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Liang W, Xu F, Li L, Peng C, Sun H, Qiu J, Sun J. Epigenetic control of skeletal muscle atrophy. Cell Mol Biol Lett 2024; 29:99. [PMID: 38978023 PMCID: PMC11229277 DOI: 10.1186/s11658-024-00618-1] [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: 03/25/2024] [Accepted: 06/26/2024] [Indexed: 07/10/2024] Open
Abstract
Skeletal muscular atrophy is a complex disease involving a large number of gene expression regulatory networks and various biological processes. Despite extensive research on this topic, its underlying mechanisms remain elusive, and effective therapeutic approaches are yet to be established. Recent studies have shown that epigenetics play an important role in regulating skeletal muscle atrophy, influencing the expression of numerous genes associated with this condition through the addition or removal of certain chemical modifications at the molecular level. This review article comprehensively summarizes the different types of modifications to DNA, histones, RNA, and their known regulators. We also discuss how epigenetic modifications change during the process of skeletal muscle atrophy, the molecular mechanisms by which epigenetic regulatory proteins control skeletal muscle atrophy, and assess their translational potential. The role of epigenetics on muscle stem cells is also highlighted. In addition, we propose that alternative splicing interacts with epigenetic mechanisms to regulate skeletal muscle mass, offering a novel perspective that enhances our understanding of epigenetic inheritance's role and the regulatory network governing skeletal muscle atrophy. Collectively, advancements in the understanding of epigenetic mechanisms provide invaluable insights into the study of skeletal muscle atrophy. Moreover, this knowledge paves the way for identifying new avenues for the development of more effective therapeutic strategies and pharmaceutical interventions.
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Affiliation(s)
- Wenpeng Liang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 26001, China
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, 226001, China
| | - Feng Xu
- Department of Endocrinology, Affiliated Hospital 2 of Nantong University and First People's Hospital of Nantong City, Nantong, 226001, China
| | - Li Li
- Nantong Center for Disease Control and Prevention, Medical School of Nantong University, Nantong, 226001, China
| | - Chunlei Peng
- Department of Medical Oncology, Tumor Hospital Affiliated to Nantong University, Nantong, 226000, China
| | - Hualin Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 26001, China
| | - Jiaying Qiu
- Department of Prenatal Screening and Diagnosis Center, Affiliated Maternity and Child Health Care Hospital of Nantong University, Nantong, 226001, China.
| | - Junjie Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-Innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, Nantong, 26001, China.
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2
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Zebrauskiene D, Sadauskiene E, Dapkunas J, Kairys V, Balciunas J, Konovalovas A, Masiuliene R, Petraityte G, Valeviciene N, Mataciunas M, Barysiene J, Mikstiene V, Tomkuviene M, Preiksaitiene E. Aortic disease and cardiomyopathy in patients with a novel DNMT3A gene variant causing Tatton-Brown-Rahman syndrome. Clin Epigenetics 2024; 16:76. [PMID: 38845031 PMCID: PMC11157947 DOI: 10.1186/s13148-024-01686-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: 04/05/2024] [Accepted: 05/27/2024] [Indexed: 06/09/2024] Open
Abstract
Tatton-Brown-Rahman syndrome (TBRS) is a rare congenital genetic disorder caused by autosomal dominant pathogenic variants in the DNA methyltransferase DNMT3A gene. Typical TBRS clinical features are overgrowth, intellectual disability, and minor facial anomalies. However, since the syndrome was first described in 2014, a widening spectrum of abnormalities is being described. Cardiovascular abnormalities are less commonly reported but can be a major complication of the syndrome. This article describes a family of three individuals diagnosed with TBRS in adulthood and highlights the variable expression of cardiovascular features. A 34-year-old proband presented with progressive aortic dilatation, mitral valve (MV) regurgitation, left ventricular (LV) dilatation, and ventricular arrhythmias. The affected family members (mother and brother) were diagnosed with MV regurgitation, LV dilatation, and arrhythmias. Exome sequencing and computational protein analysis suggested that the novel familial DNMT3A mutation Ser775Tyr is located in the methyltransferase domain, however, distant from the active site or DNA-binding loops. Nevertheless, this bulky substitution may have a significant effect on DNMT3A protein structure, dynamics, and function. Analysis of peripheral blood cfDNA and transcriptome showed shortened mononucleosome fragments and altered gene expression in a number of genes related to cardiovascular health and of yet undescribed function, including several lncRNAs. This highlights the importance of epigenetic regulation by DNMT3A on cardiovascular system development and function. From the clinical perspective, we suggest that new patients diagnosed with congenital DNMT3A variants and TBRS require close examination and follow-up for aortic dilatation and valvular disease because these conditions can progress rapidly. Moreover, personalized treatments, based on the specific DNMT3A variants and the different pathways of their function loss, can be envisioned in the future.
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Affiliation(s)
- Dovile Zebrauskiene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania.
| | - Egle Sadauskiene
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Justas Dapkunas
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Visvaldas Kairys
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Joris Balciunas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania
| | | | | | - Gunda Petraityte
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania
| | - Nomeda Valeviciene
- Department of Radiology, Nuclear Medicine and Medical Physics, Institute of Biomedical Sciences, Vilnius University Faculty of Medicine, Vilnius, Lithuania
| | - Mindaugas Mataciunas
- Department of Radiology, Nuclear Medicine and Medical Physics, Institute of Biomedical Sciences, Vilnius University Faculty of Medicine, Vilnius, Lithuania
| | - Jurate Barysiene
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Violeta Mikstiene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania
| | - Migle Tomkuviene
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio 7, 10257, Vilnius, Lithuania.
| | - Egle Preiksaitiene
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariskiu 2, 08661, Vilnius, Lithuania
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3
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Engal E, Sharma A, Aviel U, Taqatqa N, Juster S, Jaffe-Herman S, Bentata M, Geminder O, Gershon A, Lewis R, Kay G, Hecht M, Epsztejn-Litman S, Gotkine M, Mouly V, Eiges R, Salton M, Drier Y. DNMT3B splicing dysregulation mediated by SMCHD1 loss contributes to DUX4 overexpression and FSHD pathogenesis. SCIENCE ADVANCES 2024; 10:eadn7732. [PMID: 38809976 PMCID: PMC11135424 DOI: 10.1126/sciadv.adn7732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024]
Abstract
Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is a noncanonical SMC protein and an epigenetic regulator. Mutations in SMCHD1 cause facioscapulohumeral muscular dystrophy (FSHD), by overexpressing DUX4 in muscle cells. Here, we demonstrate that SMCHD1 is a key regulator of alternative splicing in various cell types. We show how SMCHD1 loss causes splicing alterations of DNMT3B, which can lead to hypomethylation and DUX4 overexpression. Analyzing RNA sequencing data from muscle biopsies of patients with FSHD and Smchd1 knocked out cells, we found mis-splicing of hundreds of genes upon SMCHD1 loss. We conducted a high-throughput screen of splicing factors, revealing the involvement of the splicing factor RBM5 in the mis-splicing of DNMT3B. Subsequent RNA immunoprecipitation experiments confirmed that SMCHD1 is required for RBM5 recruitment. Last, we show that mis-splicing of DNMT3B leads to hypomethylation of the D4Z4 region and to DUX4 overexpression. These results suggest that DNMT3B mis-splicing due to SMCHD1 loss plays a major role in FSHD pathogenesis.
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Affiliation(s)
- Eden Engal
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Military Medicine and “Tzameret”, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Aveksha Sharma
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Uria Aviel
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
| | - Nadeen Taqatqa
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Sarah Juster
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Shiri Jaffe-Herman
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Mercedes Bentata
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ophir Geminder
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
- Department of Military Medicine and “Tzameret”, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Adi Gershon
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Reyut Lewis
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Merav Hecht
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Silvina Epsztejn-Litman
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
| | - Marc Gotkine
- Department of Neurology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 9112002, Israel
| | - Vincent Mouly
- UPMC University Paris 06, Inserm UMRS974, CNRS FRE3617, Center for Research in Myology, Sorbonne University,75252 Paris, France
| | - Rachel Eiges
- Stem Cell Research Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yotam Drier
- The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
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Tibben BM, Rothbart SB. Mechanisms of DNA Methylation Regulatory Function and Crosstalk with Histone Lysine Methylation. J Mol Biol 2024; 436:168394. [PMID: 38092287 PMCID: PMC10957332 DOI: 10.1016/j.jmb.2023.168394] [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: 09/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
DNA methylation is a well-studied epigenetic modification that has key roles in regulating gene expression, maintaining genome integrity, and determining cell fate. Precisely how DNA methylation patterns are established and maintained in specific cell types at key developmental stages is still being elucidated. However, research over the last two decades has contributed to our understanding of DNA methylation regulation by other epigenetic processes. Specifically, lysine methylation on key residues of histone proteins has been shown to contribute to the allosteric regulation of DNA methyltransferase (DNMT) activities. In this review, we discuss the dynamic interplay between DNA methylation and histone lysine methylation as epigenetic regulators of genome function by synthesizing key recent studies in the field. With a focus on DNMT3 enzymes, we discuss mechanisms of DNA methylation and histone lysine methylation crosstalk in the regulation of gene expression and the maintenance of genome integrity. Further, we discuss how alterations to the balance of various sites of histone lysine methylation and DNA methylation contribute to human developmental disorders and cancers. Finally, we provide perspectives on the current direction of the field and highlight areas for continued research and development.
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Affiliation(s)
- Bailey M Tibben
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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5
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Qin Y, Li T, An P, Ren Z, Xi J, Tang B. Important role of DNA methylation hints at significant potential in tuberculosis. Arch Microbiol 2024; 206:177. [PMID: 38494532 DOI: 10.1007/s00203-024-03888-7] [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: 12/02/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/19/2024]
Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis (Mtb) infection, has persisted as a major global public health threat for millennia. Until now, TB continues to challenge efforts aimed at controlling it, with drug resistance and latent infections being the two main factors hindering treatment efficacy. The scientific community is still striving to understand the underlying mechanisms behind Mtb's drug resistance and latent infection. DNA methylation, a critical epigenetic modification occurring throughout an individual's growth and development, has gained attention following advances in high-throughput sequencing technologies. Researchers have observed abnormal DNA methylation patterns in the host genome during Mtb infection. Given the escalating issue of drug-resistant Mtb, delving into the role of DNA methylation in TB's development is crucial. This review article explores DNA methylation's significance in human growth, development and disease, and its role in regulating Mtb's evolution and infection processes. Additionally, it discusses potential applications of DNA methylation research in tuberculosis.
