H3 K36 Research Articles

Histone methyltransferase NSD modulates gene silencing mechanisms on Drosophila chromosome 4

The nuclear receptor-binding SET domain protein (NSD) gene family encodes histone methyltransferases that mono- and di-methylate lysine 36 on histone H3 (H3K36). Here, we examine the effects of NSD loss-of-function on transcription and heterochromatin formation in Drosophila to elucidate the role of NSD in chromatin structure regulation. Transcriptome analysis showed that NSD deletion activated more genes on chromosome 4, predominantly heterochromatic, than on other chromosomes. We further analyzed the position-effect variegation of fly eyes due to mini-white (mw+) transgenes inserted at various chromosomal loci and found that NSD deletion promoted mw+ transgene expression on chromosome 4. Additionally, NSD deletion reduced the binding of heterochromatin markers HP1a and H3K9 to chromosome 4. These findings suggest that NSD deletion disrupts chromosome 4 heterochromatin structure by reducing HP1a binding, implying NSD's role as an epigenetic regulator of chromosome 4 silencing.

Abstract 1718: The lysine demethylase KDM2A regulates tumor cell clustering to potentiate metastasis

Abstract Approximately 70% of patients diagnosed with non-small cell lung cancer (NSCLC) are not eligible for curative resection, often due to disseminated disease at diagnosis. Thus, the advent of novel therapeutics, especially those efficacious for metastatic disease, is of primary importance. Metastasis correlates with epigenetic alterations that drive tumor plasticity and adaptive heterogeneity in response to the multiple microenvironments metastatic cells see, yet the molecular mechanisms underlying these epigenetic alterations remain poorly understood. We performed a functional genomic screen and identified the lysine 36 on histone H3 (H3K36) demethylase KDM2A as a mediator of in vivo and in vitro metastatic competence in multiple models of NSCLC. KDM2A depletion in highly metastatic NSCLC cell lines reduces their capacity to form multi-tumor cell clusters. In vivo, KDM2A depletion does not impact lung orthotopic tumor cell growth or the total number of circulating tumor cells (CTCs) but does reduce their ability to colonize distant metastatic sites. This is consistent with the fact that human CTCs found in clusters are more metastatic than CTCs which disseminate as single-cells. Because the molecular and biological consequences of H3K36 regulation are context dependent, we performed for the first time an integrated transcriptomic-epigenomic analysis of target gene regulation, KDM2A genomic binding, H3K36 methylation, and H3K27 acetylation, in metastatic cell clusters. KDM2A enhances the expression of cell adhesion and anti-oxidant genes, while suppressing inflammatory gene responses, and this regulation preferentially occurs in tumor cell clusters. Transcriptomic analysis of CTCs from patients confirms that KDM2A regulated transcriptional responses correlate with metastatic relapse across multiple cancer types. Moreover, KDM2A may function both as a transcriptional activator and repressor in metastatic clusters. As KDM2A encodes for several domains which can independently regulate E3-ubiqutin ligation, H3K36me2 demethylation, and DNA methylation, we have also performed a structure function analysis of K2MDA in the context of metastatic phenotypes. Thus, the distinct biochemical functions of KDM2A in relation to its regulation of CTC gene transcription and histone modification will also be presented. In conclusion, we have identified KDM2A as a novel regulator of NSCLC metastatic spread. The ability to inhibit KDM2A with small molecule inhibitors may be translated into effective therapeutic interventions for NSCLC patients with metastasis disease. Citation Format: Carolyn Kravitz, Kiran D. Patel, Wesley L. Cai, Anna Arnal-Estapé, Dejian Zhao, Emily Wingrove, Laura Stevens, Thomas F. Westbrook, Qin Yan, Don X. Nguyen. The lysine demethylase KDM2A regulates tumor cell clustering to potentiate metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1718.

