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Abstract
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional small molecules that induce the ternary complex formation between a protein-of-interest (POI) and an E3 ligase, leading to targeted polyubiquitination and degradation of the POI. Particularly, PROTACs have the distinct advantage of targeting both canonical and noncanonical functions of epigenetic targets over traditional inhibitors, which typically target canonical functions only, resulting in greater therapeutic efficacy. In this review, we methodically analyze published PROTAC degraders of epigenetic writer, reader, and eraser proteins and their in vitro and in vivo effects. We highlight the mechanism of action of these degraders and their advantages in targeting both canonical and noncanonical functions of epigenetic targets in the context of cancer treatment. Furthermore, we present a future outlook for this exciting field. Overall, pharmacological degradation of epigenetic targets has emerged as an effective and attractive strategy to thwart cancer progression and growth.
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Affiliation(s)
- Md Kabir
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
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2
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Usher ET, Showalter SA. Biophysical insights into glucose-dependent transcriptional regulation by PDX1. J Biol Chem 2022; 298:102623. [PMID: 36272648 PMCID: PMC9691942 DOI: 10.1016/j.jbc.2022.102623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/22/2022] Open
Abstract
The pancreatic and duodenal homeobox 1 (PDX1) is a central regulator of glucose-dependent transcription of insulin in pancreatic β cells. PDX1 transcription factor activity is integral to the development and sustained health of the pancreas; accordingly, deciphering the complex network of cellular cues that lead to PDX1 activation or inactivation is an important step toward understanding the etiopathologies of pancreatic diseases and the development of novel therapeutics. Despite nearly 3 decades of research into PDX1 control of Insulin expression, the molecular mechanisms that dictate the function of PDX1 in response to glucose are still elusive. The transcriptional activation functions of PDX1 are regulated, in part, by its two intrinsically disordered regions, which pose a barrier to its structural and biophysical characterization. Indeed, many studies of PDX1 interactions, clinical mutations, and posttranslational modifications lack molecular level detail. Emerging methods for the quantitative study of intrinsically disordered regions and refined models for transactivation now enable us to validate and interrogate the biochemical and biophysical features of PDX1 that dictate its function. The goal of this review is to summarize existing PDX1 studies and, further, to generate a comprehensive resource for future studies of transcriptional control via PDX1.
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Affiliation(s)
- Emery T Usher
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Scott A Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.
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3
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Ma Q, Song C, Yin B, Shi Y, Ye L. The role of Trithorax family regulating osteogenic and Chondrogenic differentiation in mesenchymal stem cells. Cell Prolif 2022; 55:e13233. [PMID: 35481717 PMCID: PMC9136489 DOI: 10.1111/cpr.13233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/17/2022] [Accepted: 03/28/2022] [Indexed: 02/05/2023] Open
Abstract
Mesenchymal stem/stromal cells (MSCs) hold great promise and clinical efficacy in bone/cartilage regeneration. With a deeper understanding of stem cell biology over the past decade, epigenetics stands out as one of the most promising ways to control MSCs differentiation. Trithorax group (TrxG) proteins, including the COMPASS family, ASH1L, CBP/p300 as histone modifying factors, and the SWI/SNF complexes as chromatin remodelers, play an important role in gene expression regulation during the process of stem cell differentiation. This review summarises the components and functions of TrxG complexes. We provide an overview of the regulation mechanisms of TrxG in MSCs osteogenic and chondrogenic differentiation, and discuss the prospects of epigenetic regulation mediated by TrxG in bone and cartilage regeneration.
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Affiliation(s)
- Qingge Ma
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chenghao Song
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bei Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yu Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ling Ye
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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4
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Clapier CR. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Int J Mol Sci 2021; 22:5578. [PMID: 34070411 PMCID: PMC8197500 DOI: 10.3390/ijms22115578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions-in particular, the regulation of gene expression-and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences & Howard Hughes Medical Institute, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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5
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Odnokoz O, Wavelet-Vermuse C, Hophan SL, Bulun S, Wan Y. ARID1 proteins: from transcriptional and post-translational regulation to carcinogenesis and potential therapeutics. Epigenomics 2021; 13:809-823. [PMID: 33890484 PMCID: PMC8738980 DOI: 10.2217/epi-2020-0414] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The ARID1 proteins are mutually exclusive subunits of the BRG1/BRM-associated factor (BAF) complexes that play an important role in chromatin remodeling and regulate many fundamental cell functions. The role of ARID1s is well defined as a tumor-suppressive. The cancer cells evolve different mechanisms to downregulate ARID1s and inactivate their functions. ARID1s are frequently mutated in human cancer. The recent findings of ARID1A/B downregulation at transcriptional and translational levels along with their low levels in human cancers indicate the significance of regulatory mechanisms of ARID1s in cancers. In this review, we present the current knowledge on the regulation and alterations of ARID1 protein expression in human cancers and indicate the importance of regulators of ARID1s as a prognostic marker and in potential therapeutic strategies.
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Affiliation(s)
- Olena Odnokoz
- Department of Obstetrics & Gynecology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Pharmacology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Cindy Wavelet-Vermuse
- Department of Obstetrics & Gynecology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Pharmacology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shelby L Hophan
- Department of Obstetrics & Gynecology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Pharmacology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Serdar Bulun
- Department of Obstetrics & Gynecology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yong Wan
- Department of Obstetrics & Gynecology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Department of Pharmacology & Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA,Author for correspondence: Tel.: +1 312 503 2769;
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6
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Hartley A, Leung HY, Ahmad I. Targeting the BAF complex in advanced prostate cancer. Expert Opin Drug Discov 2021; 16:173-181. [PMID: 32936685 DOI: 10.1080/17460441.2020.1821644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/07/2020] [Indexed: 12/26/2022]
Abstract
INTRODUCTION The BRG1/BRM associated factors (BAF) complex is a chromatin remodeling SWI/SNF which is mutated in 20% of cancers. This complex has many interchangeable subunits which may have oncogenic or tumor suppressor activity in a context-dependent manner. The BAF complex is mutated in 35-50% of metastatic prostate cancer (PC); however, its role in advanced disease is unclear. This review attempts to consolidate current knowledge of the BAF complex in PC and explore potential therapeutic approaches. AREAS COVERED This review covers the known roles of some BAF subunits, their alterations, and the models which best explain their mechanisms in driving PC. Following this, the authors provide their expert perspective on how this complex could be targeted in the future with a personalized medicine approach. EXPERT OPINION Personalized medicine would allow for patient stratification to exploit synthetic lethal strategies in targeting a mutated BAF complex as shown experimentally in other cancers. BAF dependency can also be targeted in patients stratified for other molecular markers such as BRG1 targeting in phosphatase and tensin homolog (PTEN) deficient PC.
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Affiliation(s)
- Andrew Hartley
- Urology Research Group, CRUK Beatson Institute , Glasgow, UK
| | - Hing Y Leung
- Urology Research Group, CRUK Beatson Institute , Glasgow, UK
- Institue of Cancer Sciences, University of Glasgow , Glasgow, UK
| | - Imran Ahmad
- Urology Research Group, CRUK Beatson Institute , Glasgow, UK
- Institue of Cancer Sciences, University of Glasgow , Glasgow, UK
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7
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Infante A, Gener B, Vázquez M, Olivares N, Arrieta A, Grau G, Llano I, Madero L, Bueno AM, Sagastizabal B, Gerovska D, Araúzo‐Bravo MJ, Astigarraga I, Rodríguez CI. Reiterative infusions of MSCs improve pediatric osteogenesis imperfecta eliciting a pro-osteogenic paracrine response: TERCELOI clinical trial. Clin Transl Med 2021; 11:e265. [PMID: 33463067 PMCID: PMC7805402 DOI: 10.1002/ctm2.265] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Osteogenesis imperfecta (OI) is a rare genetic disease characterized by bone fragility, with a wide range in the severity of clinical manifestations. The majority of cases are due to mutations in the COL1A1 or COL1A2 genes, which encode type I collagen. Mesenchymal stem cells (MSCs), as the progenitors of the osteoblasts, the main type I collagen secreting cell type in the bone, have been proposed and tested as an innovative therapy for OI with promising but transient outcomes. METHODS To overcome the short-term effect of MSCs therapy, we performed a phase I clinical trial based on reiterative infusions of histocompatible MSCs, administered in a 2.5-year period, in two pediatric patients affected by severe and moderate OI. The aim of this study was to assess the safety and effectiveness of this cell therapy in nonimmunosuppressed OI patients. The host response to MSCs was studied by analyzing the sera from OI patients, collected before, during, and after the cell therapy. RESULTS We first demonstrated that the sequential administration of MSCs was safe and improved the bone parameters and quality of life of OI patients along the cell treatment plus 2-year follow-up period. Moreover, the study of the mechanism of action indicated that MSCs therapy elicited a pro-osteogenic paracrine response in patients, especially noticeable in the patient affected by severe OI. CONCLUSIONS Our results demonstrate the feasibility and potential of reiterative MSCs infusion for two pediatric OI and highlight the paracrine response shown by patients as a consequence of MSCs treatment.
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Affiliation(s)
- Arantza Infante
- Stem Cells and Cell Therapy LaboratoryBiocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
| | - Blanca Gener
- Stem Cells and Cell Therapy LaboratoryBiocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
- Service of GeneticsCruces University HospitalBarakaldoSpain
| | - Miguel Vázquez
- Department of PediatricsBiocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
| | - Nerea Olivares
- Department of Biochemistry, Immunology UnitCruces University HospitalBarakaldoSpain
| | - Arantza Arrieta
- Department of Biochemistry, Immunology UnitCruces University HospitalBarakaldoSpain
| | - Gema Grau
- Department of PediatricsBiocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
| | - Isabel Llano
- Service of GeneticsCruces University HospitalBarakaldoSpain
| | - Luis Madero
- Department of Pediatric Hematology, Oncology and Stem CellsNiño Jesús University Children´s HospitalMadridSpain
| | - Ana Maria Bueno
- Department of Orthopedic SurgeryGetafe University HospitalMadridSpain
| | | | - Daniela Gerovska
- Computational Biology and Systems Biomedicine Research GroupBiodonostia Health Research InstituteDonostiaSpain
| | - Marcos J Araúzo‐Bravo
- Computational Biology and Systems Biomedicine Research GroupBiodonostia Health Research InstituteDonostiaSpain
| | - Itziar Astigarraga
- Department of PediatricsBiocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
- Department of PediatricsBasque Country University UPV/EHULeioaSpain
| | - Clara I. Rodríguez
- Stem Cells and Cell Therapy LaboratoryBiocruces Bizkaia Health Research InstituteCruces University HospitalBarakaldoSpain
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8
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Chakraborty S, Sinha S, Sengupta A. Emerging trends in chromatin remodeler plasticity in mesenchymal stromal cell function. FASEB J 2020; 35:e21234. [PMID: 33337557 DOI: 10.1096/fj.202002232r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022]
Abstract
Emerging evidences highlight importance of epigenetic regulation and their integration with transcriptional and cell signaling machinery in determining tissue resident adult pluripotent mesenchymal stem/stromal cell (MSC) activity, lineage commitment, and multicellular development. Histone modifying enzymes and large multi-subunit chromatin remodeling complexes and their cell type-specific plasticity remain the central defining features of gene regulation and establishment of tissue identity. Modulation of transcription factor expression gradient ex vivo and concomitant flexibility of higher order chromatin architecture in response to signaling cues are exciting approaches to regulate MSC activity and tissue rejuvenation. Being an important constituent of the adult bone marrow microenvironment/niche, pathophysiological perturbation in MSC homeostasis also causes impaired hematopoietic stem/progenitor cell function in a non-cell autonomous mechanism. In addition, pluripotent MSCs can function as immune regulatory cells, and they reside at the crossroad of innate and adaptive immune response pathways. Research in the past few years suggest that MSCs/stromal fibroblasts significantly contribute to the establishment of immunosuppressive microenvironment in shaping antitumor immunity. Therefore, it is important to understand mesenchymal stromal epigenome and transcriptional regulation to leverage its applications in regenerative medicine, epigenetic memory-guided trained immunity, immune-metabolic rewiring, and precision immune reprogramming. In this review, we highlight the latest developments and prospects in chromatin biology in determining MSC function in the context of lineage commitment and immunomodulation.
