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Retinoblastoma Tumor Suppressor Protein Roles in Epigenetic Regulation. Cancers (Basel) 2020; 12:cancers12102807. [PMID: 33003565 PMCID: PMC7600434 DOI: 10.3390/cancers12102807] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/19/2020] [Accepted: 09/27/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Loss of function of the retinoblastoma gene (RB1) is the rate-limiting step in the initiation of both the hereditary and sporadic forms of retinoblastoma tumor. Furthermore, loss of function of the retinoblastoma tumor suppressor protein (pRB) is frequently found in most human cancers. In retinoblastoma, tumor progression is driven by epigenetic changes following pRB loss. This review focuses on the diverse functions of pRB in epigenetic regulation. Abstract Mutations that result in the loss of function of pRB were first identified in retinoblastoma and since then have been associated with the propagation of various forms of cancer. pRB is best known for its key role as a transcriptional regulator during cell cycle exit. Beyond the ability of pRB to regulate transcription of cell cycle progression genes, pRB can remodel chromatin to exert several of its other biological roles. In this review, we discuss the diverse functions of pRB in epigenetic regulation including nucleosome mobilization, histone modifications, DNA methylation and non-coding RNAs.
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Marcum RD, Reyes AA, He Y. Structural Insights into the Evolutionarily Conserved BAF Chromatin Remodeling Complex. BIOLOGY 2020; 9:biology9070146. [PMID: 32629987 PMCID: PMC7408276 DOI: 10.3390/biology9070146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/17/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022]
Abstract
The switch/sucrose nonfermentable (SWI/SNF) family of proteins acts to regulate chromatin accessibility and plays an essential role in multiple cellular processes. A high frequency of mutations has been found in SWI/SNF family subunits by exome sequencing in human cancer, and multiple studies support its role in tumor suppression. Recent structural studies of yeast SWI/SNF and its human homolog, BAF (BRG1/BRM associated factor), have provided a model for their complex assembly and their interaction with nucleosomal substrates, revealing the molecular function of individual subunits as well as the potential impact of cancer-associated mutations on the remodeling function. Here we review the structural conservation between yeast SWI/SNF and BAF and examine the role of highly mutated subunits within the BAF complex.
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Affiliation(s)
- Ryan D. Marcum
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA; (R.D.M.); (A.A.R.)
| | - Alexis A. Reyes
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA; (R.D.M.); (A.A.R.)
- Interdisciplinary Biological Sciences Program, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA; (R.D.M.); (A.A.R.)
- Interdisciplinary Biological Sciences Program, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, 676 N. St. Clair, Chicago, IL 60611, USA
- Correspondence:
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Chang Y, Cui M, Fu X, Zhang L, Li X, Li L, Wu J, Sun Z, Zhang X, Li Z, Nan F, Yan J, Zhang M. MiRNA-155 regulates lymphangiogenesis in natural killer/T-cell lymphoma by targeting BRG1. Cancer Biol Ther 2018; 20:31-41. [PMID: 30299211 DOI: 10.1080/15384047.2018.1504721] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND miR-155 was up-regulated in natural killer/T-cell lymphoma (NKTCL), an aggressive malignancy, and correlated with disease progression. However, minimal is known on biological activities and underlying mechanisms of miR-155 in NKTCL. In this study, we examined BRG1, a potential target of miR-155, and focused on the miR-155/BRG1 signaling in regulating lymphangiogenesis of NKTCL. METHODS The expression of miR-155, BRG1, VEGFC, and VEGFD was compared between two NKTCL cell lines and normal NK cells. The critical role of miR-155 and STAT3 was assessed using miR-155 inhibitor and STAT3 inhibitor S31-201, respectively. Two biological phenotypes, apoptosis and pro-lymphangiogenesis, were examined in vitro by flow cytometry and lymphatic tube formation, respectively, and in vivo using an NKTCL xenograft model. RESULTS The miR-155 level negatively correlated with BRG1, but positively with VEGFC in normal NK as well as two NKTCL cell lines. Targeting miR-155 in NKTCL cells significantly boosted BRG1 expression and decreased the activated STAT3 or VEGFC level, leading to enhanced apoptosis and reduced lymphangiogenesis. STAT3 acted downstream of BRG1 and essentially regulated miR-155-mediated up-regulation of VEGFC and pro-lymphangiogenesis. In vivo, targeting miR-155 inhibited primary xenograft growth as well as tumor-associated lymphangiogenesis. CONCLUSIONS By inhibiting BRG1 expression, miR-155 activated STAT3/VEGFC signaling and promoted lymphangiogenesis. In addition, miR-155 also controlled the viability of NKTCL cells. Therefore, targeting miR-155 provides a novel therapy for NKTCL.
