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Dreier MR, Walia J, de la Serna IL. Targeting SWI/SNF Complexes in Cancer: Pharmacological Approaches and Implications. EPIGENOMES 2024; 8:7. [PMID: 38390898 PMCID: PMC10885108 DOI: 10.3390/epigenomes8010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
SWI/SNF enzymes are heterogeneous multi-subunit complexes that utilize the energy from ATP hydrolysis to remodel chromatin structure, facilitating transcription, DNA replication, and repair. In mammalian cells, distinct sub-complexes, including cBAF, ncBAF, and PBAF exhibit varying subunit compositions and have different genomic functions. Alterations in the SWI/SNF complex and sub-complex functions are a prominent feature in cancer, making them attractive targets for therapeutic intervention. Current strategies in cancer therapeutics involve the use of pharmacological agents designed to bind and disrupt the activity of SWI/SNF complexes or specific sub-complexes. Inhibitors targeting the catalytic subunits, SMARCA4/2, and small molecules binding SWI/SNF bromodomains are the primary approaches for suppressing SWI/SNF function. Proteolysis-targeting chimeras (PROTACs) were generated by the covalent linkage of the bromodomain or ATPase-binding ligand to an E3 ligase-binding moiety. This engineered connection promotes the degradation of specific SWI/SNF subunits, enhancing and extending the impact of this pharmacological intervention in some cases. Extensive preclinical studies have underscored the therapeutic potential of these drugs across diverse cancer types. Encouragingly, some of these agents have progressed from preclinical research to clinical trials, indicating a promising stride toward the development of effective cancer therapeutics targeting SWI/SNF complex and sub-complex functions.
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Affiliation(s)
- Megan R Dreier
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3000 Arlington Ave, Toledo 43614, OH, USA
| | - Jasmine Walia
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3000 Arlington Ave, Toledo 43614, OH, USA
| | - Ivana L de la Serna
- Department of Cell and Cancer Biology, University of Toledo College of Medicine and Life Sciences, 3000 Arlington Ave, Toledo 43614, OH, USA
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Shafi O, Siddiqui G, Jaffry HA. The benign nature and rare occurrence of cardiac myxoma as a possible consequence of the limited cardiac proliferative/ regenerative potential: a systematic review. BMC Cancer 2023; 23:1245. [PMID: 38110859 PMCID: PMC10726542 DOI: 10.1186/s12885-023-11723-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Cardiac Myxoma is a primary tumor of heart. Its origins, rarity of the occurrence of primary cardiac tumors and how it may be related to limited cardiac regenerative potential, are not yet entirely known. This study investigates the key cardiac genes/ transcription factors (TFs) and signaling pathways to understand these important questions. METHODS Databases including PubMed, MEDLINE, and Google Scholar were searched for published articles without any date restrictions, involving cardiac myxoma, cardiac genes/TFs/signaling pathways and their roles in cardiogenesis, proliferation, differentiation, key interactions and tumorigenesis, with focus on cardiomyocytes. RESULTS The cardiac genetic landscape is governed by a very tight control between proliferation and differentiation-related genes/TFs/pathways. Cardiac myxoma originates possibly as a consequence of dysregulations in the gene expression of differentiation regulators including Tbx5, GATA4, HAND1/2, MYOCD, HOPX, BMPs. Such dysregulations switch the expression of cardiomyocytes into progenitor-like state in cardiac myxoma development by dysregulating Isl1, Baf60 complex, Wnt, FGF, Notch, Mef2c and others. The Nkx2-5 and MSX2 contribute predominantly to both proliferation and differentiation of Cardiac Progenitor Cells (CPCs), may possibly serve roles based on the microenvironment and the direction of cell circuitry in cardiac tumorigenesis. The Nkx2-5 in cardiac myxoma may serve to limit progression of tumorigenesis as it has massive control over the proliferation of CPCs. The cardiac cell type-specific genetic programming plays governing role in controlling the tumorigenesis and regenerative potential. CONCLUSION The cardiomyocytes have very limited proliferative and regenerative potential. They survive for long periods of time and tightly maintain the gene expression of differentiation genes such as Tbx5, GATA4 that interact with tumor suppressors (TS) and exert TS like effect. The total effect such gene expression exerts is responsible for the rare occurrence and benign nature of primary cardiac tumors. This prevents the progression of tumorigenesis. But this also limits the regenerative and proliferative potential of cardiomyocytes. Cardiac Myxoma develops as a consequence of dysregulations in these key genes which revert the cells towards progenitor-like state, hallmark of CM. The CM development in carney complex also signifies the role of TS in cardiac cells.
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Affiliation(s)
- Ovais Shafi
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan.
| | - Ghazia Siddiqui
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan
| | - Hassam A Jaffry
- Sindh Medical College - Jinnah Sindh Medical University / Dow University of Health Sciences, Karachi, Pakistan
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3
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Sun J, Yan Q, Zhang Z, Xu T, Gong Y, Li W, Mai K, Ai Q. Exploring the role of SWI/SNF complex subunit BAF60c in lipid metabolism and inflammation in fish. iScience 2023; 26:108207. [PMID: 37942006 PMCID: PMC10628743 DOI: 10.1016/j.isci.2023.108207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/26/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023] Open
Abstract
Chromatin remodeling plays an important role in regulating gene transcription, in which chromatin remodeling complex is a crucial aspect. Brg1/Brm-associated factor 60c (BAF60c) subunit forms a bridge between chromatin remodeling complexes and transcription factors in mammals; hence, it has received extensive attention. However, the roles of BAF60c in fish remain largely unexplored. In this study, we identified BAF60c-interacting proteins by using HIS-pull-down and LC-MS/MS analysis in fish. Subsequently, the RNA-seq analysis was performed to identify the overall effects of BAF60c. Then, the function of BAF60c was verified through BAF60c knockdown and overexpression experiments. We demonstrated for the first time that BAF60c interacts with glucose-regulated protein 78 (GRP78) and regulates lipid metabolism, endoplasmic reticulum (ER) stress, and inflammation. Knockdown of BAF60c reduces fatty acid biosynthesis, ER stress, and inflammation. In conclusion, the results enriched BAF60c-interacting protein network and explored the function of BAF60c in lipid metabolism and inflammation in fish.
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Affiliation(s)
- Jie Sun
- Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture and Rural Affairs) & Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, 5 Yushan Road, Qingdao, Shandong 266003, People’s Republic of China
| | - Qiuxin Yan
- Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture and Rural Affairs) & Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, 5 Yushan Road, Qingdao, Shandong 266003, People’s Republic of China
| | - Zhihao Zhang
- Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture and Rural Affairs) & Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, 5 Yushan Road, Qingdao, Shandong 266003, People’s Republic of China
| | - Ting Xu
- Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture and Rural Affairs) & Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, 5 Yushan Road, Qingdao, Shandong 266003, People’s Republic of China
| | - Ye Gong
- Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture and Rural Affairs) & Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, 5 Yushan Road, Qingdao, Shandong 266003, People’s Republic of China
| | - Weijia Li
- Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture and Rural Affairs) & Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, 5 Yushan Road, Qingdao, Shandong 266003, People’s Republic of China
| | - Kangsen Mai
- Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture and Rural Affairs) & Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, 5 Yushan Road, Qingdao, Shandong 266003, People’s Republic of China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, Shandong 266237, People’s Republic of China
| | - Qinghui Ai
- Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture and Rural Affairs) & Key Laboratory of Mariculture (Ministry of Education), Ocean University of China, 5 Yushan Road, Qingdao, Shandong 266003, People’s Republic of China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, Shandong 266237, People’s Republic of China
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Chen J, Yu N, Ou S, Wang X, Li H, Zhu H. Integrated analysis reveals SMARCD1 is a potential biomarker and therapeutic target in skin cutaneous melanoma. J Cancer Res Clin Oncol 2023; 149:11619-11634. [PMID: 37401939 DOI: 10.1007/s00432-023-05064-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023]
Abstract
OBJECTIVE SMARCD1 is a part of the SWI/SNF chromatin remodeling complex family, which consists of transcription factors that are implicated in various types of cancer. Examining SMARCD1 expression in human cancers can provide valuable insights into the development and progression of skin cutaneous melanoma (SKCM). METHODS Our study comprehensively examined the association between SMARCD1 expression and numerous factors, including prognosis, tumor microenvironment (TME), immune infiltration, tumor mutational burden (TMB), and microsatellite instability (MSI) in SKCM. Then we utilized immunohistochemical staining to measure the SMARCD1 expression in both SKCM tissues and normal skin tissues. Furthermore, we conducted in vitro experimentation to evaluate the effects of SMARCD1 knockdown on SKCM cells. RESULTS We found that aberrant expression of SMARCD1 across 16 cancers was strongly correlated with overall survival (OS) and progression-free survival (PFS). In addition, our research revealed that SMARCD1 expression is associated with multiple factors in different types of cancer, including immune infiltration, TME, immune-related genes, MSI, TMB, and sensitivity to anti-cancer drugs. SMARCD1 is likely involved in various SKCM signaling pathways and biological processes. Additionally, our research revealed that an SMARCD1-based risk factor model accurately predicted OS in SKCM patients. Furthermore, the downregulation of SMARCD1 expression demonstrated a significant inhibition of SKCM cell proliferation and migration, as well as an increase in apoptosis and cell cycle arrest. CONCLUSION We conclude that SMARCD1 is a promising diagnostic, prognostic, and therapeutic biomarker for SKCM, and its expression has significant clinical implications for the development of novel treatment strategies.
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Affiliation(s)
- Jiaoquan Chen
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, 510095, Guangdong, China
| | - Nanji Yu
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, 510095, Guangdong, China
| | - Shanshan Ou
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, 510095, Guangdong, China
| | - Xue Wang
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, 510095, Guangdong, China
| | - Huaping Li
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, 510095, Guangdong, China
| | - Huilan Zhu
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, 510095, Guangdong, China.
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Aubry A, Pearson JD, Charish J, Yu T, Sivak JM, Xirodimas DP, Avet-Loiseau H, Corre J, Monnier PP, Bremner R. Deneddylation of ribosomal proteins promotes synergy between MLN4924 and chemotherapy to elicit complete therapeutic responses. Cell Rep 2023; 42:112925. [PMID: 37552601 DOI: 10.1016/j.celrep.2023.112925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 05/29/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
The neddylation inhibitor MLN4924/Pevonedistat is in clinical trials for multiple cancers. Efficacy is generally attributed to cullin RING ligase (CRL) inhibition, but the contribution of non-CRL targets is unknown. Here, CRISPR screens map MLN4924-monotherapy sensitivity in retinoblastoma to a classic DNA damage-induced p53/E2F3/BAX-dependent death effector network, which synergizes with Nutlin3a or Navitoclax. In monotherapy-resistant cells, MLN4924 plus standard-of-care topotecan overcomes resistance, but reduces DNA damage, instead harnessing ribosomal protein nucleolar-expulsion to engage an RPL11/p21/MYCN/E2F3/p53/BAX synergy network that exhibits extensive cross-regulation. Strikingly, unneddylatable RPL11 substitutes for MLN4924 to perturb nucleolar function and enhance topotecan efficacy. Orthotopic tumors exhibit complete responses while preserving visual function. Moreover, MLN4924 plus melphalan deploy this DNA damage-independent strategy to synergistically kill multiple myeloma cells. Thus, MLN4924 synergizes with standard-of-care drugs to unlock a nucleolar death effector network across cancer types implying broad therapeutic relevance.
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Affiliation(s)
- Arthur Aubry
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada; Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Centre Hospitalo-universitaire (CHU) de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Université de Toulouse, UPS, Unité de Génomique du Myélome, Toulouse, France
| | - Joel D Pearson
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Jason Charish
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada; Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Tao Yu
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Jeremy M Sivak
- Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada; Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | | | - Hervé Avet-Loiseau
- Centre Hospitalo-universitaire (CHU) de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Université de Toulouse, UPS, Unité de Génomique du Myélome, Toulouse, France; Centre de Recherches en Cancérologie de Toulouse (CRCT), INSERM, Toulouse, France
| | - Jill Corre
- Centre Hospitalo-universitaire (CHU) de Toulouse, Institut Universitaire du Cancer de Toulouse-Oncopole (IUCT-O), Université de Toulouse, UPS, Unité de Génomique du Myélome, Toulouse, France; Centre de Recherches en Cancérologie de Toulouse (CRCT), INSERM, Toulouse, France
| | - Philippe P Monnier
- Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada; Donald K. Johnson Eye Institute, Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Rod Bremner
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada; Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Ophthalmology and Vision Science, University of Toronto, Toronto, ON, Canada.
