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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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Aanniz T, Bouyahya A, Balahbib A, El Kadri K, Khalid A, Makeen HA, Alhazmi HA, El Omari N, Zaid Y, Wong RSY, Yeo CI, Goh BH, Bakrim S. Natural bioactive compounds targeting DNA methyltransferase enzymes in cancer: Mechanisms insights and efficiencies. Chem Biol Interact 2024; 392:110907. [PMID: 38395253 DOI: 10.1016/j.cbi.2024.110907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024]
Abstract
The regulation of gene expression is fundamental to health and life and is essentially carried out at the promoter region of the DNA of each gene. Depending on the molecular context, this region may be accessible or non-accessible (possibility of integration of RNA polymerase or not at this region). Among enzymes that control this process, DNA methyltransferase enzymes (DNMTs), are responsible for DNA demethylation at the CpG islands, particularly at the promoter regions, to regulate transcription. The aberrant activity of these enzymes, i.e. their abnormal expression or activity, can result in the repression or overactivation of gene expression. Consequently, this can generate cellular dysregulation leading to instability and tumor development. Several reports highlighted the involvement of DNMTs in human cancers. The inhibition or activation of DNMTs is a promising therapeutic approach in many human cancers. In the present work, we provide a comprehensive and critical summary of natural bioactive molecules as primary inhibitors of DNMTs in human cancers. The active compounds hold the potential to be developed as anti-cancer epidrugs targeting DNMTs.
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Affiliation(s)
- Tarik Aanniz
- Medical Biotechnology Laboratory, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, B.P, 6203, Morocco.
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, 10106, Morocco.
| | - Abdelaali Balahbib
- High Institute of Nursing Professions and Health Techniques of Errachidia, Errachidia, Morocco.
| | - Kawtar El Kadri
- High Institute of Nursing Professions and Health Techniques of Errachidia, Errachidia, Morocco
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan, Saudi Arabia; Medicinal and Aromatic Plants Research Institute, National Center for Research, P.O. Box: 2424, Khartoum, 11111, Sudan.
| | - Hafiz A Makeen
- Pharmacy Practice Research Unit, Clinical Pharmacy Department, Faculty of Pharmacy, Jazan University, Jazan, Saudi Arabia.
| | - Hassan A Alhazmi
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan, Saudi Arabia; Pharmacy Practice Research Unit, Clinical Pharmacy Department, Faculty of Pharmacy, Jazan University, Jazan, Saudi Arabia.
| | - Nasreddine El Omari
- High Institute of Nursing Professions and Health Techniques of Tetouan, Tetouan, Morocco.
| | - Younes Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Morocco.
| | - Rebecca Shin-Yee Wong
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia; Department of Medical Education, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia.
| | - Chien Ing Yeo
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia.
| | - Bey Hing Goh
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia; Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, 47500, Malaysia; College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Saad Bakrim
- Geo-Bio-Environment Engineering and Innovation Laboratory, Molecular Engineering, Biotechnology and Innovation Team, Polydisciplinary Faculty of Taroudant, Ibn Zohr University, Agadir, 80000, Morocco.
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3
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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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Taglini F, Kafetzopoulos I, Rolls W, Musialik KI, Lee HY, Zhang Y, Marenda M, Kerr L, Finan H, Rubio-Ramon C, Gautier P, Wapenaar H, Kumar D, Davidson-Smith H, Wills J, Murphy LC, Wheeler A, Wilson MD, Sproul D. DNMT3B PWWP mutations cause hypermethylation of heterochromatin. EMBO Rep 2024; 25:1130-1155. [PMID: 38291337 PMCID: PMC7615734 DOI: 10.1038/s44319-024-00061-5] [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: 04/18/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
The correct establishment of DNA methylation patterns is vital for mammalian development and is achieved by the de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3B localises to H3K36me3 at actively transcribing gene bodies via its PWWP domain. It also functions at heterochromatin through an unknown recruitment mechanism. Here, we find that knockout of DNMT3B causes loss of methylation predominantly at H3K9me3-marked heterochromatin and that DNMT3B PWWP domain mutations or deletion result in striking increases of methylation in H3K9me3-marked heterochromatin. Removal of the N-terminal region of DNMT3B affects its ability to methylate H3K9me3-marked regions. This region of DNMT3B directly interacts with HP1α and facilitates the bridging of DNMT3B with H3K9me3-marked nucleosomes in vitro. Our results suggest that DNMT3B is recruited to H3K9me3-marked heterochromatin in a PWWP-independent manner that is facilitated by the protein's N-terminal region through an interaction with a key heterochromatin protein. More generally, we suggest that DNMT3B plays a role in DNA methylation homeostasis at heterochromatin, a process which is disrupted in cancer, aging and Immunodeficiency, Centromeric Instability and Facial Anomalies (ICF) syndrome.
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Affiliation(s)
- Francesca Taglini
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ioannis Kafetzopoulos
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Altos Labs, Cambridge Institute, Cambridge, UK
| | - Willow Rolls
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Kamila Irena Musialik
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, Imperial College London, London, UK
| | - Heng Yang Lee
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Endocrine Oncology Research Group, Department of Surgery, The Royal College of Surgeons RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Yujie Zhang
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Mattia Marenda
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
| | - Lyndsay Kerr
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Hannah Finan
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Swiss Federal Institute of Technology, ETH Zürich, Institute of Molecular Health Sciences, Zürich, Switzerland
| | - Cristina Rubio-Ramon
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Hannah Wapenaar
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Dhananjay Kumar
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Hazel Davidson-Smith
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Jimi Wills
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ann Wheeler
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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Kumar V, Dhanjal JK, Sari AN, Khurana M, Kaul SC, Wadhwa R, Sundar D. Effect of Withaferin-A, Withanone, and Caffeic Acid Phenethyl Ester on DNA Methyltransferases: Potential in Epigenetic Cancer Therapy. Curr Top Med Chem 2024; 24:379-391. [PMID: 37496252 DOI: 10.2174/1568026623666230726105017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND DNA methyltransferases (DNMTs) have been reported to be potential drug targets in various cancers. The major hurdle in inhibiting DNMTs is the lack of knowledge about different DNMTs and their role in the hypermethylation of gene promoters in cancer cells. Lack of information on specificity, stability, and higher toxicity of previously reported DNMT inhibitors is the major reason for inadequate epigenetic cancer therapy. DNMT1 and DNMT3A are the two DNMTs that are majorly overexpressed in cancers. OBJECTIVE In this study, we have presented computational and experimental analyses of the potential of some natural compounds, withaferin A (Wi-A), withanone (Wi-N), and caffeic acid phenethyl ester (CAPE), as DNMT inhibitors, in comparison to sinefungin (SFG), a known dual inhibitor of DNMT1 and DNMT3A. METHODS We used classical simulation methods, such as molecular docking and molecular dynamics simulations, to investigate the binding potential and properties of the test compounds with DNMT1 and DNMT3A. Cell culture-based assays were used to investigate the inactivation of DNMTs and the resulting hypomethylation of the p16INK4A promoter, a key tumour suppressor that is inactivated by hypermethylation in cancer cells, resulting in upregulation of its expression. RESULTS Among the three test compounds (Wi-A, Wi-N, and CAPE), Wi-A showed the highest binding affinity to both DNMT1 and DNMT3A; CAPE showed the highest affinity to DNMT3A, and Wi-N showed a moderate affinity interaction with both. The binding energies of Wi-A and CAPE were further compared with SFG. Expression analysis of DNMTs showed no difference between control and treated cells. Cell viability and p16INK4A expression analysis showed a dose-dependent decrease in viability, an increase in p16INK4A, and a stronger effect of Wi-A compared to Wi-N and CAPE. CONCLUSION The study demonstrated the differential binding ability of Wi-A, Wi-N, and CAPE to DNMT1 and DNMT3A, which was associated with their inactivation, leading to hypomethylation and desilencing of the p16INK4A tumour suppressor in cancer cells. The test compounds, particularly Wi-A, have the potential for cancer therapy.
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Affiliation(s)
- Vipul Kumar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110016, India
| | - Jaspreet Kaur Dhanjal
- Department of Computational Biology, Indraprastha Institute of Information Technology Delhi, Okhla Industrial Estate, Phase III, New Delhi, 110020, India
- Department of Cellular and Molecular Biotechnology, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, 3058565, Japan
| | - Anissa Nofita Sari
- Department of Cellular and Molecular Biotechnology, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, 3058565, Japan
| | - Mallika Khurana
- Department of Cellular and Molecular Biotechnology, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, 3058565, Japan
| | - Sunil C Kaul
- Department of Cellular and Molecular Biotechnology, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, 3058565, Japan
| | - Renu Wadhwa
- Department of Cellular and Molecular Biotechnology, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, 3058565, Japan
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110016, India
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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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7
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Mtetwa LM, Salifu EY, Omolo CA, Soliman ME, Faya M. Halting aberrant DNA methylation via in silico Identification of potent inhibitors of DNMT3B enzyme: Atomistic insights. Comput Biol Chem 2023; 105:107909. [PMID: 37418952 DOI: 10.1016/j.compbiolchem.2023.107909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/17/2023] [Accepted: 06/18/2023] [Indexed: 07/09/2023]
Abstract
To date, Cancer remains a global threat due to its impact on growing life expectancy. With the many efforts and methods of combating the disease, complete success remains a challenge owing to several limitations including cancer cells developing resistance through mutations, off-target effect of some cancer drugs resulting in toxicities, among many others. Aberrant DNA methylation is understood to be the primary reason for improper gene silence, which can result in neoplastic transformation, carcinogenesis, and tumour progression. DNA methyltransferase B (DNMT3B) enzyme is considered a potential target for the treatment of several cancers due to its important role in DNA methylation. However, only a few DNMT3B inhibitors have been reported to date. Herein, in silico molecular recognition techniques such as Molecular docking, Pharmacophore-based virtual screen and MD simulation were employed to identify potential inhibitors of DNMT3B that can halt aberrancy in DNA methylation. Findings initially identified 878 hit compounds based on a designed pharmacophore model from the reference compound Hypericin. Molecular docking was used to rank the hits by testing their efficiency when bound to the target enzyme and the top three (3) selected. All three (3) of the top hits showed excellent pharmacokinetic properties but two (2) (Zinc33330198 and Zinc77235130) were identified to be non-toxic. Molecular dynamic simulation of the final two hits showed good stability, flexibility, and structural rigidity of the compounds on DNMT3B. Finally, thermodynamic energy estimations show both compounds had favourable free energies comprising - 26.04 kcal/mol for Zinc77235130 and - 15.73 kcal/mol for Zinc33330198. Amongst the final two hits, Zinc77235130 showed consistency in favourable results across all the tested parameters and was thus selected as the lead compound for further experimental validation. The identification of this lead compound will form important basis for the inhibition of aberrant DNA methylation in cancer therapy.
