1
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Bakr A, Corte GD, Veselinov O, Kelekçi S, Chen MJM, Lin YY, Sigismondo G, Iacovone M, Cross A, Syed R, Jeong Y, Sollier E, Liu CS, Lutsik P, Krijgsveld J, Weichenhan D, Plass C, Popanda O, Schmezer P. ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response. Nucleic Acids Res 2024; 52:5698-5719. [PMID: 38587186 PMCID: PMC11162808 DOI: 10.1093/nar/gkae233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/27/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024] Open
Abstract
AT-rich interaction domain protein 1A (ARID1A), a SWI/SNF chromatin remodeling complex subunit, is frequently mutated across various cancer entities. Loss of ARID1A leads to DNA repair defects. Here, we show that ARID1A plays epigenetic roles to promote both DNA double-strand breaks (DSBs) repair pathways, non-homologous end-joining (NHEJ) and homologous recombination (HR). ARID1A is accumulated at DSBs after DNA damage and regulates chromatin loops formation by recruiting RAD21 and CTCF to DSBs. Simultaneously, ARID1A facilitates transcription silencing at DSBs in transcriptionally active chromatin by recruiting HDAC1 and RSF1 to control the distribution of activating histone marks, chromatin accessibility, and eviction of RNAPII. ARID1A depletion resulted in enhanced accumulation of micronuclei, activation of cGAS-STING pathway, and an increased expression of immunomodulatory cytokines upon ionizing radiation. Furthermore, low ARID1A expression in cancer patients receiving radiotherapy was associated with higher infiltration of several immune cells. The high mutation rate of ARID1A in various cancer types highlights its clinical relevance as a promising biomarker that correlates with the level of immune regulatory cytokines and estimates the levels of tumor-infiltrating immune cells, which can predict the response to the combination of radio- and immunotherapy.
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Affiliation(s)
- Ali Bakr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Giuditta Della Corte
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Olivera Veselinov
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Simge Kelekçi
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Mei-Ju May Chen
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Yu-Yu Lin
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), INF581, 69120 Heidelberg, Germany
| | - Marika Iacovone
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Alice Cross
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Rabail Syed
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Yunhee Jeong
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Etienne Sollier
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Chun- Shan Liu
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), INF581, 69120 Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), INF280, 69120 Heidelberg, Germany
| | - Odilia Popanda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
| | - Peter Schmezer
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), INF280, 69120 Heidelberg, Germany
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2
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Wu Z, Jiang S, Chen Y. Non-coding RNA and Drug resistance in cholangiocarcinoma. Noncoding RNA Res 2024; 9:194-202. [PMID: 38125756 PMCID: PMC10730441 DOI: 10.1016/j.ncrna.2023.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/23/2023] Open
Abstract
Cholangiocarcinoma is a highly aggressive cancer with a dismal prognosis and limited resectability. Chemotherapy has demonstrated tremendous benefits for patients with advanced and inoperable cancer, but drug resistance poses a significant obstacle. Despite recent progress in cancer therapy, the mechanisms driving drug resistance are multifaceted and not completely comprehended. Non-coding RNA refers to RNA molecules that are endogenous and do not code for proteins. Particularly microRNAs, long non-coding RNAs, circular RNAs, are widely acknowledged to be involved in cancer initiation, proliferation, and metastasis. Recently, evidences suggests that abnormal expression of non-coding RNAs contributes to resistance to different type of cancer therapies in cholangiocarcinoma. This occurs via the rewiring of signaling pathways including the reduction of anticancer drugs, apoptosis, interaction between cholangiocarcinoma and tumor-infiltrating immune cells, and cancer stemness. Thus, our review aims to demonstrate the potential of targeting non-coding RNA to override drug resistance and summarize the molecular mechanisms of how non-coding RNA contributes to drug resistance in cholangiocarcinoma.
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Affiliation(s)
- Zhaowei Wu
- Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Medical College Street, Yuzhong District, 404100, Chongqing, China
| | - Shiming Jiang
- Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Medical College Street, Yuzhong District, 404100, Chongqing, China
| | - Yong Chen
- Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Medical College Street, Yuzhong District, 404100, Chongqing, China
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3
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Picketts D, Mirzaa G, Yan K, Relator R, Timpano S, Yalcin B, Collins S, Ziegler A, Pao E, Oyama N, Brischoux-Boucher E, Piard J, Monaghan K, Sacoto MG, Dobyns W, Park K, Fernández-Mayoralas D, Fernández-Jaén A, Jayakar P, Brusco A, Antona V, Giorgio E, Kvarnung M, Isidor B, Conrad S, Cogné B, Deb W, Stuurman KE, Sterbova K, Smal N, Weckhuysen S, Oegema R, Innes M, Latsko M, Ben-Omran T, Yeh R, Kruer M, Bakhtiari S, Papavasiliou A, Moutton S, Nambot S, Chanprasert S, Paolucci S, Miller K, Burton B, Kim K, O'Heir E, Bruwer Z, Donald K, Kleefstra T, Goldstein A, Angle B, Bontempo K, Miny P, Joset P, Demurger F, Hobson E, Pang L, Carpenter L, Li D, Bonneau D, Sadikovic B. Pathogenic variants in SMARCA1 cause an X-linked neurodevelopmental disorder modulated by NURF complex composition. RESEARCH SQUARE 2023:rs.3.rs-3317938. [PMID: 37841849 PMCID: PMC10571636 DOI: 10.21203/rs.3.rs-3317938/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Pathogenic variants in ATP-dependent chromatin remodeling proteins are a recurrent cause of neurodevelopmental disorders (NDDs). The NURF complex consists of BPTF and either the SNF2H (SMARCA5) or SNF2L (SMARCA1) ISWI-chromatin remodeling enzyme. Pathogenic variants in BPTF and SMARCA5 were previously implicated in NDDs. Here, we describe 40 individuals from 30 families with de novo or maternally inherited pathogenic variants in SMARCA1. This novel NDD was associated with mild to severe ID/DD, delayed or regressive speech development, and some recurrent facial dysmorphisms. Individuals carrying SMARCA1 loss-of-function variants exhibited a mild genome-wide DNA methylation profile and a high penetrance of macrocephaly. Genetic dissection of the NURF complex using Smarca1, Smarca5, and Bptfsingle and double mouse knockouts revealed the importance of NURF composition and dosage for proper forebrain development. Finally, we propose that genetic alterations affecting different NURF components result in a NDD with a broad clinical spectrum.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Emily Pao
- Seattle Children's Research Institute
| | | | | | | | | | | | | | - Kristen Park
- University of Colorado Denver School of Medicine
| | | | - Alberto Fernández-Jaén
- Department of Pediatrics and Neurology, Hospital Universitario Quirónsalud, School of Medicine, Universidad Europea de Madrid
| | - Parul Jayakar
- Division of Genetics and Metabolism, Nicklaus Children's Hospital
| | | | | | | | | | | | | | | | | | - K E Stuurman
- Department of Clinical Genetics, Erasmus University Medical Center
| | | | | | | | | | | | - Maeson Latsko
- The Steve and Cindy Rasmussen Institute for Genomic Medicine
| | | | | | | | | | | | | | - Sophie Nambot
- Centre de Génétique et Centre de référence «Anomalies du Développement et Syndromes Malformatifs», Hôpital d'Enfants, Centre Hospitalier
| | | | | | | | | | | | | | | | - Kirsten Donald
- Division of Developmental Paediatrics, Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Klipfontein Road/Private Bag, Rondebosch, 7700/7701, Cape Town, South A
| | | | | | | | | | | | | | | | | | | | | | - Dong Li
- The Children's Hospital of Philadelphia
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, University Hospital of Angers, F-49000
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4
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Tan Y, Wang Z, Xu M, Li B, Huang Z, Qin S, Nice EC, Tang J, Huang C. Oral squamous cell carcinomas: state of the field and emerging directions. Int J Oral Sci 2023; 15:44. [PMID: 37736748 PMCID: PMC10517027 DOI: 10.1038/s41368-023-00249-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/23/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) develops on the mucosal epithelium of the oral cavity. It accounts for approximately 90% of oral malignancies and impairs appearance, pronunciation, swallowing, and flavor perception. In 2020, 377,713 OSCC cases were reported globally. According to the Global Cancer Observatory (GCO), the incidence of OSCC will rise by approximately 40% by 2040, accompanied by a growth in mortality. Persistent exposure to various risk factors, including tobacco, alcohol, betel quid (BQ), and human papillomavirus (HPV), will lead to the development of oral potentially malignant disorders (OPMDs), which are oral mucosal lesions with an increased risk of developing into OSCC. Complex and multifactorial, the oncogenesis process involves genetic alteration, epigenetic modification, and a dysregulated tumor microenvironment. Although various therapeutic interventions, such as chemotherapy, radiation, immunotherapy, and nanomedicine, have been proposed to prevent or treat OSCC and OPMDs, understanding the mechanism of malignancies will facilitate the identification of therapeutic and prognostic factors, thereby improving the efficacy of treatment for OSCC patients. This review summarizes the mechanisms involved in OSCC. Moreover, the current therapeutic interventions and prognostic methods for OSCC and OPMDs are discussed to facilitate comprehension and provide several prospective outlooks for the fields.
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Affiliation(s)
- Yunhan Tan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
- West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhihan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Mengtong Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Bowen Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Siyuan Qin
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Jing Tang
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China.
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China.
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5
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Mao X, Wu J, Zhang Q, Zhang S, Chen X, Liu X, Wei M, Wan X, Qiu L, Zeng M, Lei X, Liu C, Han J. Requirement of WDR70 for POLE3-mediated DNA double-strand breaks repair. SCIENCE ADVANCES 2023; 9:eadh2358. [PMID: 37682991 PMCID: PMC10491287 DOI: 10.1126/sciadv.adh2358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
H2BK120ub1 triggers several prominent downstream histone modification pathways and changes in chromatin structure, therefore involving it into multiple critical cellular processes including DNA transcription and DNA damage repair. Although it has been reported that H2BK120ub1 is mediated by RNF20/40 and CRL4WDR70, less is known about the underlying regulation mechanism for H2BK120ub1 by WDR70. By using a series of biochemical and cell-based studies, we find that WDR70 promotes H2BK120ub1 by interacting with RNF20/40 complex, and deposition of H2BK120ub1 and H3K79me2 in POLE3 loci is highly sensitive to POLE3 transcription. Moreover, we demonstrate that POLE3 interacts CHRAC1 to promote DNA repair by regulation on the expression of homology-directed repair proteins and KU80 recruitment and identify CHRAC1 D121Y mutation in colorectal cancer, which leads to the defect in DNA repair due to attenuated the interaction with POLE3. These findings highlight a previously unknown role for WDR70 in maintenance of genomic stability and imply POLE3 and CHRAC1 as potential therapeutic targets in cancer.
