DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation

Abstract

IntroductionOn T-cell dependent activation, resting/naive B cells (NBCs) can be induced to migrate into lymphoid follicles and form germinal centers (GCs). 1,2 GC B cells subsequently undergo massive clonal expansion and mutagenesis mediated by activation-induced cytosine deaminase (AICDA). 2 Tolerance of simultaneous proliferation and genomic instability is a hallmark of the GC B-cell phenotype and is required for development of B-cell clones able to generate high-affinity antibodies. 1,2 AICDA not only induces mutations within the immunoglobulin loci but also localizes to many other sites of the genome including promoters and coding sequences of actively transcribed genes enriched in RGYW DNA motifs. [3][4][5][6] AICDA-induced mutations can thus occur at many sites throughout the genome in normal GCs. 3,6 In accordance with these observations, AICDA has been demonstrated to play a critical role in lymphomagenesis. 7 While genetic diversity of B-cell clones within GCs is important for the emergence of cells encoding high-affinity immunoglobulins, it also provides opportunities for the emergence of malignant clones. In fact a majority of B-cell neoplasms originate from cells that have transited the GC reaction. 1 Induction of the GC phenotype requires that NBCs undergo major changes in gene expression patterning, the basis of which are not fully understood. These shifts are mediated in part by transcription factors such as BCL6 and BACH2 [8][9][10] and histone modifying enzymes such as EZH2. 11 However, differential methylation of CpG dinucleotides is also known to control tissue specific gene expression. 12,13 CpG methylation is mediated by a family of DNA methyltransferase enzymes (DNMTs). 14 Of these, DNMT1 primarily mediates maintenance methylation, because of its preference for hemimethylated DNA 15 ; while DNMT3A and 3B primarily mediate de novo DNA methylation. Differential methylation occurs at the earliest stages of lymphopoiesis 16 and Dnmt1 hypomorphic mice accordingly display skewed hematopoietic differentiation toward the myeloid lineage, 17 but the role of DNMT1 in mature B cells has not been studied in a detailed manner.Both aberrant DNA hypermethylation and hypomethylation have been shown to occur in lymphomas derived from GC B-cells such as diffuse large B-cell lymphomas (DLBCL). 18,19 Furthermore, DLBCLs with GCB (Germinal Center B-cell like) versus ABC (Activated B cell-like) gene expression signatures display distinct DNA methylation profiles, 18 suggesting that cytosine methylation may contribute to the distinct phenotypes of these tumors. Very little is known regarding mechanisms of DNA demethylation, but reports have suggested that cytosine deamination mediated by AICDA followed by base excision The online version of this article contains a data supplement.The publication costs of this article were defrayed in part by page charge payment. Therefore, and solely to indicate this fact, this article is hereby marked ''advertisement'' in accordance with 18 USC section 1734. For personal use onl...

DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation

“…Notably, immune activation-induced DMRs were dominated by loss-of-methylation events ( Fig. 2A), in agreement with a previous study profiling the status of 50,000 CpGs during activation (Shaknovich et al 2011). Substantially fewer DMRs were identified between GC B cells and memory B cells or PCs ( Fig.…”

Mechanisms of epigenetic deregulation in lymphoid neoplasms

“…The key factors responsible for DNA methylation are members of the DNA methyltransferase (DNMT) family: DNMT1, DNMT3a, and DNMT3b, which have complex patterns of expression in peripheral B cells and during GC transit. 5,6 DNMT expression is highly compartmentalized within the GC, with DNMT1 and DNMT3b being the most highly expressed within GC B cells, but not in NB cells. GC formation is dependent on the amount of DNMT1 with significant diminution of GCs in Dnmt1 hypomorphic mice.…”

“…Shaknovich et al addressed changes in epigenome during germinal center (GC) transit and revealed that transition from naïve B cells (NB) to centroblasts (CB) is associated with predominant loss of methylation in 235 differentially methylated genes that affect NF-kB and mitogen-activated protein kinase pathways. 5 These studies set the stage for interpretation of epigenetic changes in pre-GC and GC-derived lymphomas. The key factors responsible for DNA methylation are members of the DNA methyltransferase (DNMT) family: DNMT1, DNMT3a, and DNMT3b, which have complex patterns of expression in peripheral B cells and during GC transit.…”

“…GC formation is dependent on the amount of DNMT1 with significant diminution of GCs in Dnmt1 hypomorphic mice. 5 The important role of DNMTs in lymphomagenesis is underscored by the evidence from Amara et al 7 that DNMT1, DNMT3a, and DNMT3b are overexpressed in 48%, 13%, and 45% of 81 de novo diffuse large B-cell lymphomas (DLBCLs) and correlate with advanced clinical stages. Importantly, concomitant expression of DNMT1 and DNMT3b correlated with resistance to treatment, whereas DNMT3b overexpression correlated with shorter overall and progression-free survival.…”

“…Shaknovich et al demonstrated that GC B cells have higher epigenetic heterogeneity than NB cells and that this phenomenon may be dependent on activation-induced cytidine deaminase (AID). 5 It appears that AID may contribute to epigenetic instability in lymphomas through its role as a demethylase, similar to its contribution to genomic instability through its role in somatic hypermutation (SHM). [23][24][25][26][27] Another potential contributor to epigenetic instability is CCCTC-binding factor-an insulator protein that may prevent the spread of aberrant methylation in lymphomas.…”