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Affiliation(s)
- Yu Chang
- a Department of Oncology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , P.R. China
| | - Meng Cui
- b Department of Head & Neck and Thyroid , The Cancer Hospital Affiliated to Zhengzhou University , Zhengzhou , P.R. China
| | - Xiaorui Fu
- a Department of Oncology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , P.R. China
| | - Lei Zhang
- a Department of Oncology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , P.R. China
| | - Xin Li
- a Department of Oncology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , P.R. China
| | - Ling Li
- a Department of Oncology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , P.R. China
| | - Jingjing Wu
- a Department of Oncology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , P.R. China
| | - Zhenchang Sun
- a Department of Oncology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , P.R. China
| | - Xudong Zhang
- a Department of Oncology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , P.R. China
| | - Zhaoming Li
- a Department of Oncology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , P.R. China
| | - Feifei Nan
- a Department of Oncology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , P.R. China
| | - Jiaqin Yan
- a Department of Oncology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , P.R. China
| | - Mingzhi Zhang
- a Department of Oncology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , P.R. China
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Ribeiro-Silva C, Aydin ÖZ, Mesquita-Ribeiro R, Slyskova J, Helfricht A, Marteijn JA, Hoeijmakers JHJ, Lans H, Vermeulen W. DNA damage sensitivity of SWI/SNF-deficient cells depends on TFIIH subunit p62/GTF2H1. Nat Commun 2018; 9:4067. [PMID: 30287812 PMCID: PMC6172278 DOI: 10.1038/s41467-018-06402-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 09/03/2018] [Indexed: 12/11/2022] Open
Abstract
Mutations in SWI/SNF genes are amongst the most common across all human cancers, but efficient therapeutic approaches that exploit vulnerabilities caused by SWI/SNF mutations are currently lacking. Here, we show that the SWI/SNF ATPases BRM/SMARCA2 and BRG1/SMARCA4 promote the expression of p62/GTF2H1, a core subunit of the transcription factor IIH (TFIIH) complex. Inactivation of either ATPase subunit downregulates GTF2H1 and therefore compromises TFIIH stability and function in transcription and nucleotide excision repair (NER). We also demonstrate that cells with permanent BRM or BRG1 depletion have the ability to restore GTF2H1 expression. As a consequence, the sensitivity of SWI/SNF-deficient cells to DNA damage induced by UV irradiation and cisplatin treatment depends on GTF2H1 levels. Together, our results expose GTF2H1 as a potential novel predictive marker of platinum drug sensitivity in SWI/SNF-deficient cancer cells. SWI/SNF genes are commonly found to be mutated in different cancers. Here the authors report that the remodelers BRM and BRG1 are necessary for efficient nucleotide excision repair by promoting the expression of TFIIH subunit GTF2H1.
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Affiliation(s)
- Cristina Ribeiro-Silva
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Özge Z Aydin
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.,Molecular Biology and Genetics Department, Koç University, Istanbul, 34450, Turkey
| | | | - Jana Slyskova
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Angela Helfricht
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
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Targeting AURKA-CDC25C axis to induce synthetic lethality in ARID1A-deficient colorectal cancer cells. Nat Commun 2018; 9:3212. [PMID: 30097580 PMCID: PMC6086874 DOI: 10.1038/s41467-018-05694-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 07/23/2018] [Indexed: 12/14/2022] Open
Abstract
ARID1A, a component of the SWI/SNF chromatin remodeling complex, is a tumor suppressor with a high frequency of inactivating mutations in many cancers. Therefore, ARID1A deficiency has been exploited therapeutically for treating cancer. Here we show that ARID1A has a synthetic lethal interaction with aurora kinase A (AURKA) in colorectal cancer (CRC) cells. Pharmacological and genetic perturbations of AURKA selectively inhibit the growth of ARID1A-deficient CRC cells. Mechanistically, ARID1A occupies the AURKA gene promoter and negatively regulates its transcription. Cells lacking ARID1A show enhanced AURKA transcription, which leads to the persistent activation of CDC25C, a key protein for G2/M transition and mitotic entry. Inhibiting AURKA activity in ARID1A-deficient cells significantly increases G2/M arrest and induces cellular multinucleation and apoptosis. This study shows a novel synthetic lethality interaction between ARID1A and AURKA and indicates that pharmacologically inhibiting the AURKA-CDC25C axis represents a novel strategy for treating CRC with ARID1A loss-of-function mutations.