β-Carotene enhances the expression of inflammation-related genes and histone H3 K9 acetylation, K4 dimethylation, and K36 trimethylation around these genes in juvenile macrophage-like THP-1 cells

β-Carotene is converted into vitamin A in the body and can remove reactive oxygen species. However, it is still unclear whether β-carotene alters the expression levels of inflammation-related genes in macrophages and how this is regulated. In the present study, we investigated whether the administration of β-carotene under hyperglycemic conditions altered the expression level of inflammation-related genes and whether any observed differences were associated with changes in histone modifications in juvenile macrophage-like THP-1 cells. THP-1 cells (from a human monocytic leukemia cell line) were cultured in low glucose (5 mM), high glucose (25 mM), or high glucose (25 mM) + β-carotene (5 μM) media for 1 day, and mRNA expression levels of genes related to oxidative stress and inflammation, and histone modifications were determined by mRNA microarray and qRT-PCR analyses, and chromatin immunoprecipitation assays, respectively. The expression of inflammation-related genes, such as IL31RA, CD38, and NCF1B, and inflammation-associated signaling pathway genes, such as ITGAL, PRAM1, and CSF3R, were upregulated by β-carotene under high-glucose conditions. Under these conditions, histone H3 lysine 4 (K4) demethylation, H3K36 trimethylation, and H3K9 acetylation around the CD38, NCF1B, and ITGAL genes were higher in β-carotene-treated cells than in untreated cells. Treatment of juvenile macrophage-like THP-1 cells with β-carotene under these high glucose conditions induced the expression of inflammation-related genes, K9 acetylation, and K4 di- and K36 trimethylation of histone H3 around these genes.

Set2 histone methyltransferase regulates transcription coupled-nucleotide excision repair in yeast.

Helix-distorting DNA lesions, including ultraviolet (UV) light-induced damage, are repaired by the global genomic-nucleotide excision repair (GG-NER) and transcription coupled-nucleotide excision repair (TC-NER) pathways. Previous studies have shown that histone post-translational modifications (PTMs) such as histone acetylation and methylation can promote GG-NER in chromatin. Whether histone PTMs also regulate the repair of DNA lesions by the TC-NER pathway in transcribed DNA is unknown. Here, we report that histone H3 K36 methylation (H3K36me) by the Set2 histone methyltransferase in yeast regulates TC-NER. Mutations in Set2 or H3K36 result in UV sensitivity that is epistatic with Rad26, the primary TC-NER factor in yeast, and cause a defect in the repair of UV damage across the yeast genome. We further show that mutations in Set2 or H3K36 in a GG-NER deficient strain (i.e., rad16Δ) partially rescue its UV sensitivity. Our data indicate that deletion of SET2 rescues UV sensitivity in a GG-NER deficient strain by activating cryptic antisense transcription, so that the non-transcribed strand (NTS) of yeast genes is repaired by TC-NER. These findings indicate that Set2 methylation of H3K36 establishes transcriptional asymmetry in repair by promoting canonical TC-NER of the transcribed strand (TS) and suppressing cryptic TC-NER of the NTS.

Subtelomeric Chromatin in the Fission Yeast S. pombe.

Telomeres play important roles in safeguarding the genome. The specialized repressive chromatin that assembles at telomeres and subtelomeric domains is key to this protective role. However, in many organisms, the repetitive nature of telomeric and subtelomeric sequences has hindered research efforts. The fission yeast S. pombe has provided an important model system for dissection of chromatin biology due to the relative ease of genetic manipulation and strong conservation of important regulatory proteins with higher eukaryotes. Telomeres and the telomere-binding shelterin complex are highly conserved with mammals, as is the assembly of constitutive heterochromatin at subtelomeres. In this review, we seek to summarize recent work detailing the assembly of distinct chromatin structures within subtelomeric domains in fission yeast. These include the heterochromatic SH subtelomeric domains, the telomere-associated sequences (TAS), and ST chromatin domains that assemble highly condensed chromatin clusters called knobs. Specifically, we review new insights into the sequence of subtelomeric domains, the distinct types of chromatin that assemble on these sequences and how histone H3 K36 modifications influence these chromatin structures. We address the interplay between the subdomains of chromatin structure and how subtelomeric chromatin is influenced by both the telomere-bound shelterin complexes and by euchromatic chromatin regulators internal to the subtelomeric domain. Finally, we demonstrate that telomere clustering, which is mediated via the condensed ST chromatin knob domains, does not depend on knob assembly within these domains but on Set2, which mediates H3K36 methylation.

Oncohistones: a roadmap to stalled development.