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6
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Soto-Castillo JJ, Llavata-Marti L, Fort-Culillas R, Andreu-Cobo P, Moreno R, Codony C, García Del Muro X, Alemany R, Piulats JM, Martin-Liberal J. SWI/SNF Complex Alterations in Tumors with Rhabdoid Features: Novel Therapeutic Approaches and Opportunities for Adoptive Cell Therapy. Int J Mol Sci 2023; 24:11143. [PMID: 37446319 DOI: 10.3390/ijms241311143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
The SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling complex is one of the most remarkably altered epigenetic regulators in cancer. Pathogenic mutations in genes encoding SWI/SNF-related proteins have been recently described in many solid tumors, including rare and aggressive malignancies with rhabdoid features with no standard therapies in advanced or metastatic settings. In recent years, clinical trials with targeted drugs aimed at restoring its function have shown discouraging results. However, preclinical data have found an association between these epigenetic alterations and response to immune therapy. Thus, the rationale for immunotherapy strategies in SWI/SNF complex alteration-related tumors is strong. Here, we review the SWI/SNF complex and how its dysfunction drives the oncogenesis of rhabdoid tumors and the proposed strategies to revert this alteration and promising novel therapeutic approaches, including immune checkpoint inhibition and adoptive cell therapy.
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Affiliation(s)
- Juan José Soto-Castillo
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Lucía Llavata-Marti
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 17007 Girona, Spain
| | - Roser Fort-Culillas
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 17007 Girona, Spain
| | - Pablo Andreu-Cobo
- Medical Oncology Department, Parc Tauli Hospital Universitari, 08208 Sabadell, Spain
| | - Rafael Moreno
- Cancer Immunotherapy Group, iPROCURE Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Carles Codony
- Cancer Immunotherapy Group, iPROCURE Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Xavier García Del Muro
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Ramon Alemany
- Cancer Immunotherapy Group, iPROCURE Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Josep M Piulats
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
- Cancer Immunotherapy Group, iPROCURE Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
| | - Juan Martin-Liberal
- Medical Oncology Department, Catalan Institute of Oncology (ICO), 08908 Hospitalet de Llobregat, Spain
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Reddy D, Bhattacharya S, Workman JL. (mis)-Targeting of SWI/SNF complex(es) in cancer. Cancer Metastasis Rev 2023; 42:455-470. [PMID: 37093326 PMCID: PMC10349013 DOI: 10.1007/s10555-023-10102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/05/2023] [Indexed: 04/25/2023]
Abstract
The ATP-dependent chromatin remodeling complex SWI/SNF (also called BAF) is critical for the regulation of gene expression. During the evolution from yeast to mammals, the BAF complex has evolved an enormous complexity that contains a high number of subunits encoded by various genes. Emerging studies highlight the frequent involvement of altered mammalian SWI/SNF chromatin-remodeling complexes in human cancers. Here, we discuss the recent advances in determining the structure of SWI/SNF complexes, highlight the mechanisms by which mutations affecting these complexes promote cancer, and describe the promising emerging opportunities for targeted therapies.
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Affiliation(s)
- Divya Reddy
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | | | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.
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8
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Rossin F, Ciccosanti F, D'Eletto M, Occhigrossi L, Fimia GM, Piacentini M. Type 2 transglutaminase in the nucleus: the new epigenetic face of a cytoplasmic enzyme. Cell Mol Life Sci 2023; 80:52. [PMID: 36695883 PMCID: PMC9874183 DOI: 10.1007/s00018-023-04698-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/26/2023]
Abstract
One of the major mysteries in science is how it is possible to pack the cellular chromatin with a total length of over 1 m, into a small sphere with a diameter of 5 mm "the nucleus", and even more difficult to envisage how to make it functional. Although we know that compaction is achieved through the histones, however, the DNA needs to be accessible to the transcription machinery and this is allowed thanks to a variety of very complex epigenetic mechanisms. Either DNA (methylation) or post-translational modifications of histone proteins (acetylation, methylation, ubiquitination and sumoylation) play a crucial role in chromatin remodelling and consequently on gene expression. Recently the serotonylation and dopaminylation of the histone 3, catalyzed by the Transglutaminase type 2 (TG2), has been reported. These novel post-translational modifications catalyzed by a predominantly cytoplasmic enzyme opens a new avenue for future investigations on the enzyme function itself and for the possibility that other biological amines, substrate of TG2, can influence the genome regulation under peculiar cellular conditions. In this review we analyzed the nuclear TG2's biology by discussing both its post-translational modification of various transcription factors and the implications of its epigenetic new face. Finally, we will focus on the potential impact of these events in human diseases.
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Affiliation(s)
- Federica Rossin
- Department of Biology, University of Rome 'Tor Vergata', Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Fabiola Ciccosanti
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS 'L. Spallanzani', Rome, Italy
| | - Manuela D'Eletto
- Department of Biology, University of Rome 'Tor Vergata', Via Della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Luca Occhigrossi
- Department of Molecular Medicine, University of Rome "La Sapienza", Rome, Italy
| | - Gian Maria Fimia
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS 'L. Spallanzani', Rome, Italy
- Department of Molecular Medicine, University of Rome "La Sapienza", Rome, Italy
| | - Mauro Piacentini
- Department of Biology, University of Rome 'Tor Vergata', Via Della Ricerca Scientifica 1, 00133, Rome, Italy.
- Department of Epidemiology, Preclinical Research and Advanced Diagnostics, National Institute for Infectious Diseases IRCCS 'L. Spallanzani', Rome, Italy.
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Dreier MR, de la Serna IL. SWI/SNF Chromatin Remodeling Enzymes in Melanoma. EPIGENOMES 2022; 6:epigenomes6010010. [PMID: 35323214 PMCID: PMC8947417 DOI: 10.3390/epigenomes6010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022] Open
Abstract
Melanoma is an aggressive malignancy that arises from the transformation of melanocytes on the skin, mucosal membranes, and uvea of the eye. SWI/SNF chromatin remodeling enzymes are multi-subunit complexes that play important roles in the development of the melanocyte lineage and in the response to ultraviolet radiation, a key environmental risk factor for developing cutaneous melanoma. Exome sequencing has revealed frequent loss of function mutations in genes encoding SWI/SNF subunits in melanoma. However, some SWI/SNF subunits have also been demonstrated to have pro-tumorigenic roles in melanoma and to affect sensitivity to therapeutics. This review summarizes studies that have implicated SWI/SNF components in melanomagenesis and have evaluated how SWI/SNF subunits modulate the response to current therapeutics.
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DNA damage triggers the nuclear accumulation of RASSF6 tumor suppressor protein via CDK9 and BAF53 to regulate p53-target gene transcription. Mol Cell Biol 2021; 42:e0031021. [PMID: 34898277 DOI: 10.1128/mcb.00310-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RASSF6, a member of the tumor suppressor Ras-association domain family (RASSF) proteins, regulates cell cycle arrest and apoptosis via p53 and plays a tumor suppressor role. We previously reported that RASSF6 blocks MDM2-mediated p53 degradation and enhances p53 expression. In this study, we demonstrated that RASSF6 has nuclear-localization and nuclear-export signals and that DNA damage triggers the nuclear accumulation of RASSF6. We found that RASSF6 directly binds to BAF53, the component of SWI/SNF complex. DNA damage induces CDK9-mediated phosphorylation of BAF53, which enhances the interaction with RASSF6 and increases the amount of RASSF6 in the nucleus. Subsequently, RASSF6 augments the interaction between BAF53 and BAF60a, another component of SWI/SNF complex, and further promotes the interaction of BAF53 and BAF60a with p53. BAF53 silencing or BAF60a silencing attenuates RASSF6-mediated p53-target gene transcription and apoptosis. Thus, RASSF6 is involved in the regulation of DNA damage-induced complex formation including CDK9, BAF53, BAF60a, and p53.
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Jian Y, Shim WB, Ma Z. Multiple functions of SWI/SNF chromatin remodeling complex in plant-pathogen interactions. STRESS BIOLOGY 2021; 1:18. [PMID: 37676626 PMCID: PMC10442046 DOI: 10.1007/s44154-021-00019-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/22/2021] [Indexed: 09/08/2023]
Abstract
The SWI/SNF chromatin remodeling complex utilizes the energy of ATP hydrolysis to facilitate chromatin access and plays essential roles in DNA-based events. Studies in animals, plants and fungi have uncovered sophisticated regulatory mechanisms of this complex that govern development and various stress responses. In this review, we summarize the composition of SWI/SNF complex in eukaryotes and discuss multiple functions of the SWI/SNF complex in regulating gene transcription, mRNA splicing, and DNA damage response. Our review further highlights the importance of SWI/SNF complex in regulating plant immunity responses and fungal pathogenesis. Finally, the potentials in exploiting chromatin remodeling for management of crop disease are presented.
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Affiliation(s)
- Yunqing Jian
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Won-Bo Shim
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, and Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
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Li J, Xu J, Jiang H, Zhang T, Ramakrishnan A, Shen L, Xu PX. Chromatin Remodelers Interact with Eya1 and Six2 to Target Enhancers to Control Nephron Progenitor Cell Maintenance. J Am Soc Nephrol 2021; 32:2815-2833. [PMID: 34716243 PMCID: PMC8806105 DOI: 10.1681/asn.2021040525] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/26/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Eya1 is a critical regulator of nephron progenitor cell specification and interacts with Six2 to promote NPC self-renewal. Haploinsufficiency of these genes causes kidney hypoplasia. However, how the Eya1-centered network operates remains unknown. METHODS We engineered a 2×HA-3×Flag-Eya1 knock-in mouse line and performed coimmunoprecipitation with anti-HA or -Flag to precipitate the multitagged-Eya1 and its associated proteins. Loss-of-function, transcriptome profiling, and genome-wide binding analyses for Eya1's interacting chromatin-remodeling ATPase Brg1 were carried out. We assayed the activity of the cis-regulatory elements co-occupied by Brg1/Six2 in vivo. RESULTS Eya1 and Six2 interact with the Brg1-based SWI/SNF complex during kidney development. Knockout of Brg1 results in failure of metanephric mesenchyme formation and depletion of nephron progenitors, which has been linked to loss of Eya1 expression. Transcriptional profiling shows conspicuous downregulation of important regulators for nephrogenesis in Brg1-deficient cells, including Lin28, Pbx1, and Dchs1-Fat4 signaling, but upregulation of podocyte lineage, oncogenic, and cell death-inducing genes, many of which Brg1 targets. Genome-wide binding analysis identifies Brg1 occupancy to a distal enhancer of Eya1 that drives nephron progenitor-specific expression. We demonstrate that Brg1 enrichment to two distal intronic enhancers of Pbx1 and a proximal promoter region of Mycn requires Six2 activity and that these Brg1/Six2-bound enhancers govern nephron progenitor-specific expression in response to Six2 activity. CONCLUSIONS Our results reveal an essential role for Brg1, its downstream pathways, and its interaction with Eya1-Six2 in mediating the fine balance among the self-renewal, differentiation, and survival of nephron progenitors.
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Affiliation(s)
- Jun Li
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jinshu Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Huihui Jiang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ting Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aarthi Ramakrishnan
- Department of Neurosciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Li Shen
- Department of Neurosciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Pin-Xian Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York,Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York
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13
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Gao J, Qin DL, Tang CX, Kang XY, Song CJ, Zhang CT. Smarcd1 antagonizes the apoptosis of injured MES23.5 DA cells by enhancing the effect of Six2 on GDNF expression. Neurosci Lett 2021; 760:136088. [PMID: 34233203 DOI: 10.1016/j.neulet.2021.136088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/13/2021] [Accepted: 06/23/2021] [Indexed: 11/29/2022]
Abstract
Glial cell line-derived neurotrophic factor (GDNF) played critical roles in the survival and repair of dopaminergic (DA) neurons. Transcription factor Six2 could repair injured DA cells by promoting the expression of GDNF, however, the underlying molecular mechanisms remain largely unknown. In this study, we screened forty-three proteins that interacted with Six2 in MES23.5 DA cells treated with 6-OHDA by liquid chromatography - electrospray - ionization tandem mass spectrometry (LC-ESI-ITMS/MS). Among these proteins, Smarcd1 is a member of SWI/SNF chromatin-remodeling complex family. Our results confirmed that Smarcd1 formed a transcription complex with Six2, and Smarcd1 mainly binded to the 2840 bp-2933 bp region of the GDNF promoter. Furthermore, knockdown of Smarcd1 inhibited the effect of Six2 on GDNF expression, and resulted in decreased cell viability and increased the apoptosis of injured DA neurons, and the result of overexpression of Smarcd1 is opposite to knockdown. Taken together, our results indicate that smarcd1 can be recruited to the promoter region of GDNF by transcription factor Six2 to promote the effect of Six2 on GDNF expression and protect injured MES23.5 DA cells, which could be useful in identifying potential drug targets for promoting endogenous GDNF expression.