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Marquez-Vilendrer SB, Thompson K, Lu L, Reisman D. Mechanism of BRG1 silencing in primary cancers. Oncotarget 2018; 7:56153-56169. [PMID: 27486753 PMCID: PMC5302903 DOI: 10.18632/oncotarget.10593] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/19/2016] [Indexed: 11/25/2022] Open
Abstract
BRG1 (SMARCA4) is a documented tumor suppressor and a key subunit of the SWI/SNF chromatin remodeling complex that is silenced in many cancer types. Studies have shown that BRG1 is mutated in cancer-derived cell lines, which led to the assertion that BRG1 is also mutated in primary human tumors. However, the sequencing of BRG1-deficient tumors has revealed a paucity of mutations; hence, the cause of BRG1 silencing in tumors remains an enigma. We conducted immunohistochemistry (IHC) on a number of tumor microarrays to characterize the frequency of BRG1 loss in different tumor types. We also analyzed BRG1-deficient tumors by sequencing the genomic DNA and the mRNA. We then tested if BRG1 expression could be induced in BRG1-negative cell lines (i.e., that lack mutations in BRG1) after the application of several different epigenetic agents, including drugs that inhibit the AKT pathway. We found that a subset of BRG1-negative cell lines also demonstrated aberrant splicing of BRG1, and in at least 30% of BRG1-deficient tumors, BRG1 expression appeared to be suppressed due to aberrant BRG1 splicing. As the majority of BRG1-deficient tumors lack mutations or splicing defects that could drive BRG1 loss of expression, this suggests that other mechanisms underlie BRG1 silencing. To this end, we analyzed 3 BRG1-deficient nonmutated cancer cell lines and found that BRG1 was inducible in these cell lines upon inhibition of the AKT pathway. We show that the loss of BRG1 is associated with the loss of E-cadherin and up-regulation of Vimentin in primary tumors, which explains why BRG1 loss is associated with a poor prognosis in multiple tumor types.
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Affiliation(s)
| | - Kenneth Thompson
- Division of Hematology/Oncology, Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Li Lu
- Department of Pathology, University of Florida, Gainesville, Florida, USA
| | - David Reisman
- Division of Hematology/Oncology, Department of Medicine, University of Florida, Gainesville, Florida, USA
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Ouyang X, Ye XL, Wei HB. BRM promoter insertion polymorphisms increase the risk of cancer: A meta-analysis. Gene 2017; 626:420-425. [PMID: 28571677 DOI: 10.1016/j.gene.2017.05.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 05/13/2017] [Accepted: 05/22/2017] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Many studies have suggested that the BRM promoter insertion polymorphisms might be associated with susceptibility to many different types of cancer. However, previous studies reported contradictory results. This current meta-analysis was performed to address this issue. EVIDENCE ACQUISITION A comprehensive search was conducted in multiple databases, including PubMed, Embase and China National Knowledge Infrastructure (CNKI). We collected relevant articles to explore the association between the BRM insertion polymorphisms and susceptibility of cancers. EVIDENCE SYNTHESIS For the BRM-741 polymorphism, a total of 2901 cases and 3667 controls from 6 studies were included. For the BRM-1321 polymorphism, a total of 2899 cases and 3769 controls from 6 studies were included. Overall, a significant difference was observed in BRM-741 (OR 0.81; 95%CI 0.68, 0.96; P=0.02) and BRM-1321 (OR 0.76; 95%CI 0.66, 0.88; P<0.01) for allele frequency (D versus I). In the subgroup analysis, for the BRM-741, a significant difference was observed in Asian (OR 0.88; 95%CI 0.78, 0.99; P=0.03) for D versus I. Similarly, for the BRM-1321, a significant difference was observed in Asian (OR 0.43; 95%CI 0.32, 0.58; P<0.001) and Caucasian (OR 0.74; 95%CI 0.62, 0.88; P<0.001) for DD versus II. CONCLUSIONS BRM-741 and BRM-1321 insertion polymorphisms are associated with susceptibility to cancer. Further studies are warranted to verify the clinical utility of BRM promoter insertion polymorphisms in human tumors.
