Differential DNA methylation and changing cell-type proportions as fibrotic stage progresses in NAFLD

Abstract

Background Non-alcoholic fatty liver disease (NAFLD) is characterized by changes in cell composition that occur throughout disease pathogenesis, which includes the development of fibrosis in a subset of patients. DNA methylation (DNAm) is a plausible mechanism underlying these shifts, considering that DNAm profiles differ across tissues and cell types, and DNAm may play a role in cell-type differentiation. Previous work investigating the relationship between DNAm and fibrosis in NAFLD has been limited by sample size and the number of CpG sites interrogated. Results Here, we performed an epigenome-wide analysis using Infinium MethylationEPIC array data from 325 individuals with NAFLD, including 119 with severe fibrosis and 206 with no histological evidence of fibrosis. After adjustment for latent confounders, we identified 7 CpG sites whose DNAm associated with fibrosis (p < 5.96 × 10–8). Analysis of RNA-seq data collected from a subset of individuals (N = 56) revealed that gene expression at 288 genes associated with DNAm at one or more of the 7 fibrosis-related CpGs. DNAm-based estimates of cell-type proportions showed that estimated proportions of natural killer cells increased, while epithelial cell proportions decreased with disease stage. Finally, we used an elastic net regression model to assess DNAm as a biomarker of fibrotic stage and found that our model predicted fibrosis with a sensitivity of 0.93 and provided information beyond a model based solely on cell-type proportions. Conclusion These findings are consistent with DNAm as a mechanism underpinning or marking fibrosis-related shifts in cell composition and demonstrate the potential of DNAm as a possible biomarker of NAFLD fibrosis.

Diagnostic Modalities of Non-Alcoholic Fatty Liver Disease: From Biochemical Biomarkers to Multi-Omics Non-Invasive Approaches

“…Changes in DNA methylation have also been identified in NAFLD disease progression between mild and advanced status, and it has been suggested that they may be highly predictive of fibrosis [ 240 ]. Murphy et al analysed the methylome profile in patients with NAFLD and found that, in advanced NAFLD, 52,830 CpG sites (11%) were hypomethylated and 16,417 (3%) were hypermethylated, indicating that the advanced stage is characterised by loss of gene regulation [ 241 ].…”

The Potential Role of Cellular Senescence in Non-Alcoholic Fatty Liver Disease

“…The first network involves downregulated genes for transcriptional regulation and regeneration/proliferation, and the second network contains regulated genes for lipid metabolism [ 45 ]. Another study identified DNA methylation patterns related to genes involved in fibrogenesis, especially in those patients with rapidly progressing disease and high grades of fibrosis [ 46 ]. As the consequence of all these positive results, plasma DNA methylation was proposed as a potential biomarker for NASH-related fibrosis [ 47 ].…”

Modulation of Oxidative Stress-Induced Senescence during Non-Alcoholic Fatty Liver Disease

“…Differential DNA methylation patterns are associated with different stages of NAFLD: tissue-repair genes have been hypomethylated and overexpressed, whereas metabolismassociated genes have been hypermethylated and consequently downregulated [167]. A recent study showed that differential DNA methylation patterns appeared to be associated with NAFLD progression and fibrosis stage [168]. Another study revealed two differentially methylated region (DMR) networks in a cohort of NAFLD patients.…”