Polynucleotide encoding autoantigens associated with endometriosis
This invention provides a polynucleotide encoding Repro-EN-1.0 and IB1, polypeptides associated with endometriosis. Auto-antibodies against Repro-EN-1.0 and IB1 have been found in subjects diagnosed with endometriosis. This invention also provides methods of using this polynucleotide and polypeptide.
1 . A recombinant polynucleotide comprising a nucleotide sequence encoding a polypeptide epitope of at least 5 amino acids of Repro-EN-1.0 (SEQ ID NO:2), wherein the epitope specifically binds to antibodies from subjects diagnosed with endometriosis.
2 . The polynucleotide of claim 1 wherein the nucleotide sequence is selected from the Repro-EN-1.0 sequence of SEQ ID NO: 1.
3 . The polynucleotide of claim 1 wherein the nucleotide sequence is a native Repro-EN-1.0 nucleotide sequence.
4 . The polynucleotide of claim 1 wherein the nucleotide sequence is identical to nucleotides 176 to 2755 of SEQ ID NO: 1.
5 . The polynucleotide of claim 1 further comprising an expression control sequence operatively linked to the nucleotide sequence.
6 . A recombinant polynucleotide comprising a nucleotide sequence encoding a polypeptide epitope of at least 5 amino acids of IB1 (SEQ ID NO:4), wherein the epitope specifically binds to antibodies from subjects diagnosed with endometriosis.
7 . The polynucleotide of claim 6 wherein the nucleotide sequence is selected from the IB1 sequence of SEQ ID NO:3.
8 . The polynucleotide of claim 6 wherein the nucleotide sequence is a native IB1 nucleotide sequence.
9 . The polynucleotide of claim 6 wherein the nucleotide sequence is identical to nucleotides 176 to 2986 of SEQ ID NO:3.
10 . The polynucleotide of claim 6 further comprising an expression control sequence operatively linked to the nucleotide sequence.
11 . A polynucleotide primer pair which amplifies a nucleotide sequence encoding a polypeptide eptiope of at least 5 amino acids of Repro-EN-1.0, wherein the epitope specifically binds to antibodies from subjects diagnosed with endometriosis, the pair comprising:
1 ) a 3′ primer of at least 7 nucleotides that specifically hybridizes to a 3′ end of the nucleotide sequence or downstream from the sequence, and
2) a 5′ primer of at least 7 nucleotides that specifically hybridizes to the 3′ end of the complement of the nucleotide sequence or downstream from the complement of the sequence.
12 . The polynucleotide primer pair of claim 11 wherein the 3′ primer has a sequence complementary to a nucleotide sequence selected from Repro-EN-1.0 cDNA (SEQ ID NO: 1), and the 5′ primer has a sequence identical to nucleotide sequence selected from Repro-EN-1.0 cDNA (SEQ ID NO: 1).
13 . The polynucleotide primer pair of claim 11 wherein the pair of polynucleotides are peptide nucleic acids.
14 . A polynucleotide primer pair which amplifies a nucleotide sequence encoding a polypeptide eptiope of at least 5 amino acids of IB1, wherein the epitope specifically binds to antibodies from subjects diagnosed with endometriosis, the pair comprising:
1 ) a 3′ primer of at least 7 nucleotides that specifically hybridizes to a 3′ end of the nucleotide sequence or downstream from the sequence, and
2) a 5′ primer of at least 7 nucleotides that specifically hybridizes to the 3′ end of the complement of the nucleotide sequence or downstream from the complement of the sequence.
15 . The polynucleotide primer pair of claim 14 wherein the 3′ primer has a sequence complementary to a nucleotide sequence selected from IB1 cDNA (SEQ ID NO:3), and the 5′ primer has a sequence identical to nucleotide sequence selected from IB1 cDNA (SEQ ID NO:3).
16 . The polynucleotide primer pair of claim 14 wherein the pair of polynucleotides are peptide nucleic acids.
17 . A recombinant cell comprising a recombinant polynucleotide comprising an expression control sequence operatively linked to a nucleotide sequence encoding a polypeptide epitope of at least 5 amino acids of Repro-EN-1.0 (SEQ ID NO:2), wherein the epitope specifically binds to antibodies from subjects diagnosed with endometriosis.