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Affiliation(s)
- Yuexuan Qin
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China
| | - Tianyue Li
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China
| | - Peiyan An
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China
| | - Zhi Ren
- First Affiliated Hospital of Bengbu Medical University, Bengbu, 233030, Anhui Province, China
| | - Jun Xi
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China.
| | - Bikui Tang
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China.
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6
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Li Y, Abel HJ, Cai M, LaValle TA, Yin T, Helton NM, Smith AM, Miller CA, Ley TJ. Rapid and accurate remethylation of DNA in Dnmt3a-deficient hematopoietic cells with restoration of DNMT3A activity. SCIENCE ADVANCES 2024; 10:eadk8598. [PMID: 38295174 PMCID: PMC10830114 DOI: 10.1126/sciadv.adk8598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/26/2023] [Indexed: 02/02/2024]
Abstract
Here, we characterize the DNA methylation phenotypes of bone marrow cells from mice with hematopoietic deficiency of Dnmt3a or Dnmt3b (or both enzymes) or expressing the dominant-negative Dnmt3aR878H mutation [R882H in humans; the most common DNMT3A mutation found in acute myeloid leukemia (AML)]. Using these cells as substrates, we defined DNA remethylation after overexpressing wild-type (WT) DNMT3A1, DNMT3B1, DNMT3B3 (an inactive splice isoform of DNMT3B), or DNMT3L (a catalytically inactive "chaperone" for DNMT3A and DNMT3B in early embryogenesis). Overexpression of DNMT3A for 2 weeks reverses the hypomethylation phenotype of Dnmt3a-deficient cells or cells expressing the R878H mutation. Overexpression of DNMT3L (which is minimally expressed in AML cells) also corrects the hypomethylation phenotype of Dnmt3aR878H/+ marrow, probably by augmenting the activity of WT DNMT3A encoded by the residual WT allele. DNMT3L reactivation may represent a previously unidentified approach for restoring DNMT3A activity in hematopoietic cells with reduced DNMT3A function.
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Affiliation(s)
- Yang Li
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Haley J. Abel
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michelle Cai
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | | | - Tiankai Yin
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Nichole M. Helton
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
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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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8
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Kucharski R, Ellis N, Jurkowski TP, Hurd PJ, Maleszka R. The PWWP domain and the evolution of unique DNA methylation toolkits in Hymenoptera. iScience 2023; 26:108193. [PMID: 37920666 PMCID: PMC10618690 DOI: 10.1016/j.isci.2023.108193] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/11/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
DNMT3 in Hymenoptera has a unique duplication of the essential PWWP domain. Using GST-tagged PWWP fusion proteins and histone arrays we show that these domains have gained new properties and represent the first case of PWWP domains binding to H3K27 chromatin modifications, including H3K27me3, a key modification that is important during development. Phylogenetic analyses of 107 genomes indicate that the duplicated PWWP domains separated into two sister clades, and their distinct binding capacities are supported by 3D modeling. Other features of this unique DNA methylation system include variable copies, losses, and duplications of DNMT1 and DNMT3, and combinatorial generations of DNMT3 isoforms including variants missing the catalytic domain. Some of these losses and duplications of are found only in parasitic wasps. We discuss our findings in the context of the crosstalk between DNA methylation and histone methylation, and the expanded potential of epigenomic modifications in Hymenoptera to drive evolutionary novelties.
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Affiliation(s)
- Robert Kucharski
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Nancy Ellis
- School of Biological & Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Paul J. Hurd
- School of Biological & Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ryszard Maleszka
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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9
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Behluli L, Fontanilla AM, Andessner-Angleitner L, Tolar N, Molina JM, Gahurova L. Expression analysis suggests that DNMT3L is required for oocyte de novo DNA methylation only in Muridae and Cricetidae rodents. Epigenetics Chromatin 2023; 16:43. [PMID: 37924163 PMCID: PMC10625200 DOI: 10.1186/s13072-023-00518-2] [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: 08/23/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND During early mammalian development, DNA methylation undergoes two waves of reprogramming, enabling transitions between somatic cells, oocyte and embryo. The first wave of de novo DNA methylation establishment occurs in oocytes. Its molecular mechanisms have been studied in mouse, a classical mammalian model. Current model describes DNA methyltransferase 3A (DNMT3A) and its cofactor DNMT3L as two essential factors for oocyte DNA methylation-the ablation of either leads to nearly complete abrogation of DNA methylation. However, DNMT3L is not expressed in human oocytes, suggesting that the mechanism uncovered in mouse is not universal across mammals. RESULTS We analysed available RNA-seq data sets from oocytes of multiple mammals, including our novel data sets of several rodent species, and revealed that Dnmt3l is expressed only in the oocytes of mouse, rat and golden hamster, and at a low level in guinea pigs. We identified a specific promoter sequence recognised by an oocyte transcription factor complex associated with strong Dnmt3l activity and demonstrated that it emerged in the rodent clade Eumuroida, comprising the families Muridae (mice, rats, gerbils) and Cricetidae (hamsters). In addition, an evolutionarily novel promoter emerged in the guinea pig, driving weak Dnmt3l expression, likely without functional relevance. Therefore, Dnmt3l is expressed and consequently plays a role in oocyte de novo DNA methylation only in a small number of rodent species, instead of being an essential pan-mammalian factor. In contrast to somatic cells, where catalytically inactive DNMT3B interacts with DNMT3A, forming a heterotetramer, we did not find evidence for the expression of such inactive Dnmt3b isoforms in the oocytes of the tested species. CONCLUSIONS The analysis of RNA-seq data and genomic sequences revealed that DNMT3L is likely to play a role in oocytes de novo DNA methylation only in mice, rats, gerbils and hamsters. The mechanism governing de novo DNA methylation in the oocytes of most mammalian species, including humans, occurs through a yet unknown mechanism that differs from the current model discovered in mouse.
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Affiliation(s)
- Lirik Behluli
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Alyssa M Fontanilla
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Laura Andessner-Angleitner
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Nikolas Tolar
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Julia M Molina
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
- Department of Biological Sciences, Faculty of Sciences and Languages, São Paulo State University "Júlio de Mesquita Filho" - UNESP, Assis, São Paulo, Brazil
| | - Lenka Gahurova
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic.
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Wang F, Xu Y, Wang R, Zhang B, Smith N, Notaro A, Gaerlan S, Kutschera E, Kadash-Edmondson KE, Xing Y, Lin L. TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing. Nat Commun 2023; 14:4760. [PMID: 37553321 PMCID: PMC10409798 DOI: 10.1038/s41467-023-40083-6] [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: 12/03/2022] [Accepted: 07/11/2023] [Indexed: 08/10/2023] Open
Abstract
Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. One strategy for overcoming this bottleneck is targeted long-read RNA-seq for preselected gene panels. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq utilizing isothermally linear-amplified capture probes. When performed on the Oxford nanopore platform with multiple gene panels of varying sizes, TEQUILA-seq consistently and substantially enriches transcript coverage while preserving transcript quantification. We profile full-length transcript isoforms of 468 actionable cancer genes across 40 representative breast cancer cell lines. We identify transcript isoforms enriched in specific subtypes and discover novel transcript isoforms in extensively studied cancer genes such as TP53. Among cancer genes, tumor suppressor genes (TSGs) are significantly enriched for aberrant transcript isoforms targeted for degradation via mRNA nonsense-mediated decay, revealing a common RNA-associated mechanism for TSG inactivation. TEQUILA-seq reduces the per-reaction cost of targeted capture by 2-3 orders of magnitude, as compared to a standard commercial solution. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings.
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Affiliation(s)
- Feng Wang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yang Xu
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert Wang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Beatrice Zhang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Noah Smith
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Amber Notaro
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Samantha Gaerlan
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric Kutschera
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kathryn E Kadash-Edmondson
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Lan Lin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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11
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Kawaguchi K, Ohashi T, Kobayashi N, Kanemoto K, Nose M, Shinozaki R, Kataoka T, Fujii H. Aberrant DNA methylation-mediated NF-κB/fatty acid-binding protein 5 (FABP5) feed-forward loop promotes malignancy of colorectal cancer cells. Biochim Biophys Acta Mol Cell Biol Lipids 2023:159362. [PMID: 37414211 DOI: 10.1016/j.bbalip.2023.159362] [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: 12/12/2022] [Revised: 05/15/2023] [Accepted: 06/26/2023] [Indexed: 07/08/2023]
Abstract
Fatty acid-binding proteins (FABPs) are intracellular lipid-binding proteins that play roles in fatty acid transport and the regulation of gene expression. Dysregulated FABP expression and/or activity have been associated with cancer pathogenesis; in particular, epidermal-type FABP (FABP5) is upregulated in many types of cancer. However, the mechanisms regulating FABP5 expression and its involvement in cancer remain largely unknown. Here, we examined the regulation of FABP5 gene expression in non-metastatic and metastatic human colorectal cancer (CRC) cells. We found that FABP5 expression was upregulated in metastatic compared with non-metastatic CRC cells as well as in human CRC tissues compared with adjacent normal tissue. Analysis of the DNA methylation status of the FABP5 promoter showed that hypomethylation correlated with the malignant potential of the CRC cell lines. Moreover, FABP5 promoter hypomethylation also correlated with the expression pattern of splice variants of the DNA methyltransferase DNMT3B. ChIP assays and luciferase reporter assays demonstrated that the transcription factor nuclear factor-kappa B (NF-κB) was involved in regulating FABP5 expression. FABP5 expression could be upregulated in metastatic CRC cells by sequential promotion of DNA demethylation followed by activation of NF-κB. We also found that upregulated FABP5 in turn controlled NF-κB activity through IL-8 production. Collectively, these findings suggest the existence of a DNA methylation-dependent NF-κB /FABP5 positive feed-forward loop that may lead to constitutive activation of NF-κB signaling pathway and play a crucial role in CRC progression.
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Affiliation(s)
- Koichiro Kawaguchi
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
| | - Tsubasa Ohashi
- Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Narumi Kobayashi
- Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Kotoya Kanemoto
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Makoto Nose
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Rin Shinozaki
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Takao Kataoka
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; Biomedical Research Center, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Hiroshi Fujii
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; Department of Biomedical Engineering, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan.
