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Sandhu PK, Damania B. RNA helicases, DDX5 and DDX17, facilitate lytic reactivation of gammaherpesviruses. PLoS Pathog 2025; 21:e1013009. [PMID: 40257982 PMCID: PMC12011273 DOI: 10.1371/journal.ppat.1013009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2024] [Accepted: 02/27/2025] [Indexed: 04/23/2025] Open
Abstract
Human gammaherpesviruses comprise of Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV), and are oncogenic viruses that cause life-long infections. The gammaherpesviruses utilize an extensive virus-host interaction network for facilitating viral replication, whereby virus-encoded proteins modulate host processes. Thus, identifying targets of viral proteins that aid in gammaherpesviral replication will help develop therapies to combat these viruses. We identified that host proteins DDX5 and DDX17 interact with gammaherpesviral protein kinases, KSHV-encoded vPK and EBV-encoded BGLF4. We found that DDX5 and DDX17 are required for gammaherpesviral lytic reactivation and loss of both DDX5 and DDX17 decreased KSHV and EBV lytic reactivation. Depletion of DDX5 and DDX17 lowered the transcription of KSHV RTA, the key viral gene that drives the lytic replication cascade, due to reduced occupancy of Brg1, a chromatin remodeler, at the RTA promoter. Consequently, inhibition of Brg1 decreased gammaherpesviral lytic reactivation. Here we demonstrate how gammaherpesviruses hijack the function of two host proteins to promote their lytic replication cycle.
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Affiliation(s)
- Praneet Kaur Sandhu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Blossom Damania
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Guo Z, Wang P, Han Y, Jiang S, Yang X, Cao S. SMARCA2 protein: Structure, function and perspectives of drug design. Eur J Med Chem 2025; 286:117319. [PMID: 39879937 DOI: 10.1016/j.ejmech.2025.117319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Revised: 01/21/2025] [Accepted: 01/21/2025] [Indexed: 01/31/2025]
Abstract
SMARCA2 is an ATPase that regulates chromatin structure via ATP pathways, controlling cell division and differentiation. SMARCA2's bromodomain and ATPase domain, crucial for chromatin remodeling and cell regulation, are therapeutic targets in cancer treatment. This review explores the role of SMARCA2 in cancer development by studying its protein structure and physiological functions. It further discusses the roles and distinctions of SMARCA2 and its related family proteins in cancer. Additionally, this article categorizes known SMARCA2 inhibitors into four classes based on their basic structure and examines their structure-activity relationships (SAR). This review outlines the structural mechanisms of SMARCA2 inhibitors, highlighting interactions with specific amino acids. By analyzing the SAR of inhibitors, we propose a tailored inhibitor model for the bromodomain of SMARCA2, emphasizing α, γ-H-bond donors/acceptors, and β-rigid structures as crucial for effective binding. This research provides guidance for the design and optimization of future drugs targeting the SMARCA2 protein.
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Affiliation(s)
- Zhaolin Guo
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Peng Wang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Yuxuan Han
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Sisi Jiang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Xinyu Yang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China
| | - Shuang Cao
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, P. R. China.
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Gronkowska K, Robaszkiewicz A. Genetic dysregulation of EP300 in cancers in light of cancer epigenome control - targeting of p300-proficient and -deficient cancers. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200871. [PMID: 39351073 PMCID: PMC11440307 DOI: 10.1016/j.omton.2024.200871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
Some cancer types including bladder, cervical, and uterine cancers are characterized by frequent mutations in EP300 that encode histone acetyltransferase p300. This enzyme can act both as a tumor suppressor and oncogene. In this review, we describe the role of p300 in cancer initiation and progression regarding EP300 aberrations that have been identified in TGCA Pan-Cancer Atlas studies and we also discuss possible anticancer strategies that target EP300 mutated cancers. Copy number alterations, truncating mutations, and abnormal EP300 transcriptions that affect p300 abundance and activity are associated with several pathological features such as tumor grading, metastases, and patient survival. Elevated EP300 correlates with a higher mRNA level of other epigenetic factors and chromatin remodeling enzymes that co-operate with p300 in creating permissive conditions for malignant transformation, tumor growth and metastases. The status of EP300 expression can be considered as a prognostic marker for anticancer immunotherapy efficacy, as EP300 mutations are followed by an increased expression of PDL-1.HAT activators such as CTB or YF2 can be applied for p300-deficient patients, whereas the natural and synthetic inhibitors of p300 activity, as well as dual HAT/bromodomain inhibitors and the PROTAC degradation of p300, may serve as strategies in the fight against p300-fueled cancers.
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Affiliation(s)
- Karolina Gronkowska
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
- Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Agnieszka Robaszkiewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
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Ren G, Ku WL, Ge G, Hoffman JA, Kang JY, Tang Q, Cui K, He Y, Guan Y, Gao B, Liu C, Archer TK, Zhao K. Acute depletion of BRG1 reveals its primary function as an activator of transcription. Nat Commun 2024; 15:4561. [PMID: 38811575 PMCID: PMC11137027 DOI: 10.1038/s41467-024-48911-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 05/14/2024] [Indexed: 05/31/2024] Open
Abstract
The mammalian SWI/SNF-like BAF complexes play critical roles during animal development and pathological conditions. Previous gene deletion studies and characterization of human gene mutations implicate that the complexes both repress and activate a large number of genes. However, the direct function of the complexes in cells remains largely unclear due to the relatively long-term nature of gene deletion or natural mutation. Here we generate a mouse line by knocking in the auxin-inducible degron tag (AID) to the Smarca4 gene, which encodes BRG1, the essential ATPase subunit of the BAF complexes. We show that the tagged BRG1 can be efficiently depleted by osTIR1 expression and auxin treatment for 6 to 10 h in CD4 + T cells, hepatocytes, and fibroblasts isolated from the knock-in mice. The acute depletion of BRG1 leads to decreases in nascent RNAs and RNA polymerase II binding at a large number of genes, which are positively correlated with the loss of BRG1. Further, these changes are correlated with diminished accessibility at DNase I Hypersensitive Sites (DHSs) and p300 binding. The acute BRG1 depletion results in three major patterns of nucleosome shifts leading to narrower nucleosome spacing surrounding transcription factor motifs and at enhancers and transcription start sites (TSSs), which are correlated with loss of BRG1, decreased chromatin accessibility and decreased nascent RNAs. Acute depletion of BRG1 severely compromises the Trichostatin A (TSA) -induced histone acetylation, suggesting a substantial interplay between the chromatin remodeling activity of BRG1 and histone acetylation. Our data suggest BRG1 mainly plays a direct positive role in chromatin accessibility, RNAPII binding, and nascent RNA production by regulating nucleosome positioning and facilitating transcription factor binding to their target sites.
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Affiliation(s)
- Gang Ren
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
- College of Animal Science and Technology, Northwest Agriculture and Forest University, Yangling, Xianyang, Shaanxi, China
| | - Wai Lim Ku
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Guangzhe Ge
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Jackson A Hoffman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Jee Youn Kang
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Qingsong Tang
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Yong He
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Yukun Guan
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Bin Gao
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Chengyu Liu
- Transgenic Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Trevor K Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.
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Magarifuchi N, Iwasaki T, Katayama Y, Tomonaga T, Nakashima M, Narutomi F, Kato K, Oda Y. Gene amplification of chromatin remodeling factor SMARCC2 and low protein expression of ACTL6A are unfavorable factors in ovarian high‑grade serous carcinoma. Oncol Lett 2024; 27:196. [PMID: 38516682 PMCID: PMC10955683 DOI: 10.3892/ol.2024.14329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/23/2024] [Indexed: 03/23/2024] Open
Abstract
Ovarian high-grade serous carcinoma (OHGSC) is the most common type of ovarian cancer worldwide. Genome sequencing has identified mutations in chromatin remodeling factors (CRFs) in gynecological cancer, such as clear cell carcinoma, endometrioid carcinoma and endometrial serous carcinoma. However, to the best of our knowledge, the association between CRFs and OHGSC remains unexplored. The present study aimed to investigate the clinicopathological and molecular characteristics of CRF dysfunction in OHGSC. CRF alterations were analyzed through numerous methods, including the analysis of public next-generation sequencing (NGS) data from 585 ovarian serous carcinoma cases from The Cancer Genome Atlas (TCGA), immunohistochemistry (IHC), and DNA copy number assays, which were performed on 203 surgically resected OHGSC samples. In the public NGS dataset, the most frequent genetic alteration was actin-like protein 6A (ACTL6A) amplification at 19.5%. Switch/sucrose non-fermentable related, matrix associated, actin dependent regulator of chromatin subfamily c member 2 (SMARCC2) amplification (3.1%) was associated with significantly decreased overall survival (OS). In addition, chromodomain-helicase-DNA-binding protein 4 (CHD4) amplification (5.7%) exhibited unfavorable outcome trends, although not statistically significant. IHC revealed the protein expression loss of ARID1A (2.5%), SMARCA2 (2.5%) and SMARCA4 (3.9%). The protein expression levels of ACTL6A, SMARCC2 and CHD4 were evaluated using H-score. Patients with low protein expression levels of ACTL6A showed a significantly decreased OS. Copy number gain or gene amplification was demonstrated in ACTL6A (66.2%) and SMARCC2 (33.5%), while shallow deletion or deep deletion was demonstrated in CHD4 (70.7%). However, there was no statistically significant difference in protein levels of these CRFs, between the different copy number alterations (CNAs). Overall, OHGSC exhibited CNAs and protein loss, indicating possible gene alterations in CRFs. Moreover, there was a significant association between the protein expression levels of ACTL6A and poor prognosis. Based on these findings, it is suggested that CRFs could serve as prognostic markers for OHGSC.
