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Chen Y, Liang R, Li Y, Jiang L, Ma D, Luo Q, Song G. Chromatin accessibility: biological functions, molecular mechanisms and therapeutic application. Signal Transduct Target Ther 2024; 9:340. [PMID: 39627201 PMCID: PMC11615378 DOI: 10.1038/s41392-024-02030-9] [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: 03/11/2024] [Revised: 08/04/2024] [Accepted: 10/17/2024] [Indexed: 12/06/2024] Open
Abstract
The dynamic regulation of chromatin accessibility is one of the prominent characteristics of eukaryotic genome. The inaccessible regions are mainly located in heterochromatin, which is multilevel compressed and access restricted. The remaining accessible loci are generally located in the euchromatin, which have less nucleosome occupancy and higher regulatory activity. The opening of chromatin is the most important prerequisite for DNA transcription, replication, and damage repair, which is regulated by genetic, epigenetic, environmental, and other factors, playing a vital role in multiple biological progresses. Currently, based on the susceptibility difference of occupied or free DNA to enzymatic cleavage, solubility, methylation, and transposition, there are many methods to detect chromatin accessibility both in bulk and single-cell level. Through combining with high-throughput sequencing, the genome-wide chromatin accessibility landscape of many tissues and cells types also have been constructed. The chromatin accessibility feature is distinct in different tissues and biological states. Research on the regulation network of chromatin accessibility is crucial for uncovering the secret of various biological processes. In this review, we comprehensively introduced the major functions and mechanisms of chromatin accessibility variation in different physiological and pathological processes, meanwhile, the targeted therapies based on chromatin dynamics regulation are also summarized.
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Affiliation(s)
- Yang Chen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Rui Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Yong Li
- Hepatobiliary Pancreatic Surgery, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, PR China
| | - Lingli Jiang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Di Ma
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Qing Luo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China
| | - Guanbin Song
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, PR China.
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Dai W, Qiao X, Fang Y, Guo R, Bai P, Liu S, Li T, Jiang Y, Wei S, Na Z, Xiao X, Li D. Epigenetics-targeted drugs: current paradigms and future challenges. Signal Transduct Target Ther 2024; 9:332. [PMID: 39592582 PMCID: PMC11627502 DOI: 10.1038/s41392-024-02039-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 10/14/2024] [Accepted: 10/29/2024] [Indexed: 11/28/2024] Open
Abstract
Epigenetics governs a chromatin state regulatory system through five key mechanisms: DNA modification, histone modification, RNA modification, chromatin remodeling, and non-coding RNA regulation. These mechanisms and their associated enzymes convey genetic information independently of DNA base sequences, playing essential roles in organismal development and homeostasis. Conversely, disruptions in epigenetic landscapes critically influence the pathogenesis of various human diseases. This understanding has laid a robust theoretical groundwork for developing drugs that target epigenetics-modifying enzymes in pathological conditions. Over the past two decades, a growing array of small molecule drugs targeting epigenetic enzymes such as DNA methyltransferase, histone deacetylase, isocitrate dehydrogenase, and enhancer of zeste homolog 2, have been thoroughly investigated and implemented as therapeutic options, particularly in oncology. Additionally, numerous epigenetics-targeted drugs are undergoing clinical trials, offering promising prospects for clinical benefits. This review delineates the roles of epigenetics in physiological and pathological contexts and underscores pioneering studies on the discovery and clinical implementation of epigenetics-targeted drugs. These include inhibitors, agonists, degraders, and multitarget agents, aiming to identify practical challenges and promising avenues for future research. Ultimately, this review aims to deepen the understanding of epigenetics-oriented therapeutic strategies and their further application in clinical settings.
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Affiliation(s)
- Wanlin Dai
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xinbo Qiao
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yuanyuan Fang
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Renhao Guo
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Peng Bai
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Shuang Liu
- Shenyang Maternity and Child Health Hospital, Shenyang, China
| | - Tingting Li
- Department of General Internal Medicine VIP Ward, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Yutao Jiang
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shuang Wei
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhijing Na
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.
- NHC Key Laboratory of Advanced Reproductive Medicine and Fertility (China Medical University), National Health Commission, Shenyang, China.
| | - Xue Xiao
- Department of Gynecology and Obstetrics, West China Second Hospital, Sichuan University, Chengdu, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, China.
| | - Da Li
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.
- NHC Key Laboratory of Advanced Reproductive Medicine and Fertility (China Medical University), National Health Commission, Shenyang, China.
- Key Laboratory of Reproductive Dysfunction Diseases and Fertility Remodeling of Liaoning Province, Shenyang, China.
