Passive and active demethylation in immune diseases with proliferation driving global hypomethylation

Abstract

Global DNA hypomethylation is a hallmark of immune-mediated diseases, yet its regulatory significance remains unclear. Replication-associated loss of DNA methylation at solo-WCGW (W = A/T) CpGs has recently been proposed as a consequence of cell division. Here we systematically investigated genome-wide hypomethylation patterns across seven immune-mediated diseases. Most diseases exhibited global hypomethylation, particularly at solo-WCGW CpGs in transcriptionally repressed regions, potentially reflecting increased immune cell proliferation. By contrast, CpG sites whose methylation levels were associated with cytokine exposure or SNP genotypes were predominantly located in transcriptionally active regions. To investigate whether immunological events driving immune cell proliferation may also be imprinted in transcriptionally active regions, we searched for differentially methylated regions (DMRs) correlated with an index reflecting the extent of solo-WCGW hypomethylation. In narcolepsy, we identified a DMR within the T-cell receptor alpha (TRA) locus, and greater hypomethylation was associated with increased clonality of both TRA and TRB repertoires, with a similar pattern in an independent cohort. In multiple sclerosis, a DMR was also detected within the IGH locus encoding the B-cell receptor. Together, these findings suggest that the hypomethylation index captures the impact of disease-specific immune dynamics, while reflecting a shared epigenetic signature of immune cell proliferation across diseases.