151
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Li J, Wang W, Zhang Y, Cieślik M, Guo J, Tan M, Green MD, Wang W, Lin H, Li W, Wei S, Zhou J, Li G, Jing X, Vatan L, Zhao L, Bitler B, Zhang R, Cho KR, Dou Y, Kryczek I, Chan TA, Huntsman D, Chinnaiyan AM, Zou W. Epigenetic driver mutations in ARID1A shape cancer immune phenotype and immunotherapy. J Clin Invest 2020; 130:2712-2726. [PMID: 32027624 PMCID: PMC7190935 DOI: 10.1172/jci134402] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/30/2020] [Indexed: 12/18/2022] Open
Abstract
Whether mutations in cancer driver genes directly affect cancer immune phenotype and T cell immunity remains a standing question. ARID1A is a core member of the polymorphic BRG/BRM-associated factor chromatin remodeling complex. ARID1A mutations occur in human cancers and drive cancer development. Here, we studied the molecular, cellular, and clinical impact of ARID1A aberrations on cancer immunity. We demonstrated that ARID1A aberrations resulted in limited chromatin accessibility to IFN-responsive genes, impaired IFN gene expression, anemic T cell tumor infiltration, poor tumor immunity, and shortened host survival in many human cancer histologies and in murine cancer models. Impaired IFN signaling was associated with poor immunotherapy response. Mechanistically, ARID1A interacted with EZH2 via its carboxyl terminal and antagonized EZH2-mediated IFN responsiveness. Thus, the interaction between ARID1A and EZH2 defines cancer IFN responsiveness and immune evasion. Our work indicates that cancer epigenetic driver mutations can shape cancer immune phenotype and immunotherapy.
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Affiliation(s)
- Jing Li
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Weichao Wang
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | | | - Marcin Cieślik
- Department of Pathology
- Department of Computational Medicine and Bioinformatics
- University of Michigan Rogel Cancer Center, and
| | - Jipeng Guo
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | | | - Michael D. Green
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Weimin Wang
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Heng Lin
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Wei Li
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Shuang Wei
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Jiajia Zhou
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Gaopeng Li
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | | | - Linda Vatan
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Lili Zhao
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
| | - Benjamin Bitler
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Rugang Zhang
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Kathleen R. Cho
- Department of Pathology
- University of Michigan Rogel Cancer Center, and
| | - Yali Dou
- Department of Pathology
- University of Michigan Rogel Cancer Center, and
| | - Ilona Kryczek
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Timothy A. Chan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David Huntsman
- Department of Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arul M. Chinnaiyan
- Department of Pathology
- Department of Radiation Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Department of Urology
- Michigan Center for Translational Pathology
- Howard Hughes Medical Institute, and
| | - Weiping Zou
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan Rogel Cancer Center, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
- Department of Pathology
- University of Michigan Rogel Cancer Center, and
- Graduate Program in Immunology and Graduate Program in Cancer Biology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
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152
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The SWI/SNF complex in cancer - biology, biomarkers and therapy. Nat Rev Clin Oncol 2020; 17:435-448. [PMID: 32303701 DOI: 10.1038/s41571-020-0357-3] [Citation(s) in RCA: 300] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2020] [Indexed: 12/11/2022]
Abstract
Cancer genome-sequencing studies have revealed a remarkably high prevalence of mutations in genes encoding subunits of the SWI/SNF chromatin-remodelling complexes, with nearly 25% of all cancers harbouring aberrations in one or more of these genes. A role for such aberrations in tumorigenesis is evidenced by cancer predisposition in both carriers of germline loss-of-function mutations and genetically engineered mouse models with inactivation of any of several SWI/SNF subunits. Whereas many of the most frequently mutated oncogenes and tumour-suppressor genes have been studied for several decades, the cancer-promoting role of mutations in SWI/SNF genes has been recognized only more recently, and thus comparatively less is known about these alterations. Consequently, increasing research interest is being focused on understanding the prognostic and, in particular, the potential therapeutic implications of mutations in genes encoding SWI/SNF subunits. Herein, we review the burgeoning data on the mechanisms by which mutations affecting SWI/SNF complexes promote cancer and describe promising emerging opportunities for targeted therapy, including immunotherapy with immune-checkpoint inhibitors, presented by these mutations. We also highlight ongoing clinical trials open specifically to patients with cancers harbouring mutations in certain SWI/SNF genes.
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153
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Maroufy V, Shah P, Asghari A, Deng N, Le RNU, Ramirez JC, Yaseen A, Zheng WJ, Umetani M, Wu H. Gene expression dynamic analysis reveals co-activation of Sonic Hedgehog and epidermal growth factor followed by dynamic silencing. Oncotarget 2020; 11:1358-1372. [PMID: 32341755 PMCID: PMC7170495 DOI: 10.18632/oncotarget.27547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/14/2020] [Indexed: 12/02/2022] Open
Abstract
Aberrant activation of the Sonic Hedgehog (SHH) gene is observed in various cancers. Previous studies have shown a “cross-talk” effect between the canonical Hedgehog signaling pathway and the Epidermal Growth Factor (EGF) pathway when SHH is active in the presence of EGF. However, the precise mechanism of the cross-talk effect on the entire gene population has not been investigated. Here, we re-analyzed publicly available data to study how SHH and EGF cooperate to affect the dynamic activity of the gene population. We used genome dynamic analysis to explore the expression profiles under different conditions in a human medulloblastoma cell line. Ordinary differential equations, equipped with solid statistical and computational tools, were exploited to extract the information hidden in the dynamic behavior of the gene population. Our results revealed that EGF stimulation plays a dominant role, overshadowing most of the SHH effects. We also identified cross-talk genes that exhibited expression profiles dissimilar to that seen under SHH or EGF stimulation alone. These unique cross-talk patterns were validated in a cell culture model. These cross-talk genes identified here may serve as valuable markers to study or test for EGF co-stimulatory effects in an SHH+ environment. Furthermore, these cross-talk genes may play roles in cancer progression, thus they may be further explored as cancer treatment targets.
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Affiliation(s)
- Vahed Maroufy
- Department of Biostatistics and Data Science, School of Public Heath, University of Texas Health Science Center at Houston, Houston, TX, USA.,These authors contributed equally to this work
| | - Pankil Shah
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA.,These authors contributed equally to this work
| | - Arvand Asghari
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Nan Deng
- Department of Biostatistics and Data Science, School of Public Heath, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rosemarie N U Le
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Juan C Ramirez
- Facultad de Ingeniería de Sistemas, Universidad Antonio Nariño, Bogota, Colombia
| | - Ashraf Yaseen
- Department of Biostatistics and Data Science, School of Public Heath, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - W Jim Zheng
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Michihisa Umetani
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA.,HEALTH Research Institute, University of Houston, Houston, TX, USA
| | - Hulin Wu
- Department of Biostatistics and Data Science, School of Public Heath, University of Texas Health Science Center at Houston, Houston, TX, USA
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154
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Zhao Y, Dong X, Hou R. lncRNA PICART1 alleviates progression of cervical cancer by upregulating TCF21. Oncol Lett 2020; 19:3719-3724. [PMID: 32382324 PMCID: PMC7202295 DOI: 10.3892/ol.2020.11486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/19/2019] [Indexed: 12/23/2022] Open
Abstract
Role of long non-coding RNA (lncRNA) PICART1 in alleviating the progression of cervical cancer (CC) via targeting TCF21 was elucidated. PICART1 level in CC and paracancerous tissues was determined by quantitative real-time polymerase chain reaction (qRT-PCR). Its level in CC patients with different tumor stages (stage I+II and stage III+IV) and tumor sizes (≤4 cm and >4 cm) was examined. Survival analysis was conducted in CC patients expressing high level and low level of PICART1. Changes in proliferative, migratory and invasive abilities of HeLa and SiHa cells after transfection of si-PICART1 were assessed. Prognostic value of TCF21 in CC was determined by Kaplan-Meier curves. The interaction between PICART1, TCF21 and ARID1A was investigated through RNA immunoprecipitation (RIP) and Chromatin immunoprecipitation (ChIP) assay. PICART1 was downregulated in CC tissues and cell lines. CC patients with worse TNM staging and larger tumor size presented lower level of PICART1. Low level of PICART1 in CC patients predicted a worse prognosis. Silence of PICART1 stimulated the proliferative, migratory and invasive abilities of HeLa and SiHa cells. TCF21 expression was low in CC tissues and positively regulated by PICART1. Low level of TCF21 in CC patients predicted a worse prognosis. Potential binding relationship was verified among PICART, ARID1A and TCF21. ChIP assay confirmed the decreased enrichment of ARID1A in TCF21 promoter region after PICART1 knockdown. lncRNA PICART1 recruits ARID1A to activate TCF21 expression, thus alleviating the malignant progression of CC.
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Affiliation(s)
- Yunxia Zhao
- Department of Gynaecology and Obstetrics, Weifang People's Hospital, Weifang, Shandong 261041, P.R. China
| | - Xiuxian Dong
- Department of Gynaecology and Obstetrics, Weifang People's Hospital, Weifang, Shandong 261041, P.R. China
| | - Rong Hou
- Department of Gynaecology and Obstetrics, Weifang People's Hospital, Weifang, Shandong 261041, P.R. China
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155
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Villatoro TM, Ma C, Pai RK. Switch/sucrose nonfermenting nucleosome complex-deficient colorectal carcinomas have distinct clinicopathologic features. Hum Pathol 2020; 99:53-61. [PMID: 32222462 DOI: 10.1016/j.humpath.2020.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/13/2020] [Accepted: 03/20/2020] [Indexed: 02/08/2023]
Abstract
The switch/sucrose nonfermenting (SWI/SNF) nucleosome complex consists of several proteins that are involved in cellular proliferation and tumor suppression. The aim of this study was to correlate immunohistochemical expression of four SWI/SNF complex subunits, SMARCA2, SMARCB1, SMARCA4, and ARID1A, with clinicopathologic and molecular features and patient survival in 338 patients with colorectal adenocarcinoma using a tissue microarray approach. Twenty-three (7%) colorectal adenocarcinomas demonstrated deficient SWI/SNF expression: 7 had SMARCA2 deficiency, 12 had ARID1A deficiency, and 4 had both SMARCA2 and ARID1A deficiency. No cases were SMARCB1 or SMARCA4 deficient. Twelve (52%) SWI/SNF complex-deficient tumors demonstrated mismatch repair (MMR) deficiency (p = 0.02), 6 (26%) showed medullary differentiation (p = 0.001), and 9 were negative for CDX2 expression (p < 0.001). Among the MMR-deficient SWI/SNF complex-deficient tumors, 8 were sporadic MLH1 deficient, and 4 were seen in patients with Lynch syndrome. Compared with tumors with ARID1A deficiency alone, SMARCA2-deficient tumors were less likely to exhibit MMR deficiency (27% vs. 75%, p = 0.04), medullary differentiation (0% vs. 50%, p = 0.01), and mucinous differentiation (0% vs. 42%, p = 0.04). Conventional gland-forming histology was more often identified in SMARCA2-deficient tumors (11/11, 100%) than in tumors with ARID1A deficiency alone (4/12, 33%) (p = 0.001). There was no difference in KRAS mutation, BRAF mutation, stage, disease-specific survival, or disease-free survival for patients stratified by SWI/SNF expression (all with p > 0.05). In conclusion, SMARCA2-deficient and ARID1A-deficient colorectal carcinomas had distinctly different clinicopathologic features, with ARID1A-deficient tumors exhibiting medullary and mucinous differentiation and MMR deficiency and SMARCA2-deficient tumors demonstrating conventional gland-forming histologic growth with less frequent MMR deficiency.
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Affiliation(s)
- Tatiana M Villatoro
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Changqing Ma
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Reetesh K Pai
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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156
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Grossi E, Raimondi I, Goñi E, González J, Marchese FP, Chapaprieta V, Martín-Subero JI, Guo S, Huarte M. A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions. Nat Commun 2020; 11:936. [PMID: 32071317 PMCID: PMC7028943 DOI: 10.1038/s41467-020-14623-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 01/18/2020] [Indexed: 12/14/2022] Open
Abstract
LncRNAs have been shown to be direct players in chromatin regulation, but little is known about their role at active genomic loci. We investigate the role of lncRNAs in gene activation by profiling the RNA interactome of SMARCB1-containing SWI/SNF complexes in proliferating and senescent conditions. The isolation of SMARCB1-associated transcripts, together with chromatin profiling, shows prevalent association to active regions where SMARCB1 differentially binds locally transcribed RNAs. We identify SWINGN, a lncRNA interacting with SMARCB1 exclusively in proliferating conditions, exerting a pro-oncogenic role in some tumor types. SWINGN is transcribed from an enhancer and modulates the activation of GAS6 oncogene as part of a topologically organized region, as well as a larger network of pro-oncogenic genes by favoring SMARCB1 binding. Our results indicate that SWINGN influences the ability of the SWI/SNF complexes to drive epigenetic activation of specific promoters, suggesting a SWI/SNF-RNA cooperation to achieve optimal transcriptional activation.