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Affiliation(s)
- Jin Gao
- Department of Neurobiology and Cell Biology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Deng-Li Qin
- Department of Neurobiology and Cell Biology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Chuan-Xi Tang
- Department of Neurobiology and Cell Biology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Xiao-Yu Kang
- Department of Neurobiology and Cell Biology, Xuzhou Key Laboratory of Neurobiology, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Cheng-Jie Song
- Department of Physiology, Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
| | - Can-Tang Zhang
- Department of Respiratory and Critical Care, the Affiliated Hospital of Xuzhou Medical University, Xuzhou 221004, Jiangsu, China
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14
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Zhu Y, Wang H, Fei M, Tang T, Niu W, Zhang L. Smarcd1 Inhibits the Malignant Phenotypes of Human Glioblastoma Cells via Crosstalk with Notch1. Mol Neurobiol 2021; 58:1438-1452. [PMID: 33190170 PMCID: PMC7932991 DOI: 10.1007/s12035-020-02190-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 10/29/2020] [Indexed: 11/29/2022]
Abstract
Smarcd1 is a component of an evolutionary conserved chromatin remodeling complex-SWI/SNF, which is involved in transcription factor recruitment, DNA replication, recombination, and repair. Suppression of the SWI/SNF complex required for cellular differentiation and gene regulation may be inducible for cell proliferation and tumorigenicity. However, the inhibitory role of Smarcd1 in human glioblastoma cells has not been well illustrated. Both U87 and U251 human glioblastoma cell lines were employed in the present study. The lentivirus-mediated gene knockdown and overexpression approach was conducted to determine the function of Smarcd1. The protein levels were tested by western blot, and the relative mRNA contents were detected by quantitative real-time PCR. Cell viability was tested by CCK-8 and colony-forming assay. Transwell assays were utilized to evaluate the motility and invasive ability. Flow cytometry was employed to analyze cell cycle and apoptosis. SPSS software was used for statistical analysis. Low expression of Smarcd1 was observed in glioblastoma cell lines and in patients with high-grade glioma. Importantly, the depletion of Smarcd1 promoted cell proliferation, invasion, and chemoresistance, whereas enhanced expression of Smarcd1 inhibited tumor-malignant phenotypes. Mechanistic research demonstrated that overexpression of Smarcd1 decreased the expression of Notch1, while knockdown of Notch1 increased the expression of Smarcd1 through Hes1 suppression. Hence, the crosstalk between Smarcd1 and Notch1, which formed a feedback loop, was crucial in regulation of glioblastoma malignant phenotypes. Furthermore, targeting Smarcd1 could be a potential strategy for human glioblastoma treatment.
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Affiliation(s)
- Yihao Zhu
- Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, Jiangsu, People's Republic of China
- Department of Neurosurgery, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu, People's Republic of China
| | - Handong Wang
- Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, Jiangsu, People's Republic of China.
| | - Maoxing Fei
- Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, Jiangsu, People's Republic of China
| | - Ting Tang
- Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, Jiangsu, People's Republic of China
| | - Wenhao Niu
- Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, Jiangsu, People's Republic of China
| | - Li Zhang
- Department of Neurosurgery, Jinling Hospital, Medical School of Nanjing University, 305 East Zhongshan Road, Nanjing, 210002, Jiangsu, People's Republic of China
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15
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Han J, Kim T, Moon S, Park JH, Lee W, Ko YJ, Ryu KS, Yun JH, Lee W. NMR spectroscopy uncovers direct interaction between BAF60A and p53. Biochem Biophys Res Commun 2020; 534:815-821. [PMID: 33168186 DOI: 10.1016/j.bbrc.2020.10.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 10/23/2022]
Abstract
The BRG1-associated factor 60A (BAF60A), an SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1, has been known to be important for transcriptional activation and inhibition through the alteration of the DNA nucleosome. Although the association between BAF60A and p53 plays a critical role in tumor suppression, the interaction mode is still unclear. Here, we report the detailed interactions between BAF60A and p53 by both NMR spectroscopy and pull-down analysis. Both N-terminal region (BAF60ANR) and the SWIB domain (BAF60ASWIB) of BAF60A directly interact with the tetramerization domain of p53 (p53TET). NMR data show that Ile315, Met366, Ala388, and Tyr390 of BAF60ASWIB are mostly involved in p53TET binding. The calculated dissociation constant (KD) value between BAF60ASWIB and p53TET revealed relatively weak binding affinity, at approximately 0.3 ± 0.065 mM. Our data will enhance detailed interaction mechanism to elucidate the molecular basis of p53-mediated integration via BAF60A interaction.
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Affiliation(s)
- Jeongmin Han
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Sciences & Biotechnology, Yonsei University, Seoul, 120-749, South Korea
| | - Taehee Kim
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Sciences & Biotechnology, Yonsei University, Seoul, 120-749, South Korea
| | - Sunjin Moon
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Sciences & Biotechnology, Yonsei University, Seoul, 120-749, South Korea
| | - Jae-Hyun Park
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Sciences & Biotechnology, Yonsei University, Seoul, 120-749, South Korea
| | - Wonbin Lee
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Sciences & Biotechnology, Yonsei University, Seoul, 120-749, South Korea
| | - Yoon-Joo Ko
- Nuclear Magnetic Resonance Laboratory, National Center for Inter-University Research Facilities, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-742, South Korea
| | - Kyoung-Seok Ryu
- Division of Magnetic Resonance Research, Korea Basic Science Institute, Yangcheong-Ri 804-1, Ochang-Eup, Cheongwon-Gun, Chungcheongbuk-Do, 363-883, South Korea
| | - Ji-Hye Yun
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Sciences & Biotechnology, Yonsei University, Seoul, 120-749, South Korea.
| | - Weontae Lee
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Sciences & Biotechnology, Yonsei University, Seoul, 120-749, South Korea.
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16
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Innis SM, Cabot B. GBAF, a small BAF sub-complex with big implications: a systematic review. Epigenetics Chromatin 2020; 13:48. [PMID: 33143733 PMCID: PMC7607862 DOI: 10.1186/s13072-020-00370-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/23/2020] [Indexed: 12/01/2022] Open
Abstract
ATP-dependent chromatin remodeling by histone-modifying enzymes and chromatin remodeling complexes is crucial for maintaining chromatin organization and facilitating gene transcription. In the SWI/SNF family of ATP-dependent chromatin remodelers, distinct complexes such as BAF, PBAF, GBAF, esBAF and npBAF/nBAF are of particular interest regarding their implications in cellular differentiation and development, as well as in various diseases. The recently identified BAF subcomplex GBAF is no exception to this, and information is emerging linking this complex and its components to crucial events in mammalian development. Furthermore, given the essential nature of many of its subunits in maintaining effective chromatin remodeling function, it comes as no surprise that aberrant expression of GBAF complex components is associated with disease development, including neurodevelopmental disorders and numerous malignancies. It becomes clear that building upon our knowledge of GBAF and BAF complex function will be essential for advancements in both mammalian reproductive applications and the development of more effective therapeutic interventions and strategies. Here, we review the roles of the SWI/SNF chromatin remodeling subcomplex GBAF and its subunits in mammalian development and disease.
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Affiliation(s)
- Sarah M Innis
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Birgit Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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17
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Daneshvar K, Ardehali MB, Klein IA, Hsieh FK, Kratkiewicz AJ, Mahpour A, Cancelliere SOL, Zhou C, Cook BM, Li W, Pondick JV, Gupta SK, Moran SP, Young RA, Kingston RE, Mullen AC. lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation. Nat Cell Biol 2020; 22:1211-1222. [PMID: 32895492 PMCID: PMC8008247 DOI: 10.1038/s41556-020-0572-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/05/2020] [Indexed: 01/19/2023]
Abstract
Cooperation between DNA, RNA and protein regulates gene expression and controls differentiation through interactions that connect regions of nucleic acids and protein domains and through the assembly of biomolecular condensates. Here, we report that endoderm differentiation is regulated by the interaction between the long non-coding RNA (lncRNA) DIGIT and the bromodomain and extraterminal domain protein BRD3. BRD3 forms phase-separated condensates of which the formation is promoted by DIGIT, occupies enhancers of endoderm transcription factors and is required for endoderm differentiation. BRD3 binds to histone H3 acetylated at lysine 18 (H3K18ac) in vitro and co-occupies the genome with H3K18ac. DIGIT is also enriched in regions of H3K18ac, and the depletion of DIGIT results in decreased recruitment of BRD3 to these regions. Our findings show that cooperation between DIGIT and BRD3 at regions of H3K18ac regulates the transcription factors that drive endoderm differentiation and suggest that protein-lncRNA phase-separated condensates have a broader role as regulators of transcription.
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Affiliation(s)
- Kaveh Daneshvar
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - M Behfar Ardehali
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Fu-Kai Hsieh
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Arcadia J Kratkiewicz
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Amin Mahpour
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Chan Zhou
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Wenyang Li
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Joshua V Pondick
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sweta K Gupta
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sean P Moran
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert E Kingston
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alan C Mullen
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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18
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Rashid A, Wang R, Zhang L, Yue J, Yang M, Yen A. Dissecting the novel partners of nuclear c-Raf and its role in all-trans retinoic acid (ATRA)-induced myeloblastic leukemia cells differentiation. Exp Cell Res 2020; 394:111989. [PMID: 32283065 PMCID: PMC10656057 DOI: 10.1016/j.yexcr.2020.111989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/25/2020] [Accepted: 04/02/2020] [Indexed: 01/09/2023]
Abstract
All-trans retinoic acid (ATRA) is an anti-cancer differentiation therapy agent effective for acute promyelocytic leukemia (APL) but not acute myeloid leukemia (AML) in general. Using the HL-60 human non-APL AML model where ATRA causes nuclear enrichment of c-Raf that drives differentiation and G1/G0 cell cycle arrest, we now observe that c-Raf in the nucleus showed novel interactions with several prominent regulators of the cell cycle and cell differentiation. One is cyclin-dependent kinase 2 (Cdk2). ATRA treatment caused c-Raf to dissociate from Cdk2. This was associated with enhanced binding of Cdk2 with retinoic acid receptor α (RARα). Consistent with this novel Raf/CDK2/RARα axis contributing to differentiation, CD38 expression per cell, which is transcriptionally regulated by a retinoic acid response element (RARE), is enhanced. The RB tumor suppressor, a fundamental regulator of G1 cell cycle progression or arrest, was also targeted by c-Raf in the nucleus. RB and specifically the S608 phosphorylated form (pS608RB) complexed with c-Raf. ATRA treatment induced S608RB-hypophosphorylation associated with G1/G0 cell cycle arrest and release of c-Raf from RB. We also found that nuclear c-Raf interacted with SMARCD1, a pioneering component of the SWI/SNF chromatin remodeling complex. ATRA treatment diminished the amount of this protein bound to c-Raf. The data suggest that ATRA treatment to HL-60 human cells re-directed c-Raf from its historically pro-proliferation functions in the cytoplasm to pro-differentiation functions in the nucleus.
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Affiliation(s)
- Asif Rashid
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China; Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA; Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Rui Wang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Liang Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China; Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Jianbo Yue
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Mengsu Yang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China.
| | - Andrew Yen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA.
