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Bhat KP, Vijay J, Vilas CK, Asundi J, Zou J, Lau T, Cai X, Ahmed M, Kabza M, Weng J, Fortin JP, Lun A, Durinck S, Hafner M, Costa MR, Ye X. CRISPR activation screens identify the SWI/SNF ATPases as suppressors of ferroptosis. Cell Rep 2024; 43:114345. [PMID: 38870012 DOI: 10.1016/j.celrep.2024.114345] [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: 07/25/2023] [Revised: 04/22/2024] [Accepted: 05/24/2024] [Indexed: 06/15/2024] Open
Abstract
Ferroptosis is an iron-dependent cell death mechanism characterized by the accumulation of toxic lipid peroxides and cell membrane rupture. GPX4 (glutathione peroxidase 4) prevents ferroptosis by reducing these lipid peroxides into lipid alcohols. Ferroptosis induction by GPX4 inhibition has emerged as a vulnerability of cancer cells, highlighting the need to identify ferroptosis regulators that may be exploited therapeutically. Through genome-wide CRISPR activation screens, we identify the SWI/SNF (switch/sucrose non-fermentable) ATPases BRM (SMARCA2) and BRG1 (SMARCA4) as ferroptosis suppressors. Mechanistically, they bind to and increase chromatin accessibility at NRF2 target loci, thus boosting NRF2 transcriptional output to counter lipid peroxidation and confer resistance to GPX4 inhibition. We further demonstrate that the BRM/BRG1 ferroptosis connection can be leveraged to enhance the paralog dependency of BRG1 mutant cancer cells on BRM. Our data reveal ferroptosis induction as a potential avenue for broadening the efficacy of BRM degraders/inhibitors and define a specific genetic context for exploiting GPX4 dependency.
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Affiliation(s)
- Kamakoti P Bhat
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Jinchu Vijay
- Roche Canada, Mississauga, Ontario L5N 5M8, Canada
| | - Caroline K Vilas
- Oncology Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Jyoti Asundi
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Jun Zou
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Ted Lau
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Xiaoyu Cai
- Regenerative Medicine, Genentech, South San Francisco, CA 94080, USA
| | | | - Michal Kabza
- 7N Sp. Z O. O. by order of Roche Polska, 02-670 Warsaw, Poland
| | - Julie Weng
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Jean-Philippe Fortin
- Data Science and Statistical Computing, Genentech, South San Francisco, CA 94080, USA
| | - Aaron Lun
- Data Science and Statistical Computing, Genentech, South San Francisco, CA 94080, USA
| | - Steffen Durinck
- Oncology Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Marc Hafner
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA; Oncology Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Michael R Costa
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Xin Ye
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA.
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2
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Merlini A, Rabino M, Brusco S, Pavese V, Masci D, Sangiolo D, Bironzo P, Scagliotti GV, Novello S, D'Ambrosio L. Epigenetic determinants in soft tissue sarcomas: molecular mechanisms and therapeutic targets. Expert Opin Ther Targets 2024; 28:17-28. [PMID: 38234142 DOI: 10.1080/14728222.2024.2306344] [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: 07/24/2023] [Accepted: 01/12/2024] [Indexed: 01/19/2024]
Abstract
INTRODUCTION Soft tissue sarcomas are a group of rare, mesenchymal tumors characterized by dismal prognosis in advanced/metastatic stages. Knowledge of their molecular determinants is still rather limited. However, in recent years, epigenetic regulation - the modification of gene expression/function without DNA sequence variation - has emerged as a key player both in sarcomagenesis and sarcoma progression. AREAS COVERED Herein, we describe and review the main epigenetic mechanisms involved in chromatin remodeling and their role as disease drivers in different soft tissue sarcoma histotypes, focusing on epithelioid sarcoma, synovial sarcoma, and malignant peripheral nerve sheath tumors. Focusing on chromatin-remodeling complexes, we provide an in-depth on the role of BAF complex alterations in these soft tissue sarcoma histotypes. In parallel, we highlight current state-of-the-art and future perspectives in the development of rational, innovative treatments leveraging on epigenetic dysregulation in soft tissue sarcomas. EXPERT OPINION Therapeutic options for metastatic/advanced sarcomas are to date very limited and largely represented by cytotoxic agents, with only modest results. In the continuous attempt to find novel targets and innovative, effective drugs, epigenetic mechanisms represent an emerging and promising field of research, especially for malignant peripheral nerve sheath tumors, epithelioid and synovial sarcoma.