18 . A method for detecting a target polynucleotide comprising a nucleotide sequence selected from Repro-EN-1.0 cDNA (SEQ ID NO: 1) or its complement in a sample comprising the steps of:
(a) contacting the sample with a polynucleotide probe or primer comprising a sequence of at least 7 nucleotides that specifically hybridizes to the nucleotide sequence and
(b) detecting whether the probe or primer has specifically hybridized to the target polynucleotide,
whereby specific hybridization provides a detection of the target polynucleotide in the sample.
19 . The method of claim 18 wherein the polynucleotide probe or primer is a peptide nucleic acid.
20 . A recombinant cell comprising a recombinant polynucleotide comprising an expression control sequence operatively linked to a nucleotide sequence encoding a polypeptide epitope of at least 5 amino acids of IB1 (SEQ ID NO:4), wherein the epitope specifically binds to antibodies from subjects diagnosed with endometriosis.
21 . A method for detecting a target polynucleotide comprising a nucleotide sequence selected from IB1 cDNA (SEQ ID NO:3) or its complement in a sample comprising the steps of:
(a) contacting the sample with a polynucleotide probe or primer comprising a sequence of at least 7 nucleotides that specifically hybridizes to the nucleotide sequence and
(b) detecting whether the probe or primer has specifically hybridized to the target polynucleotide, whereby specific hybridization provides a detection of the target polynucleotide in the sample.
22 . The method of claim 21 wherein the polynucleotide probe or primer is a peptide nucleic acid.
23 . A purified, recombinant Repro-EN-1.0 polypeptide whose amino acid sequence is identical to that of SEQ ID NO:2, or an allelic variant of SEQ ID NO:2.
24 . A purified, recombinant IB1 polypeptide whose amino acid sequence is identical to that of SEQ ID NO:4, or an allelic variant of SEQ ID NO:4.
25 . A purified polypeptide comprising an epitope of at least 5 amino acids of Repro-EN-1.0 (SEQ ID NO:2), wherein the epitope specifically binds to antibodies from subjects diagnosed with endometriosis.
26 . A purified polypeptide comprising an epitope of at least 5 amino acids of IB1 (SEQ ID NO:4), wherein the epitope specifically binds to antibodies from subjects diagnosed with endometriosis.
27 . A composition consisting essentially of an antibody that specifically binds to Repro-EN-1.0 polypeptide (SEQ ID NO:2).
28 . The composition of claim 27 wherein the antibodies are monoclonal antibodies.
29 . A composition consisting essentially of an antibody that specifically binds to IB1 polypeptide (SEQ ID NO:4).
30 . The composition of claim 27 wherein the antibodies are monoclonal antibodies.
31 . A method for detecting a Repro-EN-1.0 polypeptide in a sample, comprising the steps of:
(a) contacting the sample with an antibody that specifically binds to the Repro-EN-1.0 polypeptide and
(b) detecting specific binding between the antibody and Repro-EN-1.0 polypeptide,
whereby specific binding provides a detection of Repro-EN-1.0 polypeptide in the sample.
32 . A method for detecting a IB1 polypeptide in a sample, comprising the steps of:
(a) contacting the sample with an antibody that specifically binds to the IB1 polypeptide and
(b) detecting specific binding between the antibody and IB1 polypeptide,
whereby specific binding provides a detection of IB1 polypeptide in the sample.
33 . A method for diagnosing endometriosis in a subject comprising the steps of:
(a) detecting a test amount of an antibody that specifically binds to Repro-EN-1.0 polypeptide in a sample from the subject; and
(b) comparing the test amount with a normal range of the antibody in a control sample from a subject who does not suffer from endometriosis,
whereby a test amount above the normal range provides a positive indication in the diagnosis of endometriosis.
34 . The method of claim 33 wherein the sample comprises blood serum.
35 . The method of claim 33 wherein the antibody is an IgE immunoglobulin.
