DNA Methylation Analysis in Nonalcoholic Fatty Liver Disease Suggests Distinct Disease-Specific and Remodeling Signatures after Bariatric Surgery

Abstract

Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients (n = 45) with all stages of NAFLD and controls (n = 18) were analyzed by array-based DNA methylation and mRNA expression profiling. NAFLD-specific expression and methylation differences were seen for nine genes coding for key enzymes in intermediate metabolism (including PC, ACLY, and PLCG1) and insulin/insulin-like signaling (including IGF1, IGFBP2, and PRKCE) and replicated by bisulfite pyrosequening (independent n = 39). Transcription factor binding sites at NAFLD-specific CpG sites were >1,000-fold enriched for ZNF274, PGC1A, and SREBP2. Intraindividual comparison of liver biopsies before and after bariatric surgery showed NAFLD-associated methylation changes to be partially reversible. Postbariatric and NAFLD-specific methylation signatures were clearly distinct both in gene ontology and transcription factor binding site analyses, with >400-fold enrichment of NRF1, HSF1, and ESRRA sites. Our findings provide an example of treatment-induced epigenetic organ remodeling in humans.

Human liver epigenetic alterations in non-alcoholic steatohepatitis are related to insulin action

“…that has shown NAFLD-specific differences at DNA methylation levels of IGF1, a gene coding key enzymes of in insulin/insulin-like signaling. 13 This hypothesis is also partially supported by our findings that 30 out of the 67 of the differentially methylated CpG sites demonstrated a correlation of methylation on this site both with fasting insulin (n D 51) and transcription of a nearby gene. For example, the correlations between these NASH-associated CpG sites with the mRNA expression of genes such as LDHB and SQSTM1.…”

“…We were also not able to differentiate the liver cell type composition between hepatocytes and inflammatory cells, which has been also the case in previous GW studies. 13,14 Thus, some changes in individuals with NASH could be related to changes in cell type composition. Nevertheless, we observed similar strength in the relationship between top-ranking NASH-associated CpG sites with both liver fibrosis and lobular inflammation.…”

“…10 So far, the most studied epigenetic mechanisms related to NAFLD in humans are the microRNA serum/plasma profile and DNA methylation. 10,11 In human liver, very few studies have demonstrated the importance of DNA methylation in NAFLD, [12][13][14][15] from which only 2 have applied a genome-wide (GW) approach. 13,14 However, none of these GW studies have carefully explored the relation between differential methylation and clinical parameters related to NASH.…”

Obesity accelerates epigenetic aging of human liver

“…At the discovery stage, all publicly available Illumina DNAm datasets with phenotypic information on chronological age, BMI, and sex were analyzed. In these analyses of liver (12), adipose tissue (13), muscle (14), and blood (15,16), a strong positive (and expected) correlation between chronological age and DNAm age was observed with correlation coefficients ranging from 0.78 to 0.90 ( Fig. 1 A-D).…”

Non-alcoholic fatty liver disease

“…Clinical evidence has suggested that bariatric surgery was able to partially reverse epigenetic alterations in the liver associated with NAFLD. Notably, reversing differentially methylated sites in NAFLD correlates with improvement in liver histology 119 .…”