minutes to 1 hour is optional. The filter is then preferably dried and subjected to autoradiography for sufficient time to visualize the positives on the X-ray film. Other known hybridization methods can also be employed.
The positive colonies are picked, grown in culture, and plasmid DNA isolated using standard procedures. The clones can then be verified by restriction analysis, hybridization analysis, or DNA sequencing.
Fragments of the proteins of the present invention which are capable of exhibiting biological activity are also encompassed by the present invention. Fragments of the protein may be in linear form or they may be cyclized using known methods, for example, as described in H.U. Saragovi, et al., Bio/Terhnology ~Q, 773-778 (1992) and in R.S.
McDowell, et al., J. Amer. Chem. Soc. ~, 9245-9253 (1992), both of which are incorporated herein by reference. Such fragments may be fused to carrier molecules such as immunoglobulins for many purposes, including increasing the valency of protein binding sites. For example, fragments of the protein may be fused through "linker"
sequences to the Fc portion of an immunoglobulin. Far a bivalent form of the protein, such a fusion 2 0 could be to the Fc portion of an IgG molecule. Other immunoglobulin isotypes may also be used to generate such fusions. For example, a protein - IgM fusion would generate a decavalent form of the protein of the invention.
The present invention also provides both full-length and mature forms of the disclosed proteins. The full-length form of the such proteins is identified in the sequence 2 5 listing by translation of the nucleotide sequence of each disclosed clone.
The mature forms) of such protein may be obtained by expression of the disclosed full-length polynucleotide (preferably those deposited with ATCC) in a suitable mammalian cell or other host cell. The sequences) of the mature forms) of the protein may also be determinable from the amino acid sequence of the full-length form.
3 0 The present invention also provides genes corresponding to the polynucleotide sequences disclosed herein. "Corresponding genes" are the regions of the genome that are transcribed to produce the mRNAs from which cDNA polynucleotide sequences are derived and may include contiguous regions of the genome necessary for the regulated expression of such genes. Corresponding genes may therefore include but are not limited to coding sequences, 5' and 3' untranslated regions, alternatively spliced exons, introns, promoters, enhancers, and silencer or suppressor elements. The corresponding genes can be isolated in accordance with known methods using the sequence information disclosed herein. Such methods include the preparation of probes or primers from the disclosed sequence information for identification and/or amplification of genes in appropriate genomic libraries or other sources of genomic materials. An "isolated gene" is a gene that has been separated from the adjacent coding sequences, if any, present in the genome of the organism from which the gene was isolated.
The chromosomal location corresponding to the polynucleotide sequences disclosed herein may also be determined, for example by hybridizing appropriately labeled polynucleotides of the present invention to chromosomes in situ. It may also be possible to determine the corresponding chromosomal location for a disclosed polynucleotide by identifying significantly similar nucleotide sequences in public databases, such as expressed sequence tags (ESTs), that have already been mapped to particular chromosomal locations. For at least some of the polynucleotide sequences disclosed herein, public database sequences having at least some similarity to the polynudeotide of the present invention have been listed by database accession number.
Searches using the GenBank accession numbers of these public database sequences can then be performed at an Internet site provided by the National Center for Biotechnology Information having the address http://www.ncbi.nlm.nih.gov/UniGene/, in order to identify "UruGene clusters" of overlapping sequences. Many of the "UruGene clusters"
so identified will already have been mapped to particular chromosomal sites.
Organisms that have enhanced, reduced, or modified expression of the genes) corresponding to the polynucleotide. sequences disclosed herein are provided.
The 2 5 desired change in gene expression can be achieved through the use of antisense polynucleotides or ribozymes that bind and/or cleave the mRNA transcribed from the gee (Albert and Morris,1994, Trends Pharmacol. Sci.15(7): 250-254; Lavar~ky et al.,1997, Biockem. Mol. Med. 62(1):11-22; and Hampel,1998, Prog. Nucleic Acid Res. Mol.
Biol. 58:1-39; all of which are incorporated by reference herein). Transgenic animals that have 3 0 multiple copies of the genes) corresponding to the polynucleotide sequences disclosed herein, preferably produced by transformation of cells with genetic constructs that are stably maintained within the transformed cells and their progeny, are provided.
Transgenic animals that have modified genetic control regions that increase or reduce gene expression levels, or that change temporal or spatial patterns of gene expression, are also provided (see European Patent No. 0 649 464 Bl, incorporated by reference herein).
In addition, organisms are provided in which the genes) corresponding to the polynucleotide sequences disclosed herein have been partially or completely inactivated, through insertion of extraneous sequences into the corresponding genes) or through deletion of all or part of the corresponding gene(s). Partial or complete gene inactivation can be accomplished through insertion, preferably followed by imprecise excision, of transposable elements (Plasterk,1992, Bioassays 14(9): 629-633; Zwaal et nl.,1993, Proc. Natl.
Acad. Sci. LISA 90(16): 7431-7435; Dark et al.,1994, Proc. Natl. Acad. Sci.
LISA 91(2): 719-722;
all of which are incorporated by reference herein), or through homologous recombination, preferably detected by positive/negative genetic selection strategies (Mansour et al.,1988, Natscre 336: 348-352; U.S. Patent Nos. 5,464,764; 5,487,992; 5,627,059;
5,631,153; 5,614, 396;
5,616,491; and 5,679,523; all of which are incorporated by reference herein).
These organisms with altered gene expression are preferably eukaryotes and more preferably are mammals. Such organisms are useful for the development of non-human models for the study of disorders involving the corresponding gene(s), and for the development of assay systems for the identification of molecules that interact with the protein products) of the corresponding gene(s).
Where the profiein of the present invention is membrane-bound (e.g., is a receptor), the present invention also provides for soluble forms of such protein. In such forms, part 2 0 or all of the intracellular and transrnembrane domains of the protein are deleted such that the protein is fully secreted from the cell in which it is expressed. The intracellular and transmembrane domains of proteins of the invention can be identified in aa~ordance with known techniques for determination of such domains from sequence information.
For example, the TopPredII computer program can be used to predict the location of 2 5 transnnembrane domains in an amino acid sequence, domains which are described by the location of the center of the transmsmbrane domain, with at least ten transmembrane amino acids on each side of the reported central residue(s).
Proteins and protein fragments of the present invention include proteins with amino acid sequence lengths that are at least 25%{more preferably at least 50%, and most 3 0 preferably at least 75%) of the length of a disclosed profiein and have at least 609'° sequence identity (more preferably, at least 75% identity; most preferably at least 90%
or 95%
identity) with that disclosed protein, where sequence identity is determined by rnmparing the amino acid sequences of the proteins when aligned so as to maximize overlap and identity while minimizing sequence gaps. Also included in the present invention are proteins and protein fragments that contain a segment preferably comprising 8 or more (more preferably 20 or more, most preferably 30 or more) contiguous amino acids that shares at least 75% sequence identity (more preferably, at least 85% identity;
most preferably at least 95% identity) with any such segment of any of the disclosed proteins.
In particular, sequence identity may be determined using WLT-BLAST
(Washington University BLAST) version 2.0 software, which builds upon WU-BLAST
version 1.4, which in turn is based on the public domain NCBI-BLAST version 1.4 (Altschul and Gish,1996, Local alignment statistics, Doolittle ed., Methods in Enzynology 266: 460-480; Altschul et al., 1990, Basic local alignment search tool, Journal of Molecular Biology 215: 403-410; Gish and States, 1993, Identification of protein coding regions by database similarity search, Nature Genetics 3: 266-272; Karlin and Altschul, 1993, Applications and statistics for multiple high-scoring segments in molecular sequences, Proc. Natl. Acad Sci. USA 90: 5873-5877; all of which are incorporated by reference herein). WU-BLAST version 2.0 executable programs for several UNIX
platforms can be downloaded from ftp://blast.wustl.edu/blast/executables. The complete suite of search programs (BLASTP, BLASTN, BLASTX, TBLASTN, and TBLASTX) is provided at that site, in addition to several support programs. WU-BLAST 2.0 is copyrighted and may not be sold or redistributed in any form or manner without the express written consent of the author; but the posted executables may otherwise be freely 2 0 used for commercial, nonprofit, or academic purposes. In all search programs in the suite -- BLASTP, BLASTN, BLASTX, TBLASTN and TBLASTX -- the gapped alignment routines are integral to the database search itself, and thus yield much better sensitivity and selectivity while producing the more easily interpreted output. Gapping can optionally be turned off in all of these programs, if desired. The default penalty (Q) for a gap of length 2 5 one is Q~ for proteins and BLASTP, and X10 for BLASTN, but may be changed to any integer value including zero, one through eight, nine, ten, eleven, twelve through twenty, twenty-one through fifty, fifty-one through one hundred, etc. The default per-residue penalty for extending a gap (R) is R=2 for proteins and BLASTP, and R=10 for BLASTN, but may be changed to any integer value including zero, one, two, three, four, five, six, 3 0 seven, eight, nine, ten, eleven, twelve through twenty, twenty-one through fifty, fifty-one through one hundred, etc. Any combination of values for Q and R can be used in order to align sequences so as to maximize overlap and identity while minimizing sequence gaps.
The default amino acid comparison matrix is BLOSUM62, but other amino acid comparison matrices such as PAM can be utilized.
Species homologues of the disclosed polynucleotides and proteins are also provided by the present invention. As used herein, a "species homologue" is a protein or polynucleotide with a different species of origin from that of a given protein or polynucleotide, but with significant sequence similarity to the given protein or polynucleotide. Preferably, polynucleotide species homologues have at least 60% sequence identity (more preferably, at least 75% identity; most preferably at least 90%
identity) with the given polynucleotide, and protein species homologues have at least 30%
sequence identity (more preferably, at least 45% identity; most preferably at least 60%
identity) with the given protein, where sequence identity is determined by comparing the nucleotide sequences of the polynucleotides or the amino acid sequences of the proteins when aligned so as to maximize overlap and identity while minimizing sequence gaps.
Species homologues may be isolated and identified by making suitable probes or primers from the sequences provided herein and screening a suitable nucleic acid source from the desired species. Preferably, species homologues are those isolated from mammalian species. Most preferably, species homologues are those isolated from certain mammalian species such as, for example, Pan troglodytes, Gorilla gorilla, Pongo pygmaeus, Hylobates concolor, Macaca mulatto, Papio papio, Papio hamadryas, Cercopithecus aethurps, Cebus capucinus, 2 0 Aotus trivirgatus, Sanguinus Oedipus, Microcehus murinus, Mus musculus, Rattus norvegicus, Cricetulus griseus, Fells catus, Mustela visor, Cams familiaris, Oryctolagus cuniculus, Bos taurus, Ovis aries, Sus scrofa, and Equus cabalIus, for which genetic maps have been created allowing the identification of syntenic relationships between the genomic organization of genes in one species and the genomic organization of the related genes in another species 2 5 (O'Brien and Seu~nez, 1988, Ann. Rev. Genet. 22: 323-351; OBrien et al., 1993, Nature Genetics 3:103-112; Johansson et al.,1995, Genomics 25: 682-690; Lyons et al.,1997, Nature Genetics 15 ;47 56; OBrien et al.,1997, Trends in Genetics 13(10): 393-399;
Carver and Stubbs, 1997, Genome Research 7:1123-1137; all of which are incorporated by reference herein).
The invention also encompasses allelic variants of the disclosed polynucleotides 3 0 or proteins; that is, naturally-occurring alternative forms of the isolated polynucleotides which also encode proteins which are identical or have significantly similar sequences to those encoded by the disclosed polynucleotides. Preferably, allelic variants have at least 60% sequence identity (more preferably, at least 75% identity; most preferably at least 90%
identity) with the given polynucleotide, where sequence identity is determined by comparing the nucleotide sequences of the polynucleotides when aligned so as to maximize overlap and identity while minimizing sequence gaps. Allelic variants may be isolated and identified by making suitable probes or primers from the sequences provided herein and screening a suitable nucleic acid source from individuals of the appropriate species.
The invention also includes polynucleotides with sequences complementary to those of the polynucleotides disclosed herein.
The present invention also includes polynucleotides that hybridize under reduced stringency conditions, more preferably stringent conditions, and most preferably highly stringent conditions, to polynucleotides described herein. Examples of stringency conditions are shown in the table below: highly stringent conditions are those that are at least as stringent as, for example, conditions A-F; stringent conditions are at least as stringent as, for example, conditions G-L; and reduced stringency conditions are at least as stringent as, for example, conditions M-R.
StringencyPolynucleotideHybridHybridization TemperatureWash ConditionHybrid Lengthand Temperature ~P)= Buffer' and Buffer' A DNA:DNA x 50 65C; lxSSC -or- b5C; 0.3xSSC
42C; lxSSC, SO~o formamide B DNA:DNA <50 TB*; lxSSC Ts*; lxSSC
C DNA:RNA x 50 67C; ixSSC -or- 67C; 0.3xSSC
45C; lxSSC, 50% formamide D DNA:RNA t50 Tp*; lxSSC Tp*; lxSSC
E RNA:RNA x 50 70C; lxSSC -or- 70C; 03xSSC
50C; lxSSC, 50% formamide F RNA:RNA <50 TF*; ixSSC TF*; lxSSC
G DNA:DNA x 50 65C; 4xSSC -or- 65C; lxSSC
42C; 4xSSC, 509'o formamide H DNA:DNA <50 TH*; 4xSSC TH*;
I DNA:RNA x 50 67C; 4xSSC -or- 67C; lxSSC
45C; 4xSSC, 50~o formamide J DNA:RNA <50 T~*; 4xSSC T~*; ~
K RNA:RNA x 50 70C; 4xSSC -or- 67C; ixSSC
50C; 4xSSC, 50% formamide L RNA:RNA <50 T~*; 2xSSC T~*; 2~
M DNA:DNA x 50 50C; 4xSSC -or- 50C; 2xSSC
40C; 6xSSC, 50% formamide N DNA:DNA <50 TN*; 6xSSC TN*; 6xSSC
O DNA:RNA x 50 55C; 4xSSC -or- 55C; 2xSSC
42C; 6xSSC, 50% formamide P DNA:RNA <50 TP*; 6xSSC Tp*; 6xSSC
Q RNA:RNA x 50 60C; 4xSSC -or- 60C; 2xSSC
45C; 6xSSC, 50% formamide 2 R RNA:RNA <50 TR*; 4xSSC TR*; 4~
O
1: The hybrid length is that anticipated for the hybridized regions) of the hybridizing polynucleotides. When hybridizing a polynucleotide to a target polynucleotide of unknown sequence, the hybrid length is assumed to be that of the hybridizing polynucleotide. When polynucleotides of known sequence are hybridized, the 2 5 hybrid length can be determined by aligning the sequences of the polynucleotides and identifying the region or regions of optimal sequence rnmplementarity.
t: SSPE (ixSSPE is 0.15M NaCI, lOmM NaH2P0" and 1.25mM EDTA, pH 7.4) can be substituted for SSC
(lxSSC is 0.15M NaCI and l5mM sodium citrate) in the hybridization and wash buffers; washes are performed for 15 minutes after hybridization is complete.
3 0 "Ta - TR: The hybridization temperature for hybrids anticipated to be less than 50 base pairs in length should be 5-10°C less than the melting temperature (T~ of the hybrid, where Tm is determined aaording to the following equations. For hybrids less than 18 base pairs in length, Tm(°C) = 2(# of A + T bases) + 4(# of G +
C bases). For hybrids between 18 and 49 base pairs in length, Tm(°C) =
81.5 + 16.6(log,o[Na']) + 0.41(~oG+C) (600/N), where N is the number of bases in the hybrid, and [Na'] is the concentration of sodium ions in the 3 5 hybridization buffer ([Na'j for lxSSC = 0.165 M).
Additional examples of stringency conditions for polynucleotide hybridization are provided in Sambrook, J., E.F. Fritsch, and T. Maniatis, 1989, Molecular Cloning: A
Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, chapters 9 and 11, and Current Protocols in Molecular Biology,1995, F.M.
Ausubel et al., eds., John Wiley & Sons, lnc., sections 2.10 and 6.3-6.4, incorporated herein by reference.
Preferably, each such hybridizing polynucleotide has a length that is at least 25%(more preferably at least 50%, and most preferably at least 75%) of the length of the polynucleotide of the present invention to which it hybridizes, and has at least 60%
sequence identity (more preferably, at least 75% identity; most preferably at least 90% or 95% identity) with the polynucleotide of the present invention to which it hybridizes, where sequence identity is determined by comparing the sequences of the hybridizing polynucleotides when aligned so as to maximize overlap and identity while minimizing sequence gaps.
The isolated polynucleotide of the invention may be operably linked to an expression control sequence such as the pMT2 or pED expression vectors disclosed in ICaufman et al., Nucleic Acids Res. ~, 4485-4490 (1991), in order to produce the protein recombinantly. Many suitable expression control sequences are known in the art. General methods of expressing recombinant proteins are also known and are exemplified in R.
ICaufman, Methods in Enzymology ~, 537-566 (1990). As defined herein "operably 2 0 linked" means that the isolated polynucleotide of the invention and an expression control sequence are situated within a vector or cell in such a way that the protein is expressed by a host cell which has been transformed (transfected) with the ligated polynucleotide/expression control sequence.
A number of types of cells may act as suitable host cells for expression of the 2 5 profiein. Mammalian host cells include, for example, monkey COS cells, Chinese Hamster Ovary (CHO) cells, human kidney 293 cells, human epidermal A431 cells, human Co1o205 cells, 3T3 cells, CV-1 cells, other transformed primate cell lines, normal diploid cells, cell strains derived from j~ vitro culture of primary tissue, primary explants, HeLa cells, mouse L cells, BHK, HL-60, U937, HaK or Jurkat cells.
3 0. Alternatively, it may be possible to produce the protein in lower eukaryotes such as yeast or in prokaryotes such as bacteria. Potentially suitable yeast strains include Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces strains, Candida, or any yeast strain capable of expressing heberologous proteins. Potentially suitable bacterial strains include Escherichia coli, Bacillus subtilis, Salmonella typhimurium, or any bacterial strain capable of expressing heterologous proteins. If the protein is made in yeast or bacteria, it may be necessary to modify the protein produced therein, for example by phosphorylation or glycosylation of the appropriate sites, in order to obtain the functional protein. Such covalent attachments may be accomplished using known chemical or enzymatic methods.
The protein may also be produced by operably linking the isolated polynucleotide of the invention to suitable control sequences in one or more insect expression vectors, and employing an insect expression system. Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, e.g., Invitrogen, San Diego, California, U.S.A. (the MaxBac~ kit), and such methods are well known in the art, as described in Summers and Smith, '~~xas Agric~tural E
~~riment Station Bulletin No. 1555 f 19871. incorporated herein by reference. As used herein, an insect cell capable of expressing a polynucleotide of the present invention is "transformed."
The protein of the invention may be prepared by culturing transformed host cells under culture conditions suitable to express the recombinant protein. The resulting expressed protein may then be purified from such culture (i.e., from culture medium or cell extracts) using known purification processes, such as gel filtration and ion exchange chromatography. The purification of the protein may also include an affinity column 2 0 containing agents which will bind to the protein; one or more column steps over such affinity resins as concanavalin A-agarose, heparin-toyopearl~ or Cibacrom blue Sepharose~; one or more steps involving hydrophobic interaction chromatography using such resins as phenyl ether, butyl ether, or propyl ether; or immunoaffinity chromatography.
2 5 Alternatively, the protein of the invention may also be expressed in a form which will facilitate purification. For example, it may be expressed as a fusion protein, such as those of maltose binding protein (MBP), glutathione-S-transferase (GST) or thioredoxin (TRXJ. Kits for expression and purification of such fusion proteins are commercially available from New England BioLabs (Beverly, MA), Pharmacia (Piscataway, NJ) and 3 0 Invitrogen Corporation (Carlsbad, CA), respectively. The protein can also be tagged with an epitope and subsequently purified by using a specific antibody directed to such epitope. One such epitope ("Flag") is commercially available from the Eastman Kodak Company (New Haven, CT).
Finally, one or more reverse-phase high performance liquid chromatography (RP-HPLC) steps employing hydrophobic RP-HPLC media, e.g., silica gel having pendant methyl or other aliphatic groups, can be employed to further purify the protein. Some or all of the foregoing purification steps, in various combinations, can also be employed to provide a substantially homogeneous isolated recombinant protein. The protein thus purified is substantially free of other mammalian proteins and is defined in accordance with the present invention as an "isolated protein."
The protein of the invention may also be expressed as a product of transgenic animals, e.g., as a component of the mills of transgeruc cows, goats, pigs, or sheep which are characterized by somatic or germ cells containing a nucleotide sequence encoding the protein.
The protein may also be produced by known conventional chemical synthesis.
Methods for constructing the proteins of the present invention by synthetic means are known to those skilled in the art. The synthetically-constructed protein sequences, by virtue of sharing primary, secondary or tertiary structural and/or conformational characteristics with proteins may possess biological properties in common therewith, including protein activity. Thus, they may be employed as biologically active or immunological substitutes for natural, purified proteins in screening of therapeutic compounds and in immunological processes for the development of antibodies.
2 0 The proteins provided herein also include proteins characterized by amino acid sequences similar to those of purified proteins but into which modification are naturally provided or deliberately engineered. For example, modifications in the peptide or DNA
sequences can be made by those skilled in the art using known techniques.
Modifications of interest in the protein sequences may include the alteration, substitution, replacement, 2 5 insertion or deletion of a selected amino acid residue in the coding sequence. For example, one or more of the cysteine residues may be deleted or replaced with another amino acid to alter the conformation of the molecule. Techniques for such alteration, substitution, replacement, insertion or deletion are well known to those skilled in the art (see, e.g., U.S. Patent No. 4,518,584). Preferably, such alteration, substitution, replacement, 3 0 insertion or deletion retains the desired activity of the protein.
Other fragments and derivatives of the sequences of proteins which would be expected to retain protein activity in whole or in part and may thus be useful for screening or other immunological methodologies may also be easily made by those skilled in the art given the disclosures herein. Such modifications are believed to be encompassed by the present invention.
The polynucleotides and proteins of the present invention are expected to exhibit one or more of the uses or biological activities (including those associated with assays cited herein) identified below. Uses or activities described for proteins of the present invention may be provided by administration or use of such proteins or by administration or use of polynucleotides encoding such proteins (such as, for example, in gene therapies or vectors suitable for introduction of DNA).
The polynucleotides provided by the present invention can be used by the research community for various purposes. The polynucleotides can be used to express recombinant protein for analysis, characterization or therapeutic use; as markers for tissues in which the corresponding protein is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in disease states); as molecular weight markers on Southern gels; as chromosome markers or tags (when labeled) to identify cluomosomes or to map related gene positions; to compare 2 0 with endogenous DNA sequences in patients to identify potential genetic disorders; as probes to hybridize and thus discover novel, related DNA sequences; as a source of information to derive 1?CR primers for genetic fingerprinting; as a probe to "subtract-out"
known sequences in the process of discovering other novel polynucleotides; for selecting and making oligomers for attachment to a "gene chip" or other support, including for 2 5 examination of expression patterns; to raise anti-protein antibodies using DNA
immunization techniques; and as an antigen to raise anti-DNA antibodies or elicit another immune response. Where the polynucleotide encodes a protein which binds or pofientially binds to another protein (such as, for example, in a receptor-ligand interaction), the polynucleotide can also be used in interaction trap assays (such as, for example, those 3 0 described in Gyuris et al.,1993, Cell 75: 791-803 and in Rossi et al.,1997, Proc. Natl. Acad.
Sci. LISA 94: 8405-8410, all of which are incorporated by reference herein) to identify polynudeotides encoding the other protein with which binding occurs or to identify inhibitors of the binding interaction.
The proteins provided by the present invention can similarly be used in assay to determine biological activity, including in a panel of multiple proteins for high-throughput screening; to raise antibodies or to elicit another immune response; as a reagent (including the labeled reagent) in assays designed to quantitatively determine levels of the protein (or its receptor) in biological fluids; as markers for tissues in which the corresponding protein is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in a disease state); and, of course, to isolate correlative receptors or ligands. Where the protein binds or potentially binds to another protein (such as, for example, in a receptor-ligand interaction), the protein can be used to identify the other protein with which binding occurs or to identify inhibitors of the binding interaction. Proteins involved in these binding interactions can also be used to screen for peptide or small molecule inhibitors or agonists of the binding interaction.
Any or au of these research utilities are capable of being developed into reagent grade or kit format for commercialization as research products.
Methods for performing the uses listed above are well known to those skilled in the art. References disclosing such methods include without limitation "Molecular Cloning. A Laboratory Manual", 2d ed., Cold Spring Harbor Laboratory Press, Sambrook, j., E.F. Fritsch and T. Maniatis eds., 1989, and "Methods in Enzymology: Guide to 2 0 Molecular Cloning Techniques", Academic Press, Berger, S.L, and A.R.
ICimmel eds.,1987.
Polynucleotides and proteins of the present invention can also be used as nutritional sources or supplements. Such uses include without limitation use as a protein 2 5 or amino acid supplement, use as a carbon source, use as a nitrogen source and use as a sourre of carbohydrate. In such cases the protein or polynucleotide of the invention can be added to the feed of a particular organism or can be administered as a separate solid or liquid preparation, such as in the form of powder, pills, solutions, suspensions or capsules. In the case of microorganisms, the protein or polynucleotide of the invention 3 0 can be added to the medium in or on which the microorganism is cultured.
d A protein of the present invention may exhibit cytokine, cell proliferation (either inducing or inhibiting) or cell differentiation (either inducing or inhibiting) activity or may induce production of other cytokines in certain cell populations. Many protein factors discovered to date, including all known cytokines, have exhibited activity in one or more factor-dependent cell proliferation assays, and hence the assays serve as a convenient confirmation of cytokine activity. The activity of a protein of the present invention is evidenced by any one of a number of routine factor dependent cell proliferation assays for cell lines including, without limitation, 32D, DA2, DA1G, T10, B9, B9/11, BaF3, MC9/G, M+ (preB M+), 2E8, RBS, DA1,123, T1165, HT2, CTLL2, TF_l, Mo7e and CMK.
The activity of a protein of the invention may, among other means, be measured by the following methods:
Assays for T-cell or thymocyte proliferation include without limitation those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A.M.
Kruisbeek, D.H.
Margulies, E.M. Shevach, W Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7, Inununologic studies in Humans); Takai et al., J. Immunol. 137:3494-3500, 1986;
Bertagnolli et al., j. Immunol.145:1706-1712, 1990; Bertagnolli et al., Cellular Immunology 133:327-341,1991; Bertagnolli, et al., J. Immunol. 149:3778-3783,1992; Bowman et al., J.
Immunol.152: 1756-1761,1994.
Assays for cytokine production and/or proliferation of spleen cells, lymph node cells or thymocytes include, without limitation, those described in:
Polyclonal T cell 2 0 stimulation, Kruisbeek, A.M. and Shevach, E.M. In Current Protocols in Immunology. J.E.e.a.
Coligan eds. Vol 1 pp. 3.12.1-3.12.14, John Wiley and Sons, Toronto. 1994; and Measurement of mouse and human Interferon y, Schreiber, R.D. In Current Protocols in Immunology. j.E.e.a. Coligan eds. Vol 1 pp. 6.8.1-6.8.8, john Wiley and Sons, Toronto.1994.
Assays for proliferation and differentiation of hematopoietic and lymphopoietic 2 5 cells include, without limitation, those described in: Measurement of Human and Murine Interleukin 2 and Interleukin 4, Bottomly, K., Davis, L.S. and Lipsky, P.E. In Current Protocols in Immunology. j.E.e.a. Coligan eds. Vol 1 pp. 6.3.1-6.3.12, John Whey and Sons, Toronto. 1991; deVries et al., j. Exp. Med. 173:1205-1211, 1991; Moreau et al., Nature 336:690-692, 1988; Greenberger et al., Proc. Natl. Acad. Sci. U.S.A. 80:2931-2938, 1983;
3 0 Measurement of mouse and human interleukin 6 - Nordan, R. In Current Protocols in Immunology. J.E.e.a. Coligan eds. Vol 1 pp. 6.6.i-6.6.5, John Wiley and Sons, Toronto.1991;
Smith et al., Proc. Natl. Acad. Sci. U.S.A. 83:18571861, 1986; Measurement of human Interleuldn 11- Bennett, F., Giannotti, J., Clark, S.C. and Turner, K. J. In Current Protocols in Immunology. J.E.e.a. Coligan eds. Vol 1 pp. 6.15.1 John Wiley and Sons, Toronto.1991;
Measurement of mouse and human Interleukin 9 - Ciarletta, A., Giannotti, J., Clark, S.C.
and Turner, IGJ. In Current Protocols in Immunology. J.E.e.a. Coligan eds. Vol 1 pp. 6.13.1, John Wiley and Sons, Toronto.1991.
Assays for T-cell clone responses to antigens (which will identify, among others, proteins that affect APC-T cell interactions as well as direct T-cell effects by measuring proliferation and cytokine production) include, without limitation, those described in:
Current Protocols in Immunology, Ed by j. E. Coligan, A.M. ICruisbeek, D.H.
Margulies, E.M. Shevach, W Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function; Chapter 6, Cytokines and their cellular receptors; Chapter 7, Immunologic studies in Humans);
Weinberger et al., Proc. Natl. Acad. Sci. USA 77:6091-6095, 1980; Weinberger et al., Eur. J.
Immun.
Preferably, such polynucleotide comprises the nucleotide sequence of SEQ ID
N0:5 from nucleotide 615 to nucleotide 908; the nucleotide sequence of SEQ ID
N0:5 from nucleotide 774 to nucleotide 908; the nucleotide sequence of the full-length protein coding sequence of clone yb42_1 deposited under accession number ATCC 98650; or the nucleotide sequence of a mature protein coding sequence of clone yb42_1 deposited under accession number ATCC 98650. In other preferred embodiments, the polynucleotide encodes the full-length or a mature protein encoded by the cDNA insert of clone yb42_1 deposited under accession number ATCC 9$650. In further preferred embodiments, the present invention provides a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:6 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:6, or a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:6 having biological activity, the fragment comprising the amino acid sequence from amino acid 44 to amino acid 53 of SEQ
2 0 ID N0:6.
Other embodiments provide the gene corresponding to the cDNA sequence of SEQ
ID N0:5.
Further embodiments of the invention provide isolated polynucleotides produced according to a process selected from the group consisting of:
2 5 (a) a process comprising the steps of:
(i) preparing one or more polynucleotide probes that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(aa) SEQ ID N0:5, but excluding the poly(A) tail at the 3 0 3' end of SEQ ID N0:5; and (ab) the nucleotide sequence of the cDNA insert of clone yb42_i deposited under accession number ATCC 98650;
(ii) hybridizing said probes) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C; and {iii) isolating the DNA polynucleotides detected with the probe(s);
and (b) a process comprising the steps of:
(i) preparing one or more polynucleotide primers that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(ba) SEQ ID N0:5, but excluding the poly(A) tail at the 3' end of SEQ ID N0:5; and _ (bb) the nucleotide sequence of the cDNA insert of clone yb42_1 deposited under accession number ATCC 98650;
(ii) hybridizing said primers) to human genomic DNA in conditions at least as stringent as 4X S5C at 50 degrees C;
(iii) amplifying human DNA sequences; and 25 (iv) isolating the polynucleotide products of step {b)(iii).
Preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:5, and extending contiguously from a nucleotide sequence corresponding to the 5' end of SEQ ID
IV0:5 to a nucleotide sequence corresponding to the 3' end of SEQ ID N0:5 , but excluding the 2 0 poly(A) tail at the 3' end of SEQ ID N0:5. Also preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:5 from nucleotide 615 to nucleotide 908, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID N0:5 from nucleotide 615 to nucleotide 908, to a nucleotide sequence 2 5 corresponding to the 3' end of said sequence of SEQ ID N0:5 from nucleotide 615 to nucleotide 908. Also preferably the polynucleotide isolated according to the above process comprises a nucleotide sequenre corresponding to the cDNA sequence of SEQ ID
N0:5 from nucleotide 774 to nucleotide 908, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID
N0:5 from 3 0 nucleotide 774 to nucleotide 908, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID N0:5 from nucleotide 774 to nucleotide 908.
In other embodiments, the present invention provides a composition comprising a protein, whex~itt said protein comprises an amino acid sequence selected from the group consisting of:
WO 99/41284 PCT/US99l02898 (a) the amino acid sequence of SEQ ID N4:6;
(b) a fragment of the amino acid sequence of SEQ ID N0:6, the fragment comprising eight contiguous amino acids of SEQ ID N0:6; and (c) the amino acid sequence encoded by the cDNA insert of clone yb42_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins. Preferably such protein comprises the amino acid sequence of SEQ ID N0:6. In further preferred embodiments, the present invention provides a protein comprising a fragment of the amino acid sequence of SEQ ID N0:6 having biological activity, the fragment preferably comprising Wight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:6, or a protein comprising a fragment of the amino acid sequence of SEQ
ID N0:6 having biological activity, the fragment comprising the amino acid sequence from amino acid 44 to amino acid 53 of SEQ ID N0:6.
In one embodiment, the present invention provides a composition comprising an isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:7;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:7 from nucleotide 1203 to nucleotide 2327;
2 0 (c) a polynudeotide comprising the nucleotide sequence of the full-length protein coding sequence of clone yc9 1 deposited under accession number ATCC 98650;
(d) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone y~ 1 deposited under accession number ATCC 98650;
2 5 (e) a polynucleotide comprising the nucleotide sequence of a mature protein coding sequence of clone y~ 1 deposited under accession number ATCC
98650;
(f) a polynudeotide encoding a mature protein encoded by the cDNA
insert of clone y~ 1 deposited under accession number ATCC 98650;
3 0 (g) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:8;
(h) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:8 having biological activity, the fragment comprising eight contiguous amino acids of SEQ ID N0:8;
(i) a polynucleotide which is an allelic variant of a polynucleotide of {a)-(f) above;
(j) a polynudeotide which encodes a speaes homologue of the protein of (g) or (h) above ;
(k) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (ar(h); and {1) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (ar(h) and that has a length that is at least 25% of the length of SEQ ID N0:7.
