Epigenetic profiling of the HLA locus in the THP-1 monocytic cell line

Abstract

Multiple Sclerosis (MS) is a complex autoimmune disorder influenced by both genetic predisposition and environmental exposures. The HLA-DR15 haplotype – particularly the HLA-DRB1*15:01 allele which encodes MHC class II molecules that present antigens to CD4+ T-cells – exerts the strongest known genetic effect on MS susceptibility in Caucasians. Besides its structural function, studies have indicated that altered DNA methylation patterns of HLA-DRB1*15:01 contribute to the risk of developing MS. However, the genetic complexity of the HLA locus and epigenetic contributions to disease development have hindered mechanistic insights. In this study, we aimed to dissect the epigenetic landscape of the HLA class II locus and explore gene-targeted strategies to modulate HLA-DRB1*15:01 expression. We utilised a dual sequencing approach combining probe capture-based SureSelect sequencing with adaptive sampling using Oxford Nanopore Technology to fine-map CpG methylation on a haplotype specific level within the HLA locus in the THP-1 monocytic cell line carrying HLADR15 and -DR1 haplotypes. To decipher the functional role of DNA methylation, we engineered a new THP-1 cell line that constitutively expresses the dCas9-DNMT3A fusion protein. Genome-wide Enzymatic Methyl-sequencing was used to assess the off-target methylation changes following construct integration. These results could help to annotate methylation-sensitive regions in the HLA class II region that are prone to epigenome editing, with potential implications for precision immunotherapy in MS and other autoimmune conditions.