Since the discovery of recurrent mutations in histone H3 variants in paediatric brain tumours, so-called 'oncohistones' have been identified in various cancers. While their mechanism of action remains under active investigation, several studies have shed light on how they promote genome-wide epigenetic perturbations. These findings converge on altered post-translational modifications on two key lysine (K) residues of the H3 tail, K27 and K36, which regulate several cellular processes, including those linked to cell differentiation during development. We will review how these oncohistones affect the methylation of cognate residues, but also disrupt the distribution of opposing chromatin marks, creating genome-wide epigenetic changes which participate in the oncogenic process. Ultimately, tumorigenesis is promoted through the maintenance of a progenitor state at the expense of differentiation in defined cellular and developmental contexts. As these epigenetic disruptions are reversible, improved understanding of oncohistone pathogenicity can result in needed alternative therapies.

Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders.

DNA methylation (DNAme) profiling is used to establish specific biomarkers to improve the diagnosis of patients with inherited neurodevelopmental disorders and to guide mutation screening. In the specific case of mendelian disorders of the epigenetic machinery, it also provides the basis to infer mechanistic aspects with regard to DNAme determinants and interplay between histone and DNAme that apply to humans. Here, we present comparative methylomes from patients with mutations in the de novo DNA methyltransferases DNMT3A and DNMT3B, in their catalytic domain or their N-terminal parts involved in reading histone methylation, or in histone H3 lysine (K) methylases NSD1 or SETD2 (H3 K36) or KMT2D/MLL2 (H3 K4). We provide disease-specific DNAme signatures and document the distinct consequences of mutations in enzymes with very similar or intertwined functions, including at repeated sequences and imprinted loci. We found that KMT2D and SETD2 germline mutations have little impact on DNAme profiles. In contrast, the overlapping DNAme alterations downstream of NSD1 or DNMT3 mutations underlines functional links, more specifically between NSD1 and DNMT3B at heterochromatin regions or DNMT3A at regulatory elements. Together, these data indicate certain discrepancy with the mechanisms described in animal models or the existence of redundant or complementary functions unforeseen in humans.

Histone H3.3 G34 mutations promote aberrant PRC2 activity and drive tumor progression

A high percentage of pediatric gliomas and bone tumors reportedly harbor missense mutations at glycine 34 in genes encoding histone variant H3.3. We find that these H3.3 G34 mutations directly alter the enhancer chromatin landscape of mesenchymal stem cells by impeding methylation at lysine 36 on histone H3 (H3K36) by SETD2, but not by the NSD1/2 enzymes. The reduction of H3K36 methylation by G34 mutations promotes an aberrant gain of PRC2-mediated H3K27me2/3 and loss of H3K27ac at active enhancers containing SETD2 activity. This altered histone modification profile promotes a unique gene expression profile that supports enhanced tumor development in vivo. Our findings are mirrored in G34W-containing giant cell tumors of bone where patient-derived stromal cells exhibit gene expression profiles associated with early osteoblastic differentiation. Overall, we demonstrate that H3.3 G34 oncohistones selectively promote PRC2 activity by interfering with SETD2-mediated H3K36 methylation. We propose that PRC2-mediated silencing of enhancers involved in cell differentiation represents a potential mechanism by which H3.3 G34 mutations drive these tumors.

The catalytic domain of the histone methyltransferase NSD2/MMSET is required for the generation of B1 cells in mice.

Humoral immunity in mammals relies on the function of two developmentally and functionally distinct B-cell subsets-B1 and B2 cells. While B2 cells are responsible for the adaptive response to environmental antigens, B1 cells regulate the production of polyreactive and low-affinity antibodies for innate humoral immunity. The molecular mechanism of B-cell specification into different subsets is understudied. In this study, we identified lysine methyltransferase NSD2 (MMSET/WHSC1) as a critical regulator of B1 cell development. In contrast to its minor impact on B2 cells, deletion of the catalytic domain of NSD2 in primary B cells impairs the generation of B1 lineage. Thus, NSD2, a histone H3 K36 dimethylase, is the first-in-class epigenetic regulator of a B-cell lineage in mice.

Unique and Shared Roles for Histone H3K36 Methylation States in Transcription Regulation Functions

Set2 co-transcriptionally methylates lysine 36 of histone H3 (H3K36), producing mono-, di-, and trimethylation (H3K36me1/2/3). These modifications recruit or repel chromatin effector proteins important for transcriptional fidelity, mRNA splicing, and DNA repair. However, it was not known whether the different methylation states of H3K36 have distinct biological functions. Here, we use engineered forms of Set2 that produce different lysine methylation states to identify unique and shared functions for H3K36 modifications. Although H3K36me1/2 and H3K36me3 are functionally redundant in many SET2 deletion phenotypes, we found that H3K36me3 has a unique function related to Bur1 kinase activity and FACT (facilitates chromatin transcription) complex function. Further, during nutrient stress, either H3K36me1/2 or H3K36me3 represses high levels of histone acetylation and cryptic transcription that arises from within genes. Our findings uncover the potential for the regulation of diverse chromatin functions by different H3K36 methylation states.