Preferably, such polynucleotide comprises the nucleotide sequence of SEQ ID
N0:7 from nucleotide 1203 to nucleotide 2327; the nucleotide sequence of the full-length protein coding sequence of clone y~ 1 deposited under accession number ATCC
98650;
or the nucleotide sequence of a mature prntein coding sequence of clone y~ 1 deposited under accession number ATCC 98650. In other preferred embodiments, the polynucleotide encodes the full-length or a mature protein encoded by the cDNA
insert of clone y~ 1 deposited under accession number ATCC 98650. In further preferred embodiments, the present invention provides a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:8 having biological activity, the fragment preferably comprising eight (more preferably twenty, most 2 0 preferably thirty) contiguous amino ands of SEQ ID N0:8, or a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:8 having biological activity, the fragment rnmprising the amino acid sequence from amino acid 182 to amino acid 191 of SEQ ID N0:8.
Other embodiments provide the gene corresponding to the cDNA sequence of SEQ
2 5 ID N0:7.
Further embodiments of the invention provide isolated polynucleotides produced according to a process selected from the group consisting of:
(a) a process comprising the steps of:
(i) preparing one or more polynucleotide probes that hybridize 3 0 in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(aa) SEQ ID N0:7, but excluding the poly(A) tail at the 3' end of SEQ ID N0:7; and (ab) the nucleotide sequence of the cDNA insert of clone yc9_1 deposited under accession number ATCC 98650;
(ii) hybridizing said probes) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C; and (iii) isolating the DNA polynucleotides detected with the probe(s);
and (b) a process comprising the steps of:
(i) preparing one or more polynucleotide primers that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(ba) SEQ ID N0:7, but excluding the poly(A) tail at the 3' end of SEQ ID N0:7; and (bb) the nucleotide sequence of the cDNA insert of clone y~ 1 deposited under accession number ATCC 98650;
(ii) hybridizing said primers) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C;
(iii) amplifying human DNA sequences; and (iv) isolating the polynucleotide products of step (b)(iii).
2 0 Preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:7, and exfiending contiguously from a nucleotide sequence corresponding to the 5' end of SEQ ID
N0:7 to a nucleotide sequence corresponding to the 3' end of SEQ ID N0:7 , but excluding the poly(A) tail at the 3' end of SEQ ID N0:7. Also preferably the polynucleotide isolated 2 5 according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:7 from nucleotide 1203 to nucleotide 2327, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID N0:7 from nucleotide 1203 to nucleotide 2327, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID N0:7 from nucleotide 1203 to 3 0 nucleotide 2327.
In other embodiments, the present invention provides a composition comprising a protein, wherein said protein comprises an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID N0:8;
WO 99/41284 PCf/US99/OZ898 (b) a fragment of the amino acid sequence of SEQ ID N0:8, the fragment comprising eight contiguous amino acids of SEQ ID N0:8; and (c) the amino acid sequence encoded by the cDNA insert of clone y~ 1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins. Preferably such protein comprises the amino acid sequence of SEQ ID N0:8. In further preferred embodiments, the present invention provides a protein comprising a fragment of the amino acid sequence of SEQ ID N0:8 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:8, or a protein comprising a fragment of the amino acid sequence of SEQ
ID NO:B having biological activity, the fragment comprising the amino acid sequence from amino acid 182 to amino acid 191 of SEQ ID N0:8.
In one embodiment, the present invention provides a composition comprising an isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:9;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:9 from nucleotide 230 to nucleotide 823;
(c) a polynucleotide comprising the nucleotide sequence of SEQ ID
2 0 N0:9 from nucleotide 584 to nucleotide 823;
(d) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone ycl9_i deposited under accession number ATCC 98650;
(e) a polynucleotide encoding the full-length protein encoded by the 2 5 cDNA insert of clone ycl9_1 deposited under accession number ATCC 98650;
(f) a polynucleotide comprising the nucleotide sequence of a mature protein coding sequence of clone ycl9_1 deposited under accession number ATCC
98650;
(g) a polynucleotide encoding a mature protein encoded by the cDNA
3 0 insert of clone ycl9_1 deposited under accession number ATCC 98650;
(h) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:10;
(i) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:10 having biological activity, the fragment comprising eight contiguous amino acids of SEQ ID NO:10;
(j) a polynucleotide which is an allelic variant of a polynucleotide of (a)-(g) above;
(k) a polynucleotide which encodes a species homologue of the protein of (h) or (i) above ;
(1) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (a)-(i); and (m) a polynucleotide that hybridizes under stringent conditions to any one of the polynucleotides specified in (a~(i) and that has a length that is at least 25% of the length of SEQ ID N0:9.
Preferably, such polynucleotide comprises the nucleotide sequence of SEQ ID
N0:9 from nucleotide 230 to nucleotide 823; the nucleotide sequence of SEQ ID
N0:9 from nucleotide 584 to nucleotide 823; the nucleotide sequence of the full-length protein coding sequence of clone ycl9_1 deposited under accession number ATCC 98650; or the nucleotide sequence of a mature protein coding sequence of clone ycl9_1 deposited under accession number ATCC 98650. In other preferred embodiments, the polynucleotide encodes the full length or a mature protein encoded by the cDNA insert of clone ycl9_1 2 0 deposited under accession number ATCC 98650. In further preferred embodiments, the present invention provides a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:10 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids of SEQ ID N0:10, or a polynucleotide encoding a protein comprising a 2 5 fragment of the amino acid sequence of SEQ ID NO:10 having biological activity, the fragment comprising the amino acid sequence from amino acid 94 to amino acid 103 of SEQ ID NO:10.
Other embodiments provide the gene corresponding to the cDNA sequenre of SEQ
ID N0:9.
3 0 Further embodiments of the invention provide isolated polynucleotides produced according to a process selected from the group consisting of:
(a) a process comprising the steps of:
(i) preparing one or more polynucleotide probes that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(aa) SEQ ID N0:9, but excluding the poly(A) tail at the 3' end of SEQ ID N0:9; and (ab) the nucleotide sequence of the cDNA insert of clone ycl9_1 deposited under accession number ATCC 98650;
(ii) hybridizing said probes) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C; and (iii) isolating the DNA polynudeotides detected with the probe(s);
and (b) a process comprising the steps of:
(i) preparing one or more polynucleotide primers that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(ba) SEQ ID N0:9, but excluding the poly(A) tail at the 3' end of SEQ ID N0:9; and (bb) the nucleotide sequence of the cDNA insert of clone 2 0 ycl9_i deposited under accession number ATCC 98650;
(ii) hybridizing said primers) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C;
(iii) amplifying human DNA sequences; and (iv) isolating the polynudeotide products of step (b)(iii).
2 5 Preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence co~p~g to the cDNA sequence of SEQ ID N0:9, and extending contiguously from a nucleotide sequence corresponding to the 5' end of SEQ ID
N0:9 to a nucleotide sequence corresponding to the 3' end of SEQ ID N0:9 , but excluding the poly(A) tail at the 3' end of SEQ ID N0:9. Also preferably the polynucleotide isolated 3 0 according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:9 from nucleotide 230 to nucleotide 823, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID N0:9 from nucleotide 230 to nucleotide 823, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID N0:9 from nucleotide 230 to nucleotide 823. Also preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID
N0:9 from nucleotide 584 to nucleotide 823, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID
N0:9 from nucleotide 584 to nucleotide 823, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID N0:9 from nucleotide 584 to nucleotide 823.
In other embodiments, the present invention provides a composition comprising a protein, wherein said protein comprises an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID N0:10;
(b) a fragment of the amino acid sequence of SEQ ID NO:10, the fragment comprising eight contiguous amino acids of SEQ ID N0:10; and (c) the amino acid sequence encoded by the cDNA insert of clone ycl9_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins. Preferably such protein comprises the amino acid sequence of SEQ ID N0:10. In further preferred embodiments, the present invention provides a protein comprising a fragment of the amino acid sequence of SEQ ID N0:10 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids 2 0 of SEQ ID NO:10, or a protein comprising a fragment of the amino acid sequence of SEQ
ID N0:10 having biological activity, the fragment comprising the amino acid sequence from amino acid 94 to. amino acid 103 of SEQ ID NO:10.
In one embodiment, the present invention provides a composition comprising an isolated polynucleotide selected from the group consisting of:
2 5 (a) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:11;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
N0:11 from nucleotide 292 to nucleotide 534;
(c) a polynucleotide comprising the nucleotide sequence of the full-3 0 length protein coding sequence of clone yc20_1 deposited under accession number ATCC 98650;
(d) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone yc20_1 deposited under accession number ATCC 98650;
(e) a polynudeotide comprising the nucleotide sequence of a mature protein coding sequence of clone yc20_1 deposited under accession number ATCC
98650;
(f) a polynucleotide encoding a mature protein encoded by the cDNA
insert of clone yc20_1 deposited under accession number ATCC 98650;
(g) a polynudeotide encoding a protein comprising the amino acid sequence of SEQ ID N0:12;
(h) a polynudeotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:12 having biological activity, the fragment comprising eight contiguous amino acids of SEQ ID N0:12;
(i) a polynudeotide which is an allelic variant of a polynudeotide of (a)-(f) above;
(j) a polynudeotide which encodes a species homologue of the protein of (g) or (h) above ;
(k) a polynucleotide that hybridizes under stringent conditions to any one of the polynudeotides specified in (ar(h); and (I) a polynucleotide that hybridizes under stringent conditions to any one of the polynudeotides specified in (a~(h) and that has a length that is at least 25% of the length of SEQ ID N0:11.
2 0 Preferably, such polynudeotide comprises the nucleotide sequ~ce of SEQ ID
NO:11 from nucleotide 292 to nucleotide 534; the nucleotide sequence of the full-length protein coding sequence of clone yc20_1 deposited under accession number ATCC
98650;
or the nucleotide sequence of a mature protein coding sequence of clone yc20_1 deposited under accession number ATCC 98650. In other preferred embodiments, the 2 5 polynudeotide encodes the full-length or a mature protein encoded by the cDNA insert of done yc20_1 deposited under accession number ATCC 98650. In further preferred embodiments, the present invention provides a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:12 having biological activity, the fragment preferably comprising eight (more preferably twenty, most 3 0 preferably thirty) contiguous amino acids of SEQ ID N0:12, or a polynudeotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID N0:12 having biological activity, the fragment comprising the amino acid sequence from amino acid 35 to amino acid 44 of SEQ ID N0:12.
Other embodiments provide the gene corresponding to the cDNA sequeruce of SEQ
ID N0:11.
Further embodiments of the invention provide isolated polynucleotides produced according to a process selected from the group consisting of:
(a) a process comprising the steps of:
(i) preparing one or more polynucleotide probes that hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(aa) SEQ ID N0:11, but excluding the poly(A) tail at the 3' end of SEQ ID N0:11; and (ab) the nucleotide sequence of the cDNA insert of clone yc20_1 deposited under accession number-ATCC 98650;
(ii) hybridizing said probes) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C; and (iii) isolating the DNA polynucleotides detected with the probe(s);
and (b) a process comprising the steps of:
(i) preparing one or more polynucleotide primers that 2 0 hybridize in 6X SSC at 65 degrees C to a nucleotide sequence selected from the group consisting of:
(ba) SEQ ID N0:11, but excluding the poly(A) tail at the 3' end of SEQ ID NO:11; and (bb) the nucleotide sequence of the cDNA insert of clone 2 5 yc20_1 deposited under accession number ATCC 98650;
(ii) hybridizing said primers) to human genomic DNA in conditions at least as stringent as 4X SSC at 50 degrees C;
(iii) amplifying human DNA sequences; and (iv) isolating the polynucleotide products of step (b)(iii).
3 0 Fieferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:11, and extending contiguously from a nucleotide sequence corresponding to the 5' end of SEQ
ID N0:11 to a nucleotide sequence corresponding to the 3' end of SEQ ID NO:11 , but excluding the poly(A) tail at the 3' end of SEQ ID NO:11. Also preferably the polynucleotide isolated according to the above process comprises a nucleotide sequence corresponding to the cDNA sequence of SEQ ID N0:11 from nucleotide 292 to nucleotide 534, and extending contiguously from a nucleotide sequence corresponding to the 5' end of said sequence of SEQ ID N0:11 from nucleotide 292 to nucleotide 534, to a nucleotide sequence corresponding to the 3' end of said sequence of SEQ ID NO:11 from nucleotide 292 to nucleotide 534.
In other embodiments, the present invention provides a composition comprising a protein, wherein said protein comprises an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID N0:12;
(b) a fragment of the amino acid sequence of SEQ ID N0:12, the fragment comprising eight contiguous amino acids of SEQ ID N0:12; and (c) the amino acid sequence encoded by the cDNA insert of clone yc20_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins. Preferably such protein comprises the amino acid sequence of SEQ ID N0:12. In further preferred embodiments, the present invention provides a protein comprising a fragment of the amino acid sequence of SEQ ID N0:12 having biological activity, the fragment preferably comprising eight (more preferably twenty, most preferably thirty) contiguous amino acids 2 0 of SEQ ID N0:12, or a protein comprising a fragment of the amino acid sequence of SEQ
ID N0:12 having biological activity, the fragment comprising the amino acid sequence from amino acid 35 to amino acid 44 of SEQ ID N0:12.
In certain preferred embodiments, the polynucleotide is operably linked to an expression control sequence. The invention also provides a host cell, including bacterial, 2 5 yeast, insect and mannmalian cells, transformed with such polynucleotide compositions.
Also provided by the present invention are organisms that have enhanced, reduced, or modified expression of the genes) corresponding to the polynucleotide sequences disclosed herein.
Processes are also provided for producing a protein, which comprise:
3 0 (a) growing a culture of the host cell transformed with such polynucleotide compositions in a suitable culture medium; and (b) purifying the protein from the culture.
The protein produced according to such methods is also provided by the present invention.
Protein compositions of the present invention may further comprise a pharmaceutically acceptable carrier. Compositions comprising an antibody which specifically reacts with such protein are also provided by the present invention.
Methods are also provided for preventing, treating or ameliorating a medical condition which comprises administering to a mammalian subject a therapeutically effective amount of a composition comprising a protein of the present invention and a pharmaceutically acceptable carrier.
Figures 1A and 1B are schematic representations of the pED6 and pNOTs vectors, respectively, used for deposit of clones disclosed herein.
DETAILED g ~S('RTPTTC~Iu Nucleotide and amino acid sequences, as presently determined, are reported belqw for each clone and protein disclosed in the present application. The nucleotide sequence of each clone can readily be determined by sequencing of the deposited clone in accordance with known methods. The predicted amino acid sequence (both full length and mature forms) can then be determined from such nucleotide sequence. The amino 2 0 acid sequence of the protein encoded by a particular clone can also be determined by expression of the clone in a suitable host cell, collecting the protein and determining its sequence. For each disclosed protein applicants have identified what they have determined to be the reading frame best identifiable with sequence information available at the time of filing.
2 5 As used herein a "secreted" protein is one which, when expressed in a suitable host cell, is transported across or through a membrane, including transport as a result of signal sequences in its amino acid sequence. "Secreted" proteins include without limitation profieins secreted wholly (e.g., soluble profieins) or partially (e.g. , receptors) from the cell in which they are expressed. "Secreted" proteins also include without limitation proteins 3 0 which are transported across the membrane of the endoplasmic reticulum.
Clone ",L 1"
A polynucleotide of the preset invention has been identified as clone "yal5_1".
yal5_1 was isolated from a human adult testes cDNA library and was identified as encoding a seaeted or transmembrane protein on the basis of computer analysis of the amino acid sequence of the encoded protein. yal5_1 is a full-length clone, including the entire coding sequence of a secreted protein (also referred to herein as "yal5_1 protein").
The nucleotide sequence of yal5_1 as presently determined is reported in SEQ
ID
NO:1, and includes a poly(A) tail. What applicants presently believe to be the proper reading frame and the predicted amino acid sequence of the yal5_1 protein corresponding to the foregoing nucleotide sequence is reported in SEQ ID N0:2. Amino acids 8 to 20 of SEQ ID N0:2 are a possible leader/signal sequence, with the predicted mature amino acid sequence beginning at amino acid 21. Due to the hydrophobic nature of the predicted leader/signal sequence, it is likely to act as a transmembrane domain should the predicfied leader/signal sequence not be separated from the remainder of the yal5_1 protein.
The EcoRI/NotI restriction fragment obtainable from the deposit containing clone yal5_1 should be approximately 1100 bp.
The nucleotide sequence disclosed herein for yal5_1 was searched against the GenBank and GeneSeq nucleotide sequence databases using BLASTN/BLASTX and FASTA search protocols. yal5_1 demonstrated at least some sianilarity with sequences identified as 294056 (Human DNA sequence from PAC 436M11 on chromosome Xp22.11-22.2; contains a serine threonine protein phosphatase gene, ESTs and STSs).
Based upon sequence similarity, yal5_1 proteins and each similar protein or peptide may 2 0 share at least some activity. The TopPredII computer program predicts a potential transmembrane domain within the yal5_1 protein sequence centered around amino acid 40 of SEQ ID N0:2. The nucleotide sequence of yal5_1 indicates that it may contain an Alu repetitive element.
2 5 Clone "3ra24 1"
A polynucleotide of the present invention has been identified as clone "ya24_1 ".
ya24_i was isolated from a human adult testes cDNA library and was identified as encoding a secreted or transmembrane protein on the basis of rnmputer analysis of the amino acid sequence of the encoded protein. ya24_1 is a full-length clone, including the 3 0 entire coding sequence of a secreted protein (also referred to herein as "ya24_1 protein").
The nucleotide sequence of ya24_1 as presently determined is reported in SEQ
ID
N0:3, and includes a poly(A) tail. What applicants presently believe to be the proper reading frame and the predicted amino acid sequence of the ya24_1 protein corresponding to the foregoing nucleotide sequence is reported in SEQ ID N0:4. Amino acids 3 to 15 of SEQ ID N0:4 are a predicted leader/signal sequence, with the predicted mature amino aced sequence beginning at amino acid 16. Due to the hydrophobic nature of the predicted leader/signal sequence, it is likely to act as a transmembrane domain should the predicted leader/signal sequence not be separated from the remainder of the ya24_1 protein.
The EcoRI/NotI restriction fragment obtainable from the deposit containing clone ya24_1 should be approximately 750 bp.
The nucleotide sequence disclosed herein for ya24_1 was searched against the GenBank and GeneSeq nucleotide sequence databases using BLAST1V/BLAST?C and FASTA search protocols. ya24_1 demonstrated at least some similarity with sequences identified as AA537299 (vk46d03.r1 Soares mouse mammary gland NbMMG Mus musculus cDNA clone 949637 5'). Based upon sequence similarity, ya24_1 proteins and each similar protein or peptide may share at least some activity.
Clone "; 1"
A polynucleotide of the present invention has been identified as clone "yb42_1".
yb42_1 was isolated from a human fetal brain cDNA library and was identified as encoding a secreted or transmembrane protein on the basis of computer analysis of the amino acid sequence of the encoded protein. yb42_1 is a full-length clone, including the entire coding sequence of a secreted protein (also referred to herein as "yb42_1 protein").
2 0 The nucleotide sequence of yb42_1 as presently determined is reported in SEQ ID
N0:5, and includes a poly(A) tail. What applicants presently believe to be the proper reading frame and the predicted amino acid sequence of the yb42_1 protein corresponding to the foregoing nucleotide sequence is reported in SEQ ID N0:6.
Amino acids 41 to 53 of SEQ ID N0:6 are a predicted leader/signal sequence, with the predicted 2 5 mature amino acid sequence beginning at amino acid 54. Due to the hydrophobic nature of the predicted leader/signal sequence, it is likely to act as a transmembrane domain should the predicted leader/signal sequence not be separated from the remainder of the yb42_1 protein.
Another potential yb42_i reading frame and predicted amino acid sequence is 3 0 encoded by basepairs 1879 to 2220 of SEQ ID N0:5 and is reported in SEQ ID
N0:19;
amino acids 54 to 66 of SEQ ID N0:19 are a predicted leader/signal sequence, with the predicted mature amino acid sequence beginning at amino acid 67 of SEQ ID
N0:19. Due to the hydrophobic nature of this predicted leader/signal sequence, it is likely to act as a transmembrane domain should the predicted leader/signal sequence not be separated from the remainder of the protein of SEQ ID N0:19.
The EcoRI/NotI restriction fragment obtainable from the deposit containing clone yb42_1 should be approximately 3900 bp.
The nucleotide sequence disclosed herein for yb42_1 was searched against the GenBank and GeneSeq nucleotide sequence databases using BLASTN/BLASTX and FASTA search protocols. yb42_1 demonstrated at least some similarity with sequences identified as AA213992 (zn58d08.s1 Stratagene muscle 937209 Homo sapiens cDNA
clone 562383 3'). Based upon sequence similarity, yb42_1 proteins and each similar protein or peptide may share at least some activity. The nucleotide sequence of yb42_1 indicates that it may contain at least one MIR repeat sequence.
Clone ",yes 1"
A poiynucleotide of the present invention has been identified as clone "yes 1".
y~ 1 was isolated from a human fetal kidney (293 cell line) cDNA library and was identified as encoding a secreted or transmembrane protein on the basis of computer analysis of the amino acid sequence of the encoded protein. y~ 1 is a full-length clone, including the entire coding sequence of a secreted protein (also referred to herein as "yes 1 protein").
2 0 The nucleotide sequence of yc9_1 as presently defiermined is reported in SEQ ID
N0:7, and includes a poly(A) tail. What applicants presently believe to be the proper reading frame and the predicted amino acid sequence of the y~ 1 protein corresponding to the foregoing nucleotide sequence is reported in SEQ ID N0:8.
The EcoRI/NotI restriction fragment obtainable from the deposit rnntaining clone 2 5 yc9_1 should be approximately 3300 bp.
The nucleotide sequence disclosed herein for y~ 1 was searched against the GenBank and GeneSeq nucleotide sequence databases using BLASTN/BLASTX and FASTA search protocols. y~ 1 demonstrated at least some similarity with sequences identified as AA588539 (nm94a07.s1 NCI_CGAP_Co9 Homo sapiens cDNA clone 3 0 IMAGE:10~5860) and N47418 (yy88e12.r1 Homo Sapiens cDNA clone 280654 5').
The predicted amino acid sequence disclosed herein for yc9_1 was searched against the GenPept and GeneSeq amino acid sequence databases using the BLASTx search protocol.
The predicted y~ 1 protein demonstrated at least some similarity to sequences identified as X97196 (D. melanogaster X gene). Based upon sequence similarity, y~ 1 profieins and WO 99/d1284 PCT/US99102898 each similar protein or peptide may share at least some activity. The TopPredil rnmputer program predicts two potential transmembrane domains within the yc9_1 protein sequence, centered around amino acids 80 and 200 of SEQ ID N0:8, respectively.
Clone"ycl9 1"
A polynucleotide of the present invention has been identified as clone "ycl9_1".
ycl9_1 was isolated from a human fetal kidney (293 cell line) cDNA library and was identified as encoding a secreted or transmembrane protein on the basis of computer analysis of the amino acid sequence of the encoded protein. ycl9_1 is a full-length clone, including the entire coding sequence of a secreted protein (also referred to herein as "ycl9_1 protein").
The nucleotide sequence of ycl9_1 as presently determined is reported in SEQ
ID
N0:9, and includes a poly(A) tail. What applicants presently believe to be the proper reading frame and the predicted amino acid sequence of the ycl9_1 protein corresponding to the foregoing nucleotide sequence is reported in SEQ ID N0:10. Amino acids 106 to 118 of SEQ ID N0:10 are a predicted leader/signal sequence, with the predicted mature amino acid sequence beginning at amino acid 119. Due to the hydrophobic nature of the predicted leader/signal sequence, it is likely to act as a transmembrane domain should the predicted leader/signal sequence not be separated from the remainder of the ycl9_1 2 0 protein.
The EcoRI/NotI restriction fragment obtainable from the deposit containing clone ycl9_1 should be approximately 1400 bp.
The nucleotide sequence disclosed herein for ycl9_1 was searched against the GenBank and GeneSeq nucleotide sequence databases using BLASTN/BLASTX and 2 5 FASTA search protocols. ycl9_l demonstrated at least some similarity with sequences identified as AA126002 (z185a08.s1 Stratagene colon (#937204) Homo sapiens cDNA clone 511382 3') and AA3070~ (EST177917 Colon carcinoma (HCC) cell line Homo Sapiens cDNA 5' end). The predicted amino acid sequence disclosed herein for ycl9_1 was searched against the GenPept and GeneSeq amino acid sequence databases using the 3 0 BLASTX search protocol. The predicted ycl9_1 protein demonstrated at least some similarity to sequences identified as X83742 (MAP kinase phosphotase [Xenopus laevis]), and to several tyrosine phosphatases from other species. Based upon sequence similarity, ycl9_1 proteins and each similar protein or peptide may share at least some activity. The TopPredII computer program predicts an additional potential transmembrane domain within the ycl9_1 protein sequence centered around amino acid 43 of SEQ ID
NO:10; this region (amino acids 30 to 42 of SEQ ID N0:10) may also be a leader/signal sequence, with the predicted mature amino acid sequence beginning at amino acid 43.
ycl9_i protein was expressed in a COS cell expression system, and an expressed protein band of approximately 23 kDa was detected in conditioned medium and membrane fractions using SDS polyacrylamide gel electrophoresis.
one "3rc20 1"
A polynucleotide of the present invention has been identified as clone "yc20_1".
yc20_1 was isolated from a human fetal kidney (293 cell line) cDNA library and was identified as encoding a secreted or transmembrane protein on the basis of computer analysis of the amino acid sequence of the encoded protein. yc20_1 is a full-length clone, including the entire coding sequence of a secreted protein (also referred to herein as "yc20_1 protein").
The nucleotide sequence of yc20_1 as presently determined is reported in SEQ
ID
NO:11, and includes a poly(A) tail. What applicants presently believe to be the proper reading frame and the predicted amino acid sequence of the yc20_1 protein corresponding to the foregoing nucleotide sequence is reported in SEQ ID N0:12.
The EcoRI/NotI restriction fragment obtainable from the deposit containing clone 2 0 yc20_1 should be approximately 1450 bp.
The nucleotide sequence disclosed herein for yc20_1 was searched against the GenBank and GeneSeq nucleotide sequence databases using BIrASTN/BLASTX and FASTA search protocols. yc20_1 demonstrated at least some similarity with sequences identified as AA447839 (aa18c12.r1 Soares NhHM1'u Sl Homo Sapiens cDNA clone 2 5 813622 5'), N33405 (yy41e10.s1 Homo Sapiens cDNA clone 273834 3'), and T19519 (Human gene signature HLTMGS00580). Based upon sequence similarity, yc20_1 proteins and each similar protein or peptide may share at least some activity.
3 0 Clones yal5_l, ya24_l, yb42_l, y~ 1, ycl9_l, and yc20_1 were deposited on February 11, 1998 with the American Type Culture Collection (10801 University Boulevard, Mantissas, Virginia 20110-2209 U.S.A.) as an original deposit under the Budapest Treaty and were given the accession number ATCC 98650, from which each clone comprising a particular polynucleotide is obtainable. All restrictions on the availability to the public of the deposited material will be irrevocably removed upon the granting of the patent, except for the requirements specified in 37 C.F.R. ~
1.$OS(b), and the term of the deposit will complywith 37 C.F.R. ~ 1.806.
Each clone has been transfected into separate bacterial cells (E. co&~ in this composite deposit. Each clone can be removed kom the vector in which it was deposited bY Pe~o~g an EcoRI/NotI digestion (5' site, EcoRI; 3' site, NotI) to produce the appropriate fragment for such clone. Each clone was deposited in either the pED6 or pNOTs vector depicted in Figures lA and 1B, respectively. The pED6dpc2 vector ("pED6") was derived kom pED6dpc1 by insertion of a new polylinker to facilitate cDNA cloning (Kaufman et al.,1991, Nucleic Acids Res.19: 44g5-4490); the pNOTs vector was derived from pMT2 (Kaufman et al.,1989, Mol. Cell. Biol. 9: 946-958) by deletion of the DHFR sequences, insertion of a new polylinker, and i~mon of the M13 origin of replication in the CIaI site. In some instances, the deposited clone can become "flipped"
(i.e., in the reverse orientation) in the deposited isolate. In such instances, the cDNA insert can still be isolated by digestion with EcoRI and NotI. However, NotI will then produce the 5' site and EcoRI will produce the 3' site for placement of the cDNA in proper orientation for expression in a suitable vector. The cDNA may also be expressed kom the vectors in which they were deposited.
Ba~~ re~ c°ng a P~~ clone can be obtained from the composite 2 0 deposit as follows:
An oligonucleotide probe or probes should be designed to the sequence that is known for that particular clone, This sequence can be derived kom the sequences provided herein, or kom a combination of those sequences. The sequence of an oligonudeotide probe that was used to isolate or to sequence each full-length clone is 2 5 identified below, and should be most reliable in isolating the clone of interest.
Probe SeauencP
yal5_1 _ SEQ ID N0:13 ya24_1 SEQ ID N0:14 3 0 yb42_1 SEQ ID N0:15 Y~'1 SEQ ID N0:16 ycl9_1 SEQ ID N0:17 yc20_1 SEQ ID N0:18 In the sequences listed above which include an N at position 2, that position is occupied in preferred probes/primers by a biotinylated phosphoaramidite residue rather than a nucleotide (such as, for example, that produced by use of biotin phosphoramidite (1-dimethoxytrityloxy-2-(N-biotinyl-4-aminobutyl)-propyl-3-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramadite) (Glen Research, cat. no.10-1953)).
The design of the oligonucleotide probe should preferably follow these parameters:
(a) It should be designed to an area of the sequence which has the fewest ambiguous bases ("N's"), if any;
(b) It should be designed to have a T°, of approx. 80 ° C
(assuming 2° for each A or T and 4 degrees for each G or C).
The oligonucleotide should preferably be labeled with y ~P ATP (specific activity 6000 Ci/mmole) and T4 polynucleotide kinase using commonly employed techniques for labeling oligonudeotides. Other labeling techniques can also be used.
Unincorporated label should preferably be removed by gel filtration duomatography or other established methods. The amount of radioactivity incorporated into the probe should be quantitated by measurement in a scintillation counter.. Preferably, specific activity of the resulting probe should be approximately 4e+6 dpm/pmole.
The bacterial culture containing the pool of full length clones should preferably 2 0 be thawed and 100 Nl of the stock used to inoculate a sterile culture flask containing 25 ml of sterile L-broth containing ampicillin at 100 ug/ml. The culture should preferably be grown to saturation at 37°C, and the saturated culture should preferably be diluted in fresh L-broth. Aliquots of these dilutions should preferably be plated to determine the dilution and volume which will yield approximately 5000 distinct and well-separated 2 5 colonies on solid bacteriological media containing L-broth containing ampicillin at 100 pg/ml and agar at 1.5~° in a 150 mm petri dish when grown overnight at 37°C. Other known methods of obtaining distinct, well-separated colonies can also be employed.
Standard colony hybridization procedures should then be used to transfer the colonies to nitrocellulose filters and lyre, denature and bake them.
3 0 The filter is then preferably incubated at 65°C for 1 hour with gentle agitation in 6X SSC (20X stock is 175.3 g NaCI/liter, 88.2 g Na citrate/liter, adjusted to pH 7.0 with NaOH) containing 0.5% SDS,100 ug/ml of yeast RNA, and 10 mM 1,DTA
(approximately 10 mL per 150 mm filter). Preferably, the probe is then added to the hybridization mix at a concentration greater than or equal to le+6 dpm/mL. The filter is then preferably wo ~iaizsa rrrivs~roz898 incubated at 65°C with gentle agitation overnight. The filter is then preferably washed in 500 mL of 2X SSC/0.5% SDS at room temperature without agitation, preferably followed by 500 mL of 2X SSC/0.1% SDS at room temperature with gentle shaking for 15 minutes.
A third wash with O.1X SSC/0.5% SDS at 65°C for 30 minutes to 1 hour is optional. The filter is then preferably dried and subjected to autoradiography for sufficient time to visualize the positives on the X-ray film. Other known hybridization methods can also be employed.
The positive colonies are picked, grown in culture, and plasmid DNA isolated using standard procedures. The clones can then be verified by restriction analysis, hybridization analysis, or DNA sequencing.
Fragments of the proteins of the present invention which are capable of exhibiting biological activity are also encompassed by the present invention. Fragments of the protein may be in linear form or they may be cyclized using known methods, for example, as described in H.U. Saragovi, et al., Bio/Terhnology ~Q, 773-778 (1992) and in R.S.
McDowell, et al., J. Amer. Chem. Soc. ~, 9245-9253 (1992), both of which are incorporated herein by reference. Such fragments may be fused to carrier molecules such as immunoglobulins for many purposes, including increasing the valency of protein binding sites. For example, fragments of the protein may be fused through "linker"
sequences to the Fc portion of an immunoglobulin. Far a bivalent form of the protein, such a fusion 2 0 could be to the Fc portion of an IgG molecule. Other immunoglobulin isotypes may also be used to generate such fusions. For example, a protein - IgM fusion would generate a decavalent form of the protein of the invention.
The present invention also provides both full-length and mature forms of the disclosed proteins. The full-length form of the such proteins is identified in the sequence 2 5 listing by translation of the nucleotide sequence of each disclosed clone.
The mature forms) of such protein may be obtained by expression of the disclosed full-length polynucleotide (preferably those deposited with ATCC) in a suitable mammalian cell or other host cell. The sequences) of the mature forms) of the protein may also be determinable from the amino acid sequence of the full-length form.