36 . The method of claim 33 wherein the antibody is an IgG immunoglobulin.
37 . The method of claim 33 wherein the antibody is an IgG 4 immunoglobulin.
38 . The method of claim 33 wherein the step of detecting comprises capturing the antibody from the sample with an immobilized Repro-EN-1.0 or a peptide comprising an epitope of Repro-EN-1.0 and detecting captured antibody.
39 . The method of claim 33 wherein the step of detecting comprises capturing the antibody from the sample with an immobilized anti-immunoglobulin antibody and detecting captured antibody.
40 . The method of claim 38 wherein the step of detecting captured antibody comprises contacting the captured antibody with a detectable antibody that specifically binds immunoglobulins and detecting binding between the captured antibody and the detectable antibody.
41 . The method of claim 39 wherein the step of detecting captured antibody comprises contacting the captured antibody with Repro-EN-1.0 or a polypeptide comprising an epitope of Repro-EN-1.0 and detecting binding between the captured antibody and the Repro-EN-1.0 or polypeptide.
42 . A method for diagnosing endometriosis in a subject comprising the steps of:
(a) detecting a test amount of an antibody that specifically binds to IB1 polypeptide in a sample from the subject; and
(b) comparing the test amount with a normal range of the antibody in a control sample from a subject who does not suffer from endometriosis,
whereby a test amount above the normal range provides a positive indication in the diagnosis of endometriosis.
43 . The method of claim 42 wherein the sample comprises blood serum.
44 . The method of claim 42 wherein the antibody is an IgE immunoglobulin.
45 . The method of claim 42 wherein the antibody is an IgG immunoglobulin.
46 . The method of claim 42 wherein the antibody is an IgG4 immunoglobulin.
47 . The method of claim 42 wherein the step of detecting comprises capturing the antibody from the sample with an immobilized IB1 or a peptide comprising an epitope of IB1 and detecting captured antibody.
48 . The method of claim 46 wherein the step of detecting comprises capturing the antibody from the sample with an immobilized anti-immunoglobulin antibody and detecting captured antibody.
49 . The method of claim 47 wherein the step of detecting captured antibody comprises contacting the captured antibody with a detectable antibody that specifically binds immunoglobulins and detecting binding between the captured antibody and the detectable antibody.
50 . The method of claim 48 wherein the step of detecting captured antibody comprises contacting the captured antibody with IB1 or a polypeptide comprising an epitope of IB1 and detecting binding between the captured antibody and the I1 or polypeptide.
51 . A method for use in following the progress of endometriosis in a subject comprising the steps of:
(a) detecting first and second amounts of an antibody that specifically binds Repro-EN-1.0 polypeptide in samples from the subject at a first and a second time, respectively; and
(b) comparing the first and second amounts,
whereby an increase between the first and second amounts indicates progression of the endometriosis and a decrease between the first and second amounts indicates remission of the endometriosis.
52 . A method for use in following the progress of endometriosis in a subject comprising the steps of:
(a) detecting first and second amounts of an antibody that specifically binds IB1 polypeptide in samples from the subject at a first and a second time, respectively; and
(b) comparing the first and second amounts,
whereby an increase between the first and second amounts indicates progression of the endometriosis and a decrease between the first and second amounts indicates remission of the endometriosis.
53 . An isolated MHC-peptide complex comprising:
at least a portion of an MHC Class I molecule or an MHC Class II molecule, wherein the portion comprises a binding site that specifically binds a peptide having an amino acid binding motif specific to the molecule, and wherein the portion engages in CD4-mediated or CD8-mediated binding to T cells, and
a peptide of at least 8 amino acids in a sequence selected from the amino acid sequence of Repro-EN-1.0 (SEQ ID NO:2), wherein the peptide comprises the amino acid binding motif and comprises an epitope that specifically binds to a T cell receptor;
wherein the complex specifically binds a T cell having a T cell receptor that specifically binds to the epitope, and wherein specific binding induces anergy in the T cell.