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Affiliation(s)
| | - Martina Rabino
- Department of Oncology, University of Turin, Orbassano (TO), Italy
| | - Silvia Brusco
- Department of Oncology, University of Turin, Orbassano (TO), Italy
- Division of Molecular Pathology, The Institute of Cancer Research Royal Cancer Hospital, London, UK
| | - Valeria Pavese
- Department of Oncology, University of Turin, Orbassano (TO), Italy
| | - Debora Masci
- Department of Oncology, University of Turin, Orbassano (TO), Italy
| | - Dario Sangiolo
- Department of Oncology, University of Turin, Orbassano (TO), Italy
| | - Paolo Bironzo
- Department of Oncology, University of Turin, Orbassano (TO), Italy
- Medical Oncology, S. Luigi Gonzaga University Hospital, Orbassano (TO), Italy
| | - Giorgio Vittorio Scagliotti
- Department of Oncology, University of Turin, Orbassano (TO), Italy
- Medical Oncology, S. Luigi Gonzaga University Hospital, Orbassano (TO), Italy
| | - Silvia Novello
- Department of Oncology, University of Turin, Orbassano (TO), Italy
- Medical Oncology, S. Luigi Gonzaga University Hospital, Orbassano (TO), Italy
| | - Lorenzo D'Ambrosio
- Department of Oncology, University of Turin, Orbassano (TO), Italy
- Medical Oncology, S. Luigi Gonzaga University Hospital, Orbassano (TO), Italy
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3
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Medina EA, Delma CR, Yang FC. ASXL1/2 mutations and myeloid malignancies. J Hematol Oncol 2022; 15:127. [PMID: 36068610 PMCID: PMC9450349 DOI: 10.1186/s13045-022-01336-x] [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: 04/21/2022] [Accepted: 08/04/2022] [Indexed: 11/10/2022] Open
Abstract
Myeloid malignancies develop through the accumulation of genetic and epigenetic alterations that dysregulate hematopoietic stem cell (HSC) self-renewal, stimulate HSC proliferation and result in differentiation defects. The polycomb group (PcG) and trithorax group (TrxG) of epigenetic regulators act antagonistically to regulate the expression of genes key to stem cell functions. The genes encoding these proteins, and the proteins that interact with them or affect their occupancy at chromatin, are frequently mutated in myeloid malignancies. PcG and TrxG proteins are regulated by Enhancers of Trithorax and Polycomb (ETP) proteins. ASXL1 and ASXL2 are ETP proteins that assemble chromatin modification complexes and transcription factors. ASXL1 mutations frequently occur in myeloid malignancies and are associated with a poor prognosis, whereas ASXL2 mutations frequently occur in AML with t(8;21)/RUNX1-RUNX1T1 and less frequently in other subtypes of myeloid malignancies. Herein, we review the role of ASXL1 and ASXL2 in normal and malignant hematopoiesis by summarizing the findings of mouse model systems and discussing their underlying molecular mechanisms.
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Affiliation(s)
- Edward A Medina
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA.
| | - Caroline R Delma
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Feng-Chun Yang
- Department of Cell Systems and Anatomy, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health San Antonio, San Antonio, TX, 78229, USA.,Mays Cancer Center, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
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4
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Trotman JB, Braceros KCA, Cherney RE, Murvin MM, Calabrese JM. The control of polycomb repressive complexes by long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1657. [PMID: 33861025 PMCID: PMC8500928 DOI: 10.1002/wrna.1657] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/12/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023]
Abstract
The polycomb repressive complexes 1 and 2 (PRCs; PRC1 and PRC2) are conserved histone-modifying enzymes that often function cooperatively to repress gene expression. The PRCs are regulated by long noncoding RNAs (lncRNAs) in complex ways. On the one hand, specific lncRNAs cause the PRCs to engage with chromatin and repress gene expression over genomic regions that can span megabases. On the other hand, the PRCs bind RNA with seemingly little sequence specificity, and at least in the case of PRC2, direct RNA-binding has the effect of inhibiting the enzyme. Thus, some RNAs appear to promote PRC activity, while others may inhibit it. The reasons behind this apparent dichotomy are unclear. The most potent PRC-activating lncRNAs associate with chromatin and are predominantly unspliced or harbor unusually long exons. Emerging data imply that these lncRNAs promote PRC activity through internal RNA sequence elements that arise and disappear rapidly in evolutionary time. These sequence elements may function by interacting with common subsets of RNA-binding proteins that recruit or stabilize PRCs on chromatin. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Jackson B. Trotman
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Keean C. A. Braceros
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Mechanistic, Interdisciplinary Studies of Biological Systems, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rachel E. Cherney
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - McKenzie M. Murvin
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - J. Mauro Calabrese
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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5
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Fiore M, Sambri A, Spinnato P, Zucchini R, Giannini C, Caldari E, Pirini MG, De Paolis M. The Biology of Synovial Sarcoma: State-of-the-Art and Future Perspectives. Curr Treat Options Oncol 2021; 22:109. [PMID: 34687366 PMCID: PMC8541977 DOI: 10.1007/s11864-021-00914-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2021] [Indexed: 12/22/2022]
Abstract
New molecular insights are being achieved in synovial sarcoma (SS) that can provide new potential diagnostic and prognostic markers as well as therapeutic targets. In particular, the advancement of research on epigenomics and gene regulation is promising. The concrete hypothesis that the pathogenesis of SS might mainly depend on the disruption of the balance of the complex interaction between epigenomic regulatory complexes and the consequences on gene expression opens interesting new perspectives. The standard of care for primary SS is wide surgical resection combined with radiation in selected cases. The role of chemotherapy is still under refinement and can be considered in patients at high risk of metastasis or in those with advanced disease. Cytotoxic chemotherapy (anthracyclines, ifosfamide, trabectedin, and pazopanib) is the treatment of choice, despite several possible side effects. Many possible drug-able targets have been identified. However, the impact of these strategies in improving SS outcome is still limited, thus making current and future research strongly needed to improve the survival of patients with SS.
