Identification of sequences particularly useful for the diagnosis and identification of therapeutic targets for osteoarthritis

Abstract

The invention relates to the identification and selection of sequences which demonstrate particular advantage in identifying individuals having osteoarthritis (OA). The invention also provides a selection of sequences particularly useful in diagnosing the degree of advancement of osteoarthritis of an individual and in the identification of novel therapeutic targets for OA. The invention further provides for the use of these sequences as a tool to diagnose disease progression and to monitor the efficacy of therapeutic regimens.

1 . An isolated biomarker comprising 51% or more genes selected from the group consisting of the nucleic acids identified in  FIGS. 1 ,  3 ,  5 ,  6   a  and  7   a.    
     
     
         2 . An isolated biomarker comprising two or more genes selected from the group consisting of the nucleic acids identified in  FIGS. 1 ,  3 ,  5 ,  6   a  and  7   a.    
     
     
         3 . An isolated biomarker consisting essentially of the nucleic acids identified in  FIGS. 1 ,  3 ,  5 ,  6   a  and  7   a.    
     
     
         4 . An isolated biomarker comprising 51% or more genes selected from the group consisting of the nucleic acids identified in  FIG. 6   b.    
     
     
         5 . An isolated biomarker comprising two or more genes selected from the group consisting of the nucleic acids identified in  FIG. 6   b.    
     
     
         6 . An isolated biomarker consisting essentially of the nucleic acids identified in  FIG. 6   b.    
     
     
         7 . An isolated biomarker comprising 51% or more genes selected from the group consisting of the nucleic acids identified in  FIG. 6   c.    
     
     
         8 . An isolated biomarker comprising two or more genes selected from the group consisting of the nucleic acids identified in  FIG. 6   c.    
     
     
         9 . An isolated biomarker consisting essentially of the nucleic acids identified in  FIG. 6   c.    
     
     
         10 . An isolated biomarker comprising 51% or more genes selected from the group consisting of the nucleic acids identified in  FIGS. 2 ,  4 ,  5 ,  6   d  and  7   b.    
     
     
         11 . An isolated biomarker comprising two or more genes selected from the group consisting of the nucleic acids identified in  FIGS. 2 ,  4 ,  5 ,  6   d  and  7   b.    
     
     
         12 . An isolated biomarker consisting essentially of the nucleic acids identified in  FIGS. 2 ,  4 ,  5 ,  6   d  and  7   b.    
     
     
         13 . A method of diagnosing mild osteoarthritis in an individual, comprising determining the level of expression of a biomarker in a sample wherein said biomarker comprises one or more polynucleotide sequences selected from the group consisting of the nucleic acids identified in  FIGS. 1 ,  3 ,  5 ,  6   a ,  7   a , whereby a difference in said level of expression of said biomarker compared to a biomarker control is indicative or predictive of mild osteoarthritis. 
     
     
         14 . The method of  claim 13 , wherein said polynucleotide sequences are from the 5′ region of a gene selected from the group consisting of the nucleic acids identified in  FIGS. 1 ,  3 ,  5 ,  6   a ,  7   a.    
     
     
         15 . The method of  claim 13 , wherein said polynucleotide sequences are from the 3′ region of a gene selected from the group consisting of the nucleic acids identified in  FIGS. 1 ,  3 ,  5 ,  6   a ,  7   a.    
     
     
         16 . The method of  claim 13 , wherein said polynucleotide sequences are from the internal coding region of a gene selected from the group consisting of the nucleic acids identified in  FIGS. 1 ,  3 ,  5 ,  6   a ,  7   a.    
     
     
         17 . A method of diagnosing severe osteoarthritis in an individual, comprising determining the level of expression of a biomarker in a sample wherein said biomarker comprises one or more polynucleotide sequences selected from the group consisting of the nucleic acids identified in  FIGS. 2 ,  4 ,  5 ,  6   d ,  7   b  whereby a difference in said level of expression of said biomarker compared to a biomarker control is indicative or predictive of severe osteoarthritis. 
     
     
         18 . The method of  claim 17 , wherein said polynucleotide sequences are from the 5′ region of a gene selected from the group consisting of the nucleic acids identified in  FIGS. 2 ,  4 ,  5 ,  6   d ,  7   b.    
     
     
         19 . The method of  claim 17 , wherein said polynucleotide sequences are from the 3′ region of a gene selected from the group consisting of the nucleic acids identified in  FIGS. 2 ,  4 ,  5 ,  6   d ,  7   b.    
     
     
         20 . The method of  claim 17 , wherein said polynucleotide sequences are from the internal coding region of a gene selected from the group consisting of the nucleic acids identified in  FIGS. 2 ,  4 ,  5 ,  6   d ,  7   b.    
     
