Altered DNA methylation pattern characterizes the peripheral immune cells of patients with autoimmune hepatitis

Abstract Objective AIH is a chronic liver disease of unknown aetiology with favourable response to immunosuppression. Little is known about the impact of methylation modifications on disease pathogenesis. Design 10 patients with AIH at diagnosis (time-point 1; tp1), 9 with primary biliary cholangitis (PBC) and 10 healthy controls (HC) were investigated. 8/10 AIH patients were also investigated following biochemical remission (time-point 2; tp2). Peripheral CD19(+)- and CD4(+)-cells were isolated to study global DNA methylation (5 m C)/hydroxymethylation (5 hm C) by ELISA and mRNA of DNA methylation (DNMT1/3A/3B)/hydroxymethylation enzymes (TET1/2/3) by quantitative RT-PCR. Epigenome wide association study (EWAS) was performed in CD4(+)-cells (Illumina HumanMethylation 850K array) in AIH and HC. Differences in total 5 m C/5 hm C state between AIH-tp1 and HC were also assessed by immunohistochemistry (IHC) on paraffin embedded liver sections. Results Reduced TET1 and increased DNMT3A mRNA levels characterized CD19(+) and CD4(+) lymphocytes from AIH-tp1 patients compared to HC and PBC respectively, without affecting global DNA 5 m C/5 hm C. In AIH-tp1, CD4(+) DNMT3A expression was negatively correlated with serum IgG (p=0.03). In remission (AIH-tp2), DNMT3A decreased in both CD19(+) and CD4(+)-cells (p=0.02, p=0.03, respectively). EWAS in CD4(+)-cells from AIH patients confirmed important modifications in genes implicated in immune responses (HLA-DP, TNF, lnRNAs and CD86). IHC confirmed increased 5 hm C staining of periportal infiltrating lymphocytes in AIH-tp1. Conclusion Altered expression of TET1 and DNMT3A, characterizes peripheral immune cells in AIH. DNMT3A is associated with disease activity and decreased following therapeutic response. Gene specific DNA methylation modifications affect immunologic pathways that may play an important role in AIH pathogenesis. Summary box What is already known? Autoimmune hepatitis (AIH) is a non-resolving chronic liver disease of unknown aetiology and favourable response to immunosuppression. Since the interplay between the genetic background and the environment seems to be fundamental for AIH pathogenesis, epigenetic modifications may be of particular importance. What are the new findings? We found characteristic alterations of DNA methylation in peripheral immune cells of AIH patients, which were associated with disease activity and modified by immunosuppressive treatment. How might it impact on clinical practice in the foreseeable future? These results provide the first evidence that epigenetics play a role in AIH pathogenesis, which may have therapeutic implications for the management of the disease.