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Affiliation(s)
- Lusanda M Mtetwa
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Elliasu Y Salifu
- West African Centre for Computational Analysis, Accra, Ghana; Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Calvin A Omolo
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; School of Pharmacy and Health Sciences, United States International University of Africa, Nairobi, Kenya
| | - Mahmoud E Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mbuso Faya
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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8
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Baral I, Shirude MB, Jothi DL, Mukherjee A, Dutta D. Characterization of a Distinct State in the Continuum of Pluripotency Facilitated by Inhibition of PKCζ in Mouse Embryonic Stem Cells. Stem Cell Rev Rep 2023; 19:1098-1115. [PMID: 36781773 DOI: 10.1007/s12015-023-10513-5] [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] [Accepted: 01/26/2023] [Indexed: 02/15/2023]
Abstract
Inhibition of PKC (PKCi) signaling maintains pluripotency of embryonic stem cells (ESCs) across different mammalian species. However, the position of PKCi maintained ESCs in the pluripotency continuum is largely unknown. Here we demonstrate that mouse ESCs when cultured continuously, with PKCi, for 75 days are retained in naïve state of pluripotency. Gene expression analysis and proteomics studies demonstrated enhanced naïve character of PKCi maintained ESCs in comparison to classical serum/LIF (S/L) supported ESCs. Molecular analysis revealed that activation of PKCζ isoform associate with primed state of pluripotency, present in epiblast-like stem cells generated in vitro while inhibition of PKCζ phosphorylation associated with naïve state of pluripotency in vitro and in vivo. Phosphoproteomics and chromatin modification enzyme array based studies showed loss in DNA methyl transferase 3B (DNMT3B) and its phosphorylation level upon functional inhibition of PKCζ as one of the crucial components of this regulatory pathway. Unlike ground state of pluripotency maintained by MEK/GSK3 inhibitor in addition to LIF (2i/LIF), loss in DNMT3B is a reversible phenomenon in PKCi maintained ESCs. Absence of phosphorylation of c-MYC, RAF1, SPRY4 while presence of ERF, DUSP6, CIC and YAP1 phosphorylation underlined the phosphoproteomics signature of PKCi mediated maintenance of naïve pluripotency. States of pluripotency represent the developmental continuum and the existence of PKCi mediated mouse ESCs in a distinct state in the continuum of pluripotency (DiSCo) might contribute to the establishment of stages of murine embryonic development that were non-permissible till date.
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Affiliation(s)
- Ishita Baral
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India.,Manipal Academy of Higher Education, Karnataka State, Manipal, 576104, India
| | - Mayur Balkrishna Shirude
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India.,Manipal Academy of Higher Education, Karnataka State, Manipal, 576104, India
| | - Dhana Lakshmi Jothi
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India
| | - Ananda Mukherjee
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India
| | - Debasree Dutta
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, 695014, Kerala, India.
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9
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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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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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11
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Ma Z, Wang Y, Quan Y, Wang Z, Liu Y, Ding Z. Maternal obesity alters methylation level of cytosine in CpG island for epigenetic inheritance in fetal umbilical cord blood. Hum Genomics 2022; 16:34. [PMID: 36045397 PMCID: PMC9429776 DOI: 10.1186/s40246-022-00410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Over the past few decades, global maternal obesity prevalence has rapidly increased. This condition may induce long-lasting pathophysiological effects on either fetal or infant health that could be attributable to unknown unique changes in the umbilical blood composition. METHODS A total of 34 overweight/obese and 32 normal-weight pregnant women were recruited. Fifteen umbilical blood samples including 8 overweight/obese subjects and 7 normal weight women were sequenced using Targeted Bisulfite Sequencing technology to detect the average methylation level of cytosine and identify the differentially methylated region (DMR). GO and KEGG analyses were then employed to perform pathway enrichment analysis of DMR-related genes and promoters. Moreover, the mRNA levels of methylation-related genes histone deacetylases (HDACs) and DNA methyltransferases (DNMTs) were characterized in the samples obtained from these two groups. RESULTS Average methylated cytosine levels in both the CpG islands (CGI) and promoter significantly decreased in overweight/obese groups. A total of 1669 DMRs exhibited differences in their DNA methylation status between the overweight/obese and control groups. GO and KEGG analyses revealed that DMR-related genes and promoters were enriched in the metabolism, cancer and cardiomyopathy signaling pathways. Furthermore, the HDACs and DNMTs mRNA levels trended to decline in overweight/obese groups. CONCLUSIONS Decreased methylated cytosine levels in overweight/obese women induce the gene expression activity at a higher level than in the control group. DMRs between these two groups in the fetal blood may contribute to the changes in gene transcription that underlie the increased risk of metabolic disorders, cancers and cardiomyopathy in their offspring.
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Affiliation(s)
- Zhuoyao Ma
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China
| | - Yingjin Wang
- Department of Obstetrics and Gynecology, Shanghai Eighth People's Hospital, Shanghai, 200235, China
| | - Yanmei Quan
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China
| | - Zhijie Wang
- Department of Obstetrics and Gynecology, Shanghai Eighth People's Hospital, Shanghai, 200235, China.
| | - Yue Liu
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China.
| | - Zhide Ding
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China.
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12
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Muylaert C, Van Hemelrijck LA, Maes A, De Veirman K, Menu E, Vanderkerken K, De Bruyne E. Aberrant DNA methylation in multiple myeloma: A major obstacle or an opportunity? Front Oncol 2022; 12:979569. [PMID: 36059621 PMCID: PMC9434119 DOI: 10.3389/fonc.2022.979569] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/22/2022] [Indexed: 11/30/2022] Open
Abstract
Drug resistance (DR) of cancer cells leading to relapse is a huge problem nowadays to achieve long-lasting cures for cancer patients. This also holds true for the incurable hematological malignancy multiple myeloma (MM), which is characterized by the accumulation of malignant plasma cells in the bone marrow (BM). Although new treatment approaches combining immunomodulatory drugs, corticosteroids, proteasome inhibitors, alkylating agents, and monoclonal antibodies have significantly improved median life expectancy, MM remains incurable due to the development of DR, with the underlying mechanisms remaining largely ill-defined. It is well-known that MM is a heterogeneous disease, encompassing both genetic and epigenetic aberrations. In normal circumstances, epigenetic modifications, including DNA methylation and posttranslational histone modifications, play an important role in proper chromatin structure and transcriptional regulation. However, in MM, numerous epigenetic defects or so-called ‘epimutations’ have been observed and this especially at the level of DNA methylation. These include genome-wide DNA hypomethylation, locus specific hypermethylation and somatic mutations, copy number variations and/or deregulated expression patterns in DNA methylation modifiers and regulators. The aberrant DNA methylation patterns lead to reduced gene expression of tumor suppressor genes, genomic instability, DR, disease progression, and high-risk disease. In addition, the frequency of somatic mutations in the DNA methylation modifiers seems increased in relapsed patients, again suggesting a role in DR and relapse. In this review, we discuss the recent advances in understanding the involvement of aberrant DNA methylation patterns and/or DNA methylation modifiers in MM development, progression, and relapse. In addition, we discuss their involvement in MM cell plasticity, driving myeloma cells to a cancer stem cell state characterized by a more immature and drug-resistant phenotype. Finally, we briefly touch upon the potential of DNA methyltransferase inhibitors to prevent relapse after treatment with the current standard of care agents and/or new, promising (immuno) therapies.
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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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14
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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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15
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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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16
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Das AB, Seddon AR, O'Connor KM, Hampton MB. Regulation of the epigenetic landscape by immune cell oxidants. Free Radic Biol Med 2021; 170:131-149. [PMID: 33444713 DOI: 10.1016/j.freeradbiomed.2020.12.453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/21/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022]
Abstract
Excessive production of microbicidal oxidants by neutrophils can damage host tissue. The short-term response of cells to oxidative stress is well understood, but the mechanisms behind long-term consequences require further clarification. Epigenetic pathways mediate cellular adaptation, and are therefore a potential target of oxidative stress. Indeed, there is evidence that many proteins and metabolites involved in epigenetic pathways are redox sensitive. In this review we provide an overview of the epigenetic landscape and discuss the potential for redox regulation. Using this information, we highlight specific examples where neutrophil oxidants react with epigenetic pathway components. We also use published data from redox proteomics to map out known intersections between oxidative stress and epigenetics that may signpost helpful directions for future investigation. Finally, we discuss the role neutrophils play in adaptive pathologies with a focus on tumour initiation and progression. We hope this information will stimulate further discourse on the emerging field of redox epigenomics.
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Affiliation(s)
- Andrew B Das
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Annika R Seddon
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Karina M O'Connor
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
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17
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Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL. Blood 2021; 136:2319-2333. [PMID: 32573712 DOI: 10.1182/blood.2019004090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/18/2020] [Indexed: 02/08/2023] Open
Abstract
Karyotype is an important prognostic factor in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL), but the underlying pharmacogenomics remain unknown. Asparaginase is an integral component in current chemotherapy for childhood BCP-ALL. Asparaginase therapy depletes serum asparagine. Normal hematopoietic cells can produce asparagine by asparagine synthetase (ASNS) activity, but ALL cells are unable to synthesize adequate amounts of asparagine. The ASNS gene has a typical CpG island in its promoter. Thus, methylation of the ASNS CpG island could be one of the epigenetic mechanisms for ASNS gene silencing in BCP-ALL. To gain deep insights into the pharmacogenomics of asparaginase therapy, we investigated the association of ASNS methylation status with asparaginase sensitivity. The ASNS CpG island is largely unmethylated in normal hematopoietic cells, but it is allele-specifically methylated in BCP-ALL cells. The ASNS gene is located at 7q21, an evolutionally conserved imprinted gene cluster. ASNS methylation in childhood BCP-ALL is associated with an aberrant methylation of the imprinted gene cluster at 7q21. Aberrant methylation of mouse Asns and a syntenic imprinted gene cluster is also confirmed in leukemic spleen samples from ETV6-RUNX1 knockin mice. In 3 childhood BCP-ALL cohorts, ASNS is highly methylated in BCP-ALL patients with favorable karyotypes but is mostly unmethylated in BCP-ALL patients with poor prognostic karyotypes. Higher ASNS methylation is associated with higher L-asparaginase sensitivity in BCP-ALL through lower ASNS gene and protein expression levels. These observations demonstrate that silencing of the ASNS gene as a result of aberrant imprinting is a pharmacogenetic mechanism for the leukemia-specific activity of asparaginase therapy in BCP-ALL.
