1
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Gretarsson KH, Abini-Agbomson S, Gloor SL, Weinberg DN, McCuiston JL, Kumary VUS, Hickman AR, Sahu V, Lee R, Xu X, Lipieta N, Flashner S, Adeleke OA, Popova IK, Taylor HF, Noll K, Windham CL, Maryanski DN, Venters BJ, Nakagawa H, Keogh MC, Armache KJ, Lu C. Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patch. SCIENCE ADVANCES 2024; 10:eadp0975. [PMID: 39196936 PMCID: PMC11352909 DOI: 10.1126/sciadv.adp0975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 07/24/2024] [Indexed: 08/30/2024]
Abstract
During tumor development, promoter CpG islands that are normally silenced by Polycomb repressive complexes (PRCs) become DNA-hypermethylated. The molecular mechanism by which de novo DNA methyltransferase(s) [DNMT(s)] catalyze CpG methylation at PRC-regulated regions remains unclear. Here, we report a cryo-electron microscopy structure of the DNMT3A long isoform (DNMT3A1) amino-terminal region in complex with a nucleosome carrying PRC1-mediated histone H2A lysine-119 monoubiquitination (H2AK119Ub). We identify regions within the DNMT3A1 amino terminus that bind H2AK119Ub and the nucleosome acidic patch. This bidentate interaction is required for effective DNMT3A1 engagement with H2AK119Ub-modified chromatin in cells. Further, aberrant redistribution of DNMT3A1 to Polycomb target genes recapitulates the cancer-associated DNA hypermethylation signature and inhibits their transcriptional activation during cell differentiation. This effect is rescued by disruption of the DNMT3A1-acidic patch interaction. Together, our analyses reveal a binding interface critical for mediating promoter CpG island DNA hypermethylation, a major molecular hallmark of cancer.
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Affiliation(s)
- Kristjan H. Gretarsson
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Stephen Abini-Agbomson
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | | | - Daniel N. Weinberg
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | | | | | | | - Varun Sahu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Rachel Lee
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Xinjing Xu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Natalie Lipieta
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samuel Flashner
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY 10032, USA
| | | | | | | | | | | | | | | | - Hiroshi Nakagawa
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY 10032, USA
| | | | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA
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2
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Chen X, Guo Y, Zhao T, Lu J, Fang J, Wang Y, Wang GG, Song J. Structural basis for the H2AK119ub1-specific DNMT3A-nucleosome interaction. Nat Commun 2024; 15:6217. [PMID: 39043678 PMCID: PMC11266573 DOI: 10.1038/s41467-024-50526-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
Isoform 1 of DNA methyltransferase DNMT3A (DNMT3A1) specifically recognizes nucleosome monoubiquitylated at histone H2A lysine-119 (H2AK119ub1) for establishment of DNA methylation. Mis-regulation of this process may cause aberrant DNA methylation and pathogenesis. However, the molecular basis underlying DNMT3A1-nucleosome interaction remains elusive. Here we report the cryo-EM structure of DNMT3A1's ubiquitin-dependent recruitment (UDR) fragment complexed with H2AK119ub1-modified nucleosome. DNMT3A1 UDR occupies an extensive nucleosome surface, involving the H2A-H2B acidic patch, a surface groove formed by H2A and H3, nucleosomal DNA, and H2AK119ub1. The DNMT3A1 UDR's interaction with H2AK119ub1 affects the functionality of DNMT3A1 in cells in a context-dependent manner. Our structural and biochemical analysis also reveals competition between DNMT3A1 and JARID2, a cofactor of polycomb repression complex 2 (PRC2), for nucleosome binding, suggesting the interplay between different epigenetic pathways. Together, this study reports a molecular basis for H2AK119ub1-dependent DNMT3A1-nucleosome association, with important implications in DNMT3A1-mediated DNA methylation in development.
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Affiliation(s)
- Xinyi Chen
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Yiran Guo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Ting Zhao
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Jian Fang
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Gang Greg Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA.
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3
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Lu J, Guo Y, Yin J, Chen J, Wang Y, Wang GG, Song J. Structure-guided functional suppression of AML-associated DNMT3A hotspot mutations. Nat Commun 2024; 15:3111. [PMID: 38600075 PMCID: PMC11006857 DOI: 10.1038/s41467-024-47398-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
DNA methyltransferases DNMT3A- and DNMT3B-mediated DNA methylation critically regulate epigenomic and transcriptomic patterning during development. The hotspot DNMT3A mutations at the site of Arg822 (R882) promote polymerization, leading to aberrant DNA methylation that may contribute to the pathogenesis of acute myeloid leukemia (AML). However, the molecular basis underlying the mutation-induced functional misregulation of DNMT3A remains unclear. Here, we report the crystal structures of the DNMT3A methyltransferase domain, revealing a molecular basis for its oligomerization behavior distinct to DNMT3B, and the enhanced intermolecular contacts caused by the R882H or R882C mutation. Our biochemical, cellular, and genomic DNA methylation analyses demonstrate that introducing the DNMT3B-converting mutations inhibits the R882H-/R882C-triggered DNMT3A polymerization and enhances substrate access, thereby eliminating the dominant-negative effect of the DNMT3A R882 mutations in cells. Together, this study provides mechanistic insights into DNMT3A R882 mutations-triggered aberrant oligomerization and DNA hypomethylation in AML, with important implications in cancer therapy.
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Affiliation(s)
- Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Yiran Guo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA
| | - Jianbin Chen
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Gang Greg Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, USA.
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, USA.
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4
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Gretarsson KH, Abini-Agbomson S, Gloor SL, Weinberg DN, McCuiston JL, Kumary VUS, Hickman AR, Sahu V, Lee R, Xu X, Lipieta N, Flashner S, Adeleke OA, Popova IK, Taylor HF, Noll K, Windham CL, Maryanski DN, Venters BJ, Nakagawa H, Keogh MC, Armache KJ, Lu C. Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of Histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585588. [PMID: 38562823 PMCID: PMC10983913 DOI: 10.1101/2024.03.18.585588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
During tumor development, promoter CpG islands (CGIs) that are normally silenced by Polycomb repressive complexes (PRCs) become DNA hypermethylated. The molecular mechanism by which de novo DNA methyltransferase(s) catalyze CpG methylation at PRC-regulated regions remains unclear. Here we report a cryo-EM structure of the DNMT3A long isoform (DNMT3A1) N-terminal region in complex with a nucleosome carrying PRC1-mediated histone H2A lysine 119 monoubiquitination (H2AK119Ub). We identify regions within the DNMT3A1 N-terminus that bind H2AK119Ub and the nucleosome acidic patch. This bidentate interaction is required for effective DNMT3A1 engagement with H2AK119Ub-modified chromatin in cells. Furthermore, aberrant redistribution of DNMT3A1 to Polycomb target genes inhibits their transcriptional activation during cell differentiation and recapitulates the cancer-associated DNA hypermethylation signature. This effect is rescued by disruption of the DNMT3A1-acidic patch interaction. Together, our analyses reveal a binding interface critical for countering promoter CGI DNA hypermethylation, a major molecular hallmark of cancer.
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5
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Hobble HV, Schaner Tooley CE. Intrafamily heterooligomerization as an emerging mechanism of methyltransferase regulation. Epigenetics Chromatin 2024; 17:5. [PMID: 38429855 PMCID: PMC10908127 DOI: 10.1186/s13072-024-00530-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/10/2024] [Indexed: 03/03/2024] Open
Abstract
Protein and nucleic acid methylation are important biochemical modifications. In addition to their well-established roles in gene regulation, they also regulate cell signaling, metabolism, and translation. Despite this high biological relevance, little is known about the general regulation of methyltransferase function. Methyltransferases are divided into superfamilies based on structural similarities and further classified into smaller families based on sequence/domain/target similarity. While members within superfamilies differ in substrate specificity, their structurally similar active sites indicate a potential for shared modes of regulation. Growing evidence from one superfamily suggests a common regulatory mode may be through heterooligomerization with other family members. Here, we describe examples of methyltransferase regulation through intrafamily heterooligomerization and discuss how this can be exploited for therapeutic use.
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Affiliation(s)
- Haley V Hobble
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, 14203, USA
| | - Christine E Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, 14203, USA.
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6
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Lu J, Fang J, Zhu H, Liang KL, Khudaverdyan N, Song J. Structural basis for the allosteric regulation and dynamic assembly of DNMT3B. Nucleic Acids Res 2023; 51:12476-12491. [PMID: 37941146 PMCID: PMC10711551 DOI: 10.1093/nar/gkad972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/08/2023] [Accepted: 10/14/2023] [Indexed: 11/10/2023] Open
Abstract
Oligomerization of DNMT3B, a mammalian de novo DNA methyltransferase, critically regulates its chromatin targeting and DNA methylation activities. However, how the N-terminal PWWP and ADD domains interplay with the C-terminal methyltransferase (MTase) domain in regulating the dynamic assembly of DNMT3B remains unclear. Here, we report the cryo-EM structure of DNMT3B under various oligomerization states. The ADD domain of DNMT3B interacts with the MTase domain to form an autoinhibitory conformation, resembling the previously observed DNMT3A autoinhibition. Our combined structural and biochemical study further identifies a role for the PWWP domain and its associated ICF mutation in the allosteric regulation of DNMT3B tetramer, and a differential functional impact on DNMT3B by potential ADD-H3K4me0 and PWWP-H3K36me3 bindings. In addition, our comparative structural analysis reveals a coupling between DNMT3B oligomerization and folding of its substrate-binding sites. Together, this study provides mechanistic insights into the allosteric regulation and dynamic assembly of DNMT3B.
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Affiliation(s)
- Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| | - Jian Fang
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| | - Hongtao Zhu
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA
| | | | - Nelli Khudaverdyan
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA92521, USA
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7
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Sobieralski P, Wasąg B, Leszczyńska A, Żuk M, Bieniaszewska M. The molecular profile in patients with polycythemia vera and essential thrombocythemia is dynamic and correlates with disease's phenotype. Front Oncol 2023; 13:1224590. [PMID: 37671053 PMCID: PMC10475996 DOI: 10.3389/fonc.2023.1224590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/02/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction Polycythemia vera (PV) and essential thrombocythemia (ET) are diseases driven by canonical mutations in JAK2, CALR, or MPL gene. Previous studies revealed that in addition to driver mutations, patients with PV and ET can harbor other mutations in various genes, with no established impact on disease phenotype. We hypothesized that the molecular profile of patients with PV and ET is dynamic throughout the disease. Methods In this study, we performed a 37-gene targeted next-generation sequencing panel on the DNA samples collected from 49 study participants in two-time points, separated by 78-141 months. We identified 78 variants across 37 analyzed genes in the study population. Results By analyzing the change in variant allele frequencies and revealing the acquisition of new mutations during the disease, we confirmed the dynamic nature of the molecular profile of patients with PV and ET. We found connections between specific variants with the development of secondary myelofibrosis, thrombotic events, and response to treatment. We confronted our results with existing conventional and mutation-enhanced prognostic systems, showing the limited utility of available prognostic tools. Discussion The results of this study underline the significance of repeated molecular testing in patients with PV and ET and indicate the need for further research within this field to better understand the disease and improve available prognostic tools.