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12
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Li D, Xia L, Huang P, Wang Z, Guo Q, Huang C, Leng W, Qin S. Serine protease PRSS56, a novel cancer-testis antigen activated by DNA hypomethylation, promotes colorectal and gastric cancer progression via PI3K/AKT axis. Cell Biosci 2023; 13:124. [PMID: 37400936 DOI: 10.1186/s13578-023-01060-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/27/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Cancer/testis (CT) antigens/genes are usually overexpressed in cancers and exhibit high immunogenicity, making them promising targets for immunotherapy and cancer vaccines. The role of serine protease PRSS56 in cancers remains unknown to date. METHODS RNA sequencing studies were performed to screen CT genes in gastric cancer (GC) and colorectal cancer (CRC) cells exposed to DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-AZA-CdR). Bioinformatics analysis was conducted to analyze the correlation between PRSS56 expression and DNA methylation. Functional experiments were performed to explore the biological function of PRSS56 in GC and CRC. RESULTS In this study, we identified the testis-specific serine proteases PRSS56 as a novel CT antigen. PRSS56 was frequently overexpressed in various cancers, especially in gastrointestinal cancer. PRSS56 expression was negatively associated with promoter DNA methylation level, and positively associated with gene body methylation level. PRSS56 expression was significantly activated in colorectal and gastric cancer cells exposed to DNA methyltransferase inhibitors. Importantly, our finding highlights that the decreased methylation level of the CpG site cg10242318 in the PRSS56 promoter region resulted in its overexpression in GC and CRC. Additionally, functional assays verified that PRSS56 overexpression activated PI3K-AKT signaling in GC and CRC. CONCLUSION Serine protease PRSS56 is a novel CT antigen that is reactivated in cancers by promoter DNA hypomethylation. PRSS56 functions oncogenic roles in GC and CRC by activating of PI3K/AKT axis. Our results presented here represent the first data on the function of the serine protease PRSS56 in cancers.
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Affiliation(s)
- Dandan Li
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China
- Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China
| | - Lingyun Xia
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China
| | - Pan Huang
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China
- Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China
| | - Zidi Wang
- Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China
| | - Qiwei Guo
- Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China
| | - Congcong Huang
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China
- Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China
| | - Weidong Leng
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China.
| | - Shanshan Qin
- Department of Stomatology, Taihe Hospital and Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China.
- Laboratory of Tumor biology, Academy of Bio-Medicine Research, Hubei University of Medicine, Shiyan, Hubei, 442000, P.R. China.
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13
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Šikrová D, Testa AM, Willemsen I, van den Heuvel A, Tapscott SJ, Daxinger L, Balog J, van der Maarel SM. SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action. Commun Biol 2023; 6:677. [PMID: 37380887 DOI: 10.1038/s42003-023-05053-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/17/2023] [Indexed: 06/30/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is caused by the epigenetic derepression of the 4q-linked D4Z4 macrosatellite repeat resulting in inappropriate expression of the D4Z4 repeat-encoded DUX4 gene in skeletal muscle. In 5% of FSHD cases, D4Z4 chromatin relaxation is due to germline mutations in one of the chromatin modifiers SMCHD1, DNMT3B or LRIF1. The mechanism of SMCHD1- and LRIF1-mediated D4Z4 repression is not clear. We show that somatic loss-of-function of either SMCHD1 or LRIF1 does not result in D4Z4 chromatin changes and that SMCHD1 and LRIF1 form an auxiliary layer of D4Z4 repressive mechanisms. We uncover that SMCHD1, together with the long isoform of LRIF1, binds to the LRIF1 promoter and silences LRIF1 expression. The interdependency of SMCHD1 and LRIF1 binding differs between D4Z4 and the LRIF1 promoter, and both loci show different transcriptional responses to either early developmentally or somatically perturbed chromatin function of SMCHD1 and LRIF1.
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Affiliation(s)
- Darina Šikrová
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Alessandra M Testa
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
- Department of Biomedical Sciences, University of Padua, 35100, Padua, Italy
| | - Iris Willemsen
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Anita van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Stephen J Tapscott
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Judit Balog
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands
| | - Silvère M van der Maarel
- Department of Human Genetics, Leiden University Medical Center, 2333ZC, Leiden, The Netherlands.
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14
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Dar MS, Mensah IK, He M, McGovern S, Sohal IS, Whitlock HC, Bippus NE, Ceminsky M, Emerson ML, Tan HJ, Hall MC, Gowher H. Dnmt3bas coordinates transcriptional induction and alternative exon inclusion to promote catalytically active Dnmt3b expression. Cell Rep 2023; 42:112587. [PMID: 37294637 PMCID: PMC10592478 DOI: 10.1016/j.celrep.2023.112587] [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: 06/03/2022] [Revised: 03/16/2023] [Accepted: 05/16/2023] [Indexed: 06/11/2023] Open
Abstract
Embryonic expression of DNMT3B is critical for establishing de novo DNA methylation. This study uncovers the mechanism through which the promoter-associated long non-coding RNA (lncRNA) Dnmt3bas controls the induction and alternative splicing of Dnmt3b during embryonic stem cell (ESC) differentiation. Dnmt3bas recruits the PRC2 (polycomb repressive complex 2) at cis-regulatory elements of the Dnmt3b gene expressed at a basal level. Correspondingly, Dnmt3bas knockdown enhances Dnmt3b transcriptional induction, whereas overexpression of Dnmt3bas dampens it. Dnmt3b induction coincides with exon inclusion, switching the predominant isoform from the inactive Dnmt3b6 to the active Dnmt3b1. Intriguingly, overexpressing Dnmt3bas further enhances the Dnmt3b1:Dnmt3b6 ratio, attributed to its interaction with hnRNPL (heterogeneous nuclear ribonucleoprotein L), a splicing factor that promotes exon inclusion. Our data suggest that Dnmt3bas coordinates alternative splicing and transcriptional induction of Dnmt3b by facilitating the hnRNPL and RNA polymerase II (RNA Pol II) interaction at the Dnmt3b promoter. This dual mechanism precisely regulates the expression of catalytically active DNMT3B, ensuring fidelity and specificity of de novo DNA methylation.
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Affiliation(s)
- Mohd Saleem Dar
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ikjot Singh Sohal
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | | | - Nina Elise Bippus
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Madison Ceminsky
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Martin L Emerson
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Hern J Tan
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, 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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15
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Shin HJ, Hua JT, Li H. Recent advances in understanding DNA methylation of prostate cancer. Front Oncol 2023; 13:1182727. [PMID: 37234978 PMCID: PMC10206257 DOI: 10.3389/fonc.2023.1182727] [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: 03/09/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Epigenetic modifications, such as DNA methylation, is widely studied in cancer. DNA methylation patterns have been shown to distinguish between benign and malignant tumors in various cancers, including prostate cancer. It may also contribute to oncogenesis, as it is frequently associated with downregulation of tumor suppressor genes. Aberrant patterns of DNA methylation, in particular the CpG island hypermethylator phenotype (CIMP), have shown associative evidence with distinct clinical features and outcomes, such as aggressive subtypes, higher Gleason score, prostate-specific antigen (PSA), and overall tumor stage, overall worse prognosis, as well as reduced survival. In prostate cancer, hypermethylation of specific genes is significantly different between tumor and normal tissues. Methylation patterns could distinguish between aggressive subtypes of prostate cancer, including neuroendocrine prostate cancer (NEPC) and castration resistant prostate adenocarcinoma. Further, DNA methylation is detectable in cell-free DNA (cfDNA) and is reflective of clinical outcome, making it a potential biomarker for prostate cancer. This review summarizes recent advances in understanding DNA methylation alterations in cancers with the focus on prostate cancer. We discuss the advanced methodology used for evaluating DNA methylation changes and the molecular regulators behind these changes. We also explore the clinical potential of DNA methylation as prostate cancer biomarkers and its potential for developing targeted treatment of CIMP subtype of prostate cancer.
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Affiliation(s)
- Hyun Jin Shin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
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16
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Li HT, Jang HJ, Rohena-Rivera K, Liu M, Gujar H, Kulchycki J, Zhao S, Billet S, Zhou X, Weisenberger DJ, Gill I, Jones PA, Bhowmick NA, Liang G. RNA mis-splicing drives viral mimicry response after DNMTi therapy in SETD2-mutant kidney cancer. Cell Rep 2023; 42:112016. [PMID: 36662621 PMCID: PMC10034851 DOI: 10.1016/j.celrep.2023.112016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/26/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023] Open
Abstract
Tumors with mutations in chromatin regulators present attractive targets for DNA hypomethylating agent 5-aza-2'-deoxycytidine (DAC) therapy, which further disrupts cancer cells' epigenomic fidelity and reactivates transposable element (TE) expression to drive viral mimicry responses. SETD2 encodes a histone methyltransferase (H3K36me3) and is prevalently mutated in advanced kidney cancers. Here, we show that SETD2-mutant kidney cancer cells are especially sensitive in vitro and in vivo to DAC treatment. We find that the viral mimicry response are direct consequences of mis-splicing events, such as exon inclusions or extensions, triggered by DAC treatment in an SETD2-loss context. Comprehensive epigenomic analysis reveals H3K9me3 deposition, rather than DNA methylation dynamics, across intronic TEs might contribute to elevated mis-splicing rates. Through epigenomic and transcriptomic analyses, we show that SETD2-deficient kidney cancers are prone to mis-splicing, which can be therapeutically exacerbated with DAC treatment to increase viral mimicry activation and provide synergy with combinatorial immunotherapy approaches.
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Affiliation(s)
- Hong-Tao Li
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - H Josh Jang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Krizia Rohena-Rivera
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Minmin Liu
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Hemant Gujar
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Justin Kulchycki
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Shuqing Zhao
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Sandrin Billet
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Xinyi Zhou
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Inderbir Gill
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter A Jones
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
| | - Neil A Bhowmick
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; VA Greater Los Angeles Healthcare System, Los Angeles, CA 90073, USA.
| | - Gangning Liang
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA.
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17
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Sae-Lee C, Barrow TM, Colicino E, Choi SH, Rabanal-Ruiz Y, Green D, Korolchuk VI, Mathers JC, Byun HM. Genomic targets and selective inhibition of DNA methyltransferase isoforms. Clin Epigenetics 2022; 14:103. [PMID: 35987848 PMCID: PMC9392947 DOI: 10.1186/s13148-022-01325-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background DNA methylation in the human genome is established and maintained by DNA methyltransferases (DNMTs). DNMT isoforms show differential expression by cell lineage and during development, but much remains to be elucidated about their shared and unique genomic targets. Results We examined changes in the epigenome following overexpression of 13 DNMT isoforms in HEK293T cells. We observed increased methylation (Δβ > 0.2) at 43,405 CpG sites, with expression of DNMT3A2, DNMTΔ3B4 and DNMTΔ3B2 associated with the greatest impact. De novo methylation occurred primarily within open sea regions and at loci with intermediate methylation levels (β: 0.2–0.6). 53% of differentially methylated loci showed specificity towards a single DNMT subfamily, primarily DNMTΔ3B and DNMT3A and 39% towards a single isoform. These loci were significantly enriched for pathways related to neuronal development (DNMTΔ3B4), calcium homeostasis (DNMTΔ3B3) and ion transport (DNMT3L). Repetitive elements did not display differential sensitivity to overexpressed DNMTs, but hypermethylation of Alu elements was associated with their evolutionary age following overexpression of DNMT3A2, DNMT3B1, DNMT3B2 and DNMT3L. Differential methylation (Δβ > 0.1) was observed at 121 of the 353 loci associated with the Horvath ‘epigenetic clock’ model of ageing, with 51 showing isoform specificity, and was associated with reduction of epigenetic age by 5–15 years following overexpression of seven isoforms. Finally, we demonstrate the potential for dietary constituents to modify epigenetic marks through isoform-specific inhibition of methylation activity. Conclusions Our results provide insight into regions of the genome methylated uniquely by specific DNMT isoforms and demonstrate the potential for dietary intervention to modify the epigenome. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01325-4.
