Nonalcoholic Fatty Liver Disease (NAFLD) and Nonalcoholic Steatohepatitis (NASH) Biomarkers and Uses Thereof
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 - 57 . (canceled)
58 . A method of determining a score for a subject by detecting protein levels of a set of biomarker proteins in a sample from a subject, comprising:
(a) contacting a sample from a subject with a set of capture reagents, wherein one capture reagent specifically binds heat shock protein 90 kDa alpha/beta (HSP90AA1/HSP90AB1), wherein one capture reagent specifically binds kynureninase (KYNU), wherein one capture reagent specifically binds colony stimulating factor 1 receptor (CSF1R), and optionally wherein each other capture reagent specifically binds to one, two, three, or four different proteins chosen from aminoacylase 1 (ACY1), integrin, alpha 1/beta 1 (ITGA1/ITGB1), P450 cytochrome oxidoreductase (POR), and thrombospondin 2 (THBS2);
(b) detecting the amount of each capture reagent conjugated to the protein to which it specifically binds, thereby detecting one capture reagent that specifically binds HSP90AA1/HSP90AB1, one capture reagent that specifically binds KYNU, and one capture reagent that specifically binds CSF1R, and optionally detecting the one, two, three, or four capture reagents that specifically bind to the different biomarker proteins chosen from ACY1, ITGA1/ITGB1, POR, and THBS2, thereby detecting protein levels of a set of biomarker proteins in the sample from the subject; and
(c) determining a score in a statistical model based on input of the levels of the set of biomarkers measured;
wherein each capture reagent is an antibody or an aptamer.
59 . The method of claim 58 , wherein the set of capture reagents further comprises at least one additional capture reagent that specifically binds to a biomarker protein chosen from ACY1, ITGA1/ITGB1, POR, and THBS2.
60 . The method of claim 59 , wherein at least one of the additional capture reagents specifically binds to ACY1.
61 . The method of claim 58 , wherein the set of capture reagents comprises capture reagents that specifically bind to a different biomarker protein comprising ACY1, ITGA1/ITGB1, POR, and THBS2.
62 . The method of claim 58 , wherein each capture reagent is an aptamer.
63 . The method of claim 62 , wherein at least one aptamer is a slow off-rate aptamer.
64 . The method of claim 63 , 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.
65 . The method of claim 64 , 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.
66 . The method of claim 58 , wherein the sample is selected from a blood sample, a serum sample, and a plasma sample.
67 . The method of claim 58 , wherein determining the score for the subject comprises determining whether the subject has steatosis.
68 . The method of claim 58 , wherein the steatosis is mild, moderate, or severe steatosis.
69 . A method of determining a score for a subject by detecting protein levels of a set of biomarker proteins in a sample from a subject, comprising:
(a) contacting a sample from a subject with a set of capture reagents, wherein one capture reagent specifically binds heat shock protein 90 kDa alpha/beta (HSP90AA1/HSP90AB1), wherein one capture reagent specifically binds collectin (COLEC11), wherein one capture reagent specifically binds galectin-3-binding protein (LGALS3BP), and optionally wherein each other capture reagent specifically binds to one, two, three, four, five, six, or seven different proteins selected from aminoacylase 1 (ACY1), thrombospondin 2 (THBS2), integrin, alpha 1/beta 1 (ITGA1/ITGB1), antithrombin-I (SERPINC1), complement component 7 (C7), P450 cytochrome oxidoreductase (POR), and heat shock protein 90 kDa alpha/beta (HSP90AA1/HSP90AB1);
(b) detecting the amount of each capture reagent conjugated to the protein to which it specifically binds, thereby detecting one capture reagent that specifically binds HSP90AA1/HSP90AB1, one capture reagent that specifically binds COLEC11, and one capture reagent that specifically binds LGALS3BP, and optionally detecting the one, two, three, four, five, six, or seven capture reagents that specifically bind to the different biomarker proteins selected from ACY1, THBS2, ITGA1/ITGB1, SERPINC1, C7, POR, and HSP90AA1/HSP90AB1, thereby detecting protein levels of a set of biomarker proteins in the sample from the subject; and
(c) determining a score in a statistical model based on input of the levels of the set of biomarkers measured;
wherein each capture reagent is an antibody or an aptamer.
70 . The method of claim 69 , wherein the set of capture reagents further comprises at least one additional capture reagent that specifically binds to a biomarker protein chosen from ACY1, THBS2, ITGA1/ITGB1, SERPINC1, C7, POR, and HSP90AA1/HSP90AB1.
71 . The method of claim 70 , wherein at least one of the additional capture reagents specifically binds to ITGA1/ITGB1 or SERPINC1.
72 . The method of claim 69 , wherein the set of capture reagents comprises capture reagents that specifically bind to a different biomarker protein comprising ACY1, THBS2, ITGA1/ITGB1, SERPINC1, C7, POR, and HSP90AA1/HSP90AB1.
73 . The method of claim 69 , wherein each capture reagent is an aptamer.
74 . The method of claim 73 , wherein at least one aptamer is a slow off-rate aptamer.
75 . The method of claim 74 , 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, optionally 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.
76 . The method of claim 69 , wherein the sample is selected from a blood sample, a serum sample, and a plasma sample.
77 . The method of claim 69 , wherein determining the score for the subject comprises determining whether the subject has hepatocyte ballooning.