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Affiliation(s)
- Naomi Magarifuchi
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Takeshi Iwasaki
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Yoshihiro Katayama
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Takumi Tomonaga
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Miya Nakashima
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Fumiya Narutomi
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Kiyoko Kato
- Department of Gynecology and Obstetrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
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Basurto-Cayuela L, Guerrero-Martínez JA, Gómez-Marín E, Sánchez-Escabias E, Escaño-Maestre M, Ceballos-Chávez M, Reyes JC. SWI/SNF-dependent genes are defined by their chromatin landscape. Cell Rep 2024; 43:113855. [PMID: 38427563 DOI: 10.1016/j.celrep.2024.113855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 11/23/2023] [Accepted: 02/08/2024] [Indexed: 03/03/2024] Open
Abstract
SWI/SNF complexes are evolutionarily conserved, ATP-dependent chromatin remodeling machines. Here, we characterize the features of SWI/SNF-dependent genes using BRM014, an inhibitor of the ATPase activity of the complexes. We find that SWI/SNF activity is required to maintain chromatin accessibility and nucleosome occupancy for most enhancers but not for most promoters. SWI/SNF activity is needed for expression of genes with low to medium levels of expression that have promoters with (1) low chromatin accessibility, (2) low levels of active histone marks, (3) high H3K4me1/H3K4me3 ratio, (4) low nucleosomal phasing, and (5) enrichment in TATA-box motifs. These promoters are mostly occupied by the canonical Brahma-related gene 1/Brahma-associated factor (BAF) complex. These genes are surrounded by SWI/SNF-dependent enhancers and mainly encode signal transduction, developmental, and cell identity genes (with almost no housekeeping genes). Machine-learning models trained with different chromatin characteristics of promoters and their surrounding regulatory regions indicate that the chromatin landscape is a determinant for establishing SWI/SNF dependency.
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Affiliation(s)
- Laura Basurto-Cayuela
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - José A Guerrero-Martínez
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Elena Gómez-Marín
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - Elena Sánchez-Escabias
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - María Escaño-Maestre
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - María Ceballos-Chávez
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain
| | - José C Reyes
- Genome Biology Department, Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad de Sevilla-Universidad Pablo de Olavide (CSIC-USE-UPO), Av. Americo Vespucio, 41092 Seville, Spain.
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Wang B, Kaufmann B, Mogler C, Zhong S, Yin Y, Cheng Z, Schmid RM, Friess H, Hüser N, von Figura G, Hartmann D. Hepatocellular Brg1 promotes CCl4-induced liver inflammation, ECM accumulation and fibrosis in mice. PLoS One 2023; 18:e0294257. [PMID: 38033027 PMCID: PMC10688683 DOI: 10.1371/journal.pone.0294257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023] Open
Abstract
INTRODUCTION Hepatic fibrosis is a progressive pathological process involving the exhaustion of hepatocellular regenerative capacity and ultimately leading to the development of cirrhosis and even hepatocellular carcinoma. Brg1, the core subunit of the SWI/SNF chromatin-remodeling complex, was recently identified as important for liver regeneration. This study investigates the role of Brg1 in hepatic fibrosis development. METHODS Hepatocyte-specific Brg1 knockout mice were generated and injected with carbon tetrachloride (CCl4) for 4, 6, 8, and 12 weeks to induce liver fibrosis. Afterwards, liver fibrosis and liver damage were assessed. RESULTS Brg1 expression was significantly increased in the fibrotic liver tissue of wild-type mice, as compared to that of untreated wild-type mice. The livers of the Brg1 knockout animals showed reduced liver inflammation, extracellular matrix accumulation, and liver fibrosis. TNF-α and NF-κB-mediated inflammatory response was reduced in Brg1 knockout animals. CONCLUSION Brg1 promotes the progression of liver fibrosis in mice and may therefore be used as a potential therapeutic target for treating patients with liver fibrosis due to chronic injury.
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Affiliation(s)
- Baocai Wang
- Department of Surgery, TUM School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
- Department of General Surgery, The Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Benedikt Kaufmann
- Department of Surgery, TUM School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Carolin Mogler
- Institute of Pathology, TUM School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Suyang Zhong
- Department of Medicine II, TUM School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Yuhan Yin
- Department of Surgery, TUM School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Zhangjun Cheng
- Department of General Surgery, The Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Roland M. Schmid
- Department of Medicine II, TUM School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Helmut Friess
- Department of Surgery, TUM School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Norbert Hüser
- Department of Surgery, TUM School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Guido von Figura
- Department of Medicine II, TUM School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Daniel Hartmann
- Department of Surgery, TUM School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
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MacPherson RA, Shankar V, Anholt RRH, Mackay TFC. Genetic and genomic analyses of Drosophila melanogaster models of chromatin modification disorders. Genetics 2023; 224:iyad061. [PMID: 37036413 PMCID: PMC10411607 DOI: 10.1093/genetics/iyad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/10/2022] [Accepted: 03/30/2023] [Indexed: 04/11/2023] Open
Abstract
Switch/sucrose nonfermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma-Related Gene-1 associated factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce the expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration), and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, an SSRIDD-associated BAF component. k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in the behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in the discovery of drugs that ameliorate deleterious phenotypic effects.
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Affiliation(s)
- Rebecca A MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R H Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Trudy F C Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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Navickas SM, Giles KA, Brettingham-Moore KH, Taberlay PC. The role of chromatin remodeler SMARCA4/BRG1 in brain cancers: a potential therapeutic target. Oncogene 2023:10.1038/s41388-023-02773-9. [PMID: 37433987 PMCID: PMC10374441 DOI: 10.1038/s41388-023-02773-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 06/16/2023] [Accepted: 06/29/2023] [Indexed: 07/13/2023]
Abstract
The chromatin remodeler SMARCA4/BRG1 is a key epigenetic regulator with diverse roles in coordinating the molecular programs that underlie brain tumour development. BRG1 function in brain cancer is largely specific to the tumour type and varies further between tumour subtypes, highlighting its complexity. Altered SMARCA4 expression has been linked to medulloblastoma, low-grade gliomas such as oligodendroglioma, high-grade gliomas such as glioblastoma and atypical/teratoid rhabdoid tumours. SMARCA4 mutations in brain cancer predominantly occur in the crucial catalytic ATPase domain, which is associated with tumour suppressor activity. However, SMARCA4 is opposingly seen to promote tumourigenesis in the absence of mutation and through overexpression in other brain tumours. This review explores the multifaceted interaction between SMARCA4 and various brain cancer types, highlighting its roles in tumour pathogenesis, the pathways it regulates, and the advances that have been made in understanding the functional relevance of mutations. We discuss developments made in targeting SMARCA4 and the potential to translate these to adjuvant therapies able to enhance current methods of brain cancer treatment.
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Affiliation(s)
- Sophie M Navickas
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Katherine A Giles
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
- Children's Medical Research Institute, 214 Hawkesbury Road, Westmead, NSW, 2145, Australia
| | - Kate H Brettingham-Moore
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
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10
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MacPherson RA, Shankar V, Anholt RRH, Mackay TFC. Genetic and Genomic Analyses of Drosophila melanogaster Models of Chromatin Modification Disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.534923. [PMID: 37034595 PMCID: PMC10081333 DOI: 10.1101/2023.03.30.534923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Switch/Sucrose Non-Fermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma-Related Gene-1 Associated Factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration) and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, a SSRIDD-associated BAF component, k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in discovery of drugs that ameliorate deleterious phenotypic effects.
