Emerging concepts of epigenetic dysregulation in hematological malignancies

Abstract

The past decade brought a revolution in understanding of the structure, topology and disease-inducing lesions of RNA and DNA, fueled by unprecedented progress in next-generation sequencing. This technological revolution has also affected understanding of the epigenome and has provided unique opportunities for the analysis of DNA and histone modifications, as well as the first map of the non-protein-coding genome and three-dimensional (3D) chromosomal interactions. Overall, these advances have facilitated studies that combine genetic, transcriptomics and epigenomics data to address a wide range of issues ranging from understanding the role of the epigenome in development to targeting the transcription of noncoding genes in human cancer. Here we describe recent insights into epigenetic dysregulation characteristic of the malignant differentiation of blood stem cells based on studies of alterations that affect epigenetic complexes, enhancers, chromatin, long noncoding RNAs (lncRNAs), RNA splicing, nuclear topology and the 3D conformation of chromatin.

Figure 1

Genomic alterations that affect gene expression in leukemia. (a) Genetic alterations that link enhancers and super-enhancers (SE) to aberrant upregulation of oncogenes and/or downregulation of genes encoding tumor suppressors in leukemia. These include inversions and/or translocations of regulatory elements that aberrantly drive the expression of an oncogene and/or reduce the expression of genes encoding tumor suppressors (as has been shown for alterations in chromosome 3, whereby the super-enhancers for GATA2 are aberrantly linked to drive EVI1 expression); mutations in the noncoding genome that generate a novel super-enhancer to drive oncogene expression (as has been shown for TAL1) and abolish super-enhancers to reduce the expression of genes encoding tumor suppressors (as has been shown for PAX5); and duplications and/or amplifications of super-enhancers linked to an oncogene (as has been shown for MYC). (b) Chromatin is organized into topologically associated domains (TAD), which are normally restricted from one another through the action of CTCF in association with the cohesin complex. Alterations in the 3D organization of chromatin, through disruption of the binding of CTCF and/or disruption of cohesin expression, might result in aberrant promoter-enhancer interactions to drive cancer.

Figure 2

Targeting the spliceosome in myeloid neoplasms. Mutations in genes encoding spliceosomal proteins alter RNA splicing in a sequence-specific manner to drive aberrant gene expression. Mutations in the gene encoding SRSF2 result in alterations at Pro95 and result in aberrant splice-site ‘preference’ based on the nucleotide sequence of exonic splicing enhancer (ESE). In contrast, U2AF1 and SF3B1 both recognize the 3′ splice site, and mutations that affect Ser34 in U2AF1 result in altered 3′ splice-site usage based on the nucleotide sequence immediately 5′ of the canonical 3′ AG dinucleotide. In contrast, cells bearing mutations that result in the K700E substitution in SF3B1 have increased use of cryptic 3′ splice sites.

Figure 3

Physiological and leukemia-associated functions of epigenetic complexes. (a) Three main categories of epigenetic modulators: ‘writers’ add the histone marks; ‘readers’ have domains that recognize the modifications; and ‘erasers’ remove the modifications. (b) NOTCH1 is a typical example of oncogenic transcription factor in leukemia. LSD1 acts as both transcriptional corepressor (when associated with the CSL repressor complex) and a coactivator of NOTCH1 (when NOTCH is activated via demethylation of histone H3 at Lys4 and Lys9). (c) In a physiological context, MLL1 is the catalytic subunit of the COMPASS complexes and methylates histone H3 at Lys4. The DNA-binding amino terminus of MLL is a frequent partner in translocations. AF9, a member of the super elongation complex and the DOT1L elongation complex, is a frequent translocation partner of MLL (associated with MENIN and LEDGF); this lead to aberrant activation of genes that are targets of MLL. LEDGF, lens epithelium-derived growth factor.

Figure 4

Roles of the cytosine methylation and hydroxymethylation of DNA in normal and malignant hematopoiesis. The balance of the function of DNA methyltransferases (DNMTs) and TET enzymes is critical to the regulation of genome-wide localization and abundance of DNA cytosine modifications that in turn regulate gene-expression patterns required for normal hematopoiesis (top left). DNA methyltransferases catalyze the conversion of cytosine (C) into 5-methylcytosine (5mc), which serve as a substrate for the conversion of 5mC into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fmC) and 5-carboxymethylcytosine (5cmC) by TET enzymes (bottom left). Loss or mutation of genes encoding DNA methyltransferases or TET enzymes, which commonly occur in a variety of leukemias, due to somatic mutations, perturbs the genome-wide distribution of 5mC and its oxidized derivatives (bottom right) and promotes leukemogenesis (top right). For example, hypermethylation might affect promoters or enhancers and result in gene silencing, or it might disrupt CTCF-binding sites to alter chromosomal structure and allow aberrant promoter-enhancer interactions to occur. Moreover, extended regions of low methylation that span domains containing transcription-factor-binding sites (so-called ‘canyons’) might shrink or widen with alterations in TET or DNMT function. MPP, multipotent progenitor; CLP, common lymphoid progenitor; CMP, common myeloid progenitor; GMP, granulocyte-macrophage progenitor; MEP, megakaryocytic-erythroid progenitor; CGI, CpG island.