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Affiliation(s)
- Xi Ouyang
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Tianhe Road 600, Guangzhou 510630, China
| | - Xiao Long Ye
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Tianhe Road 600, Guangzhou 510630, China
| | - Hong Bo Wei
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Tianhe Road 600, Guangzhou 510630, China.
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Jin Y, Ren N, Li S, Fu X, Sun X, Men Y, Xu Z, Zhang J, Xie Y, Xia M, Gao J. Deletion of Brg1 causes abnormal hair cell planer polarity, hair cell anchorage, and scar formation in mouse cochlea. Sci Rep 2016; 6:27124. [PMID: 27255603 PMCID: PMC4891731 DOI: 10.1038/srep27124] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 05/12/2016] [Indexed: 12/28/2022] Open
Abstract
Hair cells (HCs) are mechanosensors that play crucial roles in perceiving sound, acceleration, and fluid motion. The precise architecture of the auditory epithelium and its repair after HC loss is indispensable to the function of organ of Corti (OC). In this study, we showed that Brg1 was highly expressed in auditory HCs. Specific deletion of Brg1 in postnatal HCs resulted in rapid HC degeneration and profound deafness in mice. Further experiments showed that cell-intrinsic polarity of HCs was abolished, docking of outer hair cells (OHCs) by Deiter’s cells (DCs) failed, and scar formation in the reticular lamina was deficient. We demonstrated that Brg1 ablation disrupted the Gαi/Insc/LGN and aPKC asymmetric distributions, without overt effects on the core planer cell polarity (PCP) pathway. We also demonstrated that Brg1-deficient HCs underwent apoptosis, and that leakage in the reticular lamina caused by deficient scar formation shifted the mode of OHC death from apoptosis to necrosis. Together, these data demonstrated a requirement for Brg1 activity in HC development and suggested a role for Brg1 in the proper cellular structure formation of HCs.
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Affiliation(s)
- Yecheng Jin
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan 250100, China
| | - Naixia Ren
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan 250100, China
| | - Shiwei Li
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan 250100, China
| | - Xiaolong Fu
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan 250100, China
| | - Xiaoyang Sun
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan 250100, China
| | - Yuqin Men
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan 250100, China
| | - Zhigang Xu
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan 250100, China
| | - Jian Zhang
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan 250100, China
| | - Yue Xie
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan 250100, China
| | - Ming Xia
- Department of Otolaryngology-Head and Neck Surgery, The Second Hospital of Shandong University, Jinan 250033, China
| | - Jiangang Gao
- School of Life Science and Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan 250100, China
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Haider SA, Faisal M. Human aging in the post-GWAS era: further insights reveal potential regulatory variants. Biogerontology 2015; 16:529-41. [PMID: 25895066 DOI: 10.1007/s10522-015-9575-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 04/07/2015] [Indexed: 12/27/2022]
Abstract
Human aging involves a gradual decrease in cellular integrity that contributes to multiple complex disorders such as neurodegenerative disorders, cancer, diabetes, and cardiovascular diseases. Genome-wide association studies (GWAS) play a key role in discovering genetic variations that may contribute towards disease vulnerability. However, mostly disease-associated SNPs lie within non-coding part of the genome; majority of the variants are also present in linkage disequilibrium (LD) with the genome-wide significant SNPs (GWAS lead SNPs). Overall 600 SNPs were analyzed, out of which 291 returned RegulomeDB scores of 1-6. It was observed that just 4 out of those 291 SNPs show strong evidence of regulatory effects (RegulomeDB score <3), while none of them includes any GWAS lead SNP. Nevertheless, this study demonstrates that by combining ENCODE project data along with GWAS reported information will provide important insights on the impact of a genetic variant-moving from GWAS towards understanding disease pathways. It is noteworthy that both genome-wide significant SNPs as well as the SNPs in LD must be considered for future studies; this may prove to be crucial in deciphering the potential regulatory elements involved in complex disorders and aging in particular.