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18
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Dogan F, Forsyth NR. Telomerase Regulation: A Role for Epigenetics. Cancers (Basel) 2021; 13:cancers13061213. [PMID: 33802026 PMCID: PMC8000866 DOI: 10.3390/cancers13061213] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Maintenance of telomeres is a fundamental step in human carcinogenesis and is primarily regulated by telomerase and the human telomerase reverse transcriptase gene (TERT). Improved understanding of the transcriptional control of this gene may provide potential therapeutic targets. Epigenetic modifications are a prominent mechanism to control telomerase activity and regulation of the TERT gene. TERT-targeting miRNAs have been widely studied and their function explained through pre-clinical in vivo model-based validation studies. Further, histone deacetylase inhibitors are now in pre and early clinical trials with significant clinical success. Importantly, TERT downregulation through epigenetic modifications including TERT promoter methylation, histone deacetylase inhibitors, and miRNA activity might contribute to clinical study design. This review provides an overview of the epigenetic mechanisms involved in the regulation of TERT expression and telomerase activity. Abstract Telomerase was first described by Greider and Blackburn in 1984, a discovery ultimately recognized by the Nobel Prize committee in 2009. The three decades following on from its discovery have been accompanied by an increased understanding of the fundamental mechanisms of telomerase activity, and its role in telomere biology. Telomerase has a clearly defined role in telomere length maintenance and an established influence on DNA replication, differentiation, survival, development, apoptosis, tumorigenesis, and a further role in therapeutic resistance in human stem and cancer cells including those of breast and cervical origin. TERT encodes the catalytic subunit and rate-limiting factor for telomerase enzyme activity. The mechanisms of activation or silencing of TERT remain open to debate across somatic, cancer, and stem cells. Promoter mutations upstream of TERT may promote dysregulated telomerase activation in tumour cells but additional factors including epigenetic, transcriptional and posttranscriptional modifications also have a role to play. Previous systematic analysis indicated methylation and mutation of the TERT promoter in 53% and 31%, respectively, of TERT expressing cancer cell lines supporting the concept of a key role for epigenetic alteration associated with TERT dysregulation and cellular transformation. Epigenetic regulators including DNA methylation, histone modification, and non-coding RNAs are now emerging as drivers in the regulation of telomeres and telomerase activity. Epigenetic regulation may be responsible for reversible silencing of TERT in several biological processes including development and differentiation, and increased TERT expression in cancers. Understanding the epigenetic mechanisms behind telomerase regulation holds important prospects for cancer treatment, diagnosis and prognosis. This review will focus on the role of epigenetics in telomerase regulation.
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Affiliation(s)
- Fatma Dogan
- The Guy Hilton Research Laboratories, School of Pharmacy and Bioengineering, Faculty of Medicine and Health Sciences, Keele University, Stoke on Trent ST4 7QB, UK;
| | - Nicholas R. Forsyth
- The Guy Hilton Research Laboratories, School of Pharmacy and Bioengineering, Faculty of Medicine and Health Sciences, Keele University, Stoke on Trent ST4 7QB, UK;
- School of Medicine, Tongji University, Shanghai 200092, China
- Correspondence:
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19
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Carvalho AS, Moraes MCS, Hyun Na C, Fierro-Monti I, Henriques A, Zahedi S, Bodo C, Tranfield EM, Sousa AL, Farinho A, Rodrigues LV, Pinto P, Bárbara C, Mota L, de Abreu TT, Semedo J, Seixas S, Kumar P, Costa-Silva B, Pandey A, Matthiesen R. Is the Proteome of Bronchoalveolar Lavage Extracellular Vesicles a Marker of Advanced Lung Cancer? Cancers (Basel) 2020; 12:cancers12113450. [PMID: 33233545 PMCID: PMC7699733 DOI: 10.3390/cancers12113450] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/11/2020] [Accepted: 11/19/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Bronchoalveolar lavage is routinely collected during bronchoscopy for cytology analysis in the diagnostic of lung cancer. Due to low sensitivity of this method, early-stage cancers are undetected, lowering the treatment success. In this study, we analyzed extracellular vesicles isolated from bronchoalveolar lavage of lung cancer suspects by mass spectrometry-based proteomics. The protein composition of bronchoalveolar lavage extracellular vesicles of late-stage cancer showed a higher proteome complexity associated with mortality within the two year follow-up period. We identified a potential therapeutic target DNMT3B complex which was significantly expressed in bronchoalveolar lavage extracellular vesicles as well as in tumor tissue. Bronchoalveolar lavage extracellular vesicles proteome analysis of immune markers indicates the presence of markers of innate immune and fibroblast cells. Abstract Acellular bronchoalveolar lavage (BAL) proteomics can partially separate lung cancer from non-lung cancer patients based on principal component analysis and multivariate analysis. Furthermore, the variance in the proteomics data sets is correlated mainly with lung cancer status and, to a lesser extent, smoking status and gender. Despite these advances BAL small and large extracellular vehicles (EVs) proteomes reveal aberrant protein expression in paracrine signaling mechanisms in cancer initiation and progression. We consequently present a case-control study of 24 bronchoalveolar lavage extracellular vesicle samples which were analyzed by state-of-the-art liquid chromatography-mass spectrometry (LC-MS). We obtained evidence that BAL EVs proteome complexity correlated with lung cancer stage 4 and mortality within two years´ follow-up (p value = 0.006). The potential therapeutic target DNMT3B complex is significantly up-regulated in tumor tissue and BAL EVs. The computational analysis of the immune and fibroblast cell markers in EVs suggests that patients who deceased within the follow-up period display higher marker expression indicative of innate immune and fibroblast cells (four out of five cases). This study provides insights into the proteome content of BAL EVs and their correlation to clinical outcomes.
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Affiliation(s)
- Ana Sofia Carvalho
- Computational and Experimental Biology Group, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciencias Medicas, Universidade NOVA de Lisboa, Campo dos Martires da Patria, 130, 1169-056 Lisboa, Portugal; (I.F.-M.); (A.H.); (S.Z.)
- Correspondence: (A.S.C.); (R.M.)
| | - Maria Carolina Strano Moraes
- Systems Oncology Group, Champalimaud Research, Champalimaud Centre for the Unknown, Av. Brasilia, Doca de Pedroucos, 1400-038 Lisbon, Portugal; (M.C.S.M.); (C.B.); (B.C.-S.)
| | - Chan Hyun Na
- Department of Neurology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
| | - Ivo Fierro-Monti
- Computational and Experimental Biology Group, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciencias Medicas, Universidade NOVA de Lisboa, Campo dos Martires da Patria, 130, 1169-056 Lisboa, Portugal; (I.F.-M.); (A.H.); (S.Z.)
| | - Andreia Henriques
- Computational and Experimental Biology Group, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciencias Medicas, Universidade NOVA de Lisboa, Campo dos Martires da Patria, 130, 1169-056 Lisboa, Portugal; (I.F.-M.); (A.H.); (S.Z.)
| | - Sara Zahedi
- Computational and Experimental Biology Group, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciencias Medicas, Universidade NOVA de Lisboa, Campo dos Martires da Patria, 130, 1169-056 Lisboa, Portugal; (I.F.-M.); (A.H.); (S.Z.)
| | - Cristian Bodo
- Systems Oncology Group, Champalimaud Research, Champalimaud Centre for the Unknown, Av. Brasilia, Doca de Pedroucos, 1400-038 Lisbon, Portugal; (M.C.S.M.); (C.B.); (B.C.-S.)
| | - Erin M Tranfield
- Electron Microscopy Facility, Instituto Gulbenkian de Ciência—Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; (E.M.T.); (A.L.S.)
| | - Ana Laura Sousa
- Electron Microscopy Facility, Instituto Gulbenkian de Ciência—Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal; (E.M.T.); (A.L.S.)
| | - Ana Farinho
- iNOVA4Health—Advancing Precision Medicine, CEDOC—Chronic Diseases Research Centre, NOVA Medical School/Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Campo dos Martires da Patria, 130, 1169-056 Lisboa, Portugal;
| | - Luís Vaz Rodrigues
- Department of Pneumology, Unidade Local de Saúde da Guarda (USLGuarda), 6300-659 Guarda, Portugal;
| | - Paula Pinto
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, 1649-028 Lisbon, Portugal; (P.P.); (L.M.); (T.T.d.A.); (J.S.)
| | - Cristina Bárbara
- Instituto de Saúde Ambiental (ISAMB), Faculdade de Medicina, Universidade de Lisboa, Centro Hospitalar Universitário Lisboa Norte, 1649-028 Lisbon, Portugal;
| | - Leonor Mota
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, 1649-028 Lisbon, Portugal; (P.P.); (L.M.); (T.T.d.A.); (J.S.)
| | - Tiago Tavares de Abreu
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, 1649-028 Lisbon, Portugal; (P.P.); (L.M.); (T.T.d.A.); (J.S.)
| | - Júlio Semedo
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte, 1649-028 Lisbon, Portugal; (P.P.); (L.M.); (T.T.d.A.); (J.S.)
| | - Susana Seixas
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, 4200-135 Porto, Portugal;
| | - Prashant Kumar
- Institute of Bioinformatics, Discoverer building, ITPL, Bangalore 560066, India; (P.K.); (A.P.)
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Bruno Costa-Silva
- Systems Oncology Group, Champalimaud Research, Champalimaud Centre for the Unknown, Av. Brasilia, Doca de Pedroucos, 1400-038 Lisbon, Portugal; (M.C.S.M.); (C.B.); (B.C.-S.)
| | - Akhilesh Pandey
- Institute of Bioinformatics, Discoverer building, ITPL, Bangalore 560066, India; (P.K.); (A.P.)