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Dreier MR, Walia J, de la Serna IL. Targeting SWI/SNF Complexes in Cancer: Pharmacological Approaches and Implications. EPIGENOMES 2024; 8:7. [PMID: 38390898 PMCID: PMC10885108 DOI: 10.3390/epigenomes8010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
SWI/SNF enzymes are heterogeneous multi-subunit complexes that utilize the energy from ATP hydrolysis to remodel chromatin structure, facilitating transcription, DNA replication, and repair. In mammalian cells, distinct sub-complexes, including cBAF, ncBAF, and PBAF exhibit varying subunit compositions and have different genomic functions. Alterations in the SWI/SNF complex and sub-complex functions are a prominent feature in cancer, making them attractive targets for therapeutic intervention. Current strategies in cancer therapeutics involve the use of pharmacological agents designed to bind and disrupt the activity of SWI/SNF complexes or specific sub-complexes. Inhibitors targeting the catalytic subunits, SMARCA4/2, and small molecules binding SWI/SNF bromodomains are the primary approaches for suppressing SWI/SNF function. Proteolysis-targeting chimeras (PROTACs) were generated by the covalent linkage of the bromodomain or ATPase-binding ligand to an E3 ligase-binding moiety. This engineered connection promotes the degradation of specific SWI/SNF subunits, enhancing and extending the impact of this pharmacological intervention in some cases. Extensive preclinical studies have underscored the therapeutic potential of these drugs across diverse cancer types. Encouragingly, some of these agents have progressed from preclinical research to clinical trials, indicating a promising stride toward the development of effective cancer therapeutics targeting SWI/SNF complex and sub-complex functions.
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Affiliation(s)
- Megan R Dreier
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3000 Arlington Ave, Toledo 43614, OH, USA
| | - Jasmine Walia
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3000 Arlington Ave, Toledo 43614, OH, USA
| | - Ivana L de la Serna
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3000 Arlington Ave, Toledo 43614, OH, USA
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Karl LA, Galanti L, Bantele SC, Metzner F, Šafarić B, Rajappa L, Foster B, Pires VB, Bansal P, Chacin E, Basquin J, Duderstadt KE, Kurat CF, Bartke T, Hopfner KP, Pfander B. A SAM-key domain required for enzymatic activity of the Fun30 nucleosome remodeler. Life Sci Alliance 2023; 6:e202201790. [PMID: 37468166 PMCID: PMC10355287 DOI: 10.26508/lsa.202201790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/21/2023] Open
Abstract
Fun30 is the prototype of the Fun30-SMARCAD1-ETL subfamily of nucleosome remodelers involved in DNA repair and gene silencing. These proteins appear to act as single-subunit nucleosome remodelers, but their molecular mechanisms are, at this point, poorly understood. Using multiple sequence alignment and structure prediction, we identify an evolutionarily conserved domain that is modeled to contain a SAM-like fold with one long, protruding helix, which we term SAM-key. Deletion of the SAM-key within budding yeast Fun30 leads to a defect in DNA repair and gene silencing similar to that of the fun30Δ mutant. In vitro, Fun30 protein lacking the SAM-key is able to bind nucleosomes but is deficient in DNA-stimulated ATPase activity and nucleosome sliding and eviction. A structural model based on AlphaFold2 prediction and verified by crosslinking-MS indicates an interaction of the long SAM-key helix with protrusion I, a subdomain located between the two ATPase lobes that is critical for control of enzymatic activity. Mutation of the interaction interface phenocopies the domain deletion with a lack of DNA-stimulated ATPase activation and a nucleosome-remodeling defect, thereby confirming a role of the SAM-key helix in regulating ATPase activity. Our data thereby demonstrate a central role of the SAM-key domain in mediating the activation of Fun30 catalytic activity, thus highlighting the importance of allosteric activation for this class of enzymes.
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Affiliation(s)
- Leonhard A Karl
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Susanne Cs Bantele
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Felix Metzner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Barbara Šafarić
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lional Rajappa
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Benjamin Foster
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Vanessa Borges Pires
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Priyanka Bansal
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Erika Chacin
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Jerôme Basquin
- Crystallization Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Martinsried, Germany
- Physik Department, Technische Universität München, Munich, Germany
| | - Christoph F Kurat
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Till Bartke
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
| | - Boris Pfander
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Genome Stability in Ageing and Disease, CECAD Research Center, University of Cologne, Cologne, Germany
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Iyer DR, Arige V, Ananthamohan K, Venkatasubramaniam S, Tokinoya K, Akoi K, Kurtz CL, Sethupathy P, Takekoshi K, Mahapatra NR. Cyclic-AMP response element binding protein (CREB) and microRNA miR-29b regulate renalase gene expression under catecholamine excess conditions. Life Sci 2023:121859. [PMID: 37315838 DOI: 10.1016/j.lfs.2023.121859] [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: 04/20/2023] [Revised: 06/09/2023] [Accepted: 06/09/2023] [Indexed: 06/16/2023]
Abstract
AIMS Renalase, a key mediator of cross-talk between kidneys and sympathetic nervous system, exerts protective roles in various cardiovascular/renal disease states. However, molecular mechanisms underpinning renalase gene expression remain incompletely understood. Here, we sought to identify the key molecular regulators of renalase under basal/catecholamine-excess conditions. MATERIALS AND METHODS Identification of the core promoter domain of renalase was carried out by promoter-reporter assays in N2a/HEK-293/H9c2 cells. Computational analysis of the renalase core promoter domain, over-expression of cyclic-AMP-response-element-binding-protein (CREB)/dominant negative mutant of CREB, ChIP assays were performed to determine the role of CREB in transcription regulation. Role of the miR-29b-mediated-suppression of renalase was validated in-vivo by using locked-nucleic-acid-inhibitors of miR-29. qRT-PCR and Western-blot analyses measured the expression of renalase, CREB, miR-29b and normalization controls in cell lysates/ tissue samples under basal/epinephrine-treated conditions. KEY FINDINGS CREB, a downstream effector in epinephrine signaling, activated renalase expression via its binding to the renalase-promoter. Physiological doses of epinephrine and isoproteronol enhanced renalase-promoter activity and endogenous renalase protein level while propranolol diminished the promoter activity and endogenous renalase protein level indicating a potential role of beta-adrenergic receptor in renalase gene regulation. Multiple animal models (acute exercise, genetically hypertensive/stroke-prone mice/rat) displayed directionally-concordant expression of CREB and renalase. Administration of miR-29b inhibitor in mice upregulated endogenous renalase expression. Moreover, epinephrine treatment down-regulated miR-29b promoter-activity/transcript levels. SIGNIFICANCE This study provides evidence for renalase gene regulation by concomitant transcriptional activation via CREB and post-transcriptional attenuation via miR-29b under excess epinephrine conditions. These findings have implications for disease states with dysregulated catecholamines.
