Deep characterization of paired chromatin and transcriptomes in four immune cell types from multiple sclerosis patients.
PMID 34676774 | DOI 10.2217/epi-2021-0205 · Epigenomics · 2021 · View on PubMed ↗
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-sequencing 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 patients 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.
Validated evidence
| Type | Entity | Source evidence | Confidence | Extractor |
|---|---|---|---|---|
| gene | CD4 | “Material & methods: We generated paired assay for transposase-accessible chromatin sequencing and RNA-sequencing profiles from sorted blood immune CD4+ and CD8+ T cells, CD14+ monocytes and CD19+ B cells from healthy controls (HCs) and MS patients.” | 0.98 | hgnc_dict_v1 |
| gene | CD14 | “Material & methods: We generated paired assay for transposase-accessible chromatin sequencing and RNA-sequencing profiles from sorted blood immune CD4+ and CD8+ T cells, CD14+ monocytes and CD19+ B cells from healthy controls (HCs) and MS patients.” | 0.98 | hgnc_dict_v1 |
| gene | CD19 | “Material & methods: We generated paired assay for transposase-accessible chromatin sequencing and RNA-sequencing profiles from sorted blood immune CD4+ and CD8+ T cells, CD14+ monocytes and CD19+ B cells from healthy controls (HCs) and MS patients.” | 0.98 | hgnc_dict_v1 |
| gene | SERTAD1 | “The top two dysregulated genes identified in this multilayer analysis were CCDC114 and SERTAD1.” | 0.98 | hgnc_dict_v1 |
| phenotype | multiple sclerosis | “Deep characterization of paired chromatin and transcriptomes in four immune cell types from multiple sclerosis patients.” | 0.98 | phenotype_alias_lexicon_v2 |