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19
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Targeting chromatin dysregulation in organ fibrosis. Cytokine Growth Factor Rev 2020; 57:64-72. [PMID: 32900600 DOI: 10.1016/j.cytogfr.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Fibrosis leads to destruction of organ architecture accompanied by chronic inflammation and loss of function. Fibrosis affects nearly every organ in the body and accounts for ∼45% of total deaths worldwide. Over the past decade, tremendous progress has been made in understanding the basic mechanisms leading to organ fibrosis. However, we are limited with therapeutic options and there is a significant need to develop highly effective anti-fibrotic therapies. Recent advances in sequencing technologies have advanced the burgeoning field of epigenetics towards molecular understanding at a higher resolution. Here we provide a comprehensive review of the recent advances in chromatin regulatory processes, specifically DNA methylation, post-translational modification of histones, and chromatin remodeling complexes in kidney, liver and lung fibrosis. Although this research field is young, we discuss new strategies for potential therapeutic interventions for treating organ fibrosis.
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20
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Chang Z, Zhao G, Zhao Y, Lu H, Xiong W, Liang W, Sun J, Wang H, Zhu T, Rom O, Guo Y, Fan Y, Chang L, Yang B, Garcia-Barrio MT, Lin JD, Chen YE, Zhang J. BAF60a Deficiency in Vascular Smooth Muscle Cells Prevents Abdominal Aortic Aneurysm by Reducing Inflammation and Extracellular Matrix Degradation. Arterioscler Thromb Vasc Biol 2020; 40:2494-2507. [PMID: 32787523 DOI: 10.1161/atvbaha.120.314955] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Currently, there are no approved drugs for abdominal aortic aneurysm (AAA) treatment, likely due to limited understanding of the primary molecular mechanisms underlying AAA development and progression. BAF60a-a unique subunit of the SWI/SNF (switch/sucrose nonfermentable) chromatin remodeling complex-is a novel regulator of metabolic homeostasis, yet little is known about its function in the vasculature and pathogenesis of AAA. In this study, we sought to investigate the role and underlying mechanisms of vascular smooth muscle cell (VSMC)-specific BAF60a in AAA formation. Approach and Results: BAF60a is upregulated in human and experimental murine AAA lesions. In vivo studies revealed that VSMC-specific knockout of BAF60a protected mice from both Ang II (angiotensin II)-induced and elastase-induced AAA formation with significant suppression of vascular inflammation, monocyte infiltration, and elastin fragmentation. Through RNA sequencing and pathway analysis, we found that the expression of inflammatory response genes in cultured human aortic smooth muscle cells was significantly downregulated by small interfering RNA-mediated BAF60a knockdown while upregulated upon adenovirus-mediated BAF60a overexpression. BAF60a regulates VSMC inflammation by recruiting BRG1 (Brahma-related gene-1)-a catalytic subunit of the SWI/SNF complex-to the promoter region of NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells) target genes. Furthermore, loss of BAF60a in VSMCs prevented the upregulation of the proteolytic enzyme cysteine protease CTSS (cathepsin S), thus ameliorating ECM (extracellular matrix) degradation within the vascular wall in AAA. CONCLUSIONS Our study demonstrated that BAF60a is required to recruit the SWI/SNF complex to facilitate the epigenetic regulation of VSMC inflammation, which may serve as a potential therapeutic target in preventing and treating AAA.
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Affiliation(s)
- Ziyi Chang
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor.,Department of Metabolism and Endocrinology (Z.C.), The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Guizhen Zhao
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Yang Zhao
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Haocheng Lu
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Wenhao Xiong
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Wenying Liang
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Jinjian Sun
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor.,Department of Cardiovascular Medicine (J.S.), The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Huilun Wang
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Tianqing Zhu
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Oren Rom
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Yanhong Guo
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Yanbo Fan
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Lin Chang
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Bo Yang
- Department of Cardiac Surgery (B.Y.), University of Michigan Medical Center, Ann Arbor
| | - Minerva T Garcia-Barrio
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Jiandie D Lin
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor (J.D.L.)
| | - Y Eugene Chen
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
| | - Jifeng Zhang
- Department of Internal Medicine, Frankel Cardiovascular Center (Z.C., G.Z., Y.Z., H.L., W.X., W.L., J.S., H.W., T.Z., O.R., Y.G., Y.F., L.C., M.T.G.-B., Y.E.C., J.Z.), University of Michigan Medical Center, Ann Arbor
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21
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Wang WF, Zhang YL. PfSWIB, a potential chromatin regulator for var gene regulation and parasite development in Plasmodium falciparum. Parasit Vectors 2020; 13:48. [PMID: 32019597 PMCID: PMC7001229 DOI: 10.1186/s13071-020-3918-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/29/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Various transcription factors are involved in the process of mutually exclusive expression and clonal variation of the Plasmodium multigene (var) family. Recent studies revealed that a P. falciparum SWI/SNF-related matrix-associated actin-dependent regulator of chromatin (PfSWIB) might trigger stage-specific programmed cell death (PCD), and was not only crucial for the survival and development of parasite, but also had profound effects on the parasite by interacting with other unknown proteins. However, it remains unclear whether PfSIWB is involved in transcriptional regulation of this virulence gene and its functional properties. METHODS A conditional knockdown system "PfSWIB-FKBP-LID" was introduced to the parasite clone 3D7, and an integrated parasite line "PfSWIB-HA-FKBP-LID" was obtained by drug cycling and clone screening. Growth curve analysis (GCA) was performed to investigate the growth and development of different parasite lines during 96 h in vitro culturing, by assessing parasitemia. Finally, we performed qPCR assays to detect var gene expression profiling in various comparison groups, as well as the mutually exclusive expression pattern of the var genes within a single 48 h life-cycle of P. falciparum in different parasite lines. In addition, RNA-seq was applied to analyze the var gene expression in different lines. RESULTS GCA revealed that conditional knockdown of PfSWIB could interfere with the growth and development of P. falciparum. The parasitemia of PfSWIB∆ showed a significant decline at 96 h during in vitro culture compared with the PfSWIB and 3D7 lines (P < 0.0001). qPCR and RNA-seq analysis confirmed that depletion of PfSWIB not only silences upsA, upsC and partial upsB var genes, as well as removes the silencing of partial upsB var genes at the ring stage in PfSWIB∆ line, but also leads to aberrant expression of upsA and partial upsB/upsC var genes at the mature stage of P. falciparum, during a single 48-h life-cycle. CONCLUSIONS We demonstrated that PfSWIB was involved in the process of clonal variation in var gene expression, and crucial for the survival and development of Plasmodium parasite. These findings could provide better understanding of the mechanism and function of PfSWIB contributing to the pathogenesis in malaria parasites.
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Affiliation(s)
- Wei-Feng Wang
- Central Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200072, China.,Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, China
| | - Yi-Long Zhang
- Department of Tropical Diseases, Faculty of Naval Medicine, Second Military Medical University, Shanghai, 200433, China. .,Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200092, China.
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22
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Cai W, Su L, Liao L, Liu ZZ, Langbein L, Dulaimi E, Testa JR, Uzzo RG, Zhong Z, Jiang W, Yan Q, Zhang Q, Yang H. PBRM1 acts as a p53 lysine-acetylation reader to suppress renal tumor growth. Nat Commun 2019; 10:5800. [PMID: 31863007 PMCID: PMC6925188 DOI: 10.1038/s41467-019-13608-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023] Open
Abstract
p53 acetylation is indispensable for its transcriptional activity and tumor suppressive function. However, the identity of reader protein(s) for p53 acetylation remains elusive. PBRM1, the second most highly mutated tumor suppressor gene in kidney cancer, encodes PBRM1. Here, we identify PBRM1 as a reader for p53 acetylation on lysine 382 (K382Ac) through its bromodomain 4 (BD4). Notably, mutations on key residues of BD4 disrupt recognition of p53 K382Ac. The mutation in BD4 also reduces p53 binding to promoters of target genes such as CDKN1A (p21). Consequently, the PBRM1 BD4 mutant fails to fully support p53 transcriptional activity and is defective as a tumor suppressor. We also find that expressions of PBRM1 and p21 correlate with each other in human kidney cancer samples. Our findings uncover a tumor suppressive mechanism of PBRM1 in kidney cancer and provide a mechanistic insight into the crosstalk between p53 and SWI/SNF complexes.
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Affiliation(s)
- Weijia Cai
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Liya Su
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Lili Liao
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
- Department of Pathology, Yale University, New Haven, CT, 06520, USA
| | - Zongzhi Z Liu
- Department of Pathology, Yale University, New Haven, CT, 06520, USA
| | - Lauren Langbein
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Essel Dulaimi
- Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | - Robert G Uzzo
- Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Zhijiu Zhong
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Wei Jiang
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Qin Yan
- Department of Pathology, Yale University, New Haven, CT, 06520, USA
| | - Qing Zhang
- Department of Pathology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Haifeng Yang
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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23
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Hasan N, Ahuja N. The Emerging Roles of ATP-Dependent Chromatin Remodeling Complexes in Pancreatic Cancer. Cancers (Basel) 2019; 11:E1859. [PMID: 31769422 PMCID: PMC6966483 DOI: 10.3390/cancers11121859] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/08/2023] Open
Abstract
Pancreatic cancer is an aggressive cancer with low survival rates. Genetic and epigenetic dysregulation has been associated with the initiation and progression of pancreatic tumors. Multiple studies have pointed to the involvement of aberrant chromatin modifications in driving tumor behavior. ATP-dependent chromatin remodeling complexes regulate chromatin structure and have critical roles in stem cell maintenance, development, and cancer. Frequent mutations and chromosomal aberrations in the genes associated with subunits of the ATP-dependent chromatin remodeling complexes have been detected in different cancer types. In this review, we summarize the current literature on the genomic alterations and mechanistic studies of the ATP-dependent chromatin remodeling complexes in pancreatic cancer. Our review is focused on the four main subfamilies: SWItch/sucrose non-fermentable (SWI/SNF), imitation SWI (ISWI), chromodomain-helicase DNA-binding protein (CHD), and INOsitol-requiring mutant 80 (INO80). Finally, we discuss potential novel treatment options that use small molecules to target these complexes.
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Affiliation(s)
| | - Nita Ahuja
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06520, USA;
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24
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Adduri RSR, George SA, Kavadipula P, Bashyam MD. SMARCD1
is a transcriptional target of specific non‐hotspot mutant p53 forms. J Cell Physiol 2019; 235:4559-4570. [DOI: 10.1002/jcp.29332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Raju S. R. Adduri
- Laboratory of Molecular Oncology Centre for DNA Fingerprinting and Diagnostics Hyderabad Telangana India
- Graduate Studies Manipal Academy of Higher Education Manipal Karnataka India
| | - Sara A. George
- Laboratory of Molecular Oncology Centre for DNA Fingerprinting and Diagnostics Hyderabad Telangana India
- Graduate Studies Regional Centre for Biotechnology Faridabad Haryana India
| | - Padmavathi Kavadipula
- Laboratory of Molecular Oncology Centre for DNA Fingerprinting and Diagnostics Hyderabad Telangana India
| | - Murali D. Bashyam
- Laboratory of Molecular Oncology Centre for DNA Fingerprinting and Diagnostics Hyderabad Telangana India
- Adjunct Faculty Regional Centre for Biotechnology Faridabad Haryana India
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25
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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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26
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Jayaprakash S, Drakulic S, Zhao Z, Sander B, Golas MM. The ATPase BRG1/SMARCA4 is a protein interaction platform that recruits BAF subunits and the transcriptional repressor REST/NRSF in neural progenitor cells. Mol Cell Biochem 2019; 461:171-182. [DOI: 10.1007/s11010-019-03600-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/08/2019] [Indexed: 10/26/2022]
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27
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Orlando KA, Nguyen V, Raab JR, Walhart T, Weissman BE. Remodeling the cancer epigenome: mutations in the SWI/SNF complex offer new therapeutic opportunities. Expert Rev Anticancer Ther 2019; 19:375-391. [PMID: 30986130 DOI: 10.1080/14737140.2019.1605905] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Cancer genome sequencing studies have discovered mutations in members of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling complex in nearly 25% of human cancers. The SWI/SNF complex, first discovered in S. cerevisiae, shows strong conservation from yeast to Drosophila to mammals, contains approximately 10-12 subunits and regulates nucleosome positioning through the energy generated by its ATPase subunits. The unexpected finding of frequent mutations in the complex has fueled studies to identify the mechanisms that drive tumor development and the accompanying therapeutic vulnerabilities. Areas covered: In the review, we focus upon the potential roles different SWI/SNF subunit mutations play in human oncogenesis, their common and unique mechanisms of transformation and the potential for translating these mechanisms into targeted therapies for SWI/SNF-mutant tumors. Expert opinion: We currently have limited insights into how mutations in different SWI/SNF subunits drive the development of human tumors. Because the SWI/SNF complex participates in a broad range of normal cellular functions, defining specific oncogenic pathways has proved difficult. In addition, therapeutic options for SWI/SNF-mutant cancers have mainly evolved from high-throughput screens of cell lines with mutations in different subunits. Future studies should follow a more coherent plan to pinpoint common vulnerabilities among these tumors.