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Affiliation(s)
- Dhanya R Iyer
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Vikas Arige
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Kalyani Ananthamohan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - S Venkatasubramaniam
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Katsuyuki Tokinoya
- Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Kai Akoi
- Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - C Lisa Kurtz
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Kazuhiro Takekoshi
- Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Nitish R Mahapatra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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Bisht D, Patne K, Rakesh R, Muthuswami R. On the Interaction Between SMARCAL1 and BRG1. Front Cell Dev Biol 2022; 10:870815. [PMID: 35784471 PMCID: PMC9243424 DOI: 10.3389/fcell.2022.870815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/30/2022] [Indexed: 11/18/2022] Open
Abstract
SMARCAL1 and BRG1, both classified as ATP-dependent chromatin remodeling proteins, play a role in double-strand break DNA damage response pathways. Mutations in SMARCAL1 cause Schimke Immuno-osseous Dysplasia (SIOD) while mutations in BRG1 are associated with Coffin-Siris Syndrome (CSS4). In HeLa cells, SMARCAL1 and BRG1 co-regulate the expression of ATM, ATR, and RNAi genes on doxorubicin-induced DNA damage. Both the proteins are found to be simultaneously present on the promoter of these genes. Based on these results we hypothesized that SMARCAL1 and BRG1 interact with each other forming a complex. In this paper, we validate our hypothesis and show that SMARCAL1 and BRG1 do indeed interact with each other both in the absence and presence of doxorubicin. The formation of these complexes is dependent on the ATPase activity of both SMARCAL1 and BRG1. Using deletion constructs, we show that the HARP domains of SMARCAL1 mediate interaction with BRG1 while multiple domains of BRG1 are probably important for binding to SMARCAL1. We also show that SIOD-associated mutants fail to form a complex with BRG1. Similarly, CSS4-associated mutants of BRG1 fail to interact with SMARCAL1, thus, possibly contributing to the failure of the DNA damage response pathway and pathophysiology associated with SIOD and CSS4.
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Rakesh R, Chanana UB, Hussain S, Sharma S, Goel K, Bisht D, Patne K, Swer PB, Hockensmith JW, Muthuswami R. Altering mammalian transcription networking with ADAADi: An inhibitor of ATP-dependent chromatin remodeling. PLoS One 2021; 16:e0251354. [PMID: 33999958 PMCID: PMC8128233 DOI: 10.1371/journal.pone.0251354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/23/2021] [Indexed: 11/30/2022] Open
Abstract
Active DNA-dependent ATPase A Domain inhibitor (ADAADi) is the only known inhibitor of ATP-dependent chromatin remodeling proteins that targets the ATPase domain of these proteins. The molecule is synthesized by aminoglycoside phosphotransferase enzyme in the presence of aminoglycosides. ADAADi interacts with ATP-dependent chromatin remodeling proteins through motif Ia present in the conserved helicase domain, and thus, can potentially inhibit all members of this family of proteins. We show that mammalian cells are sensitive to ADAADi but with variable responses in different cell lines. ADAADi can be generated from a wide variety of aminoglycosides; however, cells showed differential response to ADAADi generated from various aminoglycosides. Using HeLa and DU145 cells as model system we have explored the effect of ADAADi on cellular functions. We show that the transcriptional network of a cell type is altered when treated with sub-lethal concentration of ADAADi. Although ADAADi has no known effects on DNA chemical and structural integrity, expression of DNA-damage response genes was altered. The transcripts encoding for the pro-apoptotic proteins were found to be upregulated while the anti-apoptotic genes were found to be downregulated. This was accompanied by increased apoptosis leading us to hypothesize that the ADAADi treatment promotes apoptotic-type of cell death by upregulating the transcription of pro-apoptotic genes. ADAADi also inhibited migration of cells as well as their colony forming ability leading us to conclude that the compound has effective anti-tumor properties.
