Biomarkers For Fatty Liver Disease And Methods Using The Same

Abstract

The present invention provides various biomarkers of fatty liver disease, including steatosis and steatohepatitis. The present invention also provides various methods of using the biomarkers, including methods for diagnosis of fatty liver disease, methods of determining predisposition to fatty liver disease, methods of monitoring progression/regression of fatty liver disease, methods of assessing efficacy of compositions for treating fatty liver disease, methods of screening compositions for activity in modulating biomarkers of fatty liver disease, methods of treating fatty liver disease, as well as other methods based on biomarkers of fatty liver disease.

1 . A method of diagnosing whether a subject has steatohepatitis, comprising:
 analyzing a biological sample from a subject to determine the level(s) of one or more biomarkers for steatohepatitis in the sample, wherein the one or more biomarkers are selected from Tables 1, 3, 4B, 6B, 9, 10, 11, 12, 13, and 15 and  FIGS. 2 ,  3 ,  12 , and  13 ; and   comparing the level(s) of the one or more biomarkers in the sample to steatohepatitis-positive and/or steatohepatitis-negative reference levels of the one or more biomarkers in order to diagnose whether the subject has steatohepatitis.   
     
     
         2 . The method of  claim 1 , wherein the one or more biomarkers are selected from those biomarkers in Tables 1, 3, 4B, 6B, 9, 10, 11, 12, 13, and 15 and  FIGS. 2 ,  3 ,  12 , and  13  having p values of less than 0.05 and/or those biomarkers in Tables 1, 3, 4B, 6B, 9, 10, 11, 12, 13, and  FIGS. 2 and 3  having q values of less than 0.10. 
     
     
         3 . The method of  claim 1 , wherein the sample analyzed is from a male subject and the biomarkers are selected from Table 12. 
     
     
         4 . The method of  claim 1 , wherein the sample analyzed is from a female subject and the biomarkers are selected from Table 13. 
     
     
         5 . The method of  claim 1 , wherein the sample is analyzed using one or more techniques selected from the group consisting of mass spectrometry, enzymatic or biochemical reactions, clinical chemistry, ELISA, and antibody linkage. 
     
     
         6 . The method of  claim 1 , wherein the one or more biomarkers are selected from the group consisting of glycochenodeoxycholate, glycocholate, taurocholate, butyryl carnitine, gamma glutamyltyrosine, kynurenine, glutamyl valine, gamma glutamylphenylalanine, gamma glutamylleucine, glutamate, carnitine, propionylcarnitine, cysteine-glutathione disulfide, cholate, taurochenodeoxycholate, taurodeoxycholate, glycodeoxycholate, and combinations thereof. 
     
     
         7 . The method of  claim 1 , wherein the biological sample is a plasma sample or a urine sample. 
     
     
         8 . The method of  claim 1 , wherein the one or more biomarkers are selected from Tables 1, 4B, 6B, 10, 11, 12, 13, and 15 and  FIGS. 2 ,  3 ,  12 , and  13 . 
     
     
         9 . The method of  claim 8 , wherein the one or more biomarkers are selected from Tables 1, 6B, 10, 12, 13, and 15 and  FIGS. 2 and 13 . 
     
     
         10 . The method of  claim 8 , wherein the one or more biomarkers are selected from Tables 4B, 11, 12, 13, and 15 and  FIGS. 3 and 12 . 
     
     
         11 . A method of determining whether a subject is predisposed to developing steatohepatitis, comprising:
 analyzing a biological sample from a subject to determine the level(s) of one or more biomarkers for steatohepatitis in the sample, wherein the one or more biomarkers are selected from Tables 1, 3, 4B, 6B, 9, 10, 11, 12, 13, and 15 and  FIGS. 2 ,  3 ,  12 , and  13 ; and   comparing the level(s) of the one or more biomarkers in the sample to steatohepatitis-positive and/or steatohepatitis-negative reference levels of the one or more biomarkers in order to determine whether the subject is predisposed to developing steatohepatitis.   
     
     
         12 . A method of monitoring progression/regression of steatohepatitis in a subject comprising:
 analyzing a first biological sample from a subject to determine the level(s) of one or more biomarkers for steatohepatitis in the sample, wherein the one or more biomarkers are selected from Tables 1, 3, 4B, 6B, 9, 10, 11, 12, 13, and 15 and  FIGS. 2 ,  3 ,  12 , and  13  and the first sample is obtained from the subject at a first time point;   analyzing a second biological sample from a subject to determine the level(s) of the one or more biomarkers, wherein the second sample is obtained from the subject at a second time point; and   comparing the level(s) of one or more biomarkers in the first sample to the level(s) of the one or more biomarkers in the second sample in order to monitor the progression/regression of steatohepatitis in the subject.   
     