A Click Chemistry Approach to Reveal the chromatin‐Dependent Histone H3 K36 Deacetylase Nature of SIRT7

Using an engineered pyrrolysyl‐tRNA synthetase mutant together with tRNAPyl, we have genetically encoded Ne‐(7‐azidoheptanoyl)‐L‐lysine (AzHeK) by amber codon in Escherichia coli for recombinant expression of a number of AzHeK‐containing histone H3 proteins. We assembled in vitro acyl‐nucleosomes from these recombinant acyl‐H3 histones. All these acyl‐nucleosomes contained an azide functionality that allowed quick click labeling with a strained alkyne dye for in‐gel fluorescence analysis. Using these acyl‐nucleosomes as substrates and click labeling as a detection method, we systematically investigated chromatin deacylation activities of SIRT7, a class III NAD+‐dependent histone deacylase with roles in aging and cancer biology. Besides confirming the previously reported histone H3K18 deacylation activity, our results revealed that SIRT7 has an astonishingly high activity to catalyze deacylation of H3K36 and is also catalytically active to deacylate H3K37. We further demonstrated that this H3K36 deacylation activity is nucleosome dependent and can be significantly enhanced when appending the acyl‐nucleosome substrate with a short double‐stranded DNA that mimics the bridging DNA between nucleosomes in native chromatin. By overexpressing SIRT7 in human cells, we verified that SIRT7 natively removes acetylation from histone H3K36. Moreover, SIRT7‐deficient cells exhibited H3K36 hyperacetylation in whole cell extracts, at rDNA sequences in nucleoli, and at select SIRT7 target loci, demonstrating the physiologic importance of SIRT7 in determining endogenous H3K36 acetylation levels. H3K36 acetylation has been detected at active gene promoters, but little is understood about its regulation and functions. Our findings establish H3K36 as a physiologic substrate of SIRT7 and implicate this modification in potential SIRT7 pathways in heterochromatin silencing and genomic stability.Support or Funding InformationNIH GM121584, NIH AG050997, NIH GM086703, Welch A‐1715Figure 1

The Paf1 Complex Broadly Impacts the Transcriptome of Saccharomyces cerevisiae.

The Polymerase Associated Factor 1 complex (Paf1C) is a multifunctional regulator of eukaryotic gene expression important for the coordination of transcription with chromatin modification and post-transcriptional processes. In this study, we investigated the extent to which the functions of Paf1C combine to regulate the Saccharomyces cerevisiae transcriptome. While previous studies focused on the roles of Paf1C in controlling mRNA levels, here, we took advantage of a genetic background that enriches for unstable transcripts, and demonstrate that deletion of PAF1 affects all classes of PolII transcripts including multiple classes of noncoding RNAs (ncRNAs). By conducting a de novo differential expression analysis independent of gene annotations, we found that Paf1 positively and negatively regulates antisense transcription at multiple loci. Comparisons with nascent transcript data revealed that many, but not all, changes in RNA levels detected by our analysis are due to changes in transcription instead of post-transcriptional events. To investigate the mechanisms by which Paf1 regulates protein-coding genes, we focused on genes involved in iron and phosphate homeostasis, which were differentially affected by PAF1 deletion. Our results indicate that Paf1 stimulates phosphate gene expression through a mechanism that is independent of any individual Paf1C-dependent histone modification. In contrast, the inhibition of iron gene expression by Paf1 correlates with a defect in H3 K36 trimethylation. Finally, we showed that one iron regulon gene, FET4, is coordinately controlled by Paf1 and transcription of upstream noncoding DNA. Together, these data identify roles for Paf1C in controlling both coding and noncoding regions of the yeast genome.