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Affiliation(s)
- Patryk Sobieralski
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Bartosz Wasąg
- Department of Biology and Medical Genetics, Faculty of Medicine, Medical University of Gdańsk, Gdansk, Poland
- Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Aleksandra Leszczyńska
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
| | - Monika Żuk
- Department of Biology and Medical Genetics, Faculty of Medicine, Medical University of Gdańsk, Gdansk, Poland
- Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Maria Bieniaszewska
- Department of Hematology and Transplantology, Medical University of Gdansk, Gdansk, Poland
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8
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Lee D, Koo B, Yang J, Kim S. Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments. PLoS Comput Biol 2023; 19:e1010946. [PMID: 36940213 PMCID: PMC10062925 DOI: 10.1371/journal.pcbi.1010946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/30/2023] [Accepted: 02/13/2023] [Indexed: 03/21/2023] Open
Abstract
Phased DNA methylation states within bisulfite sequencing reads are valuable source of information that can be used to estimate epigenetic diversity across cells as well as epigenomic instability in individual cells. Various measures capturing the heterogeneity of DNA methylation states have been proposed for a decade. However, in routine analyses on DNA methylation, this heterogeneity is often ignored by computing average methylation levels at CpG sites, even though such information exists in bisulfite sequencing data in the form of phased methylation states, or methylation patterns. In this study, to facilitate the application of the DNA methylation heterogeneity measures in downstream epigenomic analyses, we present a Rust-based, extremely fast and lightweight bioinformatics toolkit called Metheor. As the analysis of DNA methylation heterogeneity requires the examination of pairs or groups of CpGs throughout the genome, existing softwares suffer from high computational burden, which almost make a large-scale DNA methylation heterogeneity studies intractable for researchers with limited resources. In this study, we benchmark the performance of Metheor against existing code implementations for DNA methylation heterogeneity measures in three different scenarios of simulated bisulfite sequencing datasets. Metheor was shown to dramatically reduce the execution time up to 300-fold and memory footprint up to 60-fold, while producing identical results with the original implementation, thereby facilitating a large-scale study of DNA methylation heterogeneity profiles. To demonstrate the utility of the low computational burden of Metheor, we show that the methylation heterogeneity profiles of 928 cancer cell lines can be computed with standard computing resources. With those profiles, we reveal the association between DNA methylation heterogeneity and various omics features. Source code for Metheor is at https://github.com/dohlee/metheor and is freely available under the GPL-3.0 license.
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Affiliation(s)
- Dohoon Lee
- Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea
- BK21 FOUR Intelligence Computing, Seoul National University, Seoul, Republic of Korea
| | - Bonil Koo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Jeewon Yang
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, Republic of Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, Republic of Korea
- Department of Computer Science and Engineering, Seoul National University, Seoul, Republic of Korea
- MOGAM Institute for Biomedical Research, Yong-in, Republic of Korea
- * E-mail:
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9
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Chen X, Tian C, Hao Z, Pan L, Hong M, Wei W, Muyey DM, Wang H, Chen X. The impact of DNMT3A variant allele frequency and two different comutations on patients with de novo cytogenetically normal acute myeloid leukemia. Cancer Med 2023; 12:10340-10350. [PMID: 36912186 DOI: 10.1002/cam4.5764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 03/14/2023] Open
Abstract
To refine the biological and prognostic significance of DNMT3A mutations in acute myeloid leukemia (AML), we assessed the impact of DNMT3A variant allele frequency (VAF) and its comutations in this study. Using targeted next-generation sequencing, we analyzed 171 adult patients with de novo cytogenetically normal AML for DNMT3A mutations and associated comutations. DNMT3Amut was detected in 35 patients. DNMT3Amut patients were divided into DNMT3AHigh and DNMT3ALow using a cut-off VAF value of 42%. We observed that DNMT3AHigh patients at diagnosis had increasing white blood cell (WBC) counts (p < 0.001) and a higher lactate dehydrogenase (LDH) level (p = 0.027), and were associated with lower complete remission (CR) rate (p = 0.015) and shorter overall survival (OS) (p = 0.032) than DNMT3ALow patients. We classified two different comutated genetypes, including DNMT3Amut NPM1mut FLT3-ITDmut and DNMT3Amut IDH1/IDH2mut . Patients with DNMT3Amut NPM1mut FLT3-ITDmut showed worse OS (p = 0.026) and relapse-free survival (RFS) (p = 0.003) than those with DNMT3Amut IDH1/IDH2mut , and showed a shorter OS (p = 0.027) than those with DNMT3Awt NPM1mut FLT3-ITDmut . We also observed that patients with DNMT3Amut IDH1/IDH2mut had higher platelet counts (p = 0.009) and a lower BM blast percentage (p = 0.040) than those with DNMT3Awt IDH1/IDH2mut . In multivariate analyses, DNMT3AHigh was independently associated with a lower CR rate (OR = 5.883; p = 0.004) and shorter OS (HR = 3.768; p < 0.001). DNMT3Amut NPM1mut FLT3-ITDmut independently affected worse OS (HR = 6.030; p < 0.001) and RFS (HR = 8.939; p < 0.001). Our findings might be potentially useful for predicting clinical outcomes.
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Affiliation(s)
- Xian Chen
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China.,Department of Genetic Medicine, Shanxi Medical University, Jinzhong, China
| | - Chuchu Tian
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Zhuanghui Hao
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Lingang Pan
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Minglin Hong
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Wei Wei
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Daniel Muteb Muyey
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Hongwei Wang
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Xiuhua Chen
- Institute of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, China
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10
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Urabe A, Chi S, Minami Y. The Immuno-Oncology and Genomic Aspects of DNA-Hypomethylating Therapeutics in Acute Myeloid Leukemia. Int J Mol Sci 2023; 24:ijms24043727. [PMID: 36835136 PMCID: PMC9961620 DOI: 10.3390/ijms24043727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Hypomethylating agents (HMAs) have been used for decades in the treatment of hematologic neoplasms, and now, have gathered attention again in terms of their combination with potent molecular-targeted agents such as a BCL-6 inhibitor venetoclax and an IDH1 inhibitor ivosidenib, as well as a novel immune-checkpoint inhibitor (anit-CD47 antibody) megrolimab. Several studies have shown that leukemic cells have a distinct immunological microenvironment, which is at least partially due to genetic alterations such as the TP53 mutation and epigenetic dysregulation. HMAs possibly improve intrinsic anti-leukemic immunity and sensitivity to immune therapies such as PD-1/PD-L1 inhibitors and anti-CD47 agents. This review describes the immuno-oncological backgrounds of the leukemic microenvironment and the therapeutic mechanisms of HMAs, as well as current clinical trials of HMAs and/or venetoclax-based combination therapies.
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Affiliation(s)
| | | | - Yosuke Minami
- Correspondence: ; Tel.: +81-4-7133-1111; Fax: +81-7133-6502
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11
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Ling MY, Chiu LJ, Hsieh CC, Shu CC. Dimerization induces bimodality in protein number distributions. Biosystems 2023; 223:104812. [PMID: 36427705 DOI: 10.1016/j.biosystems.2022.104812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/10/2022] [Accepted: 11/10/2022] [Indexed: 11/26/2022]
Abstract
We examined gene expression with DNA switching between two states, active and inactive. Subpopulations emerge from mechanisms that do not arise from trivial transcriptional heterogeneity. Although the RNA demonstrates a unimodal distribution, dimerization intriguingly causes protein bimodality. No control loop or deterministic bistability are present. In such a situation, increasing the degradation rate of the protein does not lead to bimodality. The bimodality is achieved through the interplay between the protein monomer and the formation of protein dimer. We applied Stochastic Simulation Algorithm (SSA) and found that cells spontaneously change states at the protein level. While sweeping parameters, decreasing the rate constant of dimerization severely impairs the bimodality. We also examined the influence of DNA switching. To have bimodality, the system requires a proper ratio of DNA in the active state to the inactive state. In addition to bimodality of the monomer, tetramerization also causes the bimodality of the dimer.
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Affiliation(s)
- Ming-Yang Ling
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan
| | - Lin-Jie Chiu
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan
| | - Ching-Chu Hsieh
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan
| | - Che-Chi Shu
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan.
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12
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Sandoval JE, Ramabadran R, Stillson N, Sarah L, Fujimori DG, Goodell MA, Reich N. First-in-Class Allosteric Inhibitors of DNMT3A Disrupt Protein-Protein Interactions and Induce Acute Myeloid Leukemia Cell Differentiation. J Med Chem 2022; 65:10554-10566. [PMID: 35866897 DOI: 10.1021/acs.jmedchem.2c00725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We previously identified two structurally related pyrazolone (compound 1) and pyridazine (compound 2) allosteric inhibitors of DNMT3A through screening of a small chemical library. Here, we show that these compounds bind and disrupt protein-protein interactions (PPIs) at the DNMT3A tetramer interface. This disruption is observed with distinct partner proteins and occurs even when the complexes are acting on DNA, which better reflects the cellular context. Compound 2 induces differentiation of distinct myeloid leukemia cell lines including cells with mutated DNMT3A R882. To date, small molecules targeting DNMT3A are limited to competitive inhibitors of AdoMet or DNA and display extreme toxicity. Our work is the first to identify small molecules with a mechanism of inhibition involving the disruption of PPIs with DNMT3A. Ongoing optimization of compounds 1 and 2 provides a promising basis to induce myeloid differentiation and treatment of diseases that display aberrant PPIs with DNMT3A, such as acute myeloid leukemia.
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Affiliation(s)
- Jonathan E Sandoval
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9510, United States
| | - Raghav Ramabadran
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
- Interdepartmental Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Nathaniel Stillson
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Letitia Sarah
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Norbert Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
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13
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Probing altered enzyme activity in the biochemical characterization of cancer. Biosci Rep 2022; 42:230680. [PMID: 35048115 PMCID: PMC8819661 DOI: 10.1042/bsr20212002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/10/2022] [Accepted: 01/19/2022] [Indexed: 11/30/2022] Open
Abstract
Enzymes have evolved to catalyze their precise reactions at the necessary rates, locations, and time to facilitate our development, to respond to a variety of insults and challenges, and to maintain a healthy, balanced state. Enzymes achieve this extraordinary feat through their unique kinetic parameters, myriad regulatory strategies, and their sensitivity to their surroundings, including substrate concentration and pH. The Cancer Genome Atlas (TCGA) highlights the extraordinary number of ways in which the finely tuned activities of enzymes can be disrupted, contributing to cancer development and progression often due to somatic and/or inherited genetic alterations. Rather than being limited to the domain of enzymologists, kinetic constants such as kcat, Km, and kcat/Km are highly informative parameters that can impact a cancer patient in tangible ways—these parameters can be used to sort tumor driver mutations from passenger mutations, to establish the pathways that cancer cells rely on to drive patients’ tumors, to evaluate the selectivity and efficacy of anti-cancer drugs, to identify mechanisms of resistance to treatment, and more. In this review, we will discuss how changes in enzyme activity, primarily through somatic mutation, can lead to altered kinetic parameters, new activities, or changes in conformation and oligomerization. We will also address how changes in the tumor microenvironment can affect enzymatic activity, and briefly describe how enzymology, when combined with additional powerful tools, and can provide us with tremendous insight into the chemical and molecular mechanisms of cancer.