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Affiliation(s)
- Syed Aleem Haider
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan
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Mayes K, Qiu Z, Alhazmi A, Landry JW. ATP-dependent chromatin remodeling complexes as novel targets for cancer therapy. Adv Cancer Res 2015; 121:183-233. [PMID: 24889532 DOI: 10.1016/b978-0-12-800249-0.00005-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The progression to advanced stage cancer requires changes in many characteristics of a cell. These changes are usually initiated through spontaneous mutation. As a result of these mutations, gene expression is almost invariably altered allowing the cell to acquire tumor-promoting characteristics. These abnormal gene expression patterns are in part enabled by the posttranslational modification and remodeling of nucleosomes in chromatin. These chromatin modifications are established by a functionally diverse family of enzymes including histone and DNA-modifying complexes, histone deposition pathways, and chromatin remodeling complexes. Because the modifications these enzymes deposit are essential for maintaining tumor-promoting gene expression, they have recently attracted much interest as novel therapeutic targets. One class of enzyme that has not generated much interest is the chromatin remodeling complexes. In this review, we will present evidence from the literature that these enzymes have both causal and enabling roles in the transition to advanced stage cancers; as such, they should be seriously considered as high-value therapeutic targets. Previously published strategies for discovering small molecule regulators to these complexes are described. We close with thoughts on future research, the field should perform to further develop this potentially novel class of therapeutic target.
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Affiliation(s)
- Kimberly Mayes
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Zhijun Qiu
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Aiman Alhazmi
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Joseph W Landry
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.
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Watanabe R, Ui A, Kanno SI, Ogiwara H, Nagase T, Kohno T, Yasui A. SWI/SNF factors required for cellular resistance to DNA damage include ARID1A and ARID1B and show interdependent protein stability. Cancer Res 2014; 74:2465-75. [PMID: 24788099 DOI: 10.1158/0008-5472.can-13-3608] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The SWI/SNF chromatin-remodeling family contains various protein complexes, which regulate gene expression during cellular development and influence DNA damage response in an ATP- and complex-dependent manner, of which details remain elusive. Recent human genome sequencing of various cancer cells revealed frequent mutations in SWI/SNF factors, especially ARID1A, a variant subunit in the BRG1-associated factor (BAF) complex of the SWI/SNF family. We combined live-cell analysis and gene-suppression experiments to show that suppression of either ARID1A or its paralog ARID1B led to reduced nonhomologous end joining activity of DNA double-strand breaks (DSB), decreased accumulation of KU70/KU80 proteins at DSB, and sensitivity to ionizing radiation, as well as to cisplatin and UV. Thus, in contrast to transcriptional regulation, both ARID1 proteins are required for cellular resistance to various types of DNA damage, including DSB. The suppression of other SWI/SNF factors, namely SNF5, BAF60a, BAF60c, BAF155, or BAF170, exhibits a similar phenotype. Of these factors, ARID1A, ARID1B, SNF5, and BAF60c are necessary for the immediate recruitment of the ATPase subunit of the SWI/SNF complex to DSB, arguing that both ARID1 proteins facilitate the damage response of the complex. Finally, we found interdependent protein stability among the SWI/SNF factors, suggesting their direct interaction within the complex and the reason why multiple factors are frequently lost in parallel in cancer cells. Taken together, we show that cancer cells lacking in the expression of certain SWI/SNF factors, including ARID1A, are deficient in DNA repair and potentially vulnerable to DNA damage.
