Methods for identifying patterns of ifn induced expression and use in diagnosis, monitoring and therapy

Abstract

The present inventors identified a subpopulation of genes induced by type I and type II IFNs in a human submandibular gland (HSG) epithelial cell line. Unexpectedly, it was found that the majority of genes that are highly up-regulated by IFN-α are also highly induced by IFN-γ. In contrast, there was a substantial group of genes that are highly induced by IFN-γ only. In target tissues, this identified subpopulation of genes and probes allow different IFN patterns to be discerned, enabling more precise molecular classification of patient subpopulations. The identified gene probes are useful for selecting and monitoring therapy, and for defining efficacy of novel agents in the autoimmune rheumatic diseases.

1 - 5 . (canceled) 
     
     
         6 . A method for monitoring the treatment of a subject having a rheumatic disease comprising:
 a) preparing a protein lysate from a first tissue sample of the subject;   b) analyzing the protein lysate of a) for the presence of at least one marker of type I IFN activity selected from the group consisting of MDA5 and IFIT3, and at least one marker of type II IFN activity selected from the group consisting of: GBP1, GBP2, INDO, UBD, IRF1, RARRES3, WARS, CXCL10, IL18BP, SERPING1, and GBP5, plus a loading control protein selected from the group consisting of β-actin and vinculin, wherein detection of an amount and/or a concentration of the at least one marker is achieved by exposing the protein lysate of a) to one or more antibodies specific to the one or more markers which are markers of type I IFN activity and type II IFN activity;   c) normalizing the protein expression levels of MDA5, IFIT3, GBP1, GBP2, INDO, UBD, IRF1, RARRES3, WARS, CXCL10, IL18BP, SERPING1, and GBP5 proteins in the first tissue sample to the expression of the loading control protein in the same sample;   d) administering to the subject an immunological therapy for the rheumatic disease;   e) preparing a protein lysate from a second tissue sample of the subject; and   f) comparing the normalized protein expression levels of MDA5, IFIT3, GBP1, GBP2, INDO, UBD, IRF1, RARRES3, WARS, CXCL10, IL18BP, SERPING1, and GBP5 proteins in the first tissue sample against the expression levels of the same proteins in the second tissue sample.   
     
     
         7 . (canceled) 
     
     
         8 . The method of  claim 6 , wherein the analyzing step b) is performed by using a method comprising PCR, qPCR, centrifugation, sequencing, mutation analysis, polymorphism-analysis, or any combination thereof. 
     
     
         9 . The method of  claim 6 , wherein the rheumatic disease is Sjögren syndrome (SS), dermatomyositis (DM), polymyositis, scleroderma, or systemic lupus erythematosus (SLE). 
     
     
         10 . The method of  claim 6 , wherein step b) comprises analyzing the prepared protein lysate for the presence of both markers of type I IFN activity selected from the group consisting of MDA5 and IFIT3, and two or more markers of type II IFN activity selected from the group consisting of: GBP1, GBP2, INDO, UBD, IRF1, RARRES3, WARS, CXCL10, IL18BP, SERPING1, and GBP5. 
     
     
         11 . The method of  claim 6 , wherein step b) comprises analyzing the prepared protein lysate for the presence of both markers of type I IFN activity selected from the group consisting of MDA5 and IFIT3, and three or more markers of type II IFN activity selected from the group consisting of: GBP1, GBP2, INDO, UBD, IRF1, RARRES3, WARS, CXCL10, IL18BP, SERPING1, and GBP5. 
     
     
         12 . The method of  claim 6 , wherein step b) comprises analyzing the prepared protein lysate for the presence of both markers of type I IFN activity selected from the group consisting of MDA5 and IFIT3, and four or more markers of type II IFN activity selected from the group consisting of: GBP1, GBP2, INDO, UBD, IRF1, RARRES3, WARS, CXCL10, IL18BP, SERPING1, and GBP5. 
     
     
         13 . The method of  claim 6 , wherein step b) comprises analyzing the prepared protein lysate for the presence of both markers of type I IFN activity selected from the group consisting of MDA5 and IFIT3, and five or more markers of type II IFN activity selected from the group consisting of: GBP1, GBP2, INDO, UBD, IRF1, RARRES3, WARS, CXCL10, IL18BP, SERPING1, and GBP5. 
     
     
         14 . The method of  claim 6 , wherein step b) comprises analyzing the prepared protein lysate for the presence of both markers of type I IFN activity selected from the group consisting of MDA5 and IFIT3, and markers of type II IFN activity selected from the group consisting of GBP1 and GBP2. 
     
     
         15 . The method of  claim 6 , wherein step b) comprises analyzing the prepared protein lysate for the presence of both markers of type I IFN activity selected from the group consisting of MDA5 and IFIT3, and markers of type II IFN activity selected from the group consisting of GBP1, GBP2, and UBD. 
     
     
         16 . The method of  claim 6 , wherein step b) comprises analyzing the prepared protein lysate for the presence of both markers of type I IFN activity selected from the group consisting of MDA5 and IFIT3, and markers of type II IFN activity selected from the group consisting of GBP1, GBP2, and CXCL10. 
     
     
         17 . The method of  claim 6 , wherein step b) comprises analyzing the prepared protein lysate for the presence of both markers of type I IFN activity selected from the group consisting of MDA5 and IFIT3, and markers of type II IFN activity consisting of GBP1 and GBP2, and one or more markers selected from the group consisting of INDO, UBD, IRF1, RARRES3, WARS, CXCL10, IL18BP, SERPING1, and GBP5. 
     
     
         18 . The method of  claim 6 , wherein a tissue sample comprises a liquid sample from the subject. 
     
     
         19 . The method of  claim 18 , wherein the liquid sample comprises a blood or serum sample. 
     
     
         20 . The method of  claim 6 , wherein a tissue sample comprises a solid tissue sample from the subject. 
     
     
         21 . The method of  claim 20 , wherein the solid tissue sample comprises a salivary gland sample or a muscle tissue sample.