Deep characterization of paired chromatin and transcriptomes in four immune cell types from multiple sclerosis patients

Background: The putative involvement of chromatin states in multiple sclerosis (MS) is thus far unclear. Here we determined the association of chromatin-accessibility with concurrent genetic, epigenetic and transcriptional events. Material & methods: We generated paired assay for transposase-accessible chromatin sequencing and RNA-seq profiles from sorted blood immune CD4$^{+}$ and CD8$^{+}$ T cells, CD14$^{+}$ monocytes and CD19$^{+}$ B cells from healthy controls (HCs) and MS patients. Results: We identified differentially accessible regions between MS and HCs, primarily in CD4$^{+}$ and CD19$^{+}$. CD4$^{+}$ regions were enriched for MS-associated single nucleotide polymorphisms and differentially methylated loci. In the vicinity of differentially accessible regions of CD4$^{+}$ cells, 42 differentially expressed genes were identified. The top two dysregulated genes identified in this multilayer analysis were CCDC114 and SERTAD1. Conclusion: These findings provide new insight into the primary role of CD4$^{+}$ and CD19$^{+}$ cells in MS.