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Affiliation(s)
- Reiko Watanabe
- Authors' Affiliations: Division of Dynamic Proteome in Cancer and Aging, Institute of Development, Aging and Cancer, Tohoku University, Sendai; Division of Genome Biology, National Cancer Center Research Institute, Tokyo; and Department of Biotechnology Research, Kazusa DNA Research Institute, Chiba, Japan
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12
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Song S, Walter V, Karaca M, Li Y, Bartlett CS, Smiraglia DJ, Serber D, Sproul CD, Plass C, Zhang J, Hayes DN, Zheng Y, Weissman BE. Gene silencing associated with SWI/SNF complex loss during NSCLC development. Mol Cancer Res 2014; 12:560-70. [PMID: 24445599 DOI: 10.1158/1541-7786.mcr-13-0427] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
UNLABELLED The SWI/SNF chromatin-remodeling complex regulates gene expression and alters chromatin structures in an ATP-dependent manner. Recent sequencing efforts have shown mutations in BRG1 (SMARCA4), one of two mutually exclusive ATPase subunits in the complex, in a significant number of human lung tumor cell lines and primary non-small cell lung carcinoma (NSCLC) clinical specimens. To determine how BRG1 loss fuels tumor progression in NSCLC, molecular profiling was performed after restoration of BRG1 expression or treatment with a histone deacetylase inhibitor or a DNA methyltransferase (DNMT) inhibitor in a BRG1-deficient NSCLC cells. Importantly, validation studies from multiple cell lines revealed that BRG1 reexpression led to substantial changes in the expression of CDH1, CDH3, EHF, and RRAD that commonly undergo silencing by other epigenetic mechanisms during NSCLC development. Furthermore, treatment with DNMT inhibitors did not restore expression of these transcripts, indicating that this common mechanism of gene silencing did not account for their loss of expression. Collectively, BRG1 loss is an important mechanism for the epigenetic silencing of target genes during NSCLC development. IMPLICATIONS Inactivation of the SWI/SNF complex provides a novel mechanism to induce gene silencing during NSCLC development.
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Affiliation(s)
- Shujie Song
- Lineberger Cancer Center, Room 32-048, University of North Carolina, Chapel Hill, NC 27599-7295.
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Fiorentino FP, Marchesi I, Giordano A. On the role of retinoblastoma family proteins in the establishment and maintenance of the epigenetic landscape. J Cell Physiol 2013; 228:276-84. [PMID: 22718354 DOI: 10.1002/jcp.24141] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RB family members are negative regulators of the cell cycle, involved in numerous biological processes such as cellular senescence, development and differentiation. Disruption of RB family pathways are linked to loss of cell cycle control, cellular immortalization and cancer. RB family, and in particular the most studied member RB/p105, has been considered a tumor suppressor gene by more than three decades, and numerous efforts have been done to understand his molecular activity. However, the epigenetic mechanisms behind Rb-mediated tumor suppression have been uncovered only in recent years. In this review, the role of RB family members in cancer epigenetics will be discussed. We start with an introduction to epigenomes, chromatin modifications and cancer epigenetics. In order to provide a clear picture of the involvement of RB family in the epigenetic field, we describe the RB family role in the epigenetic landscape dynamics based on the heterochromatin variety involved, facultative or constitutive. We want to stress that, despite dissimilar modulations, RB family is involved in both mammalian varieties of heterochromatin establishment and maintenance and that disruption of RB family pathways drives to alterations of both heterochromatin structures, thus to the global epigenetic landscape.
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Affiliation(s)
- Francesco Paolo Fiorentino
- Department of Biology, Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA.
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Ondrušová L, Vachtenheim J, Réda J, Žáková P, Benková K. MITF-independent pro-survival role of BRG1-containing SWI/SNF complex in melanoma cells. PLoS One 2013; 8:e54110. [PMID: 23349796 PMCID: PMC3547967 DOI: 10.1371/journal.pone.0054110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 12/10/2012] [Indexed: 11/20/2022] Open
Abstract
Metastasized malignant melanoma has a poor prognosis because of its intrinsic resistance to chemotherapy and radiotherapy. The central role in the melanoma transcriptional network has the transcription factor MITF (microphthalmia-associated transcription factor). It has been shown recently that the expression of MITF and some of its target genes require the SWI/SNF chromatin remodeling complex. Here we demonstrate that survival of melanoma cells requires functional SWI/SNF complex not only by supporting expression of MITF and its targets and but also by activating expression of prosurvival proteins not directly regulated by MITF. Microarray analysis revealed that besides the MITF-driven genes, expression of proteins like osteopontin, IGF1, TGFß2 and survivin, the factors known to be generally associated with progression of tumors and the antiapoptotic properties, were reduced in acute BRG1-depleted 501mel cells. Western blots and RT-PCR confirmed the microarray findings. These proteins have been verified to be expressed independently of MITF, because MITF depletion did not impair their expression. Because these genes are not regulated by MITF, the data suggests that loss of BRG1-based SWI/SNF complexes negatively affects survival pathways beyond the MITF cascade. Immunohistochemistry showed high expression of both BRM and BRG1 in primary melanomas. Exogenous CDK2, osteopontin, or IGF1 each alone partly relieved the block of proliferation imposed by BRG1 depletion, implicating that more factors, besides the MITF target genes, are involved in melanoma cell survival. Together these results demonstrate an essential role of SWI/SNF for the expression of MITF-dependent and MITF-independent prosurvival factors in melanoma cells and suggest that SWI/SNF may be a potential and effective target in melanoma therapy.