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Affiliation(s)
- Elena Grossi
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Ivan Raimondi
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Enrique Goñi
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Jovanna González
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Francesco P Marchese
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Vicente Chapaprieta
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - José I Martín-Subero
- Departament de Fonaments Clinics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Shuling Guo
- Department of Antisense Drug Discovery and Clinical Development, Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain.
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain.
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157
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Gatchalian J, Liao J, Maxwell MB, Hargreaves DC. Control of Stimulus-Dependent Responses in Macrophages by SWI/SNF Chromatin Remodeling Complexes. Trends Immunol 2020; 41:126-140. [PMID: 31928914 PMCID: PMC6995420 DOI: 10.1016/j.it.2019.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 12/31/2022]
Abstract
Epigenetic regulation plays an important role in controlling the activation, timing, and resolution of innate immune responses in macrophages. Previously, SWI/SNF chromatin remodeling was found to define the kinetics and selectivity of gene activation in response to microbial ligands; however, these studies do not reflect a comprehensive understanding of SWI/SNF complex regulation. In 2018, a new variant of the SWI/SNF complex was identified with unknown function in inflammatory gene regulation. Here, we summarize the biochemical and genomic properties of SWI/SNF complex variants and the potential for increased regulatory control of innate immune transcriptional programs in light of such biochemical diversity. Finally, we review the development of SWI/SNF complex chemical inhibitors and degraders that could be used to modulate immune responses.
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Affiliation(s)
- Jovylyn Gatchalian
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jingwen Liao
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Matthew B Maxwell
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Biological Sciences Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Diana C Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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158
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He S, Wu Z, Tian Y, Yu Z, Yu J, Wang X, Li J, Liu B, Xu Y. Structure of nucleosome-bound human BAF complex. Science 2020; 367:875-881. [PMID: 32001526 DOI: 10.1126/science.aaz9761] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/10/2020] [Accepted: 01/22/2020] [Indexed: 12/14/2022]
Abstract
Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to cancers. The 3.7-angstrom-resolution cryo-electron microscopy structure of human BAF bound to the nucleosome reveals that the nucleosome is sandwiched by the base and the adenosine triphosphatase (ATPase) modules, which are bridged by the actin-related protein (ARP) module. The ATPase motor is positioned proximal to nucleosomal DNA and, upon ATP hydrolysis, engages with and pumps DNA along the nucleosome. The C-terminal α helix of SMARCB1, enriched in positively charged residues frequently mutated in cancers, mediates interactions with an acidic patch of the nucleosome. AT-rich interactive domain-containing protein 1A (ARID1A) and the SWI/SNF complex subunit SMARCC serve as a structural core and scaffold in the base module organization, respectively. Our study provides structural insights into subunit organization and nucleosome recognition of human BAF complex.
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Affiliation(s)
- Shuang He
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zihan Wu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yuan Tian
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zishuo Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jiali Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xinxin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jie Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Bijun Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China. .,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.,Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
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159
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Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1. Nat Commun 2020; 11:402. [PMID: 31964861 PMCID: PMC6972792 DOI: 10.1038/s41467-019-13960-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/10/2019] [Indexed: 12/21/2022] Open
Abstract
Establishing gene regulatory networks during differentiation or reprogramming requires master or pioneer transcription factors (TFs) such as PU.1, a prototype master TF of hematopoietic lineage differentiation. To systematically determine molecular features that control its activity, here we analyze DNA-binding in vitro and genome-wide in vivo across different cell types with native or ectopic PU.1 expression. Although PU.1, in contrast to classical pioneer factors, is unable to access nucleosomal target sites in vitro, ectopic induction of PU.1 leads to the extensive remodeling of chromatin and redistribution of partner TFs. De novo chromatin access, stable binding, and redistribution of partner TFs both require PU.1's N-terminal acidic activation domain and its ability to recruit SWI/SNF remodeling complexes, suggesting that the latter may collect and distribute co-associated TFs in conjunction with the non-classical pioneer TF PU.1.
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160
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ARID1A determines luminal identity and therapeutic response in estrogen-receptor-positive breast cancer. Nat Genet 2020; 52:198-207. [PMID: 31932695 DOI: 10.1038/s41588-019-0554-0] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 11/21/2019] [Indexed: 12/14/2022]
Abstract
Mutations in ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, are the most common alterations of the SWI/SNF complex in estrogen-receptor-positive (ER+) breast cancer. We identify that ARID1A inactivating mutations are present at a high frequency in advanced endocrine-resistant ER+ breast cancer. An epigenome CRISPR-CAS9 knockout (KO) screen identifies ARID1A as the top candidate whose loss determines resistance to the ER degrader fulvestrant. ARID1A inactivation in cells and in patients leads to resistance to ER degraders by facilitating a switch from ER-dependent luminal cells to ER-independent basal-like cells. Cellular plasticity is mediated by loss of ARID1A-dependent SWI/SNF complex targeting to genomic sites of the luminal lineage-determining transcription factors including ER, forkhead box protein A1 (FOXA1) and GATA-binding factor 3 (GATA3). ARID1A also regulates genome-wide ER-FOXA1 chromatin interactions and ER-dependent transcription. Altogether, we uncover a critical role for ARID1A in maintaining luminal cell identity and endocrine therapeutic response in ER+ breast cancer.
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161
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Hu G, Tu W, Yang L, Peng G, Yang L. ARID1A deficiency and immune checkpoint blockade therapy: From mechanisms to clinical application. Cancer Lett 2020; 473:148-155. [PMID: 31911080 DOI: 10.1016/j.canlet.2020.01.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/15/2019] [Accepted: 01/01/2020] [Indexed: 02/06/2023]
Abstract
The AT-rich interaction domain 1A (ARID1A, also known as BAF250a) is a chromatin remodeling gene, which frequently mutates across a broad spectrum of cancers with loss expression of the ARID1A protein. Recently, the association between ARID1A deficiency and immune checkpoint blockade (ICB) therapy has been reported. ARID1A deficiency contributes to the high microsatellite instability phenotype, increases tumor mutation burden, elevates expression of programmed cell death ligand 1 (PD-L1), and modulates the immune microenvironment, supporting the view that ARID1A loss might serve as a predictive biomarker for ICB. Furthermore, the therapeutic targeting strategies, which show "synthetic lethality" with ARID1A deficiency, exhibit potential synergy with ICB. We collectively reviewed the mechanisms underlying the correlation between ARID1A deficiency and ICB, the predictive function of ARID1A deficiency for ICB, and potential combined strategies of targeting agents, vulnerable for ARID1A deficiency, with ICB in cancer treatment.
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Affiliation(s)
- Guangyuan Hu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Wei Tu
- Department of Rheumatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Liu Yang
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Lin Yang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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162
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Jiang T, Chen X, Su C, Ren S, Zhou C. Pan-cancer analysis of ARID1A Alterations as Biomarkers for Immunotherapy Outcomes. J Cancer 2020; 11:776-780. [PMID: 31949479 PMCID: PMC6959029 DOI: 10.7150/jca.41296] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 11/15/2019] [Indexed: 12/22/2022] Open
Abstract
ARID1A alterations would compromise mismatch repair pathway and increase the number of tumor-infiltrating lymphocytes and PD-L1 expression in some cancers, which would cooperate with immune checkpoint inhibitors (ICIs) treatment. However, a comprehensive analysis of ARID1A alteration frequency and its predictive value for ICI treatment outcome in cancers has not yet been investigated. Hence, we performed this pan-cancer analysis to evaluate the prevalence and predictive value of ARID1A alterations across >40,000 cases in multiple cancer types. We found a high frequency (6.2%) of ARID1A, which were associated with significantly higher tumor mutation burden level across various cancers. Importantly, patients with ARID1A alterations and advanced cancers had the substantially prolonged overall survival in ICI treatment cohort, suggesting it might be used to predict a survival benefit from ICI therapy across multiple cancer types. Notably, ARID1A alterations were correlated with markedly high immune infiltrates in endometrial, stomach and colon cancer. However, patients with ARID1A-mutant renal clear cell carcinoma had dramatically lower CD8+ T cell infiltrations than those without, indicating the association between ARID1A alterations and immune infiltrates was cancer-dependent. Collectively, our findings highlight the important value of ARID1A alterations as pan-cancer predictive biomarkers for ICI treatment.
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Affiliation(s)
- Tao Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, China.,Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,These authors contributed equally to this paper
| | - Xiaoxia Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, China.,These authors contributed equally to this paper
| | - Chunxia Su
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, China.,These authors contributed equally to this paper
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, China
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163
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Waterhouse MP, Ugur R, Khaled WT. Therapeutic and Mechanistic Perspectives of Protein Complexes in Breast Cancer. Front Cell Dev Biol 2019; 7:335. [PMID: 31921847 PMCID: PMC6932950 DOI: 10.3389/fcell.2019.00335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/27/2019] [Indexed: 12/24/2022] Open
Abstract
Breast cancer affects one in eight women making it the most common cancer in the United Kingdom, accounting for 15% of all new cancer cases. One of the main challenges in treating breast cancer is the heterogeneous nature of the disease. At present, targeted therapies are available for hormone receptor- and HER2-positive tumors. However, no targeted therapies are currently available for patients with triple negative breast cancer (TNBC). This likely contributes to the poor prognostic outcome for TNBC patients. Consequently, there is a clear clinical need for the development of novel drugs that efficiently target TNBC. Extensive genomic and transcriptomic characterization of TNBC has in recent years identified a plethora of putative oncogenes. However, these driver oncogenes are often critical in other cell types and/or transcription factors making them very difficult to target directly. Therefore, other approaches may be required for developing novel therapeutics that fully exploit the specific functions of TNBC oncogenes in tumor cells. Here, we will argue that more research is needed to identify the protein-protein interactions of TNBC oncogenes as a means for (a) mechanistically understanding the biological function of these oncogenes in TNBC and (b) providing novel therapeutic targets that can be exploited for selectively inhibiting the oncogenic roles of TNBC oncogenes in cancer cells, whilst sparing normal healthy cells.
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Affiliation(s)
| | | | - Walid T. Khaled
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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164
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ARID1A prevents squamous cell carcinoma initiation and chemoresistance by antagonizing pRb/E2F1/c-Myc-mediated cancer stemness. Cell Death Differ 2019; 27:1981-1997. [PMID: 31831874 DOI: 10.1038/s41418-019-0475-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/03/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022] Open
Abstract
Squamous cell carcinoma (SCC) is defined as a category of aggressive malignancies arising from the squamous epithelium of various organs. Resistance to chemotherapies is a common feature of SCCs, which leads to a poor prognosis among SCC patients. Recently, studies have illustrated the essential tumor suppressive role of ARID1A in several cancer types, but its role in SCCs remains unclear. Cancer stemness has been recognized as a main reason for tumorigenesis and is commonly correlated with chemoresistance, yet the relationship between ARID1A and cancer stemness remains unknown. In this study, we showed that Arid1a conditional knockout mice had a high incidence of SCCs occurring in the tongue and esophagus. ARID1A depletion promoted tumor initiation and cancer stemness in human SCC cells. Mechanistic studies revealed that ARID1A blocked the interaction between cyclin-dependent kinases (CDKs) and retinoblastoma protein (Rb), reducing the phosphorylation of Rb. Dephosphorylated Rb suppressed E2F1 activity and then suppressed cancer stemness by inactivating c-Myc. Furthermore, we showed that ARID1A depletion significantly increased the chemoresistance of SCC and that a CDK inhibitor exhibited a favorable effect on rescuing the chemoresistance caused by ARID1A loss. Collectively, our study showed that ARID1A inhibits the cancer stemness of SCCs by competing with CDKs to bind with Rb to inhibit the E2F1/c-Myc pathway.
