Integrative characterization of the coding and non-coding transcriptome in human memory B cells

Abstract

Abstract An effective response against a previously experienced pathogen is contingent upon the generation of memory B cells. These display intrinsic differences over naïve B cells, including extended lifespan and rapid response to antigen, with production of high-affinity class-switched antibodies. However, the transcriptional and regulatory programs that underpin the unique features of memory B cells remain unexplored. Here, we have developed an integrated analysis of differentially expressed (DE) mRNAs, miRNAs, lncRNAs and chromatin profiles to determine how gene expression intersects with epigenetic regulatory elements to shape the identity and functions of human memory B cells. DE analysis revealed an exclusive gene signature shared by CD27+IgG+ and CD27+IgA+ B cells that segregates these memory B cells from CD27−IgD+ naïve B cells – “unswitched” CD27+IgD+memory B cells displayed a transcriptional signature of transition between naïve and switched memory B cells. While changes in DNA accessibility typically predicted changes in mRNA expression, some genes of the “memory” signature deviated from this, suggesting a layer of post-transcriptional regulation mediated by ncRNAs. Indeed, probing the miRNAome revealed downregulation of miR-181 and concomitant upregulation of five target genes (RASSF6, TOX, TRERF1, TRPV3, RORA) in switched memory B cells. In these B cells, select DE lncRNAs clustered proximal to the IgH gene locus on chr 14, suggesting a role in their regulation of BCR expression. Thus, we have identified a set of genes characteristic of memory B cells and have provided evidence these genes are subject to integrated regulation by chromatin remodeling, cis-regulatory elements and distinct sets of miRNAs and lncRNAs.