- Manipal Academy of Higher Education (MAHE), Manipal 576104, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Rune Matthiesen
- Computational and Experimental Biology Group, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciencias Medicas, Universidade NOVA de Lisboa, Campo dos Martires da Patria, 130, 1169-056 Lisboa, Portugal; (I.F.-M.); (A.H.); (S.Z.)
- Correspondence: (A.S.C.); (R.M.)
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20
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Lotesto MJ, Wallace CJ, Raimondi SL. E-Cadherin, NFATC3, and PLP2 Are Differentially Methylated in Multiple Cancers. Epigenet Insights 2020; 13:2516865720964802. [PMID: 33178991 PMCID: PMC7592331 DOI: 10.1177/2516865720964802] [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: 07/14/2020] [Accepted: 09/14/2020] [Indexed: 11/30/2022] Open
Abstract
It is well documented that cancer cells have abnormal methylation patterns often caused by faulty methylating machinery. Specifically, E-cadherin, NFATC3, and PLP2 are 3 genes known to be aberrantly methylated in cancer cells. These genes are well documented for their role in signaling pathways involved with cell proliferation, adhesion, migration, and other signs of tumor progression. Therefore, changes in gene expression of CDH1, NFATC3, and PLP2 due to aberrant methylation can lead to profound changes in cellular function and tumor formation. In order to ensure that previous in vitro and in vivo methylation studies match what is observed in the clinic, we utilized a bioinformatics approach to complete an extensive analysis of methylation patterns of these 3 genes, analyzing over 5000 patient samples, across all cancers for which both normal and tumor tissues were available. Specifically, we analyzed overall and site-specific methylation patterns, at CpG islands and shores, of all 3 genes across 14 cancer types. Furthermore, we compared these methylation levels in normal and tumor samples of both matched and unmatched patient samples in order to determine any differences between groups. Finally, we examined whether an aberrant DNA methyltransferase, DNMT3B7, known to be expressed in cancer cells and to alter methylation patterns in vitro correlated with altered overall and site-specific methylation of CDH1, NFATC3, and PLP2 in these patient samples. Our results indicate that methylation patterns of CDH1 and NFATC3 were unexpectedly varied across tumors, contrary to previous studies performed in vitro, while PLP2 showed the expected hypomethylation pattern in tumor tissues. We also observed some correlation between DNMT3B7 expression and methylation patterns of these genes, but patterns were inconsistent. Taken together, these results emphasize the necessity for in vivo and patient studies rather than a complete reliance on in vitro data and provide multiple areas of future research.
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Affiliation(s)
- Mary J Lotesto
- Department of Biology, Elmhurst University, Elmhurst, IL, USA
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21
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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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22
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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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23
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Wang J, Yang J, Li D, Li J. Technologies for targeting DNA methylation modifications: Basic mechanism and potential application in cancer. Biochim Biophys Acta Rev Cancer 2020; 1875:188454. [PMID: 33075468 DOI: 10.1016/j.bbcan.2020.188454] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/14/2020] [Accepted: 10/14/2020] [Indexed: 02/07/2023]
Abstract
DNA methylation abnormalities are regarded as critical event for cancer initiation and development. Tumor-associated genes encompassing aberrant DNA methylation alterations at specific locus are correlated with chromatin remodeling and dysregulation of gene expression in various malignancies. Thus, technologies designed to manipulate DNA methylation at specific loci of genome are necessary for the functional study and therapeutic application in the context of cancer management. Traditionally, the method for DNA methylation modifications demonstrates an unspecific feature, adversely causing global-genome epigenetic alterations and confusing the function of desired gene. Novel approaches for targeted DNA methylation regulation have a great advantage of manipulating gene epigenetic alterations in a more specific and efficient method. In this review, we described different targeting DNA methylation techniques, including both their advantages and limitations. Through a comprehensive understanding of these targeting tools, we hope to open a new perspective for cancer treatment.
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Affiliation(s)
- Jie Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jing Yang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Dandan Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, P.R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China.
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24
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Zhang Y, Li H, Xiang X, Lu Y, Sharma M, Li Z, Liu K, Wei J, Shao D, Li B, Ma Z, Qiu Y. Identification of DNMT3B2 as the Predominant Isoform of DNMT3B in Porcine Alveolar Macrophages and Its Involvement in LPS-Stimulated TNF-α Expression. Genes (Basel) 2020; 11:E1065. [PMID: 32927661 PMCID: PMC7564714 DOI: 10.3390/genes11091065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022] Open
Abstract
DNA methyltransferase 3B (DNMT3B) as one member of the DNMT family functions as a de novo methyltransferase, characterized as more than 30 splice variants in humans and mice. However, the expression patterns of DNMT3B in pig as well as the biological function of porcine DNMT3B remain to be determined. In this study, we first examined the expression patterns of DNMT3B in porcine alveolar macrophages (PAM). We demonstrated that only DNMT3B2 and DNMT3B3 were the detectable isoforms in PAM. Furthermore, we revealed that DNTM3B2 was the predominant isoform in PAM. Next, in the model of LPS (lipopolysaccharide)-activated PAM, we showed that in comparison to the unstimulated PAM, (1) expression of DNTM3B is reduced; (2) the methylation level of TNF-α gene promoter is decreased. We further establish that DNMT3B2-mediated methylation of TNF-α gene promoter restricts induction of TNF-α in the LPS-stimulated PAM. In summary, these findings reveal that DNMT3B2 is the predominant isoform in PAM and its downregulation contributes to expression of TNF-α via hypomethylation of TNF-α gene promoter in the LPS-stimulated PAM.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China; (Y.Z.); (H.L.); (X.X.); (Y.L.); (M.S.); (Z.L.); (K.L.); (J.W.); (D.S.); (B.L.); (Z.M.)
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25
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Saravanaraman P, Selvam M, Ashok C, Srijyothi L, Baluchamy S. De novo methyltransferases: Potential players in diseases and new directions for targeted therapy. Biochimie 2020; 176:85-102. [PMID: 32659446 DOI: 10.1016/j.biochi.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 06/06/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022]
Abstract
Epigenetic modifications govern gene expression by guiding the human genome on 'what to express and what not to'. DNA methyltransferases (DNMTs) establish methylation patterns on DNA, particularly in CpG islands, and such patterns play a major role in gene silencing. DNMTs are a family of proteins/enzymes (DNMT1, 2, 3A, 3B, and 3L), among which, DNMT1 (maintenance methyltransferase) and DNMT3 (de novo methyltransferases) that direct mammalian development and genome imprinting are highly investigated. In recent decades, many studies revealed a strong association of DNA methylation patterns with gene expression in various clinical conditions. Differential expression of DNMT3 family proteins and their splice variants result in changes in methylation patterns and such alterations have been associated with the initiation and progression of various diseases, especially cancer. This review will discuss the aberrant modifications generated by DNMT3 proteins under various clinical conditions, suggesting a potential signature for de novo methyltransferases in targeted disease therapy. Further, this review discusses the possibility of using 'CpG island methylation signatures' as promising biomarkers and emphasizes 'targeted hypomethylation' by disrupting the interaction of specific DNMT-protein complexes as the future of cancer therapeutics.
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Affiliation(s)
- Ponne Saravanaraman
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Murugan Selvam
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Cheemala Ashok
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Loudu Srijyothi
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India.
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26
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Zhang H, Ying H, Wang X. Methyltransferase DNMT3B in leukemia. Leuk Lymphoma 2020; 61:263-273. [PMID: 31547729 DOI: 10.1080/10428194.2019.1666377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/04/2019] [Accepted: 09/07/2019] [Indexed: 01/23/2023]
Abstract
DNA methyltransferases (DNMTs) are highly conserved DNA-modifying enzymes that play important roles in epigenetic regulation and they are involved in cell proliferation, differentiation, and apoptosis. In mammalian cells, three active DNMTs have been identified: DNMT1 acts as a maintenance methyltransferase to replicate preexisting methylation patterns, whereas DNMT3A and DNMT3B primarily act as de novo methyltransferases that are responsible for establishing DNA methylation patterns by adding a methyl group to cytosine bases. The expression of DNMT3B is widespread in a variety of hematological cells and it is altered in each type of leukemia, which is associated with its pathogenesis, progression, treatment, and prognosis. Here, we review current information on DNMT3B in leukemia, including its expression, single-nucleotide polymorphisms, mutations, regulation, function, and clinical value for anti-leukemic therapy and prognosis.
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Affiliation(s)
- Haibin Zhang
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Houqun Ying
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xiaozhong Wang
- Department of Clinical Laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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27
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The Common Partner of Several Methyltransferases TRMT112 Regulates the Expression of N6AMT1 Isoforms in Mammalian Cells. Biomolecules 2019; 9:biom9090422. [PMID: 31466382 PMCID: PMC6769652 DOI: 10.3390/biom9090422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 12/28/2022] Open
Abstract
Methylation is a widespread modification occurring in DNA, RNA and proteins. The N6AMT1 (HEMK2) protein has DNA N6-methyladenine as well as the protein glutamine and histone lysine methyltransferase activities. The human genome encodes two different isoforms of N6AMT1, the major isoform and the alternatively spliced isoform, where the substrate binding motif is missing. Several RNA methyltransferases involved in ribosome biogenesis, tRNA methylation and translation interact with the common partner, the TRMT112 protein. In this study, we show that TRMT112 regulates the expression of N6AMT1 isoforms in mammalian cells. Both isoforms are equally expressed on mRNA level, but only isoform 1 is detected on the protein level in human cells. We show that the alternatively spliced isoform is not able to interact with TRMT112 and when translated, is rapidly degraded from the cells. This suggests that TRMT112 is involved in cellular quality control ensuring that N6AMT1 isoform with missing substrate binding domain is eliminated from the cells. The down-regulation of TRMT112 does not affect the N6AMT1 protein levels in cells, suggesting that the two proteins of TRMT112 network, WBSCR22 and N6AMT1, are differently regulated by their common cofactor.