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165
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Trizzino M, Barbieri E, Petracovici A, Wu S, Welsh SA, Owens TA, Licciulli S, Zhang R, Gardini A. The Tumor Suppressor ARID1A Controls Global Transcription via Pausing of RNA Polymerase II. Cell Rep 2019; 23:3933-3945. [PMID: 29949775 DOI: 10.1016/j.celrep.2018.05.097] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 03/20/2018] [Accepted: 05/30/2018] [Indexed: 12/17/2022] Open
Abstract
AT-rich interactive domain-containing proteins 1A and 1B (ARID1A and ARID1B) are mutually exclusive subunits of the chromatin remodeler SWI/SNF. ARID1A is the most frequently mutated chromatin regulator across all cancers, and ovarian clear cell carcinoma (OCCC) carries the highest prevalence of ARID1A mutations (∼57%). Despite evidence implicating ARID1A in tumorigenesis, the mechanism remains elusive. Here, we demonstrate that ARID1A binds active regulatory elements in OCCC. Depletion of ARID1A represses RNA polymerase II (RNAPII) transcription but results in modest changes to accessibility. Specifically, pausing of RNAPII is severely impaired after loss of ARID1A. Compromised pausing results in transcriptional dysregulation of active genes, which is compensated by upregulation of ARID1B. However, a subset of ARID1A-dependent genes is not rescued by ARID1B, including many p53 and estrogen receptor (ESR1) targets. Our results provide insight into ARID1A-mediated tumorigenesis and unveil functions of SWI/SNF in modulating RNAPII dynamics.
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Affiliation(s)
- Marco Trizzino
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Elisa Barbieri
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Ana Petracovici
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Shuai Wu
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Sarah A Welsh
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Tori A Owens
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Silvia Licciulli
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Rugang Zhang
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- The Wistar Institute, Gene Expression and Regulation Program, 3601 Spruce Street, Philadelphia, PA 19104, USA.
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166
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Genomic Perspective on Mouse Liver Cancer Models. Cancers (Basel) 2019; 11:cancers11111648. [PMID: 31731480 PMCID: PMC6895968 DOI: 10.3390/cancers11111648] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023] Open
Abstract
Selecting the most appropriate mouse model that best recapitulates human hepatocellular carcinoma (HCC) allows translation of preclinical mouse studies into clinical studies. In the era of cancer genomics, comprehensive and integrative analysis of the human HCC genome has allowed categorization of HCC according to molecular subtypes. Despite the variety of mouse models that are available for preclinical research, there is a lack of evidence for mouse models that closely resemble human HCC. Therefore, it is necessary to identify the accurate mouse models that represent human HCC based on molecular subtype as well as histologic aggressiveness. In this review, we summarize the mouse models integrated with human HCC genomic data to provide information regarding the models that recapitulates the distinct aspect of HCC biology and prognosis based on molecular subtypes.
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167
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El Hadidy N, Uversky VN. Intrinsic Disorder of the BAF Complex: Roles in Chromatin Remodeling and Disease Development. Int J Mol Sci 2019; 20:ijms20215260. [PMID: 31652801 PMCID: PMC6862534 DOI: 10.3390/ijms20215260] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/12/2019] [Accepted: 10/21/2019] [Indexed: 12/13/2022] Open
Abstract
The two-meter-long DNA is compressed into chromatin in the nucleus of every cell, which serves as a significant barrier to transcription. Therefore, for processes such as replication and transcription to occur, the highly compacted chromatin must be relaxed, and the processes required for chromatin reorganization for the aim of replication or transcription are controlled by ATP-dependent nucleosome remodelers. One of the most highly studied remodelers of this kind is the BRG1- or BRM-associated factor complex (BAF complex, also known as SWItch/sucrose non-fermentable (SWI/SNF) complex), which is crucial for the regulation of gene expression and differentiation in eukaryotes. Chromatin remodeling complex BAF is characterized by a highly polymorphic structure, containing from four to 17 subunits encoded by 29 genes. The aim of this paper is to provide an overview of the role of BAF complex in chromatin remodeling and also to use literature mining and a set of computational and bioinformatics tools to analyze structural properties, intrinsic disorder predisposition, and functionalities of its subunits, along with the description of the relations of different BAF complex subunits to the pathogenesis of various human diseases.
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Affiliation(s)
- Nashwa El Hadidy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33612, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, 142290 Moscow Region, Russia.
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168
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An Y, Guan Y, Xu Y, Han Y, Wu C, Bao C, Zhou B, Wang H, Zhang M, Liu W, Qiu L, Han Z, Chen Y, Xia X, Wang J, Liu Z, Huang W, Yi X, Huang J. The diagnostic and prognostic usage of circulating tumor DNA in operable hepatocellular carcinoma. Am J Transl Res 2019; 11:6462-6474. [PMID: 31737198 PMCID: PMC6834494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
Circulating tumor DNA (ctDNA) is a promising noninvasive biomarker for hepatocellular carcinoma (HCC). In this study, we aimed to assess the diagnostic and prognostic value of ctDNA in HCC. Twenty-six operable HCC, 10 hepatitis and 10 cirrhosis patients were enrolled in this study. Treatment-naïve blood samples were collected from all patients, nevertheless resected tissue and postoperative blood samples were only collected from HCC patients. A custom-designed sequencing panel covering 354 genes was used to identify somatic mutations. Collectively, we identified 139 somatic mutations from 25 HCC baseline plasma samples (96.2%). TP53 (50.00%) was the most common mutant gene, and R249S was the most recurrent mutation (19.2%). Twenty-three patients (88.5%) carried at least one ctDNA mutation validated in matched tissue, and the driver mutations exhibited an advanced concordance than non-driver mutations (67.6% vs. 33.8%, P = 0.0002). For HCC patients, the number of mutations in ctDNA (R2 = 0.1682, P = 0.0375), maximal variant allele frequency (VAF) in ctDNA (R2 = 0.4974, P < 0.0001) and ctDNA concentration (R2 = 0.2676, P = 0.0068) were linearly correlated with tumor size. Multiple circulating cell-free DNA (cfDNA) parameters could be used in differentiating malignant lesions from benign lesions, and the performance was no less than blood alpha-fetoprotein (AFP). HCC patients with detectable mutation in postoperative plasma had a poor DFS than those without (17.5 months vs. 6.7 months, HR = 7.655, P < 0.0001), and postoperative cfDNA status (HR = 10.293, P < 0.0001) was an independent risk factors for recurrence. In conclusion, ctDNA profiling is potentially valuable in differential diagnosis and prognostic evaluation of HCC.
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Affiliation(s)
- Yan An
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Yanfang Guan
- Geneplus-BeijingBeijing 102206, China
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University28 West Xianning Road, Xi’an 710049, China
| | - Yaping Xu
- Geneplus-BeijingBeijing 102206, China
| | - Yingxin Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Chi Wu
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
| | - Chaohui Bao
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Boping Zhou
- Shenzhen People’s Hospital, Second Clinical Medical College of Jinan UniversityShenzhen 518109, China
| | - Haiyan Wang
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
| | - Mingxia Zhang
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
| | - Weilong Liu
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
| | - Lin Qiu
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Zeguang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome at ShanghaiShanghai 201203, China
| | - Yongsheng Chen
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University28 West Xianning Road, Xi’an 710049, China
| | | | - Jiayin Wang
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University28 West Xianning Road, Xi’an 710049, China
| | | | - Wanqiu Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Xin Yi
- Geneplus-BeijingBeijing 102206, China
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
- Shenzhen People’s Hospital, Second Clinical Medical College of Jinan UniversityShenzhen 518109, China
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome at ShanghaiShanghai 201203, China
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169
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Selvanathan S, Graham G, Grego A, Baker T, Hogg J, Simpson M, Batish M, Crompton B, Stegmaier K, Tomazou E, Kovar H, Üren A, Toretsky J. EWS-FLI1 modulated alternative splicing of ARID1A reveals novel oncogenic function through the BAF complex. Nucleic Acids Res 2019; 47:9619-9636. [PMID: 31392992 PMCID: PMC6765149 DOI: 10.1093/nar/gkz699] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 07/23/2019] [Accepted: 08/01/2019] [Indexed: 12/27/2022] Open
Abstract
Connections between epigenetic reprogramming and transcription or splicing create novel mechanistic networks that can be targeted with tailored therapies. Multiple subunits of the chromatin remodeling BAF complex, including ARID1A, play a role in oncogenesis, either as tumor suppressors or oncogenes. Recent work demonstrated that EWS-FLI1, the oncogenic driver of Ewing sarcoma (ES), plays a role in chromatin regulation through interactions with the BAF complex. However, the specific BAF subunits that interact with EWS-FLI1 and the precise role of the BAF complex in ES oncogenesis remain unknown. In addition to regulating transcription, EWS-FLI1 also alters the splicing of many mRNA isoforms, but the role of splicing modulation in ES oncogenesis is not well understood. We have identified a direct connection between the EWS-FLI1 protein and ARID1A isoform protein variant ARID1A-L. We demonstrate here that ARID1A-L is critical for ES maintenance and supports oncogenic transformation. We further report a novel feed-forward cycle in which EWS-FLI1 leads to preferential splicing of ARID1A-L, promoting ES growth, and ARID1A-L reciprocally promotes EWS-FLI1 protein stability. Dissecting this interaction may lead to improved cancer-specific drug targeting.
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Affiliation(s)
- Saravana P Selvanathan
- Departments of Oncology and Pediatrics, Georgetown University, Washington, DC 20057, USA
| | - Garrett T Graham
- Departments of Oncology and Pediatrics, Georgetown University, Washington, DC 20057, USA
| | - Alexander R Grego
- Departments of Oncology and Pediatrics, Georgetown University, Washington, DC 20057, USA
| | | | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark Simpson
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, Newark, NJ 07103, USA
| | - Mona Batish
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers University, Newark, NJ 07103, USA
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Brian Crompton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Eleni M Tomazou
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Heinrich Kovar
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Aykut Üren
- Departments of Oncology and Pediatrics, Georgetown University, Washington, DC 20057, USA
| | - Jeffrey A Toretsky
- Departments of Oncology and Pediatrics, Georgetown University, Washington, DC 20057, USA
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170
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Higgins GA, Williams AM, Ade AS, Alam HB, Athey BD. Druggable Transcriptional Networks in the Human Neurogenic Epigenome. Pharmacol Rev 2019; 71:520-538. [PMID: 31530573 PMCID: PMC6750186 DOI: 10.1124/pr.119.017681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chromosome conformation capture methods have revealed the dynamics of genome architecture which is spatially organized into topologically associated domains, with gene regulation mediated by enhancer-promoter pairs in chromatin space. New evidence shows that endogenous hormones and several xenobiotics act within circumscribed topological domains of the spatial genome, impacting subsets of the chromatin contacts of enhancer-gene promoter pairs in cis and trans Results from the National Institutes of Health-funded PsychENCODE project and the study of chromatin remodeling complexes have converged to provide a clearer understanding of the organization of the neurogenic epigenome in humans. Neuropsychiatric diseases, including schizophrenia, bipolar spectrum disorder, autism spectrum disorder, attention deficit hyperactivity disorder, and other neuropsychiatric disorders are significantly associated with mutations in neurogenic transcriptional networks. In this review, we have reanalyzed the results from publications of the PsychENCODE Consortium using pharmacoinformatics network analysis to better understand druggable targets that control neurogenic transcriptional networks. We found that valproic acid and other psychotropic drugs directly alter these networks, including chromatin remodeling complexes, transcription factors, and other epigenetic modifiers. We envision a new generation of CNS therapeutics targeted at neurogenic transcriptional control networks, including druggable parts of chromatin remodeling complexes and master transcription factor-controlled pharmacogenomic networks. This may provide a route to the modification of interconnected gene pathways impacted by disease in patients with neuropsychiatric and neurodegenerative disorders. Direct and indirect therapeutic strategies to modify the master regulators of neurogenic transcriptional control networks may ultimately help extend the life span of CNS neurons impacted by disease.
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Affiliation(s)
- Gerald A Higgins
- Departments of Computational Medicine and Bioinformatics (G.A.H., A.S.A., B.D.A.), Surgery (A.M.W., H.B.A.), and Psychiatry (B.D.A.), University of Michigan Medical School, Ann Arbor, Michigan
| | - Aaron M Williams
- Departments of Computational Medicine and Bioinformatics (G.A.H., A.S.A., B.D.A.), Surgery (A.M.W., H.B.A.), and Psychiatry (B.D.A.), University of Michigan Medical School, Ann Arbor, Michigan
| | - Alex S Ade
- Departments of Computational Medicine and Bioinformatics (G.A.H., A.S.A., B.D.A.), Surgery (A.M.W., H.B.A.), and Psychiatry (B.D.A.), University of Michigan Medical School, Ann Arbor, Michigan
| | - Hasan B Alam
- Departments of Computational Medicine and Bioinformatics (G.A.H., A.S.A., B.D.A.), Surgery (A.M.W., H.B.A.), and Psychiatry (B.D.A.), University of Michigan Medical School, Ann Arbor, Michigan
| | - Brian D Athey
- Departments of Computational Medicine and Bioinformatics (G.A.H., A.S.A., B.D.A.), Surgery (A.M.W., H.B.A.), and Psychiatry (B.D.A.), University of Michigan Medical School, Ann Arbor, Michigan
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171
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Ho PJ, Lloyd SM, Bao X. Unwinding chromatin at the right places: how BAF is targeted to specific genomic locations during development. Development 2019; 146:146/19/dev178780. [PMID: 31570369 DOI: 10.1242/dev.178780] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The BAF (SWI/SNF) chromatin remodeling complex plays a crucial role in modulating spatiotemporal gene expression during mammalian development. Although its remodeling activity was characterized in vitro decades ago, the complex actions of BAF in vivo have only recently begun to be unraveled. In living cells, BAF only binds to and remodels a subset of genomic locations. This selectivity of BAF genomic targeting is crucial for cell-type specification and for mediating precise responses to environmental signals. Here, we provide an overview of the distinct molecular mechanisms modulating BAF chromatin binding, including its combinatory assemblies, DNA/histone modification-binding modules and post-translational modifications, as well as its interactions with proteins, RNA and lipids. This Review aims to serve as a primer for future studies to decode the actions of BAF in developmental processes.