3 0 The present invention also provides genes corresponding to the polynucleotide sequences disclosed herein. "Corresponding genes" are the regions of the genome that are transcribed to produce the mRNAs from which cDNA polynucleotide sequences are derived and may include contiguous regions of the genome necessary for the regulated expression of such genes. Corresponding genes may therefore include but are not limited to coding sequences, 5' and 3' untranslated regions, alternatively spliced exons, introns, promoters, enhancers, and silencer or suppressor elements. The corresponding genes can be isolated in accordance with known methods using the sequence information disclosed herein. Such methods include the preparation of probes or primers from the disclosed sequence information for identification and/or amplification of genes in appropriate genomic libraries or other sources of genomic materials. An "isolated gene" is a gene that has been separated from the adjacent coding sequences, if any, present in the genome of the organism from which the gene was isolated.
The chromosomal location corresponding to the polynucleotide sequences disclosed herein may also be determined, for example by hybridizing appropriately labeled polynucleotides of the present invention to chromosomes in situ. It may also be possible to determine the corresponding chromosomal location for a disclosed polynucleotide by identifying significantly similar nucleotide sequences in public databases, such as expressed sequence tags (ESTs), that have already been mapped to particular chromosomal locations. For at least some of the polynucleotide sequences disclosed herein, public database sequences having at least some similarity to the polynudeotide of the present invention have been listed by database accession number.
Searches using the GenBank accession numbers of these public database sequences can then be performed at an Internet site provided by the National Center for Biotechnology Information having the address http://www.ncbi.nlm.nih.gov/UniGene/, in order to identify "UruGene clusters" of overlapping sequences. Many of the "UruGene clusters"
so identified will already have been mapped to particular chromosomal sites.
Organisms that have enhanced, reduced, or modified expression of the genes) corresponding to the polynucleotide. sequences disclosed herein are provided.
The 2 5 desired change in gene expression can be achieved through the use of antisense polynucleotides or ribozymes that bind and/or cleave the mRNA transcribed from the gee (Albert and Morris,1994, Trends Pharmacol. Sci.15(7): 250-254; Lavar~ky et al.,1997, Biockem. Mol. Med. 62(1):11-22; and Hampel,1998, Prog. Nucleic Acid Res. Mol.
Biol. 58:1-39; all of which are incorporated by reference herein). Transgenic animals that have 3 0 multiple copies of the genes) corresponding to the polynucleotide sequences disclosed herein, preferably produced by transformation of cells with genetic constructs that are stably maintained within the transformed cells and their progeny, are provided.
Transgenic animals that have modified genetic control regions that increase or reduce gene expression levels, or that change temporal or spatial patterns of gene expression, are also provided (see European Patent No. 0 649 464 Bl, incorporated by reference herein).
In addition, organisms are provided in which the genes) corresponding to the polynucleotide sequences disclosed herein have been partially or completely inactivated, through insertion of extraneous sequences into the corresponding genes) or through deletion of all or part of the corresponding gene(s). Partial or complete gene inactivation can be accomplished through insertion, preferably followed by imprecise excision, of transposable elements (Plasterk,1992, Bioassays 14(9): 629-633; Zwaal et nl.,1993, Proc. Natl.
Acad. Sci. LISA 90(16): 7431-7435; Dark et al.,1994, Proc. Natl. Acad. Sci.
LISA 91(2): 719-722;
all of which are incorporated by reference herein), or through homologous recombination, preferably detected by positive/negative genetic selection strategies (Mansour et al.,1988, Natscre 336: 348-352; U.S. Patent Nos. 5,464,764; 5,487,992; 5,627,059;
5,631,153; 5,614, 396;
5,616,491; and 5,679,523; all of which are incorporated by reference herein).
These organisms with altered gene expression are preferably eukaryotes and more preferably are mammals. Such organisms are useful for the development of non-human models for the study of disorders involving the corresponding gene(s), and for the development of assay systems for the identification of molecules that interact with the protein products) of the corresponding gene(s).
Where the profiein of the present invention is membrane-bound (e.g., is a receptor), the present invention also provides for soluble forms of such protein. In such forms, part 2 0 or all of the intracellular and transrnembrane domains of the protein are deleted such that the protein is fully secreted from the cell in which it is expressed. The intracellular and transmembrane domains of proteins of the invention can be identified in aa~ordance with known techniques for determination of such domains from sequence information.
For example, the TopPredII computer program can be used to predict the location of 2 5 transnnembrane domains in an amino acid sequence, domains which are described by the location of the center of the transmsmbrane domain, with at least ten transmembrane amino acids on each side of the reported central residue(s).
Proteins and protein fragments of the present invention include proteins with amino acid sequence lengths that are at least 25%{more preferably at least 50%, and most 3 0 preferably at least 75%) of the length of a disclosed profiein and have at least 609'° sequence identity (more preferably, at least 75% identity; most preferably at least 90%
or 95%
identity) with that disclosed protein, where sequence identity is determined by rnmparing the amino acid sequences of the proteins when aligned so as to maximize overlap and identity while minimizing sequence gaps. Also included in the present invention are proteins and protein fragments that contain a segment preferably comprising 8 or more (more preferably 20 or more, most preferably 30 or more) contiguous amino acids that shares at least 75% sequence identity (more preferably, at least 85% identity;
most preferably at least 95% identity) with any such segment of any of the disclosed proteins.
In particular, sequence identity may be determined using WLT-BLAST
(Washington University BLAST) version 2.0 software, which builds upon WU-BLAST
version 1.4, which in turn is based on the public domain NCBI-BLAST version 1.4 (Altschul and Gish,1996, Local alignment statistics, Doolittle ed., Methods in Enzynology 266: 460-480; Altschul et al., 1990, Basic local alignment search tool, Journal of Molecular Biology 215: 403-410; Gish and States, 1993, Identification of protein coding regions by database similarity search, Nature Genetics 3: 266-272; Karlin and Altschul, 1993, Applications and statistics for multiple high-scoring segments in molecular sequences, Proc. Natl. Acad Sci. USA 90: 5873-5877; all of which are incorporated by reference herein). WU-BLAST version 2.0 executable programs for several UNIX
platforms can be downloaded from ftp://blast.wustl.edu/blast/executables. The complete suite of search programs (BLASTP, BLASTN, BLASTX, TBLASTN, and TBLASTX) is provided at that site, in addition to several support programs. WU-BLAST 2.0 is copyrighted and may not be sold or redistributed in any form or manner without the express written consent of the author; but the posted executables may otherwise be freely 2 0 used for commercial, nonprofit, or academic purposes. In all search programs in the suite -- BLASTP, BLASTN, BLASTX, TBLASTN and TBLASTX -- the gapped alignment routines are integral to the database search itself, and thus yield much better sensitivity and selectivity while producing the more easily interpreted output. Gapping can optionally be turned off in all of these programs, if desired. The default penalty (Q) for a gap of length 2 5 one is Q~ for proteins and BLASTP, and X10 for BLASTN, but may be changed to any integer value including zero, one through eight, nine, ten, eleven, twelve through twenty, twenty-one through fifty, fifty-one through one hundred, etc. The default per-residue penalty for extending a gap (R) is R=2 for proteins and BLASTP, and R=10 for BLASTN, but may be changed to any integer value including zero, one, two, three, four, five, six, 3 0 seven, eight, nine, ten, eleven, twelve through twenty, twenty-one through fifty, fifty-one through one hundred, etc. Any combination of values for Q and R can be used in order to align sequences so as to maximize overlap and identity while minimizing sequence gaps.
The default amino acid comparison matrix is BLOSUM62, but other amino acid comparison matrices such as PAM can be utilized.
Species homologues of the disclosed polynucleotides and proteins are also provided by the present invention. As used herein, a "species homologue" is a protein or polynucleotide with a different species of origin from that of a given protein or polynucleotide, but with significant sequence similarity to the given protein or polynucleotide. Preferably, polynucleotide species homologues have at least 60% sequence identity (more preferably, at least 75% identity; most preferably at least 90%
identity) with the given polynucleotide, and protein species homologues have at least 30%
sequence identity (more preferably, at least 45% identity; most preferably at least 60%
identity) with the given protein, where sequence identity is determined by comparing the nucleotide sequences of the polynucleotides or the amino acid sequences of the proteins when aligned so as to maximize overlap and identity while minimizing sequence gaps.
Species homologues may be isolated and identified by making suitable probes or primers from the sequences provided herein and screening a suitable nucleic acid source from the desired species. Preferably, species homologues are those isolated from mammalian species. Most preferably, species homologues are those isolated from certain mammalian species such as, for example, Pan troglodytes, Gorilla gorilla, Pongo pygmaeus, Hylobates concolor, Macaca mulatto, Papio papio, Papio hamadryas, Cercopithecus aethurps, Cebus capucinus, 2 0 Aotus trivirgatus, Sanguinus Oedipus, Microcehus murinus, Mus musculus, Rattus norvegicus, Cricetulus griseus, Fells catus, Mustela visor, Cams familiaris, Oryctolagus cuniculus, Bos taurus, Ovis aries, Sus scrofa, and Equus cabalIus, for which genetic maps have been created allowing the identification of syntenic relationships between the genomic organization of genes in one species and the genomic organization of the related genes in another species 2 5 (O'Brien and Seu~nez, 1988, Ann. Rev. Genet. 22: 323-351; OBrien et al., 1993, Nature Genetics 3:103-112; Johansson et al.,1995, Genomics 25: 682-690; Lyons et al.,1997, Nature Genetics 15 ;47 56; OBrien et al.,1997, Trends in Genetics 13(10): 393-399;
Carver and Stubbs, 1997, Genome Research 7:1123-1137; all of which are incorporated by reference herein).
The invention also encompasses allelic variants of the disclosed polynucleotides 3 0 or proteins; that is, naturally-occurring alternative forms of the isolated polynucleotides which also encode proteins which are identical or have significantly similar sequences to those encoded by the disclosed polynucleotides. Preferably, allelic variants have at least 60% sequence identity (more preferably, at least 75% identity; most preferably at least 90%
identity) with the given polynucleotide, where sequence identity is determined by comparing the nucleotide sequences of the polynucleotides when aligned so as to maximize overlap and identity while minimizing sequence gaps. Allelic variants may be isolated and identified by making suitable probes or primers from the sequences provided herein and screening a suitable nucleic acid source from individuals of the appropriate species.
The invention also includes polynucleotides with sequences complementary to those of the polynucleotides disclosed herein.
The present invention also includes polynucleotides that hybridize under reduced stringency conditions, more preferably stringent conditions, and most preferably highly stringent conditions, to polynucleotides described herein. Examples of stringency conditions are shown in the table below: highly stringent conditions are those that are at least as stringent as, for example, conditions A-F; stringent conditions are at least as stringent as, for example, conditions G-L; and reduced stringency conditions are at least as stringent as, for example, conditions M-R.
StringencyPolynucleotideHybridHybridization TemperatureWash ConditionHybrid Lengthand Temperature ~P)= Buffer' and Buffer' A DNA:DNA x 50 65C; lxSSC -or- b5C; 0.3xSSC
42C; lxSSC, SO~o formamide B DNA:DNA <50 TB*; lxSSC Ts*; lxSSC
C DNA:RNA x 50 67C; ixSSC -or- 67C; 0.3xSSC
45C; lxSSC, 50% formamide D DNA:RNA t50 Tp*; lxSSC Tp*; lxSSC
E RNA:RNA x 50 70C; lxSSC -or- 70C; 03xSSC
50C; lxSSC, 50% formamide F RNA:RNA <50 TF*; ixSSC TF*; lxSSC
G DNA:DNA x 50 65C; 4xSSC -or- 65C; lxSSC
42C; 4xSSC, 509'o formamide H DNA:DNA <50 TH*; 4xSSC TH*;
I DNA:RNA x 50 67C; 4xSSC -or- 67C; lxSSC
45C; 4xSSC, 50~o formamide J DNA:RNA <50 T~*; 4xSSC T~*; ~
K RNA:RNA x 50 70C; 4xSSC -or- 67C; ixSSC
50C; 4xSSC, 50% formamide L RNA:RNA <50 T~*; 2xSSC T~*; 2~
M DNA:DNA x 50 50C; 4xSSC -or- 50C; 2xSSC
40C; 6xSSC, 50% formamide N DNA:DNA <50 TN*; 6xSSC TN*; 6xSSC
O DNA:RNA x 50 55C; 4xSSC -or- 55C; 2xSSC
42C; 6xSSC, 50% formamide P DNA:RNA <50 TP*; 6xSSC Tp*; 6xSSC
Q RNA:RNA x 50 60C; 4xSSC -or- 60C; 2xSSC
45C; 6xSSC, 50% formamide 2 R RNA:RNA <50 TR*; 4xSSC TR*; 4~
O
1: The hybrid length is that anticipated for the hybridized regions) of the hybridizing polynucleotides. When hybridizing a polynucleotide to a target polynucleotide of unknown sequence, the hybrid length is assumed to be that of the hybridizing polynucleotide. When polynucleotides of known sequence are hybridized, the 2 5 hybrid length can be determined by aligning the sequences of the polynucleotides and identifying the region or regions of optimal sequence rnmplementarity.
t: SSPE (ixSSPE is 0.15M NaCI, lOmM NaH2P0" and 1.25mM EDTA, pH 7.4) can be substituted for SSC
(lxSSC is 0.15M NaCI and l5mM sodium citrate) in the hybridization and wash buffers; washes are performed for 15 minutes after hybridization is complete.
3 0 "Ta - TR: The hybridization temperature for hybrids anticipated to be less than 50 base pairs in length should be 5-10°C less than the melting temperature (T~ of the hybrid, where Tm is determined aaording to the following equations. For hybrids less than 18 base pairs in length, Tm(°C) = 2(# of A + T bases) + 4(# of G +
C bases). For hybrids between 18 and 49 base pairs in length, Tm(°C) =
81.5 + 16.6(log,o[Na']) + 0.41(~oG+C) (600/N), where N is the number of bases in the hybrid, and [Na'] is the concentration of sodium ions in the 3 5 hybridization buffer ([Na'j for lxSSC = 0.165 M).
Additional examples of stringency conditions for polynucleotide hybridization are provided in Sambrook, J., E.F. Fritsch, and T. Maniatis, 1989, Molecular Cloning: A
Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, chapters 9 and 11, and Current Protocols in Molecular Biology,1995, F.M.
Ausubel et al., eds., John Wiley & Sons, lnc., sections 2.10 and 6.3-6.4, incorporated herein by reference.
Preferably, each such hybridizing polynucleotide has a length that is at least 25%(more preferably at least 50%, and most preferably at least 75%) of the length of the polynucleotide of the present invention to which it hybridizes, and has at least 60%
sequence identity (more preferably, at least 75% identity; most preferably at least 90% or 95% identity) with the polynucleotide of the present invention to which it hybridizes, where sequence identity is determined by comparing the sequences of the hybridizing polynucleotides when aligned so as to maximize overlap and identity while minimizing sequence gaps.
The isolated polynucleotide of the invention may be operably linked to an expression control sequence such as the pMT2 or pED expression vectors disclosed in ICaufman et al., Nucleic Acids Res. ~, 4485-4490 (1991), in order to produce the protein recombinantly. Many suitable expression control sequences are known in the art. General methods of expressing recombinant proteins are also known and are exemplified in R.
ICaufman, Methods in Enzymology ~, 537-566 (1990). As defined herein "operably 2 0 linked" means that the isolated polynucleotide of the invention and an expression control sequence are situated within a vector or cell in such a way that the protein is expressed by a host cell which has been transformed (transfected) with the ligated polynucleotide/expression control sequence.
A number of types of cells may act as suitable host cells for expression of the 2 5 profiein. Mammalian host cells include, for example, monkey COS cells, Chinese Hamster Ovary (CHO) cells, human kidney 293 cells, human epidermal A431 cells, human Co1o205 cells, 3T3 cells, CV-1 cells, other transformed primate cell lines, normal diploid cells, cell strains derived from j~ vitro culture of primary tissue, primary explants, HeLa cells, mouse L cells, BHK, HL-60, U937, HaK or Jurkat cells.
3 0. Alternatively, it may be possible to produce the protein in lower eukaryotes such as yeast or in prokaryotes such as bacteria. Potentially suitable yeast strains include Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces strains, Candida, or any yeast strain capable of expressing heberologous proteins. Potentially suitable bacterial strains include Escherichia coli, Bacillus subtilis, Salmonella typhimurium, or any bacterial strain capable of expressing heterologous proteins. If the protein is made in yeast or bacteria, it may be necessary to modify the protein produced therein, for example by phosphorylation or glycosylation of the appropriate sites, in order to obtain the functional protein. Such covalent attachments may be accomplished using known chemical or enzymatic methods.
The protein may also be produced by operably linking the isolated polynucleotide of the invention to suitable control sequences in one or more insect expression vectors, and employing an insect expression system. Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, e.g., Invitrogen, San Diego, California, U.S.A. (the MaxBac~ kit), and such methods are well known in the art, as described in Summers and Smith, '~~xas Agric~tural E
~~riment Station Bulletin No. 1555 f 19871. incorporated herein by reference. As used herein, an insect cell capable of expressing a polynucleotide of the present invention is "transformed."
The protein of the invention may be prepared by culturing transformed host cells under culture conditions suitable to express the recombinant protein. The resulting expressed protein may then be purified from such culture (i.e., from culture medium or cell extracts) using known purification processes, such as gel filtration and ion exchange chromatography. The purification of the protein may also include an affinity column 2 0 containing agents which will bind to the protein; one or more column steps over such affinity resins as concanavalin A-agarose, heparin-toyopearl~ or Cibacrom blue Sepharose~; one or more steps involving hydrophobic interaction chromatography using such resins as phenyl ether, butyl ether, or propyl ether; or immunoaffinity chromatography.
2 5 Alternatively, the protein of the invention may also be expressed in a form which will facilitate purification. For example, it may be expressed as a fusion protein, such as those of maltose binding protein (MBP), glutathione-S-transferase (GST) or thioredoxin (TRXJ. Kits for expression and purification of such fusion proteins are commercially available from New England BioLabs (Beverly, MA), Pharmacia (Piscataway, NJ) and 3 0 Invitrogen Corporation (Carlsbad, CA), respectively. The protein can also be tagged with an epitope and subsequently purified by using a specific antibody directed to such epitope. One such epitope ("Flag") is commercially available from the Eastman Kodak Company (New Haven, CT).
Finally, one or more reverse-phase high performance liquid chromatography (RP-HPLC) steps employing hydrophobic RP-HPLC media, e.g., silica gel having pendant methyl or other aliphatic groups, can be employed to further purify the protein. Some or all of the foregoing purification steps, in various combinations, can also be employed to provide a substantially homogeneous isolated recombinant protein. The protein thus purified is substantially free of other mammalian proteins and is defined in accordance with the present invention as an "isolated protein."
The protein of the invention may also be expressed as a product of transgenic animals, e.g., as a component of the mills of transgeruc cows, goats, pigs, or sheep which are characterized by somatic or germ cells containing a nucleotide sequence encoding the protein.
The protein may also be produced by known conventional chemical synthesis.
Methods for constructing the proteins of the present invention by synthetic means are known to those skilled in the art. The synthetically-constructed protein sequences, by virtue of sharing primary, secondary or tertiary structural and/or conformational characteristics with proteins may possess biological properties in common therewith, including protein activity. Thus, they may be employed as biologically active or immunological substitutes for natural, purified proteins in screening of therapeutic compounds and in immunological processes for the development of antibodies.
2 0 The proteins provided herein also include proteins characterized by amino acid sequences similar to those of purified proteins but into which modification are naturally provided or deliberately engineered. For example, modifications in the peptide or DNA
sequences can be made by those skilled in the art using known techniques.
Modifications of interest in the protein sequences may include the alteration, substitution, replacement, 2 5 insertion or deletion of a selected amino acid residue in the coding sequence. For example, one or more of the cysteine residues may be deleted or replaced with another amino acid to alter the conformation of the molecule. Techniques for such alteration, substitution, replacement, insertion or deletion are well known to those skilled in the art (see, e.g., U.S. Patent No. 4,518,584). Preferably, such alteration, substitution, replacement, 3 0 insertion or deletion retains the desired activity of the protein.
Other fragments and derivatives of the sequences of proteins which would be expected to retain protein activity in whole or in part and may thus be useful for screening or other immunological methodologies may also be easily made by those skilled in the art given the disclosures herein. Such modifications are believed to be encompassed by the present invention.
The polynucleotides and proteins of the present invention are expected to exhibit one or more of the uses or biological activities (including those associated with assays cited herein) identified below. Uses or activities described for proteins of the present invention may be provided by administration or use of such proteins or by administration or use of polynucleotides encoding such proteins (such as, for example, in gene therapies or vectors suitable for introduction of DNA).
The polynucleotides provided by the present invention can be used by the research community for various purposes. The polynucleotides can be used to express recombinant protein for analysis, characterization or therapeutic use; as markers for tissues in which the corresponding protein is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in disease states); as molecular weight markers on Southern gels; as chromosome markers or tags (when labeled) to identify cluomosomes or to map related gene positions; to compare 2 0 with endogenous DNA sequences in patients to identify potential genetic disorders; as probes to hybridize and thus discover novel, related DNA sequences; as a source of information to derive 1?CR primers for genetic fingerprinting; as a probe to "subtract-out"
known sequences in the process of discovering other novel polynucleotides; for selecting and making oligomers for attachment to a "gene chip" or other support, including for 2 5 examination of expression patterns; to raise anti-protein antibodies using DNA
immunization techniques; and as an antigen to raise anti-DNA antibodies or elicit another immune response. Where the polynucleotide encodes a protein which binds or pofientially binds to another protein (such as, for example, in a receptor-ligand interaction), the polynucleotide can also be used in interaction trap assays (such as, for example, those 3 0 described in Gyuris et al.,1993, Cell 75: 791-803 and in Rossi et al.,1997, Proc. Natl. Acad.
Sci. LISA 94: 8405-8410, all of which are incorporated by reference herein) to identify polynudeotides encoding the other protein with which binding occurs or to identify inhibitors of the binding interaction.
The proteins provided by the present invention can similarly be used in assay to determine biological activity, including in a panel of multiple proteins for high-throughput screening; to raise antibodies or to elicit another immune response; as a reagent (including the labeled reagent) in assays designed to quantitatively determine levels of the protein (or its receptor) in biological fluids; as markers for tissues in which the corresponding protein is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in a disease state); and, of course, to isolate correlative receptors or ligands. Where the protein binds or potentially binds to another protein (such as, for example, in a receptor-ligand interaction), the protein can be used to identify the other protein with which binding occurs or to identify inhibitors of the binding interaction. Proteins involved in these binding interactions can also be used to screen for peptide or small molecule inhibitors or agonists of the binding interaction.
Any or au of these research utilities are capable of being developed into reagent grade or kit format for commercialization as research products.
Methods for performing the uses listed above are well known to those skilled in the art. References disclosing such methods include without limitation "Molecular Cloning. A Laboratory Manual", 2d ed., Cold Spring Harbor Laboratory Press, Sambrook, j., E.F. Fritsch and T. Maniatis eds., 1989, and "Methods in Enzymology: Guide to 2 0 Molecular Cloning Techniques", Academic Press, Berger, S.L, and A.R.
ICimmel eds.,1987.
Polynucleotides and proteins of the present invention can also be used as nutritional sources or supplements. Such uses include without limitation use as a protein 2 5 or amino acid supplement, use as a carbon source, use as a nitrogen source and use as a sourre of carbohydrate. In such cases the protein or polynucleotide of the invention can be added to the feed of a particular organism or can be administered as a separate solid or liquid preparation, such as in the form of powder, pills, solutions, suspensions or capsules. In the case of microorganisms, the protein or polynucleotide of the invention 3 0 can be added to the medium in or on which the microorganism is cultured.
d A protein of the present invention may exhibit cytokine, cell proliferation (either inducing or inhibiting) or cell differentiation (either inducing or inhibiting) activity or may induce production of other cytokines in certain cell populations. Many protein factors discovered to date, including all known cytokines, have exhibited activity in one or more factor-dependent cell proliferation assays, and hence the assays serve as a convenient confirmation of cytokine activity. The activity of a protein of the present invention is evidenced by any one of a number of routine factor dependent cell proliferation assays for cell lines including, without limitation, 32D, DA2, DA1G, T10, B9, B9/11, BaF3, MC9/G, M+ (preB M+), 2E8, RBS, DA1,123, T1165, HT2, CTLL2, TF_l, Mo7e and CMK.
The activity of a protein of the invention may, among other means, be measured by the following methods:
Assays for T-cell or thymocyte proliferation include without limitation those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A.M.
Kruisbeek, D.H.
Margulies, E.M. Shevach, W Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7, Inununologic studies in Humans); Takai et al., J. Immunol. 137:3494-3500, 1986;
Bertagnolli et al., j. Immunol.145:1706-1712, 1990; Bertagnolli et al., Cellular Immunology 133:327-341,1991; Bertagnolli, et al., J. Immunol. 149:3778-3783,1992; Bowman et al., J.
Immunol.152: 1756-1761,1994.
Assays for cytokine production and/or proliferation of spleen cells, lymph node cells or thymocytes include, without limitation, those described in:
Polyclonal T cell 2 0 stimulation, Kruisbeek, A.M. and Shevach, E.M. In Current Protocols in Immunology. J.E.e.a.
Coligan eds. Vol 1 pp. 3.12.1-3.12.14, John Wiley and Sons, Toronto. 1994; and Measurement of mouse and human Interferon y, Schreiber, R.D. In Current Protocols in Immunology. j.E.e.a. Coligan eds. Vol 1 pp. 6.8.1-6.8.8, john Wiley and Sons, Toronto.1994.
Assays for proliferation and differentiation of hematopoietic and lymphopoietic 2 5 cells include, without limitation, those described in: Measurement of Human and Murine Interleukin 2 and Interleukin 4, Bottomly, K., Davis, L.S. and Lipsky, P.E. In Current Protocols in Immunology. j.E.e.a. Coligan eds. Vol 1 pp. 6.3.1-6.3.12, John Whey and Sons, Toronto. 1991; deVries et al., j. Exp. Med. 173:1205-1211, 1991; Moreau et al., Nature 336:690-692, 1988; Greenberger et al., Proc. Natl. Acad. Sci. U.S.A. 80:2931-2938, 1983;
3 0 Measurement of mouse and human interleukin 6 - Nordan, R. In Current Protocols in Immunology. J.E.e.a. Coligan eds. Vol 1 pp. 6.6.i-6.6.5, John Wiley and Sons, Toronto.1991;
Smith et al., Proc. Natl. Acad. Sci. U.S.A. 83:18571861, 1986; Measurement of human Interleuldn 11- Bennett, F., Giannotti, J., Clark, S.C. and Turner, K. J. In Current Protocols in Immunology. J.E.e.a. Coligan eds. Vol 1 pp. 6.15.1 John Wiley and Sons, Toronto.1991;
Measurement of mouse and human Interleukin 9 - Ciarletta, A., Giannotti, J., Clark, S.C.
and Turner, IGJ. In Current Protocols in Immunology. J.E.e.a. Coligan eds. Vol 1 pp. 6.13.1, John Wiley and Sons, Toronto.1991.
Assays for T-cell clone responses to antigens (which will identify, among others, proteins that affect APC-T cell interactions as well as direct T-cell effects by measuring proliferation and cytokine production) include, without limitation, those described in:
Current Protocols in Immunology, Ed by j. E. Coligan, A.M. ICruisbeek, D.H.
Margulies, E.M. Shevach, W Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3, In Vitro assays for Mouse Lymphocyte Function; Chapter 6, Cytokines and their cellular receptors; Chapter 7, Immunologic studies in Humans);
Weinberger et al., Proc. Natl. Acad. Sci. USA 77:6091-6095, 1980; Weinberger et al., Eur. J.
Immun.
11:405-411,1981; Takai et al., J. Immunol. 137:3494-3500,1986; Takai et al., J. Immunol.
140:508-512, 1988.
Immun_P S 'm ~la 'n~ or ynressi_ng Acti ~it;, A protein of the present invention may also exhibit immune stimulating or immune suppressing activity, including without limitation the activities for which assays are described herein. A protein may be useful in the treatment of various immune deficiencies and disorders (including severe combined immunodeficiency (SCID)), e.g., 2 0 in regulating (up or down) growth and proliferation of T and/or B
lymphocytes, as well as effecting the cytolytic activity of NK cells and other cell populations.
These immune deficiencies may be genetic or be caused by viral (e.g., HIV) as well as bacterial or fungal infections, or may result from autoimmune disorders. More specifically, infectious diseases causes by viral, bacterial, fungal or other infection may be treatable using a protein of the present invention, including infections by HIV, hepatitis viruses, herpesvinuses, mycobacteria, Leishmania spp., malaria spp. and various fungal infections such as candidiasis. Of course, in this regard, a protein of the present invention may also be useful where a boost to the immune system generally may be desirable, i.e., in the treatment of cancer.
3 0 Autoimmune disorders which may be treated using a protein of the present invention include, for example, connective tissue disease, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, autoimmune pulmonary inflammation, Guillain-Barre syndrome, autoimmune thyroiditis, insulin dependent diabetes mellitis, myasthenia gravis, graft versus-host disease and autoimmune inflammatory eye disease.
Such a protein of the present invention may also to be useful in the treatment of allergic reactions and conditions, such as asthma (particularly allergic asthma) or other respiratory problems. Other conditions, in which immune suppression is desired (including, for example, organ transplantation), may also be treatable using a protein of the present invention.
Using the proteins of the invention it may also be possible to regulate immune responses in a number of ways. Down regulation may be in the form of inhibiting or blocking an immune response already in progress or may involve preventing the induction of an immune response. The functions of activated T cells may be inhibited by suppressing T cell responses or by inducing specific tolerance in T cells, or both.
Immunosuppression of T cell responses is generally an active, non-antigen-specific, process which requires continuous exposure of the T cells to the suppressive agent.
Tolerance, which involves inducing non-responsiveness or anergy in T cells, is distinguishable from immunosuppression in that it is generally antigen-specific and persists after exposure to the tolerizing agent has ceased. Operationally, tolerance can be demonstrated by the lack of a T cell response upon reexposure to specific antigen in the absence of the tolerizing agent.
Down regulating or preventing one or more antigen functions (including without limitation B lymphocyte antigen functions (such as , for example, B~), e.g., preventing 2 0 high level lymphokine synthesis by activated T cells, will be useful in situations of tissue, skin and organ transplantation and in graft versus-host disease (GVHD). For example, blockage of T cell function should result in reduced tissue destruction in tissue transplantation. Typically, in tissue transplants, rejection of the transplant is initiated through its recognition as foreign by T cells, followed by an immune reaction that destroys 2 5 the transplant. The administration of a molecule which inhibits or blocks interac#ion of a B7 lymphocyte antigen with its natural ligand(s) on immune cells (such as a soluble, monomeric form of a peptide having B7 2 activity alone or in conjunction with a monomeric form of a peptide having an activity of another B lymphocyte antigen (eg., B7 1, B7-3) or blocking antibody), prior to transplantation can lead to the binding of the 3 0 molecule to the natural ligand(s) on the immune cells without transmitting the corresponding costimulatory signal. Blocking B lymphocyte antigen function in this matter prevents cytokine synthesis by immune cells, such as T cells, and thus acts as an immunosuppressant. Moreover, the lack of costimulation may also be sufficient to anergize the T cells, thereby inducing tolerance in a subject. Induction of long-term WO 99/411,$4 PGTNS99/02898 tolerance by B lymphocyte antigen-blocking reagents may avoid the necessity of repeated administration of these blocking reagents. To achieve sufficient immunosuppression or tolerance in a subject, it may also be necessary to block the function of a combination of B lymphocyte antigens.
The efficacy of particular blocking reagents in preventing organ transplant rejection or GVI3D can be assessed using animal models that are predictive of efficacy in humans. Examples of appropriate systems which can be used include allogeneic cardiac grafts in rats and xenogeneic pancreatic islet cell grafts in mice, both of which have been used to examine the immunosuppressive effects of CTLA4Ig fusion proteins in vivo as described in Lenschow et al., Science 257:789-792 (1992) and Turka et al., Proc. Natl. Acad.
Sci USA, 89:11102-11105 (1992). In addition, marine models of GVI3D (see Paul ed., Fundamental Immunology, Raven Press, New York, 1989, pp. 846-847) can be used to determine the effect of blocking B lymphocyte antigen function in vivo on the development of that disease.
Blocking antigen function may also be therapeutically useful for treating autoimmune diseases. Many autoimmune disorders are the result of inappropriate activation of T cells that are reactive against self tissue and which promote the production of cytokines and autoantibodies involved in the pathology of the diseases.
Preventing the activation of autoreactive T cells may reduce or eliminate disease symptoms.
2 0 Administration of reagents which block costimulation of T cells by disrupting receptor:ligand interactions of B lymphocyte antigens can be used to inhibit T
cell activation and prevent production of autoantibodies or T cell-derived cytokines which may be involved in the disease process. Additionally, blocking reagents may induce antigen-specific tolerance of autoreactive T cells which could lead to long-term relief from 2 5 the disease. The efficacy of blockimg reagents in preventing or alleviating autoimmune disorders can be determined using a number of well-characterized animal models of human autoimmune diseases. Examples include marine experimental autoimmune encephalitis, systemic lupus erythmatosis in MRL/lpr/lpr mice or NZB hybrid mice, marine autoimmune collagen arthritis, diabetes mellitus in NOD mice and BB
rats, and 3 0 marine experimental myasthenia gravis (see Paul ed., Fundamental Immunology, Raven Press, New York,1989, pp. 840-856).
Upregulation of an antigen function (preferably a B lymphocyte antigen function), as a means of up regulating immune responses, may also be useful in therapy.
Upregulation of immune responses may be in the form of enhancing an existing immune response or eliciting an initial immune response. For example, enhancing an immune response through stimulating B lymphocyte antigen function may be useful in cases of viral infection. In addition, systemic viral diseases such as influenza, the common cold, and encephalitis might be alleviated by the administration of stimulatory forms of B
lymphocyte antigens systemically.