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Affiliation(s)
- Lubica Ondrušová
- Laboratory of Transcription and Cell Signaling, Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Jiri Vachtenheim
- Laboratory of Transcription and Cell Signaling, Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- * E-mail:
| | - Jiri Réda
- Laboratory of Transcription and Cell Signaling, Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Petra Žáková
- Laboratory of Transcription and Cell Signaling, Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Kamila Benková
- Department of Pathology, Hospital Bulovka, Prague, Czech Republic
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Wang JR, Gramling SJB, Goldstein DP, Cheng D, Chen D, Azad AK, Tse A, Hon H, Chen Z, Mirshams M, Simpson C, Huang SH, Marquez S, O'Sullivan B, Liu FF, Roberts H, Xu W, Brown DH, Gilbert RW, Gullane PJ, Irish JC, Reisman DN, Liu G. Association of two BRM promoter polymorphisms with head and neck squamous cell carcinoma risk. Carcinogenesis 2013; 34:1012-7. [PMID: 23322154 DOI: 10.1093/carcin/bgt008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The SWI/SNF chromatin remodeling complex is an important regulator of gene expression that has been linked to cancer development. Expression of Brahma (BRM), a critical catalytic subunit of SWI/SNF, is lost in a variety of solid tumors. Two novel BRM promoter polymorphisms (BRM-741 and BRM-1321) have been correlated with BRM loss and elevated cancer risk. The aim(s) of this study were to examine BRM expression in head and neck squamous cell carcinoma (HNSCC) and to correlate BRM polymorphisms with HNSCC risk. BRM expression studies were performed on eight HNSCC cell lines and 76 surgically resected tumor samples. A case-control study was conducted on 668 HNSCC patients (oral cavity, oropharynx, larynx and hypopharynx) and 700 healthy matched controls. BRM expression was lost in 25% of cell lines and 16% of tumors. The homozygous genotype of each polymorphism was significantly associated with increased HNSCC risk [BRM-741: adjusted odds ratio (aOR) 1.75, 95% CI 1.2-2.3, P < 0.001; BRM-1321: aOR 1.65, 95% CI 1.2-2.2, P < 0.001]. Individuals that were homozygous for both BRM polymorphisms had a more than 2-fold increase in the risk of HNSCC (aOR 2.23, 95% CI 1.5-3.4, P < 0.001). A particularly elevated risk was seen within the oropharynx, human papillomavirus-positive subgroup for carriers of both homozygous variants (aOR 3.09, 95% CI 1.5-6.8, P = 0.004). BRM promoter polymorphisms appear to act as susceptibility markers of HNSCC with potential utility in screening, prevention and treatment.
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Affiliation(s)
- Jennifer R Wang
- Department of Otolaryngology-Head and Neck Surgery, University Health Network, Princess Margaret Hospital, Toronto, Ontario M5G 2M9, Canada.
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Liu JX, Zhang F, Zhou P, Xia TY, Mao GP. Protein expression and gene mutation of Brg1 in Peutz-Jeghers syndrome. Shijie Huaren Xiaohua Zazhi 2012; 20:2353-2357. [DOI: 10.11569/wcjd.v20.i25.2353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the protein expression and gene mutation of Brahma-related gene 1 (Brg1) in Peutz-Jeghers syndrome (PJS), and to analyze their relation with tumor development.
METHODS: The expression of Brg1 protein in 72 cases of PJS polyps was detected by immunohistochemistry. Mutations in exons 4 and 10 of the Brg1 gene was detected by means of polymerase chain reaction-direct sequencing (PCR-DNA) in 39 cases of PJS polyps and 2 cases of carcinoma.
RESULTS: The positive rate of Brg1 protein expression in PJS (54.17%) was lower than that in adenocarcinoma (76.67%) but higher than that in normal tissue (16.67%). There was a significant difference in the positive rate of Brg1 protein expression among the three groups (P < 0.05). No Brg1 gene mutations were detected in 39 cases of PJS polyps and 2 cases of carcinoma.