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Affiliation(s)
- Rebecca A. MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R. H. Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Trudy F. C. Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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11
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Kido K, Nojima S, Motooka D, Nomura Y, Kohara M, Sato K, Ohshima K, Tahara S, Kurashige M, Umeda D, Takashima T, Kiyokawa H, Ukon K, Matsui T, Okuzaki D, Morii E. Ovarian high-grade serous carcinoma cells with low SMARCA4 expression and high SMARCA2 expression contribute to platinum resistance. J Pathol 2023; 260:56-70. [PMID: 36763038 DOI: 10.1002/path.6064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/31/2022] [Accepted: 02/08/2023] [Indexed: 02/11/2023]
Abstract
Platinum resistance is a major obstacle to the treatment of ovarian cancer and is correlated with poor clinical outcomes. Intratumor heterogeneity plays a key role in chemoresistance. Recent studies have emphasized the contributions of genetic and epigenetic factors to the development of intratumor heterogeneity. Although the clinical significance of multi-subunit chromatin remodeler, switch/sucrose nonfermenting (SWI/SNF) complexes in cancers has been reported, the impacts of SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4/subfamily A, member 2 (SMARCA4/A2) expression patterns in human cancer tissues have not been fully elucidated. Here, we show that low expression of SMARCA4 and high expression of SMARCA2 are associated with platinum resistance in ovarian high-grade serous carcinoma (HGSC) cells. We used fluorescence multiplex immunohistochemistry (fmIHC) to study resected specimens; we examined heterogeneity in human HGSC tissues at the single-cell level, which revealed that the proportion of cells with the SMARCA4low /SMARCA2high phenotype was positively correlated with clinical platinum-resistant recurrence. We used stable transfection of SMARCA2 and siRNA knockdown of SMARCA4 to generate HGSC cells with the SMARCA4low /SMARCA2high phenotype; these cells had the greatest resistance to carboplatin. Bioinformatics analyses revealed that the underlying mechanism involved in substantial alterations to chromatin accessibility and resultant fibroblast growth factor (FGF) signaling activation, MAPK pathway activation, BCL2 overexpression, and reduced carboplatin-induced apoptosis; these were confirmed by in vitro functional experiments. Furthermore, in vivo experiments in an animal model demonstrated that combination therapy with carboplatin and a fibroblast growth factor receptor (FGFR) inhibitor promoted cell death in HGSC xenografts. Taken together, these observations reveal a specific subpopulation of HGSC cells that is associated with clinical chemoresistance, which may lead to the establishment of a histopathological prediction system for carboplatin response. Our findings may facilitate the development of novel therapeutic strategies for platinum-resistant HGSC cells. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Kansuke Kido
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Satoshi Nojima
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Daisuke Motooka
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Yusuke Nomura
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Masaharu Kohara
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kazuaki Sato
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kenji Ohshima
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Shinichiro Tahara
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Masako Kurashige
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Daisuke Umeda
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Tsuyoshi Takashima
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hiroki Kiyokawa
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Koto Ukon
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takahiro Matsui
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Daisuke Okuzaki
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Eiichi Morii
- Department of Pathology, Osaka University Graduate School of Medicine, Osaka, Japan.,Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
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12
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Reddy D, Bhattacharya S, Levy M, Zhang Y, Gogol M, Li H, Florens L, Workman JL. Paraspeckles interact with SWI/SNF subunit ARID1B to regulate transcription and splicing. EMBO Rep 2023; 24:e55345. [PMID: 36354291 PMCID: PMC9827562 DOI: 10.15252/embr.202255345] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/12/2022] [Accepted: 10/20/2022] [Indexed: 11/12/2022] Open
Abstract
Paraspeckles are subnuclear RNA-protein structures that are implicated in important processes including cellular stress response, differentiation, and cancer progression. However, it is unclear how paraspeckles impart their physiological effect at the molecular level. Through biochemical analyses, we show that paraspeckles interact with the SWI/SNF chromatin-remodeling complex. This is specifically mediated by the direct interaction of the long-non-coding RNA NEAT1 of the paraspeckles with ARID1B of the cBAF-type SWI/SNF complex. Strikingly, ARID1B depletion, in addition to resulting in loss of interaction with the SWI/SNF complex, decreases the binding of paraspeckle proteins to chromatin modifiers, transcription factors, and histones. Functionally, the loss of ARID1B and NEAT1 influences the transcription and the alternative splicing of a common set of genes. Our findings reveal that dynamic granules such as the paraspeckles may leverage the specificity of epigenetic modifiers to impart their regulatory effect, thus providing a molecular basis for their function.
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Affiliation(s)
- Divya Reddy
- Stowers Institute for Medical ResearchKansas CityMOUSA
| | | | | | - Ying Zhang
- Stowers Institute for Medical ResearchKansas CityMOUSA
| | | | - Hua Li
- Stowers Institute for Medical ResearchKansas CityMOUSA
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13
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Sun J, Ye L, Shi Y, Wang X, Zhao X, Ren S, Fan J, Shao H, Qin B. MiR-6511b-5p suppresses metastasis of pMMR colorectal cancer through methylation of CD44 by directly targeting BRG1. Clin Transl Oncol 2022; 24:1940-1953. [PMID: 35590122 PMCID: PMC9418090 DOI: 10.1007/s12094-022-02845-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/19/2022] [Indexed: 11/27/2022]
Abstract
PURPOSE Distal metastases are a major cause of poor prognosis in colorectal cancer patients. Approximately 95% of metastatic colorectal cancers are defined as DNA mismatch repair proficient (pMMR). Our previous study found that miR-6511b-5p was downregulated in pMMR colorectal cancer. However, the mechanism of miR-6511b-5p in pMMR colorectal cancer metastases remain unclear. METHODS We first used quantitative real-time PCR to evaluate the role of miR-6511b-5p in colorectal cancer. Second, we conducted invasion assays and wound healing assays to investigate the role of miR-6511b-5p and CD44 in colorectal cancer cells metastases. Third, luciferase reporter assay, in situ hybridization (ISH), and immunohistochemistry assays were performed to study the relationship between miR-6511b-5p and BRG1. Finally, real-time quantitative PCR, immunohistochemistry, and chromatin immunoprecipitation (ChIP) assays were performed to analyze the relationship between BRG1 and CD44 in colorectal cancer. RESULTS We found that lower expression of miR-6511b-5p appeared more often in pMMR colorectal cancer patients compared with dMMR (mismatch repair deficient) cases, and was positively correlated with metastases. In vitro, overexpression of miR-6511b-5p inhibited metastasis by decreasing CD44 expression via directly targeting BRG1 in colorectal cancer. Furthermore, BRG1 knockdown decreased the expression of CD44 by promoting CD44 methylation in colorectal cancer cells. CONCLUSION Our data suggest that miR-6511b-5p may act as a promising biomarker and treatment target for pMMR colorectal cancer, particularly in metastatic patients. Mechanistically, miR-6511b-5p suppresses invasion and migration of colorectal cancer cells through methylation of CD44 via directly targeting BRG1.
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Affiliation(s)
- JinMing Sun
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Ling Ye
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Yuan Shi
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - XingWei Wang
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - XiaFei Zhao
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - ShengYong Ren
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China
| | - JunWei Fan
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - HuanZhang Shao
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China.
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China.
| | - BingYu Qin
- Department of Critical Care Medicine, Henan Key Laboratory for Critical Care Medicine, Zhengzhou Key Laboratory for Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, Henan, China.
- Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, Henan, China.
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14
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Naidu SR, Capitano M, Ropa J, Cooper S, Huang X, Broxmeyer HE. Chromatin remodeling subunit BRM and valine regulate hematopoietic stem/progenitor cell function and self-renewal via intrinsic and extrinsic effects. Leukemia 2022; 36:821-833. [PMID: 34599272 PMCID: PMC9212754 DOI: 10.1038/s41375-021-01426-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023]
Abstract
Little is known of hematopoietic stem (HSC) and progenitor (HPC) cell self-renewal. The role of Brahma (BRM), a chromatin remodeler, in HSC function is unknown. Bone marrow (BM) from Brm-/- mice manifested increased numbers of long- and short-term HSCs, GMPs, and increased numbers and cycling of functional HPCs. However, increased Brm-/- BM HSC numbers had decreased secondary and tertiary engraftment, suggesting BRM enhances HSC self-renewal. Valine was elevated in lineage negative Brm-/- BM cells, linking intracellular valine with Brm expression. Valine enhanced HPC colony formation, replating of human cord blood (CB) HPC-derived colonies, mouse BM and human CB HPC survival in vitro, and ex vivo expansion of normal mouse BM HSCs and HPCs. Valine increased oxygen consumption rates of WT cells. BRM through CD98 was linked to regulated import of branched chain amino acids, such as valine, in HPCs. Brm-/- LSK cells exhibited upregulated interferon response/cell cycle gene programs. Effects of BRM depletion are less apparent on isolated HSCs compared to HSCs in the presence of HPCs, suggesting cell extrinsic effects on HSCs. Thus, intracellular valine is regulated by BRM expression in HPCs, and the BRM/valine axis regulates HSC and HPC self-renewal, proliferation, and possibly differentiation fate decisions.
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Affiliation(s)
- Samisubbu R. Naidu
- Medicine, Indiana University School of Medicine,Indiana University School of Medicine, Department of Microbiology/Immunology, 950 West Walnut Street, Bldg. R2, Room 302, Indianapolis, IN 46202, Indiana University School of Medicine, Department of Medicine, 950 West Walnut Street, Bldg. R2, Room E435,These authors contributed equally to this work
| | - Maegan Capitano
- Departments of Microbiology and Immunology, Indiana University School of Medicine,These authors contributed equally to this work
| | - James Ropa
- Departments of Microbiology and Immunology, Indiana University School of Medicine,These authors contributed equally to this work
| | - Scott Cooper
- Departments of Microbiology and Immunology, Indiana University School of Medicine
| | - Xinxin Huang
- Departments of Microbiology and Immunology, Indiana University School of Medicine
| | - Hal E. Broxmeyer
- Departments of Microbiology and Immunology, Indiana University School of Medicine,Indiana University School of Medicine, Department of Microbiology/Immunology, 950 West Walnut Street, Bldg. R2, Room 302, Indianapolis, IN 46202, Indiana University School of Medicine, Department of Medicine, 950 West Walnut Street, Bldg. R2, Room E435
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15
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Laubscher D, Gryder BE, Sunkel BD, Andresson T, Wachtel M, Das S, Roschitzki B, Wolski W, Wu XS, Chou HC, Song YK, Wang C, Wei JS, Wang M, Wen X, Ngo QA, Marques JG, Vakoc CR, Schäfer BW, Stanton BZ, Khan J. BAF complexes drive proliferation and block myogenic differentiation in fusion-positive rhabdomyosarcoma. Nat Commun 2021; 12:6924. [PMID: 34836971 PMCID: PMC8626462 DOI: 10.1038/s41467-021-27176-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is a pediatric malignancy of skeletal muscle lineage. The aggressive alveolar subtype is characterized by t(2;13) or t(1;13) translocations encoding for PAX3- or PAX7-FOXO1 chimeric transcription factors, respectively, and are referred to as fusion positive RMS (FP-RMS). The fusion gene alters the myogenic program and maintains the proliferative state while blocking terminal differentiation. Here, we investigated the contributions of chromatin regulatory complexes to FP-RMS tumor maintenance. We define the mSWI/SNF functional repertoire in FP-RMS. We find that SMARCA4 (encoding BRG1) is overexpressed in this malignancy compared to skeletal muscle and is essential for cell proliferation. Proteomic studies suggest proximity between PAX3-FOXO1 and BAF complexes, which is further supported by genome-wide binding profiles revealing enhancer colocalization of BAF with core regulatory transcription factors. Further, mSWI/SNF complexes localize to sites of de novo histone acetylation. Phenotypically, interference with mSWI/SNF complex function induces transcriptional activation of the skeletal muscle differentiation program associated with MYCN enhancer invasion at myogenic target genes, which is recapitulated by BRG1 targeting compounds. We conclude that inhibition of BRG1 overcomes the differentiation blockade of FP-RMS cells and may provide a therapeutic strategy for this lethal childhood tumor.
