Non-invasive stratification of non-alcoholic fatty liver disease by whole-transcriptome cell-free mRNA characterization

Hepatic fibrosis stage is the most important determinant of outcomes in patients with non-alcoholic fatty liver disease (NAFLD). There is an urgent need for non-invasive tests that can accurately stage fibrosis and determine efficacy of interventions. Here we describe a novel cf-mRNA-Sequencing approach that can accurately and reproducibly profile low levels of circulating mRNAs and evaluate the feasibility of developing a cf-mRNA-based NAFLD fibrosis classifier. Using separate discovery and validation cohorts with biopsy-confirmed NAFLD (n=176 and 59, respectively) and healthy subjects (n=23), we performed serum cf-mRNA RNA-Seq profiling. Differential expression analysis identified 2498 dysregulated genes between NAFLD and healthy subjects and 134 fibrosis-associated genes in NAFLD patients. Comparison between cf-mRNA and liver tissues transcripts revealed significant overlap of fibrosis associated genes and pathways indicating that the circulating cf-mRNA transcriptome reflects molecu...