Nonalcoholic Fatty Liver Disease (NAFLD) and Nonalcoholic Steatohepatitis (NASH) Biomarkers and Uses Thereof

Abstract

Methods, compositions, and kits for determining whether a subject has non-alcoholic fatty liver disease (NAFLD), and more specifically one or more of the following associated conditions of steatosis, lobular inflammation, hepatocyte ballooning and fibrosis, are provided. Methods, compositions, and kits for determining whether a subject has non-alcoholic steatosis are also provided. Methods, compositions, and kits for determining whether a subject has non-alcoholic steatohepatitis (NASH) are also provided.

1 . A method of detecting protein levels of a set of biomarkers in a sample from a subject, comprising (a) forming a biomarker panel having N biomarker proteins from the biomarker proteins listed in Table 15 and Table 16; (b) contacting the biomarker proteins with a set of biomarker capture reagents, wherein each biomarker capture reagent of the set of biomarker capture reagents specifically binds to a different biomarker protein being detected; and (c) detecting the level of each of the N biomarker proteins of the panel in the sample, wherein N is at least 5. 
     
     
         2 . The method of  claim 1 , wherein N is 5 to 10, or N is 6 to 10, or N is 7 to 10, or N is 8 to 10, or N is 9 to 10, or N is at least 6, or N is at least 7, or N is at least 8, or N is at least 9, or N is 5, or N is 6, or N is 7, or N is 8, or N is 9, or N is 10. 
     
     
         3 . (canceled) 
     
     
         4 . (canceled) 
     
     
         5 . A method of detecting protein levels of a set of biomarkers in a sample from a subject, comprising: (a) contacting a sample from a subject with a set of capture reagents, wherein each capture reagent specifically binds to a protein selected from ITGA1/ITGB1 and HSP90AA1/HSP90AB1; and (b) detecting the amount of each capture reagent that bound to the protein to which it specifically binds, thereby detecting protein levels of a set of biomarkers in a sample from a subject. 
     
     
         6 . The method of  claim 5 , wherein step (a) further comprising contacting the sample with a set of at least one, at least two, at least three, at least four, at least five, at least six, or at least seven capture reagents, wherein each capture reagent specifically binds to a different protein selected from ACY1, C7, COLEC11, CSF1R, DCN, KYNU, POR and THBS2. 
     
     
         7 . The method of  claim 6 , wherein the method comprises contacting the sample with a set of capture reagents, wherein each capture reagent specifically binds to one of the proteins ITGA1/ITGB1, HSP90AA1/HSP90AB1, ACY1, COLEC11, and THBS2. 
     
     
         8 . (canceled) 
     
     
         9 . A method of detecting protein levels of a set of biomarkers in a sample from a subject, comprising: (a) contacting a sample from a subject with a set of capture reagents, wherein the set of capture reagents comprises at least three capture reagents, wherein each capture reagent specifically binds to a different protein selected from: ACY1, C7, COLEC11, CSF1R, DCN, HSP90AA1/HSP90AB1, ITGA1/ITGB1, KYNU, POR, FCGR3B, LGALS3BP, SERPINC1, IGFBP7, PIK3CA/PIK3R1, NAGK, DDC, SERPINA7, and THBS2; and (b) detecting the amount of each capture reagent conjugated to the protein to which it specifically binds, thereby detecting protein levels of a set of biomarkers in a sample from a subject. 
     
     
         10 . The method of  claim 9 , wherein the method comprises detecting the level of HSP90AA1/HSP90AB1 or ITGA1/ITGB1, or both HSP90AA1/HSP90AB1 and ITGA1/ITGB1. 
     
     
         11 . (canceled) 
     
     
         12 . (canceled) 
     
     
         13 . (canceled) 
     
     
         14 . (canceled) 
     
     
         15 . The method of  claim 9 , wherein the set of capture reagents comprises at least three capture reagents, wherein each capture reagent specifically binds to a different protein selected from ACY1, KYNU, ITGA1/ITGB1, POR, HSP90AA1/HSP90AB1, THBS2, and CSF1R. 
     