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Affiliation(s)
- Dominik Laubscher
- grid.412341.10000 0001 0726 4330Department of Oncology and Children’s Research Center, University Children’s Hospital, Zurich, Switzerland
| | - Berkley E. Gryder
- grid.48336.3a0000 0004 1936 8075Genetics Branch, NCI, NIH, Bethesda, MD USA ,grid.67105.350000 0001 2164 3847Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH USA
| | - Benjamin D. Sunkel
- grid.240344.50000 0004 0392 3476Nationwide Children’s Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH USA
| | - Thorkell Andresson
- grid.418021.e0000 0004 0535 8394Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Marco Wachtel
- grid.412341.10000 0001 0726 4330Department of Oncology and Children’s Research Center, University Children’s Hospital, Zurich, Switzerland
| | - Sudipto Das
- grid.418021.e0000 0004 0535 8394Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Bernd Roschitzki
- grid.7400.30000 0004 1937 0650Functional Genomics Center, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Witold Wolski
- grid.7400.30000 0004 1937 0650Functional Genomics Center, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Xiaoli S. Wu
- grid.225279.90000 0004 0387 3667Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - Hsien-Chao Chou
- grid.48336.3a0000 0004 1936 8075Genetics Branch, NCI, NIH, Bethesda, MD USA
| | - Young K. Song
- grid.48336.3a0000 0004 1936 8075Genetics Branch, NCI, NIH, Bethesda, MD USA
| | - Chaoyu Wang
- grid.48336.3a0000 0004 1936 8075Genetics Branch, NCI, NIH, Bethesda, MD USA
| | - Jun S. Wei
- grid.48336.3a0000 0004 1936 8075Genetics Branch, NCI, NIH, Bethesda, MD USA
| | - Meng Wang
- grid.240344.50000 0004 0392 3476Nationwide Children’s Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH USA
| | - Xinyu Wen
- grid.48336.3a0000 0004 1936 8075Genetics Branch, NCI, NIH, Bethesda, MD USA
| | - Quy Ai Ngo
- grid.412341.10000 0001 0726 4330Department of Oncology and Children’s Research Center, University Children’s Hospital, Zurich, Switzerland
| | - Joana G. Marques
- grid.412341.10000 0001 0726 4330Department of Oncology and Children’s Research Center, University Children’s Hospital, Zurich, Switzerland
| | - Christopher R. Vakoc
- grid.225279.90000 0004 0387 3667Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - Beat W. Schäfer
- grid.412341.10000 0001 0726 4330Department of Oncology and Children’s Research Center, University Children’s Hospital, Zurich, Switzerland
| | - Benjamin Z. Stanton
- grid.240344.50000 0004 0392 3476Nationwide Children’s Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH USA ,grid.261331.40000 0001 2285 7943Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH USA ,grid.261331.40000 0001 2285 7943Department of Biological Chemistry & Pharmacology, The Ohio State University College of Medicine, Columbus, OH USA
| | - Javed Khan
- Genetics Branch, NCI, NIH, Bethesda, MD, USA.
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16
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β-actin dependent chromatin remodeling mediates compartment level changes in 3D genome architecture. Nat Commun 2021; 12:5240. [PMID: 34475390 PMCID: PMC8413440 DOI: 10.1038/s41467-021-25596-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/18/2021] [Indexed: 02/07/2023] Open
Abstract
β-actin is a crucial component of several chromatin remodeling complexes that control chromatin structure and accessibility. The mammalian Brahma-associated factor (BAF) is one such complex that plays essential roles in development and differentiation by regulating the chromatin state of critical genes and opposing the repressive activity of polycomb repressive complexes (PRCs). While previous work has shown that β-actin loss can lead to extensive changes in gene expression and heterochromatin organization, it is not known if changes in β-actin levels can directly influence chromatin remodeling activities of BAF and polycomb proteins. Here we conduct a comprehensive genomic analysis of β-actin knockout mouse embryonic fibroblasts (MEFs) using ATAC-Seq, HiC-seq, RNA-Seq and ChIP-Seq of various epigenetic marks. We demonstrate that β-actin levels can induce changes in chromatin structure by affecting the complex interplay between chromatin remodelers such as BAF/BRG1 and EZH2. Our results show that changes in β-actin levels and associated chromatin remodeling activities can not only impact local chromatin accessibility but also induce reversible changes in 3D genome architecture. Our findings reveal that β-actin-dependent chromatin remodeling plays a role in shaping the chromatin landscape and influences the regulation of genes involved in development and differentiation.
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17
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OCT4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human. Nat Commun 2021; 12:5123. [PMID: 34446700 PMCID: PMC8390644 DOI: 10.1038/s41467-021-25107-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). While the protein-protein interactions of core pluripotency factors have been identified in mouse ESCs, their interactome in human ESCs (hESCs) has not to date been explored. Here we mapped the OCT4 interactomes in naïve and primed hESCs, revealing extensive connections to mammalian ATP-dependent nucleosome remodeling complexes. In naïve hESCs, OCT4 is associated with both BRG1 and BRM, the two paralog ATPases of the BAF complex. Genome-wide location analyses and genetic studies reveal that these two enzymes cooperate in a functionally redundant manner in the transcriptional regulation of blastocyst-specific genes. In contrast, in primed hESCs, OCT4 cooperates with BRG1 and SOX2 to promote chromatin accessibility at ectodermal genes. This work reveals how a common transcription factor utilizes differential BAF complexes to control distinct transcriptional programs in naïve and primed hESCs. Although the interactors of pluripotency factors have been identified in mouse embryonic stem cells (ESCs), their interactors in human ESCs remain unexplored. Here the authors map OCT4 protein interactions in naïve and primed human ESCs to find specific interactions with BAF subunits that promote an open chromatin architecture at blastocyst-associated genes and ectodermal genes, respectively.
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18
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Dong W, Zhu Y, Zhang Y, Fan Z, Zhang Z, Fan X, Xu Y. BRG1 Links TLR4 Trans-Activation to LPS-Induced SREBP1a Expression and Liver Injury. Front Cell Dev Biol 2021; 9:617073. [PMID: 33816466 PMCID: PMC8012493 DOI: 10.3389/fcell.2021.617073] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/26/2021] [Indexed: 12/12/2022] Open
Abstract
Multiple organ failure is one of the most severe consequences in patients with septic shock. Liver injury is frequently observed during this pathophysiological process. In the present study we investigated the contribution of Brahma related gene 1 (BRG1), a chromatin remodeling protein, to septic shock induced liver injury. When wild type (WT) and liver conditional BRG1 knockout (LKO) mice were injected with lipopolysaccharide (LPS), liver injury was appreciably attenuated in the LKO mice compared to the WT mice as evidenced by plasma ALT/AST levels, hepatic inflammation and apoptosis. Of interest, there was a down-regulation of sterol response element binding protein 1a (SREBP1a), known to promote liver injury, in the LKO livers compared to the WT livers. BRG1 did not directly bind to the SREBP1a promoter. Instead, BRG1 was recruited to the toll-like receptor 4 (TLR4) promoter and activated TLR4 transcription. Ectopic TLR4 restored SREBP1a expression in BRG1-null hepatocytes. Congruently, adenovirus carrying TLR4 or SREBP1a expression vector normalized liver injury in BRG1 LKO mice injected with LPS. Finally, a positive correlation between BRG1 and TLR4 expression was detected in human liver biopsy specimens. In conclusion, our data demonstrate that a BRG1-TLR4-SREBP1a axis that mediates LPS-induced liver injury in mice.
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Affiliation(s)
- Wenhui Dong
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Yuwen Zhu
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Yangxi Zhang
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China
| | - Zhiwen Fan
- Department of Pathology, Affiliated Nanjing Drum Tower Hospital of Nanjing University School of Medicine, Nanjing, China
| | - Ziyu Zhang
- Key Laboratory of Women's Reproductive Health of Jiangxi, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, China.,Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, China
| | - Xiangshan Fan
- Department of Pathology, Affiliated Nanjing Drum Tower Hospital of Nanjing University School of Medicine, Nanjing, China
| | - Yong Xu
- Key Laboratory of Targeted Invention of Cardiovascular Disease and Collaborative Innovation Center for Cardiovascular Translational Medicine, Department of Pathophysiology, Nanjing Medical University, Nanjing, China.,Institute of Biomedical Research, Liaocheng University, Liaocheng, China
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19
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Chong PSY, Chooi JY, Lim JSL, Toh SHM, Tan TZ, Chng WJ. SMARCA2 Is a Novel Interactor of NSD2 and Regulates Prometastatic PTP4A3 through Chromatin Remodeling in t(4;14) Multiple Myeloma. Cancer Res 2021; 81:2332-2344. [PMID: 33602783 DOI: 10.1158/0008-5472.can-20-2946] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/18/2020] [Accepted: 02/11/2021] [Indexed: 11/16/2022]
Abstract
NSD2 is the primary oncogenic driver in t(4;14) multiple myeloma. Using SILAC-based mass spectrometry, we demonstrate a novel role of NSD2 in chromatin remodeling through its interaction with the SWI/SNF ATPase subunit SMARCA2. SMARCA2 was primarily expressed in t(4;14) myeloma cells, and its interaction with NSD2 was noncanonical and independent of the SWI/SNF complex. RNA sequencing identified PTP4A3 as a downstream target of NSD2 and mapped NSD2-SMARCA2 complex on PTP4A3 promoter. This led to a focal increase in the permissive H3K36me2 mark and transcriptional activation of PTP4A3. High levels of PTP4A3 maintained MYC expression and correlated with a 54-gene MYC signature in t(4;14) multiple myeloma. Importantly, this mechanism was druggable by targeting the bromodomain of SMARCA2 using the specific BET inhibitor PFI-3, leading to the displacement of NSD2 from PTP4A3 promoter and inhibiting t(4;14) myeloma cell viability. In vivo, treatment with PFI-3 reduced the growth of t(4;14) xenograft tumors. Together, our study reveals an interplay between histone-modifying enzymes and chromatin remodelers in the regulation of myeloma-specific genes that can be clinically intervened. SIGNIFICANCE: This study uncovers a novel, SWI/SNF-independent interaction between SMARCA2 and NSD2 that facilitates chromatin remodeling and transcriptional regulation of oncogenes in t(4;14) multiple myeloma, revealing a therapeutic vulnerability targetable by BET inhibition.