Structural Insights into Stimulation of Ash1L's H3K36 Methyltransferase Activity through Mrg15 Binding

The evolutionarily conserved Trithorax group protein Ash1 is a SET domain histone methyltransferase that mono- and dimethylates lysine 36 of histone H3 (H3K36). Ash1 forms a complex with Mrg15 and Nurf55, and the binding of Mrg15 greatly stimulates the catalytic activity of Ash1, yet the underlying molecular mechanisms remain unknown. Here we report the crystal structure of the tandem Mrg15-interacting and SET domains of human Ash1L in complex with Mrg15. Ash1L interacts with Mrg15 principally via a segment located N-terminal to the catalytic SET domain. Surprisingly, an autoinhibitory loop in the post-SET region of Ash1L is destabilized on Mrg15 binding despite no direct contact. Dynamics of the autoinhibitory loop can be attributed to subtle structural changes of the S-adenosylmethionine (SAM) binding pocket induced by Mrg15 binding, implicating a mechanism of conformational coupling between SAM and substrate binding sites. The findings broaden the understanding of regulation of H3K36 methyltransferases.

Abstract A39: Nuclear SET domain (NSD) protein lysine methyltransferases (KMT) are higher expressed in acute myeloid leukemia

Abstract The nuclear SET domain (NSD) protein lysine methyltransferases (KMT) family is composed of three members, NSD1/KMT3B, NSD2/WHSC1/MMSET, and NSD3/WHSC1L1, which regulate gene expression through methylation of lysine 36 of histone H3 (H3K36). NSD2 overexpression was reported in multiple myeloma with t(4;14)/IgH-MMSET. NSDs gene expression profile is unknown in acute leukemias; however, NSD1 and NSD3 were described to be fused with the nucleoporin 98 gene (NUP98) in rare AML and myelodysplastic syndrome cases and both fusion proteins were associated with poor prognosis. The aims of the present study were to characterize the expression of NSD-KMTs in patients with AML and healthy controls, to determine if this expression is associated with specific genetic abnormalities and/or with treatment outcome. Bone marrow aspirates from four healthy donors and 94 AML patients (50♀, 44♂) at diagnosis were included in the study. Our cohort included 10 patients with acute promyelocytic leukemia (APL), 8 with core binding factor (CBF) leukemias [6 with t(8;21) and 4 with inv(16)], and 74 patients with non-APL non-CBF AML. NSD family gene expression was evaluated by qPCR using the comparative Ct method for analysis. A higher expression of the NSD1 gene was observed in AML cells compared to normal bone marrow (BM) samples (median [range] = 3.8835 [0.6804-11.5598] vs. 1.003 [0.7956-1.265], p=0.0243). Similarly, the expression of NSD3 was higher in AML only for the comparison between healthy BM and CBF-AML groups (median [range] = 1.070 [0.6360-1.410] vs. 2.719 [1.238-8.830], p=0.0265). No significant differences were detected in the analysis of NSD2 expression. The association between expression levels of NSD-KMT with age, gender, prognosis (favorable vs. unfavorable), presence or absence of FLT3-ITD and NPM1 mutations, and presence or absence of karyotype abnormalities was evaluated. With the exception of NSD3 and presence/absence of karyotype abnormalities, NSD-KMT gene expression levels were higher in AML subgroups when compared to healthy donors, in all above parameters. NSD2 was more expressed in AML when compared to NSD1/NSD2 groups. NPM1 mutations and FLT3 internal tandem duplications (FLT3-ITD) were detected in 19.1% (18/94) of the patients with AML. NSD1/NSD3 were more expressed in FLT3-ITD mutant vs. FLT3 wild-type group. In addition, NSD2 was frequently more observed in patients aged 65 or older. Next, patients were stratified into two groups according to the median value of each NSD-KMT evaluated. We assessed the correlation between age, white blood cells count, hemoglobin, platelets, and blasts percentage at bone marrow and NSD-KMT expression levels. A positive correlation was observec between NSD1/NSD3 and the percentage of bone marrow blasts at diagnosis (r2 = 0.08080/p-value = 0.0084, and r2 = 0.04937/p-value = 0.0410, respectively). NSD3 was also correlated to the higher number of bone marrow blasts (r2 = 0.1219/p-value = 0.0217), followed by a decrease into the platelet count (r2 = 0.09795/p-value = 0.0436). Regarding the analysis of treatment outcome, patients with non-APL AML were stratified into high and low NSD1 or NSD2 expression subgroups using the criteria above. The median overall survival of patients in the low NSD2 expression subgroup was 333.023 days (95% CI:158.541-507.505 days) whereas that of patients in the high NSD2 expression subgroup was 817.629 days (95% CI:238.702-1396.555 days) (p=0,633). No significant difference was observed between the overall survival of patients in the high and low NSD1 expression subgroups. Our data suggest a correlation between the overexpression levels of NSD-KMT with histone modifications, suggesting that this modification and not only DNA methylation can contribute to epigenomic changes associated with AML pathogenesis. Citation Format: Virginia Mara de Deus Wagatsuma, Luisa C. A. Koury, Silvia Helena Sánchez, Lorena Lobo Figueiredo-Pontes, Fernanda Borges da Silva, Fernanda Borges da Silva, Adriana Ines Dore, Ana Silvia Gouvea de Lima, Antonio Roberto Lucena-Araujo, Fabiola Traina, Felipe Saldanha-Araujo, Fabio Pittella, Eduardo Magalhães Rego. Nuclear SET domain (NSD) protein lysine methyltransferases (KMT) are higher expressed in acute myeloid leukemia [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A39.