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Affiliation(s)
- Xiaobing Mao
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jian Wu
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qin Zhang
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Su Zhang
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoshuang Chen
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xueqin Liu
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mingtian Wei
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaowen Wan
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lei Qiu
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ming Zeng
- Department of Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University hospital, Sichuan University, Chengdu 610041, China
| | - Xue Lei
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Cong Liu
- Department of Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University hospital, Sichuan University, Chengdu 610041, China
| | - Junhong Han
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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6
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Raja SJ, Van Houten B. UV-DDB as a General Sensor of DNA Damage in Chromatin: Multifaceted Approaches to Assess Its Direct Role in Base Excision Repair. Int J Mol Sci 2023; 24:10168. [PMID: 37373320 PMCID: PMC10298998 DOI: 10.3390/ijms241210168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Base excision repair (BER) is a cellular process that removes damaged bases arising from exogenous and endogenous sources including reactive oxygen species, alkylation agents, and ionizing radiation. BER is mediated by the actions of multiple proteins which work in a highly concerted manner to resolve DNA damage efficiently to prevent toxic repair intermediates. During the initiation of BER, the damaged base is removed by one of 11 mammalian DNA glycosylases, resulting in abasic sites. Many DNA glycosylases are product-inhibited by binding to the abasic site more avidly than the damaged base. Traditionally, apurinic/apyrimidinic endonuclease 1, APE1, was believed to help turn over the glycosylases to undergo multiple rounds of damaged base removal. However, in a series of papers from our laboratory, we have demonstrated that UV-damaged DNA binding protein (UV-DDB) stimulates the glycosylase activities of human 8-oxoguanine glycosylase (OGG1), MUTY DNA glycosylase (MUTYH), alkyladenine glycosylase/N-methylpurine DNA glycosylase (AAG/MPG), and single-strand selective monofunctional glycosylase (SMUG1), between three- and five-fold. Moreover, we have shown that UV-DDB can assist chromatin decompaction, facilitating access of OGG1 to 8-oxoguanine damage in telomeres. This review summarizes the biochemistry, single-molecule, and cell biology approaches that our group used to directly demonstrate the essential role of UV-DDB in BER.
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Affiliation(s)
- Sripriya J. Raja
- Molecular Pharmacology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA;
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Bennett Van Houten
- Molecular Pharmacology Graduate Program, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA;
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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7
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Bure IV, Nemtsova MV. Mutual Regulation of ncRNAs and Chromatin Remodeling Complexes in Normal and Pathological Conditions. Int J Mol Sci 2023; 24:ijms24097848. [PMID: 37175555 PMCID: PMC10178202 DOI: 10.3390/ijms24097848] [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: 03/23/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Chromatin remodeling is the one of the main epigenetic mechanisms of gene expression regulation both in normal cells and in pathological conditions. In recent years, a growing number of investigations have confirmed that epigenetic regulators are tightly connected and form a comprehensive network of regulatory pathways and feedback loops. Genes encoding protein subunits of chromatin remodeling complexes are often mutated and change their expression in diseases, as well as non-coding RNAs (ncRNAs). Moreover, different mechanisms of their mutual regulation have already been described. Further understanding of these processes may help apply their clinical potential for establishment of the diagnosis, prognosis, and treatment of the diseases. The therapeutic targeting of the chromatin structure has many limitations because of the complexity of its regulation, with the involvement of a large number of genes, proteins, non-coding transcripts, and other intermediary molecules. However, several successful strategies have been proposed to target subunits of chromatin remodeling complexes and genes encoding them, as well as the ncRNAs that regulate the operation of these complexes and direct them to the target gene regions. In our review, we focus on chromatin remodeling complexes and ncRNAs, their mutual regulation, role in cellular processes and potential clinical application.
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Affiliation(s)
- Irina V Bure
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Marina V Nemtsova
- Laboratory of Medical Genetics, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115522 Moscow, Russia
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8
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Wei J, Li M, Xue C, Chen S, Zheng L, Deng H, Tang F, Li G, Xiong W, Zeng Z, Zhou M. Understanding the roles and regulation patterns of circRNA on its host gene in tumorigenesis and tumor progression. J Exp Clin Cancer Res 2023; 42:86. [PMID: 37060016 PMCID: PMC10105446 DOI: 10.1186/s13046-023-02657-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/29/2023] [Indexed: 04/16/2023] Open
Abstract
Circular RNAs (circRNAs) are a novel type of endogenous non-coding RNAs, which are covalently closed loop structures formed by precursor mRNAs (pre-mRNAs) through back-splicing. CircRNAs are abnormally expressed in many tumors, and play critical roles in a variety of tumors as oncogenes or tumor suppressor genes by sponging miRNAs, regulating alternative splicing and transcription, cis-regulating host genes, interacting with RNA binding proteins (RBPs) or encoding polypeptides. Among them, the regulation of circRNAs on their corresponding host genes is a critical way for circRNAs to exit their functions. Accumulating evidence suggests that circRNAs are able to regulate the expression of host genes at the transcriptional level, post-transcriptional level, translational level, post-translational level, or by encoding polypeptides. Therefore, this paper mainly summarized the roles and association of circRNAs and their corresponding host genes in tumorigenesis and tumor progression, generalized the circRNAs that function synergistically or antagonistically with their host genes, and elaborated the mechanisms of mutual regulation between circRNAs and their host genes. More importantly, this review provides specific references for revealing the potential application of circRNAs combined with their host genes in tumor diagnosis, treatment and prognosis.
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Affiliation(s)
- Jianxia Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Mengna Li
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Changning Xue
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Shipeng Chen
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Lemei Zheng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Hongyu Deng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
| | - Faqing Tang
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China
- Cancer Research Institute, Central South University, Changsha, 410078, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, China.
- Cancer Research Institute, Central South University, Changsha, 410078, China.
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, 410078, China.
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9
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Pan C, Ding Z, Dai J, Yang L, Wei Y, Wang X. CircSMARCA5
functions as a potential biomarker for clinicopathology and therapy in solid tumors: A systematic review and meta‐analysis. PRECISION MEDICAL SCIENCES 2023. [DOI: 10.1002/prm2.12100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
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10
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D'Incal CP, Van Rossem KE, De Man K, Konings A, Van Dijck A, Rizzuti L, Vitriolo A, Testa G, Gozes I, Vanden Berghe W, Kooy RF. Chromatin remodeler Activity-Dependent Neuroprotective Protein (ADNP) contributes to syndromic autism. Clin Epigenetics 2023; 15:45. [PMID: 36945042 PMCID: PMC10031977 DOI: 10.1186/s13148-023-01450-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/16/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Individuals affected with autism often suffer additional co-morbidities such as intellectual disability. The genes contributing to autism cluster on a relatively limited number of cellular pathways, including chromatin remodeling. However, limited information is available on how mutations in single genes can result in such pleiotropic clinical features in affected individuals. In this review, we summarize available information on one of the most frequently mutated genes in syndromic autism the Activity-Dependent Neuroprotective Protein (ADNP). RESULTS Heterozygous and predicted loss-of-function ADNP mutations in individuals inevitably result in the clinical presentation with the Helsmoortel-Van der Aa syndrome, a frequent form of syndromic autism. ADNP, a zinc finger DNA-binding protein has a role in chromatin remodeling: The protein is associated with the pericentromeric protein HP1, the SWI/SNF core complex protein BRG1, and other members of this chromatin remodeling complex and, in murine stem cells, with the chromodomain helicase CHD4 in a ChAHP complex. ADNP has recently been shown to possess R-loop processing activity. In addition, many additional functions, for instance, in association with cytoskeletal proteins have been linked to ADNP. CONCLUSIONS We here present an integrated evaluation of all current aspects of gene function and evaluate how abnormalities in chromatin remodeling might relate to the pleiotropic clinical presentation in individual"s" with Helsmoortel-Van der Aa syndrome.
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Affiliation(s)
- Claudio Peter D'Incal
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Kirsten Esther Van Rossem
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
| | - Kevin De Man
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Anthony Konings
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium
| | - Ludovico Rizzuti
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Alessandro Vitriolo
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Giuseppe Testa
- High Definition Disease Modelling Lab, Stem Cell and Organoid Epigenetics, IEO, European Institute of Oncology, IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Human Technopole, V. Le Rita Levi-Montalcini, 1, 20157, Milan, Italy
| | - Illana Gozes
- Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, Sackler School of Medicine, 727, 69978, Tel Aviv, Israel
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling Lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium.
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Belgium.
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11
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Jiang D, Li T, Guo C, Tang TS, Liu H. Small molecule modulators of chromatin remodeling: from neurodevelopment to neurodegeneration. Cell Biosci 2023; 13:10. [PMID: 36647159 PMCID: PMC9841685 DOI: 10.1186/s13578-023-00953-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
The dynamic changes in chromatin conformation alter the organization and structure of the genome and further regulate gene transcription. Basically, the chromatin structure is controlled by reversible, enzyme-catalyzed covalent modifications to chromatin components and by noncovalent ATP-dependent modifications via chromatin remodeling complexes, including switch/sucrose nonfermentable (SWI/SNF), inositol-requiring 80 (INO80), imitation switch (ISWI) and chromodomain-helicase DNA-binding protein (CHD) complexes. Recent studies have shown that chromatin remodeling is essential in different stages of postnatal and adult neurogenesis. Chromatin deregulation, which leads to defects in epigenetic gene regulation and further pathological gene expression programs, often causes a wide range of pathologies. This review first gives an overview of the regulatory mechanisms of chromatin remodeling. We then focus mainly on discussing the physiological functions of chromatin remodeling, particularly histone and DNA modifications and the four classes of ATP-dependent chromatin-remodeling enzymes, in the central and peripheral nervous systems under healthy and pathological conditions, that is, in neurodegenerative disorders. Finally, we provide an update on the development of potent and selective small molecule modulators targeting various chromatin-modifying proteins commonly associated with neurodegenerative diseases and their potential clinical applications.
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Affiliation(s)
- Dongfang Jiang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingting Li
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Caixia Guo
- grid.9227.e0000000119573309Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Tie-Shan Tang
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongmei Liu
- grid.458458.00000 0004 1792 6416State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
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12
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Czerwinska P, Mackiewicz AA. Bromodomain (BrD) Family Members as Regulators of Cancer Stemness-A Comprehensive Review. Int J Mol Sci 2023; 24:995. [PMID: 36674511 PMCID: PMC9861003 DOI: 10.3390/ijms24020995] [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: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Epigenetic mechanisms involving DNA methylation and chromatin modifications have emerged as critical facilitators of cancer heterogeneity, substantially affecting cancer development and progression, modulating cell phenotypes, and enhancing or inhibiting cancer cell malignant properties. Not surprisingly, considering the importance of epigenetic regulators in normal stem cell maintenance, many chromatin-related proteins are essential to maintaining the cancer stem cell (CSC)-like state. With increased tumor-initiating capacities and self-renewal potential, CSCs promote tumor growth, provide therapy resistance, spread tumors, and facilitate tumor relapse after treatment. In this review, we characterized the epigenetic mechanisms that regulate the acquisition and maintenance of cancer stemness concerning selected epigenetic factors belonging to the Bromodomain (BrD) family of proteins. An increasing number of BrD proteins reinforce cancer stemness, supporting the maintenance of the cancer stem cell population in vitro and in vivo via the utilization of distinct mechanisms. As bromodomain possesses high druggable potential, specific BrD proteins might become novel therapeutic targets in cancers exhibiting de-differentiated tumor characteristics.