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Affiliation(s)
- Patric J Ho
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sarah M Lloyd
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA .,Department of Dermatology, Northwestern University, Evanston, IL 60208, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
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172
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Systematic characterization of BAF mutations provides insights into intracomplex synthetic lethalities in human cancers. Nat Genet 2019; 51:1399-1410. [PMID: 31427792 PMCID: PMC6952272 DOI: 10.1038/s41588-019-0477-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 06/04/2019] [Indexed: 12/26/2022]
Abstract
Aberrations in genes coding for subunits of the BAF chromatin remodeling complexes are highly abundant in human cancers. Currently, it is not understood how these loss-of-function mutations contribute to cancer development and how they can be targeted therapeutically. The cancer-type-specific occurrence patterns of certain subunit mutations suggest subunit-specific effects on BAF complex function, possibly by the formation of aberrant residual complexes. Here, we systematically characterize the effects of individual subunit loss on complex composition, chromatin accessibility and gene expression in a panel of knock-out cell lines deficient for 22 BAF subunits. We observe strong, specific and sometimes discordant alterations dependent on the targeted subunit and show that these explain intra-complex co-dependencies, including the synthetic lethal interactions SMARCA4-ARID2, SMARCA4-ACTB and SMARCC1-SMARCC2. These data provide insights into the role of different BAF subcomplexes in genome-wide chromatin organization and suggest approaches to therapeutically target BAF mutant cancers.
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173
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Bui CB, Le HK, Vu DM, Truong KDD, Nguyen NM, Ho MAN, Truong DQ. ARID1A-SIN3A drives retinoic acid-induced neuroblastoma differentiation by transcriptional repression of TERT. Mol Carcinog 2019; 58:1998-2007. [PMID: 31365169 DOI: 10.1002/mc.23091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/15/2019] [Accepted: 07/19/2019] [Indexed: 12/29/2022]
Abstract
Aggressive, high-risk neuroblastoma (NB) exhibits an immature differentiation state, profound epigenetic dysregulation and high telomerase activity. It has been suggested that aggressive NB may be treatable by inducing differentiation whereas therapeutic targeting of telomerase is under investigation for multiple cancer types. While epigenetic regulation of the telomerase reverse transcriptase (TERT) promoter has been described in high-risk NB, the exact molecular mechanisms are still not completely understood. Here we used quantitative real-time polymerase chain reaction (PCR), chromatin immunoprecipitation qPCR, quantitative telomeric repeat amplification protocol, and immunoblot techniques to investigate epigenetic regulation of TERT in wild-type and genetically modified NB cell lines. We demonstrated that TERT expression is reduced during 13-cis retinoic acid-induced NB differentiation and that this inversely correlated with increased expression of AT-rich interaction domain 1A (ARID1A), a subunit of the SWItch/sucrose nonfermentable chromatin remodeling complex. We showed that ARID1A directly caused suppression of TERT and was reliant on DNA binding and co-occupancy of the TERT promoter by the SIN3 transcription regulator family member A (SIN3A) repressor complex allowing NB differentiation to proceed. Finally, using data from NB patient cohorts, we reported a significant correlation between low ARID1A expression, elevated expression of TERT, and poorly differentiated, high-risk NB. These results provide insights into a key epigenetic pathway responsible for modulating TERT-driven NB progression, which could represent a target for therapeutic intervention.
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Affiliation(s)
- Chi-Bao Bui
- Laboratory of Neuroscience and Immunotherapy, University of Medicine and Pharmacy at Hochiminh city, Ho Chi Minh City, Vietnam.,Department of Molecular Oncology, City Children's Hospital, Ho Chi Minh City, Vietnam
| | - Hoa Kim Le
- Laboratory of Neuroscience and Immunotherapy, University of Medicine and Pharmacy at Hochiminh city, Ho Chi Minh City, Vietnam
| | - Diem My Vu
- Laboratory of Neuroscience and Immunotherapy, University of Medicine and Pharmacy at Hochiminh city, Ho Chi Minh City, Vietnam.,Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Kieu-Diem Dinh Truong
- Laboratory of Neuroscience and Immunotherapy, University of Medicine and Pharmacy at Hochiminh city, Ho Chi Minh City, Vietnam
| | - Nhat Manh Nguyen
- Laboratory of Neuroscience and Immunotherapy, University of Medicine and Pharmacy at Hochiminh city, Ho Chi Minh City, Vietnam
| | - Minh Anh Nguyen Ho
- Department of Molecular and Cell Biology, School of Medicine, Sungkyunkwan University, Suwon, Korea
| | - Dinh Quang Truong
- Department of Molecular Oncology, City Children's Hospital, Ho Chi Minh City, Vietnam
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174
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Gao F, Elliott NJ, Ho J, Sharp A, Shokhirev MN, Hargreaves DC. Heterozygous Mutations in SMARCA2 Reprogram the Enhancer Landscape by Global Retargeting of SMARCA4. Mol Cell 2019; 75:891-904.e7. [PMID: 31375262 PMCID: PMC7291823 DOI: 10.1016/j.molcel.2019.06.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/24/2019] [Accepted: 06/18/2019] [Indexed: 12/22/2022]
Abstract
Mammalian SWI/SNF complexes are multi-subunit chromatin remodeling complexes associated with an ATPase (either SMARCA4 or SMARCA2). Heterozygous mutations in the SMARCA2 ATPase cause Nicolaides-Baraitser syndrome (NCBRS), an intellectual disability syndrome associated with delayed speech onset. We engineered human embryonic stem cells (hESCs) to carry NCBRS-associated heterozygous SMARCA2 K755R or R1159Q mutations. While SMARCA2 mutant hESCs were phenotypically normal, differentiation to neural progenitors cells (NPCs) was severely impaired. We find that SMARCA2 mutations cause enhancer reorganization with loss of SOX3-dependent neural enhancers and prominent emergence of astrocyte-specific de novo enhancers. Changes in chromatin accessibility at enhancers were associated with an increase in SMARCA2 binding and retargeting of SMARCA4. We show that the AP-1 family member FRA2 is aberrantly overexpressed in SMARCA2 mutant NPCs, where it functions as a pioneer factor at de novo enhancers. Together, our results demonstrate that SMARCA2 mutations cause impaired differentiation through enhancer reprogramming via inappropriate targeting of SMARCA4.
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Affiliation(s)
- Fangjian Gao
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nicholas J Elliott
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Josephine Ho
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Alexzander Sharp
- Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Diana C Hargreaves
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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175
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Yan P, Wang Y, Meng X, Yang H, Liu Z, Qian J, Zhou W, Li J. Whole Exome Sequencing of Ulcerative Colitis-associated Colorectal Cancer Based on Novel Somatic Mutations Identified in Chinese Patients. Inflamm Bowel Dis 2019; 25:1293-1301. [PMID: 30794281 DOI: 10.1093/ibd/izz020] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Carcinogenesis is a severe consequence of chronic ulcerative colitis. We investigated the somatic mutations and pathway alterations in ulcerative colitis-associated colorectal cancer (CRC) in Chinese patients compared with sporadic CRCs to reveal potential therapeutic targets in ulcerative colitis-associated CRC. METHODS Whole exome sequencing was performed on archival tumor tissues and paired adjacent nondysplastic mucosa from 10 ulcerative colitis-associated CRC patients at a high risk of carcinogenesis. Genomic alteration profiles from 223 primary CRCs from The Cancer Genome Atlas served as sporadic CRC controls. A meta-analysis was performed to investigate differences in major genetic mutations between ulcerative colitis-associated and Crohn's disease-associated CRCs. RESULTS We identified 44 nonsilent recurrent somatic mutations via whole exome sequencing, including 25 deleterious mutations involved in apoptosis and the PI3K-Akt pathway (COL6A3, FN1), autophagy (ULK1), cell adhesion (PODXL, PTPRT, ZFHX4), and epigenetic regulation (ARID1A, NCOR2, KMT2D, NCOA6, MECP2, SUPT6H). In total, 11 of the 25 mutated genes significantly differed between ulcerative colitis-associated CRC and sporadic CRC (APC, APOB, MECP2, NCOR2, NTRK2, PODXL, RABGAP1, SIK3, SUPT6H, ULK1, USP48). Somatic TP53 mutations occurred in 33% of ulcerative colitis-associated CRCs. Subsequent meta-analysis revealed distinct mutation profiles for Crohn's disease- and ulcerative colitis-associated CRCs. Mutations involving the NF-kB pathway and epigenetic regulation were more common in ulcerative colitis-associated CRCs than in sporadic CRCs. CONCLUSION Distinct genomic alteration profiles of deleterious somatic mutations were found in ulcerative colitis-associated and sporadic CRCs. Mutations of epigenetic regulators, such as KMT2D and NCOA6, were common, suggesting an epigenetic pathomechanism for colitis-associated carcinoma in Chinese patients.
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Affiliation(s)
- Pengguang Yan
- Peking Union Medical College, No. 9 Dongdan Santiao, Beijing, China.,Department of Gastroenterology, Key Laboratory of Gut Microbiota Translational Medicine Research, Peking Union Medical College Hospital, Chinese Academy of Medical Science, No. 1 Shuaifuyuan, Beijing, China
| | - Yanan Wang
- Department of Gastroenterology, Key Laboratory of Gut Microbiota Translational Medicine Research, Peking Union Medical College Hospital, Chinese Academy of Medical Science, No. 1 Shuaifuyuan, Beijing, China
| | - Xiangchen Meng
- Department of Gastroenterology, Key Laboratory of Gut Microbiota Translational Medicine Research, Peking Union Medical College Hospital, Chinese Academy of Medical Science, No. 1 Shuaifuyuan, Beijing, China
| | - Hong Yang
- Department of Gastroenterology, Key Laboratory of Gut Microbiota Translational Medicine Research, Peking Union Medical College Hospital, Chinese Academy of Medical Science, No. 1 Shuaifuyuan, Beijing, China
| | - Zhanju Liu
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| | - Jiaming Qian
- Department of Gastroenterology, Key Laboratory of Gut Microbiota Translational Medicine Research, Peking Union Medical College Hospital, Chinese Academy of Medical Science, No. 1 Shuaifuyuan, Beijing, China
| | - Weixun Zhou
- Department of pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, No. 1 Shuaifuyuan, Beijing, China
| | - Jingnan Li
- Department of Gastroenterology, Key Laboratory of Gut Microbiota Translational Medicine Research, Peking Union Medical College Hospital, Chinese Academy of Medical Science, No. 1 Shuaifuyuan, Beijing, China
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176
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ARID1A Mutations Are Associated with Increased Immune Activity in Gastrointestinal Cancer. Cells 2019; 8:cells8070678. [PMID: 31277418 PMCID: PMC6678467 DOI: 10.3390/cells8070678] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 12/24/2022] Open
Abstract
Because traditional treatment strategies for advanced gastrointestinal (GI) cancers often have a limited therapeutic effect, immunotherapy could be a viable approach for the therapy of advanced GI cancers, considering the recent success of immunotherapy in treating various refractory malignancies, including the DNA mismatch repair-deficient GI cancers. However, only a subset of cancer patients currently respond to immunotherapy. Thus, it is important to identify useful biomarkers for predicting cancer immunotherapy response. The tumor suppressor gene ARID1A has a high mutation rate in GI cancers and its deficiency is correlated with the microsatellite instability (MSI) genomic feature of cancer. We investigated the correlation between ARID1A mutations and tumor immunity using three GI cancer genomics datasets by the bioinformatic approach, and found that diverse antitumor immune signatures were more highly enriched in ARID1A-mutated GI cancers than in ARID1A-wildtype GI cancers. The elevated immune activity in ARID1A-mutated GI cancers was associated with the higher tumor mutation burden and lower tumor aneuploidy level, as well as a higher proportion of MSI cancers in this GI cancer subtype. Moreover, we found that ARID1A-mutated GI cancers more highly expressed PD-L1 than ARID1A-wildtype GI cancers. The elevated antitumor immune signatures and PD-L1 expression could contribute to the more active immunotherapeutic responsiveness and better survival prognosis in ARID1A-mutated GI cancers than in ARID1A-wildtype GI cancers in the immunotherapy setting, as evidenced in three cancer cohorts receiving immunotherapy. Thus, the ARID1A mutation could be a useful biomarker for identifying GI cancer patients responsive to immunotherapy.