NSD1 Inactivation and SETD2 Mutation Drive a Convergence toward Loss of Function of H3K36 Writers in Clear Cell Renal Cell Carcinomas.

Extensive dysregulation of chromatin-modifying genes in clear cell renal cell carcinoma (ccRCC) has been uncovered through next-generation sequencing. However, a scientific understanding of the cross-talk between epigenetic and genomic aberrations remains limited. Here we identify three ccRCC epigenetic clusters, including a clear cell CpG island methylator phenotype (C-CIMP) subgroup associated with promoter methylation of VEGF genes (FLT4, FLT1, and KDR). C-CIMP was furthermore characterized by silencing of genes related to vasculature development. Through an integrative analysis, we discovered frequent silencing of the histone H3 K36 methyltransferase NSD1 as the sole chromatin-modifying gene silenced by DNA methylation in ccRCC. Notably, tumors harboring NSD1 methylation were of higher grade and stage in different ccRCC datasets. NSD1 promoter methylation correlated with SETD2 somatic mutations across and within spatially distinct regions of primary ccRCC tumors. ccRCC harboring epigenetic silencing of NSD1 displayed a specific genome-wide methylome signature consistent with the NSD1 mutation methylome signature observed in Sotos syndrome. Thus, we concluded that epigenetic silencing of genes involved in angiogenesis is a hallmark of the methylator phenotype in ccRCC, implying a convergence toward loss of function of epigenetic writers of the H3K36 histone mark as a root feature of aggressive ccRCC. Cancer Res; 77(18); 4835-45. ©2017 AACR.

Drosophila Histone Demethylase KDM4A Has Enzymatic and Non-enzymatic Roles in Controlling Heterochromatin Integrity

Eukaryotic genomes are broadly divided between gene-rich euchromatin and the highly repetitive heterochromatin domain, which is enriched for proteins critical for genome stability and transcriptional silencing. This study shows that Drosophila KDM4A (dKDM4A), previously characterized as a euchromatic histone H3 K36 demethylase and transcriptional regulator, predominantly localizes to heterochromatin and regulates heterochromatin position-effect variegation (PEV), organization of repetitive DNAs, and DNA repair. We demonstrate that dKDM4A demethylase activity is dispensable for PEV. In contrast, dKDM4A enzymatic activity is required to relocate heterochromatic double-strand breaks outside the domain, as well as for organismal survival when DNA repair is compromised. Finally, DNA damage triggers dKDM4A-dependent changes in the levels of H3K56me3, suggesting that dKDM4A demethylates this heterochromatic mark to facilitate repair. We conclude that dKDM4A, in addition to its previously characterized role in euchromatin, utilizes both enzymatic and structural mechanisms to regulate heterochromatin organization and functions.

Nuclear SET Domain (NSD) Protein Lysine Methyltransferases (KMT) Family Members Expression in Acute Myeloid Leukemia