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Affiliation(s)
| | | | - Saddam Hussain
- Chromatin Remodeling Laboratory, School of Life Sciences, JNU, New Delhi, India
| | - Soni Sharma
- Chromatin Remodeling Laboratory, School of Life Sciences, JNU, New Delhi, India
| | - Kaveri Goel
- Chromatin Remodeling Laboratory, School of Life Sciences, JNU, New Delhi, India
| | - Deepa Bisht
- Chromatin Remodeling Laboratory, School of Life Sciences, JNU, New Delhi, India
| | - Ketki Patne
- Chromatin Remodeling Laboratory, School of Life Sciences, JNU, New Delhi, India
| | - Pynskhem Bok Swer
- Chromatin Remodeling Laboratory, School of Life Sciences, JNU, New Delhi, India
| | - Joel W Hockensmith
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Rohini Muthuswami
- Chromatin Remodeling Laboratory, School of Life Sciences, JNU, New Delhi, India
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Bansal R, Hussain S, Chanana UB, Bisht D, Goel I, Muthuswami R. SMARCAL1, the annealing helicase and the transcriptional co-regulator. IUBMB Life 2020; 72:2080-2096. [PMID: 32754981 DOI: 10.1002/iub.2354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/26/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022]
Abstract
The ATP-dependent chromatin remodeling proteins play an important role in DNA repair. The energy released by ATP hydrolysis is used for myriad functions ranging from nucleosome repositioning and nucleosome eviction to histone variant exchange. In addition, the distant member of the family, SMARCAL1, uses the energy to reanneal stalled replication forks in response to DNA damage. Biophysical studies have shown that this protein has the unique ability to recognize and bind specifically to DNA structures possessing double-strand to single-strand transition regions. Mutations in SMARCAL1 have been linked to Schimke immuno-osseous dysplasia, an autosomal recessive disorder that exhibits variable penetrance and expressivity. It has long been hypothesized that the variable expressivity and pleiotropic phenotypes observed in the patients might be due to the ability of SMARCAL1 to co-regulate the expression of a subset of genes within the genome. Recently, the role of SMARCAL1 in regulating transcription has been delineated. In this review, we discuss the biophysical and functional properties of the protein that help it to transcriptionally co-regulate DNA damage response as well as to bind to the stalled replication fork and stabilize it, thus ensuring genomic stability. We also discuss the role of SMARCAL1 in cancer and the possibility of using this protein as a chemotherapeutic target.
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Affiliation(s)
- Ritu Bansal
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Saddam Hussain
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Upasana Bedi Chanana
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Deepa Bisht
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Isha Goel
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Muthuswami
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Ciechomska IA, Jayaprakash C, Maleszewska M, Kaminska B. Histone Modifying Enzymes and Chromatin Modifiers in Glioma Pathobiology and Therapy Responses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1202:259-279. [PMID: 32034718 DOI: 10.1007/978-3-030-30651-9_13] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Signal transduction pathways directly communicate and transform chromatin to change the epigenetic landscape and regulate gene expression. Chromatin acts as a dynamic platform of signal integration and storage. Histone modifications and alteration of chromatin structure play the main role in chromatin-based gene expression regulation. Alterations in genes coding for histone modifying enzymes and chromatin modifiers result in malfunction of proteins that regulate chromatin modification and remodeling. Such dysregulations culminate in profound changes in chromatin structure and distorted patterns of gene expression. Gliomagenesis is a multistep process, involving both genetic and epigenetic alterations. Recent applications of next generation sequencing have revealed that many chromatin regulation-related genes, including ATRX, ARID1A, SMARCA4, SMARCA2, SMARCC2, BAF155 and hSNF5 are mutated in gliomas. In this review we summarize newly identified mechanisms affecting expression or functions of selected histone modifying enzymes and chromatin modifiers in gliomas. We focus on selected examples of pathogenic mechanisms involving ATRX, histone methyltransferase G9a, histone acetylases/deacetylases and chromatin remodeling complexes SMARCA2/4. We discuss the impact of selected epigenetics alterations on glioma pathobiology, signaling and therapeutic responses. We assess the attempts of targeting defective pathways with new inhibitors.
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Affiliation(s)
- Iwona A Ciechomska
- Laboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Chinchu Jayaprakash
- Laboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Marta Maleszewska
- Laboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, Warsaw, Poland.
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Muthuswami R, Bailey L, Rakesh R, Imbalzano AN, Nickerson JA, Hockensmith JW. BRG1 is a prognostic indicator and a potential therapeutic target for prostate cancer. J Cell Physiol 2019; 234:15194-15205. [PMID: 30667054 PMCID: PMC6563042 DOI: 10.1002/jcp.28161] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 02/06/2023]
Abstract
Brahma-related gene 1 (BRG1) is one of two mutually exclusive ATPases that function as the catalytic subunit of human SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling enzymes. BRG1 has been identified as a tumor suppressor in some cancer types but has been shown to be expressed at elevated levels, relative to normal tissue, in other cancers. Using TCGA (The Cancer Genome Atlas) prostate cancer database, we determined that BRG1 mRNA and protein expression is elevated in prostate tumors relative to normal prostate tissue. Only 3 of 491 (0.6%) sequenced tumors showed amplification of the locus or mutation in the protein coding sequence, arguing against the idea that elevated expression due to amplification or expression of a mutant BRG1 protein is associated with prostate cancer. Kaplan-Meier survival curves showed that BRG1 expression in prostate tumors inversely correlated with survival. However, BRG1 expression did not correlate with Gleason score/International Society of Urological Pathology (ISUP) Grade Group, indicating it is an independent predictor of tumor progression/patient outcome. To experimentally assess BRG1 as a possible therapeutic target, we treated prostate cancer cells with a biologic inhibitor called ADAADi (active DNA-dependent ATPase A Domain inhibitor) that targets the activity of the SNF2 family of ATPases in biochemical assays but showed specificity for BRG1 in prior tissue culture experiments. The inhibitor decreased prostate cancer cell proliferation and induced apoptosis. When directly injected into xenografts established by injection of prostate cancer cells in mouse flanks, the inhibitor decreased tumor growth and increased survival. These results indicate the efficacy of pursuing BRG1 as both an indicator of patient outcome and as a therapeutic target.