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18
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Li W, Gao R, Ding Y, Chen X, Liu X, He J, Li F, Long J, Lu S, Yang C, Wang Y. Imbalance hepatic metabolism homeostasis in the F1 generation of endometrial DNMT3B conditional knockout female mice. Front Physiol 2022; 13:1042449. [PMCID: PMC9692016 DOI: 10.3389/fphys.2022.1042449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous studies have suggested the possibility of explaining the etiology of metabolic syndrome through DNA methylation. DNA methyltransferase 3B (DNMT3B) plays an important role in de novo DNA methylation. There was an alteration in maternal (F0) endometrial function, which might lead to growth and developmental disorder in offspring (F1). In this study, we investigated the effect of maternal endometrial DNMT3B deficiency on the metabolism in offspring. We constructed endometrial DNMT3B conditional knockout female mice (cKO) which were mated with normal C57BL/6 male mice to obtain the F1 generation. Further, to study the development of these offspring, we observed them at three different life stages which included the 6-week-old juvenile, 9-week-old sub-adult and 12-week-old adult. Follow the detection of a range of metabolism-related indicators, we found that in the cKO F1 generation, liver triglyceride level was significantly elevated in 9-week-old female mice, lipid droplet deposition was significantly increased in 9-week-old and 12-week-old mice, and the expression of lipid metabolism key factors in the liver was markedly decreased except of 6-week-old male mice. These results indicate that maternal endometrial DNMT3B conditional knockout leads to imbalance in hepatic metabolism in F1 generation, the mechanism of which requires further discussion.
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Affiliation(s)
- Weike Li
- Laboratory of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Rufei Gao
- Laboratory of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Yubin Ding
- Laboratory of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Xuemei Chen
- Laboratory of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Xueqing Liu
- Laboratory of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Junlin He
- Laboratory of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Fangfang Li
- Laboratory of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Jing Long
- Laboratory of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Siyu Lu
- Laboratory of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Chengshun Yang
- Laboratory of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
- *Correspondence: Chengshun Yang, ; Yingxiong Wang,
| | - Yingxiong Wang
- Laboratory of Reproductive Biology, School of Public Health, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
- *Correspondence: Chengshun Yang, ; Yingxiong Wang,
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Du W, Shi G, Shan CM, Li Z, Zhu B, Jia S, Li Q, Zhang Z. Mechanisms of chromatin-based epigenetic inheritance. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2162-2190. [PMID: 35792957 DOI: 10.1007/s11427-022-2120-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Multi-cellular organisms such as humans contain hundreds of cell types that share the same genetic information (DNA sequences), and yet have different cellular traits and functions. While how genetic information is passed through generations has been extensively characterized, it remains largely obscure how epigenetic information encoded by chromatin regulates the passage of certain traits, gene expression states and cell identity during mitotic cell divisions, and even through meiosis. In this review, we will summarize the recent advances on molecular mechanisms of epigenetic inheritance, discuss the potential impacts of epigenetic inheritance during normal development and in some disease conditions, and outline future research directions for this challenging, but exciting field.
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Affiliation(s)
- Wenlong Du
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guojun Shi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Chun-Min Shan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhiming Li
- Institutes of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Songtao Jia
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Zhiguo Zhang
- Institutes of Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, 10032, USA.
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20
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Expression of DNA Methyltransferase 3B Isoforms Is Associated with DNA Satellite 2 Hypomethylation and Clinical Prognosis in Advanced High-Grade Serous Ovarian Carcinoma. Int J Mol Sci 2022; 23:ijms232112759. [PMID: 36361550 PMCID: PMC9654283 DOI: 10.3390/ijms232112759] [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: 08/19/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022] Open
Abstract
Alterations in DNA methylation are critical for the carcinogenesis of ovarian tumors, especially ovarian carcinoma (OC). DNMT3B, a de novo DNA methyltransferase (DNMT), encodes for fifteen spliced protein products or isoforms. DNMT3B isoforms lack exons for the catalytic domain, with functional consequences on catalytic activity. Abnormal expression of DNMT3B isoforms is frequently observed in several types of cancer, such as breast, lung, kidney, gastric, liver, skin, leukemia, and sarcoma. However, the expression patterns and consequences of DNMT3B isoforms in OC are unknown. In this study, we analyzed each DNMT and DNMT3B isoforms expression by qPCR in 63 OC samples and their association with disease-free survival (DFS), overall survival (OS), and tumor progression. We included OC patients with the main histological subtypes of EOC and patients in all the disease stages and found that DNMTs were overexpressed in advanced stages (p-value < 0.05) and high-grade OC (p-value < 0.05). Remarkably, we found DNMT3B1 overexpression in advanced stages (p-value = 0.0251) and high-grade serous ovarian carcinoma (HGSOC) (p-value = 0.0313), and DNMT3B3 was overexpressed in advanced stages (p-value = 0.0098) and high-grade (p-value = 0.0004) serous ovarian carcinoma (SOC). Finally, we observed that overexpression of DNMT3B isoforms was associated with poor prognosis in OC and SOC. DNMT3B3 was also associated with FDS (p-value = 0.017) and OS (p-value = 0.038) in SOC patients. In addition, the ovarian carcinoma cell lines OVCAR3 and SKOV3 also overexpress DNMT3B3. Interestingly, exogenous overexpression of DNMT3B3 in OVCAR3 causes demethylation of satellite 2 sequences in the pericentromeric region. In summary, our results suggest that DNMT3B3 expression is altered in OC.
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21
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DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon. Nat Commun 2022; 13:6266. [PMID: 36271073 PMCID: PMC9587301 DOI: 10.1038/s41467-022-33844-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 10/05/2022] [Indexed: 12/25/2022] Open
Abstract
Genetic variants in the DNA methyltransferase 3 A (DNMT3A) locus have been associated with inflammatory bowel disease (IBD). DNMT3A is part of the epigenetic machinery physiologically involved in DNA methylation. We show that DNMT3A plays a critical role in maintaining intestinal homeostasis and gut barrier function. DNMT3A expression is downregulated in intestinal epithelial cells from IBD patients and upon tumor necrosis factor treatment in murine intestinal organoids. Ablation of DNMT3A in Caco-2 cells results in global DNA hypomethylation, which is linked to impaired regenerative capacity, transepithelial resistance and intercellular junction formation. Genetic deletion of Dnmt3a in intestinal epithelial cells (Dnmt3aΔIEC) in mice confirms the phenotype of an altered epithelial ultrastructure with shortened apical-junctional complexes, reduced Goblet cell numbers and increased intestinal permeability in the colon in vivo. Dnmt3aΔIEC mice suffer from increased susceptibility to experimental colitis, characterized by reduced epithelial regeneration. These data demonstrate a critical role for DNMT3A in orchestrating intestinal epithelial homeostasis and response to tissue damage and suggest an involvement of impaired epithelial DNMT3A function in the etiology of IBD.
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22
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Chromosome-specific retention of cancer-associated DNA hypermethylation following pharmacological inhibition of DNMT1. Commun Biol 2022; 5:528. [PMID: 35654826 PMCID: PMC9163065 DOI: 10.1038/s42003-022-03509-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/20/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractThe DNA methylation status of the X-chromosome in cancer cells is often overlooked because of computational difficulties. Most of the CpG islands on the X-chromosome are mono-allelically methylated in normal female cells and only present as a single copy in male cells. We treated two colorectal cancer cell lines from a male (HCT116) and a female (RKO) with increasing doses of a DNA methyltransferase 1 (DNMT1)-specific inhibitor (GSK3685032/GSK5032) over several months to remove as much non-essential CpG methylation as possible. Profiling of the remaining DNA methylome revealed an unexpected, enriched retention of DNA methylation on the X-chromosome. Strikingly, the identified retained X-chromosome DNA methylation patterns accurately predicted de novo DNA hypermethylation in colon cancer patient methylomes in the TCGA COAD/READ cohort. These results suggest that a re-examination of tumors for X-linked DNA methylation changes may enable greater understanding of the importance of epigenetic silencing of cancer related genes.
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23
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Fagg WS, Liu N, Braunschweig U, Pereira de Castro K, Chen X, Ditmars F, Widen S, Donohue JP, Modis K, Russell W, Fair JH, Weirauch M, Blencowe B, Garcia-Blanco M. Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate. Nucleic Acids Res 2022; 50:5313-5334. [PMID: 35544276 PMCID: PMC9122611 DOI: 10.1093/nar/gkac327] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/14/2022] [Accepted: 04/25/2022] [Indexed: 01/27/2023] Open
Abstract
Alternative splicing is critical for development; however, its role in the specification of the three embryonic germ layers is poorly understood. By performing RNA-Seq on human embryonic stem cells (hESCs) and derived definitive endoderm, cardiac mesoderm, and ectoderm cell lineages, we detect distinct alternative splicing programs associated with each lineage. The most prominent splicing program differences are observed between definitive endoderm and cardiac mesoderm. Integrative multi-omics analyses link each program with lineage-enriched RNA binding protein regulators, and further suggest a widespread role for Quaking (QKI) in the specification of cardiac mesoderm. Remarkably, knockout of QKI disrupts the cardiac mesoderm-associated alternative splicing program and formation of myocytes. These changes arise in part through reduced expression of BIN1 splice variants linked to cardiac development. Mechanistically, we find that QKI represses inclusion of exon 7 in BIN1 pre-mRNA via an exonic ACUAA motif, and this is concomitant with intron removal and cleavage from chromatin. Collectively, our results uncover alternative splicing programs associated with the three germ lineages and demonstrate an important role for QKI in the formation of cardiac mesoderm.