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Affiliation(s)
- Michele Fiore
- Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Andrea Sambri
- Alma Mater Studiorum - University of Bologna, Bologna, Italy. .,IRCCS Azienda Ospedaliero Universitaria di Bologna, via Massarenti 9, 40138, Bologna, Italy.
| | | | | | | | - Emilia Caldari
- IRCCS Azienda Ospedaliero Universitaria di Bologna, via Massarenti 9, 40138, Bologna, Italy
| | - Maria Giulia Pirini
- IRCCS Azienda Ospedaliero Universitaria di Bologna, via Massarenti 9, 40138, Bologna, Italy
| | - Massimiliano De Paolis
- IRCCS Azienda Ospedaliero Universitaria di Bologna, via Massarenti 9, 40138, Bologna, Italy
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6
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Aliperti V, Skonieczna J, Cerase A. Long Non-Coding RNA (lncRNA) Roles in Cell Biology, Neurodevelopment and Neurological Disorders. Noncoding RNA 2021; 7:36. [PMID: 34204536 PMCID: PMC8293397 DOI: 10.3390/ncrna7020036] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023] Open
Abstract
Development is a complex process regulated both by genetic and epigenetic and environmental clues. Recently, long non-coding RNAs (lncRNAs) have emerged as key regulators of gene expression in several tissues including the brain. Altered expression of lncRNAs has been linked to several neurodegenerative, neurodevelopmental and mental disorders. The identification and characterization of lncRNAs that are deregulated or mutated in neurodevelopmental and mental health diseases are fundamental to understanding the complex transcriptional processes in brain function. Crucially, lncRNAs can be exploited as a novel target for treating neurological disorders. In our review, we first summarize the recent advances in our understanding of lncRNA functions in the context of cell biology and then discussing their association with selected neuronal development and neurological disorders.
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Affiliation(s)
- Vincenza Aliperti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Justyna Skonieczna
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
| | - Andrea Cerase
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK;
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Takahashi K, Takenaka M, Okamoto A, Bowtell DDL, Kohno T. Treatment Strategies for ARID1A-Deficient Ovarian Clear Cell Carcinoma. Cancers (Basel) 2021; 13:1769. [PMID: 33917230 PMCID: PMC8068058 DOI: 10.3390/cancers13081769] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/27/2021] [Accepted: 03/31/2021] [Indexed: 02/06/2023] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is a histological subtype of ovarian cancer that is more frequent in Asian countries (~25% of ovarian cancers) than in US/European countries (less than 10%). OCCC is refractory to conventional platinum-based chemotherapy, which is effective against high-grade serous carcinoma (HGSC), a major histological subtype of ovarian cancer. Notably, deleterious mutations in SWI/SNF chromatin remodeling genes, such as ARID1A, are common in OCCC but rare in HGSC. Because this complex regulates multiple cellular processes, including transcription and DNA repair, molecularly targeted therapies that exploit the consequences of SWI/SNF deficiency may have clinical efficacy against OCCC. Three such strategies have been proposed to date: prioritizing a gemcitabine-based chemotherapeutic regimen, synthetic lethal therapy targeting vulnerabilities conferred by SWI/SNF deficiency, and immune checkpoint blockade therapy that exploits the high mutational burden of ARID1A-deficient tumor. Thus, ARID1A deficiency has potential as a biomarker for precision medicine of ovarian cancer.
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Affiliation(s)
- Kazuaki Takahashi
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo 105-8461, Japan; (K.T.); (M.T.); (A.O.)
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia;
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Masataka Takenaka
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo 105-8461, Japan; (K.T.); (M.T.); (A.O.)