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Affiliation(s)
- Sayan Chakraborty
- Stem Cell & Leukemia Laboratory, Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Translational Research Unit of Excellence (TRUE), Kolkata, India
| | - Sayantani Sinha
- Stem Cell & Leukemia Laboratory, Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Translational Research Unit of Excellence (TRUE), Kolkata, India
| | - Amitava Sengupta
- Stem Cell & Leukemia Laboratory, Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Translational Research Unit of Excellence (TRUE), Kolkata, India
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9
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Yoshino J, Akiyama Y, Shimada S, Ogura T, Ogawa K, Ono H, Mitsunori Y, Ban D, Kudo A, Yamaoka S, Tanabe M, Tanaka S. Loss of ARID1A induces a stemness gene ALDH1A1 expression with histone acetylation in the malignant subtype of cholangiocarcinoma. Carcinogenesis 2020; 41:734-742. [PMID: 31665232 DOI: 10.1093/carcin/bgz179] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/21/2019] [Accepted: 10/25/2019] [Indexed: 12/19/2022] Open
Abstract
Genomic analyses have recently discovered the malignant subtype of human intrahepatic cholangiocarcinoma (ICC) characterized by frequent mutations of chromatin remodeling gene ARID1A; however, the biological and molecular functions still remain obscure. We here examined the clinical and biological significances of ARID1A deficiency in human ICC. Immunohistochemical analysis demonstrated that the loss of ARID1A was an independent prognostic factor for overall survival of ICC patients (P = 0.023). We established ARID1A-knockout (KO) cells by using the CRISPR/Cas9 system from two human cholangiocarcinoma cell lines. ARID1A-KO cells exhibited significantly enhanced migration, invasion, and sphere formation activity. Microarray analysis revealed that ALDH1A1, a stemness gene, was the most significantly elevated genes in ARID1A-KO cells. In addition, ALDH enzymatic activity as a hallmark of cancer stem cells was markedly high in the KO cells. ARID1A and histone deacetylase 1 were directly recruited to the ALDH1A1 promoter region in cholangiocarcinoma cells with undetectable ALDH1A1 expression by chromatin immunoprecipitation assay. The histone H3K27 acetylation level at the ALDH1A1 promoter region was increased in cells when ARID1A was disrupted (P < 0.01). Clinically, inverse correlation between ARID1A and ALDH1A1 expression was also identified in primary ICC (P = 0.018), and ARID1A-negative and ALDH1A1-positve ICCs showed worse prognosis than only ARID1A-negative cases (P = 0.002). In conclusion, ARID1A may function as a tumor suppressor in ICC through transcriptional downregulation of ALDH1A1 expression with decreasing histone H3K27 acetylation. Our studies provide the basis for the development of new epigenetic approaches to ARID1A-negative ICC. Immunohistochemical loss of ARID1A is an independent prognostic factor in intrahepatic cholangiocarcinoma patients. ARID1A recruits HDAC1 to the promoter region of ALDH1A1, a stemness gene, and epigenetically suppresses ALDH1A1 expression with decreasing histone H3K27 acetylation in cholangiocarcinoma cells.
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Affiliation(s)
- Jun Yoshino
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo.,Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo
| | - Yoshimitsu Akiyama
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo
| | - Shu Shimada
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo
| | - Toshiro Ogura
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo
| | - Kosuke Ogawa
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo
| | - Hiroaki Ono
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo
| | - Yusuke Mitsunori
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo
| | - Daisuke Ban
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo
| | - Atsushi Kudo
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo
| | - Shoji Yamaoka
- Department of Molecular Virology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Minoru Tanabe
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo
| | - Shinji Tanaka
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo.,Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo
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10
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Sanchez JC, Zhang L, Evoli S, Schnicker NJ, Nunez-Hernandez M, Yu L, Wereszczynski J, Pufall MA, Musselman CA. The molecular basis of selective DNA binding by the BRG1 AT-hook and bromodomain. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194566. [PMID: 32376391 PMCID: PMC7350285 DOI: 10.1016/j.bbagrm.2020.194566] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 12/18/2022]
Abstract
The ATP-dependent BAF chromatin remodeling complex plays a critical role in gene regulation by modulating chromatin architecture, and is frequently mutated in cancer. Indeed, subunits of the BAF complex are found to be mutated in >20% of human tumors. The mechanism by which BAF properly navigates chromatin is not fully understood, but is thought to involve a multivalent network of histone and DNA contacts. We previously identified a composite domain in the BRG1 ATPase subunit that is capable of associating with both histones and DNA in a multivalent manner. Mapping the DNA binding pocket revealed that it contains several cancer mutations. Here, we utilize SELEX-seq to investigate the DNA specificity of this composite domain and NMR spectroscopy and molecular modelling to determine the structural basis of DNA binding. Finally, we demonstrate that cancer mutations in this domain alter the mode of DNA association.
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Affiliation(s)
- Julio C Sanchez
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States
| | - Liyang Zhang
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States; Integrated DNA Technologies IDT, Coralville, IA 52241, United States
| | - Stefania Evoli
- Department of Physics and The Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States
| | - Nicholas J Schnicker
- Protein & Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States
| | - Maria Nunez-Hernandez
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States
| | - Liping Yu
- Department of Biochemistry, Carver College of Medicine NMR Core Facility, University of Iowa, Iowa City, IA 52242, United States; The Iowa City Veterans Affairs Medical Center, Iowa City, IA 52242, United States
| | - Jeff Wereszczynski
- Department of Physics and The Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States.
| | - Miles A Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States.
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, United States; Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States.
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11
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Wu S, Ge Y, Li X, Yang Y, Zhou H, Lin K, Zhang Z, Zhao Y. BRM-SWI/SNF chromatin remodeling complex enables functional telomeres by promoting co-expression of TRF2 and TRF1. PLoS Genet 2020; 16:e1008799. [PMID: 32502208 PMCID: PMC7299400 DOI: 10.1371/journal.pgen.1008799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/17/2020] [Accepted: 04/26/2020] [Indexed: 12/20/2022] Open
Abstract
TRF2 and TRF1 are a key component in shelterin complex that associates with telomeric DNA and protects chromosome ends. BRM is a core ATPase subunit of SWI/SNF chromatin remodeling complex. Whether and how BRM-SWI/SNF complex is engaged in chromatin end protection by telomeres is unknown. Here, we report that depletion of BRM does not affect heterochromatin state of telomeres, but results in telomere dysfunctional phenomena including telomere uncapping and replication defect. Mechanistically, expression of TRF2 and TRF1 is jointly regulated by BRM-SWI/SNF complex, which is localized to promoter region of both genes and facilitates their transcription. BRM-deficient cells bear increased TRF2-free or TRF1-free telomeres due to insufficient expression. Importantly, BRM depletion-induced telomere uncapping or replication defect can be rescued by compensatory expression of exogenous TRF2 or TRF1, respectively. Together, these results identify a new function of BRM-SWI/SNF complex in enabling functional telomeres for maintaining genome stability. Human telomeres consist of repetitive “TTAGGG” DNA sequences and associated shelterin complex, which maintain genomic stability by preventing linear chromosome ends from being recognized as broken DNA. TRF1 and TRF2, as key components of shelterin complex, directly associate with double strand telomeric DNA. In this study, we discovered that both TRF1 and TRF2 are jointly regulated by BRM-SWI/SNF complex. Depletion of BRM led to insufficient amount of TRF1 and TRF2, which is associated with telomere replication defect and telomere uncapping. More importantly, these phenomena can be rescued by ectopically expressed TRF1 and TRF2. Our work demonstrates a specific role of BRM-SWI/SNF complex on safeguarding genome stability by enabling functional telomeres.
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Affiliation(s)
- Shu Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanlong Ge
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Xiaocui Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yiding Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Haoxian Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Kaixuan Lin
- Yale Stem Cell Center & Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Zepeng Zhang
- Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail:
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12
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SMARCB1 Acts as a Quiescent Gatekeeper for Cell Cycle and Immune Response in Human Cells. Int J Mol Sci 2020; 21:ijms21113969. [PMID: 32492816 PMCID: PMC7312701 DOI: 10.3390/ijms21113969] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022] Open
Abstract
Switch/sucrose non-fermentable (SWI/SNF)-related matrix-associated actin-dependent regulator of chromatin (SMARC) subfamily B member 1 (SMARCB1) is a core subunit of the switch/sucrose non-fermentable (SWI/SNF) complex, one of the adenosine triphosphate (ATP)-dependent chromatin remodeler complexes. The unique role of SMARCB1 has been reported in various cellular contexts. Here, we focused on the general role of the ubiquitous expression of SMARCB1 in a normal cell state. We selected ARPE19 (human primary retinal pigment epithelium) and IMR90 (from human fetal lung fibroblasts) cell lines as they have completely different contexts. Furthermore, although these cell lines have been immortalized, they are relatively close to normal human cells. The loss of SMARCB1 in ARPE19 and IMR90 cells reduced cell cycle progression via the upregulation of P21. Transcriptome analysis followed by SMARCB1 knockdown in both cell lines revealed that SMARCB1 was not only involved in cell maintenance but also conferred immunomodulation. Of note, SMARCB1 bound to interleukin (IL) 6 promoter in a steady state and dissociated in an active immune response state, suggesting that SMARCB1 was a direct repressor of IL6, which was further confirmed via loss- and gain-of-function studies. Taken together, we demonstrated that SMARCB1 is a critical gatekeeper molecule of the cell cycle and immune response.
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13
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Sinha S, Biswas M, Chatterjee SS, Kumar S, Sengupta A. Pbrm1 Steers Mesenchymal Stromal Cell Osteolineage Differentiation by Integrating PBAF-Dependent Chromatin Remodeling and BMP/TGF-β Signaling. Cell Rep 2020; 31:107570. [DOI: 10.1016/j.celrep.2020.107570] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/17/2020] [Accepted: 04/02/2020] [Indexed: 12/31/2022] Open
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14
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Sobczak M, Pietrzak J, Płoszaj T, Robaszkiewicz A. BRG1 Activates Proliferation and Transcription of Cell Cycle-Dependent Genes in Breast Cancer Cells. Cancers (Basel) 2020; 12:cancers12020349. [PMID: 32033115 PMCID: PMC7072512 DOI: 10.3390/cancers12020349] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/17/2020] [Accepted: 01/23/2020] [Indexed: 12/19/2022] Open
Abstract
Cancer malignancy is usually characterized by unlimited self-renewal. In some types of advanced tumors that are rapidly dividing, gene expression profiles depict elevations in pro-proliferative genes accompanied by coordinately elevated transcription of factors responsible for removal of DNA lesions. In our studies, fast proliferating breast cancer cell lines (MDA-MB-231 and MCF7), BRG1, a component of the SWI/SNF complex, emerges as an activator of functionally-linked genes responsible for activities such as mitotic cell divisions and DNA repair. Products of at least some of them are considerably overrepresented in breast cancer cells and BRG1 facilitates growth of MCF7 and MDA-MB-231 cell lines. BRG1 occurs at the promoters of genes such as CDK4, LIG1, and NEIL3, which are transcriptionally controlled by cell cycle progression and highly acetylated by EP300 in proliferating cells. As previously documented, in dividing cells BRG1 directly activates gene transcription by evicting EP300 modified nucleosomes from the promoters and, thereby, relaxing chromatin. However, the deficiency of BRG1 or EP300 activity for 48 h leads to cell growth arrest and to chromatin compaction, but also to the assembly of RB1/HDAC1/EZH2 complexes at the studied cell cycle-dependent gene promoters. Epigenetic changes include histone deacetylation and accumulation of H3K27me trimethylation, both known to repress transcription. Cell cycle arrest in G1 by inhibition of CDK4/6 phenocopies the effect of the long-term BRG1 inhibition on the chromatin structure. These results suggest that BRG1 may control gene transcription also by promoting expression of genes responsible for cell cycle progression in the studied breast cancer cells. In the current study, we show that BRG1 binding occurs at the promoters of functionally linked genes in proliferating breast cancer cells, revealing a new mechanism by which BRG1 defines gene transcription.