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Affiliation(s)
- Patrycja Czerwinska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
| | - Andrzej Adam Mackiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
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13
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Prakash Yadav R, Leskinen S, Ma L, Mäkelä JA, Kotaja N. Chromatin remodelers HELLS, WDHD1 and BAZ1A are dynamically expressed during mouse spermatogenesis. Reproduction 2023; 165:49-63. [PMID: 36194437 PMCID: PMC9782464 DOI: 10.1530/rep-22-0240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022]
Abstract
In brief Proper regulation of heterochromatin is critical for spermatogenesis. This study reveals the dynamic localization patterns of distinct chromatin regulators during spermatogenesis and disrupted sex chromatin status in spermatocytes in the absence of DICER. Abstract Heterochromatin is dynamically formed and organized in differentiating male germ cells, and its proper regulation is a prerequisite for normal spermatogenesis. While heterochromatin is generally transcriptionally silent, we have previously shown that major satellite repeat (MSR) DNA in the pericentric heterochromatin (PCH) is transcribed during spermatogenesis. We have also shown that DICER associates with PCH and is involved in the regulation of MSR-derived transcripts. To shed light on the heterochromatin regulation in the male germline, we studied the expression, localization and heterochromatin association of selected testis-enriched chromatin regulators in the mouse testis. Our results show that HELLS, WDHD1 and BAZ1A are dynamically expressed during spermatogenesis. They display limited overlap in expression, suggesting involvement in distinct heterochromatin-associated processes at different steps of differentiation. We also show that HELLS and BAZ1A interact with DICER and MSR chromatin. Interestingly, deletion of Dicer1 affects the sex chromosome heterochromatin status in late pachytene spermatocytes, as demonstrated by mislocalization of Polycomb protein family member SCML1 to the sex body. These data substantiate the importance of dynamic heterochromatin regulation during spermatogenesis and emphasize the key role of DICER in the maintenance of chromatin status in meiotic male germ cells.
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Affiliation(s)
- Ram Prakash Yadav
- 1Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Sini Leskinen
- 1Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Lin Ma
- 1Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Juho-Antti Mäkelä
- 1Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Noora Kotaja
- 1Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
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14
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Fukuda Y, Akematsu T, Bando H, Kato K. Snf2 Proteins Are Required to Generate Gamete Pronuclei in Tetrahymena thermophila. Microorganisms 2022; 10:microorganisms10122426. [PMID: 36557679 PMCID: PMC9786623 DOI: 10.3390/microorganisms10122426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
During sexual reproduction/conjugation of the ciliate Tetrahymena thermophila, the germinal micronucleus undergoes meiosis resulting in four haploid micronuclei (hMICs). All hMICs undergo post-meiotic DNA double-strand break (PM-DSB) formation, cleaving their genome. DNA lesions are subsequently repaired in only one ‘selected’ hMIC, which eventually produces gametic pronuclei. DNA repair in the selected hMIC involves chromatin remodeling by switching from the heterochromatic to the euchromatic state of its genome. Here, we demonstrate that, among the 15 Tetrahymena Snf2 family proteins, a core of the ATP-dependent chromatin remodeling complex in Tetrahymena, the germline nucleus specific Iswi in Tetrahymena IswiGTt and Rad5Tt is crucial for the generation of gametic pronuclei. In either gene knockout, the selected hMIC which shows euchromatin markers such as lysine-acetylated histone H3 does not appear, but all hMICs in which markers for DNA lesions persist are degraded, indicating that both IswiGTt and Rad5Tt have important roles in repairing PM-DSB DNA lesions and remodeling chromatin for the euchromatic state in the selected hMIC.
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Affiliation(s)
- Yasuhiro Fukuda
- Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Miyagi, Japan
- Correspondence: ; Tel.: +81-229-84-7387
| | - Takahiko Akematsu
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo 156-8550, Japan
| | - Hironori Bando
- Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Miyagi, Japan
| | - Kentaro Kato
- Graduate School of Agricultural Science, Tohoku University, Osaki 989-6711, Miyagi, Japan
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15
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The Emerging Roles and Clinical Potential of circSMARCA5 in Cancer. Cells 2022; 11:cells11193074. [PMID: 36231036 PMCID: PMC9562909 DOI: 10.3390/cells11193074] [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: 08/06/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 12/24/2022] Open
Abstract
Circular RNAs (circRNAs) are a type of endogenous non-coding RNA and a critical epigenetic regulation way that have a closed-loop structure and are highly stable, conserved, and tissue-specific, and they play an important role in the development of many diseases, including tumors, neurological diseases, and cardiovascular diseases. CircSMARCA5 is a circRNA formed by its parental gene SMARCA5 via back splicing which is dysregulated in expression in a variety of tumors and is involved in tumor development with dual functions as an oncogene or tumor suppressor. It not only serves as a competing endogenous RNA (ceRNA) by binding to various miRNAs, but it also interacts with RNA binding protein (RBP), regulating downstream gene expression; it also aids in DNA damage repair by regulating the transcription and expression of its parental gene. This review systematically summarized the expression and characteristics, dual biological functions, and molecular regulatory mechanisms of circSMARCA5 involved in carcinogenesis and tumor progression as well as the potential applications in early diagnosis and gene targeting therapy in tumors.
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16
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Corcoran ET, LeBlanc C, Huang YC, Arias Tsang M, Sarkiss A, Hu Y, Pedmale UV, Jacob Y. Systematic histone H4 replacement in Arabidopsis thaliana reveals a role for H4R17 in regulating flowering time. THE PLANT CELL 2022; 34:3611-3631. [PMID: 35879829 PMCID: PMC9516085 DOI: 10.1093/plcell/koac211] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 07/15/2022] [Indexed: 06/13/2023]
Abstract
Despite the broad array of roles for epigenetic mechanisms on regulating diverse processes in eukaryotes, no experimental system is currently available in plants for the direct assessment of histone function. In this work, we present the development of a genetic strategy in Arabidopsis (Arabidopsis thaliana) whereby modified histone H4 transgenes can completely replace the expression of endogenous histone H4 genes. Accordingly, we established a collection of plants expressing different H4 point mutants targeting residues that may be post-translationally modified in vivo. To demonstrate its utility, we screened this new H4 mutant collection to uncover substitutions in H4 that alter flowering time. We identified different mutations in the H4 tail (H4R17A) and the H4 globular domain (H4R36A, H4R39K, H4R39A, and H4K44A) that strongly accelerate the floral transition. Furthermore, we identified a conserved regulatory relationship between H4R17 and the ISWI chromatin remodeling complex in plants: As with other biological systems, H4R17 regulates nucleosome spacing via ISWI. Overall, this work provides a large set of H4 mutants to the plant epigenetics community that can be used to systematically assess histone H4 function in Arabidopsis and a roadmap to replicate this strategy for studying other histone proteins in plants.
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Affiliation(s)
- Emma Tung Corcoran
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Chantal LeBlanc
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Yi-Chun Huang
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Mia Arias Tsang
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Anthony Sarkiss
- Faculty of Arts and Sciences, Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Yuzhao Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ullas V Pedmale
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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17
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Tulsyan S, Aftab M, Sisodiya S, Khan A, Chikara A, Tanwar P, Hussain S. Molecular basis of epigenetic regulation in cancer diagnosis and treatment. Front Genet 2022; 13:885635. [PMID: 36092905 PMCID: PMC9449878 DOI: 10.3389/fgene.2022.885635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023] Open
Abstract
The global cancer cases and mortality rates are increasing and demand efficient biomarkers for accurate screening, detection, diagnosis, and prognosis. Recent studies have demonstrated that variations in epigenetic mechanisms like aberrant promoter methylation, altered histone modification and mutations in ATP-dependent chromatin remodelling complexes play an important role in the development of carcinogenic events. However, the influence of other epigenetic alterations in various cancers was confirmed with evolving research and the emergence of high throughput technologies. Therefore, alterations in epigenetic marks may have clinical utility as potential biomarkers for early cancer detection and diagnosis. In this review, an outline of the key epigenetic mechanism(s), and their deregulation in cancer etiology have been discussed to decipher the future prospects in cancer therapeutics including precision medicine. Also, this review attempts to highlight the gaps in epigenetic drug development with emphasis on integrative analysis of epigenetic biomarkers to establish minimally non-invasive biomarkers with clinical applications.
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Affiliation(s)
- Sonam Tulsyan
- Division of Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR- National Institute of Cancer Prevention and Research, Noida, India
| | - Mehreen Aftab
- Division of Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR- National Institute of Cancer Prevention and Research, Noida, India
| | - Sandeep Sisodiya
- Division of Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR- National Institute of Cancer Prevention and Research, Noida, India
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Asiya Khan
- Laboratory Oncology Unit, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Atul Chikara
- Division of Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR- National Institute of Cancer Prevention and Research, Noida, India
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Pranay Tanwar
- Laboratory Oncology Unit, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
- *Correspondence: Showket Hussain, ; Pranay Tanwar,
| | - Showket Hussain
- Division of Cellular and Molecular Diagnostics (Molecular Biology Group), ICMR- National Institute of Cancer Prevention and Research, Noida, India
- *Correspondence: Showket Hussain, ; Pranay Tanwar,
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18
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Alvarez S, da Silva Almeida AC, Albero R, Biswas M, Barreto-Galvez A, Gunning TS, Shaikh A, Aparicio T, Wendorff A, Piovan E, Van Vlierberghe P, Gygi S, Gautier J, Madireddy A, A Ferrando A. Functional mapping of PHF6 complexes in chromatin remodeling, replication dynamics, and DNA repair. Blood 2022; 139:3418-3429. [PMID: 35338774 PMCID: PMC9185155 DOI: 10.1182/blood.2021014103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/27/2022] [Indexed: 01/05/2023] Open
Abstract
The Plant Homeodomain 6 gene (PHF6) encodes a nucleolar and chromatin-associated leukemia tumor suppressor with proposed roles in transcription regulation. However, specific molecular mechanisms controlled by PHF6 remain rudimentarily understood. Here we show that PHF6 engages multiple nucleosome remodeling protein complexes, including nucleosome remodeling and deacetylase, SWI/SNF and ISWI factors, the replication machinery and DNA repair proteins. Moreover, after DNA damage, PHF6 localizes to sites of DNA injury, and its loss impairs the resolution of DNA breaks, with consequent accumulation of single- and double-strand DNA lesions. Native chromatin immunoprecipitation sequencing analyses show that PHF6 specifically associates with difficult-to-replicate heterochromatin at satellite DNA regions enriched in histone H3 lysine 9 trimethyl marks, and single-molecule locus-specific analyses identify PHF6 as an important regulator of genomic stability at fragile sites. These results extend our understanding of the molecular mechanisms controlling hematopoietic stem cell homeostasis and leukemia transformation by placing PHF6 at the crossroads of chromatin remodeling, replicative fork dynamics, and DNA repair.