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Affiliation(s)
- W Samuel Fagg
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Naiyou Liu
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | | | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Frederick S Ditmars
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - John Paul Donohue
- Sinsheimer Labs, RNA Center for Molecular Biology, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Katalin Modis
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jeffrey H Fair
- Department of Surgery, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ONM5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, ONM5S 1A8, Canada
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
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DNMT1 regulates the timing of DNA methylation by DNMT3 in an enzymatic activity-dependent manner in mouse embryonic stem cells. PLoS One 2022; 17:e0262277. [PMID: 34986190 PMCID: PMC8730390 DOI: 10.1371/journal.pone.0262277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/21/2021] [Indexed: 01/01/2023] Open
Abstract
DNA methylation (DNAme; 5-methylcytosine, 5mC) plays an essential role in mammalian development, and the 5mC profile is regulated by a balance of opposing enzymatic activities: DNA methyltransferases (DNMTs) and Ten-eleven translocation dioxygenases (TETs). In mouse embryonic stem cells (ESCs), de novo DNAme by DNMT3 family enzymes, demethylation by the TET-mediated conversion of 5mC to 5-hydroxymethylation (5hmC), and maintenance of the remaining DNAme by DNMT1 are actively repeated throughout cell cycles, dynamically forming a constant 5mC profile. Nevertheless, the detailed mechanism and physiological significance of this active cyclic DNA modification in mouse ESCs remain unclear. Here by visualizing the localization of DNA modifications on metaphase chromosomes and comparing whole-genome methylation profiles before and after the mid-S phase in ESCs lacking Dnmt1 (1KO ESCs), we demonstrated that in 1KO ESCs, DNMT3-mediated remethylation was interrupted during and after DNA replication. This results in a marked asymmetry in the distribution of 5hmC between sister chromatids at mitosis, with one chromatid being almost no 5hmC. When introduced in 1KO ESCs, the catalytically inactive form of DNMT1 (DNMT1CI) induced an increase in DNAme in pericentric heterochromatin and the DNAme-independent repression of IAPEz, a retrotransposon family, in 1KO ESCs. However, DNMT1CI could not restore the ability of DNMT3 to methylate unmodified dsDNA de novo in S phase in 1KO ESCs. Furthermore, during in vitro differentiation into epiblasts, 1KO ESCs expressing DNMT1CI showed an even stronger tendency to differentiate into the primitive endoderm than 1KO ESCs and were readily reprogrammed into the primitive streak via an epiblast-like cell state, reconfirming the importance of DNMT1 enzymatic activity at the onset of epiblast differentiation. These results indicate a novel function of DNMT1, in which DNMT1 actively regulates the timing and genomic targets of de novo methylation by DNMT3 in an enzymatic activity-dependent and independent manner, respectively.
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25
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Tajima S, Suetake I, Takeshita K, Nakagawa A, Kimura H, Song J. Domain Structure of the Dnmt1, Dnmt3a, and Dnmt3b DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:45-68. [PMID: 36350506 PMCID: PMC11025882 DOI: 10.1007/978-3-031-11454-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In mammals, three major DNA methyltransferases, Dnmt1, Dnmt3a, and Dnmt3b, have been identified. Dnmt3a and Dnmt3b are responsible for establishing DNA methylation patterns produced through their de novo-type DNA methylation activity in implantation stage embryos and during germ cell differentiation. Dnmt3-like (Dnmt3l), which is a member of the Dnmt3 family but does not possess DNA methylation activity, was reported to be indispensable for global methylation in germ cells. Once the DNA methylation patterns are established, maintenance-type DNA methyltransferase Dnmt1 faithfully propagates them to the next generation via replication. All Dnmts possess multiple domains. For instance, Dnmt3a and Dnmt3b each contain a Pro-Trp-Trp-Pro (PWWP) domain that recognizes the histone H3K36me2/3 mark, an Atrx-Dnmt3-Dnmt3l (ADD) domain that recognizes unmodified histone H3 tail, and a catalytic domain that methylates CpG sites. Dnmt1 contains an N-terminal independently folded domain (NTD) that interacts with a variety of regulatory factors, a replication foci-targeting sequence (RFTS) domain that recognizes the histone H3K9me3 mark and H3 ubiquitylation, a CXXC domain that recognizes unmodified CpG DNA, two tandem Bromo-Adjacent-homology (BAH1 and BAH2) domains that read the H4K20me3 mark with BAH1, and a catalytic domain that preferentially methylates hemimethylated CpG sites. In this chapter, the structures and functions of these domains are described.
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Affiliation(s)
- Shoji Tajima
- Institute for Protein Research, Osaka University, Osaka, Japan.
| | - Isao Suetake
- Department of Nutritional Sciences, Faculty of Nutritional Sciences, Nakamura Gakuen University, Fukuoka, Japan
| | | | - Atsushi Nakagawa
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hironobu Kimura
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Jikui Song
- Department of Biochemistry, University of California Riverside, Riverside, CA, USA.
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26
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Wedd L, Kucharski R, Maleszka R. DNA Methylation in Honey Bees and the Unresolved Questions in Insect Methylomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:159-176. [DOI: 10.1007/978-3-031-11454-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Recent Advances on DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:295-315. [DOI: 10.1007/978-3-031-11454-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:111-136. [PMID: 36350508 PMCID: PMC9815518 DOI: 10.1007/978-3-031-11454-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cytosine methylation at the C5-position-generating 5-methylcytosine (5mC)-is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80%) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation and genetic alterations in enzymes and regulators involved in DNA methylation are associated with various human diseases, including cancer and developmental disorders. In mammals, DNA methylation is mediated by two families of DNA methyltransferases (Dnmts), namely Dnmt1 and Dnmt3 proteins. Over the last three decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and human diseases.
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The Role of DNA Methylation and DNA Methyltransferases in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:317-348. [DOI: 10.1007/978-3-031-11454-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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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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31
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Farah E, Zhang Z, Utturkar SM, Liu J, Ratliff TL, Liu X. Targeting DNMTs to overcome enzalutamide resistance in prostate cancer. Mol Cancer Ther 2021; 21:193-205. [PMID: 34728570 DOI: 10.1158/1535-7163.mct-21-0581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/22/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022]
Abstract
Prostate cancer is the second leading cause of cancer death among men in the United States. The androgen receptor (AR) antagonist enzalutamide is a FDA-approved drug for treatment of patients with late-stage prostate cancer and is currently under clinical study for early-stage prostate cancer treatment. After a short positive response period to enzalutamide, tumors will develop drug resistance. In this study, we uncovered that DNA methylation was deregulated in enzalutamide-resistant cells. DNMT activity and DNMT3B expression were upregulated in resistant cell lines. Enzalutamide induced the expression of DNMT3A and DNMT3B in prostate cancer cells with a potential role of p53 and pRB in this process. The overexpression of DNMT3B3, a DNMT3B variant, promoted an enzalutamide-resistant phenotype in C4-2B cell lines. Inhibition of DNA methylation and DNMT3B knockdown induced a re-sensitization to enzalutamide. Decitabine treatment in enzalutamide-resistant cells induced a decrease of the expression of AR-V7 and changes of genes for apoptosis, DNA repair and mRNA splicing. Combination treatment of Decitabine and enzalutamide induced a decrease of tumor weight, Ki-67 and AR-V7 expression and an increase of cleaved-caspase3 levels in 22Rv1 xenografts. The collective results suggest that DNA methylation pathway is deregulated after enzalutamide resistance onset and that targeting DNA methyltransferases restores the sensitivity to enzalutamide in prostate cancer cells.
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Affiliation(s)
| | | | - Sagar M Utturkar
- Purdue University Center for Cancer Research, Purdue University West Lafayette
| | - Jinpeng Liu
- Markey Cancer Center, Department of Biostatistics, University of Kentucky
| | - Timothy L Ratliff
- Comparative Pathobiology and the Center for Cancer Research, Purdue University West Lafayette
| | - Xiaoqi Liu
- Department of Toxicology and Cancer Biology, University of Kentucky
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32
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Xiao C, Fan T, Tian H, Zheng Y, Zhou Z, Li S, Li C, He J. H3K36 trimethylation-mediated biological functions in cancer. Clin Epigenetics 2021; 13:199. [PMID: 34715919 PMCID: PMC8555273 DOI: 10.1186/s13148-021-01187-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
Histone modification is an important form of epigenetic regulation. Thereinto, histone methylation is a critical determination of chromatin states, participating in multiple cellular processes. As a conserved histone methylation mark, histone 3 lysine 36 trimethylation (H3K36me3) can mediate multiple transcriptional-related events, such as the regulation of transcriptional activity, transcription elongation, pre-mRNA alternative splicing, and RNA m6A methylation. Additionally, H3K36me3 also contributes to DNA damage repair. Given the crucial function of H3K36me3 in genome regulation, the roles of H3K36me3 and its sole methyltransferase SETD2 in pathogenesis, especially malignancies, have been emphasized in many studies, and it is conceivable that disruption of histone methylation regulatory network composed of "writer", "eraser", "reader", and the mutation of H3K36me3 codes have the capacity of powerfully modulating cancer initiation and development. Here we review H3K36me3-mediated biological processes and summarize the latest findings regarding its role in cancers. We highlight the significance of epigenetic combination therapies in cancers.
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Affiliation(s)
- Chu Xiao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tao Fan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - He Tian
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yujia Zheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zheng Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shuofeng Li
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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33
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Venney D, Mohd-Sarip A, Mills KI. The Impact of Epigenetic Modifications in Myeloid Malignancies. Int J Mol Sci 2021; 22:5013. [PMID: 34065087 PMCID: PMC8125972 DOI: 10.3390/ijms22095013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Myeloid malignancy is a broad term encapsulating myeloproliferative neoplasms (MPN), myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML). Initial studies into genomic profiles of these diseases have shown 2000 somatic mutations prevalent across the spectrum of myeloid blood disorders. Epigenetic mutations are emerging as critical components of disease progression, with mutations in genes controlling chromatin regulation and methylation/acetylation status. Genes such as DNA methyltransferase 3A (DNMT3A), ten eleven translocation methylcytosine dioxygenase 2 (TET2), additional sex combs-like 1 (ASXL1), enhancer of zeste homolog 2 (EZH2) and isocitrate dehydrogenase 1/2 (IDH1/2) show functional impact in disease pathogenesis. In this review we discuss how current knowledge relating to disease progression, mutational profile and therapeutic potential is progressing and increasing understanding of myeloid malignancies.
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Affiliation(s)
| | | | - Ken I Mills
- Patrick G Johnston Center for Cancer Research, Queens University Belfast, 97 Lisburn Road, Belfast BT9 7AE, UK; (D.V.); (A.M.-S.)