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177
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Wang W, Friedland SC, Guo B, O’Dell MR, Alexander WB, Whitney-Miller CL, Agostini-Vulaj D, Huber AR, Myers JR, Ashton JM, Dunne RF, Steiner LA, Hezel AF. ARID1A, a SWI/SNF subunit, is critical to acinar cell homeostasis and regeneration and is a barrier to transformation and epithelial-mesenchymal transition in the pancreas. Gut 2019; 68:1245-1258. [PMID: 30228219 PMCID: PMC6551318 DOI: 10.1136/gutjnl-2017-315541] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 08/07/2018] [Accepted: 08/09/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Here, we evaluate the contribution of AT-rich interaction domain-containing protein 1A (ARID1A), the most frequently mutated member of the SWItch/sucrose non-fermentable (SWI/SNF) complex, in pancreatic homeostasis and pancreatic ductal adenocarcinoma (PDAC) pathogenesis using mouse models. DESIGN Mice with a targeted deletion of Arid1a in the pancreas by itself and in the context of two common genetic alterations in PDAC, Kras and p53, were followed longitudinally. Pancreases were examined and analysed for proliferation, response to injury and tumourigenesis. Cancer cell lines derived from these models were analysed for clonogenic, migratory, invasive and transcriptomic changes. RESULTS Arid1a deletion in the pancreas results in progressive acinar-to-ductal metaplasia (ADM), loss of acinar mass, diminished acinar regeneration in response to injury and ductal cell expansion. Mutant Kras cooperates with homozygous deletion of Arid1a, leading to intraductal papillary mucinous neoplasm (IPMN). Arid1a loss in the context of mutant Kras and p53 leads to shorter tumour latency, with the resulting tumours being poorly differentiated. Cancer cell lines derived from Arid1a-mutant tumours are more mesenchymal, migratory, invasive and capable of anchorage-independent growth; gene expression analysis showed activation of epithelial-mesenchymal transition (EMT) and stem cell identity pathways that are partially dependent on Arid1a loss for dysregulation. CONCLUSIONS ARID1A plays a key role in pancreatic acinar homeostasis and response to injury. Furthermore, ARID1A restrains oncogenic KRAS-driven formation of premalignant proliferative IPMN. Arid1a-deficient PDACs are poorly differentiated and have mesenchymal features conferring migratory/invasive and stem-like properties.
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Affiliation(s)
- Wenjia Wang
- Department of Medicine, Hematology and Oncology Division, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Scott C Friedland
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, USA
| | - Bing Guo
- Department of Medicine, Hematology and Oncology Division, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Michael R O’Dell
- Department of Medicine, Hematology and Oncology Division, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - William B Alexander
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, USA
| | - Christa L Whitney-Miller
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Diana Agostini-Vulaj
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Aaron R Huber
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Jason R Myers
- Genomics Research Center, University of Rochester Medical Center, Rochester, New York, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester Medical Center, Rochester, New York, USA
| | - Richard F Dunne
- Department of Medicine, Hematology and Oncology Division, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Laurie A Steiner
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA
| | - Aram F Hezel
- Department of Medicine, Hematology and Oncology Division, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA,Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, USA
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178
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Srinivas US, Tan BWQ, Vellayappan BA, Jeyasekharan AD. ROS and the DNA damage response in cancer. Redox Biol 2019; 25:101084. [PMID: 30612957 PMCID: PMC6859528 DOI: 10.1016/j.redox.2018.101084] [Citation(s) in RCA: 1055] [Impact Index Per Article: 211.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/12/2018] [Accepted: 12/17/2018] [Indexed: 12/14/2022] Open
Abstract
Reactive oxygen species (ROS) are a group of short-lived, highly reactive, oxygen-containing molecules that can induce DNA damage and affect the DNA damage response (DDR). There is unequivocal pre-clinical and clinical evidence that ROS influence the genotoxic stress caused by chemotherapeutics agents and ionizing radiation. Recent studies have provided mechanistic insight into how ROS can also influence the cellular response to DNA damage caused by genotoxic therapy, especially in the context of Double Strand Breaks (DSBs). This has led to the clinical evaluation of agents modulating ROS in combination with genotoxic therapy for cancer, with mixed success so far. These studies point to context dependent outcomes with ROS modulator combinations with Chemotherapy and radiotherapy, indicating a need for additional pre-clinical research in the field. In this review, we discuss the current knowledge on the effect of ROS in the DNA damage response, and its clinical relevance.
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Affiliation(s)
| | - Bryce W Q Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | | | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Haematology-Oncology, National University Hospital, Singapore.
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179
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Hung YH, Hsu MC, Chen LT, Hung WC, Pan MR. Alteration of Epigenetic Modifiers in Pancreatic Cancer and Its Clinical Implication. J Clin Med 2019; 8:jcm8060903. [PMID: 31238554 PMCID: PMC6617267 DOI: 10.3390/jcm8060903] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/15/2019] [Accepted: 06/20/2019] [Indexed: 12/12/2022] Open
Abstract
The incidence of pancreatic cancer has considerably increased in the past decade. Pancreatic cancer has the worst prognosis among the cancers of the digestive tract because the pancreas is located in the posterior abdominal cavity, and most patients do not show clinical symptoms for early detection. Approximately 55% of all patients are diagnosed with pancreatic cancer only after the tumors metastasize. Therefore, identifying useful biomarkers for early diagnosis and screening high-risk groups are important to improve pancreatic cancer therapy. Recent emerging evidence has suggested that genetic and epigenetic alterations play a crucial role in the molecular aspects of pancreatic tumorigenesis. Here, we summarize recent progress in our understanding of the epigenetic alterations in pancreatic cancer and propose potential synthetic lethal strategies to target these genetic defects to treat this deadly disease.
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Affiliation(s)
- Yu-Hsuan Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan.
| | - Ming-Chuan Hsu
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan.
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan.
- Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan 704, Taiwan.
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan.
- Institute of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
| | - Mei-Ren Pan
- Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan.
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180
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Sen M, Wang X, Hamdan FH, Rapp J, Eggert J, Kosinsky RL, Wegwitz F, Kutschat AP, Younesi FS, Gaedcke J, Grade M, Hessmann E, Papantonis A, Strӧbel P, Johnsen SA. ARID1A facilitates KRAS signaling-regulated enhancer activity in an AP1-dependent manner in colorectal cancer cells. Clin Epigenetics 2019; 11:92. [PMID: 31217031 PMCID: PMC6585056 DOI: 10.1186/s13148-019-0690-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/29/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND ARID1A (AT-rich interactive domain-containing protein 1A) is a subunit of the BAF chromatin remodeling complex and plays roles in transcriptional regulation and DNA damage response. Mutations in ARID1A that lead to inactivation or loss of expression are frequent and widespread across many cancer types including colorectal cancer (CRC). A tumor suppressor role of ARID1A has been established in a number of tumor types including CRC where the genetic inactivation of Arid1a alone led to the formation of invasive colorectal adenocarcinomas in mice. Mechanistically, ARID1A has been described to largely function through the regulation of enhancer activity. METHODS To mimic ARID1A-deficient colorectal cancer, we used CRISPR/Cas9-mediated gene editing to inactivate the ARID1A gene in established colorectal cancer cell lines. We integrated gene expression analyses with genome-wide ARID1A occupancy and epigenomic mapping data to decipher ARID1A-dependent transcriptional regulatory mechanisms. RESULTS Interestingly, we found that CRC cell lines harboring KRAS mutations are critically dependent on ARID1A function. In the absence of ARID1A, proliferation of these cell lines is severely impaired, suggesting an essential role for ARID1A in this context. Mechanistically, we showed that ARID1A acts as a co-factor at enhancers occupied by AP1 transcription factors acting downstream of the MEK/ERK pathway. Consistently, loss of ARID1A led to a disruption of KRAS/AP1-dependent enhancer activity, accompanied by a downregulation of expression of the associated target genes. CONCLUSIONS We identify a previously unknown context-dependent tumor-supporting function of ARID1A in CRC downstream of KRAS signaling. Upon the loss of ARID1A in KRAS-mutated cells, enhancers that are co-occupied by ARID1A and the AP1 transcription factors become inactive, thereby leading to decreased target gene expression. Thus, targeting of the BAF complex in KRAS-mutated CRC may offer a unique, previously unknown, context-dependent therapeutic option in CRC.
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Affiliation(s)
- Madhobi Sen
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Xin Wang
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Feda H Hamdan
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Gastroenterology Research, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Jacobe Rapp
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Jessica Eggert
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Robyn Laura Kosinsky
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Ana Patricia Kutschat
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Fereshteh S Younesi
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Jochen Gaedcke
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Marian Grade
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Elisabeth Hessmann
- Department of Gastroenterology & Gastrointestinal Oncology, University Medical Center Gӧttingen, 37075, Göttingen, Germany
| | - Argyris Papantonis
- Department of Pathology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Philipp Strӧbel
- Department of Pathology, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Steven A Johnsen
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Gastroenterology Research, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.
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181
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Yu JSE, Colborne S, Hughes CS, Morin GB, Nielsen TO. The FUS-DDIT3 Interactome in Myxoid Liposarcoma. Neoplasia 2019; 21:740-751. [PMID: 31220736 PMCID: PMC6584455 DOI: 10.1016/j.neo.2019.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/13/2022] Open
Abstract
Myxoid liposarcoma is a malignant lipogenic tumor that develops in deep soft tissues. While local control rates are good, current chemotherapy options remain ineffective against metastatic disease. Myxoid liposarcoma is characterized by the FUS-DDIT3 fusion oncoprotein that is proposed to function as an aberrant transcription factor, but its exact mechanism of action has remained unclear. To identify the key functional interacting partners of FUS-DDIT3, this study utilized immunoprecipitation-mass spectrometry (IP-MS) to identify the FUS-DDIT3 interactome in whole cell lysates of myxoid liposarcoma cells, and results showed an enrichment of RNA processing proteins. Further quantitative MS analyses of FUS-DDIT3 complexes isolated from nuclear lysates showed that members of several chromatin regulatory complexes were present in the FUS-DDIT3 interactome, including NuRD, SWI/SNF, PRC1, PRC2, and MLL1 COMPASS-like complexes. Co-immunoprecipitation validated the associations of FUS-DDIT3 with BRG1/SMARCA4, BAF155/SMARCC1, BAF57/SMARCE1, and KDM1A. Data from this study provides candidates for functional validation as potential therapeutic targets, particularly for emerging epigenetic drugs.
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Affiliation(s)
- Jamie S E Yu
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada.
| | - Shane Colborne
- British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
| | | | - Gregg B Morin
- British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
| | - Torsten O Nielsen
- Department of Pathology, University of British Columbia, Vancouver, BC V5Z 1M9, Canada.
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182
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Winters BR, De Sarkar N, Arora S, Bolouri H, Jana S, Vakar-Lopez F, Cheng HH, Schweizer MT, Yu EY, Grivas P, Lee JK, Kollath L, Holt SK, McFerrin L, Ha G, Nelson PS, Montgomery RB, Wright JL, Lam HM, Hsieh AC. Genomic distinctions between metastatic lower and upper tract urothelial carcinoma revealed through rapid autopsy. JCI Insight 2019; 5:128728. [PMID: 31145100 DOI: 10.1172/jci.insight.128728] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Little is known about the genomic differences between metastatic urothelial carcinoma (LTUC) and upper tract urothelial carcinoma (UTUC). We compare genomic features of primary and metastatic UTUC and LTUC tumors in a cohort of patients with end stage disease. METHODS We performed whole exome sequencing on matched primary and metastatic tumor samples (N=37) from 7 patients with metastatic UC collected via rapid autopsy. Inter- and intra-patient mutational burden, mutational signatures, predicted deleterious mutations, and somatic copy alterations (sCNV) were analyzed. RESULTS We investigated 3 patients with UTUC (3 primary samples, 13 metastases) and 4 patients with LTUC (4 primary samples, 17 metastases). We found that sSNV burden was higher in metastatic LTUC compared to UTUC. Moreover, the APOBEC mutational signature was pervasive in metastatic LTUC and less so in UTUC. Despite a lower overall sSNV burden, UTUC displayed greater inter- and intra-individual genomic distances at the copy number level between primary and metastatic tumors than LTUC. Our data also indicate that metastatic UTUC lesions can arise from small clonal populations present in the primary cancer. Importantly, putative druggable mutations were found across patients with the majority shared across all metastases within a patient. CONCLUSIONS Metastatic UTUC demonstrated a lower overall mutational burden but greater structural variability compared to LTUC. Our findings suggest that metastatic UTUC displays a greater spectrum of copy number divergence from LTUC. Importantly, we identified druggable lesions shared across metastatic samples, which demonstrate a level of targetable homogeneity within individual patients.