     
         16 . (canceled) 
     
     
         17 . The method of  claim 15 , wherein the set of capture reagents comprises capture reagents which bind specifically to ACY1, KNYU and at least one, at least two, at least three or four additional proteins selected from ITGA1/ITGB1, POR, HSP90AA1/HSP90AB1, THBS2, and CSF1R. 
     
     
         18 . (canceled) 
     
     
         19 . (canceled) 
     
     
         20 . (canceled) 
     
     
         21 . (canceled) 
     
     
         22 . (canceled) 
     
     
         23 . The method of  claim 9 , wherein the set of capture reagents comprises capture reagents which bind specifically to ACY1, THBS2, COLEC11 and at least one or two additional proteins selected from ITGA1/ITGB1, CSF1R, KYNU, FCGR3B, and POR. 
     
     
         24 . (canceled) 
     
     
         25 . (canceled) 
     
     
         26 . (canceled) 
     
     
         27 . The method of  claim 9 , wherein the set of capture reagents comprises at least three capture reagents, wherein each capture reagent specifically binds to a different protein selected from ACY1, COLEC11, THBS2, ITGA1/ITGB1, SERPINC1, C7, POR, LGALS3BP, and HSP90AA1/HSP90AB1. 
     
     
         28 . (canceled) 
     
     
         29 . The method of  claim 27 , wherein the set of capture reagents comprises capture reagents which bind specifically to ACY1, COLEC11, THB S2 and at least one or two additional protein selected from ITGA1/ITGB1 and HSP90AA1/HSP90AB1. 
     
     
         30 . (canceled) 
     
     
         31 . The method of  claim 27 , wherein the set of capture reagents comprises capture reagents which bind specifically to ITGA1/ITGB1, COLEC11, SERPINC1, and LGALS3BP. 
     
     
         32 . The  claim 9 , wherein the set of capture reagents comprises at least three capture reagents, wherein each capture reagent specifically binds to a different protein selected from C7, COLEC11, THBS2, ITGA1/ITGB1, HSP90AA1/HSP90AB1, ACY1, CSF1R, KYNU, POR, IGFBP7, PIK3CA/PIK3R1, NAGK, DDC, SERPINA7, and DCN. 
     
     
         33 . (canceled) 
     
     
         34 . (canceled) 
     
     
         35 . The method of  claim 32 , wherein the set of capture reagents comprises capture reagents which bind specifically to C7, COLEC11, THB S2 and at least one, at least two or three additional protein selected from ITGA1/ITGB1, HSP90AA1/HSP90AB1 and DCN. 
     
     
         36 . The method of  claim 32 , wherein the set of capture reagents comprises capture reagents which bind specifically to C7, THBS2, KYNU, and SERPINA7. 
     
     
         37 . (canceled) 
     
     
         38 . (canceled) 
     
     
         39 . (canceled) 
     
     
         40 . (canceled) 
     
     
         41 . (canceled) 
     
     
         42 . (canceled) 
     
     
         43 . The method of  claim 1 , wherein each biomarker capture reagent is an antibody or an aptamer. 
     
     
         44 . The method of  claim 43 , wherein each biomarker capture reagent is an aptamer. 
     
     
         45 . The method of  claim 44 , wherein at least one aptamer is a slow off-rate aptamer. 
     
     
         46 . The method of  claim 45 , wherein at least one slow off-rate aptamer comprises at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least 10 nucleotides with modifications. 
     
     
         47 . The method of  claim 45 , wherein each slow off-rate aptamer binds to its target protein with an off rate (t 1/2 ) of ≥30 minutes, ≥60 minutes, ≥90 minutes, ≥120 minutes, ≥150 minutes, ≥180 minutes, ≥210 minutes, or ≥240 minutes. 
     
     
         48 . The method of  claim 1 , wherein the sample is a blood sample, a serum sample or a plasma sample. 
     
     
         49 . (canceled) 
     
     
         50 . (canceled) 
     
     
         51 . (canceled) 
     
     
         52 . (canceled) 
     
     
         53 . (canceled) 
     
     
         54 . (canceled) 
     
     
         55 . (canceled) 
     
     
         56 . (canceled) 
     
     
         57 . (canceled)