Alternatively, anti-viral immune responses may be enhanced in an infected patient by removing T cells from the patient, costimulating the T cells in vitro with viral antigen-pulsed APCs either expressing a peptide of the present invention or together with a stimulatory form of a soluble peptide of the present invention and reintroducing the in vitro activated T cells into the patient. Another method of enhancing anti-viral immune responses would be to isolate infected cells from a patient, transfect them with a nucleic acid encoding a protein of the present invention as described herein such that the cells express all or a portion of the protein on their surface, and reintroduce the transfected cells into the patient. The infected cells would now be capable of delivering a costimulatory signal to, and thereby activate, T cells in vivo.
In another application, up regulation or enhancement of antigen function (preferably B lymphocyte antigen function) may be useful in the induction of tumor immunity. Tumor cells (eg., sarcoma, melanoma, lymphoma, leukemia, neuroblastoma, carcinoma) transfected with a nucleic acid encoding at least one peptide of the present 2 0 invention can be administered to a subject to overcome tumor-specific tolerance in the subject. If desired, the tumor cell can be transfected to express a combination of peptides.
For example, tumor cells obtained from a patient can be transfected ex vivo with an expression vector directing the expression of a peptide having B7 2-like activity alone, or in conjunction with a peptide having B7-1-like activity and/or B7-3-like activity. The 2 5 transfected tumor reps are returned to the patient to result in expression of the peptides on the surface of the transfecbed cell. Alternatively, gene therapy techniques can be used to target a tumor cell for transfection in vivo.
The presence of the peptide of the present invention having the activity of a B
lymphocyte antigens) on the surface of the tumor cell provides the necessary 3 0 costimulation signal to T cells to induce a T cell mediated immune response against the trai~sfected tumor cells. In addition, tumor cells which lack MHC class I or MHC class II
molecules, or which fail to reexpress sufficient amounts of MHC class I or MFIC class II
molecules, can be transfected with nucleic acid encoding all or a portion of (e.g., a cytoplasmic-domain truncated portion) of an MHC class I a chain protein and ~i2 microglobulin protein or an MHC class II a chain protein and an MHC class II
~i chain protein to thereby express MHC class I or MHC class II proteins on the cell surface.
Expression of the appropriate class I or class II MHC in conjunction with a peptide having the activity of a B lymphocyte antigen (e.g., B7-1, B7-2, B7 3) induces a T
cell mediated immune response against the transfected tumor cell. Optionally, a gene encoding an antisense construct which blocks expression of an MHC class II associated protein, such as the invariant chain, can also be cotransfected with a DNA encoding a peptide having the activity of a B lymphocyte antigen to promote presentation of tumor associated antigens and induce tumor specific immunity. Thus, the induction of a T cell mediated immune response in a human subject may be sufficient to overcome tumor-specific tolerance in the subject.
The activity of a protein of the invention may, among other means, be measured by the following methods:
Suitable assays for thymocyte or splenocyte cytotoxicity include, without limitation, those described in: Current protocols in Immunology, Ed by j. E.
Coligan, A.M.
Kruisbeek, D.H. Margulies, E.M. Shevach, W Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3,1n Vitro assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7, Immunologic studies in Humans); Herrmann et al., Proc. Natl.
Acad. Sci.
USA 78:2488-2492,1981; Herrmann et al., J. Immunol.128:1968-1974,1982; Handa et al., 2 0 J. Immunol.135:1564-1572,1985; Takai et al., J. Immunol.137:3494-3500,1986; Takai et al., J. Imrnunol.140:508-512, 1988; Herrmann et al., Proc. Natl. Acad. Sci. USA
78:2488-2492, 1981; Hemnann et al., J. Immunol. 128:1968-1974, 1982; Handa et al., J.
Immunol.
135:1564-1572, 1985; Takai et al., J. lmmunol. 137:3494-3500, 1986; Bowmanet al., j.
Virology 61:1992-1998; Takai et al., J. Immunol. 140:508-512, 1988;
Bertagnolli et al., 2 5 Cellular Immunology 133:327 341,1991; Brown et al., J. Immunol.153:3079-3092, 1994.
Assays for T-cell-dependent immunoglobulin responses and isotype switching (which will identify, among others, proteins that modulate T-cell dependent antibody responses and that affect Thl /Th2 profiles) include, without limitation, those described in: Maliszewski, J. Immunol.144:3028-3033,1990; and Assays for B cell function: In vitro 3 0 antibody production, Mond, J.J. and Brunswick, M. In Current Protocols in Immunology.
J.E.e.a. Coligan eds. Vol 1 pp. 3.8.1-3.8.16, John Wiley and Sons, Toronto.1994.
Mixed lymphocyte reaction (MLR) assays (which will identify, among others, proteins that generate predominantly Thl and CTL responses) include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A.M.
ICruisbeek, wo 99iaizsa rcrnrs~ro2s9s D.H. Margulies, E.M. Shevach, W Strober, Pub. Greene Publishing Associates and Wiley-lnterscience (Chapfier 3, In Vitro assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7, Immunologic studies in Humans); Takai et al., J. Immunol.137:3494-3500,1986; Takai et al., J. Immunol.140:508-512, 1988; Bertagnolli et al., J. Immunol.149:3778-3783,1992.
Dendritic cell-dependent assays (which will identify, among others, proteins expressed by dendritic cells that activate naive T-cells) include, without limitation, those described in: Guery et al., J. hnmunol. 134:536-544, 1995; Inaba et al., Journal of Experimental Medicine 173:549-559, 1991; Macatonia et al., Journal of Immunology 154:5071-5079,1995; Porgador et al., Journal of Experimental Medicine 182:255-260,1995;
Nair et al., Journal of Virology 67:4062-4069, 1993; Huang et al., Science 264:961-965, 1994; Macatonia et al., Journal of Experimental Medicine 169:1255-1264,1989;
Bhardwaj et al., Journal of Clinical Investigation 94:797-807, 1994; and lnaba et al., journal of Experimental Medicine 172:631-640,1990.
Assays for lymphocyte survival/apoptosis (which will identify, among others, proteins that prevent apoptosis after superantigen induction and proteins that regulate lymphocyte homeostasis) include, without limitation, those described in:
Darzynkiewicz et al., Cytometry 13:795-808,1992; Gorczyca et al., Leukemia 7:659-670,1993;
Gorczyca et al., Cancer Research 53:1945-1951, 1993; Itoh et al., Cell 66:233-243, 1991;
Zacharchuk, Journal of Immunology 145:4037-4045, 1990; Zamai et al., Cytometry 14:891-897, 1993;
2 0 Gorczyca et al., International Journal of Oncology 1:639-648,1992.
Assays for proteins that influence early steps of T-cell commitment and development include, without limitation, those described in: Antica et al., Blood 84:111-117, 1994; Fine et al., Cellular Immunology 155:111-122,1994; Galy et al., Blood 85:2770-2778,1995; Toki et al., Proc. Nat. Acad Sci. USA 88:7548-7551,1991.
HematopoiesL ReeLati-ng A
A protein of the present invention may be useful in regulation of hematopoiesis and, consequently, in the treatment of myeloid or lymphoid cell deficiencies.
Even marginal biological activity in support of colony forming cells or of factor-dependent cell 3 0 lines indicafies involvement in regulating heznatopoiesis, e.g. in supporting the growth and proliferation of erythroid progenitor cells alone or in combination with other cytokines, thereby indicating utility, for example, in treating various anemias or for use in conjunction with irradiation/chemotherapy to stimulate the production of erythroid precursors and/or erythroid cells; in supporting the growth and proliferation of myeloid cells such as granulocyfies and monocytes/macrophages (i.e., traditional CSF
activity) useful, for example, in conjunction with chemotherapy to prevent or treat consequent myelo-suppression; in supporting the growth and proliferation of megakaryocytes and consequently of platelets thereby allowing prevention or treatment of various platelet disorders such as thrombocytopenia, and generally for use in place of or complimentary to platelet transfusions; and/or in supporting the growth and proliferation of hematopoietic stem cells which are capable of maturing to any and all of the above-mentioned hematopoietic cells and therefore find therapeutic utility in various stem cell disorders (such as those usually treated with transplantation, including, without limitation, aplastic anemia and paroxysmal nocturnal hemoglobinuria), as well as in repopulating the stem cell compartment post irradiation/chemotherapy, either in-vivo or ex-vivo (i.e., in conjunction with bone marrow transplantation or with peripheral progenitor cell transplantation (homologous or heterologous)) as normal cells or genetically manipulated for gene therapy.
The activity of a protein of the invention may, among other means, be measured by the following methods:
Suitable assays for proliferation and differentiation of various hematopoietic lines are cited above.
Assays for embryonic stem cell differentiation (which will identify, among others, 2 0 proteins that influence embryonic differentiation hematopoiesis) include, without limitation, those described in: Johansson et al. Cellular Biology 15:141-151,1995; Keller et al., Molecular and Cellular Biology 13:473-486, 1993; McClanahan et al., Blood 81:2903-2915,1993.
Assays for stem cell survival and differentiation {which will identify, among 2 5 others, proteins that regulate lympho-hematopoiesis) include, without limitation, those described in: Methylcellulose colony forming assays, Freshney, M.G. In Culture of Hematopoietic Cells. R.I. Freshney, et al. eds. Vol pp. 265-268, Whey-Liss, Inc., New York, NY. 1994; Hirayama et al., Proc. Natl. Acad. Sci. USA 89:5907 5911, 1992;
Primitive hematopoietic colony forming cells with high proliferative potential, McNiece, LK. and 3 0 Briddell, R.A. In Culture of Hemutopoietic Cells. R.I. Freshney, et al.
eds. Vol pp. 23-39, Wiley-Liss, Inc., New York, NY.1994; Neben et al., Experimental Hematology 22:353-359, 1994; Cobblestone area forming cell assay, Ploemacher, R.E. In Culture of Hematopoietic Cells. R.I. Freshney, et al. eds. Vol pp.1-21, Whey Liss, Inc.., New York, NY.1994; Long term bone marrow cultures in the presence of stromal cells, Spooncer, E., Dexter, M. and Allen, T. In Culture of Hemutopoietic Cells. R.I. Freshney, et al. eds. Vol pp. 163-179, Hliley-hiss, Inc., New York, NY.1994; Long term culture initiating cell assay, Sutherland, H.J. In Culture of Hematopoietic Cells. RI. Freshney, et al. eds. Vol pp.139-162, Wiley-Liss, Inc., New York, NY.1994.
A protein of the present invention also may have utility in compositions used for bone, cartilage, tendon, ligament and / or nerve tissue growth or regeneration, as well as for wound healing and tissue repair and replacement, and in the treatment of burns, incisions and ulcers.
A protein of the present invention, which induces cartilage and/or bone growth in circumstances where bone is not normally formed, has application in the healing of bone fractures and cartilage damage or defects in humans and other animals.
Such a preparation employing a protein of the invention may have prophylactic use in closed as well as open fracture reduction and also in the improved fixation of artificial joints. De novo bone formation induced by an osteogeruc agent contributes to the repair of congenital, trauma induced, or oncologic resection induced craniofacial defects, and also is useful in cosmetic plastic surgery.
A protein of this invention may also be used in the treatment of periodontal 2 0 disease, and in other tooth repair processes. Such agents may provide an environment to attract bone-forming cells, stimulate growth of bone-forming cells or induce differentiation of progenitors of bone-forming cells. A protein of the invention may also be useful in the treatment of osteoporosis or osteoarthritis, such as through stimulation of bone and/or cartilage repair or by blocking inflammation or processes of tissue destruction (collagenase activity, osteoclast activity, etc.) mediated by inflammatory processes.
Another category of tissue regeneration activity that may be attributable to the protein of the present invention is tendon/ligament formation. A protein of the present invention, which induces tendon/ligament-like tissue or other tissue formation in 3 0 circumstances where such tissue is not normally formed, has application in the healing of tendon or ligament tears, deformities and other tendon or ligament defects in humans and other animals. Such a preparation employing a tendon/ligament like tissue inducing protein may have prophylactic use in preventing damage to tendon or ligament tissue, as well as use in the improved fixation of tendon or ligament to bone or other tissues, and in repairing defects to tendon or ligament tissue. De novo tsndon/ligament like tissue formation induced by a composition of the present invention contributes to the repair of congenital, trauma induced, or other tendon or ligament defects of other origin, and is also useful in cosmetic plastic surgery for attachment or repair of tendons or ligaments. The compositions of the present invention may provide an environment to attract tendon- or ligament forming cells, stimulate growth of tendon- or ligament-forming cells, induce differentiation of progenitors of tendon or ligament-forming cells, or induce growth of tendon/ligament cells or progenitors ex vivo for return in vivo to effect tissue repair. The compositions of the invention may also be useful in the treatment of tendinitis, carpal tunnel syndrome and other tendon or ligament defects. The compositions may also include an appropriate matrix and/or sequestering agent as a carrier as is well known in the art.
The protein of the present invention may also be useful for proliferation of neural cells and for regeneration of nerve and brain tissue, i.e. for the treatment of central and peripheral nervous system diseases and neuropathies, as well as mechanical and traumatic disorders, which involve degeneration, death or trauma to neural cells or nerve tissue. More specifically, a protein may be used in the treatment of diseases of the peripheral nervous system, such as peripheral nerve injuries, peripheral neuropathy and localized neuropathies, and central nervous system diseases, such as Alzheimer's, 2 0 Parkinson s disease, Huntington's disease, amyotrophic lateral sclerosis, and Shy-Drager syndrome. Further conditions which may be treated in accordance with the present invention include mechanical and traumatic disorders, such as spinal cord disorders, head trauma and cerebrovasculai diseases such as stroke. Peripheral neuropathies resulting from chemotherapy or other medical therapies may also be treatable using a protein of the 2 5 invention.
Proteins of the invention may also be useful to promote better or faster closure of non-healing wounds, including without limitation pressure ulcers, ulcers associated with vascular insufficiency, surgical and traumatic wounds, and the like.
It is expected that a protein of the present invention may also exhibit activity for 3 0 generation or regeneration of other tissues, such as organs (including, for example, pancreas, liver, intestine, kidney, skin, endothelium), muscle (smooth, skeletal or cardiac) and vascular (including vascular endothelium) tissue, or for promoting the growth of cells comprising such tissues. Part of the desired effects may be by inhibition or modulation WO 99/41284 PG"f/US99/02898 of fibrotic scarring to allow normal tissue to regenerate. A protein of the invention may also exhibit angiogenic activity.
A protein of the present invention may also be useful for gut protection or regeneration and treatment of lung or liver fibrosis, reperfusion injury in various tissues, and conditions resulting from systemic cytokine damage.
A protein of the present invention may also be useful for promoting or inhibiting differentiation of tissues described above from precursor tissues or cells; or for inhibiting the growth of tissues described above.
The activity of a protein of the invention may, among other means, be measured by the following methods:
Assays for tissue generation activity include, without limitation, those described in: International Patent Publication No. W095/16035 (bone, cartilage, tendon);
Infiernational Patent Publication No. W095/05846 (nerve, neuronal);
International Patent Publication No. W091/07491 (skin, endothelium ).
Assays for wound healing activity include, without limitation, those described in:
Winter, ~idermal Wound Healing. pps. 71-112 (Maibach, HI and Rovee, DT, eds.), Year Book Medical Publishers, Inc., Chicago, as modified by Eaglstein and Mertz, J.
Invest.
Dermatol 71:382-84 (1978).
2 0 ~,ctivin/Inhibin ActiY~
A protein of the present invention may also exhibit activin- or inhibin-related activities. Inhibins are characterized by their ability to inhibit the release of follicle stimulating hormone (FSH), while activins and are characterized by their ability to stimulate the release of follicle stimulating hormone (FSH). Thus, a protein of the present 2 5 invention, alone or in heterodimers with a member of the inhibin a family, may be useful as a contraceptive based on the ability of inhibins to decrease fertility in female mammals and decrease spermatogenesis in male mammals. Administration of sufficient amounts of other inhibins can induce infertility in these mammals. Alternatively, the protein of the invention, as a homodimer or as a heterodimer with other protein subunits of the inhibin-3 0 (3 group, may be useful as a fertility inducing therapeutic, based upon the ability of activin molecules in stimulating FSH release from cells of the anterior pituitary.
See, for example, United States Patent 4,798,885. A protein of the invention may also be useful for advancement of the onset of fertility in sexually immature mammals, so as to increase the lifetime reproductive performance of domestic animals such as cows, sheep and pigs.
The activity of a protein of the invention may, among other means, be measured by the following methods:
Assays for activin/inh~in activity include, without limitation, those described in:
Vale et al., Endocrinology 91:562-572,1972; Ling et al., Nature 321:779-782,1986; Vale et al., Nature 321:776-779,1986; Mason et al., Nature 318:659-663,1985; Forage et al., Proc.
Nail. Acad. Sci. USA 83:3091-3095,1986.
A protein of the present invention may have chemotactic or chemokinetic activity (e.g., act as a chemokine) for mammalian cells, including, for example, monocytes, fibroblasts, neutrophils, T-cells, mast cells, eosinophils, epithelial and/or endothelial cells.
Glemotactic and chemokinetic proteins can be used to mobilize or attract a desired cell population to a desired site of action. Chemotactic or chemokinetic proteins provide particular advantages in treatment of wounds and other trauma to tissues, as well as in treatment of localized infections. For example, attraction of lymphocytes, monocytes or neutrophils to tumors or sites of infection may result in improved immune responses against the tumor or infecting agent.
A protein or peptide has chemotactic activity for a particular cell population if it can stimulate, directly or indirectly, the directed orientation or movement of such cell 2 0 population. Preferably, the protein or peptide has the ability to directly stimulate directed movement of cells. Whether a particular prod ~ ~~o~~c activity for a population of cells can be readily determined by employing such protein or peptide in any known assay for cell chemotaxis.
The activity of a protein of the invention may, among other means, be measured 2 5 by the following methods:
Assays for chemotactic activity (which will identify proteins that induce or prevent chemotaxis) consist of assays that measure the ability of a protein to induce the migration of cells across a membrane as well as the ability of a protein to induce the adhesion of one cell population to another cell population. Suitable assays for movement and adhesion 3 0 include, without limitation, those described in: Current Protocols in Immunology, Ed by J.E. Coligan, A.M. Kruisbeek, D.H. Margulies, E.M. Shevach, W.Strober, Pub.
Greene Publishing Associates and Wiley Interscience (Chapter 6.12, Measurement of alpha and beta Chemokines 6.12.1-6.12.28; Taub et al. J. Gin. Invest. 95:1370-1376,1995;
Lind et al.
APMIS 103:140-146,1995; Muller et al Eur. J. Immunol. 25: 1744-1748; Gruber et al. J. of Immunol.152:5860-5867,1994; Johnston et al. J. of Immunol.153:1762-1768,1994.
Hemostatic and Thrombolytic Activity A protein of the invention may also exhibit hemostatic or thrombolytic activity.
As a result, such a protein is expected to be useful in treatment of various rnagulation disorders (including hereditary disorders, such as hemophiliac) or to enhance coagulation and other hemostatic events in treating wounds resulting from trauma, surgery or other causes. A protein of the invention may also be useful for dissolving or inhibiting formation of thromboses and for treatment and prevention of conditions resulting therefrom (such as, for example, infarction of cardiac and central nervous system vessels (e.g., stroke).
The activity of a protein of the invention may, among other means, be measured by the following methods:
Assay for hemostatic and thrombolytic activity include, without limitation, those described in: Linet et al., J. Clin. Pharmacol. 26:131-140,1986; Burdick et al., Thrombosis Res. 45:413-419,1987; Humphrey et al., Fibrinolysis 5:71-79 (I991); Schaub, Prostaglandins 35:467-474,1988.
2 0 ~tor /Ligand A protein of the present invention may also demonstrate activity as receptors, receptor ligands or inhibitors or agonises of receptor/ligand interactions.
Examples of such receptors and ligands include, without limitation, cytokine receptors and their ligands, receptor kinases and their ligands, receptor phosphatases and their ligands, 2 5 receptors involved in cell-cell interactions and their ligands (including without limitation, cellular adhesion molecules (such as selectins, integrins and their ligands) and receptor/ligand pairs involved in antigen presentation, antigen recognition and development of rellular and humoral immune responses). Receptors and ligands are also useful for screening of potential peptide or small molecule inhibitors of the relevant 3 0 receptor/ligand interaction. A protein of the present invention (including, without limitation, fragments of receptors and ligands) may themselves be useful as inhibitors of receptor/ligand interactions.
The activity of a protein of the invention may, among other means, be measured by the following methods:
WO 99/41284 PC"T/US99/OZ898 Suitable assays for receptor-ligand activity include without limitation those described in:Current Protocols in Immunology, Ed by J.E. Coligan, A.M.
ICruisbeek, D.H.
Margulies, E.M. Shevach, W.Strober, Pub. Greene Publishing Associates and Wiley-Intersrience (Chapter 7.28, Measurement of Cellular Adhesion under static conditions 7.28.1-7.28.22), Takai et al., Proc. Natl. Acad. Sci. USA 84:6864-6868, 1987;
Bierer et al., J. Exp. Med.168:1145-1156, 1988; Rosenstein et al., J. Exp.
Med.169:149-160 1989; Stoltenborg et al., J. Immunol. Methods 175:59-68,1994; Stitt et al., Cell 80:661-670, 1995.
Proteins of the present invention may also exhibit anti-inflammatory activity.
The anti-inflammatory activity may be achieved by providing a stimulus to cells involved in the inNamnnatory response, by inhibiting or promoting cell-cell interactions (such as, for example, cell adhesion), by inhibiting or promoting chemotaxis of cells involved in the inflammatory process, inhibiting or promoting cell extravasation, or by stimulating or suppressing production of other factors which more directly inhibit or promote an inflammatory response. Proteins exhibiting such activities can be used to treat inflammatory conditions including chronic or acute conditions), including without limitation inflammation associated with infection (such as septic shock, sepsis or systemic 2 0 inflammatory response syndrome (SIRS)), ischemia-reperfusion injury, endotoxin lethality, arthritis, complement mediated hyperacute rejection, nephritis, cytokine or chemokine-induced lung injury, inflammatory bowel disease, Crohn's disease or resulting fpm over production of cytokines such as TNF or ILrl. Proteins of the invention may also be useful to treat anaphylaxis and hypexsensitivity to an antigenic substance or material.
Cadherins are calcium-dependent adhesion molecules that appear to play major roles during development, particularly in defining specific cell types. Loss or alteration of normal cadherin expression can lead to changes in cell adhesion properties linked to 3 0 tumor growth and metastasis. Cadherin malfunction is also implicated in other human diseases, such as pemphigus vulgaris and pemphigus foliaceus (auto-immune blistering skin diseases), Crohn's disease, and some developmental abnormalities.
The cadherin superfamily includes well over forty members, each with a distinct pattern of expression. All members of the superfamily have in common conserved extracellular repeats (cadherin domains), but structural differences are found in other parts of the molecule. The cadherin domains bind calcium to form their tertiary structure and thus calcium is required to mediate their adhesion. Only a few amino acids in the first cadherin domain provide the basis for homophilic adhesion; modification of this recognition site can change the specificity of a cadherin so that instead of recognizing only itself, the mutant molecule can now also bind to a different cadherin. In addition, some cadherins engage in heterophilic adhesion with other cadherins.
E-cadherin, one member of the cadherin supex~family, is expressed in epithelial cell types. Pathologically, if E-cadherin expression is lost in a tumor, the malignant cells become invasive and the cancer metastasizes. Transfection of cancer cell lines with polynucleotides expressing E-cadherin has reversed cancer-associated changes by returning altered cell shapes to normal, restoring cells adhesiveness to each other and to their substrate, decreasing the cell growth rate, and drastically reducing anchorage-independent cell growth. Thus, reintroducing E-cadherin expression reverts carcinomas to a less advanced stage. It is likely that other cadherins have the same invasion suppressor role in carcinomas derived from other tissue types. Therefore, proteins of the present invention with cadherin activity, and polynucleotides of the present invention encoding such proteins, can be used to treat cancer. Introducing such proteins or polynucleotides into cancer cells can reduce or eliminate the cancerous changes observed 2 0 in these cells by providing normal cadherin expression.
Cancer cells have also been shown to express cadherins of a different tissue type than their' origin, thus allowing these cells to invade and metastasize in a different tissue in the body. Proteins of the present invention with cadherin activity, and polynucleotides of the present invention encoding such proteins, can be substituted in these cells for the 2 5 inappropriately expressed cadherins, restoring normal cell adhesive properties and reducing or eliminating the tendency of the cells to metastasize.
Additionally, proteins of the present invention with cadherirt activity, and poiynucleotides of the present invention encoding such proteins, can used to generate antibodies recognizing and binding to cadherins. Such antibodies can be used to block 3 0 the adhesion of inappropriately expressed tumor-cell cadherins, preventing the cells from forming a tumor elsewhere. Such an anti-cadherin antibody can also be used as a r~.~r for the grade, pathological type, and prognosis of a cancer, i.e. the more progressed the cancer, the less cadherin expression there will be, and this decrease in cadherin expression can be detected by the use of a cadherin-binding antibody.
Fragments of profieins of the present invention with cadherin activity, preferably a polypeptide comprising a decapeptide of the cadherin recognition site, and poly-nucleotides of the present invention encoding such protein fragments, can also be used to block cadherin function by binding to cadherins and preventing them from binding in ways that produce undesirable effects. Additionally, fragments of proteins of the present invention with cadherin activity, preferably truncated soluble cadherin fragments which have been found to be stable in the circulation of cancer patients, and polynucleotides encoding such protein fragments, can be used to disturb proper cell-cell adhesion.
Assays for cadherin adhesive and invasive suppressor activity include, without limitation, those described in: Hortsch et al. J Biol Chem 270 (32): 18809-18817, 1995;
Miyaki et al. Oncogene 11: 2547-2552,1995; C~zawa et al. Cell 63:1033-1038,1990.
In addition to the activities described above for immunological treatment or prevention of tumors, a protein of the invention may exhibit other anti-tumor activities.
A protein may inhibit tumor growth directly or indirectly (such as, for example, via antibody-dependent cell-mediated cytotoxicity (ADCC)). A protein may exhibit its tumor inhibitory activity by acting on tumor tissue or tumor precursor tissue, by inhibiting formation of tissues necessary to support tumor growth {such as, for example, by 2 0 iWu'biting angiogenesis), by causing production of other factors, agents or cell types which inhibit tumor growth, or by suppressing, eliminating or inhibiting factors, agents or cell types which promote tumor growth.
2 5 A protein of the invention may also exh~it one or more of the following additional activities or effects: inhibiting the growth, infection or function of, or killing, infectious agents, including, without limitation, bacteria, viruses, fungi and other parasites; effecting {suppressing or enhancing) bodily characteristics, including, without limitation, height, weight, hair rnlor, eye color, skin, fat to lean ratio or other tissue pigmentation, or organ 3 0 or body part size or shape (such as, for example, breast augmentation or diminution, change in bone form or shape); effecting biorhythms or caricadic cycles or rhythms;
effecting the fertility of male or female subjects; effecting the metabolism, catabolism, anabolism, processing, utilization, storage or elimination of dietary fat, lipid, profiein, carbohydrate, vitamins, minerals, cofactors or other nutritional factors or component(s);
effecting behavioral characteristics, including, without limitation, appetite, libido, stress, cognition (including cognitive disorders), depression (including depressive disorders) and violent behaviors; providing analgesic effects or other pain reducing effects;
promoting differentiation and growth of embryonic stem cells in lineages other than hematopoietic lineages; hormonal or endocrine activity; in the case of enzymes, correcting deficiencies of the enzyme and treating deficiency-related diseases; treatment of hyperproliferative disorders (such as, for example, psoriasis); immunoglobulin-like activity (such as, for example, the ability to bind antigens or complement); and the ability to act as an antigen in a vaccine composition to raise an immune response against such protein or another material or entity which is cross-reactive with such protein.
A protein of the present invention (from whatever source derived, including without limitation from recombinant and non-recombinant sources) may be used in a pharmaceutical composition when combined with a pharmaceutically acceptable carrier.
Such a composition may also contain (in addition to protein and a Garner) diluents, fillers, salts, buffers, stabilizers, solubiiizers, and other materials well known in the art. The term "pharmaceutically acceptable" means a non toxic mafierial that does not interfere with the effectiveness of the biological activity of the active ingredient(s). The characteristics of the 2 0 Garner will depend on the route of administration. The pharmaceutical composition of the invention may also contain cytokines, lymphokines, or other hematopoietic factors such as M-CSF, GM-CSF, TNF, IL-1, IL-2, ILr3, IL-4, IL-5, ILr6, IL-7, ILr8, IL.-9, IL~-10, ILrl l, l:Lrl2, ILrl3, fLrl4, IL-15, TFN, TNFU, TNFl, TNF2, G-CSF, Meg-CSF, thrombopoietin, stem cell factor, and erythropoietin. The pharmaceutical composition may contain other 2 5 agents which either enhance the activity of the protein or compliment its activity or use in treatment. Such additional factors and/or agents may be included in the pharmaceutical comp~ition to produce a synergistic effect with protein of the invention, or to minimize side effects. Conversely, protein of the present invention may be included in formulations of the particular cytokine, lymphokine, other hematopoietic factor, 3 0 thrombolytic or anti-thrombotic factor, or anti-inflammatory agent to minimize side effects of the cytokine, lymphokine, other hematopoietic factor, thrombolytic or anti-thrombotic factor, or anti-inflammatory agent.
A protein of the present invention may be active in multimers (e.g., heterodimers or homodimers) or complexes with itself or other proteins. As a result, pharmaceutical compositions of the invention may comprise a protein of the invention in such multimeric or complexed form.
The pharmaceutical composition of the invention may be in the form of a complex of the proteins) of present invention along with protein or peptide antigens.
The protein and/or peptide antigen will deliver a stimulatory signal to both B and T
lymphocytes. B
lymphocytes will respond to antigen through their surface immunoglobulin receptor. T
lymphocytes will respond to antigen through the T cell receptor (TCR) following presentation of the antigen by MHC proteins. MHC and structurally related proteins including those encoded by class I and class II MHC genes on host cells will serve to present the peptide antigens) to T lymphocytes. The antigen components could also be supplied as purified MFiC-peptide complexes alone or with co-stimulatory molecules that can directly signal T cells. Alternatively antibodies able to bind surface immunolgobulin and other molecules on B cells as well as antibodies able to bind the TCR and other molecules on T cells can be combined with the pharmaceutical composition of the invention.
The pharmaceutical composition of the invention may be in the form of a liposome in which protein of the present invention is combined, in addition to other pharniaceutically acceptable carriers, with amphipathic agents such as lipids which exist in aggregated form as micelles, insoluble monolayers, liquid crystals, or lamellar layers 2 0 in aqueous solution. Suitable lipids for liposomal formulation include, without limitation, monoglycerides, diglycerides, sulfatides, lysolecithin, phospholipids, saponin, bile acids, and the like. Preparation of such liposomal formulations is within the level of skill in the art, as disclosed, for example, in U.S. Patent No. 4,235,871; U.S. Pafient No.
4,501,728; U.S.
Patent No. 4,837,028; and U.S. Patent No. 4,737,323, all of which are incorporated herein 2 5 by reference.
As used herein, the term "therapeutically effective amount" means the total amount of each active component of the pharmaceutical composition or method that is sufficient to show a meaningful patient benefit, i.e., treatment, healing, prevention or amelioration of the relevant medical condition, or an incrnase in rate of treatment, healing, 3 0 prevention or amelioration of such conditions. When applied to an individual active ingredient, administered alone, the term refers to that ingredient alone. When applied to a combination, the term refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.
In practicing the method of treatment or use of the present invention, a therapeutically effective amount of protein of the present invention is administered to a mammal having a condition to be treated. Protein of the present invention may be administered in accordance with the method of the invention either alone or in combination with other therapies such as treatments employing cytolcines, lympholcines or other hematopoietic factors. When co-administered with one or more rytolcines, lymphokines or other hematopoietic factors, protein of the present invention may be administered either simultaneously with the cytolcine(s), lympholcine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic factors, or sequentially. If administered sequentially, the attending physician will decide on the appropriate sequence of administering protein of the present invention in combination with cytokine(s), lympholcine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic factors.
Administration of protein of the present invention used in the pharmaceutical composition or to practice the method of the present invention can be carned out in a variety of conventional ways, such as oral ingestion, inhalation, topical application or cutaneous, subcutaneous, intraperitoneal, parenteral or intravenous injection.
Intravenous administration to the patient is preferred.
When a therapeutically effective amount of protein of the present invention is 2 0 administered orally, protein of the present invention will be in the form of a tablet, capsule, powder, solution or elixir. When administered in tablet form, the pharmaceutical composition of the invention may additionally contain a solid Garner such as a gelatin or an adjuvant. The tablet, capsule, and powder contain from about 5 to 95%
protein of the present invention, and preferably from about 25 to 90~° protein of the present invention.
2 5 When administered in liquid form, a liquid carrier such as water, petroleum, oils of animal or plant origin such as peanut oil, mineral oil, soybean oil, or sesame oil, or synthetic oils may be added. The liquid form of the pharmaceutical composition may further contain physiological saline solution, dextrose or other saccharide solution, or glycols such as ethylene glycol, propylene glycol or polyethylene glycol. When administered in liquid 3 0 form, the pharmaceutical composition contains from about 0.5 to 90% by weight of protein of the present invention, and preferably from about 1 to 50% protein of the present invention.
When a therapeutically effective amount of protein of the present invention is administered by intravenous, cutaneous or subcutaneous injection, protein of the present wo m4m Pc-riusmoas98 invention will be in the form of a pyrogen-free, parenterally acceptable aqueous solution.
The preparation of such parenterally acceptable protein solutions, having due regard to pH, isotonicity, stability, and the like, is within the skill in the art. A
preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection should contain, in addition to protein of the present invention, an isotonic vehicle such as Sodium Chloride Injection, Ringer's Injection, Dextrose Injection, Dextrose and Sodium Chloride Injection, Lactated Ringer's Injection, or other vehicle as known in the art.
The pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additives known to those of skill in the art.
The amount of protein of the present invention in the pharmaceutical composition of the present invention will depend upon the nature and severity of the condition being treated, and on the nature of prior treatments which the patient has undergone.
Ultimately, the attending physician will decide the amount of protein of the present invention with which to treat each individual patient. Initially, the attending physician will administer low doses of protein of the present invention and observe the patient's response. Larger doses of protein of the present invention may be administered until the optimal therapeutic effect is obtained for the patient, and at that point the dosage is not increased further. It is contemplated that the various pharmaceutical compositions used to practice the method of the present invention should rnntain about 0.01 pg to about 100 2 0 mg (preferably about O.lng to about 10 mg, more preferably about 0.1 pg to about 1 mg) of protein of the present invention per kg body weight.
The duration of intravenous therapy using the pharmaceutical composition of the present invention will vary, depending on the severity of the disease being treated and the condition and potential idiosyncratic response of each individual patient.
It is 2 5 contemplated that the duration of each application of the protein of the present invention will be in the range of 12 to 24 hours of continuous intravenous administration.
Ultimately the attending physician will decide on the appropriate duration of intravenous therapy using the pharmaceutical composition of the present invention.
Protein of the invention may also be used to immunize animals to obtain 3 0 polyclonal and monoclonal antibodies which specifically react with the protein. Such antibodies may be obtained using either the entire protein or fragments thereof as an immunogen. The peptide immunogens additionally may contain a cysteine residue at the carboxyl terminus, and are conjugated to a hapten such as keyhole limpet hemocyanin ~. Methods for synthesizing such peptides are known in the art, for example, as in R.P. Merrifield, J. Amer.Chem.Soc. $~, 2149-2154 (1963); J.L. ICrstenansky, et al., FEBS Lett.
~1, 10 (198. Monoclonal antibodies binding to the protein of the invention may be useful diagnostic agents for the immunodetection of the protein. Neutralizing monoclonal antibodies binding to the protein may also be useful therapeutics for both conditions associated with the protein and also in the treatment of some forms of cancer where abnormal expression of the protein is involved. In the case of cancerous cells or leukemic cells, neutralizing monoclonal antibodies against the protein may be useful in detecting and preventing the metastatic spread of the cancerous cells, which may be mediated by the protein.
For compositions of the present invention which are useful for bone, cartilage, tendon or ligament regeneration, the therapeutic method includes administering the composition topically, systematically, or locally as an implant or device.
When administered, the therapeutic composition for use in this invention is, of course, in a pyrogen free, physiologically acceptable form. Further, the composition may desirably be encapsulated or injected in a viscous form for delivery to the site of bone, cartilage or tissue damage. Topical administration may be suitable for wound healing and tissue repair. Therapeutically useful agents other than a protein of the invention which may also optionally be included in the composition as described above, may alternatively or additionally, be administered simultaneously or sequentially with the composition in the 2 0 methods of the invention. Preferably for bone and/or cartilage formation, the composition would include a matrix capable of delivering the protein-containing composition to the site of bone and/or cartilage damage, providing a structure for the developing bone and cartilage and optimally capable of being resorted into the body.
Such matrices may be formed of materials presently in use for other implanted medical 2 5 applications.
The choice of matrix material is based on biocompati'bility, biodegradability, mechanical properties, cosmetic appearance and interface properties. The particular application of the compositions will define the appropriate formulation.
Potential matrices for the compositions may be biodegradable and chemically defined calcium 3 0 sulfate, tricalciumphosphate, hydroxyapatite, polylactic acid, polyglycolic acid and polyanhydrides. Other potential materials are biodegradable and biologically well-defined, such as bone or dermal collagen. Further matrices are comprised of pure proteins or extracellular matrix components. Other potential matrices are nonbiodegradable and chemically defined, such as sintered hydroxapatite, bioglass, aluminates, or other ceramics. Matrices may be comprised of combinations of any of the above mentioned types of material, such as polylactic acid and hydroxyapatite or rnllagen and tricalciumphosphate. The bioceramics may be altered in composition, such as in calcium aluminate-phosphate and processing to alter pore size, particle size, particle shape, and biodegradability.
Presently preferred is a 50:50 (mole weight) copolymer of lactic acid and glycolic acid in the form of porous particles having diameters ranging from 150 to 800 microns.
In some applications, it will be useful to utilize a sequestering agent, such as carboxymethyl cellulose or autologous blood clot, to prevent the protein compositions from disassociating from the matrix.
A preferred family of sequestering agents is cellulosic materials such as alkylcelluloses (including hydroxyalkylcelluloses), including methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropylcellulose, hydroxypropyl-methylcellulose, and carboxymethylcellulose, the most preferred being cationic salts of carboxymethylcellulose (CMC). Other preferred sequestering agents include hyaluronic acid, sodium alginate, polyethylene glycol), polyoxyethylene oxide, carboxyvinyl polymer and polyvinyl alcohol). The amount of sequestering agent useful herein is 0.5-20 wt%, preferably 1-10 wt% based on total formulation weight, which represents the amount necessary to prevent desorbtion of the protein from the polymer matrix and to 2 0 provide appropriate handling of the composition, yet not so much that the progenitor cells are prevented from infiltrating the matrix, thereby providing the protein the opportunity to assist the osteogenic activity of the progenitor cells.
In further compositions, proteins of the invention may be combined with other agents beneficial to the treatment of the bone and/or cartilage defect, wound, or tissue in question. These agents include various growth factors such as epidermal growth factor (EGF), platelet derived growth factor (PDGF), transforming growth factors (TGF-a and TGR~), and insulin like growth factor (IGF).
The therapeutic compositions are also presently valuable for veterinary applications. Particularly domestic animals and thoroughbred horses, in addition to 3 0 humans, are desired patients for such treatment with proteins of the present invention.
The dosage regimen of a protein-containing pharmaceutical composition to be used in tissue regeneration will be determined by the attending physician considering various factors which modify the action of the proteins, e.g., amount of tissue weight desired to be formed, the site of damage, the condition of the damaged tissue, the size of a wound, type of damaged tissue (e.g., bone), the patient's age, sex, and diet, the severity of any infection, time of administration and other clinical factors. The dosage may vary with the type of matrix used in the reconstitution and with inclusion of other proteins in the pharmaceutical composition. For example, the addition of other known growth factors, such as IGF I (insulin like growth factor I), to the final composition, may also effect the dosage. Progress can be monitored by periodic assessment of tissue/bone growth and/or repair, for example, X-rays, histomorphometric determinations and tetracycline labeling.
Polynucleotides of the present invention can also be used for gene therapy.
Such polynudeotides can be introduced either in vivo or ex vivo into cells for expression in a mammalian subject. Polynucleotides of the invention may also be administered by other known methods for introduction of nucleic acid into a cell or organism (including, without limitation, in the form of viral vectors or naked DNA).
Cells may also be cultured ex vivo in the presence of proteins of the present invention in order to proliferate or to produce a desired effect on or activity in such cells.
Treated cells can then be introduced in vivo for therapeutic purposes.
Patent and literature references cited herein are incorporated by reference as if fully set forth.
63.
SEQUENCE LISTING
<110> Wong, Cordon G.
Clark, Hilary Fechtel, Rim Agostino, Michael J.
Genetics Institute. Inc.
<120> SECRETED PROTEINS AND POLYNUCLEOTIDES ENCODING THEM
<130> GI 6300A
<140>
< 141 > "mss MaH' mailirrp I~el numk~: Err~_ ~ fro bra 90 ~ u~
Date of OepoatlL i l 99 9 i hereby certify that this papa or fee is befnQ
<160> 19 depOSis~ with the United States Postal Service "f=xpress Mail Post Ot'~e to Addn~stse' aervioe <170> Patentln Ver. 2.0 under 37 CFR 1 10 on the date indtcabd above end is addrossad to the Assistant Comn~ionar <210> 1 Fa nts, lfYashin D. . 20231 <211> 1051 <212> DNA
<213> Homo sapiens <400> 1 taggccatga aggccgcttg ctattattat gcaaataagt gttgtattac acatactaat 60 ttatgcatgg ttagattatg cagatgcatc acaaacatgg ttattgaata ataggatggg 120 gctcattctc tctaccatct ttataagcag ttttaagcaa attctcctgg taccaatgtg 180 gacatttaaa gaccctttac tcaatgaaat gtctctttcg tattcttttg ctttcatagt 240 taaagccatc agataagtgg aagagaaatc gtccaagttg ttaggttcaa gagtgttagt 300 ctcacttttc aaattcgtag acttttttgt ttaaatgtaa tcttttcctt atagagaaaa 360 tctaaaatgc agttgcttgg catgaatgct ggcatttagt gagattttag tgtatatagc 420 cttgctgctt agctctaggt aacccatcaa attaaaatta cattttcagg atttatagct 480 cattagaata tttatcttgg taagcttctt attctgtcag taatttctaa acaattcagc 540 ttggccaatt tgtgaaatcc cctaaaattt tgaaagtgaa ctcacaagcc ctatgcagta 600 tatttctcaa acaaatctta gtagaaaact tataagccat ccagtaaaaa ttccaaaggt 660 tgagaatgta gcaatattct tgagattcct aatgtctaga gtagttaatc agtgagattt 720 gatgggtgat gagtctaaga aatggatttt gccatggcca ggtgcagtgg cttacgcctg 780 taatcccagc actttgggag gccgaggtgg gcggatcacg aggtcaggag attgagacca 840 tcctggctaa catggtgaaa cccygtctct actaaaaata caaaaaaaaa aaattagccg 900 ggcgtggtgg cgggcacctg tagtccctgc tgaggcagga gaatggcttg aacccgggag 960 gtggagcttg cagtgagccg agatcacgcc actgcactcc agcctgggca acagagcaag 1020 attccgtctc aaaaacaaaa aaaaaaaaaa a 1051 <210> 2 <211> 75 <212> PRT
<213> Homo sapiens <400> 2 Met Gln Ile Ser Val Val Leu His Ile Leu Ile Tyr Ala Trp Leu Aap Tyr Ala Asp Ala Ser Gln Thr Trp Leu Leu Asn Asn Arg Met Gly Leu Ile Leu Ser Thr Ile Phe Ile Ser Ser Phe Lys Gln Ile Leu Leu Val Pro Met Trp Thr Phe Lys Asp Pro Leu Leu Asn Glu Met Ser Leu Ser Tyr Ser Phe Ala Phe Ile Val Lys Ala Ile Arg <210> 3 <211> 711 <212> DNA
<213> Homo Sapiens <400> 3 ttcaggttta gtgctattgt cattgaacac tggtattttc tgtatcatat naaacattaa 60 aattcaaata attataagca tttggcaaaa acaagagaaa agaaacttgc catattttac 120 aagctgcaat tttagaaaag ctttaactta atgatagttt tatcattgtt ttcttgtccc 180 aaacttatcc agggccatag aagtatgaat ctaattaaaa cagaaatggg aattattgca 240 cagaaatggg aaataactaa ttttaaatca gtcmaattgg cttcttatta aatacaataa 300 ttcttatgaa aatcatagta ccctattttc agacacagct gccagtttac acatttctca 360 gtatcctgaa aggaaaaaag tatagcccca cttatactat gtaaaattac caataaaata 420 tttttatgac tacagatttt gcatttttgt ttacaactat ttaaagagtt ttatgttgta 480 tttagaattt caacctagaa accacacagt acttaaattc tcctggggtc tcctgctttc 540 tcttaaccat ttgcttaata tatatctacc taaaggagac ttctgaattg taaatgaact 600 taaaaataga atgtggatgc aaaatatcac ataagacatc atgataacat ttgaagaaaa 660 aataaaactg tagaccctaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa a 711 <210> 4 <211> 46 <212> PRT
<213> Homo sapiens <220>
<221> UNSURE
<222> (42) <400> 4 Met Ile Val Leu Ser Leu Phe Ser Cys Pro Lys Leu Ile Gln Gly His Arg Ser Met Asn Leu Ile Lys Thr Glu Met Gly Ile Ile Ala Gln Lys Trp Glu Ile Thr Asn Phe Lys Ser Val Xaa Leu Ala Ser Tyr <210> 5 <211> 4529 <212> DaJA
<213> Homo sapiens <400> 5 cacctgggac ctctcacagg tggcatgccc ttccaagacc aggagagaac accacaactt 60 tgcaggacca gcatctctca gcctgcctcc tccctttctc catatcaata tgatatggat 120 gagtactcat ccagcattgg atgatatgga tgaatggtca tccatcccag agcactgtcc 180 ctactccagt tccagggcac tcttagtctg ttcttggcac atacagcttt gcatctgtca 240 gtgtccatgc aaaagccaac acaagctgtg atggactgtg cattgggtag ccaccagagg 300 taactgccac ttatctatca gtcagccttt gacaggcctc acgtagatac gtacctccca 360 tcacctccaa gctggaatac actttactca tctgtaaaat gggtatgaac atgcctcctt 420 tgcagarctt ttttgaagat tctgcattta ctagtttaac aactgttcag tacctattat 480 gggcctagct accggcacat agtaaacact cagttacaat agctttaaga aaatctgtct 540 wo ~i4ms4 rcTNS~rozs9s tagacaaagg agtttcaaaa ctatgtgaag agtatacaag aagtagtagt ccaaactgtt 600 ttttcagttg tttaatgatc tctatgataa agatgttcag ggagaggaat atcttgcgtg 660 ataactggag taaaacccac ttagatttct atgtccccaa acctctggtg tggtcagggt 720 tggcacctgc cctctcaacc atttgtctca ctgtacatgc atcttgtcta tgtcttccac 780 tagagaccat gagggcagag atcagaccta tgtacgttgc acattgctgt ccccagtacc 840 tagcacagca ccttgcccca gtacgcactt catatatatt tcctggacta cggcaggtga 900 gccctttgtg agggttccac ctgcccactg gcctggcctt taatgtcagg ggagcatttc 960 tgatatatta atgcccctct aattgtgctg cattcgttta cataggcagt gcagcagcct 1020 ggctttggtg tttaaagacc ggattgcagt caeagctctg ctgtttgctg gctatgaact 1080 ccaggtaagt tgccaggttc ctctgagcac taatgataat attacctgcc tcacagggtt 1140 gttttgagag cagcttctgc tgctgcccca tgccccagaa ttatggaaaa ccattttgta 1200 aacttcaagt cacttcctct ccatagtaca gatcaatggt agaccagtga tcagggagga 1260 tacaaatcat aaccccaaaa aaggcttctt tgttgtattt tacctcaagt gttttcttag 1320 agaacctcaa caaaccacac tattttctag taatcagcca cttatcccac catttgcagt 1380 aaggaaaact gaggcacgcc ttgatggctt attcagcatc agcagcctca caaaagacag 1440 aagtctcctt tggattagct ttatcatctt tcccttaagc agagatgatg gtgcctttct 1500 cgctgctctg gctcagttaa gaagtcaagt ctgatttatt ggtcatccta actatcgttt 1560 cctgaaggcc cgaagccctg taatgctgtt gtctggcttc ccagatttat gaccatggtt 1620 tctggccccc aacaatatct ggagttcggt ttacatattc acttccacca tccaatccaa 1680 atcctcccag gcagcaatca agctggggct gattcctcat ccatttgtgg gctcactttt 1740 tctggcaagt cagccttcat tctccaggac gcttagaagc cgcatgttgg cggtggattg 1800 tgctacggga aagagtgaat gtgtagcctg cacatttgaa gccttgctgg ggtagagagc 1860 aacgctactg ctcctggaat gtccaggcca ctgttagaaa ggccatctta ttccttagaa 1920 gagtctagcc ctgctgcagg cttcagaaac gtgtgctcta agctcgttcc tgctcatttg 1980 aagcagtctt ctgaaaaggt ctgcagaaac ctgcctttac cctctccctc atcctgcgtg 2040 gcctttgtca catccttcct ccaaggttcc tctggtggtg gtagtaggga ggctgccacc 2100 tggctttgca tgtgggaaag cccagcctct tccctccacc ctcacagcag gacagccaaa 2160 cttggatttt ttcatgagga agcaactctt atgagctctc tggttcagct ctctggttaa 2220 aagaccatac tgtgctgttt ctggggcagc acagacctgg ttgatcgtgt ccacaggaag 2280 aacagccttt gggattcatt agtctggtta agaccagccc tgcagcctcc tctgccagct 2340 atagaactat gtgttagagt tggtgctgaa gccagtcgca aacccatccc agatgcgtct 2400 ggtcttgttg atgttcaaat gccacctcct cctccaggaa gacttcacca cctccccaag 2460 gctgccttat gggctccttc tctgttccct ctcgactctc cccctctatc actatggcca 2520 ttttatagaa ttttaattat tgtctcgggt gtctccacta gactgtaagt atcaagtgtg 2580 tagagacttt tgtttcaact ctgtatcccc aaaattcagc atagttcata gcacatacag 2640 tactctcaat gcctgttgaa tgaataaaga gtctgcttgc atgtaaaact acagtggttt 2700 ggtcttggag acacttgttt tggaattctt ctactgatat ggacagcatc aagatgatgg 2760 gaaatgtatt ggtctgggat ttgttttgcc tacaaagttt cttatgttgg ctcatctcca 2820 actagataaa accctgagtc taggcttccc cttctaacaa agctgctata cctttatgga 2880 cctccatttt cctgtctgta aaatgagagt gtgggctagc tagaaaaatt tctggtgtcc 2940 cccttgctgc tttgtaattc tggagtacgt tcggagaaca ccccaatgtg acasaggatc 3000 tggaaattct tcatasaata ttcagggagg gagacaactc agggaacatg acaactgtct 3060 ggaattattt gaggggttgt catgtagasg atgaaaagga ttagattatc ttgaaaggcc 3120 ccacaggtta taaataagac caattattaa ttcattcaac aaatatttga gtacctgcca 3180 tgtgcaaggc actattctaa gcaataatga tgcagtaatg aatacaacag acaaaaatct 3240 tgttgccttt atggagttga cattctagtg aacagaaaca attcaaaaac aaacacaatg 3300 gagaggagct tcttggaccc tcaaaacgag ctgcctgtga actattgagc tctttgtgtt 3360 caggaatacg tttagtactt agaaatctgc ttccagtggc tgcttagact aaatgacctt 3420 gttaggtttt tttagcccag caatcccatg aatctaaggc tagcgaagat gtgtgatctc 3480 tctattctaa caccactaag ccaaatcatg acetcctctc aatggtaact gtcactctaa 3540 aaagagagat aaggtagatg cagtgggctg ttcttatgaa aaggcaccta aaaaatagta 3600 ctttagaaac atgcattgtg gtgggggtct gggtggaggg gttgcttttt cttgagatcc 3660 ctgtgatatt gaggatgaag aaagagaaac acagggggtg ggcaacttcc ttgaaggacc 3720 agagagagtg agtcatgagg aagagaagga ggagacagag aacaggagag ttggggatga 3780 agcctttgat gaggggagtg aggaggggca gaagtaggag acagacatga ggaaaccacc 3840 aactgaagtc ccagaaaccc agcctccgtc ccctctaggt cctactgccg tcatcctctt 3900 tctgtaaagg tgagagtcta ggtgcagtgt cccaggttcc aaacacaagt tcatactcat 3960 tgactagtgg gatgcccact gtgagagcag gaaggagggc tagagagatc taagagggca 4020 gaagccctgc cctgccagta ttttttgcct ccagccacct gctctgttct gagacatgcc 4080 tgagaccagc tgcctacagg gggaccaggg tctgtttctg ctgttaacct tggttccctc 4140 WO 99/41284 PGTNS99/02$98 ctgcattcct gcatgtgggg atgtagacag gaagcctgca ggtatggagc aattgaagca 4200 gagtctagat agagcccaga ctccttactt cccatagtac tattctgcat tttgtagtgc 4260 tgcttatgct tttcagtgtt tccacatcta tttactaata acatcatagt acaacagcaa 4320 gaacatggcc tcagaactca aagttctgga attctaatat tttatttgat tgtcagtatt 4380 tctgtgagat agataaaata ggaattattt cctctgatct gcaggtgagg aaactcagtc 4440 acagggagca catttatcca tacttgtgga gctatagtat aactagtatt aggacaagga 4500 tagccaacat agttaaaaaa aaaaaaaaa 4529 <210> 6 <211> 98 <212> PRT
<213> Homo sapiens <400> 6 Met Ile Ser Met Ile Lys Met Phe Arg Glu Arg Asn Ile Leu Arg Asp Asn Trp Ser Lys Thr His Leu Asp Phe Tyr Val Pro Lys Pro Leu Val 20 25 ~ 30 Trp Ser Gly Leu Ala Pro Ala Leu Ser Thr Ile Cys Leu Thr Val His Ala Ser Cys Leu Cys Leu Pro Leu Glu Thr Met Arg Ala Glu Ile Arg Pro Met Tyr Val Ala His Cys Cys Pro Gln Tyr Leu Ala Gln His Leu Ala Pro Val Arg Thr Ser Tyr Ile Phe Pro Gly Leu Arg Gln Val Ser Pro Leu <210> 7 <211> 3537 <212> DNA
<213> Homo sapiens <400> 7 aacttagatt tcttaaaact gtatacagat aactaatttt tattttgaaa tagcttttat 60 gttcttgtgt ttatgtaata gtcacattaa ttttgctctt ttggctttgt gttgtgttta 120 tttgatgact gttttattcg gtttaatttt ttcttgattt tgcaaattca tttttatcat 180 ctttaagtgg tggagtggcc atttcagctt gaaatatttc actgtcttta taatttcatt 240 ccatgcatgt gttttgtgtt tgtgacggtg tggtggtatt tagtctatag aagaacatgt 300 ggagcaggtc aaccaaaact gcatagcaga agattgccac atcaaggtag tattccaaga 360 tcttgtattt agctcattct ttaaagttca aggagctaac gcctcatctc tgatactaac 420 catgacctgc ccaactggct aactactcag agaactcata gtactcccat accacttcag 480 tggcacaggg gaggagatgc ttcactgtat ctggcttgct ctgtcttgcc cttggttctt 540 ctctttcttg ctccctgtcc catcttcact tgtcactttt tctgttttaa gcatggctgt 600 ttcatcttct tgattctgcc ttttctttcc ttcccatcac caaccctaag ccattgcatc 660 ttcctctcat cagtctcttt tattcctttc gaagtatccc tctttccaac ttttccttat 720 ttctgtctca ccacccttac ttcaaagggt ggtttctttg cggttttcta tggcttttta 780 ctccactctg tgcctcttaa tgtatacaca ttcttattgc agaatattta tgcacttttg 840 gaagagctaa gagagacata ctactgtata aattactaat aaaaatatat tagccatgtt 900 ttataattaa tcagtatctt accatcacag tggaaattgg ggtgattaca ggacatcaga 960 gaatttaagc aaattttcca aagctagttt tcaacacatt aaagttactc ttaccctttt 1020 ttcttgctgc tgctgctgct gctacatttt cttcttatcc tacatttaaa tcttatggga 1080 tgtgcataac tctaaataga gctgtgctgc agcaactaaa actgctgatg aatgttttct 1140 aggttgaagc tgatctgggc tatccaggtg gaaaggcgaa agtcatccat aaggaatctg 1200 atatgatcat ggcattttct gttaataagg caaattgtaa tgaaattgtt ttggcttcaa 1260 cacatgatgt tcaagaactt gatgttactt ctctactggc ctgtcagtca tacatatgga 1320 tcggagaaga atatgacaga gaatccaaaa gttcagatga tgttgattat cgtggttcca 1380 ctacaactct ttatcaaccc agtgcaacat cctattcagc aagtcaggtg catccacctt 1440 catctctgcc atggctgggc actggacaga ctagcactgg agctagtgtg cttatgaaaa 1500 ggaatctaca tsatgttaag agaatgactt cacacccagt ccatcsatac tatcttacag 1560 gtgctcagga cggcagtgta cgaatgtttg aatggacgcg gcctcagcaa cttgtctgct 1620 ttcgtcaagc tggcaatgca agagttacta gattatattt taattcacaa ggcaacaagt 1680 gtggtgttgc ggatggagag ggttttctga gtatctggca agttaaccaa actgcatcaa 1740 atcctaaacc ttatatgagt tggcagtgcc acagtaaagc cacaagtgac tttgcattta 1800 ttacctcttc aagtctagtt gccacatctg gacactccaa tgacaataga aatgtttgcc 1860 tctgggacac attaatatca cccggaaaca gcctcattca tggtttcacg tgccacgatc 1920 atggtgccac ggtactgcag tatgcaccca aacagcaact cctaatctcg gggggtagga 1980 aaggacacgt ctgcattttt gacatcaggc aaaggcagct cattcacacg ttccaggccc 2040 atgactcagc tattaaggct ctggccttgg atccctatga ggaatatttt accacaggtt 2100 cagcagaagg taacataaag gtttggagat tgacaggcca tggcctaatt cattcattta 2160 aaagtgaaca tgctaagcag tccatatttc gaaacattgg ggctggagtc atgcagattg 2220 acatcatcca gggcaatcgg ctcttctcct gtggtgcaga tggcacgctg aaaaccaggg 2280 ttttgcccaa tgcttttaac atccctsaca gaattcttga cattctataa agattggggt 2340 tttattttta tatacatttc agttaaaagg cacactacag tcatcactag gcaattctgc 2400 tttctaagca gttgtattga aaacagagaa tctctgtgta gaatttgaat atgacccaag 2460 ctgagtatta tctaaacagg ttggtggaat gaatgcgcat gtaccttatt atgctgacat 2520 actaaaaaaa ataaaaccta gtattgtatg aaggatagct attctttaca gcatttagca 2580 aacctgattc agaaaacatt tgagattagc aaattagtaa cttgaaataa tgaaaaggac 2640 gtttatacca aattaaggaa gaaaatgttg ctgatttggg tttttcttcc tgttcttacc 2700 actgactgaa gcatgcctgc agtctcctcc tctgttgaat gaaggataat cataaggtgt 2760 ttgttaggag cgctagacca cctggaaaac tttcttagct gtggagcagt gcgcagtgac 2820 cagttctctg ctgtgagagg ccgtttccat tctttcctgc tgaatatttt tcctgttagt 2880 gtttatactg agctagtact gtaacttgca aatgagtgca aatttaaatg caatgtttta 2940 ctcacaattt gcacattcac attttttgga ctgctagttt ttctatttaa atatttgcct 3000 tcatgttagg aatgtactat gtgaacatga catatttgta gttaaccaaa cacaccttct 3060 tagtccagtt tagtactttt tcttttcgtg tattcaaggt taaacaccca aacatttaag 3120 gatatgttga aactacacca atagagcatt tcatatcata attaaaatga atgttaggct 3180 tcttgtggcc agttaatagt tgatgagatt ggtgacatta tttattgcca cagcctattg 3240 tataaactat gcagagttaa atatttgctt gtaaaatatt agccaatgtt gtcattattt 3300 tgatgtattt ccttggttat gaccaaaaat atgttgagat actgaaacta atgtctgtgt 3360 gtttaaatgt ttaccagcaa attgtcttat catgttaatg agaatgttca atgcctgtgt 3420 ggtaaatagt aaatacaatg gcataaaagt aactttctct gaagatgtga tgttcaggct 3480 gtgaaatata tatgtaaaag aaaaataaat gttatttgtt agaaasaaaa aaaaaaa 3537 <210> 8 <211> 375 <212> PRT
<213> Homo sapiens <400> 8 Met Ile Met Ala Phe Ser Val Asn Lys Ala Asn Cys Asn Glu Ile Val Leu Ala Ser Thr His Asp Val Gln Glu Leu Asp Val Thr Ser Leu Leu Ala Cys Gln Ser Tyr Ile Trp Ile Gly Glu Glu Tyr Asp Arg Glu Ser Lys Ser Ser Asp Asp Val Asp Tyr Arg Gly Ser Thr Thr Thr Leu Tyr Gln Pro Ser Ala Thr Ser Tyr Ser Ala Ser Gln Val His Pro Pro Ser Ser Leu Pro Trp Leu Gly Thr Gly Gln Thr Ser Thr Gly Ala Ser Val Leu Met Lys Arg Asn Leu His Asn Val Lys Arg Met Thr Ser His Pro Val His Gln Tyr Tyr Leu Thr Gly Ala Gln Asp Gly Ser Val Arg Met Phe Glu Trp Thr Arg Pro Gln Gln Leu Val Cys Phe Arg Gln Ala Gly Asn Ala Arg Val Thr Arg Leu Tyr Phe Asn Ser Gln Gly Asn Lys Cys Gly Val Ala Asp Gly Glu Gly Phe Leu Ser Ile Trp Gln Val Asn Gln Thr Ala Ser Asn Pro Lys Pro Tyr Met Ser Trp Gln Cys His Ser Lys Ala Thr Ser Asp Phe Ala Phe Ile Thr Ser Ser Ser Leu Val Ala Thr Ser Gly His Ser Asn Asp Asn Arg Asn Val Cys Leu Trp Asp Thr Leu Ile Ser Pro Gly Asn Ser Leu Ile His Gly Phe Thr Cys His Asp His Gly Ala Thr Val Leu Gln Tyr Ala Pro Lys Gln Gln Leu Leu Ile Ser Gly Gly Arg Lys Gly His Val Cys Ile Phe Asp Ile Arg Gln Arg Gln Leu Ile His Thr Phe Gln Ala His Asp Ser Ala Ile Lys Ala Leu Ala Leu Asp Pro Tyr Glu Giu Tyr Phe Thr Thr Gly Ser Ala Glu Gly Asn Ile Lys Val Trp Arg Leu Thr Gly His Gly Leu Ile His Ser Phe Lys Ser Glu His Ala Lys Gln Ser Ile Phe Arg Asn Ile Gly Ala Gly Val Met Gln Ile Asp Ile Ile Gln Gly Asn Arg Leu Phe Ser Cys Gly Ala Asp Gly Thr Leu Lys Thr Arg Val Leu Pro Asn Ala Phe Asn Ile Pro Asn Arg Ile Leu Asp Ile Leu <210> 9 <211> 1466 <212> DNA
<213> Homo sapiens <400> 9 ccgcgcagga ggacggagcc ctaaccgcaa cccgcgccgc gccgcgccga tttgatttgt 60 atccactgtc accagcactg ctcacttagg actttctgga tccggaccca ggcagcgcac 120 actggactct tgaggaagaa ggagactcta attttggatt ccttggtgga ggaaaataaa 180 acactctggt cttgccgcca acgatgcaag tgtgactgct ggcgtcttca tgagctccag 240 aggtcacagc acgctaccaa ggactctcat ggcccctcgg atgatttccg agggagacat 300 argaggcatt gctcaaatca cctcctctct attcctgggc agaggcagtg tggcctccaa 360 tcggcacctc ctccaggctc gtggcatcac ctgcattgtt aatgctacca ttgagatccc 420 taatttcaac tggccccaat ttgagtatgt taaagtgcct ctggctgaca tgccgcatgc 480 ccccattgga ctgtactttg acaccgtggc tgacaagatc cacagtgtga gcaggaagca 540 cggggccacc ttggtgcact gtgctgcagg ggtgagccgc tcagccacgc tgtgtatcgc 600 gtacctgatg aaattccaca acgtgtgcct gctggaggcg tacaactggg tgaaagcccg 660 gcgacctgtc atcaggccca acgtaggctt ctggaggcaa ctgatagact acgagcgcca 720 gctctttggg aagtcgacag ttaaaatggt acagacacct tatggcatag ttcccgacgt 780 ctatgagaag gagtcccgac acctgatgcc ttactggggg atttagtgcc actgaagcct 840 gcgtcagcag cccgagcggg gccggcatct gctccccgcc gtctgctccc tctccactct 900 cttctcaaat ggctgacttc tggttctccc tcaagtgttt tttacactgg gtgttcaaat 960 ttattttaag agatagggag ggaggggaca taaagggaat gcatacattg ctagtcacat 1020 ttttaaaatt aacattttgg aatagtgttt atggaaatct ttagctttta atcattttta 1080 ccaatttgaa cagtttaata aactggttct gctctcttct gaatctcakg ccttkggcac 1140 cttggtaggt gcaggaggag ctcagtgcaa aaatcacttt ggggcctcat taacccttta 1200 gagacaagyt ttgccccagg ytgcggacca gacagatgyt tagggaaggt tgataccagc 1260 ttcagtctct astggattag ccctactctt tcctttcccc tccattattt agtgactctg 1320 taagtaagtt aaatacaccc ttattattta gctgttaagt aactataatg aaatctgctg 1380 caaaatctct cttggaatcc atgtgcccag gattatatta gcattatttt taataaatct 1440 atatgcttaa caaaaaaaaa aaaaaa 1466 <210> 10 <211> 198 <212> PRT
<213> Homo sapiens <220>
<221> UNSURE
<222> (25) <400> 10 Met Ser Ser Arg Gly His Ser Thr Leu Pro Arg Thr Leu Met Ala Pro Arg Met Ile Ser Glu Gly Asp .Ile Xaa Gly Ile Ala Gln Ile Thr Ser Ser Leu Phe Leu Gly Arg Gly Ser Val Ala Ser Asn Arg His Leu Leu Gln Ala Arg Gly Ile Thr Cys Ile Val Asn Ala Thr Ile Glu Ile Pro Asn Phe Asn Trp Pro Gln Phe Glu Tyr Val Lys Val Pro Leu Ala Asp Met Pro His Ala Pro Ile Gly Leu Tyr Phe Asp Thr Val Ala Asp Lys Ile His Ser Val Ser Arg Lys His Gly Als Thr Leu Val His Cys Ala Ala Gly VaI Ser Arg Ser Ala Thr Leu Cys Ile Ala Tyr Leu Met Lys Phe His Asn Val Cys Leu Leu Glu Ala Tyr Asn Trp Val Lys Ala Arg Arg Pro Val Ile Arg Pro Asn Val Gly Phe Trp Arg Gln Leu Ile Asp Tyr Glu Arg Gln Leu Phe Gly Lys Ser Thr Val Lys Met Val Gln Thr Pro Tyr Gly Ile Val Pro Asp Val Tyr Glu Lys Glu Ser Arg His Leu Met Pro Tyr Trp Gly Ile <210> 11 <211> 1521 <212> DNA
<213> Homo eapiens <400> 11 aatttcttgg gcatttaccc atgccagaag gctaacctgg ggggaggggg gcgcttgtgc 60 tggtgaggca cttggataca tactgatgct gcaagttcag gggatttttc ttactcttag 120 gtttaaccaa gaacactgag cagggaaaaa ccctgccttt cctaactgca tgtatttttt 180 cctttttgga aaggtggtag agactcagaa gctttccttg ttttcttcag gcctgctccc 240 agttttctta acagtttctt ttgttgcttt ctctctccct tgttgctttc catggcagta 300 atcctcctag agtccaagca gtctgttgta tggagcaggg tgtgtgggtt ttctgggccc 360 atcattatgg ctgcttcaga gtcagaagaa agccataggg cagtagggga gctcctattg 420 cctarcccct ctccctttgt ggctcccact ctagctgcct atttttgctc atcagctggt 480 gagtcagtat gggccagcag ttctccctcc ctaagccctt gctactttat gggttagctt 540 tgcaggtttg gtggcttgag gggtgggggc aactcaccac tgccaggtaa ctccctgaag 600 ggtgggagtg gattatcttc taggctctta cccgcggtag ggaagggcat caacactgtc 660 ttccttccat tctcctttcc cccatcccat ttagtgctgc cacagggcag aagcacacaa 720 accaaccaca cagtctctga cttctcctaa gcactttgag ttgttgaatg gggctcaggg 780 gcaagagttt ttgctgccct ccccagcgtg gtcacagggt tattgaactg cctgcacttg 840 tttctcatgc aactccagca ttttccccag aagttgaact atggatagca gcttggtatg 900 gatttcctaa atcttaacat ttgaagcagc ttcttgaggc tggcaactat cctggtttct 960 gtcttggagg gggtggtttg tttgctgggg cccaacgtct gtcccaagtg gtggggtgag 1020 agtaagttaa ctttggtgcc aggtgagagg tgggggctct ttgcttagac tccctatcat 1080 ggaaagattg gagttttcta tgcagggcac tggggaaaag gattgctgat tctgactgac 1140 cctgatcaga gagattagga ttgtattttg acataggatt tggaacccat ctaaatgttg 1200 aagttccctg agacrgctct ccagctgctg agcctgcgcc aggggytaag cagcccctaa 1260 tgagaggctc tgctcccttt cccacctcgc caatgttgtt gttgctgcct ttttgatttg 1320 tatcctctgt tatagacatt ttttraaaac gatttcctct ttcattgtgc acaagtgctg 1380 agagtctgag gccccatttc tgctgtgtat atatatcctg actcggggct tttattcagc 1440 aaactgttca ttcttctgtc agacaatgtc atattcaact ctgttcatat taaaccactg 1500 tgaagcaaaa aaaaaaaaaa a 1521 <210> 12 <211> 81 <212> PRT
<213> Homo sapiens g <220>
<221> UNSURE
<222> (45) <400> 12 Met Ala Val Ile Leu Leu Glu Ser Lys Gln Ser Val Val Trp Ser Arg Val C)rs Gly Phe Ser Gly Pro Ile Ile Met Ala Ala Ser Glu Ser Glu Glu Ser His Arg Ala Val Gly Glu Leu Leu Leu Pro Xaa Pro Ser Pro Phe Val Ala Pro Thr Leu Ala Ala Tyr Phe Cys Ser Ser Ala Gly Glu Ser Val Trp Ala Ser Ser Ser Pro Ser Leu Ser Pro Cys Tyr Phe Met 65 70 75 gp Gly <210> 13 <211> 19 <212> DNA
<213> Artificial Sequence <220>
<223> oligonucleotide <400> 13 ggatggggct cattctctc 19 <210> 14 <211> 20 <212> DNA
<213> Artificial Sequence <220>
<223> oligonucleotide <400> 14 gaaatgtgta aactggcagc 20 <210> 15 <211> 21 <212> DNA
<213> Artificial Sequence <220>
<223> oligonucleotide <400> 15 gaatgcagca caattagagg g 21 <210> 16 <211> 21 <212> DT1A
<213> Artificial Sequence <220>
<223> oligonucleotide <400> 16 ctgcttagaa agcagaattg c 21 <210> 17 <211> 19 <212> DNA
<213> Artificial Sequence <220>
<223> oligonucleotfde <400> 17 tgtgactagc aatgtatgc 19 <210> 18 <211> 20 <212> DNA
<213> Artificial Sequence <220>
<223> oligonucleotide <400> 18 tcagaagaaa gccatagggc 20 <210> 19 <211> 113 <212> PRT
<213> Homo sapiens <400> 19 Met Ser Arg pro Leu Leu Glu Arg pro Ser Tyr Ser Leu Glu Glu Ser Ser Pro Ala Ala Gly Phe Arg Asn Val Cys Ser Lya Leu Val Pro Ala His Leu Lys Gln Ser Ser Glu Lys Val Cys Arg Asn Leu Pro Leu Pro Ser Pro Ser Ser Cys Val Ala Phe Val Thr Ser Phe Leu Gln Gly Ser Ser Gly Gly Gly Ser Arg Glu Ala Ala Thr Trp Leu Cys Met Trp Glu Ser Pro Ala Ser Ser Leu His Pro His Ser Arg Thr Ala Lys Leu Gly Phe Phe His Glu Glu Ala Thr Leu Met Ser Ser Leu Val Gln Leu Ser Gly
140:508-512, 1988.