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28
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Tan HK, Wu CS, Li J, Tan ZH, Hoffman JR, Fry CJ, Yang H, Di Ruscio A, Tenen DG. DNMT3B shapes the mCA landscape and regulates mCG for promoter bivalency in human embryonic stem cells. Nucleic Acids Res 2019; 47:7460-7475. [PMID: 31219573 PMCID: PMC6698669 DOI: 10.1093/nar/gkz520] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/30/2019] [Accepted: 06/17/2019] [Indexed: 12/30/2022] Open
Abstract
DNMT3B is known as a de novo DNA methyltransferase. However, its preferential target sites for DNA methylation are largely unknown. Our analysis on ChIP-seq experiment in human embryonic stem cells (hESC) revealed that DNMT3B, mCA and H3K36me3 share the same genomic distribution profile. Deletion of DNMT3B or its histone-interacting domain (PWWP) demolished mCA in hESCs, suggesting that PWWP domain of DNMT3B directs the formation of mCA landscape. In contrast to the common presumption that PWWP guides DNMT3B-mediated mCG deposition, we found that deleting PWWP does not affect the mCG landscape. Nonetheless, DNMT3B knockout led to the formation of 2985 de novo hypomethylated regions at annotated promoter sites. Upon knockout, most of these promoters gain the bivalent marks, H3K4me3 and H3K27me3. We call them spurious bivalent promoters. Gene ontology analysis associated spurious bivalent promoters with development and cell differentiation. Overall, we found the importance of DNMT3B for shaping the mCA landscape and for maintaining the fidelity of the bivalent promoters in hESCs.
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Affiliation(s)
- Hong Kee Tan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599
- National University of Singapore Graduate School for Integrative Sciences and Engineering, 21 Lower Kent Ridge, Singapore 119077
| | - Chan-Shuo Wu
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599
| | - Jia Li
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Zi Hui Tan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599
| | | | | | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599
| | - Annalisa Di Ruscio
- Department of Translational Medicine, University of Eastern Piedmont, Novara, NO 28100, Italy
- Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599
- Harvard Stem Cell Institute, Boston, MA 02115, USA
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29
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The Roles of Human DNA Methyltransferases and Their Isoforms in Shaping the Epigenome. Genes (Basel) 2019; 10:genes10020172. [PMID: 30813436 PMCID: PMC6409524 DOI: 10.3390/genes10020172] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/16/2019] [Accepted: 02/19/2019] [Indexed: 12/20/2022] Open
Abstract
A DNA sequence is the hard copy of the human genome and it is a driving force in determining the physiological processes in an organism. Concurrently, the chemical modification of the genome and its related histone proteins is dynamically involved in regulating physiological processes and diseases, which overall constitutes the epigenome network. Among the various forms of epigenetic modifications, DNA methylation at the C-5 position of cytosine in the cytosine–guanine (CpG) dinucleotide is one of the most well studied epigenetic modifications. DNA methyltransferases (DNMTs) are a family of enzymes involved in generating and maintaining CpG methylation across the genome. In mammalian systems, DNA methylation is performed by DNMT1 and DNMT3s (DNMT3A and 3B). DNMT1 is predominantly involved in the maintenance of DNA methylation during cell division, while DNMT3s are involved in establishing de novo cytosine methylation and maintenance in both embryonic and somatic cells. In general, all DNMTs require accessory proteins, such as ubiquitin-like containing plant homeodomain (PHD) and really interesting new gene (RING) finger domain 1 (UHRF1) or DNMT3-like (DNMT3L), for their biological function. This review mainly focuses on the role of DNMT3B and its isoforms in de novo methylation and maintenance of DNA methylation, especially with respect to their role as an accessory protein.
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30
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Gagliardi M, Strazzullo M, Matarazzo MR. DNMT3B Functions: Novel Insights From Human Disease. Front Cell Dev Biol 2018; 6:140. [PMID: 30406101 PMCID: PMC6204409 DOI: 10.3389/fcell.2018.00140] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/02/2018] [Indexed: 11/13/2022] Open
Abstract
DNA methylation plays important roles in gene expression regulation and chromatin structure. Its proper establishment and maintenance are essential for mammalian development and cellular differentiation. DNMT3B is the major de novo DNA methyltransferase expressed and active during the early stage of embryonic development, including implantation. In addition to its well-known role to methylate centromeric, pericentromeric, and subtelomeric repeats, recent observations suggest that DNMT3B acts as the main enzyme methylating intragenic regions of active genes. Although largely studied, much remains unknown regarding how these specific patterns of de novo CpG methylation are established in mammalian cells, and which are the rules governing DNMT3B recruitment and activity. Latest evidence indicates that DNMT3B recruitment is regulated by numerous mechanisms including chromatin modifications, transcription levels, non-coding RNAs, and the presence of DNA-binding factors. DNA methylation abnormalities are a common mark of human diseases involving chromosomal and genomic instabilities, such as inherited disease and cancer. The autosomal recessive Immunodeficiency, Centromeric instability and Facial anomalies syndrome, type I (ICF-1), is associated to hypomorphic mutations in DNMT3B gene, while its altered expression has been correlated with the development of tumors. In both cases, this implies that abnormal DNA hypomethylation and hypermethylation patterns affect gene expression and genomic architecture contributing to the pathological states. We will provide an overview of the most recent research aimed at deciphering the molecular mechanisms by which DNMT3B abnormalities are associated with the onset and progression of these pathologies.
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Affiliation(s)
- Miriam Gagliardi
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy.,Max Planck Institute of Psychiatry, Munich, Germany
| | - Maria Strazzullo
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
| | - Maria R Matarazzo
- Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR, Naples, Italy
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31
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Saldívar-González FI, Gómez-García A, Chávez-Ponce de León DE, Sánchez-Cruz N, Ruiz-Rios J, Pilón-Jiménez BA, Medina-Franco JL. Inhibitors of DNA Methyltransferases From Natural Sources: A Computational Perspective. Front Pharmacol 2018; 9:1144. [PMID: 30364171 PMCID: PMC6191485 DOI: 10.3389/fphar.2018.01144] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/21/2018] [Indexed: 12/15/2022] Open
Abstract
Naturally occurring small molecules include a large variety of natural products from different sources that have confirmed activity against epigenetic targets. In this work we review chemoinformatic, molecular modeling, and other computational approaches that have been used to uncover natural products as inhibitors of DNA methyltransferases, a major family of epigenetic targets with therapeutic interest. Examples of computational approaches surveyed in this work are docking, similarity-based virtual screening, and pharmacophore modeling. It is also discussed the chemoinformatic-guided exploration of the chemical space of naturally occurring compounds as epigenetic modulators which may have significant implications in epigenetic drug discovery and nutriepigenetics.
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Affiliation(s)
| | - Alejandro Gómez-García
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | | | - Norberto Sánchez-Cruz
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - Javier Ruiz-Rios
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - B Angélica Pilón-Jiménez
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
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32
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Siddiqui S, White MW, Schroeder AM, DeLuca NV, Leszczynski AL, Raimondi SL. Aberrant DNMT3B7 expression correlates to tissue type, stage, and survival across cancers. PLoS One 2018; 13:e0201522. [PMID: 30071066 PMCID: PMC6072033 DOI: 10.1371/journal.pone.0201522] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/17/2018] [Indexed: 11/19/2022] Open
Abstract
Cancer cells are known for aberrant methylation patterns leading to altered gene expression and tumor progression. DNA methyltransferases (DNMTs) are responsible for regulating DNA methylation in normal cells. However, many aberrant versions of DNMTs have been identified to date and their role in cancer continues to be elucidated. It has been previously shown that an aberrant version of a de novo methylase, DNMT3B7, is expressed in many cancer cell lines and has a functional role in the progression of breast cancer, neuroblastoma, and lymphoma. It is clear that DNMT3B7 is important to tumor development in vitro and in vivo, but it is unknown if expression of the transcript in all of these cell lines translates to relevant clinical results. In this study, a bioinformatics approach was utilized to test the hypothesis that DNMT3B7 expression corresponds to tumor progression in patient samples across cancer types. Gene expression and clinical data were obtained from the Genomic Data Commons for the 33 cancer types available and analyzed for DNMT3B7 expression with relation to tissue type in matched and unmatched samples, staging of tumors, and patient survival. Here we present the results of this analysis indicating a role for DNMT3B7 in tumor progression of many additional cancer types. Based on these data, future in vitro and in vivo studies can be prioritized to examine DNMT3B7 in cancer and, hopefully, develop novel therapeutics to target this aberrant transcript across multiple tumor types.
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Affiliation(s)
- Safia Siddiqui
- Department of Biology, Elmhurst College, Elmhurst, Illinois, United States of America
| | - Michael W. White
- Department of Biology, Elmhurst College, Elmhurst, Illinois, United States of America
| | - Aimee M. Schroeder
- Department of Biology, Elmhurst College, Elmhurst, Illinois, United States of America
| | - Nicholas V. DeLuca
- Department of Biology, Elmhurst College, Elmhurst, Illinois, United States of America
| | - Andrew L. Leszczynski
- Department of Biology, Elmhurst College, Elmhurst, Illinois, United States of America
| | - Stacey L. Raimondi
- Department of Biology, Elmhurst College, Elmhurst, Illinois, United States of America
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33
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Lyko F. The DNA methyltransferase family: a versatile toolkit for epigenetic regulation. Nat Rev Genet 2017; 19:81-92. [PMID: 29033456 DOI: 10.1038/nrg.2017.80] [Citation(s) in RCA: 784] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The DNA methyltransferase (DNMT) family comprises a conserved set of DNA-modifying enzymes that have a central role in epigenetic gene regulation. Recent studies have shown that the functions of the canonical DNMT enzymes - DNMT1, DNMT3A and DNMT3B - go beyond their traditional roles of establishing and maintaining DNA methylation patterns. This Review analyses how molecular interactions and changes in gene copy numbers modulate the activity of DNMTs in diverse gene regulatory functions, including transcriptional silencing, transcriptional activation and post-transcriptional regulation by DNMT2-dependent tRNA methylation. This mechanistic diversity enables the DNMT family to function as a versatile toolkit for epigenetic regulation.