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Affiliation(s)
- Phyllis S Y Chong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Jing Yuan Chooi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Julia S L Lim
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Sabrina Hui Min Toh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Wee-Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore. .,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Heamatology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore
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20
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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: 1.0] [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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21
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Yan X, Han D, Chen Z, Han C, Dong W, Han L, Zou L, Zhang J, Liu Y, Chai J. RUNX2 interacts with BRG1 to target CD44 for promoting invasion and migration of colorectal cancer cells. Cancer Cell Int 2020; 20:505. [PMID: 33071648 PMCID: PMC7559818 DOI: 10.1186/s12935-020-01544-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/07/2020] [Indexed: 12/16/2022] Open
Abstract
Background Cancer stem cells (CSCs) play an important role in tumor invasion and metastasis. CD44 is the most commonly used marker of CSCs, with the potential to act as a determinant against the invasion and migration of CSCs and as the key factor in epithelial-mesenchymal transition (EMT)-like changes that occur in colorectal cancer (CRC). Runt-related transcription factor-2 (RUNX2) is a mesenchymal stem marker for cancer that is involved in stem cell biology and tumorigenesis. However, whether RUNX2 is involved in CSC and in inducing EMT-like changes in CRC remains uncertain, warranting further investigation. Methods We evaluated the role of RUNX2 in the invasion and migration of CRC cells as a promoter of CD44-induced stem cell- and EMT-like modifications. For this purpose, western blotting was employed to analyze the expression of differential proteins in CRC cells. We conducted sphere formation, wound healing, and transwell assays to investigate the biological functions of RUNX2 in CRC cells. Cellular immunofluorescence and coimmunoprecipitation (co-IP) assays were performed to study the relationship between RUNX2 and BRG1. Real-time quantitative PCR (RT-qPCR) and immunohistochemistry (IHC) were performed to analyze the expressions of RUNX2, BRG1, and CD44 in the CRC tissues. Results We found that RUNX2 could markedly induce the CRC cell sphere-forming ability and EMT. Interestingly, the RUNX2-mediated EMT in CRC cell may be associated with the activation of CD44. Furthermore, RUNX2 was found to interact with BRG1 to promote the recruitment of RUNX2 to the CD44 promoter. Conclusions Our cumulative findings suggest that RUNX2 and BRG1 can form a compact complex to regulate the transcription and expression of CD44, which has possible involvement in the invasion and migration of CRC cells.
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Affiliation(s)
- Xiaodong Yan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069 China
| | - Dali Han
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117 Shandong Province China
| | - Zhiqiang Chen
- Department of General Surgery, Xuanwu Hospital, Capital Medical University, Beijing, 100069 China
| | - Chao Han
- Department of Gastrointestinal Surgery, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, 046000 Shanxi Province China
| | - Wei Dong
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117 Shandong Province China
| | - Li Han
- Internal Medicine-Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117 Shandong Province China
| | - Lei Zou
- Department of Gastrointestinal Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117 Shandong Province China
| | - Jianbo Zhang
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117 Shandong Province China
| | - Yan Liu
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117 Shandong Province China
| | - Jie Chai
- Department of Gastrointestinal Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, No. 440 Ji-Yan Road, Jinan, 250117 Shandong Province China.,Tianjin Medical University, Tianjin, 300070 China
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22
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Patty BJ, Hainer SJ. Non-Coding RNAs and Nucleosome Remodeling Complexes: An Intricate Regulatory Relationship. BIOLOGY 2020; 9:E213. [PMID: 32784701 PMCID: PMC7465399 DOI: 10.3390/biology9080213] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 12/17/2022]
Abstract
Eukaryotic genomes are pervasively transcribed, producing both coding and non-coding RNAs (ncRNAs). ncRNAs are diverse and a critical family of biological molecules, yet much remains unknown regarding their functions and mechanisms of regulation. ATP-dependent nucleosome remodeling complexes, in modifying chromatin structure, play an important role in transcriptional regulation. Recent findings show that ncRNAs regulate nucleosome remodeler activities at many levels and that ncRNAs are regulatory targets of nucleosome remodelers. Further, a series of recent screens indicate this network of regulatory interactions is more expansive than previously appreciated. Here, we discuss currently described regulatory interactions between ncRNAs and nucleosome remodelers and contextualize their biological functions.
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Affiliation(s)
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA;
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23
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Xue Y, Zhu X, Meehan B, Venneti S, Martinez D, Morin G, Maïga RI, Chen H, Papadakis AI, Johnson RM, O'Sullivan MJ, Erdreich-Epstein A, Gotlieb WH, Park M, Judkins AR, Pelletier J, Foulkes WD, Rak J, Huang S. SMARCB1 loss induces druggable cyclin D1 deficiency via upregulation of MIR17HG in atypical teratoid rhabdoid tumors. J Pathol 2020; 252:77-87. [PMID: 32558936 DOI: 10.1002/path.5493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/27/2020] [Accepted: 06/10/2020] [Indexed: 01/04/2023]
Abstract
Atypical teratoid rhabdoid tumor (ATRT) is a fatal pediatric malignancy of the central neural system lacking effective treatment options. It belongs to the rhabdoid tumor family and is usually caused by biallelic inactivation of SMARCB1, encoding a key subunit of SWI/SNF chromatin remodeling complexes. Previous studies proposed that SMARCB1 loss drives rhabdoid tumor by promoting cell cycle through activating transcription of cyclin D1 while suppressing p16. However, low cyclin D1 protein expression is observed in most ATRT patient tumors. The underlying mechanism and therapeutic implication of this molecular trait remain unknown. Here, we show that SMARCB1 loss in ATRT leads to the reduction of cyclin D1 expression by upregulating MIR17HG, a microRNA (miRNA) cluster known to generate multiple miRNAs targeting CCND1. Furthermore, we find that this cyclin D1 deficiency in ATRT results in marked in vitro and in vivo sensitivity to the CDK4/6 inhibitor palbociclib as a single agent. Our study identifies a novel genetic interaction between SMARCB1 and MIR17HG in regulating cyclin D1 in ATRT and suggests a rationale to treat ATRT patients with FDA-approved CDK4/6 inhibitors. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Yibo Xue
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Xianbing Zhu
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Brian Meehan
- Department of Pediatrics, McGill University, and Research Institute of McGill University Health Centre, Montreal Children's Hospital, Montreal, Canada
| | - Sriram Venneti
- Pathology and Neuropathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Daniel Martinez
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Geneviève Morin
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Rayelle I Maïga
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Hongbo Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, PR China
| | - Andreas I Papadakis
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Radia M Johnson
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Maureen J O'Sullivan
- School of Medicine, University of Dublin, Trinity College, Dublin, Ireland.,Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Anat Erdreich-Epstein
- Departments of Pediatrics and Pathology, The Saban Research Institute at Children's Hospital Los Angeles and the Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Walter H Gotlieb
- Division of Gynecologic Oncology, Segal Cancer Center, Jewish General Hospital, McGill University, Montreal, Canada
| | - Morag Park
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Canada.,Department of Medical Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Canada.,Department of Medical Genetics and Cancer Research Program, McGill University Health Centre, Montreal, Canada
| | - Janusz Rak
- Department of Pediatrics, McGill University, and Research Institute of McGill University Health Centre, Montreal Children's Hospital, Montreal, Canada
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, Canada.,Goodman Cancer Research Centre, McGill University, Montreal, Canada
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24
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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: 1.0] [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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25
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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: 9] [Impact Index Per Article: 1.8] [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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26
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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: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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27
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Jancewicz I, Siedlecki JA, Sarnowski TJ, Sarnowska E. BRM: the core ATPase subunit of SWI/SNF chromatin-remodelling complex-a tumour suppressor or tumour-promoting factor? Epigenetics Chromatin 2019; 12:68. [PMID: 31722744 PMCID: PMC6852734 DOI: 10.1186/s13072-019-0315-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/31/2019] [Indexed: 02/07/2023] Open
Abstract
BRM (BRAHMA) is a core, SWI2/SNF2-type ATPase subunit of SWI/SNF chromatin-remodelling complex (CRC) involved in various important regulatory processes including development. Mutations in SMARCA2, a BRM-encoding gene as well as overexpression or epigenetic silencing were found in various human diseases including cancer. Missense mutations in SMARCA2 gene were recently connected with occurrence of Nicolaides-Baraitser genetics syndrome. By contrast, SMARCA2 duplication rather than mutations is characteristic for Coffin-Siris syndrome. It is believed that BRM usually acts as a tumour suppressor or a tumour susceptibility gene. However, other studies provided evidence that BRM function may differ depending on the cancer type and the disease stage, where BRM may play a role in the disease progression. The existence of alternative splicing forms of SMARCA2 gene, leading to appearance of truncated functional, loss of function or gain-of-function forms of BRM protein suggest a far more complicated mode of BRM-containing SWI/SNF CRCs actions. Therefore, the summary of recent knowledge regarding BRM alteration in various types of cancer and highlighting of differences and commonalities between BRM and BRG1, another SWI2/SNF2 type ATPase, will lead to better understanding of SWI/SNF CRCs function in cancer development/progression. BRM has been recently proposed as an attractive target for various anticancer therapies including the use of small molecule inhibitors, synthetic lethality induction or proteolysis-targeting chimera (PROTAC). However, such attempts have some limitations and may lead to severe side effects given the homology of BRM ATPase domain to other ATPases, as well as due to the tissue-specific appearance of BRM- and BRG1-containing SWI/SNF CRC classes. Thus, a better insight into BRM-containing SWI/SNF CRCs function in human tissues and cancers is clearly required to provide a solid basis for establishment of new safe anticancer therapies.
