Epigenetics of the antibody response

Abstract

Epigenetic marks, such as DNA methylation, histone post-translational modifications and miRNAs, are induced in B cells by the same stimuli that drive the antibody response. They play major roles in regulating somatic hypermutation (SHM), class switch DNA recombination (CSR), and differentiation to plasma cells or long-lived memory B cells. Histone modifications target the CSR and, possibly, SHM machinery to the immunoglobulin locus; they together with DNA methylation and miRNAs modulate the expression of critical elements of that machinery, such as activation-induced cytidine deaminase (AID), as well as factors central to plasma cell differentiation, such as B lymphocyte-induced maturation protein-1 (Blimp-1). These inducible B cell-intrinsic epigenetic marks instruct the maturation of antibody responses. Their dysregulation plays an important role in aberrant antibody responses to foreign antigens, such as those of microbial pathogens, and self-antigens, such as those targeted in autoimmunity, and B cell neoplasia.

Keywords: AID; B cell; Blimp-1; CSR; SHM; antibody; autoimmunity; epigenetic; immunoglobulin; memory B cell; neoplasia; plasma cell.

Figure 1

Expression of selected microRNAs and their regulation of genes critical for different stages of peripheral B cell differentiation. Naïve mature B cells in peripheral lymphoid organs are activated by primary stimuli to undergo SHM and CSR (e.g., to IgG1, depicted) and to differentiate into plasma cells and memory B cells. In addition to DNA demethylation and histone modifications, which instruct genetic programs to specify expression of genes that drive distinct B cell differentiation stages, microRNAs play an important role in gene regulation through direct targeting of the 3’ UTR of transcripts of those genes, thereby regulating sequential B cell differentiation stages. Multiple microRNA molecules can cooperatively target one gene; an individual microRNA molecule can target multiple genes. Upregulation (red arrow) or downregulation (black arrow) of microRNAs results in alterations in the expression of key genes.

Figure 2

Epigenetic targeting of SHM and CSR. The SHM and CSR machinery are targeted to the Igh locus VDJ and S regions, respectively (the human IgH locus is depicted; the SHM machinery also targets VκJκ or VλJλ region DNA in the Igκ and Igλ loci, as depicted). In resting naïve B cells as well as activated B cells, recombined V_HDJ_H region chromatin displays DNA hypomethylation and activating histone marks, e.g., H3K4me3 (depicted here), H3K9ac/K14ac and H4K8ac. In B cells induced to undergo SHM, V_HDJ_H region is enriched in H2AK119ub, H2BK120ub and H2B14ph, which probably recruit DNA repair factors to these regions for SHM. The Sμ region in the Igh locus is constitutively transcribed and marked by activating histone modifications, e.g., H3K4me3 (depicted here), H3K9ac/K14ac, H3K27ac, H3K36me3, H4K8ac and H2BK5ac, and combinatorial histone H3K9acS10ph modification (depicted here), starting in resting naïve B cells, in which all downstream S regions are marked by repressive histone modifications (e.g., H3K27me3, as depicted). In B cell undergoing CSR, the cytokine-selected acceptor S region(s) undergo high levels of germline I_H-S-C_H transcription, lose repressive histone modifications, acquire activating histone modifications, including H3K4me3 and combinatorial histone H3K9acS10ph modification (depicted here). H3K9acS10ph directly interacts with 14-3-3 proteins and stabilizes these adaptors and, therefore, AID on the donor Sμ and acceptor S region DNA for CSR to unfold. Also, H3K9me3, a repressive histone mark in general, occurs at low levels in Sμ and recruit the KAP1-HP1γ complex to stabilize AID in Sμ, but not downstream S regions.

Figure 3

Epigenetic changes in B cells in response to primary and secondary (CSR-inducing) stimuli. Primary stimuli include CD40 engagement by CD154, dual TLR/BCR engagement by MAMPs and antigenic epitopes, respectively, on bacteria or viruses (a bacterium is depicted here; bacterial LPS engages both TLR4 and BCR through its monophosphoryl lipid A moiety and polysaccharidic moiety, respectively), and dual engagement of TACI (by BAFF or APRIL) and TLR, BCR or CD40. They induce histone-modifying enzymes, which catalyze activating histone modifications (e.g., H3K4me3 and H3K9ac/K14ac) in the promoter of microRNA host genes and genes encoding AID and other SHM/CSR factors, thereby creating an open chromatin state. This together with transcription factors activated by primary stimuli induce the expression of those genes. Induced microRNAs regulate expression of SHM/CSR factors. Histone-modifying enzymes also catalyze histone modifications, such as H2B14ph, in the Igh, Igλ and Igκ V(D)J regions for SHM targeting (depicted are V_HDJ_H and VκJκ). When enabled by primary stimuli, secondary stimuli, e.g., the cytokines IL-4, TGF-β or IFN-γ, activate transcription factors that specifically bind selected Igh intervening (I_H) promoters to initiate germline I_H-S-C_H transcription in the acceptor S region (depicted is recombination from Sμ to Sγ1). This allows primary stimuli-induced histone-modifying enzymes to ride on RNA polymerase II to reach Sγ1 region and catalyze activating histone modifications in this S region for CSR targeting. Inset: writing and erasure of histone acetylation by histone acetyltransferases (HATs) and histone deacetylases (HDACs, which are inhibited by HDAC inhibitors, HDIs), histone methylation by histone methyltransferases (HMTs) and histone demetylases (HDMs), histone phosphorylation by kinase and phosphatases, and histone ubiquitination by Ub ligases and deubiquitinases (DUBs). DNA methylation is catalyzed by DNA methyltransferase (DNMTs).