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Affiliation(s)
- Maciej Sobczak
- Department of General Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (M.S.); (J.P.)
| | - Julita Pietrzak
- Department of General Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (M.S.); (J.P.)
| | - Tomasz Płoszaj
- Department of Clinical and Laboratory Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland;
| | - Agnieszka Robaszkiewicz
- Department of General Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (M.S.); (J.P.)
- Correspondence: ; Tel./Fax: +48-42-6354449
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15
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Chabanon RM, Morel D, Postel-Vinay S. Exploiting epigenetic vulnerabilities in solid tumors: Novel therapeutic opportunities in the treatment of SWI/SNF-defective cancers. Semin Cancer Biol 2019; 61:180-198. [PMID: 31568814 DOI: 10.1016/j.semcancer.2019.09.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/12/2022]
Abstract
Mammalian switch/sucrose non-fermentable (mSWI/SNF) family complexes are pivotal elements of the chromatin remodeling machinery, which contribute to the regulation of several major cellular functions. Large-scale exome-wide sequencing studies have identified mutations in genes encoding mSWI/SNF subunits in 20% of all human cancers, establishing mSWI/SNF deficiency as a recurrent oncogenic alteration. Accumulating evidence now supports that several mSWI/SNF defects represent targetable vulnerabilities in cancer; notably, recent research advances have unveiled unexpected synthetic lethal opportunities that foster the development of novel biomarker-driven and mechanism-based therapeutic approaches for the treatment of mSWI/SNF-deficient tumors. Here, we review the latest breakthroughs and discoveries that inform our understanding of the mSWI/SNF complexes biology in carcinogenesis, and discuss the most promising therapeutic strategies to target mSWI/SNF defects in human solid malignancies.
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Affiliation(s)
- Roman M Chabanon
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, France; ATIP-Avenir Group, Inserm Unit U981, Gustave Roussy, Villejuif, France; The Breast Cancer Now Toby Robins Breast Cancer Research Centre, France; CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Daphné Morel
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, France; ATIP-Avenir Group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Sophie Postel-Vinay
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, France; ATIP-Avenir Group, Inserm Unit U981, Gustave Roussy, Villejuif, France; DITEP (Département d'Innovations Thérapeutiques et Essais Précoces), Gustave Roussy, Villejuif, France.
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16
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Yang Y, Liu L, Fang M, Bai H, Xu Y. The chromatin remodeling protein BRM regulates the transcription of tight junction proteins: Implication in breast cancer metastasis. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:547-556. [PMID: 30946989 DOI: 10.1016/j.bbagrm.2019.03.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/28/2019] [Accepted: 03/06/2019] [Indexed: 12/31/2022]
Abstract
Claudins are a group of cell tight junction proteins that play versatile roles in cancer biology. Recent studies have correlated down-regulation of Claudins with augmented breast cancer malignancy and poor prognosis. The mechanism underlying repression of Claudin transcription in breast cancer cells is not well understood. Here we report that expression levels of Brahma (BRM) were down-regulated in triple negative breast cancer cells (MDA-231) compared to the less malignant MCF-7 cells and in high-grade human breast cancer specimens compared to low-grade ones. TGF-β treatment in MCF-7 cells repressed BRM transcription likely through targeting C/EBPβ. BRM over-expression suppressed whereas BRM knockdown promoted TGF-β induced migration and invasion of MCF-7 cells. BRM down-regulation was accompanied by the loss of a panel of Claudins in breast cancer cells. BRM directly bound to the promoter region of Claudin genes via interacting with Sp1 and activated transcription by modulating histone modifications. Together, our data have identified a novel epigenetic pathway that links Claudin transcription to breast cancer metastasis.
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Affiliation(s)
- Yuyu Yang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China; Institute of Biomedical Research, Liaocheng University, Liaocheng, China
| | - Li Liu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Innovative Collaboration Center for Cardiovascular Disease Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Mingming Fang
- Institute of Biomedical Research, Liaocheng University, Liaocheng, China; Key Laboratory of Targeted Intervention of Cardiovascular Disease and Innovative Collaboration Center for Cardiovascular Disease Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China; Department of Clinical Medicine, Jiangsu Health Vocational College, Nanjing, China
| | - Hui Bai
- Key Laboratory of Targeted Intervention of Cardiovascular Disease and Innovative Collaboration Center for Cardiovascular Disease Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Yong Xu
- Institute of Biomedical Research, Liaocheng University, Liaocheng, China; Key Laboratory of Targeted Intervention of Cardiovascular Disease and Innovative Collaboration Center for Cardiovascular Disease Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.
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17
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Wu S, Fatkhutdinov N, Fukumoto T, Bitler BG, Park PH, Kossenkov AV, Trizzino M, Tang HY, Zhang L, Gardini A, Speicher DW, Zhang R. SWI/SNF catalytic subunits' switch drives resistance to EZH2 inhibitors in ARID1A-mutated cells. Nat Commun 2018; 9:4116. [PMID: 30297712 PMCID: PMC6175882 DOI: 10.1038/s41467-018-06656-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 09/13/2018] [Indexed: 12/30/2022] Open
Abstract
Inactivation of the subunits of SWI/SNF complex such as ARID1A is synthetically lethal with inhibition of EZH2 activity. However, mechanisms of de novo resistance to EZH2 inhibitors in cancers with inactivating SWI/SNF mutations are unknown. Here we show that the switch of the SWI/SNF catalytic subunits from SMARCA4 to SMARCA2 drives resistance to EZH2 inhibitors in ARID1A-mutated cells. SMARCA4 loss upregulates anti-apoptotic genes in the EZH2 inhibitor-resistant cells. EZH2 inhibitor-resistant ARID1A-mutated cells are hypersensitive to BCL2 inhibitors such as ABT263. ABT263 is sufficient to overcome resistance to an EZH2 inhibitor. In addition, ABT263 synergizes with an EZH2 inhibitor in vivo in ARID1A-inactivated ovarian tumor mouse models. Together, these data establish that the switch of the SWI/SNF catalytic subunits from SMARCA4 to SMARCA2 underlies the acquired resistance to EZH2 inhibitors. They suggest BCL2 inhibition alone or in combination with EZH2 inhibition represents urgently needed therapeutic strategy for ARID1A-mutated cancers. The mechanism of resistance to EZH2 inhibitors in cancers with inactivating SWI/SNF mutations is unknown. Here, the authors demonstrate that the switch of the SWI/SNF catalytic subunits from SMARCA4 to SMARCA2 drives resistance to EZH2 inhibitors in ARID1A-mutated ovarian cancer cells.
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Affiliation(s)
- Shuai Wu
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Nail Fatkhutdinov
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA.,Kazan Federal University, Kazan, 420008, Russia
| | - Takeshi Fukumoto
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Benjamin G Bitler
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Pyoung Hwa Park
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Andrew V Kossenkov
- Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Marco Trizzino
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Lin Zhang
- Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Alessandro Gardini
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - David W Speicher
- Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, 19104, USA.,Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Rugang Zhang
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, 19104, USA.
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18
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Tibshirani M, Zhao B, Gentil BJ, Minotti S, Marques C, Keith J, Rogaeva E, Zinman L, Rouaux C, Robertson J, Durham HD. Dysregulation of chromatin remodelling complexes in amyotrophic lateral sclerosis. Hum Mol Genet 2018; 26:4142-4152. [PMID: 28973294 DOI: 10.1093/hmg/ddx301] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/21/2017] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis is a fatal neurodegenerative disease with paralysis resulting from dysfunction and loss of motor neurons. A common neuropathological finding is attrition of motor neuron dendrites, which make central connections vital to motor control. The chromatin remodelling complex, neuronal Brahma-related gene 1 (Brg1)-associated factor complex (nBAF), is critical for neuronal differentiation, dendritic extension and synaptic function. We have identified loss of the crucial nBAF subunits Brg1, Brg1-associated factor 53b and calcium responsive transactivator in cultured motor neurons expressing FUS or TAR-DNA Binding Protein 43 (TDP-43) mutants linked to familial ALS. When plasmids encoding wild-type or mutant human FUS or TDP-43 were expressed in motor neurons of dissociated spinal cord cultures prepared from E13 mice, mutant proteins in particular accumulated in the cytoplasm. Immunolabelling of nBAF subunits was reduced in proportion to loss of nuclear FUS or TDP-43 and depletion of Brg1 was associated with nuclear retention of Brg1 mRNA. Dendritic attrition (loss of intermediate and terminal dendritic branches) occurred in motor neurons expressing mutant, but not wild-type, FUS or TDP-43. This attrition was delayed by ectopic over-expression of Brg1 and was reproduced by inhibiting Brg1 activity either through genetic manipulation or treatment with the chemical inhibitor, (E)-1-(2-Hydroxyphenyl)-3-((1R, 4R)-5-(pyridin-2-yl)-2, 5-diazabicyclo[2.2.1]heptan-2-yl)prop-2-en-1-one, demonstrating the importance of Brg1 to maintenance of dendritic architecture. Loss of nBAF subunits was also documented in spinal motor neurons in autopsy tissue from familial amyotrophic sclerosis (chromosome 9 open reading frame 72 with G4C2 nucleotide expansion) and from sporadic cases with no identified mutation, pointing to dysfunction of nBAF chromatin remodelling in multiple forms of ALS.
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Affiliation(s)
- Michael Tibshirani
- Department of Neurology and Neurosurgery and the Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B3, Canada
| | - Beibei Zhao
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Benoit J Gentil
- Department of Neurology and Neurosurgery and the Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B3, Canada
| | - Sandra Minotti
- Department of Neurology and Neurosurgery and the Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B3, Canada
| | - Christine Marques
- Inserm U1118, Faculté de Médecine, Université de Strasbourg, 67 085 Strasbourg Cedex, France
| | - Julia Keith
- Department of Laboratory Medicine and Pathobiology, Sunnybrook Health Sciences Center, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Lorne Zinman
- Department of Laboratory Medicine and Pathobiology, Sunnybrook Health Sciences Center, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Caroline Rouaux
- Inserm U1118, Faculté de Médecine, Université de Strasbourg, 67 085 Strasbourg Cedex, France
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Toronto, ON M5T 2S8, Canada.,Department of Laboratory Medicine and Pathobiology, Sunnybrook Health Sciences Center, University of Toronto, Toronto, ON M4N 3M5, Canada
| | - Heather D Durham
- Department of Neurology and Neurosurgery and the Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B3, Canada
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19
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Raab JR, Runge JS, Spear CC, Magnuson T. Co-regulation of transcription by BRG1 and BRM, two mutually exclusive SWI/SNF ATPase subunits. Epigenetics Chromatin 2017; 10:62. [PMID: 29273066 PMCID: PMC5740901 DOI: 10.1186/s13072-017-0167-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/30/2017] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND SWI/SNF is a large heterogeneous multi-subunit chromatin remodeling complex. It consists of multiple sets of mutually exclusive components. Understanding how loss of one sibling of a mutually exclusive pair affects the occupancy and function of the remaining complex is needed to understand how mutations in a particular subunit might affect tumor formation. Recently, we showed that the members of the ARID family of SWI/SNF subunits (ARID1A, ARID1B and ARID2) had complex transcriptional relationships including both antagonism and cooperativity. However, it remains unknown how loss of the catalytic subunit(s) affects the binding and genome-wide occupancy of the remainder complex and how changes in occupancy affect transcriptional output. RESULTS We addressed this gap by depleting BRG1 and BRM, the two ATPase subunits in SWI/SNF, and characterizing the changes to chromatin occupancy of the remaining subunit and related this to transcription changes induced by loss of the ATPase subunits. We show that depletion of one subunit frequently leads to loss of the remaining subunit. This could cause either positive or negative changes in gene expression. At a subset of sites, the sibling subunit is either retained or gained. Additionally, we show genome-wide that BRG1 and BRM have both cooperative and antagonistic interactions with respect to transcription. Importantly, at genes where BRG1 and BRM antagonize one another we observe a nearly complete rescue of gene expression changes in the combined BRG/BRM double knockdown. CONCLUSION This series of experiments demonstrate that mutually exclusive SWI/SNF complexes have heterogeneous functional relationships and highlight the importance of considering the role of the remaining SWI/SNF complexes following loss or depletion of a single subunit.
