The language of chromatin modification in human cancers

Abstract

The genetic information of human cells is stored in the context of chromatin, which is subjected to DNA methylation and various histone modifications. Such a 'language' of chromatin modification constitutes a fundamental means of gene and (epi)genome regulation, underlying a myriad of cellular and developmental processes. In recent years, mounting evidence has demonstrated that miswriting, misreading or mis-erasing of the modification language embedded in chromatin represents a common, sometimes early and pivotal, event across a wide range of human cancers, contributing to oncogenesis through the induction of epigenetic, transcriptomic and phenotypic alterations. It is increasingly clear that cancer-related metabolic perturbations and oncohistone mutations also directly impact chromatin modification, thereby promoting cancerous transformation. Phase separation-based deregulation of chromatin modulators and chromatin structure is also emerging to be an important underpinning of tumorigenesis. Understanding the various molecular pathways that underscore a misregulated chromatin language in cancer, together with discovery and development of more effective drugs to target these chromatin-related vulnerabilities, will enhance treatment of human malignancies.

Figure 1.. The misregulated ‘language’ of chromatin modification in cancer.

a. Overview of key writers, erasers and readers of histone H3 methylations at K4, K9, K27, K36 and K79. Note that this list is not exclusive; many other modifications such as acetylation, phosphorylation, ubiquitylation and arginine methylation also occur in all histones, which are not shown in the figure. b. A mis-regulated ‘language’ of chromatin modification underlies oncogenesis. In addition to cancer-related mutations of chromatin modification writers, erasers or readers, the oncohistone and chromatin remodeler mutations alter numerous fundamental aspects of chromatin, as illustrated by the ‘paper’ that the ‘language’ of chromatin modification operates on. Moreover, cellular metabolites and oncometabolites form essential cofactors for erasers, and also represent the ‘paint and ink’ used by writers (and in some cases erasers) to modify histones and DNA. A versatile set of readers allow cells to recognise and engage various chromatin marks such as lysine methylation, acetylation, crotonylation, and more. Similar to a process of ‘stapling and bookbinding’, chromatin looping and phase separation-based regulation are involved in the high-order organization of chromatin and regulation of (epi)-genome, processes frequently altered in cancers. Altogether, a collection of deregulated mechanisms converge, resulting in a mis-regulated chromatin ‘language’.

Figure 2.. Miswriting of chromatin modification promotes oncogenic development.

a. Active enhancer is marked by H3K4me1 and H3K27ac, which are generated by mixed lineage leukemia 3 (MLL3) and MLL4, and histone acetyltransferases such as CREBBP and EP300. Enhancers are bound by transcription factors (TF), mediators and transcription coactivators such as BRD4, which activate RNA polymerase II (Pol II) for mediating productive transcription from promoters and generating enhancer RNA (eRNA) to facilitate gene activation. Enhancer-promoter looping underlies activation of gene transcription. Loss or inactivation mutation of CREBBP or EP300 and/or MLL3 or MLL4 is characteristic of cancers such as B-cell lymphoma, resulting in decreased H3K27ac and/or H3K4me1 at enhancers and reduced expression of genes related to tumor suppression, cell differentiation and/or antitumor immunity. b. Wildtype MLL1 uses a N-terminal region for interacting with chromatin-binding cofactors, menin and PSIP1. MLL1 or its partial tandem duplication (PTD) results in elevated H3K4me3 at oncogenes such as HOX, promoting acute leukaemogenesis. MLL1 fusion oncoprotein gains a C-terminal segment from its fusion partner, such as AF9, ENL or AF4, which recruits DOT1L complex (DotCom) for catalyzing H3K79 methylation and/or the super elongation complex (SEC) for catalyzing serine 2 phosphorylation (Ser2ph) of the C-terminal domain (CTD) of RNA Polymerase II (Pol II). H3K79me and Pol-II CTD Ser2ph, possibly with other activators such as PAF1, promote expression of oncogenes such as those of the HOX family. c. A collective action of wildtype EZH2 and its gain-of-function mutation, Y646X (X= F, C, H, S or N), causes abnormal elevation of H3K27me3 in lymphoma, leading to downregulation of transcripts related to cell cycle control and B cell differentiation. d. Regulatory roles of H3K36me2/3 modifications at gene body, intergenic regions and CpG islands. First, intergenic H3K36me2, installed by NSD family proteins, and SETD2-mediated H3K36me3 at gene body both antagonizes H3K27me3. Meanwhile, H3K36me2/3 serves as a docking site of the DNMT3A/3B PWWP domain, resulting in co-localization of H3K36me2/3 with DNA 5mC at gene body and intergenic regions. Additionally, recognition of H3K36me3/2 by the Tudor domain of PHD finger protein 1 (PHF1) or PHF19 provides a possible mechanism for PRC2 complex to establish de novo H3K27me3. Deregulation of NSD family proteins, SETD2, PRC2, PHF1/19 and DNMT3A is frequent among various human tumors. e. In breast cancer, overexpressed DOT1L interacts with MYC and EP300 to antagonize histone deacetylases (HDACs) and DNMT1, leading to the elevated H3K79me and H3Kac levels at epithelial-to-mesenchymal transition (EMT)-promoting oncogenes such as SNAIL and ZEB1.