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Affiliation(s)
- Krystal A Orlando
- a Department of Pathology and Laboratory Medicine , University of North Carolina , Chapel Hill , NC , USA
| | - Vinh Nguyen
- b Curriculum in Toxicology and Environmental Medicine , University of North Carolina , Chapel Hill , NC , USA
| | - Jesse R Raab
- c Department of Genetics , University of North Carolina , Chapel Hill , NC , USA
| | - Tara Walhart
- d Lineberger Comprehensive Cancer Center , University of North Carolina , Chapel Hill , NC , USA
| | - Bernard E Weissman
- a Department of Pathology and Laboratory Medicine , University of North Carolina , Chapel Hill , NC , USA.,b Curriculum in Toxicology and Environmental Medicine , University of North Carolina , Chapel Hill , NC , USA.,d Lineberger Comprehensive Cancer Center , University of North Carolina , Chapel Hill , NC , USA
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28
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Howard TP, Arnoff TE, Song MR, Giacomelli AO, Wang X, Hong AL, Dharia NV, Wang S, Vazquez F, Pham MT, Morgan AM, Wachter F, Bird GH, Kugener G, Oberlick EM, Rees MG, Tiv HL, Hwang JH, Walsh KH, Cook A, Krill-Burger JM, Tsherniak A, Gokhale PC, Park PJ, Stegmaier K, Walensky LD, Hahn WC, Roberts CWM. MDM2 and MDM4 Are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors. Cancer Res 2019; 79:2404-2414. [PMID: 30755442 DOI: 10.1158/0008-5472.can-18-3066] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/28/2018] [Accepted: 02/07/2019] [Indexed: 12/21/2022]
Abstract
Malignant rhabdoid tumors (MRT) are highly aggressive pediatric cancers that respond poorly to current therapies. In this study, we screened several MRT cell lines with large-scale RNAi, CRISPR-Cas9, and small-molecule libraries to identify potential drug targets specific for these cancers. We discovered MDM2 and MDM4, the canonical negative regulators of p53, as significant vulnerabilities. Using two compounds currently in clinical development, idasanutlin (MDM2-specific) and ATSP-7041 (MDM2/4-dual), we show that MRT cells were more sensitive than other p53 wild-type cancer cell lines to inhibition of MDM2 alone as well as dual inhibition of MDM2/4. These compounds caused significant upregulation of the p53 pathway in MRT cells, and sensitivity was ablated by CRISPR-Cas9-mediated inactivation of TP53. We show that loss of SMARCB1, a subunit of the SWI/SNF (BAF) complex mutated in nearly all MRTs, sensitized cells to MDM2 and MDM2/4 inhibition by enhancing p53-mediated apoptosis. Both MDM2 and MDM2/4 inhibition slowed MRT xenograft growth in vivo, with a 5-day idasanutlin pulse causing marked regression of all xenografts, including durable complete responses in 50% of mice. Together, these studies identify a genetic connection between mutations in the SWI/SNF chromatin-remodeling complex and the tumor suppressor gene TP53 and provide preclinical evidence to support the targeting of MDM2 and MDM4 in this often-fatal pediatric cancer. SIGNIFICANCE: This study identifies two targets, MDM2 and MDM4, as vulnerabilities in a deadly pediatric cancer and provides preclinical evidence that compounds inhibiting these proteins have therapeutic potential.
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Affiliation(s)
- Thomas P Howard
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Taylor E Arnoff
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Melinda R Song
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew O Giacomelli
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Xiaofeng Wang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Andrew L Hong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Su Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | | | - Minh-Tam Pham
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ann M Morgan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Franziska Wachter
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gregory H Bird
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Elaine M Oberlick
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Matthew G Rees
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Hong L Tiv
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Justin H Hwang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Katherine H Walsh
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - April Cook
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Prafulla C Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Charles W M Roberts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Oncology, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee
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29
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Akrami H, Mehdizadeh K, Moradi B, Borzabadi Farahani D, Mansouri K, Ghalib Ibraheem Alnajar S. PlGF knockdown induced apoptosis through Wnt signaling pathway in gastric cancer stem cells. J Cell Biochem 2018; 120:3268-3276. [PMID: 30203564 DOI: 10.1002/jcb.27593] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/07/2018] [Indexed: 12/19/2022]
Abstract
Despite the fact that much research has focused on gastric cancer, it is still a worldwide concern, because of the difficulties with factors such as signaling pathway crosstalk and gastric cancer stem cell (GCSC). Placental growth factor (PlGF) is one of these factors, and its tumorigenicity potential still remains a question. As a result, we have investigated the effect of PlGF knockdown on apoptosis and genes involved in the Wnt signaling pathway, and apoptosis in cancer stem cells derived from AGS an MKN-45 gastric cancer cell lines. We isolated GCSCs from MKN-45 and AGS cell lines on a nonadherent surface. Then the cell viability, the real-time reverse transcription-polymerase chain reaction data of the genes involved in the Wnt signaling pathway, and apoptosis were evaluated. Furthermore, DNA laddering was used to show the apoptotic effect and DNA fragmentation caused by the PlGF knockdown. Our investigation revealed that the PlGF knockdown with PlGF-specific small interfering RNA at 40 pmol for GCSCs derived from MKN-45 and AGS at 24 hours can significantly affect the cell viability, the Wnt signaling pathway, and the apoptosis-related genes expression. In conclusion, we showed the PlGF knockdown may induce apoptosis via the Wnt signaling pathway in GCSCs.
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Affiliation(s)
- Hassan Akrami
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.,Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Kiumars Mehdizadeh
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Behrouz Moradi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | | | - Kamran Mansouri
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
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30
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Akrami H, Moradi B, Borzabadi Farahani D, Mehdizadeh K. Ibuprofen reduces cell proliferation through inhibiting Wnt/β catenin signaling pathway in gastric cancer stem cells. Cell Biol Int 2018; 42:949-958. [PMID: 29512256 DOI: 10.1002/cbin.10959] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 03/05/2018] [Indexed: 12/15/2022]
Abstract
Nowadays, most studies focused on cancer stem cells (CSCs) through their abilities to cause tumorigenicity, drug resistance, and cancer recurrence. On the other side, nonsteroidal anti-inflammatory drugs (NSAIDs) have been taken into consideration because of cheapness and availability. For the reasons mentioned above, we have studied the effect of ibuprofen as an NSAID on CSCs derived from AGS and MKN-45 gastric cancer cell lines to perform effective cancer therapy. We evaluated cell viability, spheroid body formation, monolayer, and soft agar colony formation to express the anti-cancer effect of ibuprofen on CSCs. Also, real-time RT-PCR data of stemness markers and genes affected on, or downstream of Wnt signaling pathway were evaluated. Our findings suggest that ibuprofen at 1,000 μM for 48 h can reduce cell proliferation, stemness features in CSCs by changing the expression level of CD44, OCT3/4, SOX2, Nanog, and KLF4 as stemness markers. Furthermore, ibuprofen can have an inhibitory role in Wnt signaling pathway by changing the expression level of some genes, including CTNNB1, CTNNBIP1, SMARCD1, PYGO2, SUFU, CASK, and KREMEN1. According to our study, ibuprofen has an anti-proliferative effect on CSCs derived from AGS and MKN-45 cells.
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Affiliation(s)
- Hassan Akrami
- Faculty of Science, Department of Biology, Razi University, Kermanshah, Iran
| | - Behrouz Moradi
- Faculty of Science, Department of Biology, Razi University, Kermanshah, Iran
| | | | - Kiumars Mehdizadeh
- Faculty of Science, Department of Biology, Razi University, Kermanshah, Iran
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31
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Wang RR, Pan R, Zhang W, Fu J, Lin JD, Meng ZX. The SWI/SNF chromatin-remodeling factors BAF60a, b, and c in nutrient signaling and metabolic control. Protein Cell 2018; 9:207-215. [PMID: 28688083 PMCID: PMC5818368 DOI: 10.1007/s13238-017-0442-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 06/21/2017] [Indexed: 01/29/2023] Open
Abstract
Metabolic syndrome has become a global epidemic that adversely affects human health. Both genetic and environmental factors contribute to the pathogenesis of metabolic disorders; however, the mechanisms that integrate these cues to regulate metabolic physiology and the development of metabolic disorders remain incompletely defined. Emerging evidence suggests that SWI/SNF chromatin-remodeling complexes are critical for directing metabolic reprogramming and adaptation in response to nutritional and other physiological signals. The ATP-dependent SWI/SNF chromatin-remodeling complexes comprise up to 11 subunits, among which the BAF60 subunit serves as a key link between the core complexes and specific transcriptional factors. The BAF60 subunit has three members, BAF60a, b, and c. The distinct tissue distribution patterns and regulatory mechanisms of BAF60 proteins confer each isoform with specialized functions in different metabolic cell types. In this review, we summarize the emerging roles and mechanisms of BAF60 proteins in the regulation of nutrient sensing and energy metabolism under physiological and disease conditions.
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Affiliation(s)
- Ruo-Ran Wang
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Chronic Disease Research Institute of School of Public Health, Zhejiang University, Hangzhou, 310058, China
| | - Ran Pan
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Chronic Disease Research Institute of School of Public Health, Zhejiang University, Hangzhou, 310058, China
| | - Wenjing Zhang
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Chronic Disease Research Institute of School of Public Health, Zhejiang University, Hangzhou, 310058, China
| | - Junfen Fu
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jiandie D Lin
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan Medical Center, Ann Arbor, MI, 48109, USA
| | - Zhuo-Xian Meng
- Department of Pathology and Pathophysiology, Key Laboratory of Disease Proteomics of Zhejiang Province, School of Medicine, Chronic Disease Research Institute of School of Public Health, Zhejiang University, Hangzhou, 310058, China.
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan Medical Center, Ann Arbor, MI, 48109, USA.
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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: 25] [Impact Index Per Article: 4.2] [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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Abstract
Since its discovery in 1979, p53 has been on the forefront of cancer research. It is considered a master gene of cancer suppression and is found mutated in around 50% of all human tumors. In addition, the progressive identification of p53-related transcription factors p63 and p73 as well as their multiple isoforms have added further layers of complexity to an already dense network. Among the numerous models used to unravel the p53 family mysteries, S. cerevisiae has been particularly useful. This seemingly naive model allows the expression of a functional human p53 and thus the assessment of p53 intrinsic transcriptional activity. The aim of this article is to review the various contributions that the budding yeast has made to the understanding of p53, p63 and p73 biology and to envision new possible directions for yeast-based assays in the field of cancer as well as other p53-family-related diseases.
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Ji S, Zhu L, Gao Y, Zhang X, Yan Y, Cen J, Li R, Zeng R, Liao L, Hou C, Gao Y, Gao S, Wei G, Hui L. Baf60b-mediated ATM-p53 activation blocks cell identity conversion by sensing chromatin opening. Cell Res 2017; 27:642-656. [PMID: 28303890 PMCID: PMC5520852 DOI: 10.1038/cr.2017.36] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 02/07/2017] [Accepted: 02/10/2017] [Indexed: 12/13/2022] Open
Abstract
Lineage conversion by expression of lineage-specific transcription factors is a process of epigenetic remodeling that has low efficiency. The mechanism by which a cell resists lineage conversion is largely unknown. Using hepatic-specific transcription factors Foxa3, Hnf1α and Gata4 (3TF) to induce hepatic conversion in mouse fibroblasts, we showed that 3TF induced strong activation of the ATM-p53 pathway, which led to proliferation arrest and cell death, and it further prevented hepatic conversion. Notably, ATM activation, independent of DNA damage, responded to chromatin opening during hepatic conversion. By characterizing the early molecular events during hepatic conversion, we found that Baf60b, a member of the SWI/SNF chromatin remodeling complex, links chromatin opening to ATM activation by facilitating ATM recruitment to the open chromatin regions of a panel of hepatic gene loci. These findings shed light on cellular responses to lineage conversion by revealing a function of the ATM-p53 pathway in sensing chromatin opening.
