Molecular characterization and cell type composition deconvolution of fibrosis in NAFLD

Abstract

Non-alcoholic fatty liver disease (NAFLD) is the most common cause of liver disease worldwide. In adults with NAFLD, fibrosis can develop and progress to liver cirrhosis and liver failure. However, the underlying molecular mechanisms of fibrosis progression are not fully understood. Using total RNA-Seq, we investigated the molecular mechanisms of NAFLD and fibrosis. We sequenced liver tissue from 143 adults across the full spectrum of fibrosis stage including those with stage 4 fibrosis (cirrhosis). We identified gene expression clusters that strongly correlate with fibrosis stage including four genes that have been found consistently across previously published transcriptomic studies on NASH i.e. COL1A2, EFEMP2, FBLN5 and THBS2. Using cell type deconvolution, we estimated the loss of hepatocytes versus gain of hepatic stellate cells, macrophages and cholangiocytes with advancing fibrosis stage. Hepatocyte-specific functional analysis indicated increase of pro-apoptotic pathways and markers of bipotent hepatocyte/cholangiocyte precursors. Regression modelling was used to derive predictors of fibrosis stage. This study elucidated molecular and cell composition changes associated with increasing fibrosis stage in NAFLD and defined informative gene signatures for the disease.

Transplantation of umbilical cord-derived mesenchymal stem cells promotes the recovery of thin endometrium in rats

“…Integrin alpha ( ITGA ) was identified as hub genes in network analysis and predicted to be involved in binding laminin and collagen, which played key roles in ECM-receptor interaction and focal adhesion pathways 44 , 45 . thrombospondin-2 ( THBS2 ), as an extracellular matrix protein encoding gene, can encode a secreted ECM glycoprotein, which has a certain correlation with the severity of tissue fibrosis 46 , 47 . Von Willebrand factor ( VWF ) promoted shear stress-regulated platelet aggregation and platelet clearance, mediated platelet adhesion to damaged blood vessels and stabilized blood coagulation factor 48 , 49 .…”

Cell-Type Resolved Insights into the Cis-Regulatory Genome of NAFLD

“…Failure of the parenchymal hepatocytes to cope with the chronically high lipid load is a critical event in NAFLD pathology, and the consequential lipotoxicity triggers a cascade of pathogenic events in the non-parenchymal cell populations such as the activation of Kupffer cells (KCs), immune cell infiltration, liver sinusoidal endothelial cell (LSEC) capillarization, hepatic stellate cell (HSC) activation, and epithelial ductular reaction comprising activation, proliferation, and potential transdifferentiation amongst cholangiocytes, bipotent biliary progenitor cells or hepatocytes, or a combination of these [ 2 , 4 , 5 , 6 , 7 , 8 ]. This causes dramatic alterations of tissue architecture and function that ultimately may lead to NASH and can result in cirrhosis and liver failure [ 2 , 9 ]. These cellular behaviors are in part orchestrated by complex gene regulatory networks that change the gene expression signature of individual cells through extensive chromatin remodeling events, altered transcription factor (TF) binding patterns, and histone modifications [ 10 , 11 , 12 ].…”

Expanded transcriptomic analysis of human hepatic stellate cells links novel coding and noncoding products to human liver fibrosis

“…HSC myofibroblasts are the primary cell type responsible for the production of the ECM that leads to fibrosis in chronic liver disease. We next applied our deeper understanding of the HSC transcriptome to evaluate changes that occur with the development of liver fibrosis in patients with non-alcoholic fatty liver disease (NAFLD) (Pantano et al 2021).…”

“…We first evaluated lncRNA expression in total liver across a range of fibrosis levels associated with NAFLD (Figure 5A). RNA-seq data was analyzed from liver samples of individuals with no steatosis, those with steatosis and no fibrosis (F0), and those with steatosis and different stages of fibrosis (F1-F4), with F4 representing cirrhosis (Pantano et al 2021). We identified 251 lncRNA transcripts that are enriched with more severe liver fibrosis, and 92 of these lncRNAs represent transcripts that were previously not annotated in Gencode.…”

“…We then evaluated expression of circRNAs identified in HSC myofibroblasts with the development of liver fibrosis. We were able to perform this analysis because the RNA-seq analysis for NAFLD patients was performed on rRNA-depleted rather than polyA-enriched RNA (Pantano et al 2021). We first identified all BSJ in patient samples, and then identified BSJs that are enriched in F4 fibrosis (Figure 5C).…”