Genome-wide analysis of DNA methylation in human peripheral leukocytes identifies potential biomarkers of nonalcoholic fatty liver disease

Abstract

The aim of the present study was to uncover the role of leukocytic DNA methylation in the evaluation of nonalcoholic fatty liver disease (NAFLD). Patients with biopsy-proven NAFLD (n=35) and normal controls (n=30) were recruited from Chinese Han population. Their DNA methylation in peripheral leukocytes was subjected to genome-wide profiling. The association between differential methylation of CpG sites and NAFLD was further investigated on the basis of histopathological classification, bioinformatics, and pyrosequencing. A panel of 863 differentially methylated CpG sites dominated by global hypomethylation, characterized the NAFLD patients. Hypomethylated CpG sites of Acyl-CoA synthetase long-chain family member 4 (ACSL4) (cg15536552) and carnitine palmitoyltransferase 1C (CPT1C) (cg21604803) associated with the increased risk of NAFLD [cg15536552, odds ratio (OR): 11.44, 95% confidence interval (CI): 1.04‑125.37, P=0.046; cg21604803, OR: 6.57, 95% CI: 1.02-42.15, P=0.047] at cut-off β-values of <3.36 (ACSL4 cg15536552) and <3.54 (CPT1C cg21604803), respectively, after the adjustment of age, sex, body mass index (BMI) and homeostasis model assessment of insulin resistant (HOMA-IR). Their methylation levels also served as biomarkers of NAFLD (ACSL4 cg15536552, AUC: 0.80, 95% CI: 0.62-0.98, P=0.009; CPT1C cg21604803, AUC: 0.78, 95% CI: 0.65-0.91, P=0.001). Pathologically, lowered methylation level (β-values <3.26) of ACSL4 (cg15536552) conferred susceptibility to nonalcoholic steatohepatitis (NASH). Taken together, genome-wide hypomethylation of peripheral leukocytes may differentiate NAFLD patients from normal controls. The leukocytic hypomethylated ACSL4 (cg15536552) was suggested to be a biomarker for the pathological characteristics of NAFLD.

Altered DNA Methylation Sites in Peripheral Blood Leukocytes from Patients with Simple Steatosis and Nonalcoholic Steatohepatitis (NASH)

“…Upregulation of the ACSL4 gene accelerates lipogenesis, whereas downregulation of ACSL4 prevents the accumulation of cellular cholesterol [ 34 ]. Previous study also reported leukocytic hypomethylated ACSL4 an index for borderline/definitive NASH, with odds ratio (OR) at 11.44 and 95% confidence interval (CI) from 1.04 to 125.37 (P=0.046) [ 35 ]. In that study, the NAFLD Activity Score (NAS) scoring system has been used for the stratification of clinical phenotypes of NAFLD.…”

Genetic Alteration, Prognostic and Immunological Role of Acyl-CoA Synthetase Long-Chain Family Member 4 in a Pan-Cancer Analysis

“…This is consistent with the correlation between ASLC4 mRNA expression and prognosis in LIHC, that is, high expression of ACSL4 leads to worse prognosis. A previous study also found that hypomethylated CpG sites of ACSL4 were associated with an increased risk of non-alcoholic fatty liver disease (NAFLD) ( Zhang et al, 2018 ). These results suggest that hypomethylation of ACSL4 may be one of the epigenetic regulatory mechanisms in many cancers.…”

Deciphering the role of aberrant DNA methylation in NAFLD and NASH

“…Hypomethylation of Acyl-CoA synthetase long chain family member 4 ( ACSL4 ) and carnitinepalmitoyltransferase 1 C ( CPT1C ) were linked to a heightened risk of NAFLD and might serve as biomarkers for NAFLD. Further, leukocytichypomethylated ACSL 4 might be a useful biomarker for pathological traits of NAFLD [ 102 ]. In an exploration by Wu et al., using epigenome wide association studies (EWAS) six differentially methylated CpG sites in ACSL4, CRLS1 , CTP1A, SIGIRR, SSBP1 and ZNF622 were identified which could serve as serum biomarkers to distinguish between those with NASH and simple steatosis [ 103 ].…”