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Li Y, Chen X, Lu C. The interplay between DNA and histone methylation: molecular mechanisms and disease implications. EMBO Rep 2021; 22:e51803. [PMID: 33844406 PMCID: PMC8097341 DOI: 10.15252/embr.202051803] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/16/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
Methylation of cytosine in CpG dinucleotides and histone lysine and arginine residues is a chromatin modification that critically contributes to the regulation of genome integrity, replication, and accessibility. A strong correlation exists between the genome-wide distribution of DNA and histone methylation, suggesting an intimate relationship between these epigenetic marks. Indeed, accumulating literature reveals complex mechanisms underlying the molecular crosstalk between DNA and histone methylation. These in vitro and in vivo discoveries are further supported by the finding that genes encoding DNA- and histone-modifying enzymes are often mutated in overlapping human diseases. Here, we summarize recent advances in understanding how DNA and histone methylation cooperate to maintain the cellular epigenomic landscape. We will also discuss the potential implication of these insights for understanding the etiology of, and developing biomarkers and therapies for, human congenital disorders and cancers that are driven by chromatin abnormalities.
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Affiliation(s)
- Yinglu Li
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Xiao Chen
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
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35
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Qin L, Qiao C, Sheen V, Wang Y, Lu J. DNMT3L promotes neural differentiation by enhancing STAT1 and STAT3 phosphorylation independent of DNA methylation. Prog Neurobiol 2021; 201:102028. [PMID: 33636226 DOI: 10.1016/j.pneurobio.2021.102028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/10/2021] [Accepted: 02/21/2021] [Indexed: 01/13/2023]
Abstract
Previously, we reported global hypermethylation in DS might be attributed to the overexpression of HSA21 gene DNMT3L, which can enhance DNMT3A and DNMT3B activities in DNA methylation. To test this hypothesis, we compared the DNA methylation and RNA expression profiles of early-differentiated human neuroprogenitors with and without DNMT3L overexpression. We found DNMT3L overexpression only moderately increased the DNA methylation of limited genes, yet significantly altered global RNA expression of genes involved in neural differentiation. We further found that DNMT3L bound STAT1 or STAT3, and increased its phosphorylation and nuclear translocation, which in turn activated the expression of transcription factors including HES3, ASCL1, NEUROD2 and NEUROG2 and CDK inhibitor CDKN1A, which promoted cell cycle exit and neural differentiation. This phenomenon was also confirmed in Dnmt3l conditional knockin mice, which could be rescued by STAT1 and STAT3 phosphorylation inhibitors (Fludarabine and SH-4-54) but not DNA methylation inhibitor (Decitabine). These results suggest that DNMT3L play an important role during neurodevelopment independent of DNA methylation, which may contribute to the abnormal phenotypes observed in Down syndrome cortex.
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Affiliation(s)
- Lin Qin
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, 110122, China; Department of Obstetrics & Gynecology, Shenyang Women & Children's Hospital, Shenyang, Liaoning Province, 110121, China.
| | - Chong Qiao
- Department of Obstetrics & Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, 110004, China.
| | - Volney Sheen
- Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA.
| | - Yu Wang
- Department of Obstetrics & Gynecology, Shenyang Women & Children's Hospital, Shenyang, Liaoning Province, 110121, China.
| | - Jie Lu
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, Shenyang, Liaoning Province, 110122, China.
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Masalmeh RHA, Taglini F, Rubio-Ramon C, Musialik KI, Higham J, Davidson-Smith H, Kafetzopoulos I, Pawlicka KP, Finan HM, Clark R, Wills J, Finch AJ, Murphy L, Sproul D. De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG islands. Nat Commun 2021; 12:694. [PMID: 33514701 PMCID: PMC7846778 DOI: 10.1038/s41467-020-20716-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
The aberrant gain of DNA methylation at CpG islands is frequently observed in colorectal tumours and may silence the expression of tumour suppressors such as MLH1. Current models propose that these CpG islands are targeted by de novo DNA methyltransferases in a sequence-specific manner, but this has not been tested. Using ectopically integrated CpG islands, here we find that aberrantly methylated CpG islands are subject to low levels of de novo DNA methylation activity in colorectal cancer cells. By delineating DNA methyltransferase targets, we find that instead de novo DNA methylation activity is targeted primarily to CpG islands marked by the histone modification H3K36me3, a mark associated with transcriptional elongation. These H3K36me3 marked CpG islands are heavily methylated in colorectal tumours and the normal colon suggesting that de novo DNA methyltransferase activity at CpG islands in colorectal cancer is focused on similar targets to normal tissues and not greatly remodelled by tumourigenesis.
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Affiliation(s)
| | - Francesca Taglini
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Cristina Rubio-Ramon
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Kamila I Musialik
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Jonathan Higham
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | | | - Ioannis Kafetzopoulos
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Kamila P Pawlicka
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Hannah M Finan
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Richard Clark
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Jimi Wills
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
| | - Andrew J Finch
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Duncan Sproul
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, IGMM, University of Edinburgh, Edinburgh, UK.
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Venugopal K, Feng Y, Shabashvili D, Guryanova OA. Alterations to DNMT3A in Hematologic Malignancies. Cancer Res 2021; 81:254-263. [PMID: 33087320 PMCID: PMC7855745 DOI: 10.1158/0008-5472.can-20-3033] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
In the last decade, large-scale genomic studies in patients with hematologic malignancies identified recurrent somatic alterations in epigenetic modifier genes. Among these, the de novo DNA methyltransferase DNMT3A has emerged as one of the most frequently mutated genes in adult myeloid as well as lymphoid malignancies and in clonal hematopoiesis. In this review, we discuss recent advances in our understanding of the biochemical and structural consequences of DNMT3A mutations on DNA methylation catalysis and binding interactions and summarize their effects on epigenetic patterns and gene expression changes implicated in the pathogenesis of hematologic malignancies. We then review the role played by mutant DNMT3A in clonal hematopoiesis, accompanied by its effect on immune cell function and inflammatory responses. Finally, we discuss how this knowledge informs therapeutic approaches for hematologic malignancies with mutant DNMT3A.
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Affiliation(s)
- Kartika Venugopal
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida
| | - Yang Feng
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida
| | - Daniil Shabashvili
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida
| | - Olga A Guryanova
- Department of Pharmacology and Therapeutics, University of Florida (UF) College of Medicine, Gainesville, Florida.
- University of Florida Health Cancer Center, Gainesville, Florida
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38
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Mallona I, Ilie IM, Karemaker ID, Butz S, Manzo M, Caflisch A, Baubec T. Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Res 2021; 49:145-157. [PMID: 33290556 PMCID: PMC7797059 DOI: 10.1093/nar/gkaa1168] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/22/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Mammalian de novo DNA methyltransferases (DNMT) are responsible for the establishment of cell-type-specific DNA methylation in healthy and diseased tissues. Through genome-wide analysis of de novo methylation activity in murine stem cells we uncover that DNMT3A prefers to methylate CpGs followed by cytosines or thymines, while DNMT3B predominantly methylates CpGs followed by guanines or adenines. These signatures are further observed at non-CpG sites, resembling methylation context observed in specialised cell types, including neurons and oocytes. We further show that these preferences result from structural differences in the catalytic domains of the two de novo DNMTs and are not a consequence of differential recruitment to the genome. Molecular dynamics simulations suggest that, in case of human DNMT3A, the preference is due to favourable polar interactions between the flexible Arg836 side chain and the guanine that base-pairs with the cytosine following the CpG. By exchanging arginine to a lysine, the corresponding side chain in DNMT3B, the sequence preference is reversed, confirming the requirement for arginine at this position. This context-dependent enzymatic activity provides additional insights into the complex regulation of DNA methylation patterns.
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Affiliation(s)
- Izaskun Mallona
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich 8057, Switzerland
- SIB Swiss Institute of Bioinformatics, Zurich 8057, Switzerland
| | - Ioana Mariuca Ilie
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Ino Dominiek Karemaker
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
| | - Stefan Butz
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Massimiliano Manzo
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
- Life Science Zurich Graduate School, University of Zurich, Zurich 8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich 8057, Switzerland
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Lopusna K, Nowialis P, Opavska J, Abraham A, Riva A, Opavsky R. Dnmt3b catalytic activity is critical for its tumour suppressor function in lymphomagenesis and is associated with c-Met oncogenic signalling. EBioMedicine 2021; 63:103191. [PMID: 33418509 PMCID: PMC7804970 DOI: 10.1016/j.ebiom.2020.103191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND DNA methylation regulates gene transcription in many physiological processes in mammals including development and haematopoiesis. It is catalysed by several DNA methyltransferases, including Dnmt3b that mediates both methylation-dependant and independent gene repression. Dnmt3b is critical for mouse embryogenesis and functions as a tumour suppressor in haematologic malignancies in mice. However, the extent to which Dnmt3b's catalytic activity (CA) is involved in development and cancer is unclear. METHODS We used a mouse model expressing catalytically inactive Dnmt3b (Dnmt3bCI) to study a role of Dnmt3b's CA in development and cancer. We utilized global approaches including Whole-genome Bisulfite sequencing and RNA-seq to analyse DNA methylation and gene expression to identify putative targets of Dnmt3b's CA. To analyse postnatal development and haematopoiesis, we used tissue staining, histological and FACS analysis. To determine potential involvement of selected genes in lymphomagenesis, we used overexpression and knock down approaches followed by in vitro growth assays. FINDINGS We show that mice expressing Dnmt3bCI only, survive postnatal development and develop ICF (the immunodeficiency-centromeric instability-facial anomalies) -like syndrome. The lack of Dnmt3b's CA promoted fibroblasts transformation in vitro, accelerated MLL-AF9 driven Acute Myeloid Leukaemia and MYC-induced T-cell lymphomagenesis in vivo. The elimination of Dnmt3b's CA resulted in decreased methylation of c-Met promoter and its upregulation, activated oncogenic Met signalling, Stat3 phosphorylation and up-regulation of Lin28b promoting lymphomagenesis. INTERPRETATION Our data demonstrates that Dnmt3b's CA is largely dispensable for mouse development but critical to prevent tumourigenesis by controlling events involved in cellular transformation. FUNDING This study was supported by Department of Anatomy and Cell Biology and Cancer Centre at the University of Florida start-up funds, NIH/NCI grant 1R01CA188561-01A1 (R.O.).
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Affiliation(s)
- Katarina Lopusna
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States
| | - Pawel Nowialis
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States
| | - Jana Opavska
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States
| | - Ajay Abraham
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States
| | - Alberto Riva
- ICBR Bioinformatics, Cancer and Genetics Research Complex, University of Florida, P.O. Box 103622. Gainesville, FL 32610, United States
| | - Rene Opavsky
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, 2033 Mowry Rd, CGRC 258, Gainesville, FL 32610, United States.