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Affiliation(s)
- Silvia Alvarez
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | - Robert Albero
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Mayukh Biswas
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | - Thomas S Gunning
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Anam Shaikh
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | - Tomas Aparicio
- Institute for Cancer Genetics, Columbia University, New York, NY
| | | | - Erich Piovan
- UOC Immunologia e Diagnostica Molecolare Oncologica, Istituto Oncologico Veneto-Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Padova, Italy
- Dipartimento di Scienze Chirurgiche, Oncologiche e Gastroenterologiche, Sezione di Oncologia, Università di Padova, Padova, Italy
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Steven Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Genetics and Development, College of Physicians and Surgeons, and
| | | | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Systems Biology, Columbia University, New York, NY; and
- Department of Pediatrics and
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
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Thakur S, Cahais V, Turkova T, Zikmund T, Renard C, Stopka T, Korenjak M, Zavadil J. Chromatin Remodeler Smarca5 Is Required for Cancer-Related Processes of Primary Cell Fitness and Immortalization. Cells 2022; 11:808. [PMID: 35269430 PMCID: PMC8909548 DOI: 10.3390/cells11050808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 12/04/2022] Open
Abstract
Smarca5, an ATPase of the ISWI class of chromatin remodelers, is a key regulator of chromatin structure, cell cycle and DNA repair. Smarca5 is deregulated in leukemia and breast, lung and gastric cancers. However, its role in oncogenesis is not well understood. Chromatin remodelers often play dosage-dependent roles in cancer. We therefore investigated the epigenomic and phenotypic impact of controlled stepwise attenuation of Smarca5 function in the context of primary cell transformation, a process relevant to tumor formation. Upon conditional single- or double-allele Smarca5 deletion, the cells underwent both accelerated growth arrest and senescence entry and displayed gradually increased sensitivity to genotoxic insults. These phenotypic characteristics were explained by specific remodeling of the chromatin structure and the transcriptome in primary cells prior to the immortalization onset. These molecular programs implicated Smarca5 requirement in DNA damage repair, telomere maintenance, cell cycle progression and in restricting apoptosis and cellular senescence. Consistent with the molecular programs, we demonstrate for the first time that Smarca5-deficient primary cells exhibit dramatically decreased capacity to bypass senescence and immortalize, an indispensable step during cell transformation and cancer development. Thus, Smarca5 plays a crucial role in key homeostatic processes and sustains cancer-promoting molecular programs and cellular phenotypes.
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Affiliation(s)
- Shefali Thakur
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France; (S.T.); (V.C.); (C.R.)
- Faculty of Science, Charles University, 128 43 Prague, Czech Republic; (S.T.)
- Biocev, First Faculty of Medicine, Charles University, 252 50 Vestec, Czech Republic; (T.T.); (T.Z.); (T.S.)
| | - Vincent Cahais
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France; (S.T.); (V.C.); (C.R.)
| | - Tereza Turkova
- Biocev, First Faculty of Medicine, Charles University, 252 50 Vestec, Czech Republic; (T.T.); (T.Z.); (T.S.)
| | - Tomas Zikmund
- Biocev, First Faculty of Medicine, Charles University, 252 50 Vestec, Czech Republic; (T.T.); (T.Z.); (T.S.)
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum, D-81377 München, Germany; (T.Z.)
| | - Claire Renard
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France; (S.T.); (V.C.); (C.R.)
| | - Tomáš Stopka
- Biocev, First Faculty of Medicine, Charles University, 252 50 Vestec, Czech Republic; (T.T.); (T.Z.); (T.S.)
| | - Michael Korenjak
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France; (S.T.); (V.C.); (C.R.)
| | - Jiri Zavadil
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France; (S.T.); (V.C.); (C.R.)
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Kumar N, Theil AF, Roginskaya V, Ali Y, Calderon M, Watkins SC, Barnes RP, Opresko PL, Pines A, Lans H, Vermeulen W, Van Houten B. Global and transcription-coupled repair of 8-oxoG is initiated by nucleotide excision repair proteins. Nat Commun 2022; 13:974. [PMID: 35190564 PMCID: PMC8861037 DOI: 10.1038/s41467-022-28642-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 02/03/2022] [Indexed: 12/17/2022] Open
Abstract
UV-DDB, consisting of subunits DDB1 and DDB2, recognizes UV-induced photoproducts during global genome nucleotide excision repair (GG-NER). We recently demonstrated a noncanonical role of UV-DDB in stimulating base excision repair (BER) which raised several questions about the timing of UV-DDB arrival at 8-oxoguanine (8-oxoG), and the dependency of UV-DDB on the recruitment of downstream BER and NER proteins. Using two different approaches to introduce 8-oxoG in cells, we show that DDB2 is recruited to 8-oxoG immediately after damage and colocalizes with 8-oxoG glycosylase (OGG1) at sites of repair. 8-oxoG removal and OGG1 recruitment is significantly reduced in the absence of DDB2. NER proteins, XPA and XPC, also accumulate at 8-oxoG. While XPC recruitment is dependent on DDB2, XPA recruitment is DDB2-independent and transcription-coupled. Finally, DDB2 accumulation at 8-oxoG induces local chromatin unfolding. We propose that DDB2-mediated chromatin decompaction facilitates the recruitment of downstream BER proteins to 8-oxoG lesions. Nucleotide excision repair proteins are involved in the repair of UV-induced DNA damage. Here, the authors show that NER proteins, DDB2, XPC, and XPA play a vital role in the 8-oxoguanine repair by coordinating with base excision repair protein OGG1.
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21
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Karl LA, Peritore M, Galanti L, Pfander B. DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling. Front Genet 2022; 12:821543. [PMID: 35096025 PMCID: PMC8790285 DOI: 10.3389/fgene.2021.821543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
DNA double strand breaks (DSBs) are repaired in eukaryotes by one of several cellular mechanisms. The decision-making process controlling DSB repair takes place at the step of DNA end resection, the nucleolytic processing of DNA ends, which generates single-stranded DNA overhangs. Dependent on the length of the overhang, a corresponding DSB repair mechanism is engaged. Interestingly, nucleosomes-the fundamental unit of chromatin-influence the activity of resection nucleases and nucleosome remodelers have emerged as key regulators of DSB repair. Nucleosome remodelers share a common enzymatic mechanism, but for global genome organization specific remodelers have been shown to exert distinct activities. Specifically, different remodelers have been found to slide and evict, position or edit nucleosomes. It is an open question whether the same remodelers exert the same function also in the context of DSBs. Here, we will review recent advances in our understanding of nucleosome remodelers at DSBs: to what extent nucleosome sliding, eviction, positioning and editing can be observed at DSBs and how these activities affect the DSB repair decision.
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Affiliation(s)
- Leonhard Andreas Karl
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martina Peritore
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
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22
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Mandigo AC, Tomlins SA, Kelly WK, Knudsen KE. Relevance of pRB Loss in Human Malignancies. Clin Cancer Res 2022; 28:255-264. [PMID: 34407969 PMCID: PMC9306333 DOI: 10.1158/1078-0432.ccr-21-1565] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/24/2021] [Accepted: 08/10/2021] [Indexed: 01/07/2023]
Abstract
The retinoblastoma tumor suppressor protein (pRB) is a known regulator of cell-cycle control; however, recent studies identified critical functions for pRB in regulating cancer-associated gene networks that influence the DNA damage response, apoptosis, and cell metabolism. Understanding the impact of these pRB functions on cancer development and progression in the clinical setting will be essential, given the prevalence of pRB loss of function across disease types. Moreover, the current state of evidence supports the concept that pRB loss results in pleiotropic effects distinct from tumor proliferation. Here, the implications of pRB loss (and resultant pathway deregulation) on disease progression and therapeutic response will be reviewed, based on clinical observation. Developing a better understanding of the pRB-regulated pathways that underpin the aggressive features of pRB-deficient tumors will be essential for further developing pRB as a biomarker of disease progression and for stratifying pRB-deficient tumors into more effective treatment regimens.
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Affiliation(s)
- Amy C. Mandigo
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Scott A. Tomlins
- Departments of Pathology and Urology, Michigan Center for Translational Pathology, Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - William K. Kelly
- Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E. Knudsen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.,Department of Medical Oncology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.,Corresponding Author: Karen E. Knudsen, Thomas Jefferson University, 233 South 10th Street, BLSB 1050, Philadelphia, PA 19107. Phone: 215-503-5692; E-mail:
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23
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Li Y, Gong H, Wang P, Zhu Y, Peng H, Cui Y, Li H, Liu J, Wang Z. The emerging role of ISWI chromatin remodeling complexes in cancer. J Exp Clin Cancer Res 2021; 40:346. [PMID: 34736517 PMCID: PMC8567610 DOI: 10.1186/s13046-021-02151-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Disordered chromatin remodeling regulation has emerged as an essential driving factor for cancers. Imitation switch (ISWI) family are evolutionarily conserved ATP-dependent chromatin remodeling complexes, which are essential for cellular survival and function through multiple genetic and epigenetic mechanisms. Omics sequencing and a growing number of basic and clinical studies found that ISWI family members displayed widespread gene expression and genetic status abnormalities in human cancer. Their aberrant expression is closely linked to patient outcome and drug response. Functional or componential alteration in ISWI-containing complexes is critical for tumor initiation and development. Furthermore, ISWI-non-coding RNA regulatory networks and some non-coding RNAs derived from exons of ISWI member genes play important roles in tumor progression. Therefore, unveiling the transcriptional regulation mechanism underlying ISWI family sparked a booming interest in finding ISWI-based therapies in cancer. This review aims at describing the current state-of-the-art in the role of ISWI subunits and complexes in tumorigenesis, tumor progression, immunity and drug response, and presenting deep insight into the physiological and pathological implications of the ISWI transcription machinery in cancers.
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Affiliation(s)
- Yanan Li
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Han Gong
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Pan Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Yu Zhu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Hongling Peng
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yajuan Cui
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Heng Li
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Zi Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China.
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24
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Wang M, Li S, Guo W, Wang L, Huang J, Zhuo J, Lai B, Liao C, Ge T, Nie Y, Jin S, Wang M, Zhang Y, Liu Y, Li X, Zhang H. CHRAC1 promotes human lung cancer growth through regulating YAP transcriptional activity. Carcinogenesis 2021; 43:264-276. [PMID: 34718437 DOI: 10.1093/carcin/bgab103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/01/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
ATP-dependent chromatin remodeling complexes regulate chromatin structure and play important roles in gene expression, differentiation, development and cancer progression. Dysregulation in the subunits of the complexes often has been found in different cancers, but how they influence cancer initiation and progression is not fully understood. Here we show that Chromatin Accessibility Complex Subunit 1 (CHRAC1), the accessory subunit of chromatin remodeling complex, is highly expressed in lung cancer tissues, which correlates with poor prognosis in lung cancer patients. CHRAC1 overexpression promotes lung cancer cell proliferation and migration in vitro and tumor growth in genetically engineered Kras G12D.LSL lung adenocarcinoma mouse model. Consistent with this, CHRAC1 silencing inhibits cell proliferation and migration in lung cancer cells and suppresses tumor growth in xenograft mouse model. Further, CHRAC1 binds to the transcription co-activator Yes-associated protein (YAP), enhances the transcription of downstream target oncogenes in Hippo pathway and thus promotes the tumor growth. Together, our study defines a critical role of CHRAC1 in promoting YAP transcriptional activity and lung cancer tumorigenesis, which makes it a potential target for lung cancer.