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Affiliation(s)
- Rohini Muthuswami
- Department of Biochemistry and Molecular GeneticsUniversity of Virginia School of MedicineCharlottesvilleVirginia,School of Life Sciences, Jawaharlal Nehru UniversityNew DelhiIndia
| | - LeeAnn Bailey
- Department of Biochemistry and Molecular GeneticsUniversity of Virginia School of MedicineCharlottesvilleVirginia
| | | | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular PharmacologyUniversity of Massachusetts Medical SchoolWorcesterMassachusetts
| | - Jeffrey A. Nickerson
- Department of PediatricsUniversity of Massachusetts Medical SchoolWorcesterMassachusetts
| | - Joel W. Hockensmith
- Department of Biochemistry and Molecular GeneticsUniversity of Virginia School of MedicineCharlottesvilleVirginia
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11
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Adult Cardiac Stem Cell Aging: A Reversible Stochastic Phenomenon? OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:5813147. [PMID: 30881594 PMCID: PMC6383393 DOI: 10.1155/2019/5813147] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/08/2018] [Indexed: 12/17/2022]
Abstract
Aging is by far the dominant risk factor for the development of cardiovascular diseases, whose prevalence dramatically increases with increasing age reaching epidemic proportions. In the elderly, pathologic cellular and molecular changes in cardiac tissue homeostasis and response to injury result in progressive deteriorations in the structure and function of the heart. Although the phenotypes of cardiac aging have been the subject of intense study, the recent discovery that cardiac homeostasis during mammalian lifespan is maintained and regulated by regenerative events associated with endogenous cardiac stem cell (CSC) activation has produced a crucial reconsideration of the biology of the adult and aged mammalian myocardium. The classical notion of the adult heart as a static organ, in terms of cell turnover and renewal, has now been replaced by a dynamic model in which cardiac cells continuously die and are then replaced by CSC progeny differentiation. However, CSCs are not immortal. They undergo cellular senescence characterized by increased ROS production and oxidative stress and loss of telomere/telomerase integrity in response to a variety of physiological and pathological demands with aging. Nevertheless, the old myocardium preserves an endogenous functionally competent CSC cohort which appears to be resistant to the senescent phenotype occurring with aging. The latter envisions the phenomenon of CSC ageing as a result of a stochastic and therefore reversible cell autonomous process. However, CSC aging could be a programmed cell cycle-dependent process, which affects all or most of the endogenous CSC population. The latter would infer that the loss of CSC regenerative capacity with aging is an inevitable phenomenon that cannot be rescued by stimulating their growth, which would only speed their progressive exhaustion. The resolution of these two biological views will be crucial to design and develop effective CSC-based interventions to counteract cardiac aging not only improving health span of the elderly but also extending lifespan by delaying cardiovascular disease-related deaths.
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12
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Zernickel E, Sak A, Riaz A, Klein D, Groneberg M, Stuschke M. Targeting of BRM Sensitizes BRG1-Mutant Lung Cancer Cell Lines to Radiotherapy. Mol Cancer Ther 2018; 18:656-666. [PMID: 30478150 DOI: 10.1158/1535-7163.mct-18-0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 06/30/2018] [Accepted: 11/15/2018] [Indexed: 11/16/2022]
Abstract
Targeting of epigenetic regulators as the chromatin remodeler SWI/SNF is proving to be a promising therapeutic strategy for individualized treatment of cancer patients. Here, we tested whether targeting one of the two mutually exclusive subdomains of the SWI/SNF complex BRM/SMARCA2 can sensitize specifically non-small cell lung carcinoma (NSCLC) cells with mutations in the other subunit BRG1/SMARCA4 toward ionizing radiation (IR). Knockdown of BRM with siRNA or shRNA and its consequences for radiation sensitivity as measured by clonogenic survival and plaque-monolayer control was studied in different NSCLC lines with or without BRG1 mutations and in primary fibroblasts. Furthermore, the effect on double-strand break (DSB) repair markers measured by immunofluorescence staining of 53BP1-, γ-H2AX-, and Rad51-foci was investigated. BRG1-mutated cell lines showed an increased surviving fraction compared with BRG1 proficient cells. Depletion of BRM (i) leads to a decreased proliferation rate and plating efficiency specifically in BRG1-mutated cells, (ii) specifically sensitized BRG1-mutant NSCLC cells toward IR as characterized by a survival reducing factor of 0.63 [95% confidence interval (CI), 0.57-0.69] in the dose range between 2 and 6 Gy, and (iii) decreased the tumor control doses after daily fractionation at 4 Gy in BRG1-mutant NSCLC cell lines A549 and H1299 in minimonolayers by 9.9% ± 1.3% and 13.6% ± 1.8%, respectively. In addition, an increase of residual Rad51-foci at 24 hours after irradiation in BRG1-mutant cells was demonstrated. Therefore, targeting of BRM in combination with radiotherapy is supposed to improve the therapeutic outcome of lung cancer patients harboring BRG1 mutations.The present study shows that the moderate radioresponsiveness of NSCLC cells with BRG1 mutations can be increased upon BRM depletion that is associated with a prolonged Rad51-foci prevalence at DNA DSBs.
