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

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.

Rad52 mediates class-switch DNA recombination to IgD

“…In all flow cytometry experiments, cells were appropriately gated on forward and side scattering to exclude dead cells and debris. Cell analyses were performed using a LSR-II or Celesta flow cytometer (BD Biosciences), and data were analyzed using FlowJo software (TreeStar) 67 . All experiments were performed in triplicates.…”

“…After the sequencing run, demultiplexing with CASAVA was employed to generate the Fastq file for each sample. All sequencing reads were aligned with their reference genome (UCSC mouse genome build mm9) using TopHat2 default settings, and the Bam files from alignment were processed using HTSeq-count to obtain the counts per gene in all samples 67 . Quality control statistical analysis of outliers, intergroup variability and distribution levels, were performed for statistical validation of the experimental data.…”

B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV

“…Specifically, the TC1 marker genes FCER2 (CD23) and TCL1A are known to be highly expressed in mature naive B cells (Figure 4A; Table S4) (Horns et al, 2020), consistent with an enrichment in TC1 of IgD + and IgM + B cells (36% and 63% of cells, respectively) (Figure S4E) with low levels of inferred somatic mutations (Figure S4F) and minimal clonal expansion (Figures S4G and S4H). In TC3 and TC4, CD27 and CD80, both expressed in MBCs (Moroney et al, 2020;Zuccarino-Catania et al, 2014), were highly expressed (Figure S5A), and the majority of cells in these clusters were IgG1 + (53% and 73% of cells, respectively) (Figure S4E), somatically mutated (Figure S4F) and more clonally expanded than cells in TC1 (Figures S4G and S4H). Cells in TC3 and TC4 also highly expressed CXCR3, a chemokine receptor found on some class switched B cells that is believed to facilitate migration to sites of inflammation (Moroney et al, 2020;Muehlinghaus et al, 2005) and CD70, which is upregulated on stimulated B cells where its interaction with CD27 on effector T cells plays an important role in antiviral T cell responses (Izawa et al, 2017;van Gisbergen et al, 2011) (Figures 4A and S5A).…”

Tracking Immunoglobulin Repertoire and Transcriptomic Changes in Germinal Center B Cells by Single-Cell Analysis

“…Conversely, a much larger set of genes was induced in the switched cells including genes involved in antigen presentation ( SCIMP , IFI30 , and several HLA molecules), BCR signaling ( CD22 , CD53 , MEF2C ) and focal adhesion ( ITGB2 , FERMT3 , VASP , ARPC5 , ARPC5L1 ) ( Figure 3D ). In addition, we identified TOX , a high mobility group box protein that has been reported to be upregulated in switched memory B cells ( 38 ), to be induced in the large majority of switched cells in the GC including DZ, LZ and PreM ( Figure 3D ). Of note, the genes displayed in Figure 3D are associated with the specified isotype class regardless of the mutational load in the variable regions.…”