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Affiliation(s)
- Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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34
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Singh P, Sailu S, Palchamy E, Coumar MS, Baluchamy S. Identification of a novel leukemic-specific splice variant of DNMT3B and its stability. Med Oncol 2017; 34:145. [PMID: 28730333 DOI: 10.1007/s12032-017-1008-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 07/18/2017] [Indexed: 11/29/2022]
Abstract
DNA methyltransferases make use of alternative splicing mechanism to generate various splice variants, but their role(s) in modulating DNA methylation patterns in the cells is unclear. Notably, DNMT3B alone contains nearly 40 different splice variants. In this study, we have identified a novel splice variant of DNMT3B, which lacks exon 7 and 10 from leukemic cell lines which we termed as DNMT3B9. The exon 7 codes for the major part of PWWP domain, and exon 10 inclusion serves as a pluripotent marker. By quantitative RT-PCR using exon-exon junction-specific primers, we showed higher level of DNMT3B9 transcripts in several leukemic cell lines. However, DNMT3B9 expression was less in other tested cancer cell lines indicating that DNMT3B9 might serve as a leukemic-specific biomarker. Surprisingly, endogenous protein for DNMT3B9 was not detected in leukemic cells suggesting the unidentified RNA-related function(s) for DNMT3B9. In addition, we showed that DNMT3B9 protein lacks PWWP domain is less stable compared to other DNMT3B variants which contain PWWP domain through computational predictions and by cycloheximide half-life experiment. Taken together, we demonstrated the existence of novel leukemic-specific splice variant of DNMT3B and provide the evidence for the role of PWWP domain in the stability of DNMT3B. The findings reported here have relevance in epigenetic therapy, which is aimed to target the DNMT3B in cancer cells.
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Affiliation(s)
- Prachi Singh
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Sarvagalla Sailu
- Centre for Bioinformatics, Pondicherry Central University, Pondicherry, 605014, India
| | - Elango Palchamy
- Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | | | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India.
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35
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Liang G, Weisenberger DJ. DNA methylation aberrancies as a guide for surveillance and treatment of human cancers. Epigenetics 2017; 12:416-432. [PMID: 28358281 DOI: 10.1080/15592294.2017.1311434] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
DNA methylation aberrancies are hallmarks of human cancers and are characterized by global DNA hypomethylation of repetitive elements and non-CpG rich regions concomitant with locus-specific DNA hypermethylation. DNA methylation changes may result in altered gene expression profiles, most notably the silencing of tumor suppressors, microRNAs, endogenous retorviruses and tumor antigens due to promoter DNA hypermethylation, as well as oncogene upregulation due to gene-body DNA hypermethylation. Here, we review DNA methylation aberrancies in human cancers, their use in cancer surveillance and the interplay between DNA methylation and histone modifications in gene regulation. We also summarize DNA methylation inhibitors and their therapeutic effects in cancer treatment. In this context, we describe the integration of DNA methylation inhibitors with conventional chemotherapies, DNA repair inhibitors and immune-based therapies, to bring the epigenome closer to its normal state and increase sensitivity to other therapeutic agents to improve patient outcome and survival.
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Affiliation(s)
- Gangning Liang
- a Department of Urology , University of Southern California, USC Norris Comprehensive Cancer Center , Los Angeles , CA , USA
| | - Daniel J Weisenberger
- b Department of Biochemistry and Molecular Medicine , University of Southern California, USC Norris Comprehensive Cancer Center , Los Angeles , CA , USA
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36
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Liu Y, Sun L, Fong P, Yang J, Zhang Z, Yin S, Jiang S, Liu X, Ju H, Huang L, Bai J, Gong K, Yan S, Zhang C, Shao G. An association between overexpression of DNA methyltransferase 3B4 and clear cell renal cell carcinoma. Oncotarget 2017; 8:19712-19722. [PMID: 28160561 PMCID: PMC5386716 DOI: 10.18632/oncotarget.14966] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/03/2017] [Indexed: 12/20/2022] Open
Abstract
It is well known that abnormal DNA methylations occur frequently in kidney cancer. However, it remains unclear exactly which types of DNA methyltransferases (DNMT) contribute to the pathologies of kidney cancers. In order to determine the functions of DNA methyltransferase in kidney tumorigenesis on the molecular level, we examined the mRNA expression levels of DNMT1, DNMT3A, DNMT3B, and DNMT3B variants in renal cell carcinoma tissue. Both mRNA and protein levels of DNMT3B4, a splice variant of DNMT3B, were increased in renal cell carcinoma tissue compared with adjacent control tissues. Additionally, Alu elements and long interspersed nuclear elements (LINE-1) were hypomethylated in renal cell carcinoma tissue. Meanwhile, methylation of the promoter for RASSF1A, a tumor suppressor gene, was moderately increased in renal cell carcinoma tissue, while RASSF1A expression was decreased. Thus, our data suggest that the overexpression of DNMT3B4 may play an important role in human kidney tumorigenesis through chromosomal instability and methylation of RASSF1A.
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Affiliation(s)
- You Liu
- Biomedicine Research Center and Basic Medical College, Baotou Medical College, Inner Mongolia, PRC
| | - Liantao Sun
- Biomedicine Research Center and Basic Medical College, Baotou Medical College, Inner Mongolia, PRC
| | - Peter Fong
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Jie Yang
- Biomedicine Research Center and Basic Medical College, Baotou Medical College, Inner Mongolia, PRC
| | - Zhuxia Zhang
- Biomedicine Research Center and Basic Medical College, Baotou Medical College, Inner Mongolia, PRC
| | - Shuihui Yin
- Biomedicine Research Center and Basic Medical College, Baotou Medical College, Inner Mongolia, PRC
| | - Shuyuan Jiang
- Biomedicine Research Center and Basic Medical College, Baotou Medical College, Inner Mongolia, PRC
| | - Xiaolei Liu
- Biomedicine Research Center and Basic Medical College, Baotou Medical College, Inner Mongolia, PRC
| | - Hongge Ju
- Biomedicine Research Center and Basic Medical College, Baotou Medical College, Inner Mongolia, PRC
| | - Lihua Huang
- Biomedicine Research Center and Basic Medical College, Baotou Medical College, Inner Mongolia, PRC
| | - Jing Bai
- Biomedicine Research Center and Basic Medical College, Baotou Medical College, Inner Mongolia, PRC
| | - Kerui Gong
- Department of Oral and Maxillofacial Surgery, University of California San Francsico, San Francisco, CA, USA
| | - Shaochun Yan
- Biomedicine Research Center and Basic Medical College, Baotou Medical College, Inner Mongolia, PRC
| | - Chunyang Zhang
- Department of Neurology, First Affiliated Hospital of Baotou Medical College, Inner Mongolia, PRC
| | - Guo Shao
- Biomedicine Research Center and Basic Medical College, Baotou Medical College, Inner Mongolia, PRC
- Institute for Hypoxia Medicine, Capital Medical University, Beijing, PRC
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37
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Misregulation of DNA Methylation Regulators in Cancer. DNA AND HISTONE METHYLATION AS CANCER TARGETS 2017. [DOI: 10.1007/978-3-319-59786-7_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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38
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Najafi H, Soltani BM, Dokanehiifard S, Nasiri S, Mowla SJ. Alternative splicing of the OCC-1 gene generates three splice variants and a novel exonic microRNA, which regulate the Wnt signaling pathway. RNA (NEW YORK, N.Y.) 2017; 23:70-85. [PMID: 27986894 PMCID: PMC5159651 DOI: 10.1261/rna.056317.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 10/10/2016] [Indexed: 06/06/2023]
Abstract
The Wnt signaling pathway is hyperactivated in most colorectal cancers (CRC). Finding new regulators of this pathway represents the potential for cancer diagnosis or treatment. OCC-1 was initially reported as an up-regulated gene in colon carcinoma, without knowing its mechanism of action. Here, two novel transcript variants and an exonic microRNA that originated from the OCC-1 gene are reported, showing positive effects on Wnt activity. Up-regulation of the known OCC-1 variant (assigned as OCC-1A/B) was limited to CRC, and its overexpression increased survival of CRC-originated SW480 cells (Wnt+), while resulting in apoptosis of Wnt-suppressed SW480 cells or HeLa cells (Wnt-) detected by PI staining. Immunocytochemistry showed that the OCC-1A/B-encoded peptide was localized to the nucleus, where its overexpression resulted in Wnt signaling up-regulation, detected by TOP/FOPflash assay. The noncoding portion of the OCC-1A/B transcript had a suppressive effect on Wnt activity and had a negative correlation with APPL2 neighboring gene expression. Unlike OCC-1A/B, the novel OCC-1C splice variant had no expression alteration in CRC, and it seemed to encode a smaller peptide with cytoplasmic localization. A 60-nucleotide (nt) fragment containing an AUG start codon is spliced out to produce an OCC-1D noncoding RNA variant. The 60-nt RNA was validated as the precursor of a novel microRNA, which we named miR-ex1 Both OCC-1D and miR-ex1 were coordinately up-regulated in CRC. MiR-ex1 functional analysis revealed that it is targeting the APC2 tumor suppressor gene and is an activator of the Wnt signaling pathway. Overall, the OCC-1 gene is now introduced as a novel Wnt signaling regulator and as a potential therapeutic target.
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Affiliation(s)
- Hadi Najafi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-116 Tehran, Iran
| | - Bahram M Soltani
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-116 Tehran, Iran
| | - Sadat Dokanehiifard
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-116 Tehran, Iran
| | - Shirzad Nasiri
- Tehran University of Medical Sciences, Shariati Hospital, 1411713135 Tehran, Iran
| | - Seyed Javad Mowla
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, 14115-116 Tehran, Iran
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39
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Abstract
Epigenetic mechanisms play important roles in properly occurring mammalian oogenesis. One of these mechanisms is DNA methylation adding a methyl group to the fifth carbon atom of the cytosine residues using S-adenosyl-L-methionine as a methyl donor. DNA methylation generally takes place at cytosine-phosphate-guanine (CpG) dinucleotide sites and rarely occurs at cytosine-phosphate-thymine (CpT), cytosine-phosphate-adenine (CpA), or cytosine-phosphate-cytosine sites, known as non-CpG sites. Basically, two different DNA methylation processes are identified: de novo methylation and maintenance methylation. While the de novo methylation functions in methylation of unmethylated DNA strands, maintenance methylation is capable of methylating hemi-methylated DNA strands following DNA replication. Both DNA methylation processes are catalyzed by special DNA methyltransferase (DNMT) enzymes. To date, five different DNMTs have been identified: DNMT1, DNMT3A, DNMT3B, DNMT3L, and DNMT2. In this chapter, we focus particularly on temporal and spatial expression of DNMTs in mammalian oocytes and granulosa cells.