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Affiliation(s)
- Mingwei Wang
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shasha Li
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wencong Guo
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lulu Wang
- Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430040, China
| | - Jiaxin Huang
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Junzhe Zhuo
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Botao Lai
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chenqi Liao
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tianlan Ge
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuxuan Nie
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Su Jin
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Manxiang Wang
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yanggeling Zhang
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yimeng Liu
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaowen Li
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huixia Zhang
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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25
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Lee HS, Min S, Jung YE, Chae S, Heo J, Lee JH, Kim T, Kang HC, Nakanish M, Cha SS, Cho H. Spatiotemporal coordination of the RSF1-PLK1-Aurora B cascade establishes mitotic signaling platforms. Nat Commun 2021; 12:5931. [PMID: 34635673 PMCID: PMC8505570 DOI: 10.1038/s41467-021-26220-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 09/15/2021] [Indexed: 12/03/2022] Open
Abstract
The chromatin remodeler RSF1 enriched at mitotic centromeres is essential for proper chromosome alignment and segregation and underlying mechanisms remain to be disclosed. We here show that PLK1 recruitment by RSF1 at centromeres creates an activating phosphorylation on Thr236 in the activation loop of Aurora B and this is indispensable for the Aurora B activation. In structural modeling the phosphorylated Thr236 enhances the base catalysis by Asp200 nearby, facilitating the Thr232 autophosphorylation. Accordingly, RSF1-PLK1 is central for Aurora B-mediated microtubule destabilization in error correction. However, under full microtubule-kinetochore attachment RSF1-PLK1 positions at kinetochores, halts activating Aurora B and phosphorylates BubR1, regardless of tension. Spatial movement of RSF1-PLK1 to kinetochores is triggered by Aurora B-mediated phosphorylation of centromeric histone H3 on Ser28. We propose a regulatory RSF1-PLK1 axis that spatiotemporally controls on/off switch on Aurora B. This feedback circuit among RSF1-PLK1-Aurora B may coordinate dynamic microtubule-kinetochore attachment in early mitosis when full tension yet to be generated.
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Affiliation(s)
- Ho-Soo Lee
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea.
| | - Sunwoo Min
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea
| | - Ye-Eun Jung
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Sunyoung Chae
- Institute of Medical Science, Ajou University School of Medicine, Suwon, 16499, Korea
| | - June Heo
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea
- Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, 16499, Korea
| | - Jae-Ho Lee
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea
- Institute of Medical Science, Ajou University School of Medicine, Suwon, 16499, Korea
| | - TaeSoo Kim
- Department of Life Science, Ewha Womans University, Seoul, 03760, Korea
| | - Ho-Chul Kang
- Department of Physiology, Ajou University School of Medicine, Suwon, Korea
| | - Makoto Nakanish
- Division of Cancer Cell Biology, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Sun-Shin Cha
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Hyeseong Cho
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, Korea.
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26
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Sharif SB, Zamani N, Chadwick BP. BAZ1B the Protean Protein. Genes (Basel) 2021; 12:genes12101541. [PMID: 34680936 PMCID: PMC8536118 DOI: 10.3390/genes12101541] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 02/02/2023] Open
Abstract
The bromodomain adjacent to the zinc finger domain 1B (BAZ1B) or Williams syndrome transcription factor (WSTF) are just two of the names referring the same protein that is encoded by the WBSCR9 gene and is among the 26-28 genes that are lost from one copy of 7q11.23 in Williams syndrome (WS: OMIM 194050). Patients afflicted by this contiguous gene deletion disorder present with a range of symptoms including cardiovascular complications, developmental defects as well as a characteristic cognitive and behavioral profile. Studies in patients with atypical deletions and mouse models support BAZ1B hemizygosity as a contributing factor to some of the phenotypes. Focused analysis on BAZ1B has revealed this to be a versatile nuclear protein with a central role in chromatin remodeling through two distinct complexes as well as being involved in the replication and repair of DNA, transcriptional processes involving RNA Polymerases I, II, and III as well as possessing kinase activity. Here, we provide a comprehensive review to summarize the many aspects of BAZ1B function including its recent link to cancer.
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Affiliation(s)
- Shahin Behrouz Sharif
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA;
| | - Nina Zamani
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA;
| | - Brian P. Chadwick
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA;
- Correspondence:
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27
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28
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Song Z, Lin J, Li Z, Huang C. The nuclear functions of long noncoding RNAs come into focus. Noncoding RNA Res 2021; 6:70-79. [PMID: 33898883 PMCID: PMC8053782 DOI: 10.1016/j.ncrna.2021.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), defined as untranslated and tightly-regulated transcripts with a length exceeding 200 nt, are common outputs of the eukaryotic genome. It is becoming increasingly apparent that many lncRNAs likely serve as important regulators in a variety of biological processes. In particular, some of them accumulate in the nucleus and function in diverse nuclear events, including chromatin remodeling, transcriptional regulation, RNA processing, DNA damage repair, etc. Here, we unite recent progresses on the functions of nuclear lncRNAs and provide insights into the future research directions of this field.
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Affiliation(s)
- Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
- Corresponding author. School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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29
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Neve B, Jonckheere N, Vincent A, Van Seuningen I. Long non-coding RNAs: the tentacles of chromatin remodeler complexes. Cell Mol Life Sci 2021; 78:1139-1161. [PMID: 33001247 PMCID: PMC11072783 DOI: 10.1007/s00018-020-03646-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 09/12/2020] [Indexed: 02/07/2023]
Abstract
Chromatin remodeler complexes regulate gene transcription, DNA replication and DNA repair by changing both nucleosome position and post-translational modifications. The chromatin remodeler complexes are categorized into four families: the SWI/SNF, INO80/SWR1, ISWI and CHD family. In this review, we describe the subunits of these chromatin remodeler complexes, in particular, the recently identified members of the ISWI family and novelties of the CHD family. Long non-coding (lnc) RNAs regulate gene expression through different epigenetic mechanisms, including interaction with chromatin remodelers. For example, interaction of lncBRM with BRM inhibits the SWI/SNF complex associated with a differentiated phenotype and favors assembly of a stem cell-related SWI/SNF complex. Today, over 50 lncRNAs have been shown to affect chromatin remodeler complexes and we here discuss the mechanisms involved.
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Affiliation(s)
- Bernadette Neve
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France.
| | - Nicolas Jonckheere
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
| | - Audrey Vincent
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
| | - Isabelle Van Seuningen
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
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30
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Johann PD. Invited Review: Dysregulation of chromatin remodellers in paediatric brain tumours - SMARCB1 and beyond. Neuropathol Appl Neurobiol 2021; 46:57-72. [PMID: 32307752 DOI: 10.1111/nan.12616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/21/2020] [Indexed: 12/13/2022]
Abstract
Mutations in chromatin remodelling genes occur in approximately 25% of all human tumours (Kadoch et al. Nat Genet 45: 592-601, 2013). The spectrum of alterations is broad and comprises single nucleotide variants, insertion/deletions and more complex structural variations. The single most often affected remodelling complex is the SWI/SNF complex (SWItch/sucrose non-fermentable). In the field of paediatric neuro-oncology, the spectrum of affected genes implicated in epigenetic remodelling is narrower with SMARCB1 and SMARCA4 being the most frequent. The low mutation frequencies in many of the SWI/SNF mutant entities underline the fact that perturbed chromatin remodelling is the most salient factor in tumourigenesis and could thus be a potential therapeutic opportunity. Here, I review the genetic basis of aberrant chromatin remodelling in paediatric brain tumours and discuss their impact on the epigenome in the respective entities, mainly medulloblastomas and rhabdoid tumours.
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Affiliation(s)
- P D Johann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Heidelberg, Germany.,Department of Paediatric Haematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
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31
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Li CF, Chan TC, Wang CI, Fang FM, Lin PC, Yu SC, Huang HY. RSF1 requires CEBP/β and hSNF2H to promote IL-1β-mediated angiogenesis: the clinical and therapeutic relevance of RSF1 overexpression and amplification in myxofibrosarcomas. Angiogenesis 2021; 24:533-548. [PMID: 33496909 DOI: 10.1007/s10456-020-09764-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/20/2020] [Indexed: 12/12/2022]
Abstract
Myxofibrosarcoma is genetically complex and lacks effective nonsurgical treatment strategies; thus, elucidation of novel molecular drivers is urgently needed. Reanalyzing public myxofibrosarcoma datasets, we identified mRNA upregulation and recurrent gain of RSF1 and characterized this chromatin remodeling gene. Myxofibrosarcoma cell lines were employed to elucidate the oncogenic mechanisms of RSF1 by genetic manipulation and two IL-1β-neutralizing antibodies (RD24, P2D7KK), highlighting the regulatory basis and targetability of downstream IL-1β-mediated angiogenesis. Tumor samples were assessed for RSF1, IL-1β, and microvascular density (MVD) by immunohistochemistry and for RSF1 gene status by FISH. In vivo, RSF1-silenced and P2D7KK-treated xenografts were analyzed for tumor-promoting effects and the IL-1β-linked therapeutic relevance of RSF1, respectively. In vitro, RSF1 overexpression promoted invasive and angiogenic phenotypes with a stronger proangiogenic effect. RT-PCR profiling identified IL1B as a top-ranking candidate upregulated by RSF1. RSF1 required hSNF2H and CEBP/β to cotransactivate the IL1B promoter, which increased the IL1B mRNA level, IL-1β secretion and angiogenic capacity. Angiogenesis induced by RSF1-upregulated IL-1β was counteracted by IL1B knockdown and both IL-1β-neutralizing antibodies. Clinically, RSF1 overexpression was highly associated with RSF1 amplification, IL-1β overexpression, increased MVD and higher grades (all P ≤ 0.01) and independently predicted shorter disease-specific survival (P = 0.019, hazard ratio: 4.556). In vivo, both RSF1 knockdown and anti-IL-1β P2D7KK (200 μg twice weekly) enabled significant growth inhibition and devascularization in xenografts. In conclusion, RSF1 overexpression, partly attributable to RSF1 amplification, contributes a novel proangiogenic function by partnering with CEBP/β to cotransactivate IL1B, highlighting its prognostic, pathogenetic, and therapeutic relevance in myxofibrosarcomas.
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Affiliation(s)
- Chien-Feng Li
- Department of Pathology, Chi Mei Medical Center, Tainan, Taiwan.,National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan.,Institute of Precision Medicine, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Ti-Chen Chan
- Department of Pathology, Chi Mei Medical Center, Tainan, Taiwan.,National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Cheng-I Wang
- Singapore Immunology Network; Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Fu-Min Fang
- Department of Radiation Oncology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Po-Chun Lin
- Department of Orthopedics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shih-Chen Yu
- Department of Anatomic Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd., Niao-Sung District, Kaohsiung, Taiwan
| | - Hsuan-Ying Huang
- Department of Anatomic Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, 123, Ta-Pei Rd., Niao-Sung District, Kaohsiung, Taiwan.