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo 105-8461, Japan; (K.T.); (M.T.); (A.O.)
| | - David D. L. Bowtell
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia;
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
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8
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Leitner K, Tsibulak I, Wieser V, Knoll K, Reimer D, Marth C, Fiegl H, Zeimet AG. Clinical impact of EZH2 and its antagonist SMARCA4 in ovarian cancer. Sci Rep 2020; 10:20412. [PMID: 33230143 PMCID: PMC7684284 DOI: 10.1038/s41598-020-77532-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
SMARCA4 and EZH2 are two functional key players of their respective antagonizing chromatin remodeling complexes SWI/SNF and PRC2. EZH2 inhibitory drugs may abrogate pro-oncogenic features of PRC2 and turn the balance to cell differentiation via SWI/SNF activity in cancers. SMARCA4 and EZH2 expression was assessed by RT-PCR in 238 epithelial ovarian cancers (OCs) and put in relation to clinico-pathological parameters and patients' outcome. Optimal thresholds for high and low expression of both variables were calculated by the Youden's index based on receiver operating characteristic (ROC) curves. High SMARCA4 mRNA expression was independently associated with favorable progression-free survival (PFS) (P = 0.03) and overall survival (OS) (P = 0.018). As Youden's threshold determination for EZH2 yielded a S-shaped ROC-curve, two cut-off points (29th and 94th percentile) predicting opposite features were defined. Whereas EZH2 mRNA levels beyond the 29th percentile independently predicted poor PFS (P = 0.034), Cox-regression in EZH2 transcripts above the 94th percentile revealed a conversion from unfavorable to favorable PFS and OS (P = 0.009 and P = 0.032, respectively). High SMARCA4 expression associates with improved survival, whereas moderate/high EZH2 expression predicts poor outcome, which converts to favorable survival in ultra-high expressing OCs. This small OC subgroup could be characterized by REV7-abrogated platinum hypersensitivity but concomitant PARP-inhibitor resistance.
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Affiliation(s)
- Katharina Leitner
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Anichstraße 35, 6020, Innsbruck, Austria
| | - Irina Tsibulak
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Anichstraße 35, 6020, Innsbruck, Austria
| | - Verena Wieser
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Anichstraße 35, 6020, Innsbruck, Austria
| | - Katharina Knoll
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Anichstraße 35, 6020, Innsbruck, Austria
| | - Daniel Reimer
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Anichstraße 35, 6020, Innsbruck, Austria
| | - Christian Marth
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Anichstraße 35, 6020, Innsbruck, Austria
| | - Heidi Fiegl
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Anichstraße 35, 6020, Innsbruck, Austria
| | - Alain G Zeimet
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Anichstraße 35, 6020, Innsbruck, Austria.
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9
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Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes. Nat Commun 2020; 11:5947. [PMID: 33230107 PMCID: PMC7683540 DOI: 10.1038/s41467-020-19722-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 10/12/2020] [Indexed: 12/19/2022] Open
Abstract
Histone posttranslational modifications are key regulators of chromatin-associated processes including gene expression, DNA replication and DNA repair. Monoubiquitinated histone H2A, H2Aub (K118 in Drosophila or K119 in vertebrates) is catalyzed by the Polycomb group (PcG) repressive complex 1 (PRC1) and reversed by the PcG-repressive deubiquitinase (PR-DUB)/BAP1 complex. Here we critically assess the current knowledge regarding H2Aub deposition and removal, its crosstalk with PcG repressive complex 2 (PRC2)-mediated histone H3K27 methylation, and the recent attempts toward discovering its readers and solving its enigmatic functions. We also discuss mounting evidence of the involvement of H2A ubiquitination in human pathologies including cancer, while highlighting some knowledge gaps that remain to be addressed. Histone H2A monoubiquitination on lysine 119 in vertebrate and lysine 118 in Drosophila (H2Aub) is an epigenomic mark usually associated with gene repression by Polycomb group factors. Here the authors review the current knowledge on the deposition and removal of H2Aub, its function in transcription and other DNA-associated processes as well as its relevance to human disease.
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10
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The mechanisms of action of chromatin remodelers and implications in development and disease. Biochem Pharmacol 2020; 180:114200. [DOI: 10.1016/j.bcp.2020.114200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/09/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
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11
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Abstract
Predicting regulatory potential from primary DNA sequences or transcription factor binding patterns is not possible. However, the annotation of the genome by chromatin proteins, histone modifications, and differential compaction is largely sufficient to reveal the locations of genes and their differential activity states. The Polycomb Group (PcG) and Trithorax Group (TrxG) proteins are the central players in this cell type-specific chromatin organization. PcG function was originally viewed as being solely repressive and irreversible, as observed at the homeotic loci in flies and mammals. However, it is now clear that modular and reversible PcG function is essential at most developmental genes. Focusing mainly on recent advances, we review evidence for how PcG and TrxG patterns change dynamically during cell type transitions. The ability to implement cell type-specific transcriptional programming with exquisite fidelity is essential for normal development.