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Affiliation(s)
- Iga Jancewicz
- Department of Molecular and Translational Oncology, The Maria Sklodowska-Curie Institute-Oncology Center in Warsaw, Wawelska 15B, 02-034, Warsaw, Poland
| | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, The Maria Sklodowska-Curie Institute-Oncology Center in Warsaw, Wawelska 15B, 02-034, Warsaw, Poland
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland.
| | - Elzbieta Sarnowska
- Department of Molecular and Translational Oncology, The Maria Sklodowska-Curie Institute-Oncology Center in Warsaw, Wawelska 15B, 02-034, Warsaw, Poland.
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28
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Menon DU, Shibata Y, Mu W, Magnuson T. Mammalian SWI/SNF collaborates with a polycomb-associated protein to regulate male germline transcription in the mouse. Development 2019; 146:dev174094. [PMID: 31043422 PMCID: PMC6803380 DOI: 10.1242/dev.174094] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/23/2019] [Indexed: 12/25/2022]
Abstract
A deficiency in BRG1, the catalytic subunit of the SWI/SNF chromatin remodeling complex, results in a meiotic arrest during spermatogenesis. Here, we explore the causative mechanisms. BRG1 is preferentially enriched at active promoters of genes essential for spermatogonial pluripotency and meiosis. In contrast, BRG1 is also associated with the repression of somatic genes. Chromatin accessibility at these target promoters is dependent upon BRG1. These results favor a model in which BRG1 coordinates spermatogenic transcription to ensure meiotic progression. In spermatocytes, BRG1 interacts with SCML2, a testis-specific PRC1 factor that is associated with the repression of somatic genes. We present evidence to suggest that BRG1 and SCML2 concordantly regulate genes during meiosis. Furthermore, BRG1 is required for the proper localization of SCML2 and its associated deubiquitylase, USP7, to the sex chromosomes during pachynema. SCML2-associated mono-ubiquitylation of histone H2A lysine 119 (H2AK119ub1) and acetylation of histone lysine 27 (H3K27ac) are elevated in Brg1cKO testes. Coincidentally, the PRC1 ubiquitin ligase RNF2 is activated while a histone H2A/H2B deubiquitylase USP3 is repressed. Thus, BRG1 impacts the male epigenome by influencing the localization and expression of epigenetic modifiers. This mechanism highlights a novel paradigm of cooperativity between SWI/SNF and PRC1.
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Affiliation(s)
- Debashish U Menon
- Department of Genetics, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7264, USA
| | - Yoichiro Shibata
- Department of Genetics, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7264, USA
| | - Weipeng Mu
- Department of Genetics, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7264, USA
| | - Terry Magnuson
- Department of Genetics, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7264, USA
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Shorstova T, Marques M, Su J, Johnston J, Kleinman CL, Hamel N, Huang S, Alaoui-Jamali MA, Foulkes WD, Witcher M. SWI/SNF-Compromised Cancers Are Susceptible to Bromodomain Inhibitors. Cancer Res 2019; 79:2761-2774. [PMID: 30877105 DOI: 10.1158/0008-5472.can-18-1545] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/18/2018] [Accepted: 03/12/2019] [Indexed: 11/16/2022]
Abstract
The antitumor activity of bromodomain and extraterminal motif protein inhibitors (BETi) has been demonstrated across numerous types of cancer. As such, these inhibitors are currently undergoing widespread clinical evaluation. However, predictive biomarkers allowing the stratification of tumors into responders and nonresponders to BETi are lacking. Here, we showed significant antiproliferative effects of low dosage BETi in vitro and in vivo against aggressive ovarian and lung cancer models lacking SMARCA4 and SMARCA2, key components of SWI/SNF chromatin remodeling complexes. Restoration of SMARCA4 or SMARCA2 promoted resistance to BETi in these models and, conversely, knockdown of SMARCA4 sensitized resistant cells to BETi. Transcriptomic analysis revealed that exposure to BETi potently downregulated a network of genes involved in receptor tyrosine kinase (RTK) signaling in SMARCA4/A2-deficient cells, including the oncogenic RTK HER3. Repression of signaling downstream of HER3 was found to be an important determinant of response to BETi in SMARCA4/A2-deficient cells. Overall, we propose that BETi represent a rational therapeutic strategy in poor-prognosis, SMARCA4/A2-deficient cancers. SIGNIFICANCE: These findings address an unmet clinical need by identifying loss of SMARCA4/A2 as biomarkers of hypersensitivity to BETi.
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Affiliation(s)
- Tatiana Shorstova
- Departments of Oncology and Experimental Medicine, McGill University, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Maud Marques
- Departments of Oncology and Experimental Medicine, McGill University, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Jie Su
- Departments of Oncology and Experimental Medicine, McGill University, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Jake Johnston
- Departments of Oncology and Experimental Medicine, McGill University, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Nancy Hamel
- Departments of Oncology and Human Genetics, McGill University, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Sidong Huang
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
| | - Moulay A Alaoui-Jamali
- Departments of Oncology and Experimental Medicine, McGill University, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - William D Foulkes
- Departments of Oncology and Human Genetics, McGill University, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Michael Witcher
- Departments of Oncology and Experimental Medicine, McGill University, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.
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Ribeiro-Silva C, Vermeulen W, Lans H. SWI/SNF: Complex complexes in genome stability and cancer. DNA Repair (Amst) 2019; 77:87-95. [PMID: 30897376 DOI: 10.1016/j.dnarep.2019.03.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 01/25/2023]
Abstract
SWI/SNF complexes are among the most studied ATP-dependent chromatin remodeling complexes, mostly due to their critical role in coordinating chromatin architecture and gene expression. Mutations in genes encoding SWI/SNF subunits are frequently observed in a large variety of human cancers, suggesting that one or more of the multiple SWI/SNF functions protect against tumorigenesis. Chromatin remodeling is an integral component of the DNA damage response (DDR), which safeguards against DNA damage-induced genome instability and tumorigenesis by removing DNA damage through interconnected DNA repair and signaling pathways. SWI/SNF has been implicated in facilitating repair of double-strand breaks, by non-homologous end-joining as well as homologous recombination, and repair of helix-distorting DNA damage by nucleotide excision repair. Here, we review current knowledge on SWI/SNF activity in the DDR and discuss the potential of exploiting DDR-related vulnerabilities due to SWI/SNF dysfunction for precision cancer therapy.
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Affiliation(s)
- Cristina Ribeiro-Silva
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands.
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, the Netherlands.
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31
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Wang B, Kaufmann B, Engleitner T, Lu M, Mogler C, Olsavszky V, Öllinger R, Zhong S, Geraud C, Cheng Z, Rad RR, Schmid RM, Friess H, Hüser N, Hartmann D, von Figura G. Brg1 promotes liver regeneration after partial hepatectomy via regulation of cell cycle. Sci Rep 2019; 9:2320. [PMID: 30787318 PMCID: PMC6382836 DOI: 10.1038/s41598-019-38568-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/21/2018] [Indexed: 12/29/2022] Open
Abstract
Brahma-related gene 1 (Brg1), a catalytic subunit of the SWItch/Sucrose Non-Fermentable (SWI/SNF) complex, is known to be involved in proliferative cell processes. Liver regeneration is initiated spontaneously after injury and leads to a strong proliferative response. In this study, a hepatocyte-specific Brg1 gene knockout mouse model was used to analyse the role of Brg1 in liver regeneration by performing a 70% partial hepatectomy (PH). After PH, Brg1 was significantly upregulated in wildtype mice. Mice with hepatocyte-specific Brg1 gene knockout showed a significantly lower liver to body weight ratio 48 h post-PH concomitant with a lower hepatocellular proliferation rate compared to wildtype mice. RNA sequencing demonstrated that Brg1 controlled hepatocyte proliferation through the regulation of the p53 pathway and several cell cycle genes. The data of this study reveal a crucial role of Brg1 for liver regeneration by promoting hepatocellular proliferation through modulation of cell cycle genes and, thus, identify Brg1 as potential target for therapeutic approaches.
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Affiliation(s)
- Baocai Wang
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany.,Department of General Surgery, the Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210000, China
| | - Benedikt Kaufmann
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, Department of Medicine II and TranslaTUM Cancer Center, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Miao Lu
- Department of General Surgery, the Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210000, China
| | - Carolin Mogler
- Institute of Pathology, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Victor Olsavszky
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University and Center of Excellence in Dermatology, Mannheim, 68135, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Department of Medicine II and TranslaTUM Cancer Center, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Suyang Zhong
- Department of Medicine II, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Cyrill Geraud
- Department of Dermatology, Venereology, and Allergology, University Medical Center and Medical Faculty Mannheim, Heidelberg University and Center of Excellence in Dermatology, Mannheim, 68135, Germany
| | - Zhangjun Cheng
- Department of General Surgery, the Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210000, China
| | - Roland R Rad
- Institute of Molecular Oncology and Functional Genomics, Department of Medicine II and TranslaTUM Cancer Center, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Roland M Schmid
- Department of Medicine II, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Helmut Friess
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Norbert Hüser
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany
| | - Daniel Hartmann
- Department of Surgery, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany.
| | - Guido von Figura
- Department of Medicine II, TUM School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, 81675, Germany.