The Nuclear SET Domain (NSD) Protein Lysine Methyltransferases (KMT) family is composed of three members: NSD1/KMT3B, NSD2/WHSC1/MMSET and NSD3/WHSC1L1 which regulate gene expression through methylation of lysine 36 of histone H3 (H3K36). NSD2 overexpression was reported in multiple myeloma with t(4;14)/IgH-MMSET. NSDs gene expression profile is unknown in acute leukemias, however NSD1 and NSD3 were described to be fused with the nucleoporin 98 gene (NUP98) in rare AML and myelodysplastic syndrome cases and, both fusion proteins were associated with poor prognosis. The aims of the present study were to characterize the expression of NSD-KMTs in patients with AML and healthy controls, to determine if this expression is associated with specific genetic abnormalities and/or with treatment outcome.A total of four healthy donors and 45 AML patients (27♀, 18♂) at diagnosis were included in the study. Our cohort included 8 patients with acute promyelocytic leukemia (APL), 8 with core binding factor (CBF) leukemias [4 with t(8;21) and 4 with inv(16)], and 29 patients with non-APL non-CBF AML. NSD family gene expression was evaluated by qPCR using the comparative Ct method for analysis. A higher expression of the NSD1 gene was observed in AML cells compared to normal bone marrow (BM) samples {median [range] = 3.202 [0.6804-0.096] vs. 1.003 [:0.7956-1.265], p=0.0243}. Similarly, the expression of NSD3 was higher in AML, but the difference was significant only for the comparison between healthy BM and CBF-AML groups {median [range] = 1.070 [0.6360-1.410] vs. 2.719 [1.238-8.830], p=0.0265}. No significant differences were detected in the analysis of NSD2 expression. Considering the three groups of AML patients, no correlation was found between NSD1, NSD2 or NSD3 expression levels and age, gender, leukocyte counts at diagnosis, karyotype (normal vs. abnormal), frequency of specific genetic abnormalities (t(15;17)/PML-RARA; t(8;21)/RUNX1-RUNX1T1; inv(16)/CBFB-MYH11) or percentage of blasts in bone marrow. NPM1 mutations and FLT3 internal tandem duplications (FLT3-ITD) were detected in 29.6% (13/44) and 21% (9/43) of the patients with AML, respectively. We observed a significant increase in NSD1, NSD2 and NSD3 expression in blasts from patients with FLT3-ITD (p=0.0177), but not in those with NPM1 mutations. These differences remained significant when APL cases were excluded from the analysis. Next, patients were grouped according to NSD1 or NSD2 expression. Patients with NSD1 or NSD2 expression higher or lower than the median value (3.25 and 3.16, respectively), showed no significant differences regarding age distribution, leukocyte counts or percentage of blasts in bone marrow at diagnosis, or presence of genetic abnormalities. Regarding the analysis of treatment outcome, patients with non-APL AML were stratified into high and low NSD1 or NSD2 expression subgroups using the criteria above. The median overall survival of patients in the low NSD2 expression subgroup was of 333,023 days [95% CI:158,541-507,505 days] whereas patients in the high NSD2 expression subgroup was of 817,629 days [95% CI:238,702-1396,555 days] (p=0,633). No significant difference observed between the overall survival of patients in the high and low NSD1 expression subgroups. In order to determine if NSD-KMT levels were associated with changes at histone H3 lysine 4 (H4K4) and H3K36 (known to activate gene transcription), as well at histone H3 lysine 9 (H3K9), H3K27, H3K79 and H4K29, associated to regulatory repression, we ran an experiment using Illumina Infinium Methylation 450k arrays. The comparison between normal and leukemic cells revealed specific histone methylation profiles. There is experimental evidence that histone methylation is a prerequisite for DNA methylation and transcriptional regulation, suggesting interplay between histone and DNA methylation. Our data correlate overexpression levels of NSD-KMT with histone modifications, suggesting that this modification and not only DNA methylation can contribute for epigenomic changes associated to AML pathogenesis. DisclosuresNo relevant conflicts of interest to declare.

SETD2: an epigenetic modifier with tumor suppressor functionality.

In the past decade important progress has been made in our understanding of the epigenetic regulatory machinery. It has become clear that genetic aberrations in multiple epigenetic modifier proteins are associated with various types of cancer. Moreover, targeting the epigenome has emerged as a novel tool to treat cancer patients. Recently, the first drugs have been reported that specifically target SETD2-negative tumors. In this review we discuss the studies on the associated protein, Set domain containing 2 (SETD2), a histone modifier for which mutations have only recently been associated with cancer development. Our review starts with the structural characteristics of SETD2 and extends to its corresponding function by combining studies on SETD2 function in yeast, Drosophila, Caenorhabditis elegans, mice, and humans. SETD2 is now generally known as the single human gene responsible for trimethylation of lysine 36 of Histone H3 (H3K36). H3K36me3 readers that recruit protein complexes to carry out specific processes, including transcription elongation, RNA processing, and DNA repair, determine the impact of this histone modification. Finally, we describe the prevalence of SETD2-inactivating mutations in cancer, with the highest frequency in clear cell Renal Cell Cancer, and explore how SETD2-inactivation might contribute to tumor development.