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Affiliation(s)
- Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Hyuckjoon Kang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Sandip De
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Judith A Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
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12
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Sasaki M, Ogiwara H. Synthetic lethal therapy based on targeting the vulnerability of SWI/SNF chromatin remodeling complex-deficient cancers. Cancer Sci 2020; 111:774-782. [PMID: 31955490 PMCID: PMC7060479 DOI: 10.1111/cas.14311] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/17/2019] [Accepted: 01/08/2020] [Indexed: 12/19/2022] Open
Abstract
The SWI/SNF chromatin remodeling complex is composed of approximately 15 subunits, and approximately 20% of all cancers carry mutations in the genes encoding these subunits. Most of the genetic alterations in these genes are loss‐of‐function mutations. The identification of vulnerability based on synthetic lethality in cancers with SWI/SNF chromatin remodeling complex deficiency contributes to precision medicine. The SWI/SNF chromatin remodeling complex is involved in transcription, DNA repair, DNA replication, and chromosomal segregation. Cancers with deficiency in the SWI/SNF chromatin remodeling complex show increased vulnerability derived from the loss of these functions. Synthetic lethal targets have been identified based on vulnerabilities in the functions of the SWI/SNF chromatin remodeling complex. In this review article, we propose a precision medicine strategy using chemotherapeutic methods, such as molecular targeted therapy and immunotherapy, based on harnessing synthetic lethality in cancers with deficiency in the SWI/SNF chromatin remodeling complex.
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Affiliation(s)
- Mariko Sasaki
- Division of Cancer Therapeutics, National Cancer Center Research Institute, Tokyo, Japan.,Molecular Oncology, Jikei University Graduate School of Medicine, Tokyo, Japan
| | - Hideaki Ogiwara
- Division of Cancer Therapeutics, National Cancer Center Research Institute, Tokyo, Japan
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13
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Blackledge NP, Fursova NA, Kelley JR, Huseyin MK, Feldmann A, Klose RJ. PRC1 Catalytic Activity Is Central to Polycomb System Function. Mol Cell 2020; 77:857-874.e9. [PMID: 31883950 PMCID: PMC7033600 DOI: 10.1016/j.molcel.2019.12.001] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/21/2019] [Accepted: 12/02/2019] [Indexed: 01/01/2023]
Abstract
The Polycomb repressive system is an essential chromatin-based regulator of gene expression. Despite being extensively studied, how the Polycomb system selects its target genes is poorly understood, and whether its histone-modifying activities are required for transcriptional repression remains controversial. Here, we directly test the requirement for PRC1 catalytic activity in Polycomb system function. To achieve this, we develop a conditional mutation system in embryonic stem cells that completely removes PRC1 catalytic activity. Using this system, we demonstrate that catalysis by PRC1 drives Polycomb chromatin domain formation and long-range chromatin interactions. Furthermore, we show that variant PRC1 complexes with DNA-binding activities occupy target sites independently of PRC1 catalytic activity, providing a putative mechanism for Polycomb target site selection. Finally, we discover that Polycomb-mediated gene repression requires PRC1 catalytic activity. Together these discoveries provide compelling evidence that PRC1 catalysis is central to Polycomb system function and gene regulation.
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Affiliation(s)
- Neil P Blackledge
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Nadezda A Fursova
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Jessica R Kelley
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Miles K Huseyin
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Angelika Feldmann
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK.
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14
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Barrett CM, McCracken R, Elmer J, Haynes KA. Components from the Human c-myb Transcriptional Regulation System Reactivate Epigenetically Repressed Transgenes. Int J Mol Sci 2020; 21:E530. [PMID: 31947658 PMCID: PMC7014047 DOI: 10.3390/ijms21020530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/07/2020] [Accepted: 01/07/2020] [Indexed: 11/16/2022] Open
Abstract
A persistent challenge for mammalian cell engineering is the undesirable epigenetic silencing of transgenes. Foreign DNA can be incorporated into closed chromatin before and after it has been integrated into a host cell's genome. To identify elements that mitigate epigenetic silencing, we tested components from the c-myb and NF-kB transcriptional regulation systems in transiently transfected DNA and at chromosomally integrated transgenes in PC-3 and HEK 293 cells. DNA binding sites for MYB (c-myb) placed upstream of a minimal promoter enhanced expression from transiently transfected plasmid DNA. We targeted p65 and MYB fusion proteins to a chromosomal transgene, UAS-Tk-luciferase, that was silenced by ectopic Polycomb chromatin complexes. Transient expression of Gal4-MYB induced an activated state that resisted complete re-silencing. We used custom guide RNAs and dCas9-MYB to target MYB to different positions relative to the promoter and observed that transgene activation within ectopic Polycomb chromatin required proximity of dCas9-MYB to the transcriptional start site. Our report demonstrates the use of MYB in the context of the CRISPR-activation system, showing that DNA elements and fusion proteins derived from c-myb can mitigate epigenetic silencing to improve transgene expression in engineered cell lines.