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Xue Y, Meehan B, Fu Z, Wang XQD, Fiset PO, Rieker R, Levins C, Kong T, Zhu X, Morin G, Skerritt L, Herpel E, Venneti S, Martinez D, Judkins AR, Jung S, Camilleri-Broet S, Gonzalez AV, Guiot MC, Lockwood WW, Spicer JD, Agaimy A, Pastor WA, Dostie J, Rak J, Foulkes WD, Huang S. SMARCA4 loss is synthetic lethal with CDK4/6 inhibition in non-small cell lung cancer. Nat Commun 2019; 10:557. [PMID: 30718506 PMCID: PMC6362083 DOI: 10.1038/s41467-019-08380-1] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 01/03/2019] [Indexed: 12/23/2022] Open
Abstract
Tumor suppressor SMARCA4 (BRG1), a key SWI/SNF chromatin remodeling gene, is frequently inactivated in cancers and is not directly druggable. We recently uncovered that SMARCA4 loss in an ovarian cancer subtype causes cyclin D1 deficiency leading to susceptibility to CDK4/6 inhibition. Here, we show that this vulnerability is conserved in non-small cell lung cancer (NSCLC), where SMARCA4 loss also results in reduced cyclin D1 expression and selective sensitivity to CDK4/6 inhibitors. In addition, SMARCA2, another SWI/SNF subunit lost in a subset of NSCLCs, also regulates cyclin D1 and drug response when SMARCA4 is absent. Mechanistically, SMARCA4/2 loss reduces cyclin D1 expression by a combination of restricting CCND1 chromatin accessibility and suppressing c-Jun, a transcription activator of CCND1. Furthermore, SMARCA4 loss is synthetic lethal with CDK4/6 inhibition both in vitro and in vivo, suggesting that FDA-approved CDK4/6 inhibitors could be effective to treat this significant subgroup of NSCLCs.
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Affiliation(s)
- Yibo Xue
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
- The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Brian Meehan
- Department of Pediatrics, McGill University, and Research Institute of McGill University Health Centre, Montreal Children's Hospital, Montreal, QC, H4A 3J1, Canada
| | - Zheng Fu
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
- The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Xue Qing D Wang
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Pierre Olivier Fiset
- Department of Pathology, Glen Site, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Ralf Rieker
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, 91054, Erlangen, Germany
| | - Cameron Levins
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
| | - Tim Kong
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
- The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Xianbing Zhu
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
- The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Geneviève Morin
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
- The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Lashanda Skerritt
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
- The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Esther Herpel
- Tissue Bank of the National Center for Tumor Diseases (NCT) Heidelberg, and Institute of Pathology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Sriram Venneti
- Pathology and Neuropathology, University of Michigan Medical School, Ann Arbor, MI, 48109-0605, USA
| | - Daniel Martinez
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, 19104, USA
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA, 90027, USA
| | - Sungmi Jung
- Department of Pathology, Glen Site, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Sophie Camilleri-Broet
- Department of Pathology, Glen Site, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Anne V Gonzalez
- Division of Respiratory Medicine, Montreal Chest Institute, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - Marie-Christine Guiot
- Department of Pathology, Montreal Neurological Hospital/Institute, McGill University Health Centre, Montreal, QC, H4A 3J1, Canada
| | - William W Lockwood
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Jonathan D Spicer
- Department of Surgery, McGill University Health Center, Montreal, QC, H4A 3J1, Canada
| | - Abbas Agaimy
- Institute of Pathology, Friedrich-Alexander-University Erlangen-Nürnberg, University Hospital, 91054, Erlangen, Germany
| | - William A Pastor
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
- The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, H3A 1A3, Canada
| | - Josée Dostie
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada
| | - Janusz Rak
- Department of Pediatrics, McGill University, and Research Institute of McGill University Health Centre, Montreal Children's Hospital, Montreal, QC, H4A 3J1, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
- Department of Medical Genetics, and Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, H3T 1E2, Canada
- Department of Medical Genetics and Cancer Research Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, H4A 3J1, Canada
| | - Sidong Huang
- Department of Biochemistry, McGill University, Montreal, QC, H3G 1Y6, Canada.
- The Rosalind & Morris Goodman Cancer Research Centre, McGill University, Montreal, QC, H3A 1A3, Canada.
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33
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Machol K, Rousseau J, Ehresmann S, Garcia T, Nguyen TTM, Spillmann RC, Sullivan JA, Shashi V, Jiang YH, Stong N, Fiala E, Willing M, Pfundt R, Kleefstra T, Cho MT, McLaughlin H, Rosello Piera M, Orellana C, Martínez F, Caro-Llopis A, Monfort S, Roscioli T, Nixon CY, Buckley MF, Turner A, Jones WD, van Hasselt PM, Hofstede FC, van Gassen KL, Brooks AS, van Slegtenhorst MA, Lachlan K, Sebastian J, Madan-Khetarpal S, Sonal D, Sakkubai N, Thevenon J, Faivre L, Maurel A, Petrovski S, Krantz ID, Tarpinian JM, Rosenfeld JA, Lee BH, Campeau PM, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, et alMachol K, Rousseau J, Ehresmann S, Garcia T, Nguyen TTM, Spillmann RC, Sullivan JA, Shashi V, Jiang YH, Stong N, Fiala E, Willing M, Pfundt R, Kleefstra T, Cho MT, McLaughlin H, Rosello Piera M, Orellana C, Martínez F, Caro-Llopis A, Monfort S, Roscioli T, Nixon CY, Buckley MF, Turner A, Jones WD, van Hasselt PM, Hofstede FC, van Gassen KL, Brooks AS, van Slegtenhorst MA, Lachlan K, Sebastian J, Madan-Khetarpal S, Sonal D, Sakkubai N, Thevenon J, Faivre L, Maurel A, Petrovski S, Krantz ID, Tarpinian JM, Rosenfeld JA, Lee BH, Campeau PM, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Handley LH, Herzog MR, Holm IA, Hom J, Howerton EM, Huang Y, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Kohane IS, Krasnewich DM, Krieg EL, Krier JB, Lalani SR, Lau CC, Lazar J, Lee BH, Lee H, Levy SE, Lewis RA, Lincoln SA, Lipson A, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Marom R, Martínez-Agosto JA, Marwaha S, May T, McConkie-Rosell A, McCormack CE, McCray AT, Might M, Moretti PM, Morimoto M, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Parker NH, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Reuter CM, Robertson AK, Rodan LH, Rosenfeld JA, Sampson JB, Samson SL, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Signer R, Silverman EK, Sinsheimer JS, Smith KS, Spillmann RC, Splinter K, Stoler JM, Stong N, Sullivan JA, Sweetser DA, Tifft CJ, Toro C, Tran AA, Urv TK, Valivullah ZM, Vilain E, Vogel TP, Wahl CE, Walley NM, Walsh CA, Ward PA, Waters KM, Westerfield M, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zastrow DB, Zheng A. Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay. Am J Hum Genet 2019; 104:164-178. [PMID: 30580808 DOI: 10.1016/j.ajhg.2018.11.007] [Show More Authors] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022] Open
Abstract
SMARCC2 (BAF170) is one of the invariable core subunits of the ATP-dependent chromatin remodeling BAF (BRG1-associated factor) complex and plays a crucial role in embryogenesis and corticogenesis. Pathogenic variants in genes encoding other components of the BAF complex have been associated with intellectual disability syndromes. Despite its significant biological role, variants in SMARCC2 have not been directly associated with human disease previously. Using whole-exome sequencing and a web-based gene-matching program, we identified 15 individuals with variable degrees of neurodevelopmental delay and growth retardation harboring one of 13 heterozygous variants in SMARCC2, most of them novel and proven de novo. The clinical presentation overlaps with intellectual disability syndromes associated with other BAF subunits, such as Coffin-Siris and Nicolaides-Baraitser syndromes and includes prominent speech impairment, hypotonia, feeding difficulties, behavioral abnormalities, and dysmorphic features such as hypertrichosis, thick eyebrows, thin upper lip vermilion, and upturned nose. Nine out of the fifteen individuals harbor variants in the highly conserved SMARCC2 DNA-interacting domains (SANT and SWIRM) and present with a more severe phenotype. Two of these individuals present cardiac abnormalities. Transcriptomic analysis of fibroblasts from affected individuals highlights a group of differentially expressed genes with possible roles in regulation of neuronal development and function, namely H19, SCRG1, RELN, and CACNB4. Our findings suggest a novel SMARCC2-related syndrome that overlaps with neurodevelopmental disorders associated with variants in BAF-complex subunits.
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SWI/SNF remains localized to chromatin in the presence of SCHLAP1. Nat Genet 2018; 51:26-29. [PMID: 30510238 PMCID: PMC6339527 DOI: 10.1038/s41588-018-0272-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/05/2018] [Indexed: 12/22/2022]
Abstract
SCHLAP1 is a long-noncoding RNA that is reported to function by depleting the SWI/SNF complex from the genome. We investigated the hypothesis that SCHLAP1 affects only specific compositions of SWI/SNF. Using several assays we found that SWI/SNF is not depleted from the genome by SCHLAP1, and that SWI/SNF is associated with many coding and non-coding RNAs, suggesting SCHLAP1 may function in a SWI/SNF independent manner.
