Methods and compositions for detecting autoimmune disorders

Abstract

The invention provides methods and compositions useful for detecting autoimmune disorders.

1 . A method comprising determining whether a subject comprises a cell that expresses at least 2 of the genes listed in Table 1, 2 and/or 3 at a level greater than the expression level of the respective genes in a normal reference sample, wherein presence of said cell indicates that the subject has an autoimmune disorder.  
     
     
         2 . A method of predicting responsiveness of a subject to autoimmune disease therapy, said method comprising determining whether the subject comprises a cell that expresses at least 2 of the genes listed in Table 1, 2 and/or 3 at a level greater than the expression level of the respective genes in a normal reference sample, wherein presence of said cell indicates that the subject would be responsive to the autoimmune disease therapy.  
     
     
         3 . (canceled)  
     
     
         4 . A method for detecting an autoimmune disease state in a subject, said method comprising determining whether the subject comprises a cell that expresses at least 2 of the genes listed in Table 1, 2 and/or 3 at a level greater than the expression level of the respective genes in a normal reference sample, wherein detection of said cell is indicative of presence of an autoimmune disease state in the subject.  
     
     
         5 . A method for assessing predisposition of a subject to develop an autoimmune disorder, said method comprising determining whether the subject comprises a cell that expresses at least 2 of the genes listed in Table 1, 2 and/or 3 at a level greater than the expression level of the respective genes in a normal reference sample, wherein detection of said cell is indicative of a predisposition for the subject to develop the autoimmune disorder.  
     
     
         6 . A method for diagnosing an autoimmune disorder in a subject, said method comprising determining whether the subject comprises a cell that expresses at least 2 of the genes listed in Table 1, 2 and/or 3 at a level greater than the expression level of the respective genes in a normal reference sample, wherein detection of said cell indicates that the subject has said autoimmune disorder.  
     
     
         7 . The method of  claim 1 , wherein said at least 2 genes comprise (i) OAS3 and HERC5; or (ii) ESPTI1 and HERC5; or (iii) ESPTI1 and TYKI; or HERC5 and TYKI.  
     
     
         8 . The method of  claim 1 , wherein said at least 2 genes comprises a 3-gene combination as listed in Table 4B.  
     
     
         9 . The method of  claim 8 , wherein the 3-gene combination comprises (1) IFIT4, OAS1, and MX1; or (2) OASL, CHMP5, and ZBP1; or (3) IFI44L, OASL, and CIG5; or (4) IFI44L, CIG5, and ZBP1; or (5) EPSTI1, TYKI, and MX1; or (6) IFIT4, HERC5, and TYKI; or (7) IFIT4, TYKI, and XIAP; or (8) IFI44L, OASL, and ZBP1; or (9) IFI44L, IFIT4, and OASL; or (10) IFI4, OAS1, and IFIT1; or (11) EPSTI1, HERC5, and TYKI; or (12) IFI44L, EPSTI1, and OASL; or (13) IFI44L, EPSTI1, and OAS3; or (14) EPSTI1, TYKI, and IFIT1; or (15) G1P2, SAMD9L, and SP110.  
     
     
         10 . The method of  claim 1 , further comprising the use of a housekeeping gene.  
     
     
         11 . The method of  claim 1 , wherein the normal reference sample comprises a healthy cell or tissue.  
     
     
         12 . A composition comprising polynucleotides capable of specifically hybridizing to at least 2 of the genes listed in Table 1, 2, 3 and/or 4A or complements of said genes.  
     
     
         13 . The composition of  claim 12 , wherein the polynucleotides are provided as an array, a gene chip, or gene set.  
     
     
         14 . The composition of  claim 12  comprising polynucleotides capable of specifically hybridizing to at least 3 genes listed in Table 1, 2, 3 and/or 4A or complements of said genes.  
     
     
         15 . The composition of  claim 14 , wherein said at least 3 genes comprises a 3-gene combination listed in Table 4B.  
     
     
         16 . The composition of  claim 15 , wherein the 3-gene combination comprises (1) IFIT4, OAS1, and MX1; or (2) OASL, CHMP5, and ZBP1; or (3) IFI44L, OASL, and CIG5; or (4) IFI44L, CIG5, and ZBP1; or (5) EPSTI1, TYKI, and MX1; or (6) IFIT4, HERC5, and TYKI; or (7) IFIT4, TYKI, and XIAP; or (8) IFI44L, OASL, and ZBP1; or (9) IFI44L, IFIT4, and OASL; or (10) IFI4, OAS1, and IFIT1; or (11) EPSTI1, HERC5, and TYKI; or (12) IFI44L, EPSTI1, and OASL; or (13) IFI44L, EPSTI1, and OAS3; or (14) EPSTI1, TYKI, and IFIT1; or (15) G1P2, SAMD9L, and SP110.  
     
     
         17 . The composition of  claim 12 , further comprising a housekeeping gene.  
     
     
         18 . A kit comprising the composition of  claim 12 , and instructions for using the composition to detect an autoimmune disorder by determining whether expression of the genes provided is at a level greater than the expression level of the respective genes in a normal reference sample.  
     
     
         19 . The kit of any of  claim 18 , wherein the normal reference sample comprises a healthy cell or tissue.  
     
     
         20 - 25 . (canceled)