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Affiliation(s)
- Shuyi Ji
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Linying Zhu
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yimeng Gao
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoran Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yupeng Yan
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jin Cen
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Rongxia Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Rong Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Chunhui Hou
- Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong 518055, China
| | - Yawei Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lijian Hui
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China
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Pfister NT, Prives C. Transcriptional Regulation by Wild-Type and Cancer-Related Mutant Forms of p53. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026054. [PMID: 27836911 DOI: 10.1101/cshperspect.a026054] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
TP53 missense mutations produce a mutant p53 protein that cannot activate the p53 tumor suppressive transcriptional response, which is the primary selective pressure for TP53 mutation. Specific codons of TP53, termed hotspot mutants, are mutated at elevated frequency. Hotspot forms of mutant p53 possess oncogenic properties in addition to being deficient in tumor suppression. Such p53 mutants accumulate to high levels in the cells they inhabit, causing transcriptional alterations that produce pro-oncogenic activities, such as increased pro-growth signaling, invasiveness, and metastases. These forms of mutant p53 very likely use features of wild-type p53, such as interactions with the transcriptional machinery, to produce oncogenic effects. In this review, we discuss commonalities between wild-type and mutant p53 proteins with an emphasis on transcriptional processes.
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Affiliation(s)
- Neil T Pfister
- Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, New York 10027
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Marquez-Vilendrer SB, Rai SK, Gramling SJ, Lu L, Reisman DN. BRG1 and BRM loss selectively impacts RB and P53, respectively: BRG1 and BRM have differential functions in vivo. Oncoscience 2016; 3:337-350. [PMID: 28105458 PMCID: PMC5235922 DOI: 10.18632/oncoscience.333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 09/23/2016] [Indexed: 12/11/2022] Open
Abstract
The SWI/SNF complex is an important regulator of gene expression that functions by interacting with a diverse array of cellular proteins. The catalytic subunits of SWI/SNF, BRG1 and BRM, are frequently lost alone or concomitantly in a range of different cancer types. This loss abrogates SWI/SNF complex function as well as the functions of proteins that are required for SWI/SNF function, such as RB1 and TP53. Yet while both proteins are known to be dependent on SWI/SNF, we found that BRG1, but not BRM, is functionally linked to RB1, such that loss of BRG1 can directly or indirectly inactivate the RB1 pathway. This newly discovered dependence of RB1 on BRG1 is important because it explains why BRG1 loss can blunt the growth-inhibitory effect of tyrosine kinase inhibitors (TKIs). We also observed that selection for Trp53 mutations occurred in Brm-positive tumors but did not occur in Brm-negative tumors. Hence, these data indicate that, during cancer development, Trp53 is functionally dependent on Brm but not Brg1. Our findings show for the first time the key differences in Brm- and Brg1-specific SWI/SNF complexes and help explain why concomitant loss of Brg1 and Brm frequently occurs in cancer, as well as how their loss impacts cancer development.
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Affiliation(s)
| | - Sudhir K Rai
- Department of Hematology/Oncology, Medicine, University of Florida, Gainesville, FL, USA
| | - Sarah Jb Gramling
- Department of Hematology/Oncology, Medicine, University of Florida, Gainesville, FL, USA
| | - Li Lu
- Department of Hematology/Oncology, Medicine, University of Florida, Gainesville, FL, USA; Department of Pathology, University of Florida, Gainesville, FL, USA
| | - David N Reisman
- Department of Hematology/Oncology, Medicine, University of Florida, Gainesville, FL, USA
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Ertl I, Porta-de-la-Riva M, Gómez-Orte E, Rubio-Peña K, Aristizábal-Corrales D, Cornes E, Fontrodona L, Osteikoetxea X, Ayuso C, Askjaer P, Cabello J, Cerón J. Functional Interplay of Two Paralogs Encoding SWI/SNF Chromatin-Remodeling Accessory Subunits During Caenorhabditis elegans Development. Genetics 2016; 202:961-75. [PMID: 26739451 PMCID: PMC4788132 DOI: 10.1534/genetics.115.183533] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/21/2015] [Indexed: 12/16/2022] Open
Abstract
SWI/SNF ATP-dependent chromatin-remodeling complexes have been related to several cellular processes such as transcription, regulation of chromosomal stability, and DNA repair. The Caenorhabditis elegans gene ham-3 (also known as swsn-2.1) and its paralog swsn-2.2 encode accessory subunits of SWI/SNF complexes. Using RNA interference (RNAi) assays and diverse alleles we investigated whether ham-3 and swsn-2.2 have different functions during C. elegans development since they encode proteins that are probably mutually exclusive in a given SWI/SNF complex. We found that ham-3 and swsn-2.2 display similar functions in vulva specification, germline development, and intestinal cell proliferation, but have distinct roles in embryonic development. Accordingly, we detected functional redundancy in some developmental processes and demonstrated by RNA sequencing of RNAi-treated L4 animals that ham-3 and swsn-2.2 regulate the expression of a common subset of genes but also have specific targets. Cell lineage analyses in the embryo revealed hyper-proliferation of intestinal cells in ham-3 null mutants whereas swsn-2.2 is required for proper cell divisions. Using a proteomic approach, we identified SWSN-2.2-interacting proteins needed for early cell divisions, such as SAO-1 and ATX-2, and also nuclear envelope proteins such as MEL-28. swsn-2.2 mutants phenocopy mel-28 loss-of-function, and we observed that SWSN-2.2 and MEL-28 colocalize in mitotic and meiotic chromosomes. Moreover, we demonstrated that SWSN-2.2 is required for correct chromosome segregation and nuclear reassembly after mitosis including recruitment of MEL-28 to the nuclear periphery.
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Affiliation(s)
- Iris Ertl
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Montserrat Porta-de-la-Riva
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain C. elegans Core Facility, Bellvitge Biomedical Research Institute-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Eva Gómez-Orte
- Center for Biomedical Research of La Rioja (CIBIR), 26006 Logroño, Spain
| | - Karinna Rubio-Peña
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - David Aristizábal-Corrales
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Eric Cornes
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laura Fontrodona
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xabier Osteikoetxea
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Ayuso
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Juan Cabello
- Center for Biomedical Research of La Rioja (CIBIR), 26006 Logroño, Spain
| | - Julián Cerón
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
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38
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Zinzalla G. A New Way Forward in Cancer Drug Discovery: Inhibiting the SWI/SNF Chromatin Remodelling Complex. Chembiochem 2016; 17:677-82. [PMID: 26684344 DOI: 10.1002/cbic.201500565] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 12/24/2022]
Abstract
Mutations in subunits of the SWI/SNF chromatin remodelling complex are found in 20 % of human cancers. At face value, this would appear to indicate that this multiprotein complex is a potent tumour suppressor. However, it has recently emerged that some mutations in the SWI/SNF complex can have a gain-of-function effect and that in other tumours, such as pancreatic cancer, leukaemia, and breast cancer, the wild-type complex is used to drive cancer. Thus, paradoxically, this "tumour suppressor" has become an attractive target for developing anticancer agents. The SWI/SNF complex makes several protein-protein interactions both within the complex and with a wide range of transcription factors, and targeting these protein-protein interactions is emerging as the best approach to modulating the activity of the complex selectively.
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Affiliation(s)
- Giovanna Zinzalla
- Microbiology, Tumour and Cell Biology (MTC), and Science for Life Laboratory (SciLifeLab), Karolinska Institutet, Tomtebodavägen 23A, Stockholm, 171 65, Sweden.
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Vieira WA, Coetzer TL. Localization and interactions of Plasmodium falciparum SWIB/MDM2 homologues. Malar J 2016; 15:32. [PMID: 26791088 PMCID: PMC4721021 DOI: 10.1186/s12936-015-1065-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 12/22/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Malaria remains a global health problem and the majority of deaths are caused by Plasmodium falciparum parasites. Due to the rapid emergence of drug-resistant strains, novel avenues of research on the biology of the parasite are needed. The massive proliferation of asexual, intra-erythrocytic parasites every 48 h could kill the human host prior to transmission of slow-developing gametocytes to the mosquito vector. A self-induced P. falciparum programmed cell death mechanism has been hypothesized to maintain this balance between the parasite and its two hosts, but molecular participants of the cell death pathway in P. falciparum have not been characterized. Proteins with SWIB/MDM2 domains play a key role in metazoan programmed cell death and this study provides the first evaluation of two parasite SWIB/MDM2 homologues, PF3D7_0518200 (PfMDM2) and PF3D7_0611400 (PfSWIB). METHODS The function of these proteins was assessed by predicting their structural topology with the aid of bioinformatics and determining their location within live transgenic parasites, expressing green fluorescent protein-tagged PfMDM2 and PfSWIB under normal and elevated temperatures, which mimic fever and which are known to induce a programmed cell death response. Additionally, P. falciparum phage display library technology was used to identify binding partners for the two parasite SWIB/MDM2 domains. RESULTS Structural features of the SWIB/MDM2 domains of PfMDM2 and PfSWIB, suggested that they are chromatin remodelling factors. The N-terminal signal sequence of PfMDM2 directed the protein to the mitochondrion under both normal and heat stress conditions. Plasmodium falciparum phage display library technology revealed that the C-terminal SWIB/MDM2 domain of PfMDM2 interacted with a conserved protein containing a LisH domain. PfSWIB localized to the cytoplasm under normal growth conditions, while approximately 10% of the heat-stressed trophozoite-stage parasites presented a rapid but short-lived nuclear localization pattern. Two PfSWIB binding partners, a putative Aurora-related kinase and a member of the inner membrane complex, were identified. CONCLUSION These novel data provide insight into the function of two parasite SWIB/MDM2 homologues and suggest that PfMDM2 plays a role within the mitochondrion and that PfSWIB is involved in a stage-specific, heat-stress, response pathway.
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Affiliation(s)
- Warren Antonio Vieira
- Wits Research Institute for Malaria, Wits Medical School, 7 York Road Parktown, Johannesburg, 2193, South Africa. .,Plasmodium Molecular Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Thérèsa L Coetzer
- Wits Research Institute for Malaria, Wits Medical School, 7 York Road Parktown, Johannesburg, 2193, South Africa. .,Plasmodium Molecular Research Unit, Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,National Health Laboratory Service, Johannesburg, South Africa.
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40
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Hong CF, Lin SY, Chou YT, Wu CW. MicroRNA-7 Compromises p53 Protein-dependent Apoptosis by Controlling the Expression of the Chromatin Remodeling Factor SMARCD1. J Biol Chem 2015; 291:1877-1889. [PMID: 26542803 DOI: 10.1074/jbc.m115.667568] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Indexed: 01/19/2023] Open
Abstract
We previously demonstrated that the epidermal growth factor receptor (EGFR) up-regulated miR-7 to promote tumor growth during lung cancer oncogenesis. Several lines of evidence have suggested that alterations in chromatin remodeling components contribute to cancer initiation and progression. In this study, we identified SMARCD1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily d, member 1) as a novel target gene of miR-7. miR-7 expression reduced SMARCD1 protein expression in lung cancer cell lines. We used luciferase reporters carrying wild type or mutated 3'UTR of SMARCD1 and found that miR-7 blocked SMARCD1 expression by binding to two seed regions in the 3'UTR of SMARCD1 and down-regulated SMARCD1 mRNA expression. Additionally, upon chemotherapy drug treatment, miR-7 down-regulated p53-dependent apoptosis-related gene BAX (BCL2-associated X protein) and p21 expression by interfering with the interaction between SMARCD1 and p53, thereby reducing caspase3 cleavage and the downstream apoptosis cascades. We found that although SMARCD1 sensitized lung cancer cells to chemotherapy drug-induced apoptosis, miR-7 enhanced the drug resistance potential of lung cancer cells against chemotherapy drugs. SMARCD1 was down-regulated in patients with non-small cell lung cancer and lung adenocarcinoma cell lines, and SMARCD1 and miR-7 expression levels were negatively correlated in clinical samples. Our investigation into the involvement of the EGFR-regulated microRNA pathway in the SWI/SNF chromatin remodeling complex suggests that EGFR-mediated miR-7 suppresses the coupling of the chromatin remodeling factor SMARCD1 with p53, resulting in increased chemo-resistance of lung cancer cells.