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35
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Pietrzak J, Płoszaj T, Pułaski Ł, Robaszkiewicz A. EP300-HDAC1-SWI/SNF functional unit defines transcription of some DNA repair enzymes during differentiation of human macrophages. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:198-208. [PMID: 30414852 DOI: 10.1016/j.bbagrm.2018.10.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/17/2018] [Accepted: 10/31/2018] [Indexed: 01/31/2023]
Abstract
Differentiation of human macrophages predisposes these cells to numerous tasks, i.e. killing invading pathogens, and this entails the need for enhanced intracellular defences against stress, including conditions that may increase DNA damage. Our study shows that expression of DNA repair enzymes, such as PARP1, BRCA1 and XRCC1, are activated during macrophage development by the SWI/SNF chromatin remodelling complex, which serves as a histone acetylation sensor. It recognises and displaces epigenetically marked nucleosomes, thereby enabling transcription. Acetylation is controlled both in monocytes and macrophages by the co-operation of EP300 and HDAC1 activities. Differentiation modulates the activities of individual components of EP300-HDAC1-SWI/SNF functional unit and entails recruitment of PBAF to gene promoters. In monocytes, histone-deacetylated promoters of repressed PARP1, BRCA1 and XRCC1 respond only to HDAC inhibition, with an opening of the chromatin structure by BRM, whereas in macrophages both EP300 and HDAC1 contribute to the fine-tuning of nucleosomal acetylation, with HDAC1 remaining active and the balance of EP300 and HDAC1 activities controlling nucleosome eviction by BRG1-containing SWI/SNF. Since EP300-HDAC1-SWI/SNF operates at the level of gene promoters characterized simultaneously by the presence of E2F binding site(s) and CpG island(s), this allows cells to adjust PARP1, BRCA1 and XRCC1 transcription to the differentiation mode and to restart cell cycle progression. Thus, mutual interdependence between acetylase and deacetylase activities defines the acetylation-dependent code for regulation of histone density and gene transcription by SWI/SNF, notably on gene promoters of DNA repair enzymes.
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Affiliation(s)
- 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
| | - Tomasz Płoszaj
- Department of Clinical and Laboratory Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland
| | - Łukasz Pułaski
- Laboratory of Transcriptional Regulation, Institute of Medical Biology PAS, Lodowa 106, 93-232 Lodz, Poland; Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 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.
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36
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Ribeiro-Silva C, Aydin ÖZ, Mesquita-Ribeiro R, Slyskova J, Helfricht A, Marteijn JA, Hoeijmakers JHJ, Lans H, Vermeulen W. DNA damage sensitivity of SWI/SNF-deficient cells depends on TFIIH subunit p62/GTF2H1. Nat Commun 2018; 9:4067. [PMID: 30287812 PMCID: PMC6172278 DOI: 10.1038/s41467-018-06402-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 09/03/2018] [Indexed: 12/11/2022] Open
Abstract
Mutations in SWI/SNF genes are amongst the most common across all human cancers, but efficient therapeutic approaches that exploit vulnerabilities caused by SWI/SNF mutations are currently lacking. Here, we show that the SWI/SNF ATPases BRM/SMARCA2 and BRG1/SMARCA4 promote the expression of p62/GTF2H1, a core subunit of the transcription factor IIH (TFIIH) complex. Inactivation of either ATPase subunit downregulates GTF2H1 and therefore compromises TFIIH stability and function in transcription and nucleotide excision repair (NER). We also demonstrate that cells with permanent BRM or BRG1 depletion have the ability to restore GTF2H1 expression. As a consequence, the sensitivity of SWI/SNF-deficient cells to DNA damage induced by UV irradiation and cisplatin treatment depends on GTF2H1 levels. Together, our results expose GTF2H1 as a potential novel predictive marker of platinum drug sensitivity in SWI/SNF-deficient cancer cells. SWI/SNF genes are commonly found to be mutated in different cancers. Here the authors report that the remodelers BRM and BRG1 are necessary for efficient nucleotide excision repair by promoting the expression of TFIIH subunit GTF2H1.
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Affiliation(s)
- Cristina Ribeiro-Silva
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Özge Z Aydin
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Molecular Biology and Genetics Department, Koç University, Istanbul, 34450, Turkey
| | | | - Jana Slyskova
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Angela Helfricht
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
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Chen ES. Targeting epigenetics using synthetic lethality in precision medicine. Cell Mol Life Sci 2018; 75:3381-3392. [PMID: 30003270 PMCID: PMC11105276 DOI: 10.1007/s00018-018-2866-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/30/2018] [Accepted: 07/03/2018] [Indexed: 12/31/2022]
Abstract
Technological breakthroughs in genomics have had a significant impact on clinical therapy for human diseases, allowing us to use patient genetic differences to guide medical care. The "synthetic lethal approach" leverages on cancer-specific genetic rewiring to deliver a therapeutic regimen that preferentially targets malignant cells while sparing normal cells. The utility of this system is evident in several recent studies, particularly in poor prognosis cancers with loss-of-function mutations that become "treatable" when two otherwise discrete and unrelated genes are targeted simultaneously. This review focuses on the chemotherapeutic targeting of epigenetic alterations in cancer cells and consolidates a network that outlines the interplay between epigenetic and genetic regulators in DNA damage repair. This network consists of numerous synergistically acting relationships that are druggable, even in recalcitrant triple-negative breast cancer. This collective knowledge points to the dawn of a new era of personalized medicine.
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Affiliation(s)
- Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- National University Health System (NUHS), Singapore, 119228, Singapore.
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore.
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 117456, Singapore.
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Kobayashi H, Kawahara N, Ogawa K, Yamada Y, Iwai K, Niiro E, Morioka S. Conceptual frameworks of synthetic lethality in clear cell carcinoma of the ovary. Biomed Rep 2018; 9:112-118. [PMID: 30013776 DOI: 10.3892/br.2018.1114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022] Open
Abstract
Targeting non-oncogenes may result in the selective death of cancer cells. Clear cell carcinoma of the ovary (CCC) may exhibit resistance against conventional chemotherapy and is associated with poor prognosis. The aim of the present report was to review synthetic lethality-based therapies for CCC. Previous English-language studies were reviewed to accumulate preclinical and clinical data on targeting synthetic lethal partners. Synthetic lethal interactions have a variety of types, involving components of a backup or parallel pathway with overlapping functions, components encoded by paralogous pairs, subunit components that form heteromeric complexes and components that are arranged in a single linear pathway. A set of candidate gene targets potentially resulting in synthetic lethality have been previously identified. HNF class homeobox, AT-rich interaction domain 1A, ATR serine/threonine kinase, ATM serine/threonine kinase, checkpoint kinase 1 and phosphatase and tensin homolog may be the key partner genes. A variety of loss of function genes in CCC are driver or passenger events and may function as synthetic lethal pairs under replication stress conditions. Further clinical studies will be required to investigate the safety and therapeutic effect of synthetic lethality pairs in CCC tumor types with replication stress.
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Affiliation(s)
- Hiroshi Kobayashi
- Department of Obstetrics and Gynecology, Nara Medical University, Nara 634-8522, Japan
| | - Naoki Kawahara
- Department of Obstetrics and Gynecology, Nara Medical University, Nara 634-8522, Japan
| | - Kenji Ogawa
- Department of Obstetrics and Gynecology, Nara Medical University, Nara 634-8522, Japan
| | - Yuki Yamada
- Department of Obstetrics and Gynecology, Nara Medical University, Nara 634-8522, Japan
| | - Kana Iwai
- Department of Obstetrics and Gynecology, Nara Medical University, Nara 634-8522, Japan
| | - Emiko Niiro
- Department of Obstetrics and Gynecology, Nara Medical University, Nara 634-8522, Japan
| | - Sachiko Morioka
- Department of Obstetrics and Gynecology, Nara Medical University, Nara 634-8522, Japan
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Identification of Two Distinct Classes of the Human INO80 Complex Genome-Wide. G3-GENES GENOMES GENETICS 2018; 8:1095-1102. [PMID: 29432129 PMCID: PMC5873900 DOI: 10.1534/g3.117.300504] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chromatin remodeling and histone modifying enzymes play a critical role in shaping the regulatory output of a cell. Although much is known about these classes of proteins, identifying the mechanisms by which they coordinate gene expression programs remains an exciting topic of investigation. One factor that may contribute to the targeting and activity of chromatin regulators is local chromatin landscape. We leveraged genomic approaches and publically-available datasets to characterize the chromatin landscape at targets of the human INO80 chromatin remodeling complex (INO80-C). Our data revealed two classes of INO80-C targets with distinct chromatin signatures. The predominant INO80-C class was enriched for open chromatin, H3K27ac, and representative subunits from each of the three INO80-C modules (RUVBL1, RUVBL2, MCRS1, YY1). We named this class Canonical INO80. Notably, we identified an unexpected class of INO80-C targets that contained only the INO80 ATPase and harbored a repressive chromatin signature characterized by inaccessible chromatin, H3K27me3, and the methyltransferase EZH2. We named this class Non-Canonical INO80 (NC-INO80). Biochemical approaches indicated that INO80-C and the H3K27 acetyltransferase P300 physically interact, suggesting INO80-C and P300 may jointly coordinate chromatin accessibility at Canonical INO80 sites. No interaction was detected between INO80-C and EZH2, indicating INO80-C and EZH2 may engage in a separate form of regulatory crosstalk at NC-INO80 targets. Our data indicate that INO80-C is more compositionally heterogenous at its genomic targets than anticipated. Moreover, our data suggest there is an important link between INO80-C and histone modifying enzymes that may have consequences in developmental and pathological contexts.
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