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Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology, School of Medicine, Akdeniz University, Campus, 07070, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, School of Medicine, Akdeniz University, Campus, 07070, Antalya, Turkey.
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40
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Gromek SM, deMayo JA, Maxwell AT, West AM, Pavlik CM, Zhao Z, Li J, Wiemer AJ, Zweifach A, Balunas MJ. Synthesis and biological evaluation of santacruzamate A analogues for anti-proliferative and immunomodulatory activity. Bioorg Med Chem 2016; 24:5183-5196. [PMID: 27614919 PMCID: PMC5065774 DOI: 10.1016/j.bmc.2016.08.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/17/2016] [Accepted: 08/22/2016] [Indexed: 01/17/2023]
Abstract
Santacruzamate A (SCA) is a natural product isolated from a Panamanian marine cyanobacterium, previously reported to have potent and selective histone deacetylase (HDAC) activity. To optimize the enzymatic and cellular activity, 40 SCA analogues were synthesized in a systematic exploration of the zinc-binding group (ZBG), cap terminus, and linker region. Two cap group analogues inhibited proliferation of MCF-7 breast cancer cells, with analogous increased degranulation of cytotoxic T cells (CTLs), while one cap group analogue reduced CTL degranulation, indicative of suppression of the immune response. Additional testing of these analogues resulted in reevaluation of the previously reported SCA mechanism of action. These analogues and the resulting structure-activity relationships will be of interest for future studies on cell proliferation and immune modulation.
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Affiliation(s)
- Samantha M Gromek
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd, Storrs, CT 06269, USA
| | - James A deMayo
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd, Storrs, CT 06269, USA
| | - Andrew T Maxwell
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd, Storrs, CT 06269, USA
| | - Ashley M West
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd, Storrs, CT 06269, USA
| | - Christopher M Pavlik
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd, Storrs, CT 06269, USA
| | - Ziyan Zhao
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd, Storrs, CT 06269, USA
| | - Jin Li
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd, Storrs, CT 06269, USA
| | - Andrew J Wiemer
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd, Storrs, CT 06269, USA
| | - Adam Zweifach
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd, Storrs, CT 06269, USA
| | - Marcy J Balunas
- Division of Medicinal Chemistry, Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd, Storrs, CT 06269, USA.
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41
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Herold T, Metzeler KH, Vosberg S, Hartmann L, Jurinovic V, Opatz S, Konstandin NP, Schneider S, Zellmeier E, Ksienzyk B, Graf A, Krebs S, Blum H, Cristina Sauerland M, Büchner T, Berdel WE, Wörmann BJ, Mansmann U, Hiddemann W, Bohlander SK, Spiekermann K, Greif PA. Acute myeloid leukemia with del(9q) is characterized by frequent mutations of NPM1, DNMT3A, WT1 and low expression of TLE4. Genes Chromosomes Cancer 2016; 56:75-86. [PMID: 27636548 DOI: 10.1002/gcc.22418] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/26/2016] [Accepted: 08/27/2016] [Indexed: 12/17/2022] Open
Abstract
Deletions of the long arm of chromosome 9 [del(9q)] are a rare but recurring aberration in acute myeloid leukemia (AML). Del(9q) can be found as the sole abnormality or in combination with other cytogenetic aberrations such as t(8;21) and t(15;17). TLE1 and TLE4 were identified to be critical genes contained in the 9q region. We performed whole exome sequencing of 5 patients with del(9q) as the sole abnormality followed by targeted amplicon sequencing of 137 genes of 26 patients with del(9q) as sole or combined with other aberrations. We detected frequent mutations in NPM1 (10/26; 38%), DNMT3A (8/26; 31%), and WT1 (8/26; 31%) but only few FLT3-ITDs (2/26; 8%). All mutations affecting NPM1 and DNMT3A were exclusively identified in patients with del(9q) as the sole abnormality and were significantly more frequent compared to 111 patients classified as intermediate-II according to the European LeukemiaNet (10/14, 71% vs. 22/111, 20%; P < 0.001, 8/14, 57% vs. 26/111, 23%; P = 0.02). Furthermore, we identified DNMT3B to be rarely but recurrently targeted by truncating mutations in AML. Gene expression analysis of 13 patients with del(9q) and 454 patients with normal karyotype or various cytogenetic aberrations showed significant down regulation of TLE4 in patients with del(9q) (P = 0.02). Interestingly, downregulation of TLE4 was not limited to AML with del(9q), potentially representing a common mechanism in AML pathogenesis. Our comprehensive genetic analysis of the del(9q) subgroup reveals a unique mutational profile with the frequency of DNMT3A mutations in the del(9q) only subset being the highest reported so far in AML, indicating oncogenic cooperativity. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Tobias Herold
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU) München, München, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Center Munich for Environmental Health, München, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Klaus H Metzeler
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU) München, München, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Center Munich for Environmental Health, München, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sebastian Vosberg
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU) München, München, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Center Munich for Environmental Health, München, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Luise Hartmann
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU) München, München, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Center Munich for Environmental Health, München, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vindi Jurinovic
- Institute for Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität (LMU) München, München, Germany
| | - Sabrina Opatz
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU) München, München, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Center Munich for Environmental Health, München, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nikola P Konstandin
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU) München, München, Germany
| | - Stephanie Schneider
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU) München, München, Germany
| | - Evelyn Zellmeier
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU) München, München, Germany
| | - Bianka Ksienzyk
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU) München, München, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) München, München, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) München, München, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität (LMU) München, München, Germany
| | | | - Thomas Büchner
- Department of Medicine A-Hematology, Oncology and Pneumology, University of Münster, Münster, Germany
| | - Wolfgang E Berdel
- Department of Medicine A-Hematology, Oncology and Pneumology, University of Münster, Münster, Germany
| | - Bernhard J Wörmann
- Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine, Campus Virchow, Berlin, Germany
| | - Ulrich Mansmann
- German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute for Medical Informatics, Biometry and Epidemiology, Ludwig-Maximilians-Universität (LMU) München, München, Germany
| | - Wolfgang Hiddemann
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU) München, München, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Center Munich for Environmental Health, München, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan K Bohlander
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
| | - Karsten Spiekermann
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU) München, München, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Center Munich for Environmental Health, München, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Philipp A Greif
- Department of Internal Medicine 3, University Hospital Grosshadern, Ludwig-Maximilians-Universität (LMU) München, München, Germany.,Clinical Cooperative Group Leukemia, Helmholtz Center Munich for Environmental Health, München, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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42
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Uysal F, Akkoyunlu G, Ozturk S. DNA methyltransferases exhibit dynamic expression during spermatogenesis. Reprod Biomed Online 2016; 33:690-702. [PMID: 27687053 DOI: 10.1016/j.rbmo.2016.08.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/12/2023]
Abstract
DNA methylation is one of the epigenetic marks and plays critically important functions during spermatogenesis in mammals. DNA methylation is catalysed by DNA methyltransferase (DNMT) enzymes, which are responsible for the addition of a methyl group to the fifth carbon atom of the cytosine residues within cytosine-phosphate-guanine (CpG) and non-CpG dinucleotide sites. Structurally and functionally five different DNMT enzymes have been identified in mammals, including DNMT1, DNMT2, DNMT3A, DNMT3B and DNMT3L. These enzymes mainly play roles in two DNA methylation processes: maintenance and de novo. While DNMT1 is primarily responsible for maintenance methylation via transferring methyl groups to the hemi-methylated DNA strands following DNA replication, both DNMT3A and DNMT3B are capable of methylating unmodified cytosine residues, known as de novo methylation. However, DNMT3L indirectly participates in de novo methylation, and DNMT2 carries out methylation of the cytosine 38 in the anticodon loop of aspartic acid transfer RNA. To date, many studies have been performed to determine spatial and temporal expression levels and functional features of the DNMT in the male germ cells. This review article comprehensively discusses dynamic expression of the DNMT during spermatogenesis and their relationship with male infertility development in the light of existing investigations.
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Affiliation(s)
- Fatma Uysal
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Campus 07070, Antalya, Turkey
| | - Gokhan Akkoyunlu
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Campus 07070, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University, School of Medicine, Campus 07070, Antalya, Turkey.
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43
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Plourde KV, Labrie Y, Ouellette G, Pouliot MC, Durocher F. Genome-wide methylation analysis of DNMT3B gene isoforms revealed specific methylation profiles in breast cell lines. Epigenomics 2016; 8:1209-26. [PMID: 27586997 DOI: 10.2217/epi-2016-0013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
AIM The goal of this study is to characterize the specific methylation profile triggered by DNMT3B protein isoforms expressed at different levels in breast cell lines. MATERIALS & METHODS Microarray DNA methylation data were analyzed and associated with functional genome annotation data. RESULTS A large spectrum of DNMT3B3/DNMT3B2 expression ratio values was observed in parental breast cell lines. According to their methylation profiles, hierarchical clustering of untransfected cell lines revealed clustering based on their ER/PR status. Overexpression of DNMT3B3 triggered methylation changes of thousands of CpG sites in breast cells. Based on the trend of methylation changes, the results suggest an antiproliferative action of the DNMT3B3 isoform through a dominant negative effect on its wild-type counterpart DNMT3B2. CONCLUSION This study revealed specific pathways modulated by DNMT3B isoforms, which could regulate cell proliferation and other biological mechanisms. This illustrates the importance of multiple interactions between isoforms in the complexity of methylation processes.