     
         13 . The method of  claim 12 , wherein the method further comprises comparing the level(s) of one or more biomarkers in the first sample, the level(s) of one or more biomarkers in the second sample, and/or the results of the comparison of the level(s) of the one or more biomarkers in the first and second samples to steatohepatitis-positive and/or steatohepatitis-negative reference levels of the one or more biomarkers. 
     
     
         14 . A method of assessing the efficacy of a composition for treating steatohepatitis comprising:
 analyzing, from a subject having steatohepatitis and currently or previously being treated with a composition, a biological sample to determine the level(s) of one or more biomarkers for steatohepatitis selected from Tables 1, 3, 4B, 6B, 9, 10, 11, 12, 13, and 15 and  FIGS. 2 ,  3 ,  12 , and  13 ; and   comparing the level(s) of the one or more biomarkers in the sample to (a) levels of the one or more biomarkers in a previously-taken biological sample from the subject, wherein the previously-taken biological sample was obtained from the subject before being treated with the composition, (b) steatohepatitis-positive reference levels of the one or more biomarkers, and/or (c) steatohepatitis-negative reference levels of the one or more biomarkers.   
     
     
         15 . A method for assessing the efficacy of a composition in treating steatohepatitis, comprising:
 analyzing a first biological sample from a subject to determine the level(s) of one or more biomarkers for steatohepatitis selected from Tables 1, 3, 4B, 6B, 9, 10, 11, 12, 13, and 15 and  FIGS. 2 ,  3 ,  12 , and a 3 , the first sample obtained from the subject at a first time point;   administering the composition to the subject;   analyzing a second biological sample from the subject to determine the level(s) of the one or more biomarkers, the second sample obtained from the subject at a second time point after administration of the composition; and   comparing the level(s) of one or more biomarkers in the first sample to the level(s) of the one or more biomarkers in the second sample in order to assess the efficacy of the composition for treating steatohepatitis.   
     
     
         16 . A method for screening a composition for activity in modulating one or more biomarkers of steatohepatitis, comprising:
 contacting one or more cells with a composition;   analyzing at least a portion of the one or more cells or a biological sample associated with the cells to determine the level(s) of one or more biomarkers of steatohepatitis selected from Tables 1, 3, 4B, 6B, 9, 10, 11, 12, 13, and 15 and  FIGS. 2 ,  3 ,  12 , and  13 ; and   comparing the level(s) of the one or more biomarkers with predetermined standard levels for the biomarkers to determine whether the composition modulated the level(s) of the one or more biomarkers.   
     
     
         17 . The method of  claim 16 , wherein the predetermined standard levels for the biomarkers are level(s) of the one or more biomarkers in the one or more cells in the absence of the composition. 
     
     
         18 . The method of  claim 16 , wherein the predetermined standard levels for the biomarkers are level(s) of the one or more biomarkers in one or more control cells not contacted with the composition. 
     
     
         19 . The method of  claim 16 , wherein the method is conducted in vivo. 
     
     
         20 . The method of  claim 16 , wherein the method is conducted in vitro. 
     
     
         21 . A method for treating a subject having steatohepatitis comprising administering to the subject an effective amount of one or more biomarkers selected from Tables 1, 3, 4B, 6B, 9, 10, 11, 12, 13, and 15 and  FIGS. 2 ,  3 ,  12 , and  13  that are decreased in steatohepatitis. 
     
     
         22 . A method of distinguishing steatosis from NASH in a subject having liver disease or disorder, comprising:
 analyzing a biological sample from a subject to determine the level(s) of one or more biomarkers for steatosis and/or NASH in the sample, wherein the one or more biomarkers are selected from Tables 1, 2, 3, 4B, 5B, 6B, 8, 9, 10, 11, 12, 13, and 15 and  FIGS. 1 ,  2 ,  3 ,  12 , and  13 ; and   comparing the level(s) of the one or more biomarkers in the sample to steatosis-positive reference levels that distinguish over NASH and/or to NASH-positive reference levels that distinguish over steatosis in order to determine whether the subject has NASH.   
     
     
         23 . The method of  claim 22 , wherein the one or more biomarkers are selected from Tables 3, 9, 12, 13, and 15. 
     
     
         24 . The method of  claim 22 , wherein the one or more biomarkers are selected from Tables 4B, 11, 12, 13, and 15 and  FIGS. 3 and 12 . 
     
     
         25 . A method of diagnosing whether a subject has NASH, comprising:
 analyzing a biological sample from a subject to determine the level(s) of one or more biomarkers for NASH in the sample, wherein the one or more biomarkers are selected from Tables 1, 3, 4B, 6B, 9, 10, 11, 12, 13, and 15 and  FIGS. 2 ,  3 ,  12 , and  13 ; and   comparing the level(s) of the one or more biomarkers in the sample to NASH-positive and/or NASH-negative reference levels of the one or more biomarkers in order to diagnose whether the subject has NASH.