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14
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Zhang X, Jacobs D. OUP accepted manuscript. Genome Biol Evol 2022; 14:6519162. [PMID: 35104341 PMCID: PMC8857923 DOI: 10.1093/gbe/evab284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2021] [Indexed: 11/14/2022] Open
Abstract
DNA methylation, an important component of eukaryotic epigenetics, varies in pattern and function across Metazoa. Notably, bilaterian vertebrates and invertebrates differ dramatically in gene body methylation (GbM). Using the frequency of cytosine-phospho-guanines (CpGs), which are lost through mutation when methylated, we report the first broad survey of DNA methylation in Cnidaria, the ancient sister group to Bilateria. We find that: 1) GbM differentially relates to expression categories as it does in most bilaterian invertebrates, but distributions of GbM are less discretely bimodal. 2) Cnidarians generally have lower CpG frequencies on gene bodies than bilaterian invertebrates potentially suggesting a compensatory mechanism to replace CpG lost to mutation in Bilateria that is lacking in Cnidaria. 3) GbM patterns show some consistency within taxonomic groups such as the Scleractinian corals; however, GbM patterns variation across a range of taxonomic ranks in Cnidaria suggests active evolutionary change in GbM within Cnidaria. 4) Some but not all GbM variation is associated with life history change and genome expansion, whereas GbM loss is evident in endoparasitic cnidarians. 5) Cnidarian repetitive elements are less methylated than gene bodies, and methylation of both correlate with genome repeat content. 6) These observations reinforce claims that GbM evolved in stem Metazoa. Thus, this work supports overlap between DNA methylation processes in Cnidaria and Bilateria, provides a framework to compare methylation within and between Cnidaria and Bilateria, and demonstrates the previously unknown rapid evolution of cnidarian methylation.
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Affiliation(s)
- Xinhui Zhang
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - David Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
- Corresponding author: E-mail:
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15
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Mensah IK, Norvil AB, AlAbdi L, McGovern S, Petell CJ, He M, Gowher H. Misregulation of the expression and activity of DNA methyltransferases in cancer. NAR Cancer 2021; 3:zcab045. [PMID: 34870206 PMCID: PMC8634572 DOI: 10.1093/narcan/zcab045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
In mammals, DNA methyltransferases DNMT1 and DNMT3's (A, B and L) deposit and maintain DNA methylation in dividing and nondividing cells. Although these enzymes have an unremarkable DNA sequence specificity (CpG), their regional specificity is regulated by interactions with various protein factors, chromatin modifiers, and post-translational modifications of histones. Changes in the DNMT expression or interacting partners affect DNA methylation patterns. Consequently, the acquired gene expression may increase the proliferative potential of cells, often concomitant with loss of cell identity as found in cancer. Aberrant DNA methylation, including hypermethylation and hypomethylation at various genomic regions, therefore, is a hallmark of most cancers. Additionally, somatic mutations in DNMTs that affect catalytic activity were mapped in Acute Myeloid Leukemia cancer cells. Despite being very effective in some cancers, the clinically approved DNMT inhibitors lack specificity, which could result in a wide range of deleterious effects. Elucidating distinct molecular mechanisms of DNMTs will facilitate the discovery of alternative cancer therapeutic targets. This review is focused on: (i) the structure and characteristics of DNMTs, (ii) the prevalence of mutations and abnormal expression of DNMTs in cancer, (iii) factors that mediate their abnormal expression and (iv) the effect of anomalous DNMT-complexes in cancer.
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Affiliation(s)
- Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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16
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Khrabrova DA, Yakubovskaya MG, Gromova ES. AML-Associated Mutations in DNA Methyltransferase DNMT3A. BIOCHEMISTRY (MOSCOW) 2021; 86:307-318. [PMID: 33838631 DOI: 10.1134/s000629792103007x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In mammals, DNA methylation is an essential epigenetic modification necessary for the maintenance of genome stability, regulation of gene expression, and other processes. Carcinogenesis is accompanied by multiple changes in the DNA methylation pattern and DNA methyltransferase (DNMT) genes; these changes are often associated with poor disease prognosis. Human DNA methyltransferase DNMT3A is responsible for de novo DNA methylation. Missense mutations in the DNMT3A gene occur frequently at the early stages of tumor development and are often observed in hematologic malignances, especially in acute myeloid leukemia (AML), with a prevalence of the R882H mutation. This mutation is the only one that has been extensively studied using both model DNA substrates and cancer cell lines. Biochemical characterization of other DNMT3A mutants is necessary to assess their potential effects on the DNMT3A functioning. In this review, we describe DNMT3A mutations identified in AML with special emphasis on the missense mutations in the DNMT3A catalytic domain. The impact of R882H and less common missense mutations on the DNMT3A activity toward model DNA substrates and in cancer cell lines is discussed together with the underlying molecular mechanisms. Understanding general features of these mechanisms will be useful for further development of novel approaches for early diagnostics of hematologic diseases and personalized cancer therapy.
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Affiliation(s)
- Dariya A Khrabrova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Marianna G Yakubovskaya
- Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, 115478, Russia
| | - Elizaveta S Gromova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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17
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Sandoval JE, Reich NO. p53 and TDG are dominant in regulating the activity of the human de novo DNA methyltransferase DNMT3A on nucleosomes. J Biol Chem 2020; 296:100058. [PMID: 33172892 PMCID: PMC7948466 DOI: 10.1074/jbc.ra120.016125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/03/2020] [Accepted: 11/10/2020] [Indexed: 11/07/2022] Open
Abstract
DNA methylation and histone tail modifications are interrelated mechanisms involved in a wide range of biological processes, and disruption of this crosstalk is linked to diseases such as acute myeloid leukemia. In addition, DNA methyltransferase 3A (DNMT3A) activity is modulated by several regulatory proteins, including p53 and thymine DNA glycosylase (TDG). However, the relative role of histone tails and regulatory proteins in the simultaneous coordination of DNMT3A activity remains obscure. We observed that DNMT3A binds H3 tails and p53 or TDG at distinct allosteric sites to form DNMT3A–H3 tail-p53 or –TDG multiprotein complexes. Functional characterization of DNMT3A–H3 tail-p53 or –TDG complexes on human-derived synthetic histone H3 tails, mononucleosomes, or polynucleosomes shows p53 and TDG play dominant roles in the modulation of DNMT3A activity. Intriguingly, this dominance occurs even when DNMT3A is actively methylating nucleosome substrates. The activity of histone modifiers is influenced by their ability to sense modifications on histone tails within the same nucleosome or histone tails on neighboring nucleosomes. In contrast, we show here that DNMT3A acts on DNA within a single nucleosome, on nucleosomal DNA within adjacent nucleosomes, and DNA not associated with the DNMT3A–nucleosome complex. Our findings have direct bearing on how the histone code drives changes in DNA methylation and highlight the complex interplay between histone tails, epigenetic enzymes, and modulators of enzymatic activity.
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Affiliation(s)
- Jonathan E Sandoval
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA.
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18
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Wang Z, Chen K, Jia Y, Chuang JC, Sun X, Lin YH, Celen C, Li L, Huang F, Liu X, Castrillon DH, Wang T, Zhu H. Dual ARID1A/ARID1B loss leads to rapid carcinogenesis and disruptive redistribution of BAF complexes. ACTA ACUST UNITED AC 2020; 1:909-922. [PMID: 34386776 DOI: 10.1038/s43018-020-00109-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SWI/SNF chromatin remodelers play critical roles in development and cancer. The causal links between SWI/SNF complex disassembly and carcinogenesis are obscured by redundancy between paralogous components. Canonical cBAF-specific paralogs ARID1A and ARID1B are synthetic lethal in some contexts, but simultaneous mutations in both ARID1s are prevalent in cancer. To understand if and how cBAF abrogation causes cancer, we examined the physiologic and biochemical consequences of ARID1A/ARID1B loss. In double knockout liver and skin, aggressive carcinogenesis followed de-differentiation and hyperproliferation. In double mutant endometrial cancer, add-back of either induced senescence. Biochemically, residual cBAF subcomplexes resulting from loss of ARID1 scaffolding were unexpectedly found to disrupt polybromo containing pBAF function. 37 of 69 mutations in the conserved scaffolding domains of ARID1 proteins observed in human cancer caused complex disassembly, partially explaining their mutation spectra. ARID1-less, cBAF-less states promote carcinogenesis across tissues, and suggest caution against paralog-directed therapies for ARID1-mutant cancer.
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Affiliation(s)
- Zixi Wang
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Yuemeng Jia
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jen-Chieh Chuang
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xuxu Sun
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yu-Hsuan Lin
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cemre Celen
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lin Li
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Fang Huang
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xin Liu
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Diego H Castrillon
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Hao Zhu
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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19
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Hoang NM, Rui L. DNA methyltransferases in hematological malignancies. J Genet Genomics 2020; 47:361-372. [PMID: 32994141 PMCID: PMC7704698 DOI: 10.1016/j.jgg.2020.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 04/05/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
Abstract
DNA methyltransferases (DNMTs) are an evolutionarily conserved family of DNA methylases, transferring a methyl group onto the fifth carbon of a cytosine residue. The mammalian DNMT family includes three major members that have functional methylation activities, termed DNMT1, DNMT3A, and DNMT3B. DNMT3A and DNMT3B are responsible for methylation establishment, whereas DNMT1 maintains methylation during DNA replication. Accumulating evidence demonstrates that regulation of DNA methylation by DNMTs is critical for normal hematopoiesis. Aberrant DNA methylation due to DNMT dysregulation and mutations is known as an important molecular event of hematological malignancies, such as DNMT3A mutations in acute myeloid leukemia. In this review, we first describe the basic methylation mechanisms of DNMTs and their functions in lymphocyte maturation and differentiation. We then discuss the current understanding of DNA methylation heterogeneity in leukemia and lymphoma to highlight the importance of studying DNA methylation targets. We also discuss DNMT mutations and pathogenic roles in human leukemia and lymphoma. We summarize the recent understanding of how DNMTs interact with transcription factors or cofactors to repress the expression of tumor suppressor genes. Finally, we highlight current clinical studies using DNMT inhibitors for the treatment of these hematological malignancies.