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Hou X, Yang L, Wang K, Zhou Y, Li Q, Kong F, Liu X, He J. HELLS, a chromatin remodeler is highly expressed in pancreatic cancer and downregulation of it impairs tumor growth and sensitizes to cisplatin by reexpressing the tumor suppressor TGFBR3. Cancer Med 2021; 10:350-364. [PMID: 33280236 PMCID: PMC7826454 DOI: 10.1002/cam4.3627] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/20/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022] Open
Abstract
Pancreatic cancer (PC) is the most malignant cancer type in the digestive system with a poor prognosis. Chemotherapy such as cisplatin is the last chance for PC patients diagnosed with advanced or metastatic disease. Obtaining a deep understanding of the molecular mechanism underlying PC tumorigenesis and identifying optimal biomarkers to estimate chemotherapy sensitivity are essential for PC treatment. The chromatin remodeler HELLS was found to regulate various tumor suppressors through an epigenetic pathway in several cancers. We analyzed HELLS expression in clinical samples by Western blotting and immunohistochemical staining. Next, we identified the variation in tumor growth and cisplatin sensitivity after knockdown of HELLS and explored the downstream mediators of HELLS in PC via RNA-seq, chromatin immunoprecipitation, and gain- and loss-of-function assays. We found that HELLS is upregulated in PC tissues and correlates with advanced clinical stage and a poor prognosis, and the knockdown of HELLS leads to tumor growth arrest and increased sensitivity to cisplatin. Mechanistically, the tumor suppressor TGFBR3 is markedly reexpressed after HELLS knockdown; conversely, compromising TGFBR3 rescues HELLS knockdown-mediated effects in PC cells. Thus, our data provide evidence that HELLS can serve as a potential oncogene and suitable biomarker to evaluate chemotherapy sensitivity via epigenetically silencing the tumor suppressor TGFBR3 in PC.
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Affiliation(s)
- Xuyang Hou
- Department of General SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Leping Yang
- Department of General SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Kunpeng Wang
- Department of General SurgeryTaizhou Central HospitalTaizhou University HospitalTaizhouZhejiangChina
| | - Yan Zhou
- Department of General SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Qinglong Li
- Department of General SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Fanhua Kong
- Department of General SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Xi Liu
- Department of General SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Jun He
- Department of General SurgeryThe Second Xiangya HospitalCentral South UniversityChangshaHunanChina
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Magaña-Acosta M, Valadez-Graham V. Chromatin Remodelers in the 3D Nuclear Compartment. Front Genet 2020; 11:600615. [PMID: 33329746 PMCID: PMC7673392 DOI: 10.3389/fgene.2020.600615] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/07/2020] [Indexed: 12/15/2022] Open
Abstract
Chromatin remodeling complexes (CRCs) use ATP hydrolysis to maintain correct expression profiles, chromatin stability, and inherited epigenetic states. More than 20 CRCs have been described to date, which encompass four large families defined by their ATPase subunits. These complexes and their subunits are conserved from yeast to humans through evolution. Their activities depend on their catalytic subunits which through ATP hydrolysis provide the energy necessary to fulfill cellular functions such as gene transcription, DNA repair, and transposon silencing. These activities take place at the first levels of chromatin compaction, and CRCs have been recognized as essential elements of chromatin dynamics. Recent studies have demonstrated an important role for these complexes in the maintenance of higher order chromatin structure. In this review, we present an overview of the organization of the genome within the cell nucleus, the different levels of chromatin compaction, and importance of the architectural proteins, and discuss the role of CRCs and how their functions contribute to the dynamics of the 3D genome organization.
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Affiliation(s)
- Mauro Magaña-Acosta
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Viviana Valadez-Graham
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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López-Contreras AK, Martínez-Ruiz MG, Olvera-Montaño C, Robles-Rivera RR, Arévalo-Simental DE, Castellanos-González JA, Hernández-Chávez A, Huerta-Olvera SG, Cardona-Muñoz EG, Rodríguez-Carrizalez AD. Importance of the Use of Oxidative Stress Biomarkers and Inflammatory Profile in Aqueous and Vitreous Humor in Diabetic Retinopathy. Antioxidants (Basel) 2020; 9:antiox9090891. [PMID: 32962301 PMCID: PMC7555116 DOI: 10.3390/antiox9090891] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 09/03/2020] [Accepted: 09/10/2020] [Indexed: 12/23/2022] Open
Abstract
Diabetic retinopathy is one of the leading causes of visual impairment and morbidity worldwide, being the number one cause of blindness in people between 27 and 75 years old. It is estimated that ~191 million people will be diagnosed with this microvascular complication by 2030. Its pathogenesis is due to alterations in the retinal microvasculature as a result of a high concentration of glucose in the blood for a long time which generates numerous molecular changes like oxidative stress. Therefore, this narrative review aims to approach various biomarkers associated with the development of diabetic retinopathy. Focusing on the molecules showing promise as detection tools, among them we consider markers of oxidative stress (TAC, LPO, MDA, 4-HNE, SOD, GPx, and catalase), inflammation (IL-6, IL-1ß, IL-8, IL-10, IL-17A, TNF-α, and MMPs), apoptosis (NF-kB, cyt-c, and caspases), and recently those that have to do with epigenetic modifications, their measurement in different biological matrices obtained from the eye, including importance, obtaining process, handling, and storage of these matrices in order to have the ability to detect the disease in its early stages.
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Affiliation(s)
- Ana Karen López-Contreras
- Department of Physiology, Health Sciences University Center, Institute of Clinical and Experimental Therapeutics, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico; (A.K.L.-C.); (M.G.M.-R.); (C.O.-M.); (R.R.R.-R.); (D.E.A.-S.); (J.A.C.-G.); (A.H.-C.); (E.G.C.-M.)
| | - María Guadalupe Martínez-Ruiz
- Department of Physiology, Health Sciences University Center, Institute of Clinical and Experimental Therapeutics, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico; (A.K.L.-C.); (M.G.M.-R.); (C.O.-M.); (R.R.R.-R.); (D.E.A.-S.); (J.A.C.-G.); (A.H.-C.); (E.G.C.-M.)
| | - Cecilia Olvera-Montaño
- Department of Physiology, Health Sciences University Center, Institute of Clinical and Experimental Therapeutics, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico; (A.K.L.-C.); (M.G.M.-R.); (C.O.-M.); (R.R.R.-R.); (D.E.A.-S.); (J.A.C.-G.); (A.H.-C.); (E.G.C.-M.)
| | - Ricardo Raúl Robles-Rivera
- Department of Physiology, Health Sciences University Center, Institute of Clinical and Experimental Therapeutics, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico; (A.K.L.-C.); (M.G.M.-R.); (C.O.-M.); (R.R.R.-R.); (D.E.A.-S.); (J.A.C.-G.); (A.H.-C.); (E.G.C.-M.)
| | - Diana Esperanza Arévalo-Simental
- Department of Physiology, Health Sciences University Center, Institute of Clinical and Experimental Therapeutics, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico; (A.K.L.-C.); (M.G.M.-R.); (C.O.-M.); (R.R.R.-R.); (D.E.A.-S.); (J.A.C.-G.); (A.H.-C.); (E.G.C.-M.)
- Department of Ophthalmology, Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara, Jalisco 44280, Mexico
| | - José Alberto Castellanos-González
- Department of Physiology, Health Sciences University Center, Institute of Clinical and Experimental Therapeutics, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico; (A.K.L.-C.); (M.G.M.-R.); (C.O.-M.); (R.R.R.-R.); (D.E.A.-S.); (J.A.C.-G.); (A.H.-C.); (E.G.C.-M.)
- Department of Ophthalmology, Specialties Hospital of the National Occidental Medical Center, Mexican Institute of Social Security, Guadalajara, Jalisco 44329, Mexico
| | - Abel Hernández-Chávez
- Department of Physiology, Health Sciences University Center, Institute of Clinical and Experimental Therapeutics, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico; (A.K.L.-C.); (M.G.M.-R.); (C.O.-M.); (R.R.R.-R.); (D.E.A.-S.); (J.A.C.-G.); (A.H.-C.); (E.G.C.-M.)
| | - Selene Guadalupe Huerta-Olvera
- Medical and Life Sciences Department, La Ciénega University Center, University of Guadalajara, Ocotlán, Jalisco 47810, Mexico;
| | - Ernesto German Cardona-Muñoz
- Department of Physiology, Health Sciences University Center, Institute of Clinical and Experimental Therapeutics, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico; (A.K.L.-C.); (M.G.M.-R.); (C.O.-M.); (R.R.R.-R.); (D.E.A.-S.); (J.A.C.-G.); (A.H.-C.); (E.G.C.-M.)
| | - Adolfo Daniel Rodríguez-Carrizalez
- Department of Physiology, Health Sciences University Center, Institute of Clinical and Experimental Therapeutics, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico; (A.K.L.-C.); (M.G.M.-R.); (C.O.-M.); (R.R.R.-R.); (D.E.A.-S.); (J.A.C.-G.); (A.H.-C.); (E.G.C.-M.)
- Correspondence:
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Xu X, Zhang J, Tian Y, Gao Y, Dong X, Chen W, Yuan X, Yin W, Xu J, Chen K, He C, Wei L. CircRNA inhibits DNA damage repair by interacting with host gene. Mol Cancer 2020; 19:128. [PMID: 32838810 PMCID: PMC7446195 DOI: 10.1186/s12943-020-01246-x] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/12/2020] [Indexed: 01/01/2023] Open
Abstract
Background Deregulated circular RNAs (circRNAs) are associated with the development of cancer and therapy resistance. However, functional research of circRNAs mostly focus on potential miRNA or protein binding and more potential regulation of circRNA on host gene DNA in cancers are yet to be inspected. Method We performed total RNA sequencing on clinical breast cancer samples and identified the expression patterns of circRNAs and corresponding host genes in patient blood, tumor and adjacent normal tissues. qPCR, northern blot and in situ hybridization were used to validate the dysregulation of circRNA circSMARCA5. A series of procedures including R-loop dot-blotting, DNA-RNA immunoprecipitation and mass spectrum, etc. were conducted to explore the regulation of circSMARCA5 on the transcription of exon 15 of SMARCA5. Moreover, immunofluorescence and in vivo experiments were executed to investigate the overexpression of circSMARCA5 with drug sensitivities. Results We found that circRNAs has average higher expression over its host linear genes in peripheral blood. Compared to adjacent normal tissues, circSMARCA5 is decreased in breast cancer tissues, contrary to host gene SMARCA5. The enforced expression of circSMARCA5 induced drug sensitivity of breast cancer cell lines in vitro and in vivo. Furthermore, we demonstrated that circSMARCA5 can bind to its parent gene locus, forming an R-loop, which results in transcriptional pausing at exon 15 of SMARCA5. CircSMARCA5 expression resulted in the downregulation of SMARCA5 and the production of a truncated nonfunctional protein, and the overexpression of circSMARCA5 was sufficient to improve sensitivity to cytotoxic drugs. Conclusion Our results revealed a new regulatory mechanism for circRNA on its host gene and provided evidence that circSMARCA5 may serve as a therapeutic target for drug-resistant breast cancer patients.
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Affiliation(s)
- Xiaolong Xu
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Jingwei Zhang
- Hubei Key Laboratory of Tumor Biological Behaviors, Department of Breast and Thyroid Surgery, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Yihao Tian
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Yang Gao
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Xin Dong
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Wenbo Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Xiaoning Yuan
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Weinan Yin
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Jinjing Xu
- Hubei Key Laboratory of Tumor Biological Behaviors, Department of Breast and Thyroid Surgery, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, 430071, Hubei, China
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Chunjiang He
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China. .,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Lei Wei
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China. .,Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, 430071, Hubei, China.