Immun_P S 'm ~la 'n~ or ynressi_ng Acti ~it;, A protein of the present invention may also exhibit immune stimulating or immune suppressing activity, including without limitation the activities for which assays are described herein. A protein may be useful in the treatment of various immune deficiencies and disorders (including severe combined immunodeficiency (SCID)), e.g., 2 0 in regulating (up or down) growth and proliferation of T and/or B
lymphocytes, as well as effecting the cytolytic activity of NK cells and other cell populations.
These immune deficiencies may be genetic or be caused by viral (e.g., HIV) as well as bacterial or fungal infections, or may result from autoimmune disorders. More specifically, infectious diseases causes by viral, bacterial, fungal or other infection may be treatable using a protein of the present invention, including infections by HIV, hepatitis viruses, herpesvinuses, mycobacteria, Leishmania spp., malaria spp. and various fungal infections such as candidiasis. Of course, in this regard, a protein of the present invention may also be useful where a boost to the immune system generally may be desirable, i.e., in the treatment of cancer.
3 0 Autoimmune disorders which may be treated using a protein of the present invention include, for example, connective tissue disease, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, autoimmune pulmonary inflammation, Guillain-Barre syndrome, autoimmune thyroiditis, insulin dependent diabetes mellitis, myasthenia gravis, graft versus-host disease and autoimmune inflammatory eye disease.
Such a protein of the present invention may also to be useful in the treatment of allergic reactions and conditions, such as asthma (particularly allergic asthma) or other respiratory problems. Other conditions, in which immune suppression is desired (including, for example, organ transplantation), may also be treatable using a protein of the present invention.
Using the proteins of the invention it may also be possible to regulate immune responses in a number of ways. Down regulation may be in the form of inhibiting or blocking an immune response already in progress or may involve preventing the induction of an immune response. The functions of activated T cells may be inhibited by suppressing T cell responses or by inducing specific tolerance in T cells, or both.
Immunosuppression of T cell responses is generally an active, non-antigen-specific, process which requires continuous exposure of the T cells to the suppressive agent.
Tolerance, which involves inducing non-responsiveness or anergy in T cells, is distinguishable from immunosuppression in that it is generally antigen-specific and persists after exposure to the tolerizing agent has ceased. Operationally, tolerance can be demonstrated by the lack of a T cell response upon reexposure to specific antigen in the absence of the tolerizing agent.
Down regulating or preventing one or more antigen functions (including without limitation B lymphocyte antigen functions (such as , for example, B~), e.g., preventing 2 0 high level lymphokine synthesis by activated T cells, will be useful in situations of tissue, skin and organ transplantation and in graft versus-host disease (GVHD). For example, blockage of T cell function should result in reduced tissue destruction in tissue transplantation. Typically, in tissue transplants, rejection of the transplant is initiated through its recognition as foreign by T cells, followed by an immune reaction that destroys 2 5 the transplant. The administration of a molecule which inhibits or blocks interac#ion of a B7 lymphocyte antigen with its natural ligand(s) on immune cells (such as a soluble, monomeric form of a peptide having B7 2 activity alone or in conjunction with a monomeric form of a peptide having an activity of another B lymphocyte antigen (eg., B7 1, B7-3) or blocking antibody), prior to transplantation can lead to the binding of the 3 0 molecule to the natural ligand(s) on the immune cells without transmitting the corresponding costimulatory signal. Blocking B lymphocyte antigen function in this matter prevents cytokine synthesis by immune cells, such as T cells, and thus acts as an immunosuppressant. Moreover, the lack of costimulation may also be sufficient to anergize the T cells, thereby inducing tolerance in a subject. Induction of long-term WO 99/411,$4 PGTNS99/02898 tolerance by B lymphocyte antigen-blocking reagents may avoid the necessity of repeated administration of these blocking reagents. To achieve sufficient immunosuppression or tolerance in a subject, it may also be necessary to block the function of a combination of B lymphocyte antigens.
The efficacy of particular blocking reagents in preventing organ transplant rejection or GVI3D can be assessed using animal models that are predictive of efficacy in humans. Examples of appropriate systems which can be used include allogeneic cardiac grafts in rats and xenogeneic pancreatic islet cell grafts in mice, both of which have been used to examine the immunosuppressive effects of CTLA4Ig fusion proteins in vivo as described in Lenschow et al., Science 257:789-792 (1992) and Turka et al., Proc. Natl. Acad.
Sci USA, 89:11102-11105 (1992). In addition, marine models of GVI3D (see Paul ed., Fundamental Immunology, Raven Press, New York, 1989, pp. 846-847) can be used to determine the effect of blocking B lymphocyte antigen function in vivo on the development of that disease.
Blocking antigen function may also be therapeutically useful for treating autoimmune diseases. Many autoimmune disorders are the result of inappropriate activation of T cells that are reactive against self tissue and which promote the production of cytokines and autoantibodies involved in the pathology of the diseases.
Preventing the activation of autoreactive T cells may reduce or eliminate disease symptoms.
2 0 Administration of reagents which block costimulation of T cells by disrupting receptor:ligand interactions of B lymphocyte antigens can be used to inhibit T
cell activation and prevent production of autoantibodies or T cell-derived cytokines which may be involved in the disease process. Additionally, blocking reagents may induce antigen-specific tolerance of autoreactive T cells which could lead to long-term relief from 2 5 the disease. The efficacy of blockimg reagents in preventing or alleviating autoimmune disorders can be determined using a number of well-characterized animal models of human autoimmune diseases. Examples include marine experimental autoimmune encephalitis, systemic lupus erythmatosis in MRL/lpr/lpr mice or NZB hybrid mice, marine autoimmune collagen arthritis, diabetes mellitus in NOD mice and BB
rats, and 3 0 marine experimental myasthenia gravis (see Paul ed., Fundamental Immunology, Raven Press, New York,1989, pp. 840-856).
Upregulation of an antigen function (preferably a B lymphocyte antigen function), as a means of up regulating immune responses, may also be useful in therapy.
Upregulation of immune responses may be in the form of enhancing an existing immune response or eliciting an initial immune response. For example, enhancing an immune response through stimulating B lymphocyte antigen function may be useful in cases of viral infection. In addition, systemic viral diseases such as influenza, the common cold, and encephalitis might be alleviated by the administration of stimulatory forms of B
lymphocyte antigens systemically.
Alternatively, anti-viral immune responses may be enhanced in an infected patient by removing T cells from the patient, costimulating the T cells in vitro with viral antigen-pulsed APCs either expressing a peptide of the present invention or together with a stimulatory form of a soluble peptide of the present invention and reintroducing the in vitro activated T cells into the patient. Another method of enhancing anti-viral immune responses would be to isolate infected cells from a patient, transfect them with a nucleic acid encoding a protein of the present invention as described herein such that the cells express all or a portion of the protein on their surface, and reintroduce the transfected cells into the patient. The infected cells would now be capable of delivering a costimulatory signal to, and thereby activate, T cells in vivo.
In another application, up regulation or enhancement of antigen function (preferably B lymphocyte antigen function) may be useful in the induction of tumor immunity. Tumor cells (eg., sarcoma, melanoma, lymphoma, leukemia, neuroblastoma, carcinoma) transfected with a nucleic acid encoding at least one peptide of the present 2 0 invention can be administered to a subject to overcome tumor-specific tolerance in the subject. If desired, the tumor cell can be transfected to express a combination of peptides.
For example, tumor cells obtained from a patient can be transfected ex vivo with an expression vector directing the expression of a peptide having B7 2-like activity alone, or in conjunction with a peptide having B7-1-like activity and/or B7-3-like activity. The 2 5 transfected tumor reps are returned to the patient to result in expression of the peptides on the surface of the transfecbed cell. Alternatively, gene therapy techniques can be used to target a tumor cell for transfection in vivo.
The presence of the peptide of the present invention having the activity of a B
lymphocyte antigens) on the surface of the tumor cell provides the necessary 3 0 costimulation signal to T cells to induce a T cell mediated immune response against the trai~sfected tumor cells. In addition, tumor cells which lack MHC class I or MHC class II
molecules, or which fail to reexpress sufficient amounts of MHC class I or MFIC class II
molecules, can be transfected with nucleic acid encoding all or a portion of (e.g., a cytoplasmic-domain truncated portion) of an MHC class I a chain protein and ~i2 microglobulin protein or an MHC class II a chain protein and an MHC class II
~i chain protein to thereby express MHC class I or MHC class II proteins on the cell surface.
Expression of the appropriate class I or class II MHC in conjunction with a peptide having the activity of a B lymphocyte antigen (e.g., B7-1, B7-2, B7 3) induces a T
cell mediated immune response against the transfected tumor cell. Optionally, a gene encoding an antisense construct which blocks expression of an MHC class II associated protein, such as the invariant chain, can also be cotransfected with a DNA encoding a peptide having the activity of a B lymphocyte antigen to promote presentation of tumor associated antigens and induce tumor specific immunity. Thus, the induction of a T cell mediated immune response in a human subject may be sufficient to overcome tumor-specific tolerance in the subject.
The activity of a protein of the invention may, among other means, be measured by the following methods:
Suitable assays for thymocyte or splenocyte cytotoxicity include, without limitation, those described in: Current protocols in Immunology, Ed by j. E.
Coligan, A.M.
Kruisbeek, D.H. Margulies, E.M. Shevach, W Strober, Pub. Greene Publishing Associates and Wiley-Interscience (Chapter 3,1n Vitro assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7, Immunologic studies in Humans); Herrmann et al., Proc. Natl.
Acad. Sci.
USA 78:2488-2492,1981; Herrmann et al., J. Immunol.128:1968-1974,1982; Handa et al., 2 0 J. Immunol.135:1564-1572,1985; Takai et al., J. Immunol.137:3494-3500,1986; Takai et al., J. Imrnunol.140:508-512, 1988; Herrmann et al., Proc. Natl. Acad. Sci. USA
78:2488-2492, 1981; Hemnann et al., J. Immunol. 128:1968-1974, 1982; Handa et al., J.
Immunol.
135:1564-1572, 1985; Takai et al., J. lmmunol. 137:3494-3500, 1986; Bowmanet al., j.
Virology 61:1992-1998; Takai et al., J. Immunol. 140:508-512, 1988;
Bertagnolli et al., 2 5 Cellular Immunology 133:327 341,1991; Brown et al., J. Immunol.153:3079-3092, 1994.
Assays for T-cell-dependent immunoglobulin responses and isotype switching (which will identify, among others, proteins that modulate T-cell dependent antibody responses and that affect Thl /Th2 profiles) include, without limitation, those described in: Maliszewski, J. Immunol.144:3028-3033,1990; and Assays for B cell function: In vitro 3 0 antibody production, Mond, J.J. and Brunswick, M. In Current Protocols in Immunology.
J.E.e.a. Coligan eds. Vol 1 pp. 3.8.1-3.8.16, John Wiley and Sons, Toronto.1994.
Mixed lymphocyte reaction (MLR) assays (which will identify, among others, proteins that generate predominantly Thl and CTL responses) include, without limitation, those described in: Current Protocols in Immunology, Ed by J. E. Coligan, A.M.
ICruisbeek, wo 99iaizsa rcrnrs~ro2s9s D.H. Margulies, E.M. Shevach, W Strober, Pub. Greene Publishing Associates and Wiley-lnterscience (Chapfier 3, In Vitro assays for Mouse Lymphocyte Function 3.1-3.19; Chapter 7, Immunologic studies in Humans); Takai et al., J. Immunol.137:3494-3500,1986; Takai et al., J. Immunol.140:508-512, 1988; Bertagnolli et al., J. Immunol.149:3778-3783,1992.
Dendritic cell-dependent assays (which will identify, among others, proteins expressed by dendritic cells that activate naive T-cells) include, without limitation, those described in: Guery et al., J. hnmunol. 134:536-544, 1995; Inaba et al., Journal of Experimental Medicine 173:549-559, 1991; Macatonia et al., Journal of Immunology 154:5071-5079,1995; Porgador et al., Journal of Experimental Medicine 182:255-260,1995;
Nair et al., Journal of Virology 67:4062-4069, 1993; Huang et al., Science 264:961-965, 1994; Macatonia et al., Journal of Experimental Medicine 169:1255-1264,1989;
Bhardwaj et al., Journal of Clinical Investigation 94:797-807, 1994; and lnaba et al., journal of Experimental Medicine 172:631-640,1990.
Assays for lymphocyte survival/apoptosis (which will identify, among others, proteins that prevent apoptosis after superantigen induction and proteins that regulate lymphocyte homeostasis) include, without limitation, those described in:
Darzynkiewicz et al., Cytometry 13:795-808,1992; Gorczyca et al., Leukemia 7:659-670,1993;
Gorczyca et al., Cancer Research 53:1945-1951, 1993; Itoh et al., Cell 66:233-243, 1991;
Zacharchuk, Journal of Immunology 145:4037-4045, 1990; Zamai et al., Cytometry 14:891-897, 1993;
2 0 Gorczyca et al., International Journal of Oncology 1:639-648,1992.
Assays for proteins that influence early steps of T-cell commitment and development include, without limitation, those described in: Antica et al., Blood 84:111-117, 1994; Fine et al., Cellular Immunology 155:111-122,1994; Galy et al., Blood 85:2770-2778,1995; Toki et al., Proc. Nat. Acad Sci. USA 88:7548-7551,1991.
HematopoiesL ReeLati-ng A
A protein of the present invention may be useful in regulation of hematopoiesis and, consequently, in the treatment of myeloid or lymphoid cell deficiencies.
Even marginal biological activity in support of colony forming cells or of factor-dependent cell 3 0 lines indicafies involvement in regulating heznatopoiesis, e.g. in supporting the growth and proliferation of erythroid progenitor cells alone or in combination with other cytokines, thereby indicating utility, for example, in treating various anemias or for use in conjunction with irradiation/chemotherapy to stimulate the production of erythroid precursors and/or erythroid cells; in supporting the growth and proliferation of myeloid cells such as granulocyfies and monocytes/macrophages (i.e., traditional CSF
activity) useful, for example, in conjunction with chemotherapy to prevent or treat consequent myelo-suppression; in supporting the growth and proliferation of megakaryocytes and consequently of platelets thereby allowing prevention or treatment of various platelet disorders such as thrombocytopenia, and generally for use in place of or complimentary to platelet transfusions; and/or in supporting the growth and proliferation of hematopoietic stem cells which are capable of maturing to any and all of the above-mentioned hematopoietic cells and therefore find therapeutic utility in various stem cell disorders (such as those usually treated with transplantation, including, without limitation, aplastic anemia and paroxysmal nocturnal hemoglobinuria), as well as in repopulating the stem cell compartment post irradiation/chemotherapy, either in-vivo or ex-vivo (i.e., in conjunction with bone marrow transplantation or with peripheral progenitor cell transplantation (homologous or heterologous)) as normal cells or genetically manipulated for gene therapy.
The activity of a protein of the invention may, among other means, be measured by the following methods:
Suitable assays for proliferation and differentiation of various hematopoietic lines are cited above.
Assays for embryonic stem cell differentiation (which will identify, among others, 2 0 proteins that influence embryonic differentiation hematopoiesis) include, without limitation, those described in: Johansson et al. Cellular Biology 15:141-151,1995; Keller et al., Molecular and Cellular Biology 13:473-486, 1993; McClanahan et al., Blood 81:2903-2915,1993.
Assays for stem cell survival and differentiation {which will identify, among 2 5 others, proteins that regulate lympho-hematopoiesis) include, without limitation, those described in: Methylcellulose colony forming assays, Freshney, M.G. In Culture of Hematopoietic Cells. R.I. Freshney, et al. eds. Vol pp. 265-268, Whey-Liss, Inc., New York, NY. 1994; Hirayama et al., Proc. Natl. Acad. Sci. USA 89:5907 5911, 1992;
Primitive hematopoietic colony forming cells with high proliferative potential, McNiece, LK. and 3 0 Briddell, R.A. In Culture of Hemutopoietic Cells. R.I. Freshney, et al.
eds. Vol pp. 23-39, Wiley-Liss, Inc., New York, NY.1994; Neben et al., Experimental Hematology 22:353-359, 1994; Cobblestone area forming cell assay, Ploemacher, R.E. In Culture of Hematopoietic Cells. R.I. Freshney, et al. eds. Vol pp.1-21, Whey Liss, Inc.., New York, NY.1994; Long term bone marrow cultures in the presence of stromal cells, Spooncer, E., Dexter, M. and Allen, T. In Culture of Hemutopoietic Cells. R.I. Freshney, et al. eds. Vol pp. 163-179, Hliley-hiss, Inc., New York, NY.1994; Long term culture initiating cell assay, Sutherland, H.J. In Culture of Hematopoietic Cells. RI. Freshney, et al. eds. Vol pp.139-162, Wiley-Liss, Inc., New York, NY.1994.
A protein of the present invention also may have utility in compositions used for bone, cartilage, tendon, ligament and / or nerve tissue growth or regeneration, as well as for wound healing and tissue repair and replacement, and in the treatment of burns, incisions and ulcers.
A protein of the present invention, which induces cartilage and/or bone growth in circumstances where bone is not normally formed, has application in the healing of bone fractures and cartilage damage or defects in humans and other animals.
Such a preparation employing a protein of the invention may have prophylactic use in closed as well as open fracture reduction and also in the improved fixation of artificial joints. De novo bone formation induced by an osteogeruc agent contributes to the repair of congenital, trauma induced, or oncologic resection induced craniofacial defects, and also is useful in cosmetic plastic surgery.
A protein of this invention may also be used in the treatment of periodontal 2 0 disease, and in other tooth repair processes. Such agents may provide an environment to attract bone-forming cells, stimulate growth of bone-forming cells or induce differentiation of progenitors of bone-forming cells. A protein of the invention may also be useful in the treatment of osteoporosis or osteoarthritis, such as through stimulation of bone and/or cartilage repair or by blocking inflammation or processes of tissue destruction (collagenase activity, osteoclast activity, etc.) mediated by inflammatory processes.
Another category of tissue regeneration activity that may be attributable to the protein of the present invention is tendon/ligament formation. A protein of the present invention, which induces tendon/ligament-like tissue or other tissue formation in 3 0 circumstances where such tissue is not normally formed, has application in the healing of tendon or ligament tears, deformities and other tendon or ligament defects in humans and other animals. Such a preparation employing a tendon/ligament like tissue inducing protein may have prophylactic use in preventing damage to tendon or ligament tissue, as well as use in the improved fixation of tendon or ligament to bone or other tissues, and in repairing defects to tendon or ligament tissue. De novo tsndon/ligament like tissue formation induced by a composition of the present invention contributes to the repair of congenital, trauma induced, or other tendon or ligament defects of other origin, and is also useful in cosmetic plastic surgery for attachment or repair of tendons or ligaments. The compositions of the present invention may provide an environment to attract tendon- or ligament forming cells, stimulate growth of tendon- or ligament-forming cells, induce differentiation of progenitors of tendon or ligament-forming cells, or induce growth of tendon/ligament cells or progenitors ex vivo for return in vivo to effect tissue repair. The compositions of the invention may also be useful in the treatment of tendinitis, carpal tunnel syndrome and other tendon or ligament defects. The compositions may also include an appropriate matrix and/or sequestering agent as a carrier as is well known in the art.
The protein of the present invention may also be useful for proliferation of neural cells and for regeneration of nerve and brain tissue, i.e. for the treatment of central and peripheral nervous system diseases and neuropathies, as well as mechanical and traumatic disorders, which involve degeneration, death or trauma to neural cells or nerve tissue. More specifically, a protein may be used in the treatment of diseases of the peripheral nervous system, such as peripheral nerve injuries, peripheral neuropathy and localized neuropathies, and central nervous system diseases, such as Alzheimer's, 2 0 Parkinson s disease, Huntington's disease, amyotrophic lateral sclerosis, and Shy-Drager syndrome. Further conditions which may be treated in accordance with the present invention include mechanical and traumatic disorders, such as spinal cord disorders, head trauma and cerebrovasculai diseases such as stroke. Peripheral neuropathies resulting from chemotherapy or other medical therapies may also be treatable using a protein of the 2 5 invention.
Proteins of the invention may also be useful to promote better or faster closure of non-healing wounds, including without limitation pressure ulcers, ulcers associated with vascular insufficiency, surgical and traumatic wounds, and the like.
It is expected that a protein of the present invention may also exhibit activity for 3 0 generation or regeneration of other tissues, such as organs (including, for example, pancreas, liver, intestine, kidney, skin, endothelium), muscle (smooth, skeletal or cardiac) and vascular (including vascular endothelium) tissue, or for promoting the growth of cells comprising such tissues. Part of the desired effects may be by inhibition or modulation WO 99/41284 PG"f/US99/02898 of fibrotic scarring to allow normal tissue to regenerate. A protein of the invention may also exhibit angiogenic activity.
A protein of the present invention may also be useful for gut protection or regeneration and treatment of lung or liver fibrosis, reperfusion injury in various tissues, and conditions resulting from systemic cytokine damage.
A protein of the present invention may also be useful for promoting or inhibiting differentiation of tissues described above from precursor tissues or cells; or for inhibiting the growth of tissues described above.
The activity of a protein of the invention may, among other means, be measured by the following methods:
Assays for tissue generation activity include, without limitation, those described in: International Patent Publication No. W095/16035 (bone, cartilage, tendon);
Infiernational Patent Publication No. W095/05846 (nerve, neuronal);
International Patent Publication No. W091/07491 (skin, endothelium ).
Assays for wound healing activity include, without limitation, those described in:
Winter, ~idermal Wound Healing. pps. 71-112 (Maibach, HI and Rovee, DT, eds.), Year Book Medical Publishers, Inc., Chicago, as modified by Eaglstein and Mertz, J.
Invest.
Dermatol 71:382-84 (1978).
2 0 ~,ctivin/Inhibin ActiY~
A protein of the present invention may also exhibit activin- or inhibin-related activities. Inhibins are characterized by their ability to inhibit the release of follicle stimulating hormone (FSH), while activins and are characterized by their ability to stimulate the release of follicle stimulating hormone (FSH). Thus, a protein of the present 2 5 invention, alone or in heterodimers with a member of the inhibin a family, may be useful as a contraceptive based on the ability of inhibins to decrease fertility in female mammals and decrease spermatogenesis in male mammals. Administration of sufficient amounts of other inhibins can induce infertility in these mammals. Alternatively, the protein of the invention, as a homodimer or as a heterodimer with other protein subunits of the inhibin-3 0 (3 group, may be useful as a fertility inducing therapeutic, based upon the ability of activin molecules in stimulating FSH release from cells of the anterior pituitary.
See, for example, United States Patent 4,798,885. A protein of the invention may also be useful for advancement of the onset of fertility in sexually immature mammals, so as to increase the lifetime reproductive performance of domestic animals such as cows, sheep and pigs.
The activity of a protein of the invention may, among other means, be measured by the following methods:
Assays for activin/inh~in activity include, without limitation, those described in:
Vale et al., Endocrinology 91:562-572,1972; Ling et al., Nature 321:779-782,1986; Vale et al., Nature 321:776-779,1986; Mason et al., Nature 318:659-663,1985; Forage et al., Proc.
Nail. Acad. Sci. USA 83:3091-3095,1986.
A protein of the present invention may have chemotactic or chemokinetic activity (e.g., act as a chemokine) for mammalian cells, including, for example, monocytes, fibroblasts, neutrophils, T-cells, mast cells, eosinophils, epithelial and/or endothelial cells.
Glemotactic and chemokinetic proteins can be used to mobilize or attract a desired cell population to a desired site of action. Chemotactic or chemokinetic proteins provide particular advantages in treatment of wounds and other trauma to tissues, as well as in treatment of localized infections. For example, attraction of lymphocytes, monocytes or neutrophils to tumors or sites of infection may result in improved immune responses against the tumor or infecting agent.
A protein or peptide has chemotactic activity for a particular cell population if it can stimulate, directly or indirectly, the directed orientation or movement of such cell 2 0 population. Preferably, the protein or peptide has the ability to directly stimulate directed movement of cells. Whether a particular prod ~ ~~o~~c activity for a population of cells can be readily determined by employing such protein or peptide in any known assay for cell chemotaxis.
The activity of a protein of the invention may, among other means, be measured 2 5 by the following methods:
Assays for chemotactic activity (which will identify proteins that induce or prevent chemotaxis) consist of assays that measure the ability of a protein to induce the migration of cells across a membrane as well as the ability of a protein to induce the adhesion of one cell population to another cell population. Suitable assays for movement and adhesion 3 0 include, without limitation, those described in: Current Protocols in Immunology, Ed by J.E. Coligan, A.M. Kruisbeek, D.H. Margulies, E.M. Shevach, W.Strober, Pub.
Greene Publishing Associates and Wiley Interscience (Chapter 6.12, Measurement of alpha and beta Chemokines 6.12.1-6.12.28; Taub et al. J. Gin. Invest. 95:1370-1376,1995;
Lind et al.
APMIS 103:140-146,1995; Muller et al Eur. J. Immunol. 25: 1744-1748; Gruber et al. J. of Immunol.152:5860-5867,1994; Johnston et al. J. of Immunol.153:1762-1768,1994.
Hemostatic and Thrombolytic Activity A protein of the invention may also exhibit hemostatic or thrombolytic activity.
As a result, such a protein is expected to be useful in treatment of various rnagulation disorders (including hereditary disorders, such as hemophiliac) or to enhance coagulation and other hemostatic events in treating wounds resulting from trauma, surgery or other causes. A protein of the invention may also be useful for dissolving or inhibiting formation of thromboses and for treatment and prevention of conditions resulting therefrom (such as, for example, infarction of cardiac and central nervous system vessels (e.g., stroke).
The activity of a protein of the invention may, among other means, be measured by the following methods:
Assay for hemostatic and thrombolytic activity include, without limitation, those described in: Linet et al., J. Clin. Pharmacol. 26:131-140,1986; Burdick et al., Thrombosis Res. 45:413-419,1987; Humphrey et al., Fibrinolysis 5:71-79 (I991); Schaub, Prostaglandins 35:467-474,1988.
2 0 ~tor /Ligand A protein of the present invention may also demonstrate activity as receptors, receptor ligands or inhibitors or agonises of receptor/ligand interactions.
Examples of such receptors and ligands include, without limitation, cytokine receptors and their ligands, receptor kinases and their ligands, receptor phosphatases and their ligands, 2 5 receptors involved in cell-cell interactions and their ligands (including without limitation, cellular adhesion molecules (such as selectins, integrins and their ligands) and receptor/ligand pairs involved in antigen presentation, antigen recognition and development of rellular and humoral immune responses). Receptors and ligands are also useful for screening of potential peptide or small molecule inhibitors of the relevant 3 0 receptor/ligand interaction. A protein of the present invention (including, without limitation, fragments of receptors and ligands) may themselves be useful as inhibitors of receptor/ligand interactions.
The activity of a protein of the invention may, among other means, be measured by the following methods:
WO 99/41284 PC"T/US99/OZ898 Suitable assays for receptor-ligand activity include without limitation those described in:Current Protocols in Immunology, Ed by J.E. Coligan, A.M.
ICruisbeek, D.H.
Margulies, E.M. Shevach, W.Strober, Pub. Greene Publishing Associates and Wiley-Intersrience (Chapter 7.28, Measurement of Cellular Adhesion under static conditions 7.28.1-7.28.22), Takai et al., Proc. Natl. Acad. Sci. USA 84:6864-6868, 1987;
Bierer et al., J. Exp. Med.168:1145-1156, 1988; Rosenstein et al., J. Exp.
Med.169:149-160 1989; Stoltenborg et al., J. Immunol. Methods 175:59-68,1994; Stitt et al., Cell 80:661-670, 1995.
Proteins of the present invention may also exhibit anti-inflammatory activity.
The anti-inflammatory activity may be achieved by providing a stimulus to cells involved in the inNamnnatory response, by inhibiting or promoting cell-cell interactions (such as, for example, cell adhesion), by inhibiting or promoting chemotaxis of cells involved in the inflammatory process, inhibiting or promoting cell extravasation, or by stimulating or suppressing production of other factors which more directly inhibit or promote an inflammatory response. Proteins exhibiting such activities can be used to treat inflammatory conditions including chronic or acute conditions), including without limitation inflammation associated with infection (such as septic shock, sepsis or systemic 2 0 inflammatory response syndrome (SIRS)), ischemia-reperfusion injury, endotoxin lethality, arthritis, complement mediated hyperacute rejection, nephritis, cytokine or chemokine-induced lung injury, inflammatory bowel disease, Crohn's disease or resulting fpm over production of cytokines such as TNF or ILrl. Proteins of the invention may also be useful to treat anaphylaxis and hypexsensitivity to an antigenic substance or material.