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Abstract
Methylation of DNA at cytosine bases is an important DNA modification underlying normal development and disease states. Despite decades of research into the biological function of DNA methylation, most of the observations so far have relied primarily on associative data between observed changes in DNA methylation states and local changes in transcriptional activity or chromatin state processes. This is primarily due to the lack of molecular tools to precisely modify DNA methylation in the genome. Recent advances in genome editing technologies have allowed repurposing the CRISPR-Cas9 system for epigenome editing by fusing the catalytically dead Cas9 (dCas9) to epigenome modifying enzymes. Moreover, methods of recruiting multiple protein domains, including the SunTag system, have increased the efficacy of epigenome editing at target sites. Here, we describe an end-to-end protocol for efficient targeted removal of DNA methylation by recruiting multiple catalytic domain of TET1 enzymes to the target sites with the dCas9-SunTag system, including sgRNA design, molecular cloning, delivery of plasmid into mammalian cells, and targeted DNA methylation analysis.
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Affiliation(s)
- Trung Viet Nguyen
- ARC Center of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
- The Harry Perkins Institute of Medical Research, Perth, WA, Australia
| | - Ryan Lister
- ARC Center of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.
- The Harry Perkins Institute of Medical Research, Perth, WA, Australia.
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41
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Lopusna K, Nowialis P, Opavska J, Abraham A, Riva A, Haney SL, Opavsky R. Decreases in different Dnmt3b activities drive distinct development of hematologic malignancies in mice. J Biol Chem 2021; 296:100285. [PMID: 33450231 PMCID: PMC7949038 DOI: 10.1016/j.jbc.2021.100285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 12/20/2022] Open
Abstract
DNA methylation regulates gene transcription and is involved in various physiological processes in mammals, including development and hematopoiesis. It is catalyzed by DNA methyltransferases including Dnmt1, Dnmt3a, and Dnmt3b. For Dnmt3b, its effects on transcription can result from its own DNA methylase activity, the recruitment of other Dnmts to mediate methylation, or transcription repression in a methylation-independent manner. Low-frequency mutations in human DNMT3B are found in hematologic malignancies including cutaneous T-cell lymphomas, hairy cell leukemia, and diffuse large B-cell lymphomas. Moreover, Dnmt3b is a tumor suppressor in oncogene-driven lymphoid and myeloid malignancies in mice. However, it is poorly understood how the different Dnmt3b activities contribute to these outcomes. We modulated Dnmt3b activity in vivo by generating Dnmt3b+/- mice expressing one wild-type allele as well as Dnmt3b+/CI and Dnmt3bCI/CI mice where one or both alleles express catalytically inactive Dnmt3bCI. We show that 43% of Dnmt3b+/- mice developed T-cell lymphomas, chronic lymphocytic leukemia, and myeloproliferation over 18 months, thus resembling phenotypes previously observed in Dnmt3a+/- mice, possibly through regulation of shared target genes. Interestingly, Dnmt3b+/CI and Dnmt3bCI/CI mice survived postnatal development and were affected by B-cell rather than T-cell malignancies with decreased penetrance. Genome-wide hypomethylation, increased expression of oncogenes such as Jdp2, STAT1, and Trip13, and p53 downregulation were major events contributing to Dnmt3b+/- lymphoma development. We conclude that Dnmt3b catalytic activity is critical to prevent B-cell transformation in vivo, whereas accessory and methylation-independent repressive functions are important to prevent T-cell transformation.
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MESH Headings
- ATPases Associated with Diverse Cellular Activities/genetics
- ATPases Associated with Diverse Cellular Activities/metabolism
- Animals
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- DNA (Cytosine-5-)-Methyltransferases/deficiency
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA Methylation
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Heterozygote
- Homozygote
- Humans
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/enzymology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, B-Cell/enzymology
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/pathology
- Lymphoma, T-Cell/enzymology
- Lymphoma, T-Cell/genetics
- Lymphoma, T-Cell/pathology
- Male
- Mice
- Mice, Knockout
- Myeloproliferative Disorders/enzymology
- Myeloproliferative Disorders/genetics
- Myeloproliferative Disorders/pathology
- Neoplasms, Experimental/enzymology
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/pathology
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- STAT1 Transcription Factor/genetics
- STAT1 Transcription Factor/metabolism
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- DNA Methyltransferase 3B
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Affiliation(s)
- Katarina Lopusna
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Pawel Nowialis
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Jana Opavska
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Ajay Abraham
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Alberto Riva
- ICBR Bioinformatics, Cancer and Genetics Research Complex, University of Florida, Gainesville, Florida, USA
| | - Staci L Haney
- Department of Internal Medicine, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska, USA
| | - Rene Opavsky
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, Florida, USA.
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Iguchi E, Takai A, Takeda H, Kumagai K, Arasawa S, Eso Y, Shimizu T, Ueda Y, Marusawa H, Seno H. DNA methyltransferase 3B plays a protective role against hepatocarcinogenesis caused by chronic inflammation via maintaining mitochondrial homeostasis. Sci Rep 2020; 10:21268. [PMID: 33277576 PMCID: PMC7719166 DOI: 10.1038/s41598-020-78151-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/20/2020] [Indexed: 12/24/2022] Open
Abstract
Most hepatocellular carcinomas (HCCs) develop on the basis of chronic hepatitis, but the mechanism of epigenetic regulation in inflammatory hepatocarcinogenesis has yet to be elucidated. Among de novo DNA methyltransferases (DNMTs), DNMT3B has lately been reported to act specifically on actively transcribed genes, suggesting the possibility that it plays a role in the pathogenesis of cancer. We confirmed that DNMT3B isoforms lacking its catalytic domain were highly expressed in HCCs compared with non-tumorous liver tissue. To elucidate the role of DNMT3B in hepatocarcinogenesis, we generated a genetically engineered mouse model with hepatocyte-specific Dnmt3b deletion. The liver of the Dnmt3b-deficient mice exhibited an exacerbation of thioacetamide-induced hepatitis, progression of liver fibrosis and a higher incidence of HCC compared with the liver of the control mice. Whole-genome bisulfite sequencing verified a lower CG methylation level in the Dnmt3b-deficient liver, demonstrating differentially methylated regions throughout the genome. Transcriptome analysis revealed decreased expression of genes related to oxidative phosphorylation in the Dnmt3b-deficient liver. Moreover, primary hepatocytes isolated from the Dnmt3b-deficient mice showed reduced mitochondrial respiratory capacity, leading to the enhancement of oxidative stress in the liver tissue. Our findings suggest the protective role of DNMT3B against chronic inflammation and HCC development via maintaining mitochondrial homeostasis.
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Affiliation(s)
- Eriko Iguchi
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Atsushi Takai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Haruhiko Takeda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Ken Kumagai
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Soichi Arasawa
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Yuji Eso
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Takahiro Shimizu
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Yoshihide Ueda
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kobe University, Hyogo, Japan
| | - Hiroyuki Marusawa
- Department of Gastroenterology and Hepatology, Osaka Red Cross Hospital, Osaka, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
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43
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Zeng Y, Ren R, Kaur G, Hardikar S, Ying Z, Babcock L, Gupta E, Zhang X, Chen T, Cheng X. The inactive Dnmt3b3 isoform preferentially enhances Dnmt3b-mediated DNA methylation. Genes Dev 2020; 34:1546-1558. [PMID: 33004415 PMCID: PMC7608744 DOI: 10.1101/gad.341925.120] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022]
Abstract
The de novo DNA methyltransferases Dnmt3a and Dnmt3b play crucial roles in developmental and cellular processes. Their enzymatic activities are stimulated by a regulatory protein Dnmt3L (Dnmt3-like) in vitro. However, genetic evidence indicates that Dnmt3L functions predominantly as a regulator of Dnmt3a in germ cells. How Dnmt3a and Dnmt3b activities are regulated during embryonic development and in somatic cells remains largely unknown. Here we show that Dnmt3b3, a catalytically inactive Dnmt3b isoform expressed in differentiated cells, positively regulates de novo methylation by Dnmt3a and Dnmt3b with a preference for Dnmt3b. Dnmt3b3 is equally potent as Dnmt3L in stimulating the activities of Dnmt3a2 and Dnmt3b2 in vitro. Like Dnmt3L, Dnmt3b3 forms a complex with Dnmt3a2 with a stoichiometry of 2:2. However, rescue experiments in Dnmt3a/3b/3l triple-knockout (TKO) mouse embryonic stem cells (mESCs) reveal that Dnmt3b3 prefers Dnmt3b2 over Dnmt3a2 in remethylating genomic sequences. Dnmt3a2, an active isoform that lacks the N-terminal uncharacterized region of Dnmt3a1 including a nuclear localization signal, has very low activity in TKO mESCs, indicating that an accessory protein is absolutely required for its function. Our results suggest that Dnmt3b3 and perhaps similar Dnmt3b isoforms facilitate de novo DNA methylation during embryonic development and in somatic cells.
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Affiliation(s)
- Yang Zeng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Gundeep Kaur
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Zhengzhou Ying
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Lance Babcock
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Esha Gupta
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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de Oliveira DT, Guerra-Sá R. Uncovering epigenetic landscape: a new path for biomarkers identification and drug development. Mol Biol Rep 2020; 47:9097-9122. [PMID: 33089404 DOI: 10.1007/s11033-020-05916-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/10/2020] [Indexed: 12/31/2022]
Abstract
Scientific advances in recent decades have revealed an incredible degree of plasticity in gene expression in response to various environmental, nutritional, physiological, pathological, and behavioral conditions. Epigenetics emerges in this sense, as the link between the internal (genetic) and external (environmental) factors underlying the expression of the phenotype. Methylation of DNA and histone post-translationa modifications are canonical epigenetic events. Additionally, noncoding RNAs molecules (microRNAs and lncRNAs) have also been proposed as another layer of epigenetic regulation. Together, these events are responsible for regulating gene expression throughout life, controlling cellular fate in both normal and pathological development. Despite being a relatively recent science, epigenetics has been arousing the interest of researchers from different segments of the life sciences and the general public. This review highlights the recent advances in the characterization of the epigenetic events and points promising use of these brands for the diagnosis, prognosis, and therapy of diseases. We also present several classes of epigenetic modifying compounds with therapeutic applications (so-call epidrugs) and their current status in clinical trials and approved by the FDA. In summary, hopefully, we provide the reader with theoretical bases for a better understanding of the epigenetic mechanisms and of the promising application of these marks and events in the medical clinic.