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Scacchetti A, Becker PB. Loss of nucleosome remodelers CHRAC/ACF does not sensitize early Drosophila embryos to X-rays. MICROPUBLICATION BIOLOGY 2020; 2020:10.17912/micropub.biology.000287. [PMID: 32760884 PMCID: PMC7396160 DOI: 10.17912/micropub.biology.000287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alessandro Scacchetti
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University, Munich, Germany
| | - Peter B. Becker
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University, Munich, Germany,
Correspondence to: Peter B. Becker ()
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Interaction of Deubiquitinase 2A-DUB/MYSM1 with DNA Repair and Replication Factors. Int J Mol Sci 2020; 21:ijms21113762. [PMID: 32466590 PMCID: PMC7312997 DOI: 10.3390/ijms21113762] [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: 04/11/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023] Open
Abstract
The deubiquitination of histone H2A on lysine 119 by 2A-DUB/MYSM1, BAP1, USP16, and other enzymes is required for key cellular processes, including transcriptional activation, apoptosis, and cell cycle control, during normal hematopoiesis and tissue development, and in tumor cells. Based on our finding that MYSM1 colocalizes with γH2AX foci in human peripheral blood mononuclear cells, leukemia cells, and melanoma cells upon induction of DNA double-strand breaks with topoisomerase inhibitor etoposide, we applied a mass spectrometry-based proteomics approach to identify novel 2A-DUB/MYSM1 interaction partners in DNA-damage responses. Differential display of MYSM1 binding proteins significantly enriched after exposure of 293T cells to etoposide revealed an interacting network of proteins involved in DNA damage and replication, including factors associated with poor melanoma outcome. In the context of increased DNA-damage in a variety of cell types in Mysm1-deficient mice, in bone marrow cells upon aging and in UV-exposed Mysm1-deficient skin, our current mass spectrometry data provide additional evidence for an interaction between MYSM1 and key DNA replication and repair factors, and indicate a potential function of 2A-DUB/MYSM1 in DNA repair processes.
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Díaz-Olmos Y, Batista M, Ludwig A, Marchini FK. Characterising ISWI chromatin remodeler in Trypanosoma cruzi. Mem Inst Oswaldo Cruz 2020; 115:e190457. [PMID: 32428081 PMCID: PMC7233268 DOI: 10.1590/0074-02760190457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/23/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Imitation SWItch (ISWI) ATPase is the catalytic subunit in diverse chromatin remodeling complexes. These complexes modify histone-DNA interactions and therefore play a pivotal role in different DNA-dependent processes. In Trypanosoma cruzi, a protozoan that controls gene expression principally post-transcriptionally, the transcriptional regulation mechanisms mediated by chromatin remodeling are poorly understood. OBJECTIVE To characterise the ISWI remodeler in T. cruzi (TcISWI). METHODS A new version of pTcGW vectors was constructed to express green fluorescent protein (GFP)-tagged TcISWI. CRISPR-Cas9 system was used to obtain parasites with inactivated TcISWI gene and we determined TcISWI partners by cryomilling-affinity purification-mass spectrometry (MS) assay as an approximation to start to unravel the function of this protein. FINDINGS Our approach identified known ISWI partners [nucleoplasmin-like protein (NLP), regulator of chromosome condensation 1-like protein (RCCP) and phenylalanine/tyrosine-rich protein (FYRP)], previously characterised in T. brucei, and new components in TcISWI complex [DRBD2, DHH1 and proteins containing a domain characteristic of structural maintenance of chromosomes (SMC) proteins]. Data are available via ProteomeXchange with identifier PXD017869. MAIN CONCLUSIONS In addition to its participation in transcriptional silencing, as it was reported in T. brucei, the data generated here provide a framework that suggests a role for TcISWI chromatin remodeler in different nuclear processes in T. cruzi, including mRNA nuclear export control and chromatin compaction. Further work is necessary to clarify the TcISWI functional diversity that arises from this protein interaction study.
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Affiliation(s)
- Yirys Díaz-Olmos
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
| | - Michel Batista
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
| | - Adriana Ludwig
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
| | - Fabricio K Marchini
- Laboratório de Ciências e Tecnologias Aplicadas em Saúde, Instituto Carlos Chagas, Fundação Oswaldo Cruz-Fiocruz, Curitiba, PR, Brazil
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Höflmayer D, Hamuda M, Schroeder C, Hube-Magg C, Simon R, Göbel C, Hinsch A, Weidemann S, Möller K, Izbicki JR, Jacobsen F, Mandelkow T, Blessin NC, Lutz F, Viehweger F, Sauter G, Burandt E, Lebok P, Lennartz M, Fraune C, Minner S, Bonk S, Huland H, Graefen M, Schlomm T, Büscheck F. High RSF1 protein expression is an independent prognostic feature in prostate cancer. Acta Oncol 2020; 59:268-273. [PMID: 31687881 DOI: 10.1080/0284186x.2019.1686537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Background: Remodelling and spacing factor 1 (RSF1) is involved in the regulation of chromatin remodelling and represents a potential therapeutic target. High RSF1 expression has been linked to adverse tumour features in many cancer types, but its role in prostate cancer is uncertain.Methods: In this study, RSF1 expression was analysed by immunohistochemistry on a tissue microarray with 17,747 prostate cancers.Results: Nuclear RSF1 staining of 16,456 interpetable cancers was considered strong, moderate, weak and negative in 25.2%, 48.7%, 5.3% and 20.8% of cancers respectively. Positive RSF1 expression was associated with advanced tumour stage, high Gleason grade, lymph node metastasis (p < .0001 each), early biochemical recurrence (p < .0003) and more frequent in the ERG positive than in the ERG negative subset (88% versus 71%; p < .0001). Subset analysis revealed, that associations between RSF1 expression and unfavourable tumour phenotype and PSA recurrence were present in both subgroups but stronger in the ERG negative than in the ERG positive subset. The univariate Cox proportional hazard ratio for PSA recurrence-free survival for strong versus negative RSF1 expression was a weak 1.60 compared with 5.91 for the biopsy Gleason grade ≥4 + 4 versus ≤3 + 3. The positive association of RSF1 protein detection with deletion of 3p13, 10q23 (PTEN), 12p13, 16q23, and 17p13 (p < .0001 each) suggest a role of high RSF1 expression in the development of genomic instability.Conclusion: In summary, the results of our study identify RSF1 as an independent prognostic marker in prostate cancer with a particularly strong role in ERG negative cases.
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Affiliation(s)
- Doris Höflmayer
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Moslim Hamuda
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Cornelia Schroeder
- General, Visceral and Thoracic Surgery Department and Clinic, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Cosima Göbel
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Andrea Hinsch
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Sören Weidemann
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Möller
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Jacob R. Izbicki
- General, Visceral and Thoracic Surgery Department and Clinic, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Frank Jacobsen
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Tim Mandelkow
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Niclas C. Blessin
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Lutz
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Viehweger
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Eike Burandt
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Patrick Lebok
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Maximilian Lennartz
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Fraune
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Sarah Minner
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Sarah Bonk
- General, Visceral and Thoracic Surgery Department and Clinic, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Hartwig Huland
- Martini-Clinic, Prostate Cancer Centre, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Graefen
- Martini-Clinic, Prostate Cancer Centre, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Schlomm
- Department of Urology, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Franziska Büscheck
- Institute of Pathology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
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Srivastava A, Mishra RK. Interactome of vertebrate GAF/ThPOK reveals its diverse functions in gene regulation and DNA repair. J Biosci 2020. [DOI: 10.1007/s12038-020-0014-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Histone demethylase JMJD1C is phosphorylated by mTOR to activate de novo lipogenesis. Nat Commun 2020; 11:796. [PMID: 32034158 PMCID: PMC7005700 DOI: 10.1038/s41467-020-14617-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 01/20/2020] [Indexed: 01/28/2023] Open
Abstract
Fatty acid and triglyceride synthesis increases greatly in response to feeding and insulin. This lipogenic induction involves coordinate transcriptional activation of various enzymes in lipogenic pathway, including fatty acid synthase and glycerol-3-phosphate acyltransferase. Here, we show that JMJD1C is a specific histone demethylase for lipogenic gene transcription in liver. In response to feeding/insulin, JMJD1C is phosphorylated at T505 by mTOR complex to allow direct interaction with USF-1 for recruitment to lipogenic promoter regions. Thus, by demethylating H3K9me2, JMJD1C alters chromatin accessibility to allow transcription. Consequently, JMJD1C promotes lipogenesis in vivo to increase hepatic and plasma triglyceride levels, showing its role in metabolic adaption for activation of the lipogenic program in response to feeding/insulin, and its contribution to development of hepatosteatosis resulting in insulin resistance. In response to insulin, liver cells increase de novo lipogenesis via the transcription factors USF-1 and SREBP. Here the authors show that USF-1 recruits JMJD1C, after its phosphorylation by mTOR, to lipogenic promoters where JMJD1C demethylates histone H3, contributing to lipogenesis by an epigenetic mechanism.
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Delamarre A, Barthe A, de la Roche Saint-André C, Luciano P, Forey R, Padioleau I, Skrzypczak M, Ginalski K, Géli V, Pasero P, Lengronne A. MRX Increases Chromatin Accessibility at Stalled Replication Forks to Promote Nascent DNA Resection and Cohesin Loading. Mol Cell 2020; 77:395-410.e3. [PMID: 31759824 DOI: 10.1016/j.molcel.2019.10.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/09/2019] [Accepted: 10/17/2019] [Indexed: 01/04/2023]
Abstract
The recovery of stalled replication forks depends on the controlled resection of nascent DNA and on the loading of cohesin. These processes operate in the context of nascent chromatin, but the impact of nucleosome structure on a fork restart remains poorly understood. Here, we show that the Mre11-Rad50-Xrs2 (MRX) complex acts together with the chromatin modifiers Gcn5 and Set1 and the histone remodelers RSC, Chd1, and Isw1 to promote chromatin remodeling at stalled forks. Increased chromatin accessibility facilitates the resection of nascent DNA by the Exo1 nuclease and the Sgs1 and Chl1 DNA helicases. Importantly, increased ssDNA promotes the recruitment of cohesin to arrested forks in a Scc2-Scc4-dependent manner. Altogether, these results indicate that MRX cooperates with chromatin modifiers to orchestrate the action of remodelers, nucleases, and DNA helicases, promoting the resection of nascent DNA and the loading of cohesin, two key processes involved in the recovery of arrested forks.
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Affiliation(s)
- Axel Delamarre
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Antoine Barthe
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Christophe de la Roche Saint-André
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France
| | - Pierre Luciano
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France
| | - Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Ismaël Padioleau
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), CNRS, INSERM, Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue contre le Cancer, 13273 Marseille, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France.
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labellisée Ligue contre le Cancer, Montpellier, France.