Cadherins are calcium-dependent adhesion molecules that appear to play major roles during development, particularly in defining specific cell types. Loss or alteration of normal cadherin expression can lead to changes in cell adhesion properties linked to 3 0 tumor growth and metastasis. Cadherin malfunction is also implicated in other human diseases, such as pemphigus vulgaris and pemphigus foliaceus (auto-immune blistering skin diseases), Crohn's disease, and some developmental abnormalities.
The cadherin superfamily includes well over forty members, each with a distinct pattern of expression. All members of the superfamily have in common conserved extracellular repeats (cadherin domains), but structural differences are found in other parts of the molecule. The cadherin domains bind calcium to form their tertiary structure and thus calcium is required to mediate their adhesion. Only a few amino acids in the first cadherin domain provide the basis for homophilic adhesion; modification of this recognition site can change the specificity of a cadherin so that instead of recognizing only itself, the mutant molecule can now also bind to a different cadherin. In addition, some cadherins engage in heterophilic adhesion with other cadherins.
E-cadherin, one member of the cadherin supex~family, is expressed in epithelial cell types. Pathologically, if E-cadherin expression is lost in a tumor, the malignant cells become invasive and the cancer metastasizes. Transfection of cancer cell lines with polynucleotides expressing E-cadherin has reversed cancer-associated changes by returning altered cell shapes to normal, restoring cells adhesiveness to each other and to their substrate, decreasing the cell growth rate, and drastically reducing anchorage-independent cell growth. Thus, reintroducing E-cadherin expression reverts carcinomas to a less advanced stage. It is likely that other cadherins have the same invasion suppressor role in carcinomas derived from other tissue types. Therefore, proteins of the present invention with cadherin activity, and polynucleotides of the present invention encoding such proteins, can be used to treat cancer. Introducing such proteins or polynucleotides into cancer cells can reduce or eliminate the cancerous changes observed 2 0 in these cells by providing normal cadherin expression.
Cancer cells have also been shown to express cadherins of a different tissue type than their' origin, thus allowing these cells to invade and metastasize in a different tissue in the body. Proteins of the present invention with cadherin activity, and polynucleotides of the present invention encoding such proteins, can be substituted in these cells for the 2 5 inappropriately expressed cadherins, restoring normal cell adhesive properties and reducing or eliminating the tendency of the cells to metastasize.
Additionally, proteins of the present invention with cadherirt activity, and poiynucleotides of the present invention encoding such proteins, can used to generate antibodies recognizing and binding to cadherins. Such antibodies can be used to block 3 0 the adhesion of inappropriately expressed tumor-cell cadherins, preventing the cells from forming a tumor elsewhere. Such an anti-cadherin antibody can also be used as a r~.~r for the grade, pathological type, and prognosis of a cancer, i.e. the more progressed the cancer, the less cadherin expression there will be, and this decrease in cadherin expression can be detected by the use of a cadherin-binding antibody.
Fragments of profieins of the present invention with cadherin activity, preferably a polypeptide comprising a decapeptide of the cadherin recognition site, and poly-nucleotides of the present invention encoding such protein fragments, can also be used to block cadherin function by binding to cadherins and preventing them from binding in ways that produce undesirable effects. Additionally, fragments of proteins of the present invention with cadherin activity, preferably truncated soluble cadherin fragments which have been found to be stable in the circulation of cancer patients, and polynucleotides encoding such protein fragments, can be used to disturb proper cell-cell adhesion.
Assays for cadherin adhesive and invasive suppressor activity include, without limitation, those described in: Hortsch et al. J Biol Chem 270 (32): 18809-18817, 1995;
Miyaki et al. Oncogene 11: 2547-2552,1995; C~zawa et al. Cell 63:1033-1038,1990.
In addition to the activities described above for immunological treatment or prevention of tumors, a protein of the invention may exhibit other anti-tumor activities.
A protein may inhibit tumor growth directly or indirectly (such as, for example, via antibody-dependent cell-mediated cytotoxicity (ADCC)). A protein may exhibit its tumor inhibitory activity by acting on tumor tissue or tumor precursor tissue, by inhibiting formation of tissues necessary to support tumor growth {such as, for example, by 2 0 iWu'biting angiogenesis), by causing production of other factors, agents or cell types which inhibit tumor growth, or by suppressing, eliminating or inhibiting factors, agents or cell types which promote tumor growth.
2 5 A protein of the invention may also exh~it one or more of the following additional activities or effects: inhibiting the growth, infection or function of, or killing, infectious agents, including, without limitation, bacteria, viruses, fungi and other parasites; effecting {suppressing or enhancing) bodily characteristics, including, without limitation, height, weight, hair rnlor, eye color, skin, fat to lean ratio or other tissue pigmentation, or organ 3 0 or body part size or shape (such as, for example, breast augmentation or diminution, change in bone form or shape); effecting biorhythms or caricadic cycles or rhythms;
effecting the fertility of male or female subjects; effecting the metabolism, catabolism, anabolism, processing, utilization, storage or elimination of dietary fat, lipid, profiein, carbohydrate, vitamins, minerals, cofactors or other nutritional factors or component(s);
effecting behavioral characteristics, including, without limitation, appetite, libido, stress, cognition (including cognitive disorders), depression (including depressive disorders) and violent behaviors; providing analgesic effects or other pain reducing effects;
promoting differentiation and growth of embryonic stem cells in lineages other than hematopoietic lineages; hormonal or endocrine activity; in the case of enzymes, correcting deficiencies of the enzyme and treating deficiency-related diseases; treatment of hyperproliferative disorders (such as, for example, psoriasis); immunoglobulin-like activity (such as, for example, the ability to bind antigens or complement); and the ability to act as an antigen in a vaccine composition to raise an immune response against such protein or another material or entity which is cross-reactive with such protein.
A protein of the present invention (from whatever source derived, including without limitation from recombinant and non-recombinant sources) may be used in a pharmaceutical composition when combined with a pharmaceutically acceptable carrier.
Such a composition may also contain (in addition to protein and a Garner) diluents, fillers, salts, buffers, stabilizers, solubiiizers, and other materials well known in the art. The term "pharmaceutically acceptable" means a non toxic mafierial that does not interfere with the effectiveness of the biological activity of the active ingredient(s). The characteristics of the 2 0 Garner will depend on the route of administration. The pharmaceutical composition of the invention may also contain cytokines, lymphokines, or other hematopoietic factors such as M-CSF, GM-CSF, TNF, IL-1, IL-2, ILr3, IL-4, IL-5, ILr6, IL-7, ILr8, IL.-9, IL~-10, ILrl l, l:Lrl2, ILrl3, fLrl4, IL-15, TFN, TNFU, TNFl, TNF2, G-CSF, Meg-CSF, thrombopoietin, stem cell factor, and erythropoietin. The pharmaceutical composition may contain other 2 5 agents which either enhance the activity of the protein or compliment its activity or use in treatment. Such additional factors and/or agents may be included in the pharmaceutical comp~ition to produce a synergistic effect with protein of the invention, or to minimize side effects. Conversely, protein of the present invention may be included in formulations of the particular cytokine, lymphokine, other hematopoietic factor, 3 0 thrombolytic or anti-thrombotic factor, or anti-inflammatory agent to minimize side effects of the cytokine, lymphokine, other hematopoietic factor, thrombolytic or anti-thrombotic factor, or anti-inflammatory agent.
A protein of the present invention may be active in multimers (e.g., heterodimers or homodimers) or complexes with itself or other proteins. As a result, pharmaceutical compositions of the invention may comprise a protein of the invention in such multimeric or complexed form.
The pharmaceutical composition of the invention may be in the form of a complex of the proteins) of present invention along with protein or peptide antigens.
The protein and/or peptide antigen will deliver a stimulatory signal to both B and T
lymphocytes. B
lymphocytes will respond to antigen through their surface immunoglobulin receptor. T
lymphocytes will respond to antigen through the T cell receptor (TCR) following presentation of the antigen by MHC proteins. MHC and structurally related proteins including those encoded by class I and class II MHC genes on host cells will serve to present the peptide antigens) to T lymphocytes. The antigen components could also be supplied as purified MFiC-peptide complexes alone or with co-stimulatory molecules that can directly signal T cells. Alternatively antibodies able to bind surface immunolgobulin and other molecules on B cells as well as antibodies able to bind the TCR and other molecules on T cells can be combined with the pharmaceutical composition of the invention.
The pharmaceutical composition of the invention may be in the form of a liposome in which protein of the present invention is combined, in addition to other pharniaceutically acceptable carriers, with amphipathic agents such as lipids which exist in aggregated form as micelles, insoluble monolayers, liquid crystals, or lamellar layers 2 0 in aqueous solution. Suitable lipids for liposomal formulation include, without limitation, monoglycerides, diglycerides, sulfatides, lysolecithin, phospholipids, saponin, bile acids, and the like. Preparation of such liposomal formulations is within the level of skill in the art, as disclosed, for example, in U.S. Patent No. 4,235,871; U.S. Pafient No.
4,501,728; U.S.
Patent No. 4,837,028; and U.S. Patent No. 4,737,323, all of which are incorporated herein 2 5 by reference.
As used herein, the term "therapeutically effective amount" means the total amount of each active component of the pharmaceutical composition or method that is sufficient to show a meaningful patient benefit, i.e., treatment, healing, prevention or amelioration of the relevant medical condition, or an incrnase in rate of treatment, healing, 3 0 prevention or amelioration of such conditions. When applied to an individual active ingredient, administered alone, the term refers to that ingredient alone. When applied to a combination, the term refers to combined amounts of the active ingredients that result in the therapeutic effect, whether administered in combination, serially or simultaneously.
In practicing the method of treatment or use of the present invention, a therapeutically effective amount of protein of the present invention is administered to a mammal having a condition to be treated. Protein of the present invention may be administered in accordance with the method of the invention either alone or in combination with other therapies such as treatments employing cytolcines, lympholcines or other hematopoietic factors. When co-administered with one or more rytolcines, lymphokines or other hematopoietic factors, protein of the present invention may be administered either simultaneously with the cytolcine(s), lympholcine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic factors, or sequentially. If administered sequentially, the attending physician will decide on the appropriate sequence of administering protein of the present invention in combination with cytokine(s), lympholcine(s), other hematopoietic factor(s), thrombolytic or anti-thrombotic factors.
Administration of protein of the present invention used in the pharmaceutical composition or to practice the method of the present invention can be carned out in a variety of conventional ways, such as oral ingestion, inhalation, topical application or cutaneous, subcutaneous, intraperitoneal, parenteral or intravenous injection.
Intravenous administration to the patient is preferred.
When a therapeutically effective amount of protein of the present invention is 2 0 administered orally, protein of the present invention will be in the form of a tablet, capsule, powder, solution or elixir. When administered in tablet form, the pharmaceutical composition of the invention may additionally contain a solid Garner such as a gelatin or an adjuvant. The tablet, capsule, and powder contain from about 5 to 95%
protein of the present invention, and preferably from about 25 to 90~° protein of the present invention.
2 5 When administered in liquid form, a liquid carrier such as water, petroleum, oils of animal or plant origin such as peanut oil, mineral oil, soybean oil, or sesame oil, or synthetic oils may be added. The liquid form of the pharmaceutical composition may further contain physiological saline solution, dextrose or other saccharide solution, or glycols such as ethylene glycol, propylene glycol or polyethylene glycol. When administered in liquid 3 0 form, the pharmaceutical composition contains from about 0.5 to 90% by weight of protein of the present invention, and preferably from about 1 to 50% protein of the present invention.
When a therapeutically effective amount of protein of the present invention is administered by intravenous, cutaneous or subcutaneous injection, protein of the present wo m4m Pc-riusmoas98 invention will be in the form of a pyrogen-free, parenterally acceptable aqueous solution.
The preparation of such parenterally acceptable protein solutions, having due regard to pH, isotonicity, stability, and the like, is within the skill in the art. A
preferred pharmaceutical composition for intravenous, cutaneous, or subcutaneous injection should contain, in addition to protein of the present invention, an isotonic vehicle such as Sodium Chloride Injection, Ringer's Injection, Dextrose Injection, Dextrose and Sodium Chloride Injection, Lactated Ringer's Injection, or other vehicle as known in the art.
The pharmaceutical composition of the present invention may also contain stabilizers, preservatives, buffers, antioxidants, or other additives known to those of skill in the art.
The amount of protein of the present invention in the pharmaceutical composition of the present invention will depend upon the nature and severity of the condition being treated, and on the nature of prior treatments which the patient has undergone.
Ultimately, the attending physician will decide the amount of protein of the present invention with which to treat each individual patient. Initially, the attending physician will administer low doses of protein of the present invention and observe the patient's response. Larger doses of protein of the present invention may be administered until the optimal therapeutic effect is obtained for the patient, and at that point the dosage is not increased further. It is contemplated that the various pharmaceutical compositions used to practice the method of the present invention should rnntain about 0.01 pg to about 100 2 0 mg (preferably about O.lng to about 10 mg, more preferably about 0.1 pg to about 1 mg) of protein of the present invention per kg body weight.
The duration of intravenous therapy using the pharmaceutical composition of the present invention will vary, depending on the severity of the disease being treated and the condition and potential idiosyncratic response of each individual patient.
It is 2 5 contemplated that the duration of each application of the protein of the present invention will be in the range of 12 to 24 hours of continuous intravenous administration.
Ultimately the attending physician will decide on the appropriate duration of intravenous therapy using the pharmaceutical composition of the present invention.
Protein of the invention may also be used to immunize animals to obtain 3 0 polyclonal and monoclonal antibodies which specifically react with the protein. Such antibodies may be obtained using either the entire protein or fragments thereof as an immunogen. The peptide immunogens additionally may contain a cysteine residue at the carboxyl terminus, and are conjugated to a hapten such as keyhole limpet hemocyanin ~. Methods for synthesizing such peptides are known in the art, for example, as in R.P. Merrifield, J. Amer.Chem.Soc. $~, 2149-2154 (1963); J.L. ICrstenansky, et al., FEBS Lett.
~1, 10 (198. Monoclonal antibodies binding to the protein of the invention may be useful diagnostic agents for the immunodetection of the protein. Neutralizing monoclonal antibodies binding to the protein may also be useful therapeutics for both conditions associated with the protein and also in the treatment of some forms of cancer where abnormal expression of the protein is involved. In the case of cancerous cells or leukemic cells, neutralizing monoclonal antibodies against the protein may be useful in detecting and preventing the metastatic spread of the cancerous cells, which may be mediated by the protein.
For compositions of the present invention which are useful for bone, cartilage, tendon or ligament regeneration, the therapeutic method includes administering the composition topically, systematically, or locally as an implant or device.
When administered, the therapeutic composition for use in this invention is, of course, in a pyrogen free, physiologically acceptable form. Further, the composition may desirably be encapsulated or injected in a viscous form for delivery to the site of bone, cartilage or tissue damage. Topical administration may be suitable for wound healing and tissue repair. Therapeutically useful agents other than a protein of the invention which may also optionally be included in the composition as described above, may alternatively or additionally, be administered simultaneously or sequentially with the composition in the 2 0 methods of the invention. Preferably for bone and/or cartilage formation, the composition would include a matrix capable of delivering the protein-containing composition to the site of bone and/or cartilage damage, providing a structure for the developing bone and cartilage and optimally capable of being resorted into the body.
Such matrices may be formed of materials presently in use for other implanted medical 2 5 applications.
The choice of matrix material is based on biocompati'bility, biodegradability, mechanical properties, cosmetic appearance and interface properties. The particular application of the compositions will define the appropriate formulation.
Potential matrices for the compositions may be biodegradable and chemically defined calcium 3 0 sulfate, tricalciumphosphate, hydroxyapatite, polylactic acid, polyglycolic acid and polyanhydrides. Other potential materials are biodegradable and biologically well-defined, such as bone or dermal collagen. Further matrices are comprised of pure proteins or extracellular matrix components. Other potential matrices are nonbiodegradable and chemically defined, such as sintered hydroxapatite, bioglass, aluminates, or other ceramics. Matrices may be comprised of combinations of any of the above mentioned types of material, such as polylactic acid and hydroxyapatite or rnllagen and tricalciumphosphate. The bioceramics may be altered in composition, such as in calcium aluminate-phosphate and processing to alter pore size, particle size, particle shape, and biodegradability.
Presently preferred is a 50:50 (mole weight) copolymer of lactic acid and glycolic acid in the form of porous particles having diameters ranging from 150 to 800 microns.
In some applications, it will be useful to utilize a sequestering agent, such as carboxymethyl cellulose or autologous blood clot, to prevent the protein compositions from disassociating from the matrix.
A preferred family of sequestering agents is cellulosic materials such as alkylcelluloses (including hydroxyalkylcelluloses), including methylcellulose, ethylcellulose, hydroxyethylcellulose, hydroxypropylcellulose, hydroxypropyl-methylcellulose, and carboxymethylcellulose, the most preferred being cationic salts of carboxymethylcellulose (CMC). Other preferred sequestering agents include hyaluronic acid, sodium alginate, polyethylene glycol), polyoxyethylene oxide, carboxyvinyl polymer and polyvinyl alcohol). The amount of sequestering agent useful herein is 0.5-20 wt%, preferably 1-10 wt% based on total formulation weight, which represents the amount necessary to prevent desorbtion of the protein from the polymer matrix and to 2 0 provide appropriate handling of the composition, yet not so much that the progenitor cells are prevented from infiltrating the matrix, thereby providing the protein the opportunity to assist the osteogenic activity of the progenitor cells.
In further compositions, proteins of the invention may be combined with other agents beneficial to the treatment of the bone and/or cartilage defect, wound, or tissue in question. These agents include various growth factors such as epidermal growth factor (EGF), platelet derived growth factor (PDGF), transforming growth factors (TGF-a and TGR~), and insulin like growth factor (IGF).
The therapeutic compositions are also presently valuable for veterinary applications. Particularly domestic animals and thoroughbred horses, in addition to 3 0 humans, are desired patients for such treatment with proteins of the present invention.
The dosage regimen of a protein-containing pharmaceutical composition to be used in tissue regeneration will be determined by the attending physician considering various factors which modify the action of the proteins, e.g., amount of tissue weight desired to be formed, the site of damage, the condition of the damaged tissue, the size of a wound, type of damaged tissue (e.g., bone), the patient's age, sex, and diet, the severity of any infection, time of administration and other clinical factors. The dosage may vary with the type of matrix used in the reconstitution and with inclusion of other proteins in the pharmaceutical composition. For example, the addition of other known growth factors, such as IGF I (insulin like growth factor I), to the final composition, may also effect the dosage. Progress can be monitored by periodic assessment of tissue/bone growth and/or repair, for example, X-rays, histomorphometric determinations and tetracycline labeling.
Polynucleotides of the present invention can also be used for gene therapy.
Such polynudeotides can be introduced either in vivo or ex vivo into cells for expression in a mammalian subject. Polynucleotides of the invention may also be administered by other known methods for introduction of nucleic acid into a cell or organism (including, without limitation, in the form of viral vectors or naked DNA).
Cells may also be cultured ex vivo in the presence of proteins of the present invention in order to proliferate or to produce a desired effect on or activity in such cells.
Treated cells can then be introduced in vivo for therapeutic purposes.
Patent and literature references cited herein are incorporated by reference as if fully set forth.
63.
SEQUENCE LISTING
<110> Wong, Cordon G.
Clark, Hilary Fechtel, Rim Agostino, Michael J.
Genetics Institute. Inc.
<120> SECRETED PROTEINS AND POLYNUCLEOTIDES ENCODING THEM
<130> GI 6300A
<140>
< 141 > "mss MaH' mailirrp I~el numk~: Err~_ ~ fro bra 90 ~ u~
Date of OepoatlL i l 99 9 i hereby certify that this papa or fee is befnQ
<160> 19 depOSis~ with the United States Postal Service "f=xpress Mail Post Ot'~e to Addn~stse' aervioe <170> Patentln Ver. 2.0 under 37 CFR 1 10 on the date indtcabd above end is addrossad to the Assistant Comn~ionar <210> 1 Fa nts, lfYashin D. . 20231 <211> 1051 <212> DNA
<213> Homo sapiens <400> 1 taggccatga aggccgcttg ctattattat gcaaataagt gttgtattac acatactaat 60 ttatgcatgg ttagattatg cagatgcatc acaaacatgg ttattgaata ataggatggg 120 gctcattctc tctaccatct ttataagcag ttttaagcaa attctcctgg taccaatgtg 180 gacatttaaa gaccctttac tcaatgaaat gtctctttcg tattcttttg ctttcatagt 240 taaagccatc agataagtgg aagagaaatc gtccaagttg ttaggttcaa gagtgttagt 300 ctcacttttc aaattcgtag acttttttgt ttaaatgtaa tcttttcctt atagagaaaa 360 tctaaaatgc agttgcttgg catgaatgct ggcatttagt gagattttag tgtatatagc 420 cttgctgctt agctctaggt aacccatcaa attaaaatta cattttcagg atttatagct 480 cattagaata tttatcttgg taagcttctt attctgtcag taatttctaa acaattcagc 540 ttggccaatt tgtgaaatcc cctaaaattt tgaaagtgaa ctcacaagcc ctatgcagta 600 tatttctcaa acaaatctta gtagaaaact tataagccat ccagtaaaaa ttccaaaggt 660 tgagaatgta gcaatattct tgagattcct aatgtctaga gtagttaatc agtgagattt 720 gatgggtgat gagtctaaga aatggatttt gccatggcca ggtgcagtgg cttacgcctg 780 taatcccagc actttgggag gccgaggtgg gcggatcacg aggtcaggag attgagacca 840 tcctggctaa catggtgaaa cccygtctct actaaaaata caaaaaaaaa aaattagccg 900 ggcgtggtgg cgggcacctg tagtccctgc tgaggcagga gaatggcttg aacccgggag 960 gtggagcttg cagtgagccg agatcacgcc actgcactcc agcctgggca acagagcaag 1020 attccgtctc aaaaacaaaa aaaaaaaaaa a 1051 <210> 2 <211> 75 <212> PRT
<213> Homo sapiens <400> 2 Met Gln Ile Ser Val Val Leu His Ile Leu Ile Tyr Ala Trp Leu Aap Tyr Ala Asp Ala Ser Gln Thr Trp Leu Leu Asn Asn Arg Met Gly Leu Ile Leu Ser Thr Ile Phe Ile Ser Ser Phe Lys Gln Ile Leu Leu Val Pro Met Trp Thr Phe Lys Asp Pro Leu Leu Asn Glu Met Ser Leu Ser Tyr Ser Phe Ala Phe Ile Val Lys Ala Ile Arg <210> 3 <211> 711 <212> DNA
<213> Homo Sapiens <400> 3 ttcaggttta gtgctattgt cattgaacac tggtattttc tgtatcatat naaacattaa 60 aattcaaata attataagca tttggcaaaa acaagagaaa agaaacttgc catattttac 120 aagctgcaat tttagaaaag ctttaactta atgatagttt tatcattgtt ttcttgtccc 180 aaacttatcc agggccatag aagtatgaat ctaattaaaa cagaaatggg aattattgca 240 cagaaatggg aaataactaa ttttaaatca gtcmaattgg cttcttatta aatacaataa 300 ttcttatgaa aatcatagta ccctattttc agacacagct gccagtttac acatttctca 360 gtatcctgaa aggaaaaaag tatagcccca cttatactat gtaaaattac caataaaata 420 tttttatgac tacagatttt gcatttttgt ttacaactat ttaaagagtt ttatgttgta 480 tttagaattt caacctagaa accacacagt acttaaattc tcctggggtc tcctgctttc 540 tcttaaccat ttgcttaata tatatctacc taaaggagac ttctgaattg taaatgaact 600 taaaaataga atgtggatgc aaaatatcac ataagacatc atgataacat ttgaagaaaa 660 aataaaactg tagaccctaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa a 711 <210> 4 <211> 46 <212> PRT
<213> Homo sapiens <220>
<221> UNSURE
<222> (42) <400> 4 Met Ile Val Leu Ser Leu Phe Ser Cys Pro Lys Leu Ile Gln Gly His Arg Ser Met Asn Leu Ile Lys Thr Glu Met Gly Ile Ile Ala Gln Lys Trp Glu Ile Thr Asn Phe Lys Ser Val Xaa Leu Ala Ser Tyr <210> 5 <211> 4529 <212> DaJA
<213> Homo sapiens <400> 5 cacctgggac ctctcacagg tggcatgccc ttccaagacc aggagagaac accacaactt 60 tgcaggacca gcatctctca gcctgcctcc tccctttctc catatcaata tgatatggat 120 gagtactcat ccagcattgg atgatatgga tgaatggtca tccatcccag agcactgtcc 180 ctactccagt tccagggcac tcttagtctg ttcttggcac atacagcttt gcatctgtca 240 gtgtccatgc aaaagccaac acaagctgtg atggactgtg cattgggtag ccaccagagg 300 taactgccac ttatctatca gtcagccttt gacaggcctc acgtagatac gtacctccca 360 tcacctccaa gctggaatac actttactca tctgtaaaat gggtatgaac atgcctcctt 420 tgcagarctt ttttgaagat tctgcattta ctagtttaac aactgttcag tacctattat 480 gggcctagct accggcacat agtaaacact cagttacaat agctttaaga aaatctgtct 540 wo ~i4ms4 rcTNS~rozs9s tagacaaagg agtttcaaaa ctatgtgaag agtatacaag aagtagtagt ccaaactgtt 600 ttttcagttg tttaatgatc tctatgataa agatgttcag ggagaggaat atcttgcgtg 660 ataactggag taaaacccac ttagatttct atgtccccaa acctctggtg tggtcagggt 720 tggcacctgc cctctcaacc atttgtctca ctgtacatgc atcttgtcta tgtcttccac 780 tagagaccat gagggcagag atcagaccta tgtacgttgc acattgctgt ccccagtacc 840 tagcacagca ccttgcccca gtacgcactt catatatatt tcctggacta cggcaggtga 900 gccctttgtg agggttccac ctgcccactg gcctggcctt taatgtcagg ggagcatttc 960 tgatatatta atgcccctct aattgtgctg cattcgttta cataggcagt gcagcagcct 1020 ggctttggtg tttaaagacc ggattgcagt caeagctctg ctgtttgctg gctatgaact 1080 ccaggtaagt tgccaggttc ctctgagcac taatgataat attacctgcc tcacagggtt 1140 gttttgagag cagcttctgc tgctgcccca tgccccagaa ttatggaaaa ccattttgta 1200 aacttcaagt cacttcctct ccatagtaca gatcaatggt agaccagtga tcagggagga 1260 tacaaatcat aaccccaaaa aaggcttctt tgttgtattt tacctcaagt gttttcttag 1320 agaacctcaa caaaccacac tattttctag taatcagcca cttatcccac catttgcagt 1380 aaggaaaact gaggcacgcc ttgatggctt attcagcatc agcagcctca caaaagacag 1440 aagtctcctt tggattagct ttatcatctt tcccttaagc agagatgatg gtgcctttct 1500 cgctgctctg gctcagttaa gaagtcaagt ctgatttatt ggtcatccta actatcgttt 1560 cctgaaggcc cgaagccctg taatgctgtt gtctggcttc ccagatttat gaccatggtt 1620 tctggccccc aacaatatct ggagttcggt ttacatattc acttccacca tccaatccaa 1680 atcctcccag gcagcaatca agctggggct gattcctcat ccatttgtgg gctcactttt 1740 tctggcaagt cagccttcat tctccaggac gcttagaagc cgcatgttgg cggtggattg 1800 tgctacggga aagagtgaat gtgtagcctg cacatttgaa gccttgctgg ggtagagagc 1860 aacgctactg ctcctggaat gtccaggcca ctgttagaaa ggccatctta ttccttagaa 1920 gagtctagcc ctgctgcagg cttcagaaac gtgtgctcta agctcgttcc tgctcatttg 1980 aagcagtctt ctgaaaaggt ctgcagaaac ctgcctttac cctctccctc atcctgcgtg 2040 gcctttgtca catccttcct ccaaggttcc tctggtggtg gtagtaggga ggctgccacc 2100 tggctttgca tgtgggaaag cccagcctct tccctccacc ctcacagcag gacagccaaa 2160 cttggatttt ttcatgagga agcaactctt atgagctctc tggttcagct ctctggttaa 2220 aagaccatac tgtgctgttt ctggggcagc acagacctgg ttgatcgtgt ccacaggaag 2280 aacagccttt gggattcatt agtctggtta agaccagccc tgcagcctcc tctgccagct 2340 atagaactat gtgttagagt tggtgctgaa gccagtcgca aacccatccc agatgcgtct 2400 ggtcttgttg atgttcaaat gccacctcct cctccaggaa gacttcacca cctccccaag 2460 gctgccttat gggctccttc tctgttccct ctcgactctc cccctctatc actatggcca 2520 ttttatagaa ttttaattat tgtctcgggt gtctccacta gactgtaagt atcaagtgtg 2580 tagagacttt tgtttcaact ctgtatcccc aaaattcagc atagttcata gcacatacag 2640 tactctcaat gcctgttgaa tgaataaaga gtctgcttgc atgtaaaact acagtggttt 2700 ggtcttggag acacttgttt tggaattctt ctactgatat ggacagcatc aagatgatgg 2760 gaaatgtatt ggtctgggat ttgttttgcc tacaaagttt cttatgttgg ctcatctcca 2820 actagataaa accctgagtc taggcttccc cttctaacaa agctgctata cctttatgga 2880 cctccatttt cctgtctgta aaatgagagt gtgggctagc tagaaaaatt tctggtgtcc 2940 cccttgctgc tttgtaattc tggagtacgt tcggagaaca ccccaatgtg acasaggatc 3000 tggaaattct tcatasaata ttcagggagg gagacaactc agggaacatg acaactgtct 3060 ggaattattt gaggggttgt catgtagasg atgaaaagga ttagattatc ttgaaaggcc 3120 ccacaggtta taaataagac caattattaa ttcattcaac aaatatttga gtacctgcca 3180 tgtgcaaggc actattctaa gcaataatga tgcagtaatg aatacaacag acaaaaatct 3240 tgttgccttt atggagttga cattctagtg aacagaaaca attcaaaaac aaacacaatg 3300 gagaggagct tcttggaccc tcaaaacgag ctgcctgtga actattgagc tctttgtgtt 3360 caggaatacg tttagtactt agaaatctgc ttccagtggc tgcttagact aaatgacctt 3420 gttaggtttt tttagcccag caatcccatg aatctaaggc tagcgaagat gtgtgatctc 3480 tctattctaa caccactaag ccaaatcatg acetcctctc aatggtaact gtcactctaa 3540 aaagagagat aaggtagatg cagtgggctg ttcttatgaa aaggcaccta aaaaatagta 3600 ctttagaaac atgcattgtg gtgggggtct gggtggaggg gttgcttttt cttgagatcc 3660 ctgtgatatt gaggatgaag aaagagaaac acagggggtg ggcaacttcc ttgaaggacc 3720 agagagagtg agtcatgagg aagagaagga ggagacagag aacaggagag ttggggatga 3780 agcctttgat gaggggagtg aggaggggca gaagtaggag acagacatga ggaaaccacc 3840 aactgaagtc ccagaaaccc agcctccgtc ccctctaggt cctactgccg tcatcctctt 3900 tctgtaaagg tgagagtcta ggtgcagtgt cccaggttcc aaacacaagt tcatactcat 3960 tgactagtgg gatgcccact gtgagagcag gaaggagggc tagagagatc taagagggca 4020 gaagccctgc cctgccagta ttttttgcct ccagccacct gctctgttct gagacatgcc 4080 tgagaccagc tgcctacagg gggaccaggg tctgtttctg ctgttaacct tggttccctc 4140 WO 99/41284 PGTNS99/02$98 ctgcattcct gcatgtgggg atgtagacag gaagcctgca ggtatggagc aattgaagca 4200 gagtctagat agagcccaga ctccttactt cccatagtac tattctgcat tttgtagtgc 4260 tgcttatgct tttcagtgtt tccacatcta tttactaata acatcatagt acaacagcaa 4320 gaacatggcc tcagaactca aagttctgga attctaatat tttatttgat tgtcagtatt 4380 tctgtgagat agataaaata ggaattattt cctctgatct gcaggtgagg aaactcagtc 4440 acagggagca catttatcca tacttgtgga gctatagtat aactagtatt aggacaagga 4500 tagccaacat agttaaaaaa aaaaaaaaa 4529 <210> 6 <211> 98 <212> PRT
<213> Homo sapiens <400> 6 Met Ile Ser Met Ile Lys Met Phe Arg Glu Arg Asn Ile Leu Arg Asp Asn Trp Ser Lys Thr His Leu Asp Phe Tyr Val Pro Lys Pro Leu Val 20 25 ~ 30 Trp Ser Gly Leu Ala Pro Ala Leu Ser Thr Ile Cys Leu Thr Val His Ala Ser Cys Leu Cys Leu Pro Leu Glu Thr Met Arg Ala Glu Ile Arg Pro Met Tyr Val Ala His Cys Cys Pro Gln Tyr Leu Ala Gln His Leu Ala Pro Val Arg Thr Ser Tyr Ile Phe Pro Gly Leu Arg Gln Val Ser Pro Leu <210> 7 <211> 3537 <212> DNA