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Affiliation(s)
- Jesse R Raab
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - John S Runge
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Curriculum for Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Camarie C Spear
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Terry Magnuson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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20
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Hoffmeister H, Fuchs A, Erdel F, Pinz S, Gröbner-Ferreira R, Bruckmann A, Deutzmann R, Schwartz U, Maldonado R, Huber C, Dendorfer AS, Rippe K, Längst G. CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality. Nucleic Acids Res 2017; 45:10534-10554. [PMID: 28977666 PMCID: PMC5737555 DOI: 10.1093/nar/gkx711] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/08/2017] [Indexed: 12/22/2022] Open
Abstract
CHD3 and CHD4 (Chromodomain Helicase DNA binding protein), two highly similar representatives of the Mi-2 subfamily of SF2 helicases, are coexpressed in many cell lines and tissues and have been reported to act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). Besides CHD proteins, NuRD contains several repressors like HDAC1/2, MTA2/3 and MBD2/3, arguing for a role as a transcriptional repressor. However, the subunit composition varies among cell- and tissue types and physiological conditions. In particular, it is unclear if CHD3 and CHD4 coexist in the same NuRD complex or whether they form distinct NuRD complexes with specific functions. We mapped the CHD composition of NuRD complexes in mammalian cells and discovered that they are isoform-specific, containing either the monomeric CHD3 or CHD4 ATPase. Both types of complexes exhibit similar intranuclear mobility, interact with HP1 and rapidly accumulate at UV-induced DNA repair sites. But, CHD3 and CHD4 exhibit distinct nuclear localization patterns in unperturbed cells, revealing a subset of specific target genes. Furthermore, CHD3 and CHD4 differ in their nucleosome remodeling and positioning behaviour in vitro. The proteins form distinct CHD3- and CHD4-NuRD complexes that do not only repress, but can just as well activate gene transcription of overlapping and specific target genes.
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Affiliation(s)
- Helen Hoffmeister
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Andreas Fuchs
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Fabian Erdel
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Sophia Pinz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Regina Gröbner-Ferreira
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Rainer Deutzmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Uwe Schwartz
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Rodrigo Maldonado
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Claudia Huber
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Anne-Sarah Dendorfer
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Karsten Rippe
- BioQuant, University of Heidelberg, 69120 Heidelberg, Germany
| | - Gernot Längst
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
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21
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PRC2-mediated repression of SMARCA2 predicts EZH2 inhibitor activity in SWI/SNF mutant tumors. Proc Natl Acad Sci U S A 2017; 114:12249-12254. [PMID: 29087303 DOI: 10.1073/pnas.1703966114] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Subunits of the SWI/SNF chromatin remodeling complex are frequently mutated in human cancers leading to epigenetic dependencies that are therapeutically targetable. The dependency on the polycomb repressive complex (PRC2) and EZH2 represents one such vulnerability in tumors with mutations in the SWI/SNF complex subunit, SNF5; however, whether this vulnerability extends to other SWI/SNF subunit mutations is not well understood. Here we show that a subset of cancers harboring mutations in the SWI/SNF ATPase, SMARCA4, is sensitive to EZH2 inhibition. EZH2 inhibition results in a heterogenous phenotypic response characterized by senescence and/or apoptosis in different models, and also leads to tumor growth inhibition in vivo. Lower expression of the SMARCA2 paralog was associated with cellular sensitivity to EZH2 inhibition in SMARCA4 mutant cancer models, independent of tissue derivation. SMARCA2 is suppressed by PRC2 in sensitive models, and induced SMARCA2 expression can compensate for SMARCA4 and antagonize PRC2 targets. The induction of SMARCA2 in response to EZH2 inhibition is required for apoptosis, but not for growth arrest, through a mechanism involving the derepression of the lysomal protease cathepsin B. Expression of SMARCA2 also delineates EZH2 inhibitor sensitivity for other SWI/SNF complex subunit mutant tumors, including SNF5 and ARID1A mutant cancers. Our data support monitoring SMARCA2 expression as a predictive biomarker for EZH2-targeted therapies in the context of SWI/SNF mutant cancers.
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Abstract
Skeletal muscle regeneration is an efficient stem cell-based repair system that ensures healthy musculature. For this repair system to function continuously throughout life, muscle stem cells must contribute to the process of myofiber repair as well as repopulation of the stem cell niche. The decision made by the muscle stem cells to commit to the muscle repair or to remain a stem cell depends upon patterns of gene expression, a process regulated at the epigenetic level. Indeed, it is well accepted that dynamic changes in epigenetic landscapes to control DNA accessibility and expression is a critical component during myogenesis for the effective repair of damaged muscle. Changes in the epigenetic landscape are governed by various posttranslational histone tail modifications, nucleosome repositioning, and DNA methylation events which collectively allow the control of changes in transcription networks during transitions of satellite cells from a dormant quiescent state toward terminal differentiation. This chapter focuses upon the specific epigenetic changes that occur during muscle stem cell-mediated regeneration to ensure myofiber repair and continuity of the stem cell compartment. Furthermore, we explore open questions in the field that are expected to be important areas of exploration as we move toward a more thorough understanding of the epigenetic mechanism regulating muscle regeneration.
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Affiliation(s)
- Daniel C L Robinson
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada; University of Ottawa, Ottawa, ON, Canada
| | - Francis J Dilworth
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada; University of Ottawa, Ottawa, ON, Canada.
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23
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Downregulation of PARP1 transcription by promoter-associated E2F4-RBL2-HDAC1-BRM complex contributes to repression of pluripotency stem cell factors in human monocytes. Sci Rep 2017; 7:9483. [PMID: 28842672 PMCID: PMC5572705 DOI: 10.1038/s41598-017-10307-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 07/27/2017] [Indexed: 01/10/2023] Open
Abstract
Differentiation of certain cell types is followed by a downregulation of PARP1 expression. We show that the reduction in the abundance of PARP1 in hematopoietic progenitor cells and monocytes is tightly controlled by the cell cycle. The differentiation-associated cell cycle exit induces E2F1 replacement with E2F4 at the PARP1 promoter and the assembly of an E2F4-RBL2-HDAC1-BRM(SWI/SNF) repressor complex which deacetylates nucleosomes and compacts chromatin. In G1 arrested cells, PARP1 transcription is reduced by the recruitment of E2F1-RB1-HDAC1-EZH2(PRC2)-BRM/BRG1(SWI/SNF), which additionally trimethylates H3K27 and causes an even higher increase in nucleosome density. The re-establishment of an active chromatin structure by treating post-mitotic monocytes with the HDAC inhibitor and G1 arrested cells with a combination of HDAC and EZH2 inhibitors restores PARP1 expression completely but does not affect the interaction between the components of the repressor complex with chromatin. This suggests that RB1 and RBL2, as well as PRC2, SWI/SNF and HDAC1, do not interfere with the transcription machinery. Interestingly, reinstatement of PARP1 expression by the silencing of RBL2 or by the inhibition of HDACs in monocytes and by transfection with the PARP1 expression vector in differentiated THP-1 cells substantially increased transcription of pluripotency stem cell factors such as POU5F1, SOX2 and NANOG.
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Ge M, Chen H, Zhu Q, Cai J, Chen C, Yuan D, Jin Y, Yao W, Hei Z. Propofol post-conditioning alleviates hepatic ischaemia reperfusion injury via BRG1-mediated Nrf2/HO-1 transcriptional activation in human and mice. J Cell Mol Med 2017; 21:3693-3704. [PMID: 28749008 PMCID: PMC5706583 DOI: 10.1111/jcmm.13279] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/18/2017] [Indexed: 12/12/2022] Open
Abstract
To explore the effects of propofol post-conditioning (PPC) on hepatic ischaemia/reperfusion injury (HIRI) and the potential mechanisms that might be involved in the interaction of Brahma-related gene1(BRG1) and Nuclear-related factor 2(Nrf2). Patients were randomized into PPC(n = 16) and non-PPC(NPC)( n = 21) groups. Propofol(2 mg/kg) was infused within 10 min. of the onset of liver reperfusion during liver transplantation in the PPC group. Liver function tests, as well as Brg1, Nrf2, Heme oxygenase-1(HO-1) and NADPH:quinone oxidoreductase1(NQO1) expression levels were evaluated. CMV-Brg1 mice were designed to investigate the role of Brg1 overexpression during HIRI. Brg1 and Nrf2 siRNA were used to examine the relationship between Brg1 and Nrf2/HO-1 pathways in propofol-mediated effects in a human hepatocyte(L02) hypoxia/reoxygenation(H/R) model. In patients, PPC attenuated both donor liver pathological and function injury, and reducing oxidative stress markers, compared to the NPC group, 24 hrs after surgery. PPC increased liver Brg1, Nrf2, HO-1 and NQO1 expression. In mice, PPC reduced HIRI by decreasing liver oxidative stress and activating Nrf2/HO-1 pathway, accompanied by up-regulation of BRG1 expression. BRG1 overexpression activated Nrf2/HO-1 transcription in CMV-BRG1 mice during HIRI. In vitro, PPC significantly elevated expression of Nrf2, HO-1 and NQO1, resulting in a reduction of cell DCFH-DA and 8-isoprostane levels and decreased lactate dehydrogenase levels, leading to an overall increase in cell viability. Moreover, the protective effects of propofol were partially abrogated in Nrf2-knock-down or BRG1-knock-down hepatocytes. Nrf2-knock-down drastically reduced protein expression of HO-1 and NQO1, while Brg1-knock-down decreased HO-1 expression. Propofol post-conditioning alleviates HIRI through BRG1-mediated Nrf2/HO-1 transcriptional activation.
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Affiliation(s)
- Mian Ge
- Department of Anesthesiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huixin Chen
- Department of Anesthesiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qianqian Zhu
- Department of Anesthesiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jun Cai
- Department of Anesthesiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chaojin Chen
- Department of Anesthesiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dongdong Yuan
- Department of Anesthesiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yi Jin
- Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weifeng Yao
- Department of Anesthesiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ziqing Hei
- Department of Anesthesiology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Priam P, Krasteva V, Rousseau P, D'Angelo G, Gaboury L, Sauvageau G, Lessard JA. SMARCD2 subunit of SWI/SNF chromatin-remodeling complexes mediates granulopoiesis through a CEBPɛ dependent mechanism. Nat Genet 2017; 49:753-764. [PMID: 28369034 DOI: 10.1038/ng.3812] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 02/14/2017] [Indexed: 12/15/2022]
Abstract
Recent studies suggest that individual subunits of chromatin-remodeling complexes produce biologically specific meaning in different cell types through combinatorial assembly. Here we show that granulocyte development requires SMARCD2, a subunit of ATP-dependent SWI/SNF (BAF) chromatin-remodeling complexes. Smarcd2-deficient mice fail to generate functionally mature neutrophils and eosinophils, a phenotype reminiscent of neutrophil-specific granule deficiency (SGD) in humans, for which loss-of-function mutations in CEBPE (encoding CEBPɛ) have been reported. SMARCD2-containing SWI/SNF complexes are necessary for CEBPɛ transcription factor recruitment to the promoter of neutrophilic secondary granule genes and for granulocyte differentiation. The homologous SMARCD1 protein (63% identical at the amino acid level) cannot replace the role of SMARCD2 in granulocyte development. We find that SMARCD2 functional specificity is conferred by its divergent coiled-coil 1 and SWIB domains. Strikingly, both CEBPE and SMARCD2 loss-of-function mutations identified in patients with SGD abolish the interaction with SWI/SNF and thereby secondary granule gene expression, thus providing a molecular basis for this disease.