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Affiliation(s)
- Erika Zernickel
- Department of Radiotherapy, University of Duisburg-Essen, University Hospital, Essen, Germany.
| | - Ali Sak
- Department of Radiotherapy, University of Duisburg-Essen, University Hospital, Essen, Germany
| | - Assad Riaz
- Department of Radiotherapy, University of Duisburg-Essen, University Hospital, Essen, Germany
| | - Diana Klein
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, University Hospital, Essen, Germany
| | - Michael Groneberg
- Department of Radiotherapy, University of Duisburg-Essen, University Hospital, Essen, Germany
| | - Martin Stuschke
- Department of Radiotherapy, University of Duisburg-Essen, University Hospital, Essen, Germany
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13
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Wu Q, Madany P, Dobson JR, Schnabl JM, Sharma S, Smith TC, van Wijnen AJ, Stein JL, Lian JB, Stein GS, Muthuswami R, Imbalzano AN, Nickerson JA. The BRG1 chromatin remodeling enzyme links cancer cell metabolism and proliferation. Oncotarget 2018; 7:38270-38281. [PMID: 27223259 PMCID: PMC5122388 DOI: 10.18632/oncotarget.9505] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/01/2016] [Indexed: 12/20/2022] Open
Abstract
Cancer cells reprogram cellular metabolism to meet the demands of growth. Identification of the regulatory machinery that regulates cancer-specific metabolic changes may open new avenues for anti-cancer therapeutics. The epigenetic regulator BRG1 is a catalytic ATPase for some mammalian SWI/SNF chromatin remodeling enzymes. BRG1 is a well-characterized tumor suppressor in some human cancers, but is frequently overexpressed without mutation in other cancers, including breast cancer. Here we demonstrate that BRG1 upregulates de novo lipogenesis and that this is crucial for cancer cell proliferation. Knockdown of BRG1 attenuates lipid synthesis by impairing the transcription of enzymes catalyzing fatty acid and lipid synthesis. Remarkably, exogenous addition of palmitate, the key intermediate in fatty acid synthesis, rescued the cancer cell proliferation defect caused by BRG1 knockdown. Our work suggests that targeting BRG1 to reduce lipid metabolism and, thereby, to reduce proliferation, has promise for epigenetic therapy in triple negative breast cancer.
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Affiliation(s)
- Qiong Wu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Pasil Madany
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jason R Dobson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jake M Schnabl
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Soni Sharma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Tara C Smith
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Andre J van Wijnen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Janet L Stein
- Department of Biochemistry and Vermont Cancer Center for Basic and Translational Research, University of Vermont College of Medicine, Burlington, WA, USA
| | - Jane B Lian
- Department of Biochemistry and Vermont Cancer Center for Basic and Translational Research, University of Vermont College of Medicine, Burlington, WA, USA
| | - Gary S Stein
- Department of Biochemistry and Vermont Cancer Center for Basic and Translational Research, University of Vermont College of Medicine, Burlington, WA, USA
| | - Rohini Muthuswami
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jeffrey A Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
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14
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Wu Q, Sharma S, Cui H, LeBlanc SE, Zhang H, Muthuswami R, Nickerson JA, Imbalzano AN. Targeting the chromatin remodeling enzyme BRG1 increases the efficacy of chemotherapy drugs in breast cancer cells. Oncotarget 2017; 7:27158-75. [PMID: 27029062 PMCID: PMC5053639 DOI: 10.18632/oncotarget.8384] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/16/2016] [Indexed: 12/31/2022] Open
Abstract
Brahma related gene product 1 (BRG1) is an ATPase that drives the catalytic activity of a subset of the mammalian SWI/SNF chromatin remodeling enzymes. BRG1 is overexpressed in most human breast cancer tumors without evidence of mutation and is required for breast cancer cell proliferation. We demonstrate that knockdown of BRG1 sensitized triple negative breast cancer cells to chemotherapeutic drugs used to treat breast cancer. An inhibitor of the BRG1 bromodomain had no effect on breast cancer cell viability, but an inhibitory molecule that targets the BRG1 ATPase activity recapitulated the increased drug efficacy observed in the presence of BRG1 knockdown. We further demonstrate that inhibition of BRG1 ATPase activity blocks the induction of ABC transporter genes by these chemotherapeutic drugs and that BRG1 binds to ABC transporter gene promoters. This inhibition increased intracellular concentrations of the drugs, providing a likely mechanism for the increased chemosensitivity. Since ABC transporters and their induction by chemotherapy drugs are a major cause of chemoresistance and treatment failure, these results support the idea that targeting the enzymatic activity of BRG1 would be an effective adjuvant therapy for breast cancer.