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43
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Srivastava A, Mishra RK. Interactome of vertebrate GAF/ThPOK reveals its diverse functions in gene regulation and DNA repair. J Biosci 2020; 45:38. [PMID: 32098917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
GAGA associated factor (GAF) is a sequence-specific DNA binding transcription factor that is evolutionarily conserved from flies to humans. Emerging evidence shows a context-dependent function of vertebrate GAF (vGAF, a.k.a. ThPOK) in multiple processes like gene activation, repression, and enhancer-blocking. We hypothesize that context-dependent interaction of vGAF with a diverse set of proteins forms the basis for the multifunctional nature of vGAF. To this end, we deciphered the protein-protein interactome of vGAF and show that vGAF interacts with chromatin remodelers, RNA metabolic machinery, transcriptional activators/ repressors, and components of DNA repair machinery. We further validated the biological significance of our protein-protein interaction data with functional studies and established a novel role of vGAF in DNA repair and cell-survival after UV-induced DNA damage. One of the major risk factors for skin cutaneous melanoma is prolonged exposure of UV and subsequent DNA damage. vGAF is highly expressed in normal skin tissue. Interestingly, our analysis of high-throughput RNA-sequencing data shows that vGAF is heavily downregulated across all major stages of skin cutaneous melanoma suggesting its potential as a diagnostic biomarker. Taken together, our study provides a plausible explanation for the diverse gene regulatory functions of vGAF and unravels its novel role in DNA repair.
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Affiliation(s)
- Avinash Srivastava
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad 500 007, India
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44
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Abstract
In eukaryotes, DNA is highly compacted within the nucleus into a structure known as chromatin. Modulation of chromatin structure allows for precise regulation of gene expression, and thereby controls cell fate decisions. Specific chromatin organization is established and preserved by numerous factors to generate desired cellular outcomes. In embryonic stem (ES) cells, chromatin is precisely regulated to preserve their two defining characteristics: self-renewal and pluripotent state. This action is accomplished by a litany of nucleosome remodelers, histone variants, epigenetic marks, and other chromatin regulatory factors. These highly dynamic regulatory factors come together to precisely define a chromatin state that is conducive to ES cell maintenance and development, where dysregulation threatens the survival and fitness of the developing organism.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States.
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45
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Lu Q, Fang T. Circular RNA SMARCA5 correlates with favorable clinical tumor features and prognosis, and increases chemotherapy sensitivity in intrahepatic cholangiocarcinoma. J Clin Lab Anal 2019; 34:e23138. [PMID: 31880360 PMCID: PMC7171308 DOI: 10.1002/jcla.23138] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023] Open
Abstract
Objective This present study aimed to investigate the correlation of circular RNA SMARCA5 (circ‐SMARCA5) with clinicopathological features and overall survival (OS), and the effect of circ‐SMARCA5 on cell proliferation and chemotherapy sensitivity to cisplatin/gemcitabine in intrahepatic cholangiocarcinoma (ICC). Methods Totally 92 primary ICC patients who underwent resection were recruited, and their tumor tissues and adjacent tissues were collected for circ‐SMARCA5 detection. The effect of circ‐SMARCA5 on cell proliferation and chemotherapy sensitivity was detected after circ‐SMARCA5 overexpression plasmid transfection into TFK‐1 and HuH‐28 ICC cells. Results Circ‐SMARCA5 expression was reduced in ICC tumor tissues compared to adjacent tissues. Tumor circ‐SMARCA5 high expression was negatively associated with Eastern Cooperative Oncology Group performance score, T stage, N stage, TNM stage, and abnormal CA199 status. Furthermore, OS was increased in patients with tumor circ‐SMARCA5 high expression compared with those with low expression, and further multivariate Cox's regression demonstrated that tumor circ‐SMARCA5 high expression was an independent predictive factor for longer OS. In TFK‐1 and HuH‐28 ICC cells, circ‐SMARCA5 upregulation decreased cell proliferation, reduced relative cell viability in cisplatin‐treated as well as gemcitabine‐treated cells, and also decreased inhibitory concentration by 50% value (IC50) of cisplatin and gemcitabine. Conclusion The correlation of circ‐SMARCA5 with favorable clinical tumor features, survival profile, and its promoting effect on chemotherapy sensitivity implies its potential as a valuable biomarker in monitoring disease progression and prognosis of ICC.
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Affiliation(s)
- Qi Lu
- Department of Hepatobiliary and Pancreatic Surgery, Huangshi Central Hospital of Edong Healthcare Group, Hubei Polytechnic University, Huangshi, China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Huangshi, China
| | - Tao Fang
- Department of Hepatobiliary and Pancreatic Surgery, Huangshi Central Hospital of Edong Healthcare Group, Hubei Polytechnic University, Huangshi, China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Huangshi, China
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46
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Chittori S, Hong J, Bai Y, Subramaniam S. Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome. Nucleic Acids Res 2019; 47:9400-9409. [PMID: 31402386 PMCID: PMC6755096 DOI: 10.1093/nar/gkz670] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/11/2019] [Accepted: 08/03/2019] [Indexed: 12/15/2022] Open
Abstract
ATP-dependent chromatin remodeling factors of SWI/SNF2 family including ISWI, SNF2, CHD1 and INO80 subfamilies share a conserved but functionally non-interchangeable ATPase domain. Here we report cryo-electron microscopy (cryo-EM) structures of the nucleosome bound to an ISWI fragment with deletion of the AutoN and HSS regions in nucleotide-free conditions and the free nucleosome at ∼ 4 Å resolution. In the bound conformation, the ATPase domain interacts with the super helical location 2 (SHL 2) of the nucleosomal DNA, with the N-terminal tail of H4 and with the α1 helix of H3. Density for other regions of ISWI is not observed, presumably due to disorder. Comparison with the structure of the free nucleosome reveals that although the histone core remains largely unchanged, remodeler binding causes perturbations in the nucleosomal DNA resulting in a bulge near the SHL2 site. Overall, the structure of the nucleotide-free ISWI-nucleosome complex is similar to the corresponding regions of the recently reported ADP bound ISWI-nucleosome structures, which are significantly different from that observed for the ADP-BeFx bound structure. Our findings are relevant to the initial step of ISWI binding to the nucleosome and provide additional insights into the nucleosome remodeling process driven by ISWI.
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Affiliation(s)
- Sagar Chittori
- Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.,University of British Columbia, Vancouver, British Columbia, Canada
| | - Jingjun Hong
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Sriram Subramaniam
- University of British Columbia, Vancouver, British Columbia, Canada.,Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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47
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Ting X, Xia L, Yang J, He L, Si W, Shang Y, Sun L. USP11 acts as a histone deubiquitinase functioning in chromatin reorganization during DNA repair. Nucleic Acids Res 2019; 47:9721-9740. [PMID: 31504778 PMCID: PMC6765148 DOI: 10.1093/nar/gkz726] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 08/03/2019] [Accepted: 08/19/2019] [Indexed: 12/27/2022] Open
Abstract
How chromatin dynamics is regulated to ensure efficient DNA repair remains to be understood. Here, we report that the ubiquitin-specific protease USP11 acts as a histone deubiquitinase to catalyze H2AK119 and H2BK120 deubiquitination. We showed that USP11 is physically associated with the chromatin remodeling NuRD complex and functionally involved in DNA repair process. We demonstrated that USP11-mediated histone deubiquitination and NuRD-associated histone deacetylation coordinate to allow timely termination of DNA repair and reorganization of the chromatin structure. As such, USP11 is involved in chromatin condensation, genomic stability, and cell survival. Together, these observations indicate that USP11 is a chromatin modifier critically involved in DNA damage response and the maintenance of genomic stability.
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Affiliation(s)
- Xia Ting
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lu Xia
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Wenzhe Si
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing 100191, China
| | - Yongfeng Shang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Luyang Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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48
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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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49
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Chromatin regulators mediate anthracycline sensitivity in breast cancer. Nat Med 2019; 25:1721-1727. [PMID: 31700186 PMCID: PMC7220800 DOI: 10.1038/s41591-019-0638-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 09/12/2019] [Indexed: 12/26/2022]
Abstract
Anthracyclines are a highly effective component of curative breast cancer chemotherapy, but are associated with significant morbidity1,2. Since anthracyclines work in part via inhibition of topoisomerase-II (TOP2) on accessible DNA3,4, we hypothesized that chromatin regulatory genes (CRGs) that mediate DNA accessibility might predict anthracycline response. We elucidate the role of CRGs in anthracycline sensitivity in breast cancer through integrative analysis of patient and cell line data. We identify a consensus set of 38 CRGs associated with anthracycline response across ten cell line datasets. Evaluating the interaction between expression and treatment in predicting survival in a metacohort of 1006 early-stage breast cancer patients, we identify 54 CRGs whose expression levels dictate anthracycline benefit across the clinical subgroups, 12 of which overlapped with those identified in vitro. CRGs that promote DNA accessibility, including Trithorax complex members, were associated with anthracycline sensitivity when highly expressed, whereas CRGs that reduce accessibility such as Polycomb complex proteins, were associated with decreased anthracycline sensitivity. We show that KDM4B modulates TOP2 accessibility to chromatin, elucidating a mechanism of TOP2 inhibitor sensitivity. These findings indicate that CRGs mediate anthracycline benefit by modulating DNA accessibility with implications for breast cancer patient stratification and treatment decision making.
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50
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Alvarez-Saavedra M, Yan K, De Repentigny Y, Hashem LE, Chaudary N, Sarwar S, Yang D, Ioshikhes I, Kothary R, Hirayama T, Yagi T, Picketts DJ. Snf2h Drives Chromatin Remodeling to Prime Upper Layer Cortical Neuron Development. Front Mol Neurosci 2019; 12:243. [PMID: 31680852 PMCID: PMC6811508 DOI: 10.3389/fnmol.2019.00243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/20/2019] [Indexed: 01/23/2023] Open
Abstract
Alterations in the homeostasis of either cortical progenitor pool, namely the apically located radial glial (RG) cells or the basal intermediate progenitors (IPCs) can severely impair cortical neuron production. Such changes are reflected by microcephaly and are often associated with cognitive defects. Genes encoding epigenetic regulators are a frequent cause of intellectual disability and many have been shown to regulate progenitor cell growth, including our inactivation of the Smarca1 gene encoding Snf2l, which is one of two ISWI mammalian orthologs. Loss of the Snf2l protein resulted in dysregulation of Foxg1 and IPC proliferation leading to macrocephaly. Here we show that inactivation of the closely related Smarca5 gene encoding the Snf2h chromatin remodeler is necessary for embryonic IPC expansion and subsequent specification of callosal projection neurons. Telencephalon-specific Smarca5 cKO embryos have impaired cell cycle kinetics and increased cell death, resulting in fewer Tbr2+ and FoxG1+ IPCs by mid-neurogenesis. These deficits give rise to adult mice with a dramatic reduction in Satb2+ upper layer neurons, and partial agenesis of the corpus callosum. Mice survive into adulthood but molecularly display reduced expression of the clustered protocadherin genes that may further contribute to altered dendritic arborization and a hyperactive behavioral phenotype. Our studies provide novel insight into the developmental function of Snf2h-dependent chromatin remodeling processes during brain development.
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Affiliation(s)
- Matías Alvarez-Saavedra
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Yves De Repentigny
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Lukas E Hashem
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Nidhi Chaudary
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Shihab Sarwar
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Doo Yang
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Ilya Ioshikhes
- Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Rashmi Kothary
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Teruyoshi Hirayama
- KOKORO-Biology Group, Integrated Biology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Department of Anatomy and Developmental Neurobiology, Tokushima University Graduate School of Medical Sciences, Tokushima, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Integrated Biology Laboratories, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Departments of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada
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