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Affiliation(s)
- Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Veneta Krasteva
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Philippe Rousseau
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada
| | - Giovanni D'Angelo
- Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada
| | - Louis Gaboury
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Division of Hematology-Oncology, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada.,Leukemia Cell Bank of Quebec, Maisonneuve-Rosemont Hospital, Montreal, Quebec, Canada.,Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Julie A Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, Quebec, Canada.,Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
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26
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Glucocorticoid receptor-mediated cis-repression of osteogenic genes requires BRM-SWI/SNF. Bone Rep 2016; 5:222-227. [PMID: 28580390 PMCID: PMC5440962 DOI: 10.1016/j.bonr.2016.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 07/26/2016] [Accepted: 07/29/2016] [Indexed: 12/21/2022] Open
Abstract
Glucocorticoids are an effective therapy for a variety of severe inflammatory and autoimmune disorders; however, the therapeutic use of glucocorticoids is severely limited by their negative side effects, particularly on osteogenesis. Glucocorticoids regulate transcription by binding to the glucocorticoid receptor (GR), which then binds the promoters of target genes to induce either activation or repression. The gene activation effects of nuclear hormone receptors broadly require the cooperation of the chromatin remodeling complex known as SWI/SNF, which is powered by an ATPase core. The well-studied SWI/SNF ATPase, BRG1, is required for gene activation by a spectrum of nuclear hormone receptors including GR. However, glucocorticoid-induced side effects specifically related to impaired osteogenesis are mostly linked with GR-mediated repression. We have considered whether cis-repression of osteogenic genes by GR may be mediated by a distinct subclass of SWI/SNF powered by the alternative ATPase, BRM. BRM does not have an essential role in mammalian development, but plays a repressor role in osteoblast differentiation and favors adipogenic lineage selection over osteoblast commitment, effects that mirror the repressor effects of GR. The studies reported here examine three key GR cis-repression gene targets, and show that GR association with these promoters is sharply reduced in BRM deficient cells. Each of these GR-targeted genes act in a different way. Bglap encodes osteocalcin, which contributes to normal maturation of osteoblasts from committed pre-osteoblasts. The Per3 gene product acts in uncommitted mesenchymal stem cells to influence the osteoblast/adipocyte lineage selection point. Fas ligand, encoded by FasL, is a means by which osteoblasts can modulate bone degradation by osteoclasts. Repression of each of these genes by glucocorticoid favors bone loss. The essential role of BRM in cooperation with GR at each of these control points offers a novel mechanistic understanding of the role of GR in bone loss. Therapeutic use of glucocorticoids is limited by their negative effects on osteogenesis. The glucocorticoid receptor (GR) can either activate or repress gene expression. cis-Repression by GR drives a significant part of the negative osteogenic effects. The BRM-containing subclass of SWI/SNF is specifically required for cis-repression by GR. BRM depletion reduces negative effects of glucocorticoids on osteogenic gene expression.
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27
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Sarnowska E, Gratkowska DM, Sacharowski SP, Cwiek P, Tohge T, Fernie AR, Siedlecki JA, Koncz C, Sarnowski TJ. The Role of SWI/SNF Chromatin Remodeling Complexes in Hormone Crosstalk. TRENDS IN PLANT SCIENCE 2016; 21:594-608. [PMID: 26920655 DOI: 10.1016/j.tplants.2016.01.017] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/14/2015] [Accepted: 01/21/2016] [Indexed: 05/20/2023]
Abstract
SWI/SNF-type ATP-dependent chromatin remodeling complexes (CRCs) are evolutionarily conserved multiprotein machineries controlling DNA accessibility by regulating chromatin structure. We summarize here recent advances highlighting the role of SWI/SNF in the regulation of hormone signaling pathways and their crosstalk in Arabidopsis thaliana. We discuss the functional interdependences of SWI/SNF complexes and key elements regulating developmental and hormone signaling pathways by indicating intriguing similarities and differences in plants and humans, and summarize proposed mechanisms of SWI/SNF action on target loci. We postulate that, given their viability, several plant SWI/SNF mutants may serve as an attractive model for searching for conserved functions of SWI/SNF CRCs in hormone signaling, cell cycle control, and other regulatory pathways.
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Affiliation(s)
| | | | | | - Pawel Cwiek
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | | | - Csaba Koncz
- Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany; Institute of Plant Biology, Biological Research Center of Hungarian Academy, Temesvári Körút 62, 6724 Szeged, Hungary
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland.
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28
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Sinha S, Verma S, Chaturvedi MM. Differential Expression of SWI/SNF Chromatin Remodeler Subunits Brahma and Brahma-Related Gene During Drug-Induced Liver Injury and Regeneration in Mouse Model. DNA Cell Biol 2016; 35:373-84. [PMID: 27097303 DOI: 10.1089/dna.2015.3155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The chromatin remodeling activity of mammalian SWI/SNF complex is carried out by either Brahma (BRM) or Brahma-related gene (BRG-1). The BRG-1 regulates genes involved in cell proliferation, whereas BRM is associated with cell differentiation, and arrest of cell growth. Global modifications of histones and expression of genes of chromatin-remodeling subunits have not been studied in in vivo model systems. In the present study, we investigate epigenetic modifications of histones and the expression of genes in thioacetamide (TAA)-induced liver injury and regeneration in a mouse model. In the present study, we report that hepatocyte proliferation and H3S10 phosphorylation occur during 60 to 72 h post TAA treatment in mice. Furthermore, there was change in the H3K9 acetylation and H3K9 trimethylation pattern with respect to liver injury and regeneration phase. Looking into the expression pattern of Brg-1 and Brm, it is evident that they contribute substantially to the process of liver regeneration. The SWI/SNF remodeler might contain BRG-1 as its ATPase subunit during injury phase. Whereas, BRM-associated SWI/SNF remodeler might probably be predominant during decline of injury phase and initiation of regeneration phase. Furthermore, during the regeneration phase, BRG-1-containing remodeler again predominates. Considering all these observations, the present study depicts an interplay between chromatin interacting machineries in different phases of thioacetamide-induced liver injury and regeneration.
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Affiliation(s)
- Sonal Sinha
- 1 Laboratory for Chromatin Biology, Department of Zoology, University of Delhi , New Delhi, India
| | - Sudhir Verma
- 1 Laboratory for Chromatin Biology, Department of Zoology, University of Delhi , New Delhi, India
| | - Madan M Chaturvedi
- 1 Laboratory for Chromatin Biology, Department of Zoology, University of Delhi , New Delhi, India .,2 Cluster Innovation Center, Delhi University , Delhi, India
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29
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Matsumoto S, Banine F, Feistel K, Foster S, Xing R, Struve J, Sherman LS. Brg1 directly regulates Olig2 transcription and is required for oligodendrocyte progenitor cell specification. Dev Biol 2016; 413:173-87. [PMID: 27067865 DOI: 10.1016/j.ydbio.2016.04.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/28/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
The Olig2 basic-helix-loop-helix transcription factor promotes oligodendrocyte specification in early neural progenitor cells (NPCs), including radial glial cells, in part by recruiting SWI/SNF chromatin remodeling complexes to the enhancers of genes involved in oligodendrocyte differentiation. How Olig2 expression is regulated during oligodendrogliogenesis is not clear. Here, we find that the Brg1 subunit of SWI/SNF complexes interacts with a proximal Olig2 promoter and represses Olig2 transcription in the mouse cortex at E14, when oligodendrocyte progenitors (OPCs) are not yet found in this location. Brg1 does not interact with the Olig2 promoter in the E14 ganglionic eminence, where NPCs differentiate into Olig2-positive OPCs. Consistent with these findings, Brg1-null NPCs demonstrate precocious expression of Olig2 in the cortex. However, these cells fail to differentiate into OPCs. We further find that Brg1 is necessary for neuroepithelial-to-radial glial cell transition, but not neuronal differentiation despite a reduction in expression of the pro-neural transcription factor Pax6. Collectively, these and earlier findings support a model whereby Brg1 promotes neurogenic radial glial progenitor cell specification but is dispensable for neuronal differentiation. Concurrently, Brg1 represses Olig2 expression and the specification of OPCs, but is required for OPC differentiation and oligodendrocyte maturation.
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Affiliation(s)
- Steven Matsumoto
- Integrative Biosciences Department, School of Dentistry, Oregon Health & Science University, Portland, OR 97239, USA; Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave., Beaverton, OR 97006, USA
| | - Fatima Banine
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave., Beaverton, OR 97006, USA
| | - Kerstin Feistel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave., Beaverton, OR 97006, USA
| | - Scott Foster
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave., Beaverton, OR 97006, USA
| | - Rubing Xing
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave., Beaverton, OR 97006, USA
| | - Jaime Struve
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave., Beaverton, OR 97006, USA
| | - Larry S Sherman
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Ave., Beaverton, OR 97006, USA; Department of Cell, Developmental and Cancer Biology, School of Medicine, Oregon Health and Science University, Portland, OR 97239, USA.
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30
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Jin HL, Jeong KW. Regulation of aryl hydrocarbon receptor-mediated transcription in human retinal pigmented epithelial cells. Biochem Biophys Res Commun 2016; 472:366-72. [PMID: 26966070 DOI: 10.1016/j.bbrc.2016.03.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/04/2016] [Indexed: 01/07/2023]
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor with pleiotropic effects in normal physiology or vascular development, xenobiotic metabolism, and cancer. A previous study has reported that BRG1, a component of the SWI/SNF complex, is a coactivator for AHR and is recruited to the promoter region of the CYP1A1 gene in mouse hepatocytes. Recent data suggest that AHR is also expressed in human retinal pigment epithelial cells (ARPE-19), which play a crucial role in retinal physiology and the visual cycle. Multiple studies have shown that the AHR plays an important role in the pathogenesis of retinal diseases including age-related macular degeneration. However, the mechanism of AHR transcriptional activation in retinal pigment cells has not been reported. Here, we demonstrate that the AHR signaling pathway is active in ARPE-19 cells, as in hepatocytes, but with different target gene specificity. We also found that chromatin remodeling by the BRG1-containing SWI/SNF complex is required for the AHR-mediated expression of target genes in ARPE-19 cells. We identified a novel enhancer region (-12 kb) of the CYP1A1 gene in ARPE-19 cells, to which both AHR and BRG1 are recruited in a ligand-dependent manner. BRG1 is associated with the AHR in ARPE-19 cells, and the C-terminal activation domain of the AHR directly interacts with BRG1. Furthermore, depletion of BRG1 caused a reduction in chromatin accessibility at the CYP1A1 enhancer. These results suggest that ARPE-19 cells possess an AHR-mediated transcription pathway with different target gene specificity, and that BRG1 is required for AHR-mediated transcription in ARPE-19 cells.
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Affiliation(s)
- Hong Lan Jin
- Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, 191 Hambakmoero, Yeonsu-gu, Incheon 406-799, Republic of Korea
| | - Kwang Won Jeong
- Gachon Institute of Pharmaceutical Sciences, College of Pharmacy, Gachon University, 191 Hambakmoero, Yeonsu-gu, Incheon 406-799, Republic of Korea.
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31
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Ruijtenberg S, van den Heuvel S. Coordinating cell proliferation and differentiation: Antagonism between cell cycle regulators and cell type-specific gene expression. Cell Cycle 2016; 15:196-212. [PMID: 26825227 PMCID: PMC4825819 DOI: 10.1080/15384101.2015.1120925] [Citation(s) in RCA: 368] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 10/04/2015] [Accepted: 11/12/2015] [Indexed: 11/25/2022] Open
Abstract
Cell proliferation and differentiation show a remarkable inverse relationship. Precursor cells continue division before acquiring a fully differentiated state, while terminal differentiation usually coincides with proliferation arrest and permanent exit from the division cycle. Mechanistic insight in the temporal coordination between cell cycle exit and differentiation has come from studies of cells in culture and genetic animal models. As initially described for skeletal muscle differentiation, temporal coordination involves mutual antagonism between cyclin-dependent kinases that promote cell cycle entry and transcription factors that induce tissue-specific gene expression. Recent insights highlight the contribution of chromatin-regulating complexes that act in conjunction with the transcription factors and determine their activity. In particular SWI/SNF chromatin remodelers contribute to dual regulation of cell cycle and tissue-specific gene expression during terminal differentiation. We review the concerted regulation of the cell cycle and cell type-specific transcription, and discuss common mutations in human cancer that emphasize the clinical importance of proliferation versus differentiation control.