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Affiliation(s)
- Nguyet-Minh Hoang
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA
| | - Lixin Rui
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA; Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53792, USA.
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20
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Gong T, Gu X, Liu YT, Zhou Z, Zhang LL, Wen Y, Zhong WL, Xu GL, Zhou JQ. Both combinatorial K4me0-K36me3 marks on sister histone H3s of a nucleosome are required for Dnmt3a-Dnmt3L mediated de novo DNA methylation. J Genet Genomics 2020; 47:105-114. [PMID: 32173286 DOI: 10.1016/j.jgg.2019.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/18/2019] [Accepted: 12/30/2019] [Indexed: 11/28/2022]
Abstract
A nucleosome contains two copies of each histone H2A, H2B, H3 and H4. Histone H3 K4me0 and K36me3 are two key chromatin marks for de novo DNA methylation catalyzed by DNA methyltransferases in mammals. However, it remains unclear whether K4me0 and K36me3 marks on both sister histone H3s regulate de novo DNA methylation independently or cooperatively. Here, taking advantage of the bivalent histone H3 system in yeast, we examined the contributions of K4 and K36 on sister histone H3s to genomic DNA methylation catalyzed by ectopically co-expressed murine Dnmt3a and Dnmt3L. The results show that lack of both K4me0 and K36me3 on one sister H3 tail, or lack of K4me0 and K36me3 on respective sister H3s results in a dramatic reduction of 5mC, revealing a synergy of two sister H3s in DNA methylation regulation. Accordingly, the Dnmt3a or Dnmt3L mutation that disrupts the interaction of Dnmt3aADD domain-H3K4me0, Dnmt3LADD domain-H3K4me0, or Dnmt3aPWWP domain-H3K36me3 causes a significant reduction of DNA methylation. These results support the model that each heterodimeric Dnmt3a-Dnmt3L reads both K4me0 and K36me3 marks on one tail of sister H3s, and the dimer of heterodimeric Dnmt3a-Dnmt3L recognizes two tails of sister histone H3s to efficiently execute de novo DNA methylation.
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Affiliation(s)
- Ting Gong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xin Gu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yu-Ting Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhen Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ling-Li Zhang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yang Wen
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Wei-Li Zhong
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jin-Qiu Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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21
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Sandoval JE, Reich NO. The R882H substitution in the human de novo DNA methyltransferase DNMT3A disrupts allosteric regulation by the tumor supressor p53. J Biol Chem 2019; 294:18207-18219. [PMID: 31640986 DOI: 10.1074/jbc.ra119.010827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/18/2019] [Indexed: 12/14/2022] Open
Abstract
A myriad of protein partners modulate the activity of the human DNA methyltransferase 3A (DNMT3A), whose interactions with these other proteins are frequently altered during oncogenesis. We show here that the tumor suppressor p53 decreases DNMT3A activity by forming a heterotetramer complex with DNMT3A. Mutational and modeling experiments suggested that p53 interacts with the same region in DNMT3A as does the structurally characterized DNMT3L. We observed that the p53-mediated repression of DNMT3A activity is blocked by amino acid substitutions within this interface, but surprisingly, also by a distal DNMT3A residue, R882H. DNMT3A R882H occurs frequently in various cancers, including acute myeloid leukemia, and our results suggest that the effects of R882H and other DNMT3A mutations may go beyond changes in DNMT3A methylation activity. To further understand the dynamics of how protein-protein interactions modulate DNMT3A activity, we determined that p53 has a greater affinity for DNMT3A than for DNMT3L and that p53 readily displaces DNMT3L from the DNMT3A:DNMT3L heterotetramer. Interestingly, this occurred even when the preformed DNMT3A:DNMT3L complex was actively methylating DNA. The frequently identified p53 substitutions (R248W and R273H), whereas able to regulate DNMT3A function when forming the DNMT3A:p53 heterotetramer, no longer displaced DNMT3L from the DNMT3A:DNMT3L heterotetramer. The results of our work highlight the complex interplay between DNMT3A, p53, and DNMT3L and how these interactions are further modulated by clinically derived mutations in each of the interacting partners.
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Affiliation(s)
- Jonathan E Sandoval
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9510
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510.
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22
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Nguyen TV, Yao S, Wang Y, Rolfe A, Selvaraj A, Darman R, Ke J, Warmuth M, Smith PG, Larsen NA, Yu L, Zhu P, Fekkes P, Vaillancourt FH, Bolduc DM. The R882H DNMT3A hot spot mutation stabilizes the formation of large DNMT3A oligomers with low DNA methyltransferase activity. J Biol Chem 2019; 294:16966-16977. [PMID: 31582562 DOI: 10.1074/jbc.ra119.010126] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/27/2019] [Indexed: 01/04/2023] Open
Abstract
DNMT3A (DNA methyltransferase 3A) is a de novo DNA methyltransferase responsible for establishing CpG methylation patterns within the genome. DNMT3A activity is essential for normal development, and its dysfunction has been linked to developmental disorders and cancer. DNMT3A is frequently mutated in myeloid malignancies with the majority of mutations occurring at Arg-882, where R882H mutations are most frequent. The R882H mutation causes a reduction in DNA methyltransferase activity and hypomethylation at differentially-methylated regions within the genome, ultimately preventing hematopoietic stem cell differentiation and leading to leukemogenesis. Although the means by which the R882H DNMT3A mutation reduces enzymatic activity has been the subject of several studies, the precise mechanism by which this occurs has been elusive. Herein, we demonstrate that in the context of the full-length DNMT3A protein, the R882H mutation stabilizes the formation of large oligomeric DNMT3A species to reduce the overall DNA methyltransferase activity of the mutant protein as well as the WT-R882H complex in a dominant-negative manner. This shift in the DNMT3A oligomeric equilibrium and the resulting reduced enzymatic activity can be partially rescued in the presence of oligomer-disrupting DNMT3L, as well as DNMT3A point mutations along the oligomer-forming interface of the catalytic domain. In addition to modulating the oligomeric state of DNMT3A, the R882H mutation also leads to a DNA-binding defect, which may further reduce enzymatic activity. These findings provide a mechanistic explanation for the observed loss of DNMT3A activity associated with the R882H hot spot mutation in cancer.
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Affiliation(s)
| | - Shihua Yao
- H3 Biomedicine Inc., Cambridge, Massachusetts 02139
| | - Yahong Wang
- ChemPartner Co., Ltd., 998 Halei Road, Shanghai 201203, China
| | - Alan Rolfe
- H3 Biomedicine Inc., Cambridge, Massachusetts 02139
| | | | | | - Jiyuan Ke
- H3 Biomedicine Inc., Cambridge, Massachusetts 02139
| | | | | | | | - Lihua Yu
- H3 Biomedicine Inc., Cambridge, Massachusetts 02139
| | - Ping Zhu
- H3 Biomedicine Inc., Cambridge, Massachusetts 02139
| | - Peter Fekkes
- H3 Biomedicine Inc., Cambridge, Massachusetts 02139
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23
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Lu R, Wang J, Ren Z, Yin J, Wang Y, Cai L, Wang GG. A Model System for Studying the DNMT3A Hotspot Mutation (DNMT3A R882) Demonstrates a Causal Relationship between Its Dominant-Negative Effect and Leukemogenesis. Cancer Res 2019; 79:3583-3594. [PMID: 31164355 DOI: 10.1158/0008-5472.can-18-3275] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 04/03/2019] [Accepted: 05/29/2019] [Indexed: 01/01/2023]
Abstract
Mutation of DNA methyltransferase 3A at arginine 882 (DNMT3AR882mut) is prevalent in hematologic cancers and disorders. Recently, DNMT3AR882mut has been shown to have hypomorphic, dominant-negative, and/or gain-of-function effects on DNA methylation under different biological contexts. However, the causal role for such a multifaceted effect of DNMT3AR882mut in leukemogenesis remains undetermined. Here, we report TF-1 leukemia cells as a robust system useful for modeling the DNMT3AR882mut-dependent transformation and for dissecting the cause-effect relationship between multifaceted activities of DNMT3AR882mut and leukemic transformation. Ectopic expression of DNMT3AR882mut and not wild-type DNMT3A promoted TF-1 cell transformation characterized by cytokine-independent growth, and induces CpG hypomethylation predominantly at enhancers. This effect was dose dependent, acted synergistically with the isocitrate dehydrogenase 1 (IDH1) mutation, and resembled what was seen in human leukemia patients carrying DNMT3AR882mut. The transformation- and hypomethylation-inducing capacities of DNMT3AR882mut relied on a motif involved in heterodimerization, whereas its various chromatin-binding domains were dispensable. Mutation of the heterodimerization motif that interferes with DNMT3AR882mut binding to endogenous wild-type DNMT proteins partially reversed the CpG hypomethylation phenotype caused by DNMT3AR882mut, thus supporting a dominant-negative mechanism in cells. In mice, bromodomain inhibition repressed gene-activation events downstream of DNMT3AR882mut-induced CpG hypomethylation, thereby suppressing leukemogenesis mediated by DNMT3AR882mut. Collectively, this study reports a model system useful for studying DNMT3AR882mut, shows a requirement of the dominant-negative effect by DNMT3AR882mut for leukemogenesis, and describes an attractive strategy for the treatment of leukemias carrying DNMT3AR882mut. SIGNIFICANCE: These findings highlight a model system to study the functional impact of a hotspot mutation of DNMT3A at R882 in leukemia.
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Affiliation(s)
- Rui Lu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Zhihong Ren
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, California.,Department of Chemistry, University of California, Riverside, California
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California.,Department of Chemistry, University of California, Riverside, California
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina. .,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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24
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Sandoval JE, Huang YH, Muise A, Goodell MA, Reich NO. Mutations in the DNMT3A DNA methyltransferase in acute myeloid leukemia patients cause both loss and gain of function and differential regulation by protein partners. J Biol Chem 2019; 294:4898-4910. [PMID: 30705090 DOI: 10.1074/jbc.ra118.006795] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/24/2019] [Indexed: 01/08/2023] Open
Abstract
Eukaryotic DNA methylation prevents genomic instability by regulating the expression of oncogenes and tumor-suppressor genes. The negative effects of dysregulated DNA methylation are highlighted by a strong correlation between mutations in the de novo DNA methyltransferase gene DNA methyltransferase 3α (DNMT3A) and poor prognoses among acute myeloid leukemia (AML) patients. We show here that clinically observed DNMT3A mutations dramatically alter enzymatic activity, including mutations that lead to 6-fold hypermethylation and 3-fold hypomethylation of the human cyclin-dependent kinase inhibitor 2B (CDKN2B or p15) gene promoter. Our results provide insights into the clinically observed heterogeneity of p15 methylation in AML. Cytogenetically normal AML (CN-AML) constitutes 40-50% of all AML cases and is the most epigenetically diverse AML subtype with pronounced changes in non-CpG DNA methylation. We identified a subset of DNMT3A mutations that enhance the enzyme's ability to perform non-CpG methylation by 2-8-fold. Many of these mutations mapped to DNMT3A regions known to interact with proteins that themselves contribute to AML, such as thymine DNA glycosylase (TDG). Using functional mapping of TDG-DNMT3A interactions, we provide evidence that TDG and DNMT3-like (DNMT3L) bind distinct regions of DNMT3A. Furthermore, DNMT3A mutations caused diverse changes in the ability of TDG and DNMT3L to affect DNMT3A function. Cell-based studies of one of these DNMT3A mutations (S714C) replicated the enzymatic studies and revealed that it causes dramatic losses of genome-wide methylation. In summary, mutations in DNMT3A lead to diverse levels of activity, interactions with epigenetic machinery components and cellular changes.