     
         21 . A method of diagnosing moderate osteoarthritis in an individual, comprising determining the level of expression of a biomarker in a sample wherein said biomarker comprises one or more polynucleotide sequences selected from the group consisting of the nucleic acids identified in  FIG. 6   b , whereby a difference in said level of expression of said biomarker compared to a biomarker control is indicative or predictive of moderate osteoarthritis. 
     
     
         22 . The method of  claim 21 , wherein said polynucleotide sequences are from the 5′ region of a gene selected from the group consisting of the nucleic acids identified in  FIG. 6   b.    
     
     
         23 . The method of  claim 21 , wherein said polynucleotide sequences are from the 3′ region of a gene selected from the group consisting of the nucleic acids identified in  FIG. 6   b.    
     
     
         24 . The method of  claim 21 , wherein said polynucleotide sequences are from the internal coding region of a gene selected from the group consisting of the nucleic acids identified in  FIG. 6   b.    
     
     
         25 . A method of diagnosing marked osteoarthritis in an individual, comprising determining the level of expression of a biomarker in a sample wherein said biomarker comprises one or more polynucleotide sequences selected from the group consisting of the nucleic acids identified in  FIG. 6   c , whereby a difference in said level of expression of said biomarker compared to a biomarker control is indicative or predictive of marked osteoarthritis. 
     
     
         26 . The method of  claim 25 , wherein said polynucleotide sequences are from the 5′ region of a gene selected from the group consisting of the nucleic acids identified in  FIG. 6   c.    
     
     
         27 . The method of  claim 25 , wherein said polynucleotide sequences are from the 3′ region of a gene selected from the group consisting of the nucleic acids identified in  FIG. 6   c.    
     
     
         28 . The method of  claim 25 , wherein said polynucleotide sequences are from the internal coding region of a gene selected from the group consisting of the nucleic acids identified in  FIG. 6   c.    
     
     
         29 . A method for monitoring efficacy of a drug for treatment of mild osteoarthritis in a patient, comprising the steps of:
 (a) obtaining a sample from a patient before treatment and a second sample from said patient after said treatment;   (b) detecting the level of expression of the isolated biomarker of  claim 2  in said first sample and said second sample; and   (c) determining a difference in said level of expression of said biomarker in said first sample as compared with said second sample, wherein said difference is indicative of the efficacy of said drug for said treatment of mild osteoarthritis in said patient.   
     
     
         30 . A method for monitoring efficacy of a drug for treatment of moderate osteoarthritis in a patient, comprising the steps of:
 (a) obtaining a sample from a patient before treatment and a second sample from said patient after said treatment;   (b) detecting the level of expression of the isolated biomarker of  claim 5  in said first sample and said second sample; and   (c) determining a difference in said level of expression of said biomarker in said first sample as compared with said second sample, wherein said difference is indicative of the efficacy of said drug for said treatment of moderate osteoarthritis in said patient.   
     
     
         31 . A method for monitoring efficacy of a drug for treatment of marked osteoarthritis in a patient, comprising the steps of:
 (a) obtaining a sample from a patient before treatment and a second sample from said patient after said treatment;   (b) detecting the level of expression of the isolated biomarker of  claim 8  in said first sample and said second sample; and   
       determining a difference in said level of expression of said biomarker in said first sample as compared with said second sample, wherein said difference is indicative of the efficacy of said drug for said treatment of marked osteoarthritis in said patient. 
     
     
         32 . A method for monitoring efficacy of a drug for treatment of severe osteoarthritis in a patient, comprising the steps of:
 (a) obtaining a sample from a patient before treatment and a second sample from said patient after said treatment;   (b) detecting the level of expression of the isolated biomarker of  claim 11  in said first sample and said second sample; and   (c) determining a difference in said level of expression of said biomarker in said first sample as compared with said second sample, wherein said difference is indicative of the efficacy of said drug for said treatment of severe osteoarthritis in said patient.   
     
     
         33 . A method of identifying a therapeutic agent for the treatment of osteoarthritis, said method comprising:
 a) providing a sample from a patient diagnosed with osteoarthrtis;   b) measuring the level of expression of a biomarker as set out in  FIGS. 1-7  in the presence and the absence of said therapeutic agent; and   c) comparing said level of expression measured in the presence of said therapeutic agent to said level of expression measured in the absence of said therapeutic agent, wherein a decrease in the differential expression of said biomarker is indicative of a therapeutic agent for the treatment of osteoarthritis.   
     
     
         34 . The methods of  claims 13 ,  17 ,  21  and  25 , wherein said sample is human cartilage. 
     
     
         35 . The methods of  claims 13 ,  17 ,  21  and  25 , wherein said biomarker is immobilized to a micro array. 
     
     
         36 . The methods of  claims 13 ,  17 ,  21  and  25 , wherein said level of expression of said biomarker is determined by hybridization to a microarray or real time RT-PCR.