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Affiliation(s)
- Suzan Ruijtenberg
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, The Netherlands
| | - Sander van den Heuvel
- Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, The Netherlands
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32
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Raab JR, Resnick S, Magnuson T. Genome-Wide Transcriptional Regulation Mediated by Biochemically Distinct SWI/SNF Complexes. PLoS Genet 2015; 11:e1005748. [PMID: 26716708 PMCID: PMC4699898 DOI: 10.1371/journal.pgen.1005748] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/27/2015] [Indexed: 01/24/2023] Open
Abstract
Multiple positions within the SWI/SNF chromatin remodeling complex can be filled by mutually exclusive subunits. Inclusion or exclusion of these proteins defines many unique forms of SWI/SNF and has profound functional consequences. Often this complex is studied as a single entity within a particular cell type and we understand little about the functional relationship between these biochemically distinct forms of the remodeling complex. Here we examine the functional relationships among three complex-specific ARID (AT-Rich Interacting Domain) subunits using genome-wide chromatin immunoprecipitation, transcriptome analysis, and transcription factor binding maps. We find widespread overlap in transcriptional regulation and the genomic binding of distinct SWI/SNF complexes. ARID1B and ARID2 participate in wide-spread cooperation to repress hundreds of genes. Additionally, we find numerous examples of competition between ARID1A and another ARID, and validate that gene expression changes following loss of one ARID are dependent on the function of an alternative ARID. These distinct regulatory modalities are correlated with differential occupancy by transcription factors. Together, these data suggest that distinct SWI/SNF complexes dictate gene-specific transcription through functional interactions between the different forms of the SWI/SNF complex and associated co-factors. Most genes regulated by SWI/SNF are controlled by multiple biochemically distinct forms of the complex, and the overall expression of a gene is the product of the interaction between these different SWI/SNF complexes. The three mutually exclusive ARID family members are among the most frequently mutated chromatin regulators in cancer, and understanding the functional interactions and their role in transcriptional regulation provides an important foundation to understand their role in cancer.
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Affiliation(s)
- Jesse R. Raab
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Samuel Resnick
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Terry Magnuson
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Roy N, Malik S, Villanueva KE, Urano A, Lu X, Von Figura G, Seeley ES, Dawson DW, Collisson EA, Hebrok M. Brg1 promotes both tumor-suppressive and oncogenic activities at distinct stages of pancreatic cancer formation. Genes Dev 2015; 29:658-71. [PMID: 25792600 PMCID: PMC4378197 DOI: 10.1101/gad.256628.114] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Pancreatic Ductal Adenocarcinoma (PDA) develops predominantly through pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasm (IPMN) precursor lesions. Roy et al. identify critical antagonistic roles for Brg1, a catalytic subunit of the SWI/SNF complexes, during IPMN-PDA development. In mature duct cells Brg1 inhibits the dedifferentiation that precedes neoplastic transformation. In contrast, Brg1 promotes tumorigenesis in full-blown PDA by supporting a mesenchymal-like transcriptional landscape. JQ1 impairs PDA tumorigenesis by both mimicking some and inhibiting other Brg1-mediated functions. Pancreatic ductal adenocarcinoma (PDA) develops predominantly through pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasm (IPMN) precursor lesions. Pancreatic acinar cells are reprogrammed to a “ductal-like” state during PanIN-PDA formation. Here, we demonstrate a parallel mechanism operative in mature duct cells during which functional cells undergo “ductal retrogression” to form IPMN-PDA. We further identify critical antagonistic roles for Brahma-related gene 1 (Brg1), a catalytic subunit of the SWI/SNF complexes, during IPMN-PDA development. In mature duct cells, Brg1 inhibits the dedifferentiation that precedes neoplastic transformation, thus attenuating tumor initiation. In contrast, Brg1 promotes tumorigenesis in full-blown PDA by supporting a mesenchymal-like transcriptional landscape. We further show that JQ1, a drug that is currently being tested in clinical trials for hematological malignancies, impairs PDA tumorigenesis by both mimicking some and inhibiting other Brg1-mediated functions. In summary, our study demonstrates the context-dependent roles of Brg1 and points to potential therapeutic treatment options based on epigenetic regulation in PDA.
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Affiliation(s)
- Nilotpal Roy
- Diabetes Center, Department of Medicine, University of California at San Francisco, San Francisco, California 94143, USA
| | - Shivani Malik
- Department of Medicine/Hematology and Oncology, University of California at San Francisco, San Francisco, California 94143, USA
| | - Karina E Villanueva
- Diabetes Center, Department of Medicine, University of California at San Francisco, San Francisco, California 94143, USA
| | - Atsushi Urano
- Diabetes Center, Department of Medicine, University of California at San Francisco, San Francisco, California 94143, USA
| | - Xinyuan Lu
- Department of Medicine/Hematology and Oncology, University of California at San Francisco, San Francisco, California 94143, USA
| | - Guido Von Figura
- II. Medizinische Klinik und Poliklinik, Klinikum Rechts der Isar der Technischen Universität München, 81675 Munich, Germany
| | - E Scott Seeley
- Department of Pathology, University of California at San Francisco, San Francisco, California 94143, USA
| | - David W Dawson
- Department of Pathology and Laboratory Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Eric A Collisson
- Department of Medicine/Hematology and Oncology, University of California at San Francisco, San Francisco, California 94143, USA
| | - Matthias Hebrok
- Diabetes Center, Department of Medicine, University of California at San Francisco, San Francisco, California 94143, USA;
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Nguyen KH, Xu F, Flowers S, Williams EAJ, Fritton JC, Moran E. SWI/SNF-Mediated Lineage Determination in Mesenchymal Stem Cells Confers Resistance to Osteoporosis. Stem Cells 2015; 33:3028-38. [PMID: 26059320 PMCID: PMC5014198 DOI: 10.1002/stem.2064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 03/24/2015] [Indexed: 12/13/2022]
Abstract
Redirecting the adipogenic potential of bone marrow‐derived mesenchymal stem cells to other lineages, particularly osteoblasts, is a key goal in regenerative medicine. Controlling lineage selection through chromatin remodeling complexes such as SWI/SNF, which act coordinately to establish new patterns of gene expression, would be a desirable intervention point, but the requirement for the complex in essentially every lineage pathway has generally precluded selectivity. However, a novel approach now appears possible by targeting the subset of SWI/SNF powered by the alternative ATPase, mammalian brahma (BRM). BRM is not required for development, which has hindered understanding of its contributions, but knockdown genetics here, designed to explore the hypothesis that BRM‐SWI/SNF has different regulatory roles in different mesenchymal stem cell lineages, shows that depleting BRM from mesenchymal stem cells has a dramatic effect on the balance of lineage selection between osteoblasts and adipocytes. BRM depletion enhances the proportion of cells expressing markers of osteoblast precursors at the expense of cells able to differentiate along the adipocyte lineage. This effect is evident in primary bone marrow stromal cells as well as in established cell culture models. The altered precursor balance has major physiological significance, which becomes apparent as protection against age‐related osteoporosis and as reduced bone marrow adiposity in adult BRM‐null mice. Stem Cells2015;33:3028–3038
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Affiliation(s)
- Kevin Hong Nguyen
- Department of Orthopaedics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Fuhua Xu
- Department of Orthopaedics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Stephen Flowers
- Department of Orthopaedics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Edek A J Williams
- Department of Orthopaedics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - J Christopher Fritton
- Department of Orthopaedics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
| | - Elizabeth Moran
- Department of Orthopaedics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, USA
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Thompson KW, Marquez SB, Lu L, Reisman D. Induction of functional Brm protein from Brm knockout mice. Oncoscience 2015; 2:349-61. [PMID: 26097869 PMCID: PMC4468321 DOI: 10.18632/oncoscience.153] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 04/08/2015] [Indexed: 12/18/2022] Open
Abstract
Once the knockout of the Brm gene was found to be nontumorigenic in mice, the study of BRM's involvement in cancer seemed less important compared with that of its homolog, Brg1. This has likely contributed to the disparity that has been observed in the publication ratio between BRG1 and BRM. We show that a previously published Brm knockout mouse is an incomplete knockout whereby a truncated isoform of Brm is detected in normal tissue and in tumors. We show that this truncated Brm isoform has functionality comparable to wild type Brm. By immunohistochemistry (IHC), this truncated Brm is undetectable in normal lung tissue and is minimal to very low in Brmnull tumors. However, it is significant in a subset (~40%) of Brg1/Brm double knockout (DKO) tumors that robustly express this truncated BRM, which in part stems from an increase in Brm mRNA levels. Thus, it is likely that this mutant mouse model does not accurately reflect the role that Brm plays in cancer development. We suggest that the construction of a completely new mouse Brm knockout, where Brm is functionally absent, is needed to determine whether or not Brm is actually tumorigenic and if Brm might be a tumor suppressor.
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Affiliation(s)
- Kenneth W. Thompson
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Stefanie B. Marquez
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Li Lu
- Department of Pathology, University of Florida, Gainesville, Florida, USA
| | - David Reisman
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, Florida, USA
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Parnell TJ, Schlichter A, Wilson BG, Cairns BR. The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism. eLife 2015; 4:e06073. [PMID: 25821983 PMCID: PMC4423118 DOI: 10.7554/elife.06073] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/28/2015] [Indexed: 12/19/2022] Open
Abstract
ISWI family chromatin remodelers typically organize nucleosome arrays, while SWI/SNF family remodelers (RSC) typically disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism and reveal different mechanisms at two different promoter architectures. DOI:http://dx.doi.org/10.7554/eLife.06073.001 The genome of an organism can contain hundreds to thousands of genes. However, these genes are not all active at the same time. Instead, mechanisms exist that control when genes are switched off or on. One such mechanism alters how tightly DNA is packaged into a structure called chromatin. To form chromatin, DNA is wrapped around histone proteins at different points along its length; these structures are known as nucleosomes. Once formed, chromatin can either adopt a tightly packed form that represses gene activity or a less compact form associated with gene activation. The proteins that control how chromatin is packed are called ‘chromatin remodelers’. These proteins work in complexes that either disassemble chromatin—for example, by repositioning nucleosomes or removing histones—or organize chromatin by replacing nucleosomes and making it more compact. Studies in many organisms have identified two key families of chromatin remodelers. In yeast, the ISWI family of complexes assembles chromatin and a protein complex called RSC disassembles chromatin. Parnell, Schlichter et al. used a range of genetic techniques to investigate whether these two chromatin-remodeling complexes work against each other in a species of yeast called Saccharomyces cerevisiae. The results suggest that this is indeed the case. Both the ISWI complex and the RSC complex bind to regions of DNA called promoters, which are found at the start of a gene and help to regulate its activity. Parnell, Schlichter et al. found that the RSC complex helps to activate genes by establishing or maintaining regions of nucleosome-poor chromatin at a promoter. The chromatin is relaxed in these regions, which allows the proteins that activate genes to access the DNA. This effect is partially counteracted by the ISWI complex, which repositions nucleosomes across the promoters to fill the gaps created by the RSC complex. In comparison, Parnell, Schlichter et al. found that promoters that do not have regions of nucleosome-poor chromatin contain a larger number of both of the remodeling complexes and have a high turnover of histone proteins. This suggests that at these sites, the RSC proteins are needed to overcome the assembly of nucleosomes by the ISWI complex in order to activate the gene. Thus, these two chromatin remodelers, ISWI and RSC, compete at promoters to determine whether they contain or lack nucleosomes, which helps determine whether the gene is silent or active, respectively. Future work will look further at how the ‘winner’ is determined: how transcription factors or signaling systems within the cell bias the recruitment or activity of RSC or ISWI at particular promoters, to determine gene activity. DOI:http://dx.doi.org/10.7554/eLife.06073.002
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Affiliation(s)
- Timothy J Parnell
- Department of Oncological Sciences, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Alisha Schlichter
- Department of Oncological Sciences, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Boris G Wilson
- Department of Oncological Sciences, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Bradley R Cairns
- Department of Oncological Sciences, Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, United States
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McKenna B, Guo M, Reynolds A, Hara M, Stein R. Dynamic recruitment of functionally distinct Swi/Snf chromatin remodeling complexes modulates Pdx1 activity in islet β cells. Cell Rep 2015; 10:2032-42. [PMID: 25801033 DOI: 10.1016/j.celrep.2015.02.054] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 01/21/2015] [Accepted: 02/23/2015] [Indexed: 02/03/2023] Open
Abstract
Pdx1 is a transcription factor of fundamental importance to pancreas formation and adult islet β cell function. However, little is known about the positive- and negative-acting coregulators recruited to mediate transcriptional control. Here, we isolated numerous Pdx1-interacting factors possessing a wide range of cellular functions linked with this protein, including, but not limited to, coregulators associated with transcriptional activation and repression, DNA damage response, and DNA replication. Because chromatin remodeling activities are essential to developmental lineage decisions and adult cell function, our analysis focused on investigating the influence of the Swi/Snf chromatin remodeler on Pdx1 action. The two mutually exclusive and indispensable Swi/Snf core ATPase subunits, Brg1 and Brm, distinctly affected target gene expression in β cells. Furthermore, physiological and pathophysiological conditions dynamically regulated Pdx1 binding to these Swi/Snf complexes in vivo. We discuss how context-dependent recruitment of coregulatory complexes by Pdx1 could impact pancreas cell development and adult islet β cell activity.