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Affiliation(s)
- Jonathan E Sandoval
- From the Departments of Chemistry and Biochemistry and.,Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9510 and
| | - Yung-Hsin Huang
- the Program in Developmental Biology.,Stem Cells and Regenerative Medicine Center.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030
| | - Abigail Muise
- Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106-9510 and
| | - Margaret A Goodell
- the Program in Developmental Biology.,Stem Cells and Regenerative Medicine Center.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030
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25
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Boddu PC, Kadia TM. Molecular pathogenesis of acquired aplastic anemia. Eur J Haematol 2018; 102:103-110. [DOI: 10.1111/ejh.13182] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/03/2018] [Accepted: 10/04/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Prajwal C. Boddu
- Department of Leukemia University of Texas MD Anderson Cancer Center Houston Texas
| | - Tapan M. Kadia
- Department of Leukemia University of Texas MD Anderson Cancer Center Houston Texas
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26
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A Novel t(8;14)(q24;q11) Rearranged Human Cell Line as a Model for Mechanistic and Drug Discovery Studies of NOTCH1-Independent Human T-Cell Leukemia. Cells 2018; 7:cells7100160. [PMID: 30304769 PMCID: PMC6209910 DOI: 10.3390/cells7100160] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 09/26/2018] [Accepted: 10/04/2018] [Indexed: 12/22/2022] Open
Abstract
MYC-translocated T-lineage acute lymphoblastic leukemia (T-ALL) is a rare subgroup of T-ALL associated with CDKN2A/B deletions, PTEN inactivation, and absence of NOTCH1 or FBXW7 mutations. This subtype of T-ALL has been associated with induction failure and aggressive disease. Identification of drug targets and mechanistic insights for this disease are still limited. Here, we established a human NOTCH1-independent MYC-translocated T-ALL cell line that maintains the genetic and phenotypic characteristics of the parental leukemic clone at diagnosis. The University of Padua T-cell acute lymphoblastic leukemia 13 (UP-ALL13) cell line has all the main features of the above described MYC-translocated T-ALL. Interestingly, UP-ALL13 was found to harbor a heterozygous R882H DNMT3A mutation typically found in myeloid leukemia. Chromatin immunoprecipitation coupled with high-throughput sequencing for histone H3 lysine 27 (H3K27) acetylation revealed numerous putative super-enhancers near key transcription factors, including MYC, MYB, and LEF1. Marked cytotoxicity was found following bromodomain-containing protein 4 (BRD4) inhibition with AZD5153, suggesting a strict dependency of this particular subtype of T-ALL on the activity of super-enhancers. Altogether, this cell line may be a useful model system for dissecting the signaling pathways implicated in NOTCH1-independent T-ALL and for the screening of targeted anti-leukemia agents specific for this T-ALL subgroup.
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27
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Norvil AB, Petell CJ, Alabdi L, Wu L, Rossie S, Gowher H. Dnmt3b Methylates DNA by a Noncooperative Mechanism, and Its Activity Is Unaffected by Manipulations at the Predicted Dimer Interface. Biochemistry 2018; 57:4312-4324. [PMID: 27768276 PMCID: PMC5992102 DOI: 10.1021/acs.biochem.6b00964] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The catalytic domains of the de novo DNA methyltransferases Dnmt3a-C and Dnmt3b-C are highly homologous. However, their unique biochemical properties could potentially contribute to differences in the substrate preferences or biological functions of these enzymes. Dnmt3a-C forms tetramers through interactions at the dimer interface, which also promote multimerization on DNA and cooperativity. Similar to the case for processive enzymes, cooperativity allows Dnmt3a-C to methylate multiple sites on the same DNA molecule; however, it is unclear whether Dnmt3b-C methylates DNA by a cooperative or processive mechanism. The importance of the tetramer structure and cooperative mechanism is emphasized by the observation that the R882H mutation in the dimer interface of DNMT3A is highly prevalent in acute myeloid leukemia and leads to a substantial loss of its activity. Under conditions that distinguish between cooperativity and processivity, we show that in contrast to that of Dnmt3a-C, the activity of Dnmt3b-C is not cooperative and confirm the processivity of Dnmt3b-C and the full length Dnmt3b enzyme. Whereas the R878H mutation (mouse homologue of R882H) led to the loss of cooperativity of Dnmt3a-C, the activity and processivity of the analogous Dnmt3b-C R829H variant were comparable to those of the wild-type enzyme. Additionally, buffer acidification that attenuates the dimer interface interactions of Dnmt3a-C had no effect on Dnmt3b-C activity. Taken together, these results demonstrate an important mechanistic difference between Dnmt3b and Dnmt3a and suggest that interactions at the dimer interface may play a limited role in regulating Dnmt3b-C activity. These new insights have potential implications for the distinct biological roles of Dnmt3a and Dnmt3b.
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Affiliation(s)
- Allison B. Norvil
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Christopher J. Petell
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lama Alabdi
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lanchen Wu
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sandra Rossie
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Humaira Gowher
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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28
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Liang Z, Hu J, Yan W, Jiang H, Hu G, Luo C. Deciphering the role of dimer interface in intrinsic dynamics and allosteric pathways underlying the functional transformation of DNMT3A. Biochim Biophys Acta Gen Subj 2018; 1862:1667-1679. [DOI: 10.1016/j.bbagen.2018.04.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 04/03/2018] [Accepted: 04/13/2018] [Indexed: 01/06/2023]
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29
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Pflueger C, Tan D, Swain T, Nguyen T, Pflueger J, Nefzger C, Polo JM, Ford E, Lister R. A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. Genome Res 2018; 28:1193-1206. [PMID: 29907613 PMCID: PMC6071642 DOI: 10.1101/gr.233049.117] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 06/06/2018] [Indexed: 12/15/2022]
Abstract
Detection of DNA methylation in the genome has been possible for decades; however, the ability to deliberately and specifically manipulate local DNA methylation states in the genome has been extremely limited. Consequently, this has impeded our understanding of the direct effect of DNA methylation on transcriptional regulation and transcription factor binding in the native chromatin context. Thus, highly specific targeted epigenome editing tools are needed to address this. Recent adaptations of genome editing technologies, including fusion of the DNMT3A DNA methyltransferase catalytic domain to catalytically inactive Cas9 (dC9-D3A), have aimed to alter DNA methylation at desired loci. Here, we show that these tools exhibit consistent off-target DNA methylation deposition in the genome, limiting their capabilities to unambiguously assess the functional consequences of DNA methylation. To address this, we developed a modular dCas9-SunTag (dC9Sun-D3A) system that can recruit multiple DNMT3A catalytic domains to a target site for editing DNA methylation. dC9Sun-D3A is tunable, specific, and exhibits much higher induction of DNA methylation at target sites than the dC9-D3A direct fusion protein. Importantly, genome-wide characterization of dC9Sun-D3A binding sites and DNA methylation revealed minimal off-target protein binding and induction of DNA methylation with dC9Sun-D3A, compared to pervasive off-target methylation by dC9-D3A. Furthermore, we used dC9Sun-D3A to demonstrate the binding sensitivity to DNA methylation for CTCF and NRF1 in situ. Overall, this modular dC9Sun-D3A system enables precise DNA methylation deposition with the lowest off-target DNA methylation levels reported to date, allowing accurate functional determination of the role of DNA methylation at single loci.
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Affiliation(s)
- Christian Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Dennis Tan
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Tessa Swain
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Trung Nguyen
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Christian Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria 3800, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Clayton, Victoria 3800, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.,Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
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30
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Clonal expansion and myeloid leukemia progression modeled by multiplex gene editing of murine hematopoietic progenitor cells. Exp Hematol 2018; 64:33-44.e5. [PMID: 29751067 DOI: 10.1016/j.exphem.2018.04.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 01/22/2023]
Abstract
Recent advances in next-generation sequencing have identified novel mutations and revealed complex genetic architectures in human hematological malignancies. Moving forward, new methods to quickly generate animal models that recapitulate the complex genetics of human hematological disorders are needed to transform the genetic information to new therapies. Here, we used a ribonucleoprotein-based CRISPR/Cas9 system to model human clonal hematopoiesis of indeterminate potential and acute myeloid leukemia (AML). We edited multiple genes recurrently mutated in hematological disorders, including those encoding epigenetic regulators, transcriptional regulators, and signaling components in murine hematopoietic stem/progenitor cells. Tracking the clonal dynamics by sequencing the indels induced by CRISPR/Cas9 revealed clonal expansion in some recipient mice that progressed to AML initiated by leukemia-initiating cells. Our results establish that the CRISPR/Cas9-mediated multiplex mutagenesis can be used to engineer a variety of murine models of hematological malignancies with complex genetic architectures seen in human disease.
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31
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Impact of DNA methylation programming on normal and pre-leukemic hematopoiesis. Semin Cancer Biol 2017; 51:89-100. [PMID: 28964938 DOI: 10.1016/j.semcancer.2017.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 12/30/2022]
Abstract
Epigenome regulation is a critical mechanism that governs cell identity, lineage specification and developmental cell fates. With the advent of low-input and single-cell technologies as well as sophisticated cell labeling techniques, our understanding of transcriptional and epigenetic regulation of hematopoiesis is currently undergoing dramatic changes. Increasingly, evidence suggests that the epigenome conformation acts as a critical decision-making mechanism that instructs self-renewal, differentiation and developmental fates of hematopoietic progenitor cells. When dysregulated, this leads to the evolution of disease states such as leukemia. Indeed, aberrations in DNA methylation, histone modifications and genome architecture are characteristic features of many hematopoietic neoplasms in which epigenetic enzymes are frequently mutated. Sequencing studies and characterization of the epigenetic landscape in lymphomas, leukemias and in aged healthy individuals with clonal hematopoiesis have been indispensible to identify epigenetic regulators that play a role in transformation or pre-disposition to hematopoietic malignancies. In this review, we outline the current view of the hematopoietic system and the epigenetic mechanisms regulating hematopoiesis under homeostatic conditions, with a particular focus on the role of DNA methylation in this process. We will also summarize the current knowledge on the mechanisms underlying dysregulated DNA methylation in hematologic malignancies and how this contributes to our understanding of the physiological functions of epigenetic regulators in hematopoiesis.