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Affiliation(s)
| | - Navonil De Sarkar
- Department of Medicine, Division of Oncology, University of Washington School of Medicine, Seattle, Washington, USA.,Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sonali Arora
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Hamid Bolouri
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sujata Jana
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Funda Vakar-Lopez
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Heather H Cheng
- Department of Medicine, Division of Oncology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michael T Schweizer
- Department of Medicine, Division of Oncology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Evan Y Yu
- Department of Medicine, Division of Oncology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Petros Grivas
- Department of Medicine, Division of Oncology, University of Washington School of Medicine, Seattle, Washington, USA
| | - John K Lee
- Department of Medicine, Division of Oncology, University of Washington School of Medicine, Seattle, Washington, USA.,Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - Lisa McFerrin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Gavin Ha
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Peter S Nelson
- Department of Medicine, Division of Oncology, University of Washington School of Medicine, Seattle, Washington, USA.,Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Robert B Montgomery
- Department of Medicine, Division of Oncology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jonathan L Wright
- Department of Urology and.,Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Hung-Ming Lam
- Department of Urology and.,Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau (SAR), China
| | - Andrew C Hsieh
- Department of Medicine, Division of Oncology, University of Washington School of Medicine, Seattle, Washington, USA.,Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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183
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Bracken AP, Brien GL, Verrijzer CP. Dangerous liaisons: interplay between SWI/SNF, NuRD, and Polycomb in chromatin regulation and cancer. Genes Dev 2019; 33:936-959. [PMID: 31123059 PMCID: PMC6672049 DOI: 10.1101/gad.326066.119] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this review, Bracken et al. discuss the functional organization and biochemical activities of remodelers and Polycomb and explore how they work together to control cell differentiation and the maintenance of cell identity. They also discuss how mutations in the genes encoding these various chromatin regulators contribute to oncogenesis by disrupting the chromatin equilibrium. Changes in chromatin structure mediated by ATP-dependent nucleosome remodelers and histone modifying enzymes are integral to the process of gene regulation. Here, we review the roles of the SWI/SNF (switch/sucrose nonfermenting) and NuRD (nucleosome remodeling and deacetylase) and the Polycomb system in chromatin regulation and cancer. First, we discuss the basic molecular mechanism of nucleosome remodeling, and how this controls gene transcription. Next, we provide an overview of the functional organization and biochemical activities of SWI/SNF, NuRD, and Polycomb complexes. We describe how, in metazoans, the balance of these activities is central to the proper regulation of gene expression and cellular identity during development. Whereas SWI/SNF counteracts Polycomb, NuRD facilitates Polycomb repression on chromatin. Finally, we discuss how disruptions of this regulatory equilibrium contribute to oncogenesis, and how new insights into the biological functions of remodelers and Polycombs are opening avenues for therapeutic interventions on a broad range of cancer types.
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Affiliation(s)
- Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Gerard L Brien
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - C Peter Verrijzer
- Department of Biochemistry, Erasmus University Medical Center, 3000 DR Rotterdam, the Netherlands
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184
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Toumpeki C, Liberis A, Tsirkas I, Tsirka T, Kalagasidou S, Inagamova L, Anthoulaki X, Tsatsaris G, Kontomanolis EN. The Role of ARID1A in Endometrial Cancer and the Molecular Pathways Associated With Pathogenesis and Cancer Progression. In Vivo 2019; 33:659-667. [PMID: 31028182 PMCID: PMC6559907 DOI: 10.21873/invivo.11524] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/26/2019] [Accepted: 04/01/2019] [Indexed: 02/07/2023]
Abstract
AT-rich interaction domain 1A gene (ARID1A) encodes for a subunit of the switch/sucrose non-fermentable (SWI/SNF) complex, a chromatin remodeling complex, and it has been implicated in the pathogenesis of various cancer types. In this review, we discuss how ARID1A is linked to endometrial cancer and what molecular pathways are affected by mutation or inhibition of ARID1A. We also discuss the potential use of ARID1A not only as a prognostic biomarker, but also as a target for therapeutic interventions.
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Affiliation(s)
- Chrisavgi Toumpeki
- Department of Obstetrics and Gynecology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Anastasios Liberis
- Second Department of Obstetrics and Gynecology, Hippokration General Hospital, Thessaloniki, Greece
| | - Ioannis Tsirkas
- Department of Obstetrics and Gynecology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Theodora Tsirka
- Department of Molecular Biology and Genetics, University of Thrace, Alexandroupolis, Greece
| | - Sofia Kalagasidou
- Department of Obstetrics and Gynecology, Bodosakio General Hospital of Ptolemaida, Ptolemaida, Greece
| | - Lola Inagamova
- Department of Obstetrics and Gynecology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Xanthoula Anthoulaki
- Department of Obstetrics and Gynecology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Georgios Tsatsaris
- Department of Obstetrics and Gynecology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Emmanuel N Kontomanolis
- Department of Obstetrics and Gynecology, Democritus University of Thrace, Alexandroupolis, Greece
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185
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Prognostic role of ARID1A negative expression in gastric cancer. Sci Rep 2019; 9:6769. [PMID: 31043675 PMCID: PMC6494900 DOI: 10.1038/s41598-019-43293-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/16/2019] [Indexed: 02/01/2023] Open
Abstract
AT-rich interactive domain 1A (ARID1A) functions as a tumor suppressor and several therapeutic targets in ARID1A-mutated cancers are under development. Here, we investigated the prognostic value of ARID1A for gastric cancer and its association with expression of PD-L1 and p53. ARID1A expression was examined by immunohistochemistry and negative expression of ARID1A was detected in 39 (19.5%) of 200 cases in a test cohort and in 40 (18.2%) of 220 cases in a validation cohort. Negative expression of ARID1A was associated with worse overall survival in undifferentiated cases, particularly early-stage cases. Negative expression of ARID1A was detected in 11 (50%) of 22 PD-L1-positive cases and in 68 (17.1%) of 398 PD-L1-negative cases in a combined cohort. Negative expression of ARID1A was detected in 45 (22%) of 205 p53-positive cases and in 34 (15.8%) of 215 p53-negative cases in a combined cohort. In addition, expression of EZH2, a potential synthetic lethal target in ARID1A-mutated tumors, was detected in 79 ARID1A-negative cases. An ARID1A-knockdown gastric cancer cell line was subjected to microarray analysis, but no actionable targets or pathways were identified. The present results indicate that ARID1A may serve as an early-stage prognostic biomarker for undifferentiated gastric cancer.
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186
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Wu S, Fatkhutdinov N, Rosin L, Luppino JM, Iwasaki O, Tanizawa H, Tang HY, Kossenkov AV, Gardini A, Noma KI, Speicher DW, Joyce EF, Zhang R. ARID1A spatially partitions interphase chromosomes. SCIENCE ADVANCES 2019; 5:eaaw5294. [PMID: 31131328 PMCID: PMC6531001 DOI: 10.1126/sciadv.aaw5294] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 04/12/2019] [Indexed: 05/12/2023]
Abstract
ARID1A, a subunit of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling complex, localizes to both promoters and enhancers to influence transcription. However, the role of ARID1A in higher-order spatial chromosome partitioning and genome organization is unknown. Here, we show that ARID1A spatially partitions interphase chromosomes and regulates higher-order genome organization. The SWI/SNF complex interacts with condensin II, and they display significant colocalizations at enhancers. ARID1A knockout drives the redistribution of condensin II preferentially at enhancers, which positively correlates with changes in transcription. ARID1A and condensin II contribute to transcriptionally inactive B-compartment formation, while ARID1A weakens the border strength of topologically associated domains. Condensin II redistribution induced by ARID1A knockout positively correlates with chromosome sizes, which negatively correlates with interchromosomal interactions. ARID1A loss increases the trans interactions of small chromosomes, which was validated by three-dimensional interphase chromosome painting. These results demonstrate that ARID1A is important for large-scale genome folding and spatially partitions interphase chromosomes.
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Affiliation(s)
- Shuai Wu
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Nail Fatkhutdinov
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
- Kazan Federal University, Kazan, Russia
| | - Leah Rosin
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer M. Luppino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Osamu Iwasaki
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Hideki Tanizawa
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Andrew V. Kossenkov
- Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Alessandro Gardini
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Ken-ichi Noma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - David W. Speicher
- Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, USA
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Eric F. Joyce
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rugang Zhang
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
- Corresponding author.
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187
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Vymetalkova V, Vodicka P, Vodenkova S, Alonso S, Schneider-Stock R. DNA methylation and chromatin modifiers in colorectal cancer. Mol Aspects Med 2019; 69:73-92. [PMID: 31028771 DOI: 10.1016/j.mam.2019.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/11/2019] [Accepted: 04/15/2019] [Indexed: 12/15/2022]
Abstract
Colorectal carcinogenesis is a multistep process involving the accumulation of genetic alterations over time that ultimately leads to disease progression and metastasis. Binding of transcription factors to gene promoter regions alone cannot explain the complex regulation pattern of gene expression during this process. It is the chromatin structure that allows for a high grade of regulatory flexibility for gene expression. Posttranslational modifications on histone proteins such as acetylation, methylation, or phosphorylation determine the accessibility of transcription factors to DNA. DNA methylation, a chemical modification of DNA that modulates chromatin structure and gene transcription acts in concert with these chromatin conformation alterations. Another epigenetic mechanism regulating gene expression is represented by small non-coding RNAs. Only very recently epigenetic alterations have been included in molecular subtype classification of colorectal cancer (CRC). In this chapter, we will provide examples of the different epigenetic players, focus on their role for epithelial-mesenchymal transition and metastatic processes and discuss their prognostic value in CRC.
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Affiliation(s)
- Veronika Vymetalkova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00, Pilsen, Czech Republic
| | - Pavel Vodicka
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00, Pilsen, Czech Republic
| | - Sona Vodenkova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Sergio Alonso
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, (IGTP-PMPPC), Campus Can Ruti, 08916, Badalona, Barcelona, Spain
| | - Regine Schneider-Stock
- Experimental Tumorpathology, Institute of Pathology, University Hospital of Friedrich-Alexander-University Erlangen-Nürnberg, Universitätsstrasse 22, 91054, Erlangen, Germany.
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188
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Liu H, Zhao YR, Chen B, Ge Z, Huang JS. High expression of SMARCE1 predicts poor prognosis and promotes cell growth and metastasis in gastric cancer. Cancer Manag Res 2019; 11:3493-3509. [PMID: 31118775 PMCID: PMC6498956 DOI: 10.2147/cmar.s195137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/07/2019] [Indexed: 12/20/2022] Open
Abstract
Background: Gastric cancer (GC) is one of the most lethal cancers worldwide with a high risk for recurrence and metastasis. Therefore, further understanding of the metastatic mechanism and the development of treatment strategies are required. Although increasing evidence suggests that SWI/SNF Related, Matrix Associated, Actin Dependent Regulator of Chromatin, Subfamily E, Member 1 (SMARCE1) promotes cancer metastasis, its role in GC remains unclear. Materials and methods: GC samples (n=122) were used to investigate the association between SMARCE1 expression, patient clinicopathological features, and prognosis. The expression of SMARCE1 in GC tissues was measured using real-time polymerase chain reaction, western blotting, and immunohistochemistry. MGC-803 and AGS cells were transfected with lentivirus to upregulate or downregulate SMARCE1 expression. The roles of SMARCE1 in GC cell proliferation, migration, and invasion were determined using Cell Counting Kit-8 assay, colony formation assay, wound healing, transwell migration, and invasion assay. Nude mice models were established to observe tumorigenesis. The specific mitogen-activated protein kinase (MAPK) inhibitor U0126 was utilized to verify the involved pathway. Results: SMARCE1 was highly expressed in GC tissues and cell lines. High expression of SMARCE1 was correlated with the malignant clinicopathological characteristics of GC patients, including tumor size, depth of invasion, degree of differentiation, lymph node involvement, and TNM stage (all P<0.05). Kaplan–Meier survival analysis revealed that high SMARCE1 expression predicted poor prognosis in GC patients (P<0.01). Moreover, SMARCE1 was an independent risk factor of poor prognosis (P<0.01). Functional study revealed that overexpression of SMARCE1 markedly promoted the proliferation, migration, and invasion of GC cells in vitro and tumorigenesis in vivo. Furthermore, SMARCE1 activated the MAPK/ERK signaling pathway. U0126 significantly inhibited the SMARCE1-induced proliferation and mobility of GC cells. Conclusion: SMARCE1 promoted growth and metastasis of GC, indicating its potential usefulness as a prognostic biomarker and target for therapeutic intervention against this disease.
