Integrative transcriptome and chromatin landscape analysis reveals distinct epigenetic regulations in human memory B cells

Nat Commun. 2020 Oct 28;11(1):5435. doi: 10.1038/s41467-020-19242-6.

Abstract

Memory B cells (MBCs) are long-lived and produce high-affinity, generally, class-switched antibodies. Here, we use a multiparameter approach involving CD27 to segregate naïve B cells (NBC), IgD+ unswitched (unsw)MBCs and IgG+ or IgA+ class-switched (sw)MBCs from humans of different age, sex and race. Conserved antibody variable gene expression indicates that MBCs emerge through unbiased selection from NBCs. Integrative analyses of mRNAs, miRNAs, lncRNAs, chromatin accessibility and cis-regulatory elements uncover a core mRNA-ncRNA transcriptional signature shared by IgG+ and IgA+ swMBCs and distinct from NBCs, while unswMBCs display a transitional transcriptome. Some swMBC transcriptional signature loci are accessible but not expressed in NBCs. Profiling miRNAs reveals downregulated MIR181, and concomitantly upregulated MIR181 target genes such as RASSF6, TOX, TRERF1, TRPV3 and RORα, in swMBCs. Finally, lncRNAs differentially expressed in swMBCs cluster proximal to the IgH chain locus on chromosome 14. Our findings thus provide new insights into MBC transcriptional programs and epigenetic regulation, opening new investigative avenues on these critical cell elements in human health and disease.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • B-Lymphocytes / classification
  • B-Lymphocytes / immunology*
  • B-Lymphocytes / metabolism
  • Chromatin / genetics
  • Chromatin / immunology
  • Complementarity Determining Regions
  • Epigenesis, Genetic
  • Female
  • Gene Expression Profiling
  • Humans
  • Immunoglobulin Class Switching / genetics
  • Immunoglobulin Heavy Chains / genetics
  • Immunologic Memory / genetics*
  • Male
  • MicroRNAs / genetics
  • MicroRNAs / metabolism
  • Point Mutation
  • Signal Transduction / genetics
  • Transcription Factors / genetics
  • Tumor Necrosis Factor Receptor Superfamily, Member 7 / metabolism
  • Young Adult

Substances

  • Chromatin
  • Complementarity Determining Regions
  • Immunoglobulin Heavy Chains
  • MIRN-181 microRNA, human
  • MicroRNAs
  • Transcription Factors
  • Tumor Necrosis Factor Receptor Superfamily, Member 7