Histone H3K36 Methylation is Required for Efficient Pre‐mRNA Splicing in Saccharomyces cerevisiae

Proper gene expression involves multiple steps, including RNA splicing where non‐protein coding regions of RNA are removed from the RNA transcript. RNA splicing is carried out by the large and dynamic spliceosome, which is comprised of small nucleoprotein complexes (snRNPs) that assemble on an RNA molecule in a precise order. Assembly of the spliceosome occurs co‐transcriptionally and RNA splicing is tightly coordinated with transcription to ensure precise and efficient gene expression. However, the mechanisms that underlie this coordination are poorly understood. In order to identify proteins that function to coordinate RNA splicing with transcription we carried out a genetic interaction study using Saccharomyces cerevisiae. We identified negative genetic interactions between genes encoding RNA splicing factors and the SET2 gene, a histone methyltransferase that methylates lysine36 on histone H3 (H3K36) to regulate transcription. Furthermore, we show that mutations that block H3K36 methylation also have negative genetic interactions with splicing factor genes, suggesting that H3K36 methylation is important for RNA splicing. Indeed, we have shown that deletion of SET2 or point mutation of H3K36 inhibits RNA splicing and exacerbates splicing defects in yeast strains harboring deletions of splicing factor genes. Using chromatin immunoprecipitation, we demonstrate that deletion of SET2 reduces the association of snRNPs with chromatin. Furthermore, we tested for reciprocal/reverse coordination between RNA splicing and transcription. We found that mutation of Prp28, a helicase protein that normally promotes RNA splicing, alters RNA polymerase II association with DNA. We are currently testing whether perturbation of RNA splicing alters H3K36 methylation. Thus, we provide evidence that H3K36 methylation is required for appropriate RNA splicing in yeast and suggest a model in which Set2 or H3K36 methylation help to recruit splicing factors to RNA during transcription.Support or Funding InformationCottrell College Science Award from the Research Corporation for Science Advancement (#20186) to T.L.KAmerican Cancer Society (RSG‐05‐137‐01‐GMC) to S.W.S National Institutes of Health (GM084246 to S.W.S and GM110058 to B.D.S) Cancer Prevention & Research Institute of Texas (RP101501) to M.R.SGateway to Graduate School funded by The National Science Foundation (NSF‐URM) to D.M.F

Lysine demethylase 2A promotes stemness and angiogenesis of breast cancer by upregulating Jagged1.

Alterations of histone methylation dynamically regulated by methyltransferases and demethylases are frequently found in human cancers. Here, we showed that expression of lysine demethylase 2A (KDM2A) is markedly increased in human breast cancer and its overexpression is associated with tumor progression and poor prognosis. Knockdown of KDM2A in breast cancer cells reduced proliferation but not viability. Gene set enrichment analysis revealed that inhibition of KDM2A down-regulates angiogenic genes with concurrent reduction of Jagged1 (JAG1), NOTCH1 and HEY1 in the NOTCH signaling. Chromatin immunoprecipitation- quantitative polymerase chain reaction (ChIP-qPCR) demonstrated the binding of KDM2A to the JAG1 promoter and the increase of methylation of Lys-36 of histone H3 (H3K36) in KDM2A-depleted MDA-MB-231 cells. Tumorsphere formation was significantly reduced in KDM2A-depleted cells which could be reversed by ectopic expression of JAG1. A selective KDM2A inhibitor daminozide also decreased the number of tumorsphere and the number of CD24−/CD44hi cells. In addition, daminozide acted synergistically with cisplatin in cell killing. We identified SOX2 as a direct transcriptional target of KDM2A to promote cancer stemness. Depletion of KDM2A in MDA-MB-231 cells attenuated NOTCH activation and tube formation in co-cultured endothelial cells. Two pro-angiogenic factors JAG1 and PDGFA are key mediators for KDM2A to enhance angiogenesis. Finally, inhibition of KDM2A significantly decreased tumor growth and angiogenesis in orthotopic animal experiments. Collectively, we conclude that KDM2A functions as an oncogene in breast cancer by upregulating JAG1 to promote stemness, chemoresistance and angiogenesis.