CONCLUSION: Increased expression of Brg1 protein in PJS may be associated with the development of this disease. Brg1 gene mutations might be rare in PJS. Brg1 expression can be used as an important parameter for differentiating malignancy and evaluating prognosis of PJS.
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Romero OA, Setien F, John S, Gimenez-Xavier P, Gómez-López G, Pisano D, Condom E, Villanueva A, Hager GL, Sanchez-Cespedes M. The tumour suppressor and chromatin-remodelling factor BRG1 antagonizes Myc activity and promotes cell differentiation in human cancer. EMBO Mol Med 2012; 4:603-16. [PMID: 22407764 PMCID: PMC3407948 DOI: 10.1002/emmm.201200236] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 02/27/2012] [Accepted: 02/29/2012] [Indexed: 12/30/2022] Open
Abstract
BRG1, a member of the SWI/SNF complex, is mutated in cancer, but it is unclear how it promotes tumourigenesis. We report that re-expression of BRG1 in lung cancer cells up-regulates lung-specific transcripts, restoring the gene expression signature of normal lung. Using cell lines from several cancer types we found that those lacking BRG1 do not respond to retinoic acid (RA) or glucocorticoids (GC), while restoration of BRG1 restores sensitivity. Conversely, in SH-SY5Y cells, a paradigm of RA-dependent differentiation, abrogation of BRG1 prevented the response to RA. Further, our data suggest an antagonistic functional connection between BRG1 and MYC, whereby, refractoriness to RA and GC by BRG1 inactivation involves deregulation of MYC activity. Mechanistically, some of these effects are mediated by BRG1 binding to MYC and MYC-target promoters. The BRG1-MYC antagonism was also evident in primary tumours. Finally, BRG1 restoration significantly dampened invasion and progression and decreased MYC in lung cancer cells orthotopically implanted in nude mice. Thus, BRG1 inactivation enables cancer cells to sustain undifferentiated gene expression programs and prevent its response to environmental stimuli.
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Affiliation(s)
- Octavio A Romero
- Genes and Cancer Group, Cancer Epigenetics and Biology Program-PEBC, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
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Liu G, Gramling S, Munoz D, Cheng D, Azad AK, Mirshams M, Chen Z, Xu W, Roberts H, Shepherd FA, Tsao MS, Reisman D. Two novel BRM insertion promoter sequence variants are associated with loss of BRM expression and lung cancer risk. Oncogene 2011; 30:3295-304. [PMID: 21478907 DOI: 10.1038/onc.2011.81] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
SWI/SNF (SWItch/sucrose non-fermentable) complexes are ATP-dependent chromatin remodeling enzymes critically involved in the regulation of multiple functions, including gene expression, differentiation, development, DNA repair, cell adhesion and cell cycle control. BRM, a key SWI/SNF complex subunit, is silenced in 15-20% of many solid tumors. As BRM-deficient mice develop 10-fold more tumors when exposed to carcinogens, BRM is a strong candidate for a cancer susceptibility gene. In this paper, we show that BRM is regulated by transcription, thus demonstrating that the promoter region is important for BRM expression. We sequenced the BRM promoter region, finding two novel promoter indel polymorphisms, BRM -741 and BRM -1321, that are in linkage disequilibrium (D'≥0.83). The variant insertion alleles of both polymorphisms produce sequence variants that are highly homologous to myocyte enhancer factor-2 (MEF2) transcription factor-binding sites; MEF2 is known to recruit histone deacetylases that silence BRM expression. Each polymorphic BRM insertion variant is found in ~20% of Caucasians, and each correlates strongly with the loss of protein expression of BRM, both in cancer cell lines (P=0.009) and in primary human lung tumor specimens (P=0.015). With such strong functional evidence, we conducted a case-control study of 1199 smokers. We found an increased risk of lung cancer when both BRM homozygous promoter insertion variants were present: adjusted odds ratio of 2.19 (95% confidence interval, 1.40-3.43). Thus, we here demonstrate a strong functional association between these polymorphisms and loss of BRM expression. These polymorphisms thus have the potential to identify a sub-population of smokers at greater lung cancer risk, wherein this risk could be driven by an aberrant SWI/SNF chromatin-remodeling pathway.
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Affiliation(s)
- G Liu
- Department of Medicine, Division of Medical Oncology and Hematology, Ontario Cancer Institute, Princess Margaret Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada
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