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32
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Cole CB, Russler-Germain DA, Ketkar S, Verdoni AM, Smith AM, Bangert CV, Helton NM, Guo M, Klco JM, O'Laughlin S, Fronick C, Fulton R, Chang GS, Petti AA, Miller CA, Ley TJ. Haploinsufficiency for DNA methyltransferase 3A predisposes hematopoietic cells to myeloid malignancies. J Clin Invest 2017; 127:3657-3674. [PMID: 28872462 DOI: 10.1172/jci93041] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/14/2017] [Indexed: 12/12/2022] Open
Abstract
The gene that encodes de novo DNA methyltransferase 3A (DNMT3A) is frequently mutated in acute myeloid leukemia genomes. Point mutations at position R882 have been shown to cause a dominant negative loss of DNMT3A methylation activity, but 15% of DNMT3A mutations are predicted to produce truncated proteins that could either have dominant negative activities or cause loss of function and haploinsufficiency. Here, we demonstrate that 3 of these mutants produce truncated, inactive proteins that do not dimerize with WT DNMT3A, strongly supporting the haploinsufficiency hypothesis. We therefore evaluated hematopoiesis in mice heterozygous for a constitutive null Dnmt3a mutation. With no other manipulations, Dnmt3a+/- mice developed myeloid skewing over time, and their hematopoietic stem/progenitor cells exhibited a long-term competitive transplantation advantage. Dnmt3a+/- mice also spontaneously developed transplantable myeloid malignancies after a long latent period, and 3 of 12 tumors tested had cooperating mutations in the Ras/MAPK pathway. The residual Dnmt3a allele was neither mutated nor downregulated in these tumors. The bone marrow cells of Dnmt3a+/- mice had a subtle but statistically significant DNA hypomethylation phenotype that was not associated with gene dysregulation. These data demonstrate that haploinsufficiency for Dnmt3a alters hematopoiesis and predisposes mice (and probably humans) to myeloid malignancies by a mechanism that is not yet clear.
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Affiliation(s)
- Christopher B Cole
- Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David A Russler-Germain
- Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Shamika Ketkar
- Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Angela M Verdoni
- Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Amanda M Smith
- Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Celia V Bangert
- Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nichole M Helton
- Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mindy Guo
- Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shelly O'Laughlin
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Catrina Fronick
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Robert Fulton
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gue Su Chang
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Allegra A Petti
- Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, Missouri, USA.,The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christopher A Miller
- Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, Missouri, USA.,The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Timothy J Ley
- Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, Missouri, USA.,The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
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33
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Abstract
DNA methylation is an epigenetic process involved in development, aging, and cancer. Although the advent of new molecular techniques has enhanced our knowledge of how DNA methylation alters chromatin and subsequently affects gene expression, a direct link between epigenetic marks and tumorigenesis has not been established. DNMT3A is a de novo DNA methyltransferase that has recently gained relevance because of its frequent mutation in a large variety of immature and mature hematologic neoplasms. DNMT3A mutations are early events during cancer development and seem to confer poor prognosis to acute myeloid leukemia (AML) patients making this gene an attractive target for new therapies. Here, we discuss the biology of DNMT3A and its role in controlling hematopoietic stem cell fate decisions. In addition, we review how mutant DNMT3A may contribute to leukemogenesis and the clinical relevance of DNMT3A mutations in hematologic cancers.
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Affiliation(s)
- Lorenzo Brunetti
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030.,CREO, University of Perugia, 06123 Perugia, Italy
| | - Michael C Gundry
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030.,CREO, University of Perugia, 06123 Perugia, Italy.,Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas 77030
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34
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Woodcock CB, Ulashchik EA, Poopeiko NE, Shmanai VV, Reich NO, Shchepinov MS. Rational Manipulation of DNA Methylation by Using Isotopically Reinforced Cytosine. Chembiochem 2016; 17:2018-2021. [PMID: 27595234 DOI: 10.1002/cbic.201600393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 11/11/2022]
Abstract
The human DNA methyltransferase 3A (DNMT 3A) is responsible for de novo epigenetic regulation, which is essential for mammalian viability and implicated in diverse diseases. All DNA cytosine C5 methyltransferases follow a broadly conserved catalytic mechanism. We investigated whether C5 β-elimination contributes to the rate-limiting step in catalysis by DNMT3A and the bacterial M.HhaI by using deuterium substitutions of C5 and C6 hydrogens. This substitution caused a 1.59-1.83 fold change in the rate of catalysis, thus suggesting that β-elimination is partly rate-limiting for both enzymes. We used a multisite substrate to explore the consequences of slowing β-elimination during multiple cycles of catalysis. Processive catalysis was slower for both enzymes, and deuterium substitution resulted in DNMT 3A dissociating from its substrate. The decrease in DNA methylation rate by DNMT 3A provides the basis of our ongoing efforts to alter cellular DNA methylation levels without the toxicity of currently used methods.
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Affiliation(s)
- Clayton B Woodcock
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Egor A Ulashchik
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, Surganova str. 13, 220072, Minsk, Belarus
| | - Nikolai E Poopeiko
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, Surganova str. 13, 220072, Minsk, Belarus
| | - Vadim V Shmanai
- Institute of Physical Organic Chemistry, National Academy of Science of Belarus, Surganova str. 13, 220072, Minsk, Belarus
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
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35
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Cree SL, Fredericks R, Miller A, Pearce FG, Filichev V, Fee C, Kennedy MA. DNA G-quadruplexes show strong interaction with DNA methyltransferases in vitro. FEBS Lett 2016; 590:2870-83. [PMID: 27468168 DOI: 10.1002/1873-3468.12331] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 07/07/2016] [Accepted: 07/21/2016] [Indexed: 12/16/2022]
Abstract
The DNA methyltransferase enzymes (DNMTs) catalyzing cytosine methylation do so at specific locations of the genome, although with some level of redundancy. The de novo methyltransferases DNMT3A and 3B play a vital role in methylating the genome of the developing embryo in regions devoid of methylation marks. The ability of DNMTs to colocalize at sites of DNA damage is suggestive that recognition of mispaired bases and unusual structures is inherent to the function of these proteins. We provide evidence for G-quadruplex formation within imprinted gene promoters, and report high-affinity binding of recombinant human DNMTs to such DNA G-quadruplexes in vitro. These observations suggest a potential interaction of G-quadruplexes with the DNA methylation machinery, which may be of epigenetic and biological significance.
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Affiliation(s)
- Simone L Cree
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Rayleen Fredericks
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Allison Miller
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - F Grant Pearce
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Vyacheslav Filichev
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Conan Fee
- Department of Chemical and Process Engineering, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology, University of Otago, Christchurch, New Zealand
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36
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Petell CJ, Alabdi L, He M, San Miguel P, Rose R, Gowher H. An epigenetic switch regulates de novo DNA methylation at a subset of pluripotency gene enhancers during embryonic stem cell differentiation. Nucleic Acids Res 2016; 44:7605-17. [PMID: 27179026 PMCID: PMC5027477 DOI: 10.1093/nar/gkw426] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/05/2016] [Indexed: 12/30/2022] Open
Abstract
Coordinated regulation of gene expression that involves activation of lineage specific genes and repression of pluripotency genes drives differentiation of embryonic stem cells (ESC). For complete repression of pluripotency genes during ESC differentiation, chromatin at their enhancers is silenced by the activity of the Lsd1-Mi2/NuRD complex. The mechanism/s that regulate DNA methylation at these enhancers are largely unknown. Here, we investigated the affect of the Lsd1-Mi2/NuRD complex on the dynamic regulatory switch that induces the local interaction of histone tails with the Dnmt3 ATRX-DNMT3-DNMT3L (ADD) domain, thus promoting DNA methylation at the enhancers of a subset of pluripotency genes. This is supported by previous structural studies showing a specific interaction between Dnmt3-ADD domain with H3K4 unmethylated histone tails that is disrupted by histone H3K4 methylation and histone acetylation. Our data suggest that Dnmt3a activity is triggered by Lsd1-Mi2/NuRD-mediated histone deacetylation and demethylation at these pluripotency gene enhancers when they are inactivated during mouse ESC differentiation. Using Dnmt3 knockout ESCs and the inhibitors of Lsd1 and p300 histone modifying enzymes during differentiation of E14Tg2A and ZHBTc4 ESCs, our study systematically reveals this mechanism and establishes that Dnmt3a is both reader and effector of the epigenetic state at these target sites.
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Affiliation(s)
| | - Lama Alabdi
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Phillip San Miguel
- DNA Sequencing Core Facility, Purdue University, West Lafayette, IN 47907, USA
| | - Richard Rose
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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Cui Y, Choudhury SR, Irudayaraj J. Epigenetic Toxicity of Trichloroethylene: A Single-Molecule Perspective. Toxicol Res (Camb) 2016; 5:641-650. [PMID: 28944004 DOI: 10.1039/c5tx00454c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The volatile, water soluble trichloroethylene (TCE) is a hazardous industrial waste and could lead to various health problems, including cancer, neuropathy, cardiovascular defects, and immune diseases. Toxicological studies taking use of in vitro and in vivo models have been conducted to understand the biological impacts of TCE at the genetic, transcriptomic, metabolomic, and signaling levels. The epigenetic aberrations induced by TCE have also been reported in a number of model organisms, while a detailed mechanistic elucidation is lacking. In this study we uncover an unreported mechanism accounting for the epigenetic toxicity due to TCE exposure by monitoring the single-molecule dynamics of DNA methyltransferase 3a (Dnmt3a) in living cells. TCE-induced global DNA hypomethylation could be partly attributed to the disrupted Dnmt3a-DNA association. By analyzing the components of detached Dnmt3a, we found that the Dnmt3a oligomers (e.g., dimer, trimer, and high-order oligomers) dissociated from heterochromatin in a dose-dependent manner upon exposure. Thereafter the diminished DNA-binding affinity of Dnmt3a resulted in a significant decrease in 5-methylcytosine (5mC) under both acute high-dosage and chronic low-dosage TCE exposure. The resulting DNA demethylation might also be contributed by the elevated expression of ten-eleven-translocation (Tet) enzymes and reformed cysteine cycle. Besides the global effect, we further identified that a group of heterochromatin-located, cancer-related microRNAs (miRNAs) experienced promoter demethylation upon TCE exposure.