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Affiliation(s)
- Hao Liu
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Yan-Rong Zhao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Bo Chen
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Zheng Ge
- Department of General Surgery, Huaihe Hospital, Henan University, Kaifeng, Henan, People's Republic of China
| | - Jiang-Sheng Huang
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
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189
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BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors. Nat Commun 2019; 10:1881. [PMID: 31015438 PMCID: PMC6479050 DOI: 10.1038/s41467-019-09891-7] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/03/2019] [Indexed: 12/22/2022] Open
Abstract
Bromodomain-containing protein 9 (BRD9) is a recently identified subunit of SWI/SNF(BAF) chromatin remodeling complexes, yet its function is poorly understood. Here, using a genome-wide CRISPR-Cas9 screen, we show that BRD9 is a specific vulnerability in pediatric malignant rhabdoid tumors (RTs), which are driven by inactivation of the SMARCB1 subunit of SWI/SNF. We find that BRD9 exists in a unique SWI/SNF sub-complex that lacks SMARCB1, which has been considered a core subunit. While SMARCB1-containing SWI/SNF complexes are bound preferentially at enhancers, we show that BRD9-containing complexes exist at both promoters and enhancers. Mechanistically, we show that SMARCB1 loss causes increased BRD9 incorporation into SWI/SNF thus providing insight into BRD9 vulnerability in RTs. Underlying the dependency, while its bromodomain is dispensable, the DUF3512 domain of BRD9 is essential for SWI/SNF integrity in the absence of SMARCB1. Collectively, our results reveal a BRD9-containing SWI/SNF subcomplex is required for the survival of SMARCB1-mutant RTs. Mutations of the SWI/SNF chromatin-remodeling complex member SMARCB1 can cause malignant rhaboid tumors. Here the authors report a BRD9-containing SWI/SNF subcomplex that lacks SMARCB1 and its requirement for the survival of rhaboid tumors.
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190
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Ramakrishnan S, Granger V, Rak M, Hu Q, Attwood K, Aquila L, Krishnan N, Osiecki R, Azabdaftari G, Guru K, Chatta G, Gueron G, McNally L, Ohm J, Wang J, Woloszynska A. Inhibition of EZH2 induces NK cell-mediated differentiation and death in muscle-invasive bladder cancer. Cell Death Differ 2019; 26:2100-2114. [PMID: 30692641 PMCID: PMC6748105 DOI: 10.1038/s41418-019-0278-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 12/22/2022] Open
Abstract
Lysine-specific demethylase 6A (KDM6A) and members of the Switch/Sucrose Non-Fermentable (SWI/SNF) family are known to counteract the activity of Enhancer of Zeste Homolog 2 (EZH2), which is often overexpressed and is associated with poor prognosis in muscle-invasive bladder cancer. Here we provide evidence that alterations in chromatin modifying enzymes, including KDM6A and members of the SWI/SNF complex, are frequent in muscle-invasive bladder cancer. We exploit the loss of function mutations in KDM6A and SWI/SNF complex to make bladder cancer cells susceptible to EZH2-based epigenetic therapy that activates an immune response to drive tumor cell differentiation and death. We reveal a novel mechanism of action of EZH2 inhibition, alone and in combination with cisplatin, which induces immune signaling with the largest changes observed in interferon gamma (IFN-γ). This upregulation is a result of activated natural killer (NK) signaling as demonstrated by the increase in NK cell-associated genes MIP-1α, ICAM1, ICAM2, and CD86 in xenografts treated with EZH2 inhibitors. Conversely, EZH2 inhibition results in decreased expression of pluripotency markers, ALDH2 and CK5, and increased cell death. Our results reveal a novel sensitivity of muscle-invasive bladder cancer cells with KMD6A and SWI/SNF mutations to EZH2 inhibition alone and in combination with cisplatin. This sensitivity is mediated through increased NK cell-related signaling resulting in tumor cell differentiation and cell death.
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Affiliation(s)
- Swathi Ramakrishnan
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Victoria Granger
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Monika Rak
- Department of Cell Biology, Jagiellonian University, 31-007, Krakow, Poland
| | - Qiang Hu
- Department of Bioinformatics and BioStatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Kristopher Attwood
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Lanni Aquila
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Nithya Krishnan
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | | | - Gissou Azabdaftari
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Khurshid Guru
- Department of Urology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Gurkamal Chatta
- Department of Medicine-GU Center, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Geraldine Gueron
- Department of Biological Chemistry, University of Buenos Aires, IQUIBICEN-CONICET, Intendente Guiraldes 2160, CABA, 1428, Buenos Aires, Argentina
| | - Lacey McNally
- Department of Cancer Biology, Wake Forest Comprehensive Cancer Center, Winston-Salem, NC, 27157, USA
| | - Joyce Ohm
- Department of Cancer Genetics and Genomics, Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Jianmin Wang
- Department of Bioinformatics and BioStatistics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Anna Woloszynska
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
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191
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Zhou H, Tan S, Li H, Lin X. Expression and significance of EBV, ARID1A and PIK3CA in gastric carcinoma. Mol Med Rep 2019; 19:2125-2136. [PMID: 30747208 PMCID: PMC6390055 DOI: 10.3892/mmr.2019.9886] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022] Open
Abstract
AT-rich interaction domain 1A (ARID1A) and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA) serve important roles in the formation and development of numerous malignancies including gastric cancer. Accumulating evidence has demonstrated that Epstein-Barr virus (EBV) is a pathogenic virus associated with gastric cancer. The present study aimed to investigate the association between EBV infection, and the expression levels of ARID1A and PIK3CA in gastric cancer. EBER in situ hybridization was performed to detect EBV infection. Immunohistochemistry was used to assess the expression levels of ARID1A and PIK3CA in gastric cancer and adjacent normal tissues. A total of 58 gastric cancer and 10 adjacent normal tissues were tested for genetic mutations via single nucleotide polymorphism genotyping assays. Fluorescent polymerase chain reaction was used to detect EBV infection; 9.3% (28/300) of gastric cancer samples were positive for EBV, whereas, all adjacent normal tissues were negative. ARID1A and PIK3CA were negatively correlated in gastric cancer (r=−0.167). The expression levels of ARID1A and PIK3CA in gastric cancer were significantly associated with the depth of invasion of gastric cancer. A total of 62.1% (36/58) of tumor samples exhibited mutations in ARID1A, whereas, 13.8% (8/58) presented mutations in PIK3CA. Notably, EBV-associated gastric cancer (EBVaGC) samples with PIK3CA mutations additionally exhibited ARID1A mutations. Although in the present study it was identified that ARID1A and PIK3CA were negatively correlated in EBVaGC, further studies are required to investigate the association among ARID1A, PIK3CA and EBV in gastric cancer.
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Affiliation(s)
- Huan Zhou
- Department of Pathology, Central South University, Xiangya School of Medicine, Affiliated Haikou Hospital, Haikou, Hainan 570208, P.R. China
| | - Shun Tan
- Department of Pathology, Central South University, Xiangya School of Medicine, Affiliated Haikou Hospital, Haikou, Hainan 570208, P.R. China
| | - Hong Li
- Department of Pathology, Central South University, Xiangya School of Medicine, Affiliated Haikou Hospital, Haikou, Hainan 570208, P.R. China
| | - Xiangtao Lin
- Department of Pathology, Central South University, Xiangya School of Medicine, Affiliated Haikou Hospital, Haikou, Hainan 570208, P.R. China
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192
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Abstract
Inactivating mutations of Arid1a, a subunit of the Switch/sucrose nonfermentable chromatin remodeling complex, have been reported in multiple human cancers. Intestinal deletion of Arid1a has been reported to induce colorectal cancer in mice; however, its functional role in intestinal homeostasis remains unclear. We investigated the functional role of Arid1a in intestinal homeostasis in mice. We found that intestinal deletion of Arid1a results in loss of intestinal stem cells (ISCs), decreased Paneth and goblet cells, disorganized crypt-villous structures, and increased apoptosis in adult mice. Spheroids did not develop from intestinal epithelial cells deficient for Arid1a Lineage-tracing experiments revealed that Arid1a deletion in Lgr5+ ISCs leads to impaired self-renewal of Lgr5+ ISCs but does not perturb intestinal homeostasis. The Wnt signaling pathway, including Wnt agonists, receptors, and target genes, was strikingly down-regulated in Arid1a-deficient intestines. We found that Arid1a directly binds to the Sox9 promoter to support its expression. Remarkably, overexpression of Sox9 in intestinal epithelial cells abrogated the above phenotypes, although Sox9 overexpression in intestinal epithelial cells did not restore the expression levels of Wnt agonist and receptor genes. Furthermore, Sox9 overexpression permitted development of spheroids from Arid1a-deficient intestinal epithelial cells. In addition, deletion of Arid1a concomitant with Sox9 overexpression in Lgr5+ ISCs restores self-renewal in Arid1a-deleted Lgr5+ ISCs. These results indicate that Arid1a is indispensable for the maintenance of ISCs and intestinal homeostasis in mice. Mechanistically, this is mainly mediated by Sox9. Our data provide insights into the molecular mechanisms underlying maintenance of ISCs and intestinal homeostasis.
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193
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Nakamura M, Chiba T, Kanayama K, Kanzaki H, Saito T, Kusakabe Y, Kato N. Epigenetic dysregulation in hepatocellular carcinoma: an up-to-date review. Hepatol Res 2019; 49:3-13. [PMID: 30238570 DOI: 10.1111/hepr.13250] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 08/30/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022]
Abstract
Due to the advances made in research based on next generation sequencers, it is now possible to detect and analyze epigenetic abnormalities associated with cancer. DNA methylation, various histone modifications, chromatin remodeling, and non-coding RNA-associated gene silencing are considered to be transcriptional regulatory mechanisms associated with gene expression changes. The breakdown of this precise regulatory system is involved in the transition to cancer. The important role of epigenetic regulation can be observed from the high rate of genetic mutations and abnormal gene expression leading to a breakdown in epigenetic gene expression regulation seen in hepatocellular carcinoma (HCC). Based on an understanding of epigenomic abnormalities associated with pathological conditions, these findings will lead the way to diagnosis and treatment. In particular, in addition to the fact that there are few choices in terms of extant drug therapies aimed at HCC, there are limits to their antitumor effects. The clinical application of epigenetic therapeutic agents for HCC has only just begun, and future developments are expected.
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Affiliation(s)
- Masato Nakamura
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tetsuhiro Chiba
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kengo Kanayama
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroaki Kanzaki
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoko Saito
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuko Kusakabe
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
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194
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Saito S, Lin YC, Nakamura Y, Eckner R, Wuputra K, Kuo KK, Lin CS, Yokoyama KK. Potential application of cell reprogramming techniques for cancer research. Cell Mol Life Sci 2019; 76:45-65. [PMID: 30283976 PMCID: PMC6326983 DOI: 10.1007/s00018-018-2924-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 09/15/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023]
Abstract
The ability to control the transition from an undifferentiated stem cell to a specific cell fate is one of the key techniques that are required for the application of interventional technologies to regenerative medicine and the treatment of tumors and metastases and of neurodegenerative diseases. Reprogramming technologies, which include somatic cell nuclear transfer, induced pluripotent stem cells, and the direct reprogramming of specific cell lineages, have the potential to alter cell plasticity in translational medicine for cancer treatment. The characterization of cancer stem cells (CSCs), the identification of oncogene and tumor suppressor genes for CSCs, and the epigenetic study of CSCs and their microenvironments are important topics. This review summarizes the application of cell reprogramming technologies to cancer modeling and treatment and discusses possible obstacles, such as genetic and epigenetic alterations in cancer cells, as well as the strategies that can be used to overcome these obstacles to cancer research.
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Affiliation(s)
- Shigeo Saito
- Saito Laboratory of Cell Technology, Yaita, Tochigi, 329-1571, Japan
- College of Engineering, Nihon University, Koriyama, Fukushima, 963-8642, Japan
| | - Ying-Chu Lin
- School of Dentistry, College of Dental Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Richard Eckner
- Department of Biochemistry and Molecular Biology, Rutgers, New Jersey Medical School-Rutgers, The State University of New Jersey, Newark, NJ, 07101, USA
| | - Kenly Wuputra
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Kung-Kai Kuo
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, 807, Taiwan
| | - Chang-Shen Lin
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
| | - Kazunari K Yokoyama
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Faculty of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan.