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Affiliation(s)
- Chun-Fu Hong
- From the Department of Long Term Care, National Quemoy University, Kinmen County 89250
| | - Shu-Yu Lin
- the National Research Program for Genomic Medicine Core Facilities for Proteomics and Glycomics, Institute of Biological Chemistry, Academia Sinica, Taipei 11529
| | - Yu-Ting Chou
- the Institute of Biotechnology, National Tsing Hua University, HsinChu 30013,.
| | - Cheng-Wen Wu
- the Institute of Clinical Medicine,; Institute of Biochemistry and Molecular Biology, and; Institute of Microbiology and Immunology, National Yang Ming University, Taipei 11221, and; the Institute of Biomedical Science, Academia Sinica, Taipei 11221, Taiwan.
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41
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Jégu T, Domenichini S, Blein T, Ariel F, Christ A, Kim SK, Crespi M, Boutet-Mercey S, Mouille G, Bourge M, Hirt H, Bergounioux C, Raynaud C, Benhamed M. A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture. PLoS One 2015; 10:e0138276. [PMID: 26457678 PMCID: PMC4601769 DOI: 10.1371/journal.pone.0138276] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/26/2015] [Indexed: 02/07/2023] Open
Abstract
Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression.
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Affiliation(s)
- Teddy Jégu
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Séverine Domenichini
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Thomas Blein
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Federico Ariel
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Aurélie Christ
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Soon-Kap Kim
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Martin Crespi
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | | | - Grégory Mouille
- Institut Jean-Pierre Bourgin, UMR1318 INRA/AgroParisTech, Versailles, France
| | - Mickaël Bourge
- Pôle de Biologie Cellulaire, Imagif, Centre de Recherche de Gif, CNRS, IFR87, Gif-sur-Yvette, France
| | - Heribert Hirt
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Cécile Raynaud
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
- * E-mail:
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42
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Pfister NT, Fomin V, Regunath K, Zhou JY, Zhou W, Silwal-Pandit L, Freed-Pastor WA, Laptenko O, Neo SP, Bargonetti J, Hoque M, Tian B, Gunaratne J, Engebraaten O, Manley JL, Børresen-Dale AL, Neilsen PM, Prives C. Mutant p53 cooperates with the SWI/SNF chromatin remodeling complex to regulate VEGFR2 in breast cancer cells. Genes Dev 2015; 29:1298-315. [PMID: 26080815 PMCID: PMC4495400 DOI: 10.1101/gad.263202.115] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/26/2015] [Indexed: 01/15/2023]
Abstract
In this study, Pfister et al. identified a new mutant p53 target gene, VEGFR2, and demonstrated that mutant p53 stimulates expression of VEGFR2 by cooperating with the SWI/SNF chromatin remodeling complex to superactivate the VEGFR2 gene. They also show that >50% of all mutant p53-regulated gene expression is mediated by SWI/SNF, providing insight into the observation that mutant p53 alters the expression of many genes. Mutant p53 impacts the expression of numerous genes at the level of transcription to mediate oncogenesis. We identified vascular endothelial growth factor receptor 2 (VEGFR2), the primary functional VEGF receptor that mediates endothelial cell vascularization, as a mutant p53 transcriptional target in multiple breast cancer cell lines. Up-regulation of VEGFR2 mediates the role of mutant p53 in increasing cellular growth in two-dimensional (2D) and three-dimensional (3D) culture conditions. Mutant p53 binds near the VEGFR2 promoter transcriptional start site and plays a role in maintaining an open conformation at that location. Relatedly, mutant p53 interacts with the SWI/SNF complex, which is required for remodeling the VEGFR2 promoter. By both querying individual genes regulated by mutant p53 and performing RNA sequencing, the results indicate that >40% of all mutant p53-regulated gene expression is mediated by SWI/SNF. We surmise that mutant p53 impacts transcription of VEGFR2 as well as myriad other genes by promoter remodeling through interaction with and likely regulation of the SWI/SNF chromatin remodeling complex. Therefore, not only might mutant p53-expressing tumors be susceptible to anti VEGF therapies, impacting SWI/SNF tumor suppressor function in mutant p53 tumors may also have therapeutic potential.
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Affiliation(s)
- Neil T Pfister
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Vitalay Fomin
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Kausik Regunath
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Jeffrey Y Zhou
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Wen Zhou
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Laxmi Silwal-Pandit
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radiumhospital, 0310 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Faculty of Medicine, Institute for Clinical Medicine, University of Oslo, 0450 Oslo, Norway
| | - William A Freed-Pastor
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA; Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Oleg Laptenko
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Suat Peng Neo
- Quantitative Proteomics Group, Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore S138673
| | - Jill Bargonetti
- Department of Biological Sciences, Hunter College, City University of New York, New York, New York 10065, USA
| | - Mainul Hoque
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Jayantha Gunaratne
- Quantitative Proteomics Group, Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore S138673; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
| | - Olav Engebraaten
- The K.G. Jebsen Center for Breast Cancer Research, Faculty of Medicine, Institute for Clinical Medicine, University of Oslo, 0450 Oslo, Norway; Department of Oncology, Oslo University Hospital, 0424 Oslo, Norway
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radiumhospital, 0310 Oslo, Norway; The K.G. Jebsen Center for Breast Cancer Research, Faculty of Medicine, Institute for Clinical Medicine, University of Oslo, 0450 Oslo, Norway
| | - Paul M Neilsen
- Swinburne University of Technology, Kuching 93350, Sarawak, Malaysia
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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Sung H, Yang HH, Zhang H, Yang Q, Hu N, Tang ZZ, Su H, Wang L, Wang C, Ding T, Fan JH, Qiao YL, Wheeler W, Giffen C, Burdett L, Wang Z, Lee MP, Chanock SJ, Dawsey SM, Freedman ND, Abnet CC, Goldstein AM, Yu K, Taylor PR, Hyland PL. Common genetic variants in epigenetic machinery genes and risk of upper gastrointestinal cancers. Int J Epidemiol 2015; 44:1341-52. [PMID: 25921222 DOI: 10.1093/ije/dyv050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Populations in north central China are at high risk for oesophageal squamous cell carcinoma (ESCC) and gastric cancer (GC), and genetic variation in epigenetic machinery genes and pathways may contribute to this risk. METHODS We used the adaptive multilocus joint test to analyse 192 epigenetic genes involved in chromatin remodelling, DNA methylation and microRNA biosynthesis in 1942 ESCC and 1758 GC cases [1126 cardia (GCA) and 632 non-cardia adenocarcinoma (GNCA)] and 2111 controls with Chinese ancestry. We examined potential function of risk alleles using in silico and expression quantitative trait loci (eQTLs) analyses. RESULTS Suggestive pathway-based associations were observed for the overall epigenetic (P-value(PATH) = 0.034) and chromatin remodelling (P-value(PATH) = 0.039) pathways with risk of GCA, but not GC, GNCA or ESCC. Overall, 37 different epigenetic machinery genes were associated with risk of one or more upper gastrointestinal (UGI) cancer sites (P-value(GENE )< 0.05), including 14 chromatin remodelling genes whose products are involved in the regulation of HOX genes. We identified a gastric eQTL (rs12724079; rho = 0.37; P = 0.0006) which regulates mRNA expression of ASH1L. Several suggestive eQTLs were also found in oesophageal (rs10898459 in EED), gastric cardia (rs7157322 in DICER1; rs8179271 in ASH1L), and gastric non-cardia (rs1790733 in PPP1CA) tissues. CONCLUSIONS Results of our analyses provide limited but suggestive evidence for a role of epigenetic gene variation in the aetiology of UGI cancer.
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Affiliation(s)
- Hyuna Sung
- Division of Cancer Epidemiology and Genetics, and
| | - Howard H Yang
- Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Han Zhang
- Division of Cancer Epidemiology and Genetics, and
| | - Qi Yang
- Division of Cancer Epidemiology and Genetics, and
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, and
| | - Ze-Zhong Tang
- Shanxi Cancer Hospital, Taiyuan, People's Republic of China
| | - Hua Su
- Division of Cancer Epidemiology and Genetics, and
| | - Lemin Wang
- Division of Cancer Epidemiology and Genetics, and
| | - Chaoyu Wang
- Division of Cancer Epidemiology and Genetics, and
| | - Ti Ding
- Shanxi Cancer Hospital, Taiyuan, People's Republic of China
| | - Jin-Hu Fan
- Department of Epidemiology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - You-Lin Qiao
- Department of Epidemiology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | | | - Carol Giffen
- Information Management Services, Silver Spring, MD, USA and
| | - Laurie Burdett
- Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, and Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | - Maxwell P Lee
- Laboratory of Population Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | - Kai Yu
- Division of Cancer Epidemiology and Genetics, and
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Thompson KW, Marquez SB, Lu L, Reisman D. Induction of functional Brm protein from Brm knockout mice. Oncoscience 2015; 2:349-61. [PMID: 26097869 PMCID: PMC4468321 DOI: 10.18632/oncoscience.153] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 04/08/2015] [Indexed: 12/18/2022] Open
Abstract
Once the knockout of the Brm gene was found to be nontumorigenic in mice, the study of BRM's involvement in cancer seemed less important compared with that of its homolog, Brg1. This has likely contributed to the disparity that has been observed in the publication ratio between BRG1 and BRM. We show that a previously published Brm knockout mouse is an incomplete knockout whereby a truncated isoform of Brm is detected in normal tissue and in tumors. We show that this truncated Brm isoform has functionality comparable to wild type Brm. By immunohistochemistry (IHC), this truncated Brm is undetectable in normal lung tissue and is minimal to very low in Brmnull tumors. However, it is significant in a subset (~40%) of Brg1/Brm double knockout (DKO) tumors that robustly express this truncated BRM, which in part stems from an increase in Brm mRNA levels. Thus, it is likely that this mutant mouse model does not accurately reflect the role that Brm plays in cancer development. We suggest that the construction of a completely new mouse Brm knockout, where Brm is functionally absent, is needed to determine whether or not Brm is actually tumorigenic and if Brm might be a tumor suppressor.
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Affiliation(s)
- Kenneth W. Thompson
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Stefanie B. Marquez
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Li Lu
- Department of Pathology, University of Florida, Gainesville, Florida, USA
| | - David Reisman
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, Florida, USA
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45
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Alajem A, Biran A, Harikumar A, Sailaja BS, Aaronson Y, Livyatan I, Nissim-Rafinia M, Sommer AG, Mostoslavsky G, Gerbasi VR, Golden DE, Datta A, Sze SK, Meshorer E. Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation. Cell Rep 2015; 10:2019-31. [PMID: 25818293 DOI: 10.1016/j.celrep.2015.02.064] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 01/09/2015] [Accepted: 02/25/2015] [Indexed: 11/19/2022] Open
Abstract
Embryonic stem cells (ESCs) possess a distinct chromatin conformation maintained by specialized chromatin proteins. To identify chromatin regulators in ESCs, we developed a simple biochemical assay named D-CAP (differential chromatin-associated proteins), using brief micrococcal nuclease digestion of chromatin, followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Using D-CAP, we identified several differentially chromatin-associated proteins between undifferentiated and differentiated ESCs, including the chromatin remodeling protein SMARCD1. SMARCD1 depletion in ESCs led to altered chromatin and enhanced endodermal differentiation. Gene expression and chromatin immunoprecipitation sequencing (ChIP-seq) analyses suggested that SMARCD1 is both an activator and a repressor and is enriched at developmental regulators and that its chromatin binding coincides with H3K27me3. SMARCD1 knockdown caused H3K27me3 redistribution and increased H3K4me3 around the transcription start site (TSS). One of the identified SMARCD1 targets was Klf4. In SMARCD1-knockdown clones, KLF4, as well as H3K4me3 at the Klf4 locus, remained high and H3K27me3 was abolished. These results propose a role for SMARCD1 in restricting pluripotency and activating lineage pathways by regulating H3K27 methylation.
