Cell-specific epigenome-wide DNA methylation in peripheral CD4(+) lymphocytes from patients with primary biliary cholangitis

Abstract

Background/aims

Primary biliary cholangitis (PBC) is a chronic cholestatic autoimmune liver disease, triggered by a complex interplay between genetic, environmental and epigenetic factors. We investigated the methylation profile of peripheral CD4(+) lymphocytes from PBC patients compared to healthy controls (HC) and autoimmune hepatitis (AIH) patients, to elucidate gene specific epigenetic modifications that contribute to PBC pathogenesis, as similar data are limited.

Methods

CD4(+) lymphocytes were isolated from 8 PBC treatment-naïve patients, 9 HC and 10 AIH patients at diagnosis by ROBOSEP platform. Whole genome methylation analysis was performed by 850k array of Illumina. Candidate genes’ transcriptional expression was quantified by RT-PCR.

Results

Comparison between PBC patients and HC, revealed 1016 differentially methylated positions (DMPs) on autosomal chromosomes and 1203 DMPs on X chromosome (>98 % hypermethylated), corresponding to 695 and 322 genes, respectively (p < 0.05). Hypermethylation mainly affected pathways of immune cells differentiation and signalling (CAMTA1, PRKARB, LNC01993, TLR9). Methylation analysis between PBC and AIH revealed >5000 DMPs (98 % hypermethylated in PBC) corresponding to >4000 genes. Pathway analysis retrieved an enrichment of “cytokine” and “interleukin” signalling (C1GTNF3, SMAD3). Analysis of differentially methylated regions showed enrichment on gene promoters and hypermethylation of IFN-regulated genes (IFNGR2, TICAM2) in PBC patients. Genes expression at the transcriptional level showed over-expression of IFNGR2 in PBC patients.

Conclusions

Hypermethylation characterizes most genes of peripheral CD4(+) lymphocytes in PBC. The epigenetic modifications mainly affect pathways of immunological responses. The significant number of X chromosome located DMPs, further supports the role of sex in PBC pathogenesis.