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Affiliation(s)
- Cassandra M. Barrett
- School of Biological and Health Systems Engineering, Arizona State University, 501 East Tyler Mall, Tempe, AZ 85287, USA;
| | - Reilly McCracken
- Department of Chemical Engineering, Villanova University, 217 White Hall, 800 East Lancaster Avenue, Villanova, PA 19085, USA; (R.M.); (J.E.)
| | - Jacob Elmer
- Department of Chemical Engineering, Villanova University, 217 White Hall, 800 East Lancaster Avenue, Villanova, PA 19085, USA; (R.M.); (J.E.)
| | - Karmella A. Haynes
- School of Biological and Health Systems Engineering, Arizona State University, 501 East Tyler Mall, Tempe, AZ 85287, USA;
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
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15
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Hale R, Sandakly S, Shipley J, Walters Z. Epigenetic Targets in Synovial Sarcoma: A Mini-Review. Front Oncol 2019; 9:1078. [PMID: 31681608 PMCID: PMC6813544 DOI: 10.3389/fonc.2019.01078] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/30/2019] [Indexed: 01/25/2023] Open
Abstract
Synovial Sarcomas (SS) are a type of Soft Tissue Sarcoma (STS) and represent 8-10% of all STS cases. Although SS can arise at any age, it typically affects younger individuals aged 15-35 and is therefore part of both pediatric and adult clinical practices. SS occurs primarily in the limbs, often near joints, but can present anywhere. It is characterized by the recurrent pathognomonic chromosomal translocation t(X;18)(p11.2;q11.2) that most frequently fuses SSX1 or SSX2 genes with SS18. This leads to the expression of the SS18-SSX fusion protein, which causes disturbances in several interacting multiprotein complexes such as the SWItch/Sucrose Non-Fermentable (SWI/SNF) complex, also known as the BAF complex and the Polycomb Repressive Complex 1 and 2 (PRC1 and PRC2). Furthermore, this promotes widespread epigenetic rewiring, leading to aberrant gene expression that drives the pathogenesis of SS. Good prognoses are characterized predominantly by small tumor size and young patient age. Whereas, high tumor grade and an increased genomic complexity of the tumor constitute poor prognostic factors. The current therapeutic strategy relies on chemotherapy and radiotherapy, the latter of which can lead to chronic side effects for pediatric patients. We will focus on the known roles of SWI/SNF, PRC1, and PRC2 as the main effectors of the SS18-SSX-mediated genome modifications and we present existing biological rationale for potential therapeutic targets and treatment strategies.
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Affiliation(s)
- Ryland Hale
- Translational Epigenomics Team, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sami Sandakly
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Janet Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Zoë Walters
- Translational Epigenomics Team, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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16
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Alfert A, Moreno N, Kerl K. The BAF complex in development and disease. Epigenetics Chromatin 2019; 12:19. [PMID: 30898143 PMCID: PMC6427853 DOI: 10.1186/s13072-019-0264-y] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/13/2019] [Indexed: 01/16/2023] Open
Abstract
The ATP-dependent chromatin remodelling complex BAF (= mammalian SWI/SNF complex) is crucial for the regulation of gene expression and differentiation. In the course of evolution from yeast to mammals, the BAF complex evolved an immense complexity with a high number of subunits encoded by gene families. In this way, tissue-specific BAF function and regulation of development begin with the combinatorial assembly of distinct BAF complexes such as esBAF, npBAF and nBAF. Furthermore, whole-genome sequencing reveals the tremendous role BAF complex mutations have in both neurodevelopmental disorders and human malignancies. Therefore, gaining a more elaborate insight into how BAF complex assembly influences its function and which role distinct subunits play, will hopefully give rise to a better understanding of disease pathogenesis and ultimately to new treatments for many human diseases.
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Affiliation(s)
- Amelie Alfert
- Department of Paediatric Haematology and Oncology, University Children’s Hospital Muenster, Domagkstraße 24, 48149 Muenster, Germany
| | - Natalia Moreno
- Department of Paediatric Haematology and Oncology, University Children’s Hospital Muenster, Domagkstraße 24, 48149 Muenster, Germany
| | - Kornelius Kerl
- Department of Paediatric Haematology and Oncology, University Children’s Hospital Muenster, Domagkstraße 24, 48149 Muenster, Germany
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17
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Valencia AM, Kadoch C. Chromatin regulatory mechanisms and therapeutic opportunities in cancer. Nat Cell Biol 2019; 21:152-161. [PMID: 30602726 DOI: 10.1038/s41556-018-0258-1] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/30/2018] [Indexed: 12/11/2022]
Abstract
Research over the past several decades has unmasked a major contribution of disrupted chromatin regulatory processes to human disease, particularly cancer. Advances in genome-wide technologies have highlighted frequent mutations in genes encoding chromatin-associated proteins, identified unexpected synthetic lethal opportunities and enabled increasingly comprehensive structural and functional dissection. Here, we review recent progress in our understanding of oncogenic mechanisms at each level of chromatin organization and regulation, and discuss new strategies towards therapeutic intervention.