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Affiliation(s)
- Karine V Plourde
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
| | - Yvan Labrie
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
| | - Geneviève Ouellette
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
| | - Marie-Christine Pouliot
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
| | - Francine Durocher
- CHU de Québec Research Centre-Université Laval, Department of Molecular Medicine, Québec, G1V 4G2, Canada
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Chen LH, Hsu WL, Tseng YJ, Liu DW, Weng CF. Involvement of DNMT 3B promotes epithelial-mesenchymal transition and gene expression profile of invasive head and neck squamous cell carcinomas cell lines. BMC Cancer 2016; 16:431. [PMID: 27391030 PMCID: PMC4938990 DOI: 10.1186/s12885-016-2468-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 06/29/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The 5-year overall survival rates for head and neck cancer (HNC) relies on distant metastasis. Importantly, the epithelial-mesenchymal transition (EMT) is believed to be an initial step of metastasis. However, the relationship of epigenetic with EMT formation is still unexplored in HNC. This study focuses on invasive subclones of HNC cell lines through the simulation of invasion in vitro; and underlying mechanisms were analyzed including DNA methylation and gene expression profile. METHODS Invasive subclones of NHC cell lines were successfully obtained using transwell coated with Matrixgel. Cells invaded through 8 μm pore several times were subcultured and examined with EMT features including morphology, EMT marker genes expression, and invasive ability. Moreover, compared the profile of genes expression in parental and invasive cells was analyzed using mRNA expression array. RESULTS DNA methyltransferase 3B (DNMT 3B) was upregulated in invasive subclones and might control the 5' region of E-cadherin (E-cad) methylation and further inhibited E-cad protein expression. Interference of DNMT 3B by siRNA or miRNA 29b could reduce EMT and cell invasion. Expression array analysis revealed the most possible involved pathways in cell invasion including arginine and proline metabolism, TGF-beta, and focal adhesion. CONCLUSIONS DNMT 3B might control EMT by DNA methylation manner in invasive HNC cell lines. Moreover, miR-29b mimic downregulated DNMT 3B and inhibited EMT and cell invasion indicated the role of therapeutic agent for invasive HNC. Genes identified from array data and new molecules are involved in metastasis of HNC need further validation.
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Affiliation(s)
- Li-Hsuen Chen
- />Department of Life Science and the Institute of Biotechnology, National Dong Hwa University, Hualien, Taiwan
- />Department of Radiation Oncology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
| | - Wen-Lin Hsu
- />Department of Radiation Oncology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
- />School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Yen-Ju Tseng
- />Department of Life Science and the Institute of Biotechnology, National Dong Hwa University, Hualien, Taiwan
- />Department of Radiation Oncology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
| | - Dai-Wei Liu
- />Department of Radiation Oncology, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
- />School of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Ching-Feng Weng
- />Department of Life Science and the Institute of Biotechnology, National Dong Hwa University, Hualien, Taiwan
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Abstract
Vertebrate genomes are highly methylated at cytosine residues in CpG sequences. CpG
methylation plays an important role in epigenetic gene silencing and genome stability.
Compared with other epigenetic modifications, CpG methylation is thought to be relatively
stable; however, it is sometimes affected by environmental changes, leading to epigenetic
instability and disease. CpG methylation is reversible and regulated by DNA
methyltransferases and demethylases including ten-eleven translocation. Here, we discuss
CpG methylation instability and the regulation of CpG methylation by DNA
methyltransferases and ten-eleven translocation in pluripotent stem cells.
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Affiliation(s)
- Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Gunma 371-8512, Japan
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46
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Duymich CE, Charlet J, Yang X, Jones PA, Liang G. DNMT3B isoforms without catalytic activity stimulate gene body methylation as accessory proteins in somatic cells. Nat Commun 2016; 7:11453. [PMID: 27121154 PMCID: PMC4853477 DOI: 10.1038/ncomms11453] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 03/30/2016] [Indexed: 01/08/2023] Open
Abstract
Promoter DNA methylation is a key epigenetic mechanism for stable gene silencing, but is correlated with expression when located in gene bodies. Maintenance and de novo DNA methylation by catalytically active DNA methyltransferases (DNMT1 and DNMT3A/B) require accessory proteins such as UHRF1 and DNMT3L. DNMT3B isoforms are widely expressed, although some do not have active catalytic domains and their expression can be altered during cell development and tumourigenesis, questioning their biological roles. Here, we show that DNMT3B isoforms stimulate gene body methylation and re-methylation after methylation-inhibitor treatment. This occurs independently of the isoforms' catalytic activity, demonstrating a similar functional role to the accessory protein DNMT3L, which is only expressed in undifferentiated cells and recruits DNMT3A to initiate DNA methylation. This unexpected role for DNMT3B suggests that it might substitute for the absent accessory protein DNMT3L to recruit DNMT3A in somatic cells.
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Affiliation(s)
- Christopher E. Duymich
- Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Jessica Charlet
- Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Xiaojing Yang
- Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Peter A. Jones
- Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Gangning Liang
- Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
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Christinat Y, Pawłowski R, Krek W. jSplice: a high-performance method for accurate prediction of alternative splicing events and its application to large-scale renal cancer transcriptome data. Bioinformatics 2016; 32:2111-9. [PMID: 27153587 DOI: 10.1093/bioinformatics/btw145] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 03/11/2016] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION Alternative splicing represents a prime mechanism of post-transcriptional gene regulation whose misregulation is associated with a broad range of human diseases. Despite the vast availability of transcriptome data from different cell types and diseases, bioinformatics-based surveys of alternative splicing patterns remain a major challenge due to limited availability of analytical tools that combine high accuracy and rapidity. RESULTS We describe here a novel junction-centric method, jSplice, that enables de novo extraction of alternative splicing events from RNA-sequencing data with high accuracy, reliability and speed. Application to clear cell renal carcinoma (ccRCC) cell lines and 65 ccRCC patients revealed experimentally validatable alternative splicing changes and signatures able to prognosticate ccRCC outcome. In the aggregate, our results propose jSplice as a key analytic tool for the derivation of cell context-dependent alternative splicing patterns from large-scale RNA-sequencing datasets. AVAILABILITY AND IMPLEMENTATION jSplice is a standalone Python application freely available at http://www.mhs.biol.ethz.ch/research/krek/jsplice CONTACT wilhelm.krek@biol.ethz.ch SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yann Christinat
- Institute of Molecular Health Sciences, ETH Zurich, Zurich 8093, Switzerland
| | - Rafał Pawłowski
- Institute of Molecular Health Sciences, ETH Zurich, Zurich 8093, Switzerland
| | - Wilhelm Krek
- Institute of Molecular Health Sciences, ETH Zurich, Zurich 8093, Switzerland
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48
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Micevic G, Muthusamy V, Damsky W, Theodosakis N, Liu X, Meeth K, Wingrove E, Santhanakrishnan M, Bosenberg M. DNMT3b Modulates Melanoma Growth by Controlling Levels of mTORC2 Component RICTOR. Cell Rep 2016; 14:2180-2192. [PMID: 26923591 PMCID: PMC4785087 DOI: 10.1016/j.celrep.2016.02.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/29/2015] [Accepted: 01/27/2016] [Indexed: 01/22/2023] Open
Abstract
DNA methyltransferase DNMT3B is frequently overexpressed in tumor cells and plays important roles during the formation and progression of several cancer types. However, the specific signaling pathways controlled by DNMT3B in cancers, including melanoma, are poorly understood. Here, we report that DNMT3B plays a pro-tumorigenic role in human melanoma and that DNMT3B loss dramatically suppresses melanoma formation in the Braf/Pten mouse melanoma model. Loss of DNMT3B results in hypomethylation of the miR-196b promoter and increased miR-196b expression, which directly targets the mTORC2 component Rictor. Loss of RICTOR in turn prevents mTORC2 activation, which is critical for melanoma formation and growth. These findings establish Dnmt3b as a regulator of melanoma formation through its effect on mTORC2 signaling. Based on these results, DNMT3B is a potential therapeutic target in melanoma.
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Affiliation(s)
- Goran Micevic
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Viswanathan Muthusamy
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06510, USA
| | - William Damsky
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nicholas Theodosakis
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xiaoni Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Katrina Meeth
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Emily Wingrove
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Manjula Santhanakrishnan
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Marcus Bosenberg
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
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Yang Q, Mas A, Diamond MP, Al-Hendy A. The Mechanism and Function of Epigenetics in Uterine Leiomyoma Development. Reprod Sci 2016; 23:163-75. [PMID: 25922306 PMCID: PMC5933172 DOI: 10.1177/1933719115584449] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Uterine leiomyomas, also known as uterine fibroids, are the most common pelvic tumors, occurring in nearly 70% of all reproductive-aged women and are the leading indication for hysterectomy worldwide. The development of uterine leiomyomas involve a complex and heterogeneous constellation of hormones, growth factors, stem cells, genetic, and epigenetic abnormalities. An increasing body of evidence emphasizes the important contribution of epigenetics in the pathogenesis of leiomyomas. Genome-wide methylation analysis demonstrates that a subset of estrogen receptor (ER) response genes exhibit abnormal hypermethylation levels that are inversely correlated with their RNA expression. Several tumor suppressor genes, including Kruppel-like factor 11 (KLF11), deleted in lung and esophageal cancer 1 (DLEC1), keratin 19 (KRT19), and death-associated protein kinase 1 (DAPK1) also display higher hypermethylation levels in leiomyomas when compared to adjacent normal tissues. The important role of active DNA demethylation was recently identified with regard to the ten-eleven translocation protein 1 and ten-eleven translocation protein 3-mediated elevated levels of 5-hydroxymethylcytosine in leiomyoma. In addition, both histone deacetylase and histone methyltransferase are reported to be involved in the biology of leiomyomas. A number of deregulated microRNAs have been identified in leiomyomas, leading to an altered expression of their targets. More recently, the existence of side population (SP) cells with characteristics of tumor-initiating cells have been characterized in leiomyomas. These SP cells exhibit a tumorigenic capacity in immunodeficient mice when exposed to 17β-estradiol and progesterone, giving rise to fibroid-like tissue in vivo. These new findings will likely enhance our understanding of the crucial role epigenetics plays in the pathogenesis of uterine leiomyomas as well as point the way to novel therapeutic options.
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Affiliation(s)
- Qiwei Yang
- Division of Translation Research, Department of Obstetrics and Gynecology, Georgia Regents University, Medical College of Georgia, Augusta, GA, USA
| | - Aymara Mas
- Division of Translation Research, Department of Obstetrics and Gynecology, Georgia Regents University, Medical College of Georgia, Augusta, GA, USA
| | - Michael P Diamond
- Division of Translation Research, Department of Obstetrics and Gynecology, Georgia Regents University, Medical College of Georgia, Augusta, GA, USA
| | - Ayman Al-Hendy
- Division of Translation Research, Department of Obstetrics and Gynecology, Georgia Regents University, Medical College of Georgia, Augusta, GA, USA
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50
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Duymich CE, Liang G. Unique Role for a DNA Methyltransferase Isoform in Lung Cancer. EBioMedicine 2015; 2:1272-3. [PMID: 26629503 PMCID: PMC4634676 DOI: 10.1016/j.ebiom.2015.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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