<213> Homo sapiens <400> 7 aacttagatt tcttaaaact gtatacagat aactaatttt tattttgaaa tagcttttat 60 gttcttgtgt ttatgtaata gtcacattaa ttttgctctt ttggctttgt gttgtgttta 120 tttgatgact gttttattcg gtttaatttt ttcttgattt tgcaaattca tttttatcat 180 ctttaagtgg tggagtggcc atttcagctt gaaatatttc actgtcttta taatttcatt 240 ccatgcatgt gttttgtgtt tgtgacggtg tggtggtatt tagtctatag aagaacatgt 300 ggagcaggtc aaccaaaact gcatagcaga agattgccac atcaaggtag tattccaaga 360 tcttgtattt agctcattct ttaaagttca aggagctaac gcctcatctc tgatactaac 420 catgacctgc ccaactggct aactactcag agaactcata gtactcccat accacttcag 480 tggcacaggg gaggagatgc ttcactgtat ctggcttgct ctgtcttgcc cttggttctt 540 ctctttcttg ctccctgtcc catcttcact tgtcactttt tctgttttaa gcatggctgt 600 ttcatcttct tgattctgcc ttttctttcc ttcccatcac caaccctaag ccattgcatc 660 ttcctctcat cagtctcttt tattcctttc gaagtatccc tctttccaac ttttccttat 720 ttctgtctca ccacccttac ttcaaagggt ggtttctttg cggttttcta tggcttttta 780 ctccactctg tgcctcttaa tgtatacaca ttcttattgc agaatattta tgcacttttg 840 gaagagctaa gagagacata ctactgtata aattactaat aaaaatatat tagccatgtt 900 ttataattaa tcagtatctt accatcacag tggaaattgg ggtgattaca ggacatcaga 960 gaatttaagc aaattttcca aagctagttt tcaacacatt aaagttactc ttaccctttt 1020 ttcttgctgc tgctgctgct gctacatttt cttcttatcc tacatttaaa tcttatggga 1080 tgtgcataac tctaaataga gctgtgctgc agcaactaaa actgctgatg aatgttttct 1140 aggttgaagc tgatctgggc tatccaggtg gaaaggcgaa agtcatccat aaggaatctg 1200 atatgatcat ggcattttct gttaataagg caaattgtaa tgaaattgtt ttggcttcaa 1260 cacatgatgt tcaagaactt gatgttactt ctctactggc ctgtcagtca tacatatgga 1320 tcggagaaga atatgacaga gaatccaaaa gttcagatga tgttgattat cgtggttcca 1380 ctacaactct ttatcaaccc agtgcaacat cctattcagc aagtcaggtg catccacctt 1440 catctctgcc atggctgggc actggacaga ctagcactgg agctagtgtg cttatgaaaa 1500 ggaatctaca tsatgttaag agaatgactt cacacccagt ccatcsatac tatcttacag 1560 gtgctcagga cggcagtgta cgaatgtttg aatggacgcg gcctcagcaa cttgtctgct 1620 ttcgtcaagc tggcaatgca agagttacta gattatattt taattcacaa ggcaacaagt 1680 gtggtgttgc ggatggagag ggttttctga gtatctggca agttaaccaa actgcatcaa 1740 atcctaaacc ttatatgagt tggcagtgcc acagtaaagc cacaagtgac tttgcattta 1800 ttacctcttc aagtctagtt gccacatctg gacactccaa tgacaataga aatgtttgcc 1860 tctgggacac attaatatca cccggaaaca gcctcattca tggtttcacg tgccacgatc 1920 atggtgccac ggtactgcag tatgcaccca aacagcaact cctaatctcg gggggtagga 1980 aaggacacgt ctgcattttt gacatcaggc aaaggcagct cattcacacg ttccaggccc 2040 atgactcagc tattaaggct ctggccttgg atccctatga ggaatatttt accacaggtt 2100 cagcagaagg taacataaag gtttggagat tgacaggcca tggcctaatt cattcattta 2160 aaagtgaaca tgctaagcag tccatatttc gaaacattgg ggctggagtc atgcagattg 2220 acatcatcca gggcaatcgg ctcttctcct gtggtgcaga tggcacgctg aaaaccaggg 2280 ttttgcccaa tgcttttaac atccctsaca gaattcttga cattctataa agattggggt 2340 tttattttta tatacatttc agttaaaagg cacactacag tcatcactag gcaattctgc 2400 tttctaagca gttgtattga aaacagagaa tctctgtgta gaatttgaat atgacccaag 2460 ctgagtatta tctaaacagg ttggtggaat gaatgcgcat gtaccttatt atgctgacat 2520 actaaaaaaa ataaaaccta gtattgtatg aaggatagct attctttaca gcatttagca 2580 aacctgattc agaaaacatt tgagattagc aaattagtaa cttgaaataa tgaaaaggac 2640 gtttatacca aattaaggaa gaaaatgttg ctgatttggg tttttcttcc tgttcttacc 2700 actgactgaa gcatgcctgc agtctcctcc tctgttgaat gaaggataat cataaggtgt 2760 ttgttaggag cgctagacca cctggaaaac tttcttagct gtggagcagt gcgcagtgac 2820 cagttctctg ctgtgagagg ccgtttccat tctttcctgc tgaatatttt tcctgttagt 2880 gtttatactg agctagtact gtaacttgca aatgagtgca aatttaaatg caatgtttta 2940 ctcacaattt gcacattcac attttttgga ctgctagttt ttctatttaa atatttgcct 3000 tcatgttagg aatgtactat gtgaacatga catatttgta gttaaccaaa cacaccttct 3060 tagtccagtt tagtactttt tcttttcgtg tattcaaggt taaacaccca aacatttaag 3120 gatatgttga aactacacca atagagcatt tcatatcata attaaaatga atgttaggct 3180 tcttgtggcc agttaatagt tgatgagatt ggtgacatta tttattgcca cagcctattg 3240 tataaactat gcagagttaa atatttgctt gtaaaatatt agccaatgtt gtcattattt 3300 tgatgtattt ccttggttat gaccaaaaat atgttgagat actgaaacta atgtctgtgt 3360 gtttaaatgt ttaccagcaa attgtcttat catgttaatg agaatgttca atgcctgtgt 3420 ggtaaatagt aaatacaatg gcataaaagt aactttctct gaagatgtga tgttcaggct 3480 gtgaaatata tatgtaaaag aaaaataaat gttatttgtt agaaasaaaa aaaaaaa 3537 <210> 8 <211> 375 <212> PRT
<213> Homo sapiens <400> 8 Met Ile Met Ala Phe Ser Val Asn Lys Ala Asn Cys Asn Glu Ile Val Leu Ala Ser Thr His Asp Val Gln Glu Leu Asp Val Thr Ser Leu Leu Ala Cys Gln Ser Tyr Ile Trp Ile Gly Glu Glu Tyr Asp Arg Glu Ser Lys Ser Ser Asp Asp Val Asp Tyr Arg Gly Ser Thr Thr Thr Leu Tyr Gln Pro Ser Ala Thr Ser Tyr Ser Ala Ser Gln Val His Pro Pro Ser Ser Leu Pro Trp Leu Gly Thr Gly Gln Thr Ser Thr Gly Ala Ser Val Leu Met Lys Arg Asn Leu His Asn Val Lys Arg Met Thr Ser His Pro Val His Gln Tyr Tyr Leu Thr Gly Ala Gln Asp Gly Ser Val Arg Met Phe Glu Trp Thr Arg Pro Gln Gln Leu Val Cys Phe Arg Gln Ala Gly Asn Ala Arg Val Thr Arg Leu Tyr Phe Asn Ser Gln Gly Asn Lys Cys Gly Val Ala Asp Gly Glu Gly Phe Leu Ser Ile Trp Gln Val Asn Gln Thr Ala Ser Asn Pro Lys Pro Tyr Met Ser Trp Gln Cys His Ser Lys Ala Thr Ser Asp Phe Ala Phe Ile Thr Ser Ser Ser Leu Val Ala Thr Ser Gly His Ser Asn Asp Asn Arg Asn Val Cys Leu Trp Asp Thr Leu Ile Ser Pro Gly Asn Ser Leu Ile His Gly Phe Thr Cys His Asp His Gly Ala Thr Val Leu Gln Tyr Ala Pro Lys Gln Gln Leu Leu Ile Ser Gly Gly Arg Lys Gly His Val Cys Ile Phe Asp Ile Arg Gln Arg Gln Leu Ile His Thr Phe Gln Ala His Asp Ser Ala Ile Lys Ala Leu Ala Leu Asp Pro Tyr Glu Giu Tyr Phe Thr Thr Gly Ser Ala Glu Gly Asn Ile Lys Val Trp Arg Leu Thr Gly His Gly Leu Ile His Ser Phe Lys Ser Glu His Ala Lys Gln Ser Ile Phe Arg Asn Ile Gly Ala Gly Val Met Gln Ile Asp Ile Ile Gln Gly Asn Arg Leu Phe Ser Cys Gly Ala Asp Gly Thr Leu Lys Thr Arg Val Leu Pro Asn Ala Phe Asn Ile Pro Asn Arg Ile Leu Asp Ile Leu <210> 9 <211> 1466 <212> DNA
<213> Homo sapiens <400> 9 ccgcgcagga ggacggagcc ctaaccgcaa cccgcgccgc gccgcgccga tttgatttgt 60 atccactgtc accagcactg ctcacttagg actttctgga tccggaccca ggcagcgcac 120 actggactct tgaggaagaa ggagactcta attttggatt ccttggtgga ggaaaataaa 180 acactctggt cttgccgcca acgatgcaag tgtgactgct ggcgtcttca tgagctccag 240 aggtcacagc acgctaccaa ggactctcat ggcccctcgg atgatttccg agggagacat 300 argaggcatt gctcaaatca cctcctctct attcctgggc agaggcagtg tggcctccaa 360 tcggcacctc ctccaggctc gtggcatcac ctgcattgtt aatgctacca ttgagatccc 420 taatttcaac tggccccaat ttgagtatgt taaagtgcct ctggctgaca tgccgcatgc 480 ccccattgga ctgtactttg acaccgtggc tgacaagatc cacagtgtga gcaggaagca 540 cggggccacc ttggtgcact gtgctgcagg ggtgagccgc tcagccacgc tgtgtatcgc 600 gtacctgatg aaattccaca acgtgtgcct gctggaggcg tacaactggg tgaaagcccg 660 gcgacctgtc atcaggccca acgtaggctt ctggaggcaa ctgatagact acgagcgcca 720 gctctttggg aagtcgacag ttaaaatggt acagacacct tatggcatag ttcccgacgt 780 ctatgagaag gagtcccgac acctgatgcc ttactggggg atttagtgcc actgaagcct 840 gcgtcagcag cccgagcggg gccggcatct gctccccgcc gtctgctccc tctccactct 900 cttctcaaat ggctgacttc tggttctccc tcaagtgttt tttacactgg gtgttcaaat 960 ttattttaag agatagggag ggaggggaca taaagggaat gcatacattg ctagtcacat 1020 ttttaaaatt aacattttgg aatagtgttt atggaaatct ttagctttta atcattttta 1080 ccaatttgaa cagtttaata aactggttct gctctcttct gaatctcakg ccttkggcac 1140 cttggtaggt gcaggaggag ctcagtgcaa aaatcacttt ggggcctcat taacccttta 1200 gagacaagyt ttgccccagg ytgcggacca gacagatgyt tagggaaggt tgataccagc 1260 ttcagtctct astggattag ccctactctt tcctttcccc tccattattt agtgactctg 1320 taagtaagtt aaatacaccc ttattattta gctgttaagt aactataatg aaatctgctg 1380 caaaatctct cttggaatcc atgtgcccag gattatatta gcattatttt taataaatct 1440 atatgcttaa caaaaaaaaa aaaaaa 1466 <210> 10 <211> 198 <212> PRT
<213> Homo sapiens <220>
<221> UNSURE
<222> (25) <400> 10 Met Ser Ser Arg Gly His Ser Thr Leu Pro Arg Thr Leu Met Ala Pro Arg Met Ile Ser Glu Gly Asp .Ile Xaa Gly Ile Ala Gln Ile Thr Ser Ser Leu Phe Leu Gly Arg Gly Ser Val Ala Ser Asn Arg His Leu Leu Gln Ala Arg Gly Ile Thr Cys Ile Val Asn Ala Thr Ile Glu Ile Pro Asn Phe Asn Trp Pro Gln Phe Glu Tyr Val Lys Val Pro Leu Ala Asp Met Pro His Ala Pro Ile Gly Leu Tyr Phe Asp Thr Val Ala Asp Lys Ile His Ser Val Ser Arg Lys His Gly Als Thr Leu Val His Cys Ala Ala Gly VaI Ser Arg Ser Ala Thr Leu Cys Ile Ala Tyr Leu Met Lys Phe His Asn Val Cys Leu Leu Glu Ala Tyr Asn Trp Val Lys Ala Arg Arg Pro Val Ile Arg Pro Asn Val Gly Phe Trp Arg Gln Leu Ile Asp Tyr Glu Arg Gln Leu Phe Gly Lys Ser Thr Val Lys Met Val Gln Thr Pro Tyr Gly Ile Val Pro Asp Val Tyr Glu Lys Glu Ser Arg His Leu Met Pro Tyr Trp Gly Ile <210> 11 <211> 1521 <212> DNA
<213> Homo eapiens <400> 11 aatttcttgg gcatttaccc atgccagaag gctaacctgg ggggaggggg gcgcttgtgc 60 tggtgaggca cttggataca tactgatgct gcaagttcag gggatttttc ttactcttag 120 gtttaaccaa gaacactgag cagggaaaaa ccctgccttt cctaactgca tgtatttttt 180 cctttttgga aaggtggtag agactcagaa gctttccttg ttttcttcag gcctgctccc 240 agttttctta acagtttctt ttgttgcttt ctctctccct tgttgctttc catggcagta 300 atcctcctag agtccaagca gtctgttgta tggagcaggg tgtgtgggtt ttctgggccc 360 atcattatgg ctgcttcaga gtcagaagaa agccataggg cagtagggga gctcctattg 420 cctarcccct ctccctttgt ggctcccact ctagctgcct atttttgctc atcagctggt 480 gagtcagtat gggccagcag ttctccctcc ctaagccctt gctactttat gggttagctt 540 tgcaggtttg gtggcttgag gggtgggggc aactcaccac tgccaggtaa ctccctgaag 600 ggtgggagtg gattatcttc taggctctta cccgcggtag ggaagggcat caacactgtc 660 ttccttccat tctcctttcc cccatcccat ttagtgctgc cacagggcag aagcacacaa 720 accaaccaca cagtctctga cttctcctaa gcactttgag ttgttgaatg gggctcaggg 780 gcaagagttt ttgctgccct ccccagcgtg gtcacagggt tattgaactg cctgcacttg 840 tttctcatgc aactccagca ttttccccag aagttgaact atggatagca gcttggtatg 900 gatttcctaa atcttaacat ttgaagcagc ttcttgaggc tggcaactat cctggtttct 960 gtcttggagg gggtggtttg tttgctgggg cccaacgtct gtcccaagtg gtggggtgag 1020 agtaagttaa ctttggtgcc aggtgagagg tgggggctct ttgcttagac tccctatcat 1080 ggaaagattg gagttttcta tgcagggcac tggggaaaag gattgctgat tctgactgac 1140 cctgatcaga gagattagga ttgtattttg acataggatt tggaacccat ctaaatgttg 1200 aagttccctg agacrgctct ccagctgctg agcctgcgcc aggggytaag cagcccctaa 1260 tgagaggctc tgctcccttt cccacctcgc caatgttgtt gttgctgcct ttttgatttg 1320 tatcctctgt tatagacatt ttttraaaac gatttcctct ttcattgtgc acaagtgctg 1380 agagtctgag gccccatttc tgctgtgtat atatatcctg actcggggct tttattcagc 1440 aaactgttca ttcttctgtc agacaatgtc atattcaact ctgttcatat taaaccactg 1500 tgaagcaaaa aaaaaaaaaa a 1521 <210> 12 <211> 81 <212> PRT
<213> Homo sapiens g <220>
<221> UNSURE
<222> (45) <400> 12 Met Ala Val Ile Leu Leu Glu Ser Lys Gln Ser Val Val Trp Ser Arg Val C)rs Gly Phe Ser Gly Pro Ile Ile Met Ala Ala Ser Glu Ser Glu Glu Ser His Arg Ala Val Gly Glu Leu Leu Leu Pro Xaa Pro Ser Pro Phe Val Ala Pro Thr Leu Ala Ala Tyr Phe Cys Ser Ser Ala Gly Glu Ser Val Trp Ala Ser Ser Ser Pro Ser Leu Ser Pro Cys Tyr Phe Met 65 70 75 gp Gly <210> 13 <211> 19 <212> DNA
<213> Artificial Sequence <220>
<223> oligonucleotide <400> 13 ggatggggct cattctctc 19 <210> 14 <211> 20 <212> DNA
<213> Artificial Sequence <220>
<223> oligonucleotide <400> 14 gaaatgtgta aactggcagc 20 <210> 15 <211> 21 <212> DNA
<213> Artificial Sequence <220>
<223> oligonucleotide <400> 15 gaatgcagca caattagagg g 21 <210> 16 <211> 21 <212> DT1A
<213> Artificial Sequence <220>
<223> oligonucleotide <400> 16 ctgcttagaa agcagaattg c 21 <210> 17 <211> 19 <212> DNA
<213> Artificial Sequence <220>
<223> oligonucleotfde <400> 17 tgtgactagc aatgtatgc 19 <210> 18 <211> 20 <212> DNA
<213> Artificial Sequence <220>
<223> oligonucleotide <400> 18 tcagaagaaa gccatagggc 20 <210> 19 <211> 113 <212> PRT
<213> Homo sapiens <400> 19 Met Ser Arg pro Leu Leu Glu Arg pro Ser Tyr Ser Leu Glu Glu Ser Ser Pro Ala Ala Gly Phe Arg Asn Val Cys Ser Lya Leu Val Pro Ala His Leu Lys Gln Ser Ser Glu Lys Val Cys Arg Asn Leu Pro Leu Pro Ser Pro Ser Ser Cys Val Ala Phe Val Thr Ser Phe Leu Gln Gly Ser Ser Gly Gly Gly Ser Arg Glu Ala Ala Thr Trp Leu Cys Met Trp Glu Ser Pro Ala Ser Ser Leu His Pro His Ser Arg Thr Ala Lys Leu Gly Phe Phe His Glu Glu Ala Thr Leu Met Ser Ser Leu Val Gln Leu Ser Gly
Claims (21)
1. An isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:1;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:1 from nucleotide 29 to nucleotide 253;
(c) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone ya15_1 deposited under accession number ATCC 98650;
(d) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone ya15_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:2;
(f) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:2, the fragment comprising eight contiguous amino acids of SEQ ID NO:2;
(g) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 65 degrees C, or 4X SSC at 42 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)(f); and (h) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 50 degrees C, or 6X SSC at 40 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(f), and that has a length that is at least 25% of the length of SEQ ID NO:1.
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:1;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:1 from nucleotide 29 to nucleotide 253;
(c) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone ya15_1 deposited under accession number ATCC 98650;
(d) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone ya15_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:2;
(f) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:2, the fragment comprising eight contiguous amino acids of SEQ ID NO:2;
(g) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 65 degrees C, or 4X SSC at 42 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)(f); and (h) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 50 degrees C, or 6X SSC at 40 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(f), and that has a length that is at least 25% of the length of SEQ ID NO:1.
2. The polynucleotide of claim 1 wherein said polynucleotide is operably linked to at least one expression control sequence.
3. A host cell transformed with the polynucleotide of claim 2.
4. The host cell of claim 3, wherein said cell is a mammalian cell.
5. A process for producing a protein encoded by the polynucleotide of claim 2, which process comprises:
(a) growing a culture of the host cell of claim 3 in a suitable culture medium; and (b) purifying said protein from the culture.
(a) growing a culture of the host cell of claim 3 in a suitable culture medium; and (b) purifying said protein from the culture.
6. A protein produced according to the process of claim 5.
7. An isolated polynucleotide encoding the protein of claim 6.
8. The polynucleotide of claim 7, wherein the polynucleotide comprises the cDNA insert of clone ya15_1 deposited under accession number ATCC 98650.
9. A protein comprising an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID NO:2;
(b) a fragment of the amino acid sequence of SEQ ID NO:2, the fragment comprising eight contiguous amino acids of SEQ ID NO:2; and (c) the amino acid sequence encoded by the cDNA insert of done ya15_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins.
(a) the amino acid sequence of SEQ ID NO:2;
(b) a fragment of the amino acid sequence of SEQ ID NO:2, the fragment comprising eight contiguous amino acids of SEQ ID NO:2; and (c) the amino acid sequence encoded by the cDNA insert of done ya15_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins.
10. The protein of claim 9, wherein said protein comprises the amino acid sequence of SEQ ID NO:2.
11. A composition comprising the protein of claim 9 and a pharmaceutically acceptable carrier.
12. An isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:3;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:3 from nucleotide 151 to nucleotide 288;
(c) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:3 from nucleotide 196 to nucleotide 288;
(d) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone ya24_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone ya24_1 deposited under accession number ATCC 98650;
(f) a polynucleotide comprising the nucleotide sequence of the mature protein coding sequence of clone ya24_1 deposited under accession number ATCC
98650;
(g) a polynucleotide encoding the mature protein encoded by the cDNA insert of clone ya24_1 deposited under accession number ATCC 98b50;
(h) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:4;
(i) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:4, the fragment comprising eight contiguous amino acids of SEQ ID NO:4;
(j) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 65 degrees C, or 4X SSC at 42 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(i); and (k) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 50 degrees C, or 6X SSC at 40 degrees C with 50%
formamide, to any one of the polynudeotides specified in (a)-(i) and that has a length that is at least 25% of the length of SEQ ID NO:3.
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:3;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:3 from nucleotide 151 to nucleotide 288;
(c) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:3 from nucleotide 196 to nucleotide 288;
(d) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone ya24_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone ya24_1 deposited under accession number ATCC 98650;
(f) a polynucleotide comprising the nucleotide sequence of the mature protein coding sequence of clone ya24_1 deposited under accession number ATCC
98650;
(g) a polynucleotide encoding the mature protein encoded by the cDNA insert of clone ya24_1 deposited under accession number ATCC 98b50;
(h) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:4;
(i) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:4, the fragment comprising eight contiguous amino acids of SEQ ID NO:4;
(j) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 65 degrees C, or 4X SSC at 42 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(i); and (k) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 50 degrees C, or 6X SSC at 40 degrees C with 50%
formamide, to any one of the polynudeotides specified in (a)-(i) and that has a length that is at least 25% of the length of SEQ ID NO:3.
13. A protein comprising an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID NO:4;
(b) a fragment of the amino acid sequence of SEQ ID NO:4, the fragment comprising eight contiguous amino acids of SEQ ID NO:4; and (c) the amino acid sequence encoded by the cDNA insert of clone ya24_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins.
(a) the amino acid sequence of SEQ ID NO:4;
(b) a fragment of the amino acid sequence of SEQ ID NO:4, the fragment comprising eight contiguous amino acids of SEQ ID NO:4; and (c) the amino acid sequence encoded by the cDNA insert of clone ya24_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins.
14. An isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:5;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:5 from nucleotide 615 to nucleotide 908;
(c) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:5 from nucleotide 774 to nucleotide 908;
(d) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone yb42_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone yb42_1 deposited under accession number ATCC 98650;
(f) a polynucleotide comprising the nucleotide sequence of the mature protein coding sequence of clone yb42_1 deposited under accession number ATCC
98650;
(g) a polynucleotide encoding the mature protein encoded by the cDNA insert of clone yb42_1 deposited under accession number ATCC 98650;
(h) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:6;
(i) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:6, the fragment comprising eight contiguous amino acids of SEQ ID NO:6;
(j) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 65 degrees C, or 4X SSC at 42 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(i) and (k) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 50 degrees C, or 6X SSC at 40 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(i) and that has a length that is at least 25% of the length of SEQ ID NO:5.
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:5;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:5 from nucleotide 615 to nucleotide 908;
(c) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:5 from nucleotide 774 to nucleotide 908;
(d) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone yb42_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone yb42_1 deposited under accession number ATCC 98650;
(f) a polynucleotide comprising the nucleotide sequence of the mature protein coding sequence of clone yb42_1 deposited under accession number ATCC
98650;
(g) a polynucleotide encoding the mature protein encoded by the cDNA insert of clone yb42_1 deposited under accession number ATCC 98650;
(h) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:6;
(i) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:6, the fragment comprising eight contiguous amino acids of SEQ ID NO:6;
(j) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 65 degrees C, or 4X SSC at 42 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(i) and (k) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 50 degrees C, or 6X SSC at 40 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(i) and that has a length that is at least 25% of the length of SEQ ID NO:5.
15. A protein comprising an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID NO:6;
(b) a fragment of the amino acid sequence of SEQ ID NO:6, the fragment comprising eight contiguous amino acids of SEQ ID NO:6; and (c) the amino acid sequence encoded by the DNA insert of clone yb42_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins.
(a) the amino acid sequence of SEQ ID NO:6;
(b) a fragment of the amino acid sequence of SEQ ID NO:6, the fragment comprising eight contiguous amino acids of SEQ ID NO:6; and (c) the amino acid sequence encoded by the DNA insert of clone yb42_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins.
16. An isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:7;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:7 from nucleotide 1203 to nucleotide 2327;
(c) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of done yc9_1 deposited under accession number ATCC 98650;
(d) a polynucleotide encoding the full-length protein encoded by the DNA insert of clone yc9_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:8;
(f) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:8, the fragment comprising eight contiguous amino acids of SEQ ID NO:8;
(g) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 65 degrees C, or 4X SSC at 42 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(f); and (h) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 50 degrees C, or 6X SSC at 40 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(f) and that has a length that is at least 25% of the length of SEQ ID NO:7.
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:7;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:7 from nucleotide 1203 to nucleotide 2327;
(c) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of done yc9_1 deposited under accession number ATCC 98650;
(d) a polynucleotide encoding the full-length protein encoded by the DNA insert of clone yc9_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:8;
(f) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:8, the fragment comprising eight contiguous amino acids of SEQ ID NO:8;
(g) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 65 degrees C, or 4X SSC at 42 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(f); and (h) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 50 degrees C, or 6X SSC at 40 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(f) and that has a length that is at least 25% of the length of SEQ ID NO:7.
17. A protein comprising an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID NO:8;
(b) a fragment of the amino acid sequence of SEQ ID NO:8, the fragment comprising eight contiguous amino acids of SEQ ID NO:8; and (c) the amino acid sequence encoded by the cDNA insert of clone yc9_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins.
(a) the amino acid sequence of SEQ ID NO:8;
(b) a fragment of the amino acid sequence of SEQ ID NO:8, the fragment comprising eight contiguous amino acids of SEQ ID NO:8; and (c) the amino acid sequence encoded by the cDNA insert of clone yc9_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins.
18. An isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:9;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:9 from nucleotide 230 to nucleotide 823;
(c) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:9 from nucleotide 584 to nucleotide 823;
(d) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone yc19_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone yc19_1 deposited under accession number ATCC 98650;
(f) a polynucleotide comprising the nucleotide sequence of the mature protein coding sequence of clone yc19_1 deposited under accession number ATCC
98650;
(g) a polynucleotide encoding the mature protein encoded by the cDNA insert of clone yc19_1 deposited under accession number ATCC 98650;
(h) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:10;
(i) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:10, the fragment comprising eight contiguous amino acids of SEQ ID NO:10;
(j) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 65 degrees C, or 4X SSC at 42 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(i); and (k) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 50 degrees C, or 6X SSC at 40 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(i) and that has a length that is at least 25% of the length of SEQ ID NO:9.
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:9;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:9 from nucleotide 230 to nucleotide 823;
(c) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:9 from nucleotide 584 to nucleotide 823;
(d) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of clone yc19_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone yc19_1 deposited under accession number ATCC 98650;
(f) a polynucleotide comprising the nucleotide sequence of the mature protein coding sequence of clone yc19_1 deposited under accession number ATCC
98650;
(g) a polynucleotide encoding the mature protein encoded by the cDNA insert of clone yc19_1 deposited under accession number ATCC 98650;
(h) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:10;
(i) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:10, the fragment comprising eight contiguous amino acids of SEQ ID NO:10;
(j) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 65 degrees C, or 4X SSC at 42 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(i); and (k) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 50 degrees C, or 6X SSC at 40 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(i) and that has a length that is at least 25% of the length of SEQ ID NO:9.
19. A protein comprising an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID NO:10;
(b) a fragment of the amino acid sequence of SEQ ID NO:10, the fragment comprising eight contiguous amino acids of SEQ ID NO:10; and (c) the amino acid sequence encoded by the cDNA insert of clone yc19_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins.
(a) the amino acid sequence of SEQ ID NO:10;
(b) a fragment of the amino acid sequence of SEQ ID NO:10, the fragment comprising eight contiguous amino acids of SEQ ID NO:10; and (c) the amino acid sequence encoded by the cDNA insert of clone yc19_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins.
20. An isolated polynucleotide selected from the group consisting of:
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:11;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:11 from nucleotide 292 to nucleotide 534;
(c) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of done yc20_1 deposited under accession number ATCC 98650;
(d) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone yc20_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:12;
(f) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:12, the fragment comprising eight contiguous amino acids of SEQ ID NO:12;
(g) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 65 degrees C, or 4X SSC at 42 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(f); and (h) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 50 degrees C, or 6X SSC at 40 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(f) and that has a length that is at least 25% of the length of SEQ ID NO:11.
(a) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:11;
(b) a polynucleotide comprising the nucleotide sequence of SEQ ID
NO:11 from nucleotide 292 to nucleotide 534;
(c) a polynucleotide comprising the nucleotide sequence of the full-length protein coding sequence of done yc20_1 deposited under accession number ATCC 98650;
(d) a polynucleotide encoding the full-length protein encoded by the cDNA insert of clone yc20_1 deposited under accession number ATCC 98650;
(e) a polynucleotide encoding a protein comprising the amino acid sequence of SEQ ID NO:12;
(f) a polynucleotide encoding a protein comprising a fragment of the amino acid sequence of SEQ ID NO:12, the fragment comprising eight contiguous amino acids of SEQ ID NO:12;
(g) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 65 degrees C, or 4X SSC at 42 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(f); and (h) a polynucleotide that hybridizes under conditions at least as stringent as 4X SSC at 50 degrees C, or 6X SSC at 40 degrees C with 50%
formamide, to any one of the polynucleotides specified in (a)-(f) and that has a length that is at least 25% of the length of SEQ ID NO:11.
21. A protein comprising an amino acid sequence selected from the group consisting of:
(a) the amino acid sequence of SEQ ID NO:12;
(b) a fragment of the amino acid sequence of SEQ ID NO:12, the fragment comprising eight contiguous amino acids of SEQ ID NO:12; and (c) the amino acid sequence encoded by the cDNA insert of clone yc20_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins.
(a) the amino acid sequence of SEQ ID NO:12;
(b) a fragment of the amino acid sequence of SEQ ID NO:12, the fragment comprising eight contiguous amino acids of SEQ ID NO:12; and (c) the amino acid sequence encoded by the cDNA insert of clone yc20_1 deposited under accession number ATCC 98650;
the protein being substantially free from other mammalian proteins.
Applications Claiming Priority (4)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US7511898P | 1998-02-11 | 1998-02-11 | |
US60/075,118 | 1998-02-11 | ||
US09/248,059 | 1999-02-10 | ||
PCT/US1999/002898 WO1999041284A1 (en) | 1998-02-11 | 1999-02-11 | Secreted proteins and polynucleotides encoding them |
Publications (1)
Publication Number | Publication Date |
---|---|
CA2320618A1 true CA2320618A1 (en) | 1999-08-19 |
Family
ID=22123671
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
CA002320618A Abandoned CA2320618A1 (en) | 1998-02-11 | 1999-02-11 | Secreted proteins and polynucleotides encoding them |
Country Status (4)
Country | Link |
---|---|
EP (1) | EP1053252A1 (en) |
AU (1) | AU2669899A (en) |
CA (1) | CA2320618A1 (en) |
WO (1) | WO1999041284A1 (en) |
Families Citing this family (5)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US20080213778A1 (en) | 1998-12-30 | 2008-09-04 | Millennium Pharmaceuticals, Inc. | Novel genes encoding proteins having prognostic, diagnostic, preventive, therapeutic, and other uses |
US7041474B2 (en) | 1998-12-30 | 2006-05-09 | Millennium Pharmaceuticals, Inc. | Nucleic acid encoding human tango 509 |
US6852520B1 (en) | 1999-03-24 | 2005-02-08 | Ceptyr, Inc. | DSP-2 dual-specificity phosphatase |
JP2002541852A (en) * | 1999-04-20 | 2002-12-10 | セプティア, インコーポレイテッド | DSP-8 bispecific MAP kinase phosphatase |
WO2001021631A2 (en) * | 1999-09-20 | 2001-03-29 | Millennium Pharmaceuticals, Inc. | Secreted proteins and uses thereof |
Family Cites Families (4)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US5350683A (en) * | 1990-06-05 | 1994-09-27 | Immunex Corporation | DNA encoding type II interleukin-1 receptors |
US5641657A (en) * | 1994-05-19 | 1997-06-24 | Human Genome Sciences, Inc. | DNA encoding an interleukin-6 splice variant |
US5610056A (en) * | 1994-11-16 | 1997-03-11 | Amgen Inc. | Use of stem cell factor interleukin-6 and soluble interleukin-6 receptor to induce the development of hematopoietic stem cells |
US5654276A (en) * | 1995-06-07 | 1997-08-05 | Affymax Technologies N.V. | Peptides and compounds that bind to the IL-5 receptor |
-
1999
- 1999-02-11 WO PCT/US1999/002898 patent/WO1999041284A1/en not_active Application Discontinuation
- 1999-02-11 EP EP99906893A patent/EP1053252A1/en not_active Withdrawn
- 1999-02-11 AU AU26698/99A patent/AU2669899A/en not_active Abandoned
- 1999-02-11 CA CA002320618A patent/CA2320618A1/en not_active Abandoned
Also Published As
Publication number | Publication date |
---|---|
EP1053252A1 (en) | 2000-11-22 |
AU2669899A (en) | 1999-08-30 |
WO1999041284A1 (en) | 1999-08-19 |
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