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Affiliation(s)
- Alfredo M Valencia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Chemical Biology Program, Harvard University, Cambridge, MA, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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18
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Chuang JH, Yarmishyn AA, Hwang DK, Hsu CC, Wang ML, Yang YP, Chien KH, Chiou SH, Peng CH, Chen SJ. Expression profiling of cell-intrinsic regulators in the process of differentiation of human iPSCs into retinal lineages. Stem Cell Res Ther 2018; 9:140. [PMID: 29751772 PMCID: PMC5948821 DOI: 10.1186/s13287-018-0848-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 03/06/2018] [Accepted: 03/16/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Differentiation of human induced pluripotent stem cells (hiPSCs) into retinal lineages offers great potential for medical application. Therefore, it is of crucial importance to know the key intrinsic regulators of differentiation and the specific biomarker signatures of cell lineages. METHODS In this study, we used microarrays to analyze transcriptomes of terminally differentiated retinal ganglion cell (RGC) and retinal pigment epithelium (RPE) lineages, as well as intermediate retinal progenitor cells of optic vesicles (OVs) derived from hiPSCs. In our analysis, we specifically focused on the classes of transcripts that encode intrinsic regulators of gene expression: the transcription factors (TFs) and epigenetic chromatin state regulators. We applied two criteria for the selection of potentially important regulators and markers: firstly, the magnitude of fold-change of upregulation; secondly, the contrasted pattern of differential expression between OV, RGC and RPE lineages. RESULTS We found that among the most highly overexpressed TF-encoding genes in the OV/RGC lineage were three members of the Collier/Olfactory-1/Early B-cell family: EBF1, EBF2 and EBF3. Knockdown of EBF1 led to significant impairment of differentiation of hiPSCs into RGCs. EBF1 was shown to act upstream of ISL1 and BRN3A, the well-characterized regulators of RGC lineage specification. TF-encoding genes DLX1, DLX2 and INSM1 were the most highly overexpressed genes in the OVs, indicating their important role in the early stages of retinal differentiation. Along with MITF, the two paralogs, BHLHE41 and BHLHE40, were the most robust TF markers of RPE cells. The markedly contrasted expression of ACTL6B, encoding the component of chromatin remodeling complex SWI/SNF, discriminated hiPSC-derived OV/RGC and RPE lineages. CONCLUSIONS We identified novel, potentially important intrinsic regulators of RGC and RPE cell lineage specification in the process of differentiation from hiPSCs. We demonstrated the crucial role played by EBF1 in differentiation of RGCs. We identified intrinsic regulator biomarker signatures of these two retinal cell types that can be applied with high confidence to confirm the cell lineage identities.
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Affiliation(s)
- Jen-Hua Chuang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
| | - Aliaksandr A Yarmishyn
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
| | - De-Kuang Hwang
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Chien Hsu
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Mong-Lien Wang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Ping Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
| | - Ke-Hung Chien
- Department of Ophthalmology, Tri-Service General Hospital & National Defense Medical Center, Taipei, Taiwan
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chi-Hsien Peng
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan. .,Department of Ophthalmology, Shin Kong Wu Ho-Su Memorial Hospital and Fu Jen Catholic University, Taipei, Taiwan.
| | - Shih-Jen Chen
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, Taiwan. .,Department of Ophthalmology, Tri-Service General Hospital & National Defense Medical Center, Taipei, Taiwan. .,School of Medicine, National Yang-Ming University, Taipei, Taiwan.
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19
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Rybina OY, Rozovsky YM, Veselkina ER, Pasyukova EG. Polycomb/Trithorax group-dependent regulation of the neuronal gene Lim3 involved in Drosophila lifespan control. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:451-462. [PMID: 29555581 DOI: 10.1016/j.bbagrm.2018.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 02/18/2018] [Accepted: 03/14/2018] [Indexed: 12/14/2022]
Abstract
Molecular mechanisms governing gene expression and defining complex phenotypes are central to understanding the basics of development and aging. Here, we demonstrate that naturally occurring polymorphisms of the Lim3 regulatory region that are associated with variation in gene expression and Drosophila lifespan control are located exclusively in the Polycomb response element (PRE). We find that the Polycomb group (PcG) protein Polycomb (PC) is bound to the PRE only in embryos where Lim3 is present in both repressed and active states. In contrast, the Trithorax group (TrxG) protein absent, small, or homeotic discs 1 (ASH1) is bound downstream of the PRE, to a region adjacent to the Lim3 transcription start site in embryos and adult flies, in which Lim3 is in an active state. Furthermore, mutations in Pc and ash1 genes affect Lim3 expression depending on the structural integrity of the Lim3 PRE, thus confirming functional interactions between these proteins and Lim3 regulatory region. In addition, we demonstrate that the evolutionary conserved Lim3 core promoter provides basic Lim3 expression, whereas structural changes in the Lim3 PRE of distal promoter provide stage-, and tissue-specific Lim3 expression. Therefore, we hypothesize that PcG/TrxG proteins, which are directly involved in Lim3 transcription regulation, participate in lifespan control.
