Defining the serum proteomic signature of hepatic steatosis, inflammation, ballooning and fibrosis in non-alcoholic fatty liver disease

• Authors: Arun J Sanyal, Virginia Commonwealth University; Stephen A Williams, SomaLog Inc; Joel E Lavine, Columbia University; Brent A Neuschwander-Tetri, Saint Louis University; Leigh Alexander, SomaLog Inc; Rachel Ostroff, SomaLog Inc; Hannah Biegel, SomaLog Inc; Kris V Kowdley, Liver Institute Northwest; Naga Chalasani, Indiana University; Srinivasan Dasarathy, Cleveland Clinic; Anna Mae Diehl, Duke University; Rohit Loomba, University of California San Diego; Bilal Hameed, University of California San Francisco; Cynthia Behling, University of California San Diego; David E Kleiner, National Cancer Institute, National Institutes of Health, Bethesda; Saul Karpen, Emory University; Jessica Williams, SomaLog Inc; Yi Jia, SomaLog Inc; Katherine P Yates, Johns Hopkins University; James Tonascia, Johns Hopkins University
• Journal Title: JOURNAL OF HEPATOLOGY
• Volume: Volume 78, Number 4
• Publisher: ELSEVIER | 2023-03-15, Pages 693-703
• Type of Work: Article | Post-print: After Peer Review
• Publisher DOI: http://doi.org/10.1016/j.jhep.2022.11.029
• Subjects: Health Sciences, Medicine and Surgery; Health Sciences, Pathology
• Keywords: Science & Technology; Life Sciences & Biomedicine; Gastroenterology & Hepatology; Nonalcoholic fatty liver disease (NAFLD); Nonalcoholic steatohepatitis (NASH); NAFLD activity score (NAS); fibrosis stage; cirrhosis; stea-tohepatitis; steatosis; hepatocellular ballooning; lobular inflammation; fibrosis; proteomics; aptamers; OBETICHOLIC ACID; STEATOHEPATITIS; PLACEBO; ASSOCIATION; MULTICENTER; DISCOVERY; DIAGNOSIS; PROFILES; PATTERNS

Abstract

Background & Aims: Despite recent progress, non-invasive tests for the diagnostic assessment and monitoring of non-alcoholic fatty liver disease (NAFLD) remain an unmet need. Herein, we aimed to identify diagnostic signatures of the key histological features of NAFLD. Methods: Using modified-aptamer proteomics, we assayed 5,220 proteins in each of 2,852 single serum samples from 636 individuals with histologically confirmed NAFLD. We developed and validated dichotomized protein-phenotype models to identify clinically relevant severities of steatosis (grade 0 vs. 1-3), hepatocellular ballooning (0 vs. 1 or 2), lobular inflammation (0-1 vs. 2-3) and fibrosis (stages 0-1 vs. 2-4). Results: The AUCs of the four protein models, based on 37 analytes (18 not previously linked to NAFLD), for the diagnosis of their respective components (at a clinically relevant severity) in training/paired validation sets were: fibrosis (AUC 0.92/0.85); steatosis (AUC 0.95/0.79), inflammation (AUC 0.83/0.72), and ballooning (AUC 0.87/0.83). An additional outcome, at-risk NASH, defined as steatohepatitis with NAFLD activity score ≥4 (with a score of at least 1 for each of its components) and fibrosis stage ≥2, was predicted by multiplying the outputs of each individual component model (AUC 0.93/0.85). We further evaluated their ability to detect change in histology following treatment with placebo, pioglitazone, vitamin E or obeticholic acid. Component model scores significantly improved in the active therapies vs. placebo, and differential effects of vitamin E, pioglitazone, and obeticholic acid were identified. Conclusions: Serum protein scanning identified signatures corresponding to the key components of liver biopsy in NAFLD. The models developed were sufficiently sensitive to characterize the longitudinal change for three different drug interventions. These data support continued validation of these proteomic models to enable a “liquid biopsy”-based assessment of NAFLD. Clinical Trial Number: Not applicable. Impact and implications: An aptamer-based protein scan of serum proteins was performed to identify diagnostic signatures of the key histological features of non-alcoholic fatty liver disease (NAFLD), for which no approved non-invasive diagnostic tools are currently available. We also identified specific protein signatures related to the presence and severity of NAFLD and its histological components that were also sensitive to change over time. These are fundamental initial steps in establishing a serum proteome-based diagnostic signature of NASH and provide the rationale for using these signatures to test treatment response and to identify several novel targets for evaluation in the pathogenesis of NAFLD.