Figure 3.. Misinterpretation of histone modification in cancer.

a. The YEATS domain of ENL recognizes acetylated lysine (Kac). ENL, which interacts with the mixed lineage leukemia 1 (MLL1) fusion oncoprotein, recruits the Super Elongation Complex (SEC) or DotCom into target oncogenes, maintaining a potently activated state in leukaemia cells. The ENL gain-of-function mutations facilitate self-aggregation and form phase separated puncta. The concentrated ENL mutant proteins recruit more SEC for activation of oncogenes in Wilms tumor. b. The histone acetyltransferase Ada-two-A-containing (ATAC) complex contains a subunit YEATS2, recognizing H3K27ac and a subunit SAGA-associated factor 29 (SGF29), recognizing H3K4me3. The catalytic subunit consisting of histone acetyltransferase KAT2A results in elevated H3K9ac and activates expression of oncogenes in non-small cell lung cancer. The YEATS domain of GAS41 recognizes H3K27ac and H3K14ac at promoter regions. GAS41 is a subunit of chromatin remodeling complexes SRCAP and TIP60-EP400. The remodeling complex SRCAP substitutes histone H2A with histone variant H2A.Z and thus activates gene expression. c. BAH and coiled-coil domain-containing protein 1 (BAHCC1) binds to H3K27me3-marked chromatin regions through a conserved BAH domain. BAHCC1 interacts with corepressors including histone deacetylases (HDACs) and SAP30 binding protein (SAP30BP) to silence tumor suppressor genes and lineage-specification transcription factors in acute leukaemias. d. Histone modifications H3.3K36me3 and phosphorylated serine 31 on histone H3.3 (H3.3S31ph) influence chromatin localization of zinc finger MYND domain-containing protein 11 (ZMYND11). ZMYND11 specifically recognizes H3.3K36me3 at gene bodies and functions as a transcriptional corepressor by recruiting the NCOR2-HDAC3 complex. H3.3S31ph leads to the ‘ejection’ of ZMYND11 from its binding sites. A ZMYND11-MBTD1 fusion protein was identified in a subset of acute myeloid leukemia patients. The PWWP domain of ZMYND11 binds to H3K36me3 and the fusion partner (MBTD1) recruits the nucleosome acetyltransferase of H4 (NUA4)-TIP60 histone acetyltransferase complex. Elevated histone acetylation maintains the high expression of pro-leukemic genes in leukemia stem cells. e. Under normal conditions, the tumor suppressor RACK7 recognizes the H3 tail carrying lysine acetylation and/or H3K4me1 and recruits the H3K4me3 erasers KDM5C and KDM5D onto enhancer regions. Loss of the RACK7-KDM5C/5D complex fails to demethylate H3K4me3 and results in overexpression of oncogenes (such as S100A) and metastasis-linked genes (such as SLUG and VEGFA) in breast and prostate tumor cells.

Figure 4.. Mis-erasing of chromatin modification is critically involved in cancer initiation and progression.

a. In T-ALL, the expression level of KDM6B increases while the (KDM6A level decreases. Both KDM6A and KDM6B are erasers of H3K27me3. KDM6B binds to oncogenic NOTCH1 target genes, catalyzes the demethylation of H3K27me3 and antagonizes the polycomb repressor complex 2 (PRC2), an H3K27me3 writer. Decreased H3K27me3 and increased H3K4me3 facilitate the expression of oncogenic genes. In contrast, KDM6A binds to tumor suppressor genes and facilitates their expression. KDM6A thus functions as tumor suppressor in T-ALL. b. In glioblastoma stem cells (GSC), DNA adenine methylation (N⁶-mA) co-exists with H3K9me3, suppressing the neuronal differentiation-related gene-expression program. Depletion of nucleic acid dioxygenase ALKBH1 in glioblastoma facilitates silencing of oncogenic genes and thus decreases GSC proliferation.