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Affiliation(s)
- Olga Y Rybina
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurtchatov Sq. 2, Moscow 123182, Russia; Federal State-Financed Educational Institution of Higher Professional Education, Moscow State Pedagogical University, M. Pirogovskaya Str. 1/1, Moscow 119991, Russia.
| | - Yakov M Rozovsky
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurtchatov Sq. 2, Moscow 123182, Russia
| | - Ekaterina R Veselkina
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurtchatov Sq. 2, Moscow 123182, Russia
| | - Elena G Pasyukova
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurtchatov Sq. 2, Moscow 123182, Russia
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20
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McBride MJ, Kadoch C. Disruption of mammalian SWI/SNF and polycomb complexes in human sarcomas: mechanisms and therapeutic opportunities. J Pathol 2018; 244:638-649. [PMID: 29359803 DOI: 10.1002/path.5042] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 01/01/2023]
Abstract
Soft-tissue sarcomas are increasingly characterized and subclassified by genetic abnormalities that represent underlying drivers of their pathology. Hallmark tumor suppressor gene mutations and pathognomonic gene fusions collectively account for approximately one-third of all sarcomas. These genetic abnormalities most often result in global transcriptional misregulation via disruption of protein regulatory complexes which govern chromatin architecture. Specifically, alterations to mammalian SWI/SNF (mSWI/SNF or BAF) ATP-dependent chromatin remodeling complexes and polycomb repressive complexes cause disease-specific changes in chromatin architecture and gene expression across a number of sarcoma subtypes. Understanding the functions of chromatin regulatory complexes and the mechanisms underpinning their roles in oncogenesis will be required for the design and development of new therapeutic strategies in sarcomas. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Matthew J McBride
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Chemical Biology Program, Harvard University, Cambridge, MA, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
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21
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Dasari V, Srivastava S, Khan S, Mishra RK. Epigenetic factors Polycomb (Pc) and Suppressor of zeste (Su(z)2) negatively regulate longevity in Drosophila melanogaster. Biogerontology 2017; 19:33-45. [PMID: 29177687 DOI: 10.1007/s10522-017-9737-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 11/22/2017] [Indexed: 01/10/2023]
Abstract
The process of aging is a hallmark of the natural life span of all organisms and individuals within a population show variability in the measures of age related performance. Longevity and the rate of aging are influenced by several factors such as genetics, nutrition, stress, and environment. Many studies have focused on the genes that impact aging and there is increasing evidence that epigenetic factors regulate these genes to control life span. Polycomb (PcG) and trithorax (trxG) protein complexes maintain the expression profiles of developmentally important genes and regulate many cellular processes. Here, we report that mutations of PcG and trxG members affect the process of aging in Drosophila melanogaster, with perturbations mostly associated with retardation in aging. We find that mutations in polycomb repressive complex (PRC1) components Pc and Su(z)2 increase fly survival. Using an inducible UAS-GAL4 system, we show that this effect is tissue-specific; knockdown in fat body, but not in muscle or brain tissues, enhances life span. We hypothesize that these two proteins influence life span via pathways independent of their PRC1 functions, with distinct effects on response to oxidative stress. Our observations highlight the role of global epigenetic regulators in determining life span.
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Affiliation(s)
- Vasanthi Dasari
- CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Surabhi Srivastava
- CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Shagufta Khan
- CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India
| | - Rakesh K Mishra
- CSIR - Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
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22
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McLoughlin KC, Kaufman AS, Schrump DS. Targeting the epigenome in malignant pleural mesothelioma. Transl Lung Cancer Res 2017; 6:350-365. [PMID: 28713680 DOI: 10.21037/tlcr.2017.06.06] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Malignant pleural mesotheliomas (MPM) are notoriously refractory to conventional treatment modalities. Recent insights regarding epigenetic alterations in MPM provide the preclinical rationale for the evaluation of novel combinatorial regimens targeting the epigenome in these neoplasms.
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Affiliation(s)
- Kaitlin C McLoughlin
- Thoracic Epigenetics Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Andrew S Kaufman
- Thoracic Epigenetics Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - David S Schrump
- Thoracic Epigenetics Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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23
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Mammalian SWI/SNF complexes in cancer: emerging therapeutic opportunities. Curr Opin Genet Dev 2017; 42:56-67. [PMID: 28391084 DOI: 10.1016/j.gde.2017.02.004] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/23/2017] [Accepted: 02/07/2017] [Indexed: 02/08/2023]
Abstract
Mammalian SWI/SNF (BAF) chromatin remodeling complexes orchestrate a diverse set of chromatin alterations which impact transcriptional output. Recent whole-exome sequencing efforts have revealed that the genes encoding subunits of mSWI/SNF complexes are mutated in over 20% of cancers, spanning a wide range of tissue types. The majority of mutations result in loss of subunit protein expression, implicating mSWI/SNF subunits as tumor suppressors. mSWI/SNF-deficient cancers remain a therapeutic challenge, owing to a lack of potent and selective agents which target complexes or unique pathway dependencies generated by mSWI/SNF subunit perturbations. Here, we review the current landscape of mechanistic insights and emerging therapeutic opportunities for human malignancies driven by mSWI/SNF complex perturbation.
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