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Affiliation(s)
- Yi Cui
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Samrat Roy Choudhury
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Joseph Irudayaraj
- Department of Agricultural and Biological Engineering, Bindley Bioscience Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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Dabe EC, Sanford RS, Kohn AB, Bobkova Y, Moroz LL. DNA Methylation in Basal Metazoans: Insights from Ctenophores. Integr Comp Biol 2015; 55:1096-110. [PMID: 26173712 PMCID: PMC4817592 DOI: 10.1093/icb/icv086] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Epigenetic modifications control gene expression without altering the primary DNA sequence. However, little is known about DNA methylation in invertebrates and its evolution. Here, we characterize two types of genomic DNA methylation in ctenophores, 5-methyl cytosine (5-mC) and the unconventional form of methylation 6-methyl adenine (6-mA). Using both bisulfite sequencing and an ELISA-based colorimetric assay, we experimentally confirmed the presence of 5-mC DNA methylation in ctenophores. In contrast to other invertebrates studied, Mnemiopsis leidyi has lower levels of genome-wide 5-mC methylation, but higher levels of 5-mC methylation in promoters when compared with gene bodies. Phylogenetic analysis showed that ctenophores have distinct forms of DNA methyltransferase 1 (DNMT1); the zf-CXXC domain type, which localized DNMT1 to CpG sites, and is a metazoan specific innovation. We also show that ctenophores encode the full repertoire of putative enzymes for 6-mA DNA methylation, and these genes are expressed in the aboral organ of Mnemiopsis. Using an ELISA-based colorimetric assay, we experimentally confirmed the presence of 6-mA methylation in the genomes of three different species of ctenophores, M. leidyi, Beroe abyssicola, and Pleurobrachia bachei. The functional role of this novel epigenomic mark is currently unknown. In summary, despite their compact genomes, there is a wide variety of epigenomic mechanisms employed by basal metazoans that provide novel insights into the evolutionary origins of biological novelties.
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Affiliation(s)
- Emily C Dabe
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Rachel S Sanford
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Andrea B Kohn
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA
| | - Yelena Bobkova
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA
| | - Leonid L Moroz
- *The Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St Augustine, FL 32080, USA; Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
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39
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Abstract
The approval of DNA methylation inhibitors azacytidine and decitabine for the treatment of myelodysplastic syndromes and acute myeloid leukaemia has demonstrated that modulation of relatively broad epigenetic regulatory processes can show beneficial efficacy/safety profiles in defined patient groups. This chapter will focus on the biochemical mechanisms controlling DNA methylation, consequences of aberrant DNA methylation in complex chronic diseases, existing modulators of DNA methylation used in the clinic, and opportunities for new drugs targeting this central epigenetic mechanism.
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Affiliation(s)
- Tom D. Heightman
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - Michael McCullar
- Astex Pharmaceuticals Inc. 4140 Dublin Boulevard, Suite 200 Dublin CA 94568 USA
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40
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Eriksson A, Lennartsson A, Lehmann S. Epigenetic aberrations in acute myeloid leukemia: Early key events during leukemogenesis. Exp Hematol 2015; 43:609-24. [PMID: 26118500 DOI: 10.1016/j.exphem.2015.05.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 05/23/2015] [Indexed: 12/17/2022]
Abstract
As a result of the introduction of new sequencing technologies, the molecular landscape of acute myeloid leukemia (AML) is rapidly evolving. From karyotyping, which detects only large genomic aberrations of metaphase chromosomes, we have moved into an era when sequencing of each base pair allows us to define the AML genome at highest resolution. This has revealed a new complex landscape of genetic aberrations where addition of mutations in epigenetic regulators has been one of the most important contributions to the understanding of the pathogenesis of AML. These findings, together with new insights into epigenetic mechanisms, have placed dysregulated epigenetic mechanisms at the forefront of AML development. Not only have several new mutations in genes directly involved in epigenetic regulatory mechanisms been discovered, but also previously well-known gene fusions have been found to exert aberrant effects through epigenetic mechanisms. In addition, mutations in epigenetic regulators such as DNMT3A, TET2, and ASXL1 have recently been found to be the earliest known events during AML evolution and to be present as preleukemic lesions before the onset of AML. In this article, we review epigenetic changes in AML also in relation to what is known about their mechanism of action and their prognostic role.
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Affiliation(s)
- Anna Eriksson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Andreas Lennartsson
- Department of Biosciences and Nutrition, NOVUM, Karolinska Institutet, Stockholm, Sweden
| | - Sören Lehmann
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Centre of Hematology, HERM, Department of Medicine, Karolinska Institute, Huddinge, Stockholm, Sweden.
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Gale RE, Lamb K, Allen C, El-Sharkawi D, Stowe C, Jenkinson S, Tinsley S, Dickson G, Burnett AK, Hills RK, Linch DC. Simpson's Paradox and the Impact of Different DNMT3A Mutations on Outcome in Younger Adults With Acute Myeloid Leukemia. J Clin Oncol 2015; 33:2072-83. [PMID: 25964253 DOI: 10.1200/jco.2014.59.2022] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024] Open
Abstract
PURPOSE To evaluate the impact of DNMT3A mutations on outcome in younger patients with cytogenetic intermediate-risk acute myeloid leukemia. PATIENTS AND METHODS Diagnostic samples from 914 patients (97% < 60 years old) were screened for mutations in DNMT3A exons 13 to 23. Clinical outcome was evaluated according to presence or absence of a mutation and stratified according to type of mutation (R882, non-R882 missense, or truncation). RESULTS DNMT3A mutations (DNMT3A(MUT)) were identified in 272 patients (30%) and associated with a poorer prognosis than wild-type DNMT3A, but the difference was only seen when the results were stratified according to NPM1 genotype. This example of Simpson's paradox results from the high coincidence of DNMT3A and NPM1 mutations (80% of patients with DNMT3A(MUT) had NPM1 mutations), where the two mutations have opposing prognostic impact. In the stratified analyses, relapse in patients with DNMT3A(MUT) was higher (hazard ratio, 1.35; 95% CI, 1.07 to 1.72; P = .01), and overall survival was lower (hazard ratio, 1.37; 95% CI, 1.12 to 1.87; P = .002). The impact of DNMT3A(MUT) did not differ according to NPM1 genotype (test for heterogeneity: relapse, P = .4; overall survival, P = .9). Further analysis according to the type of DNMT3A mutation indicated that outcome was comparable in patients with R882 and non-R882 missense mutants, whereas in those with truncation mutants, it was comparable to wild-type DNMT3A. CONCLUSION These data confirm that presence of a DNMT3A mutation should be considered as a poor-risk prognostic factor, irrespective of the NPM1 genotype, and suggest that further consideration should be given to the type of DNMT3A mutation.
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Affiliation(s)
- Rosemary E Gale
- Rosemary E. Gale, Katarina Lamb, Christopher Allen, Dima El-Sharkawi, Cassandra Stowe, Sarah Jenkinson, Steven Tinsley, Glenda Dickson, and David C. Linch, University College London Cancer Institute, London; and Alan K. Burnett and Robert K. Hills, Cardiff University School of Medicine, Cardiff, United Kingdom.
| | - Katarina Lamb
- Rosemary E. Gale, Katarina Lamb, Christopher Allen, Dima El-Sharkawi, Cassandra Stowe, Sarah Jenkinson, Steven Tinsley, Glenda Dickson, and David C. Linch, University College London Cancer Institute, London; and Alan K. Burnett and Robert K. Hills, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Christopher Allen
- Rosemary E. Gale, Katarina Lamb, Christopher Allen, Dima El-Sharkawi, Cassandra Stowe, Sarah Jenkinson, Steven Tinsley, Glenda Dickson, and David C. Linch, University College London Cancer Institute, London; and Alan K. Burnett and Robert K. Hills, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Dima El-Sharkawi
- Rosemary E. Gale, Katarina Lamb, Christopher Allen, Dima El-Sharkawi, Cassandra Stowe, Sarah Jenkinson, Steven Tinsley, Glenda Dickson, and David C. Linch, University College London Cancer Institute, London; and Alan K. Burnett and Robert K. Hills, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Cassandra Stowe
- Rosemary E. Gale, Katarina Lamb, Christopher Allen, Dima El-Sharkawi, Cassandra Stowe, Sarah Jenkinson, Steven Tinsley, Glenda Dickson, and David C. Linch, University College London Cancer Institute, London; and Alan K. Burnett and Robert K. Hills, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Sarah Jenkinson
- Rosemary E. Gale, Katarina Lamb, Christopher Allen, Dima El-Sharkawi, Cassandra Stowe, Sarah Jenkinson, Steven Tinsley, Glenda Dickson, and David C. Linch, University College London Cancer Institute, London; and Alan K. Burnett and Robert K. Hills, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Steven Tinsley
- Rosemary E. Gale, Katarina Lamb, Christopher Allen, Dima El-Sharkawi, Cassandra Stowe, Sarah Jenkinson, Steven Tinsley, Glenda Dickson, and David C. Linch, University College London Cancer Institute, London; and Alan K. Burnett and Robert K. Hills, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Glenda Dickson
- Rosemary E. Gale, Katarina Lamb, Christopher Allen, Dima El-Sharkawi, Cassandra Stowe, Sarah Jenkinson, Steven Tinsley, Glenda Dickson, and David C. Linch, University College London Cancer Institute, London; and Alan K. Burnett and Robert K. Hills, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Alan K Burnett
- Rosemary E. Gale, Katarina Lamb, Christopher Allen, Dima El-Sharkawi, Cassandra Stowe, Sarah Jenkinson, Steven Tinsley, Glenda Dickson, and David C. Linch, University College London Cancer Institute, London; and Alan K. Burnett and Robert K. Hills, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Robert K Hills
- Rosemary E. Gale, Katarina Lamb, Christopher Allen, Dima El-Sharkawi, Cassandra Stowe, Sarah Jenkinson, Steven Tinsley, Glenda Dickson, and David C. Linch, University College London Cancer Institute, London; and Alan K. Burnett and Robert K. Hills, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - David C Linch
- Rosemary E. Gale, Katarina Lamb, Christopher Allen, Dima El-Sharkawi, Cassandra Stowe, Sarah Jenkinson, Steven Tinsley, Glenda Dickson, and David C. Linch, University College London Cancer Institute, London; and Alan K. Burnett and Robert K. Hills, Cardiff University School of Medicine, Cardiff, United Kingdom
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Abstract
DNA methylation patterns are disrupted in various malignancies, suggesting a role in the development of cancer, but genetic aberrations directly linking the DNA methylation machinery to malignancies were rarely observed, so this association remained largely correlative. Recently, however, mutations in the gene encoding DNA methyltransferase 3A (DNMT3A) were reported in patients with acute myeloid leukaemia (AML), and subsequently in patients with various other haematological malignancies, pointing to DNMT3A as a critically important new tumour suppressor. Here, we review the clinical findings related to DNMT3A, tie these data to insights from basic science studies conducted over the past 20 years and present a roadmap for future research that should advance the agenda for new therapeutic strategies.