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195
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Iqbal J, Amador C, McKeithan TW, Chan WC. Molecular and Genomic Landscape of Peripheral T-Cell Lymphoma. Cancer Treat Res 2019; 176:31-68. [PMID: 30596212 DOI: 10.1007/978-3-319-99716-2_2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Peripheral T-cell lymphoma (PTCL) is an uncommon group of lymphoma covering a diverse spectrum of entities. Little was known regarding the molecular and genomic landscapes of these diseases until recently but the knowledge is still quite spotty with many rarer types of PTCL remain largely unexplored. In this chapter, the recent findings from gene expression profiling (GEP) studies, including profiling data on microRNA, where available, will be presented with emphasis on the implication on molecular diagnosis, prognostication, and the identification of new entities (PTCL-GATA3 and PTCL-TBX21) in the PTCL-NOS group. Recent studies using next-generation sequencing have unraveled the mutational landscape in a number of PTCL entities leading to a marked improvement in the understanding of their pathogenesis and biology. While many mutations are shared among PTCL entities, the frequency varies and certain mutations are quite unique to a specific entity. For example, TET2 is often mutated but this is particularly frequent (70-80%) in angioimmunoblastic T-cell lymphoma (AITL) and IDH2 R172 mutations appear to be unique for AITL. In general, chromatin modifiers and molecular components in the CD28/T-cell receptor signaling pathways are frequently mutated. The major findings will be summarized in this chapter correlating with GEP data and clinical features where appropriate. The mutational landscape of cutaneous T-cell lymphoma, specifically on mycosis fungoides and Sezary syndrome, will also be discussed.
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Affiliation(s)
- Javeed Iqbal
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, US
| | - Catalina Amador
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, US
| | - Timothy W McKeithan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Wing C Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA.
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196
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A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation. Nat Cell Biol 2018; 20:1410-1420. [PMID: 30397315 PMCID: PMC6698386 DOI: 10.1038/s41556-018-0221-1] [Citation(s) in RCA: 255] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/21/2018] [Indexed: 12/17/2022]
Abstract
Mammalian SWI/SNF chromatin remodeling complexes exist in three distinct, final-form assemblies: canonical BAF (cBAF), PBAF, and a newly-characterized non-canonical complex, ncBAF. However, their complex-specific targeting on chromatin, functions and roles in disease remain largely undefined. Here, we comprehensively mapped complex assemblies on chromatin and found that ncBAF complexes uniquely localize to CTCF sites and promoters. We identified ncBAF subunits as synthetic lethal targets specific to synovial sarcoma (SS) and malignant rhabdoid tumor (MRT), which share in common cBAF complex (SMARCB1 subunit) perturbation. Chemical and biological depletion of the BRD9 subunit of ncBAF rapidly attenuates SS and MRT cell proliferation. Notably, in cBAF-perturbed cancers, ncBAF complexes maintain gene expression at retained CTCF-promoter sites, and function in a manner distinct from fusion oncoprotein-bound complexes. Taken together, these findings unmask the unique chromatin targeting and function of ncBAF complexes and present new cancer-specific therapeutic targets.
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197
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Hu W, Yang Y, Ge W, Zheng S. Deciphering molecular properties of hypermutated gastrointestinal cancer. J Cell Mol Med 2018; 23:370-379. [PMID: 30381870 PMCID: PMC6307802 DOI: 10.1111/jcmm.13941] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 12/17/2022] Open
Abstract
Great mutational heterogeneity is observed both across cancer types (>1000-fold) and within a given cancer type, with a fraction harboring >10 mutations per million bases, thus termed hypermutation. We determined the genome-wide effects of high mutation load on the transcriptome and methylome of two cancer types; namely, colorectal cancer (CRC) and stomach adenocarcinoma (STAD). Briefly, hierarchical clustering of the expression and methylation profiles showed that the majority of CRC and STAD hypermutated samples were mixed and separated from their respective non-hypermutated samples, exceeding the boundary of tissue specificity. Further in-detailed exploration uncovered that the underlying molecular mechanism may be related to the perturbation of chromatin remodeling genes.
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Affiliation(s)
- Wangxiong Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Yanmei Yang
- Key Laboratory of Reproductive and Genetics, Ministry of Education, Women's Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Weiting Ge
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
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198
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Garczyk S, Schneider U, Lurje I, Becker K, Vögeli TA, Gaisa NT, Knüchel R. ARID1A-deficiency in urothelial bladder cancer: No predictive biomarker for EZH2-inhibitor treatment response? PLoS One 2018; 13:e0202965. [PMID: 30138427 PMCID: PMC6107234 DOI: 10.1371/journal.pone.0202965] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/13/2018] [Indexed: 01/21/2023] Open
Abstract
Bladder cancer therapy relies on aggressive treatments highlighting the need for new, targeted therapies with reduced side effects. SWI/SNF complexes are mutated in ~20% across human cancers and dependency of SWI/SNF-deficient tumors on EZH2 has been uncovered recently. To systematically dissect the frequency of genetic alterations in SWI/SNF complexes potentially contributing to their inactivation, mutations and copy number variations in 25 SWI/SNF subunit genes were analyzed making use of publicly available sequencing data for 408 muscle-invasive bladder carcinoma samples. ARID1A truncating mutations were identified as the by far most common alterations of SWI/SNF complexes in urothelial bladder cancer. As current ARID1A protein expression data in bladder cancer are inconsistent and incomplete we examined if the frequency of truncating ARID1A mutations translates into a similar frequency of cases showing ARID1A protein loss. We applied a validated ARID1A antibody conducting a comprehensive immunohistochemistry-based expression analysis in urothelial bladder cancer (n = 362) including carcinoma in situ (CIS) cases. While observing increased median ARID1A protein levels in all carcinoma subgroups compared to normal urothelial controls (n = 21), the percentage of cases showing ARID1A protein loss was positively correlated with increasing stage and grade culminating in a rate of 14.1% in muscle-invasive disease. ARID1A-depletion did neither increase EZH2 protein or trimethylated H3K27 levels in vitro nor did ARID1A expression correlate with EZH2 or H3K27me3 amounts in human bladder carcinomas. Importantly, ARID1A-deficiency was neither associated with enhanced sensitivity towards inhibition of EZH2 enzymatic activity nor depletion of EZH2 protein. In summary, ARID1A truncating mutations, potentially translating into ARID1A protein loss in a subset of high-grade bladder cancers, are the most common SWI/SNF genetic alterations in bladder cancer. Our data do not support ARID1A-deficiency as predictive biomarker for EZH2-inhibitor treatment response in bladder cancer underlining the need for future bladder cancer-specific, drug screens for successfull discovery of ARID1A-deficiency-based targeted drugs.
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Affiliation(s)
- Stefan Garczyk
- Uropathology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
- * E-mail:
| | - Ursula Schneider
- Uropathology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Isabella Lurje
- Uropathology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Katharina Becker
- Uropathology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Thomas A. Vögeli
- Department of Urology, University Hospital RWTH Aachen, Aachen, Germany
| | - Nadine T. Gaisa
- Uropathology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
| | - Ruth Knüchel
- Uropathology Group, Institute of Pathology, University Hospital RWTH Aachen, Aachen, Germany
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199
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Fukumoto T, Magno E, Zhang R. SWI/SNF Complexes in Ovarian Cancer: Mechanistic Insights and Therapeutic Implications. Mol Cancer Res 2018; 16:1819-1825. [PMID: 30037854 DOI: 10.1158/1541-7786.mcr-18-0368] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/05/2018] [Accepted: 07/06/2018] [Indexed: 12/24/2022]
Abstract
Ovarian cancer remains the most lethal gynecologic malignancy in the developed world. Despite the unprecedented progress in understanding the genetics of ovarian cancer, cures remain elusive due to a lack of insight into the mechanisms that can be targeted to develop new therapies. SWI/SNF chromatin remodeling complexes are genetically altered in approximately 20% of all human cancers. SWI/SNF alterations vary in different histologic subtypes of ovarian cancer, with ARID1A mutation occurring in approximately 50% of ovarian clear cell carcinomas. Given the complexity and prevalence of SWI/SNF alterations, ovarian cancer represents a paradigm for investigating the molecular basis and exploring therapeutic strategies for SWI/SNF alterations. This review discusses the recent progress in understanding SWI/SNF alterations in ovarian cancer and specifically focuses on: (i) ARID1A mutation in endometriosis-associated clear cell and endometrioid histologic subtypes of ovarian cancer; (ii) SMARCA4 mutation in small cell carcinoma of the ovary, hypercalcemic type; and (iii) amplification/upregulation of CARM1, a regulator of BAF155, in high-grade serous ovarian cancer. Understanding the molecular underpinning of SWI/SNF alterations in different histologic subtypes of ovarian cancer will provide mechanistic insight into how these alterations contribute to ovarian cancer. Finally, the review discusses how these newly gained insights can be leveraged to develop urgently needed therapeutic strategies in a personalized manner.
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Affiliation(s)
- Takeshi Fukumoto
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - Elizabeth Magno
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania
| | - Rugang Zhang
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania.
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200
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Livshits G, Alonso-Curbelo D, Morris JP, Koche R, Saborowski M, Wilkinson JE, Lowe SW. Arid1a restrains Kras-dependent changes in acinar cell identity. eLife 2018; 7:35216. [PMID: 30014851 PMCID: PMC6050044 DOI: 10.7554/elife.35216] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022] Open
Abstract
Mutations in members of the SWI/SNF chromatin remodeling family are common events in cancer, but the mechanisms whereby disruption of SWI/SNF components alters tumorigenesis remain poorly understood. To model the effect of loss of function mutations in the SWI/SNF subunit Arid1a in pancreatic ductal adenocarcinoma (PDAC) initiation, we directed shRNA triggered, inducible and reversible suppression of Arid1a to the mouse pancreas in the setting of oncogenic KrasG12D. Arid1a cooperates with Kras in the adult pancreas as postnatal silencing of Arid1a following sustained KrasG12D expression induces rapid and irreversible reprogramming of acinar cells into mucinous PDAC precursor lesions. In contrast, Arid1a silencing during embryogenesis, concurrent with KrasG12D activation, leads to retention of acinar cell fate. Together, our results demonstrate Arid1a as a critical modulator of Kras-dependent changes in acinar cell identity, and underscore an unanticipated influence of timing and genetic context on the effects of SWI/SNF complex alterations in epithelial tumorigenesis. The pancreas produces many different hormones, as well as several substances important for digestion. To perform these roles, the pancreas contains different types of cells; for example, acinar cells make digestive enzymes that help to break down food. But, like other cells in the body, pancreatic cells can accumulate mutations in their DNA that cause them to divide, acquire an altered identity and form a cancerous tumor. The DNA of cells is packed into a structure called chromatin. While the DNA sequence is essentially the same across all normal cells of a given individual, chromatin can be more or less compacted in the different cell types that comprise our body tissues. A collection of proteins called the SWI/SNF complex can reorganize the chromatin to change how tightly the DNA is packed. This determines which genes in the DNA are accessible and can be activated, and which ones cannot. Around 25% of pancreatic cancers contain mutations in genes that produce proteins of the SWI/SNF complex. These mutations normally occur with an additional mutation that over-activates the gene that produces a potentially cancer-causing protein called Kras. Livshits et al. have now genetically engineered mice to investigate how one such SWI/SNF complex protein, called Arid1a, affects how pancreatic cancer develops using a genetic approach that made possible to temporarily halt the production of Arid1a in acinar cells by feeding these mice an antibiotic. The gene that produces Kras was also over-activated in the pancreases of the mice, making them more likely to develop cancer. Within just two weeks of stopping the production of Arid1a, the acinar cells stopped producing digestive enzymes and started making other proteins that are typically found in cancerous cells, indicating that Arid1a is involved in maintaining the normal identity and activity of these cells. Restoring the ability of altered acinar cells to produce normal levels of Arid1a (by removing the mice from the antibiotic diet) did not reverse these changes. Biochemical experiments showed that acinar cells with reduced levels of Arid1a have altered chromatin. In particular, the genes that produce digestive enzymes, which are normally active in healthy pancreases, were less accessible in mice who had over-active Kras and reduced levels of Arid1a. The results presented by Livshits et al. provide the first evidence of how alterations to Arid1a can lead to irreversible changes in the identity and activity of pancreatic acinar cells. These results will need to be carefully considered by researchers who are developing treatments for cancer patients with mutations in Arid1a and other SWI/SNF proteins. In particular, methods that attempt to restore the functions of absent SWI/SNF proteins to cancer cells are unlikely to treat the cancer successfully.
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Affiliation(s)
- Geulah Livshits
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Direna Alonso-Curbelo
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - John P Morris
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Richard Koche
- Center of Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Michael Saborowski
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover Medical School, Hannover, Germany
| | - John Erby Wilkinson
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, United States
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, United States.,Howard Hughes Medical Institute, New York, United States
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