54 . An isolated MHC-peptide complex comprising:
at least a portion of an MHC Class I molecule or an MHC Class II molecule, wherein the portion comprises a binding site that specifically binds a peptide having an amino acid binding motif specific to the molecule, and wherein the portion engages in CD4-mediated or CD8-mediated binding to T cells, and
a peptide of at least 8 amino acids in a sequence selected from the amino acid sequence of IB1 (SEQ ID NO:4), wherein the peptide comprises the amino acid binding motif and comprises an epitope that specifically binds to a T cell receptor;
wherein the complex specifically binds a T cell having a T cell receptor that specifically binds to the epitope, and wherein specific binding induces anergy in the T cell.
55 . A method for treating endometriosis in a subject comprising the step of inhibiting an immune response against Repro-EN-1.0 in the subject.
56 . The method of claim 55 comprising administering to the subject an immunosuppressant in an amount effective to inhibit the immune response.
57 . The method of claim 55 comprising administering to the subject an isolated MHC-peptide complex of claim 54 in an amount effective to inhibit the immune response.
58 . The method of claim 55 comprising administering to the subject an anti-idiotypic antibody that specifically binds to an antigen binding site of an antibody that specifically binds to Repro-EN-1.0 in an amount effective to inhibit the immune response.
59 . A method for treating endometriosis in a subject comprising the step of inhibiting an immune response against IB1 in the subject.
60 . The method of claim 59 comprising administering to the subject an immunosuppressant in an amount effective to inhibit the immune response.
61 . The method of claim 59 comprising administering to the subject an isolated MHC-peptide complex of claim 58 in an amount effective to inhibit the immune response.
62 . The method of claim 59 comprising administering to the subject an anti-idiotypic antibody that specifically binds to an antigen binding site of an antibody that specifically binds to IB1 in an amount effective to inhibit the immune response.
63 . A screening method for determining whether a compound increases or decreases the expression of Repro-EN-1.0 in a cell comprising contacting the cell with the compound and determining whether the production of Repro-EN-1.0 mRNA or polypeptide are increased or decreased.
64 . A screening method for determining whether a compound increases or decreases the expression of IB1 in a cell comprising contacting the cell with the compound and determining whether the production of IB1 mRNA or polypeptide are increased or decreased.
65 . A method of detecting a chromosomal translocation of a Repro-EN-1.0 gene comprising the steps of:
a) hybridizing a labeled polynucleotide probe that specifically hybridizes with the Repro-EN-1.0 nucleotide sequence of SEQ ID NO: 1 or its complement, to a chromosome spread from a cell sample to determine the pattern of hybridization and
b) determining whether the pattern of hybridization differs from a normal pattern;
whereby a difference in the pattern represents a translocation.
66 . A method of detecting a chromosomal translocation of a IB1 gene comprising the steps of:
a) hybridizing a labeled polynucleotide probe that specifically hybridizes with the IB1 nucleotide sequence of SEQ ID NO:3 or its complement, to a chromosome spread from a cell sample to determine the pattern of hybridization and
b) determining whether the pattern of hybridization differs from a normal pattern;
whereby a difference in the pattern represents a translocation.
67 . A method of detecting polymorphic forms of Repro-EN-1.0 comprising the steps of:
a) determining the identity of a nucleotide or amino acid at a selected position within the sequence of a test Repro-EN-1.0 gene or polypeptide;
b) determining the identity of the nucleotide or amino acid at the corresponding position of native Repro-EN-1.0 (SEQ ID NO: 1 or 2) gene or polypeptide; and
c) comparing the identity from the test gene or polynucleotide with the identity of the native gene or polypeptide, whereby a difference in identity indicates that the test polynucleotide is a polymorphic form of Repro-EN-1.0.
68 . A method of detecting polymorphic forms of IB1 comprising the steps of:
a) determining the identity of a nucleotide or amino acid at a selected position within the sequence of a test IB1 gene or polypeptide;
b) determining the identity of the nucleotide or amino acid at the corresponding position of native IB1 (SEQ ID NO:3 or 4) gene or polypeptide; and
c) comparing the identity from the test gene or polynucleotide with the identity of the native gene or polypeptide, whereby a difference in identity indicates that the test polynucleotide is a polymorphic form of IB1.