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Affiliation(s)
- Liubin Yang
- 1] Department of Molecular and Human Genetics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA. [2]
| | - Rachel Rau
- 1] Department of Pediatrics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA. [2]
| | - Margaret A Goodell
- 1] Department of Molecular and Human Genetics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA. [2] Department of Pediatrics, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
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43
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Holz-Schietinger C, Reich NO. De novo DNA methyltransferase DNMT3A: Regulation of oligomeric state and mechanism of action in response to pH changes. Biochim Biophys Acta Gen Subj 2015; 1850:1131-9. [PMID: 25681155 DOI: 10.1016/j.bbagen.2015.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 01/17/2015] [Accepted: 02/04/2015] [Indexed: 01/26/2023]
Abstract
BACKGROUND The oligomeric state of the human DNMT3A is functionally important and cancer cells are known to undergo changes in pH (intracellular). METHODS Light scattering, gel filtration, and fluorescence anisotropy. Also, methylation and processivity assays. CONCLUSIONS Physiologically relevant changes in pH result in changes in DNMT3A oligomer composition which have dramatic consequences on DNMT3A function. GENERAL SIGNIFICANCE The pH changes which occur within cancer cells alter the oligomeric state and function of DNMT3A which could contribute to changes in genomic DNA methylation observed in vivo.
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Affiliation(s)
- Celeste Holz-Schietinger
- Interdepartmental Program in Biomolecular Science & Engineering, University of California, Santa Barbara, CA 93106-9510, United States
| | - Norbert O Reich
- Interdepartmental Program in Biomolecular Science & Engineering, University of California, Santa Barbara, CA 93106-9510, United States; Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA 93106-9510, United States.
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44
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Prognostic significance of DNMT3A mutations in patients with acute myeloid leukemia. Blood Cells Mol Dis 2015; 54:84-9. [DOI: 10.1016/j.bcmd.2014.07.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/25/2014] [Indexed: 11/23/2022]
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45
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Uchiyama K, Watanabe D, Hayasaka M, Hanaoka K. A novel imprinted transgene located near a repetitive element that exhibits allelic imbalance in DNA methylation during early development. Dev Growth Differ 2014; 56:653-68. [PMID: 25389047 DOI: 10.1111/dgd.12182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 08/29/2014] [Accepted: 09/09/2014] [Indexed: 11/27/2022]
Abstract
A mouse line carrying a lacZ transgene driven by the human EEF1A1/EF1 alpha promoter was established. Although the promoter is known to show ubiquitous activity, only paternal transgene alleles were expressed, resulting in a transgene imprinting. At mid-gestation, the promoter sequence was differentially methylated, hypomethylated for paternal and hypermethylated for maternal alleles. In germline, the promoter was a typical differentially methylated region. After fertilization, however, both alleles were hypermethylated. Thus, the differential methylation of the promoter required for transgene imprinting was re-established during later embryonic development independently of the germline differential methylation. Furthermore, also a retroelement promoter closely-flanking imprinted transgene and its wild type counterpart displayed similar differential methylation during early development. The retroelement promoter was methylated differentially also in germline, but in an opposite pattern to the embryonic differential methylation. These results suggest that there might be an unknown epigenetic regulation inducing transgene imprinting independently of DNA methylation in the transgene insertion site. Then, besides CpG dinucleotides, non-CpG cytosines of the retroelement promoter were highly methylated especially in the transgene-active mid-gestational embryos, suggesting that an unusual epigenetic regulation might protect the active transgene against de novo methylation occurring generally in mid-gestational embryo.
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Affiliation(s)
- Koji Uchiyama
- Molecular Embryology, Department of Biosciences, School of Science, Kitasato University, Sagamihara-Shi, Japan
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46
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Emperle M, Rajavelu A, Reinhardt R, Jurkowska RZ, Jeltsch A. Cooperative DNA binding and protein/DNA fiber formation increases the activity of the Dnmt3a DNA methyltransferase. J Biol Chem 2014; 289:29602-13. [PMID: 25147181 DOI: 10.1074/jbc.m114.572032] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Dnmt3a DNA methyltransferase has been shown to bind cooperatively to DNA and to form large multimeric protein/DNA fibers. However, it has also been reported to methylate DNA in a processive manner, a property that is incompatible with protein/DNA fiber formation. We show here that the DNA methylation rate of Dnmt3a increases more than linearly with increasing enzyme concentration on a long DNA substrate, but not on a short 30-mer oligonucleotide substrate. We also show that addition of a catalytically inactive Dnmt3a mutant, which carries an amino acid exchange in the catalytic center, increases the DNA methylation rate by wild type Dnmt3a on the long substrate but not on the short one. In agreement with this finding, preincubation experiments indicate that stable protein/DNA fibers are formed on the long, but not on the short substrate. In addition, methylation experiments with substrates containing one or two CpG sites did not provide evidence for a processive mechanism over a wide range of enzyme concentrations. These data clearly indicate that Dnmt3a binds to DNA in a cooperative reaction and that the formation of stable protein/DNA fibers increases the DNA methylation rate. Fiber formation occurs at low μm concentrations of Dnmt3a, which are in the range of Dnmt3a concentrations in the nucleus of embryonic stem cells. Understanding the mechanism of Dnmt3a is of vital importance because Dnmt3a is a hotspot of somatic cancer mutations one of which has been implicated in changing Dnmt3a processivity.
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Affiliation(s)
- Max Emperle
- From the Institute of Biochemistry, Stuttgart University, D-70569 Stuttgart, Germany and
| | - Arumugam Rajavelu
- From the Institute of Biochemistry, Stuttgart University, D-70569 Stuttgart, Germany and
| | | | - Renata Z Jurkowska
- From the Institute of Biochemistry, Stuttgart University, D-70569 Stuttgart, Germany and
| | - Albert Jeltsch
- From the Institute of Biochemistry, Stuttgart University, D-70569 Stuttgart, Germany and
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47
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Russler-Germain DA, Spencer DH, Young MA, Lamprecht TL, Miller CA, Fulton R, Meyer MR, Erdmann-Gilmore P, Townsend RR, Wilson RK, Ley TJ. The R882H DNMT3A mutation associated with AML dominantly inhibits wild-type DNMT3A by blocking its ability to form active tetramers. Cancer Cell 2014; 25:442-54. [PMID: 24656771 PMCID: PMC4018976 DOI: 10.1016/j.ccr.2014.02.010] [Citation(s) in RCA: 334] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/08/2014] [Accepted: 02/19/2014] [Indexed: 10/25/2022]
Abstract
Somatic mutations in DNMT3A, which encodes a de novo DNA methyltransferase, are found in ∼30% of normal karyotype acute myeloid leukemia (AML) cases. Most mutations are heterozygous and alter R882 within the catalytic domain (most commonly R882H), suggesting the possibility of dominant-negative consequences. The methyltransferase activity of R882H DNMT3A is reduced by ∼80% compared with the WT enzyme. In vitro mixing of WT and R882H DNMT3A does not affect the WT activity, but coexpression of the two proteins in cells profoundly inhibits the WT enzyme by disrupting its ability to homotetramerize. AML cells with the R882H mutation have severely reduced de novo methyltransferase activity and focal hypomethylation at specific CpGs throughout AML cell genomes.
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Affiliation(s)
- David A Russler-Germain
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - David H Spencer
- Department of Pathology and Immunology, Washington University, St. Louis, MO 63110, USA
| | - Margaret A Young
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Tamara L Lamprecht
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | | | - Robert Fulton
- The Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Matthew R Meyer
- Division of Metabolism, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Petra Erdmann-Gilmore
- Division of Metabolism, Department of Medicine, Washington University, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63110, USA
| | - R Reid Townsend
- Division of Metabolism, Department of Medicine, Washington University, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63110, USA
| | - Richard K Wilson
- The Genome Institute, Washington University, St. Louis, MO 63110, USA; Department of Genetics, Washington University, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63110, USA
| | - Timothy J Ley
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University, St. Louis, MO 63110, USA; The Genome Institute, Washington University, St. Louis, MO 63110, USA; Department of Genetics, Washington University, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University, St. Louis, MO 63110, USA.
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48
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Abstract
Epigenetic alterations are associated with all aspects of cancer, from tumor initiation to cancer progression and metastasis. It is now well understood that both losses and gains of DNA methylation as well as altered chromatin organization contribute significantly to cancer-associated phenotypes. More recently, new sequencing technologies have allowed the identification of driver mutations in epigenetic regulators, providing a mechanistic link between the cancer epigenome and genetic alterations. Oncogenic activating mutations are now known to occur in a number of epigenetic modifiers (i.e. IDH1/2, EZH2, DNMT3A), pinpointing epigenetic pathways that are involved in tumorigenesis. Similarly, investigations into the role of inactivating mutations in chromatin modifiers (i.e. KDM6A, CREBBP/EP300, SMARCB1) implicate many of these genes as tumor suppressors. Intriguingly, a number of neoplasms are defined by a plethora of mutations in epigenetic regulators, including renal, bladder, and adenoid cystic carcinomas. Particularly striking is the discovery of frequent histone H3.3 mutations in pediatric glioma, a particularly aggressive neoplasm that has long remained poorly understood. Cancer epigenetics is a relatively new, promising frontier with much potential for improving cancer outcomes. Already, therapies such as 5-azacytidine and decitabine have proven that targeting epigenetic alterations in cancer can lead to tangible benefits. Understanding how genetic alterations give rise to the cancer epigenome will offer new possibilities for developing better prognostic and therapeutic strategies.
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49
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50
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Chen BF, Chan WY. The de novo DNA methyltransferase DNMT3A in development and cancer. Epigenetics 2014; 9:669-77. [PMID: 24589714 DOI: 10.4161/epi.28324] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA methylation, one of the best-characterized epigenetic modifications, plays essential roles in development, aging and diseases. The de novo DNA methyltransferase DNMT3A is responsible for the establishment of de novo genomic DNA methylation patterns and, as such, involved in normal development as well as in many diseases including cancer. In recent years, our understanding of this important protein has made significant progress, which was facilitated by stunning development in the analysis of the DNA methylome of multiple organs and cell types. In this review, recent developments in the characterization of DNMT3A were discussed with special emphasis on the roles of DNMT3A in development and cancer.
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Affiliation(s)
- Bi-Feng Chen
- Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics; School of Biomedical Sciences; Shenzhen Research Institute; the Chinese University of Hong Kong; Hong Kong SAR, PR China
| | - Wai-Yee Chan
- Chinese University of Hong Kong-Shandong University Joint Laboratory on Reproductive Genetics; School of Biomedical Sciences; Shenzhen Research Institute; the Chinese University of Hong Kong; Hong Kong SAR, PR China
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