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Affiliation(s)
- Daiane Teixeira de Oliveira
- Programa de Pós-graduação em Ciências Farmacêuticas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.
| | - Renata Guerra-Sá
- Programa de Pós-graduação em Ciências Farmacêuticas, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.,Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
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45
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Xu TH, Liu M, Zhou XE, Liang G, Zhao G, Xu HE, Melcher K, Jones PA. Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B. Nature 2020; 586:151-155. [PMID: 32968275 PMCID: PMC7540737 DOI: 10.1038/s41586-020-2747-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/30/2020] [Indexed: 12/31/2022]
Abstract
CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer1. These two DNMTs preferentially bind to nucleosomes, yet cannot methylate the DNA wrapped around the nucleosome core2, and they favour the methylation of linker DNA at positioned nucleosomes3,4. Here we present the cryo-electron microscopy structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3 and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds to the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur.
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Affiliation(s)
- Ting-Hai Xu
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Minmin Liu
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - X Edward Zhou
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA, USA
| | - Gongpu Zhao
- David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Institute, Grand Rapids, MI, USA
| | - H Eric Xu
- Center for Structure and Function of Drug Targets, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| | - Peter A Jones
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
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46
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Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY. The DNA methylation landscape of advanced prostate cancer. Nat Genet 2020; 52:778-789. [PMID: 32661416 PMCID: PMC7454228 DOI: 10.1038/s41588-020-0648-8] [Citation(s) in RCA: 183] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/20/2020] [Indexed: 02/08/2023]
Abstract
Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes only detectable with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hyper-methylation and somatic mutations in TET2, DNMT3B, IDH1, and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer and provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer.
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Affiliation(s)
- Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - William S Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Yale School of Medicine, New Haven, CT, USA
| | - Haolong Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Denise Playdle
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Rajdeep Das
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Chou
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Junjie T Hua
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Travis J Barnard
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adina M Bailey
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA
| | - Marc D Perry
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ha X Dang
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA
| | - Rendong Yang
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Ruhollah Moussavi-Baygi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - S Laura Chang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen E Houlahan
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Division of Hematology/Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Cancer Agency, Vancouver Centre, Vancouver, British Columbia, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert E Reiter
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew B Rettig
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA.,Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Owen Witte
- Department of Microbiology, Immunology, and Molecular Genetics at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - M Yvonne Kim
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hui Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Lisa Chesner
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Tanushree Shenoy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Irfan A Asangani
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Nupam P Mahajan
- Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Surgery, Washington University, St. Louis, MO, USA
| | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA.,Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA.,Department of Urologic Surgery, University of California Davis, Sacramento, CA, USA
| | | | | | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Housheng H He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC, USA
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Arul M Chinnaiyan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Biomedical Engineering, Washington University, St. Louis, MO, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. .,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California San Francisco, San Francisco, CA, USA.
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47
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Fan YL, Li B, Zhao HP, Zhao HC, Feng XQ. A function of fascin1 in the colony formation of mouse embryonic stem cells. Stem Cells 2020; 38:1078-1090. [PMID: 32379912 DOI: 10.1002/stem.3197] [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: 10/29/2019] [Accepted: 04/16/2020] [Indexed: 11/07/2022]
Abstract
Fascin1 is known to participate in the migration of cancer cells by binding to actin filaments. Recent studies evidenced that fascin1 also modulates processes such as the tumorigenesis and maintenance of pluripotency genes in cancer stem cells. However, the function of fascin1 in embryonic stem cells remains unclear. In this article, we report that fascin1 is highly expressed and widely distributed in mouse embryonic stem cells (mESCs), which are regulated by JAK-STAT3 and β-catenin. We found that the overexpression of fascin1 impairs the formation of mESC colonies via the downregulation of intercellular adhesion molecules, and that mimicking the dephosphorylated mutation of fascin1 or inhibiting phosphorylation with Gö6983 significantly enhances colony formation. Hyperphosphorylated fascin1 can promote the maintenance of pluripotency in mESCs via nuclear localization and suppressing DNA methyltransferase expression. Our findings demonstrate a novel function of fascin1, as a vital regulator, in the colony formation and pluripotency of mESCs and provide insights into the molecular mechanisms underlying embryonic stem cell self-organization and development in vitro.
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Affiliation(s)
- Yan-Lei Fan
- Department of Engineering Mechanics, Institute of Biomechanics and Medical Engineering, AML, Tsinghua University, Beijing, People's Republic of China
| | - Bo Li
- Department of Engineering Mechanics, Institute of Biomechanics and Medical Engineering, AML, Tsinghua University, Beijing, People's Republic of China
| | - Hong-Ping Zhao
- Department of Engineering Mechanics, Institute of Biomechanics and Medical Engineering, AML, Tsinghua University, Beijing, People's Republic of China
| | - Hu-Cheng Zhao
- Department of Engineering Mechanics, Institute of Biomechanics and Medical Engineering, AML, Tsinghua University, Beijing, People's Republic of China
| | - Xi-Qiao Feng
- Department of Engineering Mechanics, Institute of Biomechanics and Medical Engineering, AML, Tsinghua University, Beijing, People's Republic of China
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48
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Li N, Zeng Y, Huang J. Signaling pathways and clinical application of RASSF1A and SHOX2 in lung cancer. J Cancer Res Clin Oncol 2020; 146:1379-1393. [PMID: 32266538 DOI: 10.1007/s00432-020-03188-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/17/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND An increasing number of studies have focused on the early diagnostic value of the methylation of RASSF1A and SHOX2 in lung cancer. However, the intricate cellular events related to RASSF1A and SHOX2 in lung cancer are still a mystery. For researchers and clinicians aiming to more profoundly understand the diagnostic value of methylated RASSF1A and SHOX2 in lung cancer, this review will provide deeper insights into the molecular events of RASSF1A and SHOX2 in lung cancer. METHODOLOGY We searched for relevant publications in the PubMed and Google Scholar databases using the keywords "RASSF1A", "SHOX2" and "lung cancer" etc. First, we reviewed the RASSF1A and SHOX2 genes, from their family structures to the functions of their basic structural domains. Then we mainly focused on the roles of RASSF1A and SHOX2 in lung cancer, especially on their molecular events in recent decades. Finally, we compared the value of measuring RASSF1A and SHOX2 gene methylation with that of the common methods for the diagnosis of lung cancer patients. RESULTS The RASSF1A and SHOX2 genes were confirmed to be regulators or effectors of multiple cancer signaling pathways, driving tumorigenesis and lung cancer progression. The detection of RASSF1A and SHOX2 gene methylation has higher sensitivity and specificity than other commonly used methods for diagnosing lung cancer, especially in the early stage. CONCLUSIONS The RASSF1A and SHOX2 genes are critical for the processes of tumorigenesis, development, metastasis, drug resistance, and recurrence in lung cancer. The combined detection of RASSF1A and SHOX2 gene methylation was identified as an excellent method for the screening and surveillance of lung cancer that exhibits high sensitivity and specificity.
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Affiliation(s)
- Nanhong Li
- Department of Pathology, Guangdong Medical University, Zhanjiang, 524023, China
| | - Yu Zeng
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524003, China
| | - Jian Huang
- Department of Pathology, Guangdong Medical University, Zhanjiang, 524023, China.
- Pathological Diagnosis and Research Center, Affiliated Hospital, Guangdong Medical University, Zhanjiang, 524001, China.
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49
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Abstract
The mammalian genome experiences profound setting and resetting of epigenetic patterns during the life-course. This is understood best for DNA methylation: the specification of germ cells, gametogenesis, and early embryo development are characterised by phases of widespread erasure and rewriting of methylation. While mitigating against intergenerational transmission of epigenetic information, these processes must also ensure correct genomic imprinting that depends on faithful and long-term memory of gamete-derived methylation states in the next generation. This underscores the importance of understanding the mechanisms of methylation programming in the germline.
De novo methylation in the oocyte is of particular interest because of its intimate association with transcription, which results in a bimodal methylome unique amongst mammalian cells. Moreover, this methylation landscape is entirely set up in a non-dividing cell, making the oocyte a fascinating model system in which to explore mechanistic determinants of methylation. Here, we summarise current knowledge on the oocyte DNA methylome and how it is established, focussing on recent insights from knockout models in the mouse that explore the interplay between methylation and chromatin states. We also highlight some remaining paradoxes and enigmas, in particular the involvement of non-nuclear factors for correct
de novo methylation.
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Affiliation(s)
- Hannah Demond
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
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Kühnel T, Heinz HSB, Utz N, Božić T, Horsthemke B, Steenpass L. A human somatic cell culture system for modelling gene silencing by transcriptional interference. Heliyon 2020; 6:e03261. [PMID: 32021933 PMCID: PMC6994850 DOI: 10.1016/j.heliyon.2020.e03261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/06/2020] [Accepted: 01/15/2020] [Indexed: 11/30/2022] Open
Abstract
Transcriptional interference and transcription through regulatory elements (transcriptional read-through) are implicated in gene silencing and the establishment of DNA methylation. Transcriptional read-through is needed to seed DNA methylation at imprinted genes in the germ line and can lead to aberrant gene silencing by DNA methylation in human disease. To enable the study of parameters and factors influencing transcriptional interference and transcriptional read-through at human promoters, we established a somatic cell culture system. At two promoters of imprinted genes (UBE3A and SNRPN) and two promoters shown to be silenced by aberrant transcriptional read-through in human disease (MSH2 and HBA2) we tested, if transcriptional read-through is sufficient for gene repression and the acquisition of DNA methylation. Induction of transcriptional read-through from the doxycycline-inducible CMV promoter resulted in consistent repression of all downstream promoters, independent of promoter type and orientation. Repression was dependent on ongoing transcription, since withdrawal of induction resulted in reactivation. DNA methylation was not acquired at any of the promoters. Overexpression of DNMT3A and DNMT3L, factors needed for DNA methylation establishment in oocytes, was still not sufficient for the induction of DNA methylation. This indicates that induction of DNA methylation has more complex requirements than transcriptional read-through and the presence of de novo DNA methyltransferases.
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Affiliation(s)
- Theresa Kühnel
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany
| | - Helena Sophie Barbara Heinz
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany
| | - Nadja Utz
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany
- Present address: Institute of Neuropathology, Justus Liebig University Giessen, Aulweg 128, 35392 Giessen, Germany
| | - Tanja Božić
- Helmholtz Institute for Biomedical Engineering, Division of Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstr. 20, 52074 Aachen, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany
| | - Laura Steenpass
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Hufelandstr 55, 45147 Essen, Germany
- Corresponding author.
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