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Affiliation(s)
- Qiong Wu
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Soni Sharma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Hang Cui
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA.,Abace Biotech Co Ltd., Yi Zhuang Biomedical Park, BDA, Beijing, China
| | - Scott E LeBlanc
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hong Zhang
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rohini Muthuswami
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi, India
| | - Jeffrey A Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anthony N Imbalzano
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
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15
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Wu Q, Lian JB, Stein JL, Stein GS, Nickerson JA, Imbalzano AN. The BRG1 ATPase of human SWI/SNF chromatin remodeling enzymes as a driver of cancer. Epigenomics 2017; 9:919-931. [PMID: 28521512 PMCID: PMC5705788 DOI: 10.2217/epi-2017-0034] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Mammalian SWI/SNF enzymes are ATP-dependent remodelers of chromatin structure. These multisubunit enzymes are heterogeneous in composition; there are two catalytic ATPase subunits, BRM and BRG1, that are mutually exclusive, and additional subunits are incorporated in a combinatorial manner. Recent findings indicate that approximately 20% of human cancers contain mutations in SWI/SNF enzyme subunits, leading to the conclusion that the enzyme subunits are critical tumor suppressors. However, overexpression of specific subunits without apparent mutation is emerging as an alternative mechanism by which cellular transformation may occur. Here we highlight recent evidence linking elevated expression of the BRG1 ATPase to tissue-specific cancers and work suggesting that inhibiting BRG1 may be an effective therapeutic strategy.
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Affiliation(s)
- Qiong Wu
- Department of Pediatrics, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Jane B Lian
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Janet L Stein
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Gary S Stein
- Department of Biochemistry, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT 05405, USA
| | - Jeffrey A Nickerson
- Department of Pediatrics, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA
| | - Anthony N Imbalzano
- Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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16
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Nickerson JA, Wu Q, Imbalzano AN. Mammalian SWI/SNF Enzymes and the Epigenetics of Tumor Cell Metabolic Reprogramming. Front Oncol 2017; 7:49. [PMID: 28421159 PMCID: PMC5378717 DOI: 10.3389/fonc.2017.00049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/09/2017] [Indexed: 01/27/2023] Open
Abstract
Tumor cells reprogram their metabolism to survive and grow in a challenging microenvironment. Some of this reprogramming is performed by epigenetic mechanisms. Epigenetics is in turn affected by metabolism; chromatin modifying enzymes are dependent on substrates that are also key metabolic intermediates. We have shown that the chromatin remodeling enzyme Brahma-related gene 1 (BRG1), an epigenetic regulator, is necessary for rapid breast cancer cell proliferation. The mechanism for this requirement is the BRG1-dependent transcription of key lipogenic enzymes and regulators. Reduction in lipid synthesis lowers proliferation rates, which can be restored by palmitate supplementation. This work has established BRG1 as an attractive target for breast cancer therapy. Unlike genetic alterations, epigenetic mechanisms are reversible, promising gentler therapies without permanent off-target effects at distant sites.
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Affiliation(s)
- Jeffrey A Nickerson
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Qiong Wu
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA, USA
| | - Anthony N Imbalzano
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
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17
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Kwon Y, Cha J, Chiang J, Tran G, Giaever G, Nislow C, Hur JS, Kwak YS. A chemogenomic approach to understand the antifungal action of Lichen-derived vulpinic acid. J Appl Microbiol 2016; 121:1580-1591. [DOI: 10.1111/jam.13300] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/15/2016] [Accepted: 09/11/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Y. Kwon
- Division of Applied Life Science; Gyeongsang National University; Jinju Korea
| | - J. Cha
- Department of Plant Medicine and Institute of Agriculture & Life Science; Gyeongsang National University; Jinju Korea
| | - J. Chiang
- Pharmaceutical Sciences; University of British Columbia; Vancouver BC Canada
| | - G. Tran
- Pharmaceutical Sciences; University of British Columbia; Vancouver BC Canada
| | - G. Giaever
- Pharmaceutical Sciences; University of British Columbia; Vancouver BC Canada
| | - C. Nislow
- Pharmaceutical Sciences; University of British Columbia; Vancouver BC Canada
| | - J.-S. Hur
- Korean Lichen Research Institute; Suncheon National University; Suncheon Korea
| | - Y.-S. Kwak
- Department of Plant Medicine and Institute of Agriculture & Life Science; Gyeongsang National University; Jinju Korea
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18
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Haokip DT, Goel I, Arya V, Sharma T, Kumari R, Priya R, Singh M, Muthuswami R. Transcriptional Regulation of Atp-Dependent Chromatin Remodeling Factors: Smarcal1 and Brg1 Mutually Co-Regulate Each Other. Sci Rep 2016; 6:20532. [PMID: 26843359 PMCID: PMC4740806 DOI: 10.1038/srep20532] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 01/06/2016] [Indexed: 11/09/2022] Open
Abstract
The ATP-dependent chromatin remodeling factors regulate gene expression. However, it is not known whether these factors regulate each other. Given the ability of these factors to regulate the accessibility of DNA to transcription factors, we postulate that one ATP-dependent chromatin remodeling factor should be able to regulate the transcription of another ATP-dependent chromatin remodeling factor. In this paper, we show that BRG1 and SMARCAL1, both members of the ATP-dependent chromatin remodeling protein family, regulate each other. BRG1 binds to the SMARCAL1 promoter, while SMARCAL1 binds to the brg1 promoter. During DNA damage, the occupancy of SMARCAL1 on the brg1 promoter increases coinciding with an increase in BRG1 occupancy on the SMARCAL1 promoter, leading to increased brg1 and SMARCAL1 transcripts respectively. This is the first report of two ATP-dependent chromatin remodeling factors regulating each other.