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Affiliation(s)
- Adi Alajem
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alva Biran
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Arigela Harikumar
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Badi Sri Sailaja
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yair Aaronson
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ilana Livyatan
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Malka Nissim-Rafinia
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Andreia Gianotti Sommer
- Section of Gastroenterology, Department of Medicine, Center for Regenerative Medicine (CReM), Boston University School of Medicine, 670 Albany Street, Suite 209, Boston, MA 02118, USA
| | - Gustavo Mostoslavsky
- Section of Gastroenterology, Department of Medicine, Center for Regenerative Medicine (CReM), Boston University School of Medicine, 670 Albany Street, Suite 209, Boston, MA 02118, USA
| | - Vincent R Gerbasi
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA; Naval Medical Research Center, Silver Spring, MD 20910, USA
| | | | - Arnab Datta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Eran Meshorer
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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46
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Shen J, Xiao Z, Wu WKK, Wang MH, To KF, Chen Y, Yang W, Li MSM, Shin VY, Tong JH, Kang W, Zhang L, Li M, Wang L, Lu L, Chan RLY, Wong SH, Yu J, Chan MTV, Chan FKL, Sung JJY, Cheng ASL, Cho CH. Epigenetic silencing of miR-490-3p reactivates the chromatin remodeler SMARCD1 to promote Helicobacter pylori-induced gastric carcinogenesis. Cancer Res 2014; 75:754-65. [PMID: 25503559 DOI: 10.1158/0008-5472.can-14-1301] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chromatin remodeling has emerged as a hallmark of gastric cancer, but the regulation of chromatin regulators other than genetic change is unknown. Helicobacter pylori causes epigenetic dysregulation to promote gastric carcinogenesis, but the roles and functions of microRNAs (miRNA) in this multistage cascade are not fully explored. In this study, miRNA expression in preneoplastic and neoplastic lesions in murine stomachs induced by H. pylori and N-methyl-N-nitrosourea (MNU) was profiled by miRNA expression array. miR-490-3p exhibited progressive downregulation in gastritis, intestinal metaplasia, and adenocarcinoma during H. pylori and MNU-induced gastric carcinogenesis. Significant downregulation of miR-490-3p was confirmed in human gastric cancer tissues in which its regulatory region was found to be hypermethylated. miR-490-3p exerted growth- and metastasis-suppressive effects on gastric cancer cells through directly targeting SMARCD1, a SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling complex subunit. Knockdown of SMARCD1 significantly attenuated the protumorigenic effects of miR-490-3p inhibitor, whereas enforced expression of SMARCD1 promoted in vitro and in vivo oncogenic phenotypes of gastric cancer cells. SMARCD1 was markedly upregulated in gastric cancer in which its high expression was associated with shortened patients' survival independent of TNM staging. In conclusion, hypermethylation-mediated silencing of miR-490-3p reactivates SMARCD1 to confer malignant phenotypes, mechanistically linking H. pylori, chromatin remodeling, and gastric carcinogenesis.
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Affiliation(s)
- Jing Shen
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong. Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong
| | - Zhangang Xiao
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - William K K Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong. Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong. CUHK Shenzhen Research Institute, Shenzhen, China.
| | - Maggie H Wang
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong
| | - Ka F To
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong. Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong
| | - Yangchao Chen
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong. Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong
| | - Weiqin Yang
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong. Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - May S M Li
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Vivian Y Shin
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong
| | - Joanna H Tong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong
| | - Wei Kang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong
| | - Lin Zhang
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong. Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Minxing Li
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Lin Wang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Lan Lu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Ruby L Y Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Sunny H Wong
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong. Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Jun Yu
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong. Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong. CUHK Shenzhen Research Institute, Shenzhen, China
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong
| | - Francis K L Chan
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong. Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Joseph J Y Sung
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong. Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Alfred S L Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong. Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong.
| | - Chi H Cho
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong. Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong
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Zhang L, Nemzow L, Chen H, Hu JJ, Gong F. Whole genome expression profiling shows that BRG1 transcriptionally regulates UV inducible genes and other novel targets in human cells. PLoS One 2014; 9:e105764. [PMID: 25157878 PMCID: PMC4144907 DOI: 10.1371/journal.pone.0105764] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/19/2014] [Indexed: 12/16/2022] Open
Abstract
UV irradiation is known to cause cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6–4) pyrimidone photoproducts (6-4PPs), and plays a large role in the development of cancer. Tumor suppression, through DNA repair and proper cell cycle regulation, is an integral factor in maintaining healthy cells and preventing development of cancer. Transcriptional regulation of the genes involved in the various tumor suppression pathways is essential for them to be expressed when needed and to function properly. BRG1, an ATPase catalytic subunit of the SWI/SNF chromatin remodeling complex, has been identified as a tumor suppressor protein, as it has been shown to play a role in Nucleotide Excision Repair (NER) of CPDs, suppress apoptosis, and restore checkpoint deficiency, in response to UV exposure. Although BRG1 has been shown to regulate transcription of some genes that are instrumental in proper DNA damage repair and cell cycle maintenance in response to UV, its role in transcriptional regulation of the whole genome in response to UV has not yet been elucidated. With whole genome expression profiling in SW13 cells, we show that upon UV induction, BRG1 regulates transcriptional expression of many genes involved in cell stress response. Additionally, our results also highlight BRG1's general role as a master regulator of the genome, as it transcriptionally regulates approximately 4.8% of the human genome, including expression of genes involved in many pathways. RT-PCR and ChIP were used to validate our genome expression analysis. Importantly, our study identifies several novel transcriptional targets of BRG1, such as ATF3. Thus, BRG1 has a larger impact on human genome expression than previously thought, and our studies will provide inroads for future analysis of BRG1's role in gene regulation.
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Affiliation(s)
- Ling Zhang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Leah Nemzow
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Hua Chen
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Jennifer J. Hu
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Feng Gong
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- * E-mail:
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48
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Zhao J, Liu C, Zhao Z. ARID1A: a potential prognostic factor for breast cancer. Tumour Biol 2014; 35:4813-9. [PMID: 24430365 DOI: 10.1007/s13277-014-1632-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/06/2014] [Indexed: 11/24/2022] Open
Abstract
The aim of this study is to explore the expression of BAF250a protein in breast cancer and its association with the clinical and pathological characteristics and prognosis of breast cancer. The expression status of BAF250a protein was detected by Western blot analysis and immunohistochemical staining. The relationship between BAF250a proteins and clinicopathological parameters in 496 breast cancer specimens was analyzed. Western blot analysis showed that BAF250a protein had a lower expression in breast cancer specimens than in matched normal breast tissue (104.38 ± 11.65 vs. 55.94 ± 10.27; P = 0.004, t test). Among the 496 enrolled breast cancer patients, BAF250a protein expression was absent in 324 (65.3 %). Universal and multiple analyses indicated that BAF250a protein expression loss was significantly related to histological grade, metastatic nodes, tumor node metastasis (TNM) stage, and the expression of estrogen receptor (ER), progesterone receptor (PR), c-erbB-2, and p53 (all P < 0.05). For TNM stage, rank correlation coefficients were 0.199 and 0.191, respectively, (P < 0.05), but BAF250a protein deletion had either a positive or a negative correlation with ER, PR, c-erbB-2, and p53 protein expression (correlation coefficients were 0.231, 0.207, -0.098, -0.128; P < 0.05). Analysis of survival rates showed that the patients with BAF250a protein expression attained a significantly better postoperative disease-specific survival than those with BAF250a protein deletion (88.4 vs. 79.0%; P = 0.003). In the Cox regression test, BAF250a protein deletion was detected as an independent prognostic factor (P = 0.014). BAF250a protein might be a new potential target for breast cancer treatment.
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Affiliation(s)
- Jing Zhao
- Gastrointestinal Tumor Pathology Laboratory of Cancer Institute, the First Hospital of China Medical University, Shenyang, China, 110001
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49
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Kwon SJ, Park JH, Park EJ, Lee SA, Lee HS, Kang SW, Kwon J. ATM-mediated phosphorylation of the chromatin remodeling enzyme BRG1 modulates DNA double-strand break repair. Oncogene 2014; 34:303-13. [PMID: 24413084 DOI: 10.1038/onc.2013.556] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 11/15/2013] [Accepted: 11/18/2013] [Indexed: 12/25/2022]
Abstract
ATP-dependent chromatin remodeling complexes such as SWI/SNF (SWItch/Sucrose NonFermentable) have been implicated in DNA double-strand break (DSB) repair and damage responses. However, the regulatory mechanisms that control the function of chromatin remodelers in DNA damage response are largely unknown. Here, we show that ataxia telangiectasia mutated (ATM) mediates the phosphorylation of BRG1, the catalytic ATPase of the SWI/SNF complex that contributes to DSB repair by binding γ-H2AX-containing nucleosomes via interaction with acetylated histone H3 and stimulating γ-H2AX formation, at Ser-721 in response to DNA damage. ATM-mediated phosphorylation of BRG1 occurs rapidly and transiently after DNA damage. Phosphorylated BRG1 binds γ-H2AX-containing nucleosomes to form the repair foci. The Ser-721 phosphorylation of BRG1 is critical for binding γ-H2AX-containing nucleosomes and stimulating γ-H2AX formation and DSB repair. BRG1 binds to acetylated H3 peptides much better after phosphorylation at Ser-721 by DNA damage. However, the phosphorylation of Ser-721 does not significantly affect the ATPase and transcriptional activities of BRG1. These results, establishing BRG1 as a novel and functional ATM substrate, suggest that the ATM-mediated phosphorylation of BRG1 facilitates DSB repair by stimulating the association of this remodeler with γ-H2AX nucleosomes via enhancing the affinity to acetylated H3. Our work also suggests that the mechanism of BRG1 stimulation of DNA repair is independent of the remodeler's enzymatic or transcriptional activities.
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Affiliation(s)
- S-J Kwon
- Department of Life Science, College of Natural Sciences, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of Korea
| | - J-H Park
- Department of Life Science, College of Natural Sciences, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of Korea
| | - E-J Park
- Department of Life Science, College of Natural Sciences, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of Korea
| | - S-A Lee
- Department of Life Science, College of Natural Sciences, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of Korea
| | - H-S Lee
- Department of Life Science, College of Natural Sciences, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of Korea
| | - S W Kang
- Department of Life Science, College of Natural Sciences, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of Korea
| | - J Kwon
- Department of Life Science, College of Natural Sciences, The Research Center for Cellular Homeostasis, Ewha Womans University, Seoul, Republic of Korea
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50
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Streppel MM, Pai S, Campbell NR, Hu C, Yabuuchi S, Canto MI, Wang JS, Montgomery EA, Maitra A. MicroRNA 223 is upregulated in the multistep progression of Barrett's esophagus and modulates sensitivity to chemotherapy by targeting PARP1. Clin Cancer Res 2013; 19:4067-78. [PMID: 23757351 DOI: 10.1158/1078-0432.ccr-13-0601] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PURPOSE Recent microarray and RNA-sequencing studies have uncovered aberrantly expressed microRNAs (miRNA) in Barrett's esophagus-associated esophageal adenocarcinoma. The functional significance of these miRNAs in esophageal adenocarcinoma initiation and progression is largely unknown. EXPERIMENTAL DESIGN Expression levels of miR-199a/b-3p, -199a-5p, -199b-5p, -200b, -200c, -223, and -375 were determined in microdissected tissues from cardiac mucosa, Barrett's esophagus, dysplastic Barrett's esophagus, and esophageal adenocarcinoma using quantitative real-time PCR. miR-223 expression was validated in precursors and esophageal adenocarcinomas from 95 patients with esophageal adenocarcinoma by in situ hybridization (ISH). miR-223 was transfected into two esophageal adenocarcinoma cell lines, and in vitro assays were conducted. Target genes were identified using Illumina microarray, and results were validated in cell lines and human specimens. RESULTS miR-199 family members and miR-223 were significantly overexpressed in esophageal adenocarcinoma, however, only miR-223 showed a stepwise increase during esophageal adenocarcinoma carcinogenesis. A similar trend was observed by ISH, which additionally showed that miR-223 is exclusively expressed by the epithelial compartment. miR-223-overexpressing cells had statistically significantly more migratory and invasive potential than scramble sequence-transfected cells. PARP1 was identified as a direct target gene of miR-223 in esophageal adenocarcinoma cells. Increased sensitivity to chemotherapy was observed in cells with enforced miR-223 expression and reduced PARP1. CONCLUSIONS miR-223 is significantly upregulated during the Barrett's esophagus-dysplasia-esophageal adenocarcinoma sequence. Although high miR-223 levels might contribute to an aggressive phenotype, our results also suggest that patients with esophageal adenocarcinoma with high miR-223 levels might benefit from treatment with DNA-damaging agents.
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Affiliation(s)
- Mirte Mayke Streppel
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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