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Affiliation(s)
- Brian McKenna
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Min Guo
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Albert Reynolds
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Manami Hara
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Roland Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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Mehrotra A, Mehta G, Aras S, Trivedi A, de la Serna IL. SWI/SNF chromatin remodeling enzymes in melanocyte differentiation and melanoma. Crit Rev Eukaryot Gene Expr 2015; 24:151-61. [PMID: 24940768 DOI: 10.1615/critreveukaryotgeneexpr.2014007882] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epidermal melanocytes are pigment-producing cells derived from the neural crest that protects skin from the damaging effects of solar radiation. Malignant melanoma, a highly aggressive cancer, arises from melanocytes. SWI/SNF enzymes are multiprotein complexes that remodel chromatin structure and have extensive roles in cellular differentiation. Components of the complex have been found to be mutated or lost in several human cancers. This review focuses on studies that implicate SWI/SNF enzymes in melanocyte differentiation and in melanoma.
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Affiliation(s)
- A Mehrotra
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH
| | - G Mehta
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH
| | - S Aras
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH
| | - A Trivedi
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH
| | - I L de la Serna
- Department of Biochemistry and Cancer Biology, University of Toledo College of Medicine and Life Sciences, Toledo, OH
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Flowers S, Patel PJ, Gleicher S, Amer K, Himelman E, Goel S, Moran E. p107-Dependent recruitment of SWI/SNF to the alkaline phosphatase promoter during osteoblast differentiation. Bone 2014; 69:47-54. [PMID: 25182511 PMCID: PMC5222550 DOI: 10.1016/j.bone.2014.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 08/11/2014] [Accepted: 08/16/2014] [Indexed: 12/28/2022]
Abstract
The retinoblastoma protein family is intimately involved in the regulation of tissue specific gene expression during mesenchymal stem cell differentiation. The role of the following proteins, pRB, p107 and p130, is particularly significant in differentiation to the osteoblast lineage, as human germ-line mutations of RB1 greatly increase susceptibility to osteosarcoma. During differentiation, pRB directly targets certain osteogenic genes for activation, including the alkaline phosphatase-encoding gene Alpl. Chromatin immunoprecipitation (ChIP) assays indicate that Alpl is targeted by p107 in differentiating osteoblasts selectively during activation with the same dynamics as pRB, which suggests that p107 helps promote Alpl activation. Mouse models indicate overlapping roles for pRB and p107 in bone and cartilage formation, but very little is known about direct tissue-specific gene targets of p107, or the consequences of targeting by p107. Here, the roles of p107 and pRB were compared using shRNA-mediated knockdown genetics in an osteoblast progenitor model, MC3T3-E1 cells. The results show that p107 has a distinct role along with pRB in induction of Alpl. Deficiency of p107 does not impede recruitment of transcription factors recognized as pRB co-activation partners at the promoter; however, p107 is required for the efficient recruitment of an activating SWI/SNF chromatin-remodeling complex, an essential event in Alpl induction.
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Affiliation(s)
- Stephen Flowers
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA
| | - Parth J Patel
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA
| | - Stephanie Gleicher
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA
| | - Kamal Amer
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA
| | - Eric Himelman
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA
| | - Shruti Goel
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA
| | - Elizabeth Moran
- Department of Orthopaedics, New Jersey Medical School, Rutgers, the State University of New Jersey, Newark, NJ 07103, USA.
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Segalés J, Perdiguero E, Muñoz-Cánoves P. Epigenetic control of adult skeletal muscle stem cell functions. FEBS J 2014; 282:1571-88. [PMID: 25251895 DOI: 10.1111/febs.13065] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 12/12/2022]
Abstract
Skeletal muscle regeneration in the adult (de novo myogenesis) depends on a resident population of muscle stem cells (satellite cells) that are normally quiescent. In response to injury or stress, satellite cells are activated and expand as myoblast cells that differentiate and fuse to form new muscle fibers or return to quiescence to maintain the stem cell pool (self-renewal). Satellite cell-dependent myogenesis is a well-characterized multi-step process orchestrated by muscle-specific transcription factors, such as Pax3/Pax7 and members of the MyoD family of muscle regulatory factors, and epigenetically controlled by mechanisms such as DNA methylation, covalent modification of histones and non-coding RNAs. Recent results from next-generation genome-wide sequencing have increased our understanding about the highly intricate layers of epigenetic regulation involved in satellite cell maintenance, activation, differentiation and self-renewal, and their cross-talk with the muscle-specific transcriptional machinery.
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Affiliation(s)
- Jessica Segalés
- Cell Biology Group, Department of Experimental and Health Sciences, Pompeu Fabra University, Center for Networked Biomedical Research on Neurodegenerative Diseases, Barcelona, Spain
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41
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Forcales SV. The BAF60c-MyoD complex poises chromatin for rapid transcription. BIOARCHITECTURE 2014; 2:104-109. [PMID: 22880151 PMCID: PMC3414383 DOI: 10.4161/bioa.20970] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Chromatin remodeling by the SWI/SNF complex is required to activate the transcription of myogenic-specific genes. Our work addressed the details of how SWI/SNF is recruited to myogenic regulatory regions in response to differentiation signals. Surprisingly, the muscle determination factor MyoD and the SWI/SNF subunit BAF60c form a complex on the regulatory elements of MyoD-targeted genes in myogenic precursor cells. This Brg1-devoid MyoD-BAF60c complex flags the chromatin of myogenic-differentiation genes before transcription is activated. On differentiation, BAF60c phosphorylation on a conserved threonine by p38 α kinase promotes the incorporation of MyoD-BAF60c into a Brg1-based SWI/SNF complex, which remodels the chromatin and activates transcription of MyoD-target genes. Downregulation of BAF60c expression prevents MyoD access to the chromatin and the proper loading of an active myogenic transcriptosome preventing the expression of hundreds of myogenic genes. Our data support an unprecedented two-step model by which (1) pre-assembled BAF60c-MyoD complex poises the chromatin of myogenic genes for rapid transcription; (2) chromatin-bound BAF60c "senses" the myogenic differentiation cues and recruits an active SWI/SNF complex to remodel the chromatin allowing transcriptional activation.
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Affiliation(s)
- Sonia-Vanina Forcales
- Institute of Predictive and Personalized Medicine of Cancer; Badalona, Barcelona, Spain
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42
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Seth-Vollenweider T, Joshi S, Dhawan P, Sif S, Christakos S. Novel mechanism of negative regulation of 1,25-dihydroxyvitamin D3-induced 25-hydroxyvitamin D3 24-hydroxylase (Cyp24a1) Transcription: epigenetic modification involving cross-talk between protein-arginine methyltransferase 5 and the SWI/SNF complex. J Biol Chem 2014; 289:33958-70. [PMID: 25324546 DOI: 10.1074/jbc.m114.583302] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The SWI/SNF chromatin remodeling complex facilitates gene transcription by remodeling chromatin using the energy of ATP hydrolysis. Recent studies have indicated an interplay between the SWI/SNF complex and protein-arginine methyltransferases (PRMTs). Little is known, however, about the role of SWI/SNF and PRMTs in vitamin D receptor (VDR)-mediated transcription. Using SWI/SNF-defective cells, we demonstrated that Brahma-related gene 1 (BRG1), an ATPase that is a component of the SWI/SNF complex, plays a fundamental role in induction by 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) of the transcription of Cyp24a1 encoding the enzyme 25-hydroxyvitamin D3 24-hydroxylase involved in the catabolism of 1,25(OH)2D3. BRG1 was found to associate with CCAAT-enhancer-binding protein (C/EBP) β and cooperate with VDR and C/EBPβ in regulating Cyp24a1 transcription. PRMT5, a type II PRMT that interacts with BRG1, repressed Cyp24a1 transcription and mRNA expression. Our findings indicate the requirement of the C/EBP site for the inhibitory effect of PRMT5 via its methylation of H3R8 and H4R3. These findings indicate that the SWI/SNF complex and PRMT5 may be key factors involved in regulation of 1,25(OH)2D3 catabolism and therefore in the maintenance of calcium homeostasis by vitamin D. These studies also define epigenetic events linked to a novel mechanism of negative regulation of VDR-mediated transcription.
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Affiliation(s)
- Tanya Seth-Vollenweider
- From the Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey 07103 and
| | - Sneha Joshi
- From the Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey 07103 and
| | - Puneet Dhawan
- From the Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey 07103 and
| | - Said Sif
- Department of Molecular and Cellular Biochemistry, College of Medicine and Public Health, The Ohio State University, Columbus, Ohio 43210
| | - Sylvia Christakos
- From the Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers-The State University of New Jersey, Newark, New Jersey 07103 and
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Yuan Y, Wang C, Xu J, Tao J, Xu Z, Huang S. BRG1 overexpression in smooth muscle cells promotes the development of thoracic aortic dissection. BMC Cardiovasc Disord 2014; 14:144. [PMID: 25304030 PMCID: PMC4531522 DOI: 10.1186/1471-2261-14-144] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 10/03/2014] [Indexed: 01/19/2023] Open
Abstract
Background Here we investigated Brahma-related gene 1 (BRG1) expression in aortic smooth muscle cells (SMCs) and its role in the regulation of the pathological changes in aortic SMCs of thoracic arotic dissection (TAD). Methods BRG1, matrix metalloproteinase 2 (MMP2), and MMP9 mRNA and protein expression in human aortic specimens were examined by qPCR and western blot, respectively. The percentage of apoptotic and contractile SMCs in aortic specimens were determined by TUNEL assay and α-SMA immunohistochemical staining, respectively. The role of BRG1 in MMP2 and MMP9 expression, cell apoptosis, and phenotype transition in aortic SMCs were investigated using a human aortic SMC line via adenovirus mediated gene transfer. MMPs mRNA and protein levels were analyzed by qPCR and western blot, respectively. The percentage of apoptotic and contractile cells were determined through flow cytometry analysis. Results The expression level of BRG1 in the aortic walls (adventitia-removed) was significantly higher in the TAD than the normal group. BRG1 expression was positively correlated to expression of MMP2 and MMP9 and SMC apoptosis, but was negatively correlated to the percentage of contractile aortic SMCs in TAD specimens. In human aortic SMC line, BRG1 transfection led to significant upregulation of MMP2 and MMP9 expression and a concomitant increase in SMC apoptosis as well as a decrease in the percentage of contractile phenotype of cells. Conclusions BRG1 is significantly upregulated in the aortic SMCs of TAD, and its overexpression might promote the development of TAD by increasing MMP2 and MMP9 expression, inducing SMC apoptosis and the transition from contractile to synthetic phenotype.