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Affiliation(s)
| | - Isha Goel
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Vijendra Arya
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Tapan Sharma
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Reshma Kumari
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Rashmi Priya
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Manpreet Singh
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Rohini Muthuswami
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067
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19
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Sharma T, Bansal R, Haokip DT, Goel I, Muthuswami R. SMARCAL1 Negatively Regulates C-Myc Transcription By Altering The Conformation Of The Promoter Region. Sci Rep 2015; 5:17910. [PMID: 26648259 PMCID: PMC4673416 DOI: 10.1038/srep17910] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 11/09/2015] [Indexed: 12/18/2022] Open
Abstract
SMARCAL1, a member of the SWI2/SNF2 protein family, stabilizes replication forks during DNA damage. In this manuscript, we provide the first evidence that SMARCAL1 is also a transcriptional co-regulator modulating the expression of c-Myc, a transcription factor that regulates 10-15% genes in the human genome. BRG1, SMARCAL1 and RNAPII were found localized onto the c-myc promoter. When HeLa cells were serum starved, the occupancy of SMARCAL1 on the c-myc promoter increased while that of BRG1 and RNAPII decreased correlating with repression of c-myc transcription. Using Active DNA-dependent ATPase A Domain (ADAAD), the bovine homolog of SMARCAL1, we show that the protein can hydrolyze ATP using a specific region upstream of the CT element of the c-myc promoter as a DNA effector. The energy, thereby, released is harnessed to alter the conformation of the promoter DNA. We propose that SMARCAL1 negatively regulates c-myc transcription by altering the conformation of its promoter region during differentiation.
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Affiliation(s)
| | - Ritu Bansal
- School of Life Sciences, JNU, New Delhi 110067
| | | | - Isha Goel
- School of Life Sciences, JNU, New Delhi 110067
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20
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Tanti GK, Pandey S, Goswami SK. SG2NA enhances cancer cell survival by stabilizing DJ-1 and thus activating Akt. Biochem Biophys Res Commun 2015; 463:524-31. [DOI: 10.1016/j.bbrc.2015.05.069] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/18/2015] [Indexed: 01/20/2023]
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21
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Jain BP, Chauhan P, Tanti GK, Singarapu N, Ghaskadbi S, Goswami SK. Tissue specific expression of SG2NA is regulated by differential splicing, RNA editing and differential polyadenylation. Gene 2015; 556:119-126. [PMID: 25459749 DOI: 10.1016/j.gene.2014.11.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 11/05/2014] [Accepted: 11/20/2014] [Indexed: 11/21/2022]
Abstract
SG2NA belongs to a three member Striatin subfamily of WD-40 repeat superfamily. It has multiple protein-protein interaction domains that are involved in the assembly of supra-molecular signaling complexes. Earlier we had demonstrated that there are at least five variants of SG2NA, generated by alternative splicing. We now demonstrate that a 52kDa novel variant is generated by the editing of the transcript for the 82kDa isoform. The 52kDa protein is abundant in mouse tissues but it is barely present in immortalized cells, suggesting its role in cell differentiation. Besides splicing and editing, expression of SG2NAs in tissues is also regulated by differential polyadenylation and mRNA/protein stability. Further, the longer UTR is seen only in the brain mRNA from 1month old mouse and 8-10day old chick embryo. Like alternative splicing, differential polyadenylation of Sg2na transcripts is also conserved in evolution. Taken together, these results suggest a highly versatile and dynamic mode of regulation of SG2NA with potential implications in tissue development.
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Affiliation(s)
- Buddhi Prakash Jain
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pooja Chauhan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Goutam K Tanti
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Nandini Singarapu
- The University of Texas M.D. Anderson Cancer Center, Science Park, Department of Molecular Carcinogenesis, P.O. Box 389, Smithville, TX 78957, United States
| | | | - Shyamal K Goswami
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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22
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Tanti GK, Goswami SK. SG2NA recruits DJ-1 and Akt into the mitochondria and membrane to protect cells from oxidative damage. Free Radic Biol Med 2014; 75:1-13. [PMID: 25035075 DOI: 10.1016/j.freeradbiomed.2014.07.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/24/2014] [Accepted: 07/07/2014] [Indexed: 12/31/2022]
Abstract
SG2NA is a WD-40 repeat protein with multiple protein-protein interaction domains of unknown functions. We demonstrate that it associates with the antioxidant protein DJ-1 and the survival kinase Akt. The C-terminal WD-40 repeat domain of SG2NA is required for its interaction with Akt, while DJ-1 binds it further upstream. No interaction between DJ-1 and Akt occurs in the absence of SG2NA. SG2NA, DJ-1, and Akt colocalize in mitochondria and plasma membrane. Their association is enhanced by increasing levels of reactive oxygen species up to a threshold level but falters thereafter with further increase in oxidants. Mutants of DJ-1 found in patients with familial parkinsonism are not recruited by SG2NA, suggesting its role in neuroprotection. Cells depleted of SG2NA are susceptible, while those overexpressing it are resistant to apoptosis induced by oxidative stress. Our study thus unravels a novel pathway of recruitment of Akt and DJ-1 that provides protection against oxidative stress, especially in neurons.
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Affiliation(s)
- Goutam Kumar Tanti
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Shyamal K Goswami
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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23
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Marker-free plasmids for biotechnological applications – implications and perspectives. Trends Biotechnol 2013; 31:539-47. [DOI: 10.1016/j.tibtech.2013.06.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/03/2013] [Accepted: 06/03/2013] [Indexed: 11/22/2022]
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