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Affiliation(s)
- Yang Yuan
- Institute of Cardiothoracic Surgery, Changhai Hospital, Second Military Medical University, 168, Changhai Rd, Shanghai, P. R. China.
| | - Chong Wang
- Department of Cardiothoracic Surgery, Changhai Hospital, Second Military Medical University, 168, Changhai Rd., Shanghai, P. R. China.
| | - Jibin Xu
- Department of Cardiothoracic Surgery, Changhai Hospital, Second Military Medical University, 168, Changhai Rd., Shanghai, P. R. China.
| | - Jin Tao
- Institute of Cardiothoracic Surgery, Changhai Hospital, Second Military Medical University, 168, Changhai Rd, Shanghai, P. R. China.
| | - Zhiyun Xu
- Department of Cardiothoracic Surgery, Changhai Hospital, Second Military Medical University, 168, Changhai Rd., Shanghai, P. R. China.
| | - Shengdong Huang
- Institute of Cardiothoracic Surgery, Changhai Hospital, Second Military Medical University, 168, Changhai Rd, Shanghai, P. R. China.
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Helming KC, Wang X, Roberts CWM. Vulnerabilities of mutant SWI/SNF complexes in cancer. Cancer Cell 2014; 26:309-317. [PMID: 25203320 PMCID: PMC4159614 DOI: 10.1016/j.ccr.2014.07.018] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/12/2014] [Accepted: 07/23/2014] [Indexed: 01/30/2023]
Abstract
Cancer genome sequencing efforts have revealed the novel theme that chromatin modifiers are frequently mutated across a wide spectrum of cancers. Mutations in genes encoding subunits of SWI/SNF (BAF) chromatin remodeling complexes are particularly prevalent, occurring in 20% of all human cancers. As these are typically loss-of-function mutations and not directly therapeutically targetable, central goals have been to elucidate mechanism and identify vulnerabilities created by these mutations. Here, we discuss emerging data that these mutations lead to the formation of aberrant residual SWI/SNF complexes that constitute a specific vulnerability and discuss the potential for exploiting these dependencies in SWI/SNF mutant cancers.
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Affiliation(s)
- Katherine C Helming
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaofeng Wang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Charles W M Roberts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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45
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Sousa SB, Hennekam RC. Phenotype and genotype in Nicolaides-Baraitser syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2014; 166C:302-14. [PMID: 25169058 DOI: 10.1002/ajmg.c.31409] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nicolaides-Baraitser syndrome (NCBRS) is an intellectual disability (ID)/multiple congenital anomalies syndrome caused by non-truncating mutations in the ATPase region of SMARCA2, which codes for one of the two alternative catalytic subunits of the BAF chromatin remodeling complex. We analyzed 61 molecularly confirmed cases, including all previously reported patients (n = 47) and 14 additional unpublished individuals. NCBRS is clinically and genetically homogeneous. The cardinal features (ID, short stature, microcephaly, typical face, sparse hair, brachydactyly, prominent interphalangeal joints, behavioral problems and seizures), are almost universally present. There is variability however, as ID can range from severe to mild, and sparse hair may be present only in certain age groups. There may be a correlation between the severity of the ID and presence of seizures, absent speech, short stature and microcephaly. SMARCA2 mutations causing NCBRS are likely to act through a dominant-negative effect. There may be some genotype-phenotype correlations (mutations at domain VI with severe ID and seizures; mutations affecting residues Pro883, Leu946, and Ala1201 with mild phenotypes) but numbers are still too small to draw definitive conclusions.
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46
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Hohmann AF, Vakoc CR. A rationale to target the SWI/SNF complex for cancer therapy. Trends Genet 2014; 30:356-63. [PMID: 24932742 PMCID: PMC4112150 DOI: 10.1016/j.tig.2014.05.001] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/07/2014] [Accepted: 05/11/2014] [Indexed: 02/06/2023]
Abstract
SWI/SNF is a multisubunit chromatin-remodeling complex that performs fundamental roles in gene regulation, cell lineage specification, and organismal development. Mutations that inactivate SWI/SNF subunits are found in nearly 20% of human cancers, which indicates that the proper functioning of this complex is necessary to prevent tumor formation in diverse tissues. Recent studies show that SWI/SNF-mutant cancers depend on residual SWI/SNF complexes for their aberrant growth, thus revealing synthetic lethal interactions that could be exploited for therapeutic purposes. Other studies reveal that certain acute leukemias and small cell lung cancers, which lack SWI/SNF mutations, can be vulnerable to inhibition of the SWI/SNF ATPase subunit BRG1, whereas several normal and malignant cell types do not show this sensitivity. Here, we review the emerging evidence that implicates SWI/SNF as a tumor-dependency and candidate drug target in human cancer.
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Affiliation(s)
- Anja F Hohmann
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Christopher R Vakoc
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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Mehrotra A, Saladi SV, Trivedi AR, Aras S, Qi H, Jayanthy A, Setaluri V, de la Serna IL. Modulation of Brahma expression by the mitogen-activated protein kinase/extracellular signal regulated kinase pathway is associated with changes in melanoma proliferation. Arch Biochem Biophys 2014; 563:125-35. [PMID: 25026375 DOI: 10.1016/j.abb.2014.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 07/03/2014] [Accepted: 07/06/2014] [Indexed: 10/25/2022]
Abstract
Brahma (BRM) and Brahma-related gene 1(BRG1) are catalytic subunits of SWItch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes. BRM is epigenetically silenced in a wide-range of tumors. Mutations in the v-raf murine sarcoma viral oncogene homolog B1 (BRAF) gene occur frequently in melanoma and lead to constitutive activation of the mitogen-activated protein kinase (MAPK)/extracellular signal regulated kinase (ERK1/2) pathway. We tested the hypothesis that BRM expression is modulated by oncogenic BRAF and phosphorylation of ERK1/2 in melanocytes and melanoma cells. Expression of oncogenic BRAF in melanocytes and melanoma cells that are wild-type for BRAF decreased BRM expression and increased BRG1 expression. Inhibition of mitogen-activated protein/extracellular signal-regulated kinase kinase (MEK) or selective inhibition of BRAF in melanoma cells that harbor oncogenic BRAF increased BRM expression and decreased BRG1 expression. Increased BRM expression was associated with increased histone acetylation on the BRM promoter. Over-expression of BRM in melanoma cells that harbor oncogenic BRAF promoted changes in cell cycle progression and apoptosis consistent with a tumor suppressive role. Upon inhibition of BRAF(V600E) with PLX4032, BRM promoted survival. PLX4032 induced changes in BRM function were correlated with increased acetylation of the BRM protein. This study provides insights into the epigenetic consequences of inhibiting oncogenic BRAF in melanoma through modulation of SWI/SNF subunit expression and function.
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Affiliation(s)
- Aanchal Mehrotra
- University of Toledo College of Medicine, Department of Biochemistry and Cancer Biology, 3035 Arlington Ave, Toledo, OH 43614, United States
| | - Srinivas Vinod Saladi
- University of Toledo College of Medicine, Department of Biochemistry and Cancer Biology, 3035 Arlington Ave, Toledo, OH 43614, United States
| | - Archit R Trivedi
- University of Toledo College of Medicine, Department of Biochemistry and Cancer Biology, 3035 Arlington Ave, Toledo, OH 43614, United States
| | - Shweta Aras
- University of Toledo College of Medicine, Department of Biochemistry and Cancer Biology, 3035 Arlington Ave, Toledo, OH 43614, United States
| | - Huiling Qi
- University of Toledo College of Medicine, Department of Biochemistry and Cancer Biology, 3035 Arlington Ave, Toledo, OH 43614, United States
| | - Ashika Jayanthy
- University of Wisconsin, Department of Dermatology, 1300 University Avenue, #439, Madison, WI 53706, United States
| | - Vijayasaradhi Setaluri
- University of Wisconsin, Department of Dermatology, 1300 University Avenue, #439, Madison, WI 53706, United States
| | - Ivana L de la Serna
- University of Toledo College of Medicine, Department of Biochemistry and Cancer Biology, 3035 Arlington Ave, Toledo, OH 43614, United States.
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Abstract
Epigenetic alterations are associated with all aspects of cancer, from tumor initiation to cancer progression and metastasis. It is now well understood that both losses and gains of DNA methylation as well as altered chromatin organization contribute significantly to cancer-associated phenotypes. More recently, new sequencing technologies have allowed the identification of driver mutations in epigenetic regulators, providing a mechanistic link between the cancer epigenome and genetic alterations. Oncogenic activating mutations are now known to occur in a number of epigenetic modifiers (i.e. IDH1/2, EZH2, DNMT3A), pinpointing epigenetic pathways that are involved in tumorigenesis. Similarly, investigations into the role of inactivating mutations in chromatin modifiers (i.e. KDM6A, CREBBP/EP300, SMARCB1) implicate many of these genes as tumor suppressors. Intriguingly, a number of neoplasms are defined by a plethora of mutations in epigenetic regulators, including renal, bladder, and adenoid cystic carcinomas. Particularly striking is the discovery of frequent histone H3.3 mutations in pediatric glioma, a particularly aggressive neoplasm that has long remained poorly understood. Cancer epigenetics is a relatively new, promising frontier with much potential for improving cancer outcomes. Already, therapies such as 5-azacytidine and decitabine have proven that targeting epigenetic alterations in cancer can lead to tangible benefits. Understanding how genetic alterations give rise to the cancer epigenome will offer new possibilities for developing better prognostic and therapeutic strategies.
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Essential role of BRG, the ATPase subunit of BAF chromatin remodeling complexes, in leukemia maintenance. Blood 2014; 123:1720-8. [PMID: 24478402 DOI: 10.1182/blood-2013-02-483495] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In mammals, combinatorial assembly of alternative families of subunits confers functional specificity to adenosine triphosphate (ATP)-dependent SWI/SNF-like Brg/Brm-associated factor (BAF) chromatin remodeling complexes by creating distinct polymorphic surfaces for interaction with regulatory elements and DNA-binding factors. Although redundant in terms of biochemical activity, the core ATPase subunits, BRG/SMARCA4 and BRM/SMARCA2, are functionally distinct and may contribute to complex specificity. Here we show using quantitative proteomics that BAF complexes expressed in leukemia are specifically assembled around the BRG ATPase. Moreover, using a mouse model of acute myeloid leukemia, we demonstrate that BRG is essential for leukemia maintenance, as leukemic cells lacking BRG rapidly undergo cell-cycle arrest and apoptosis. Most importantly, we show that BRG is dispensable for the maintenance of immunophenotypic long-term repopulating hematopoietic stem cells, suggesting that adroit targeting of BRG in leukemia may have potent and specific therapeutic effects.
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Residual complexes containing SMARCA2 (BRM) underlie the oncogenic drive of SMARCA4 (BRG1) mutation. Mol Cell Biol 2014; 34:1136-44. [PMID: 24421395 DOI: 10.1128/mcb.01372-13] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Collectively, genes encoding subunits of the SWI/SNF (BAF) chromatin remodeling complex are mutated in 20% of all human cancers, with the SMARCA4 (BRG1) subunit being one of the most frequently mutated. The SWI/SNF complex modulates chromatin remodeling through the activity of two mutually exclusive catalytic subunits, SMARCA4 and SMARCA2 (BRM). Here, we show that a SMARCA2-containing residual SWI/SNF complex underlies the oncogenic activity of SMARCA4 mutant cancers. We demonstrate that a residual SWI/SNF complex exists in SMARCA4 mutant cell lines and plays essential roles in cellular proliferation. Further, using data from loss-of-function screening of 165 cancer cell lines, we identify SMARCA2 as an essential gene in SMARCA4 mutant cancer cell lines. Mechanistically, we reveal that Smarca4 inactivation leads to greater incorporation of the nonessential SMARCA2 subunit into the SWI/SNF complex. Collectively, these results reveal a role for SMARCA2 in oncogenesis caused by SMARCA4 loss and identify the ATPase and bromodomain-containing SMARCA2 as a potential therapeutic target in these cancers.
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