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Chauhan AS, Jhujh SS, Stewart GS. E3 ligases: a ubiquitous link between DNA repair, DNA replication and human disease. Biochem J 2024; 481:923-944. [PMID: 38985307 DOI: 10.1042/bcj20240124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 07/11/2024]
Abstract
Maintenance of genome stability is of paramount importance for the survival of an organism. However, genomic integrity is constantly being challenged by various endogenous and exogenous processes that damage DNA. Therefore, cells are heavily reliant on DNA repair pathways that have evolved to deal with every type of genotoxic insult that threatens to compromise genome stability. Notably, inherited mutations in genes encoding proteins involved in these protective pathways trigger the onset of disease that is driven by chromosome instability e.g. neurodevelopmental abnormalities, neurodegeneration, premature ageing, immunodeficiency and cancer development. The ability of cells to regulate the recruitment of specific DNA repair proteins to sites of DNA damage is extremely complex but is primarily mediated by protein post-translational modifications (PTMs). Ubiquitylation is one such PTM, which controls genome stability by regulating protein localisation, protein turnover, protein-protein interactions and intra-cellular signalling. Over the past two decades, numerous ubiquitin (Ub) E3 ligases have been identified to play a crucial role not only in the initiation of DNA replication and DNA damage repair but also in the efficient termination of these processes. In this review, we discuss our current understanding of how different Ub E3 ligases (RNF168, TRAIP, HUWE1, TRIP12, FANCL, BRCA1, RFWD3) function to regulate DNA repair and replication and the pathological consequences arising from inheriting deleterious mutations that compromise the Ub-dependent DNA damage response.
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Affiliation(s)
- Anoop S Chauhan
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Satpal S Jhujh
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
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2
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Novelli F, Yoshikawa Y, Vitto VAM, Modesti L, Minaai M, Pastorino S, Emi M, Kim JH, Kricek F, Bai F, Onuchic JN, Bononi A, Suarez JS, Tanji M, Favaron C, Zolondick AA, Xu R, Takanishi Y, Wang Z, Sakamoto G, Gaudino G, Grzymski J, Grosso F, Schrump DS, Pass HI, Atanesyan L, Smout J, Savola S, Sarin KY, Abolhassani H, Hammarström L, Pan-Hammarström Q, Giorgi C, Pinton P, Yang H, Carbone M. Germline BARD1 variants predispose to mesothelioma by impairing DNA repair and calcium signaling. Proc Natl Acad Sci U S A 2024; 121:e2405231121. [PMID: 38990952 DOI: 10.1073/pnas.2405231121] [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: 03/13/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
We report that ~1.8% of all mesothelioma patients and 4.9% of those younger than 55, carry rare germline variants of the BRCA1 associated RING domain 1 (BARD1) gene that were predicted to be damaging by computational analyses. We conducted functional assays, essential for accurate interpretation of missense variants, in primary fibroblasts that we established in tissue culture from a patient carrying the heterozygous BARD1V523A mutation. We found that these cells had genomic instability, reduced DNA repair, and impaired apoptosis. Investigating the underlying signaling pathways, we found that BARD1 forms a trimeric protein complex with p53 and SERCA2 that regulates calcium signaling and apoptosis. We validated these findings in BARD1-silenced primary human mesothelial cells exposed to asbestos. Our study elucidated mechanisms of BARD1 activity and revealed that heterozygous germline BARD1 mutations favor the development of mesothelioma and increase the susceptibility to asbestos carcinogenesis. These mesotheliomas are significantly less aggressive compared to mesotheliomas in asbestos workers.
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Affiliation(s)
- Flavia Novelli
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Yoshie Yoshikawa
- Department of Genetics, School of Medicine, Hyogo Medical University, Hyogo 663-8501, Japan
| | - Veronica Angela Maria Vitto
- Department of Medical Sciences, Laboratory for Technologies of Advanced Therapies, University of Ferrara, Ferrara 44121, Italy
| | - Lorenzo Modesti
- Department of Medical Sciences, Laboratory for Technologies of Advanced Therapies, University of Ferrara, Ferrara 44121, Italy
| | - Michael Minaai
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Sandra Pastorino
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Mitsuru Emi
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Jin-Hee Kim
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Franz Kricek
- NBS-C Bioscience & Consulting GmbH, Vienna 1230, Austria
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech University, Shanghai 201210, China
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
| | - Angela Bononi
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Joelle S Suarez
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Mika Tanji
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Cristina Favaron
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Alicia A Zolondick
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822
| | - Ronghui Xu
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Yasutaka Takanishi
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Zhanwei Wang
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Greg Sakamoto
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Giovanni Gaudino
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | | | - Federica Grosso
- Mesothelioma Unit, Azienda Ospedaliera Santo Antonio and Santo Biagio (SS) Antonio e Biagio e Cesare Arrigo, Alessandria 15121, Italy
| | - David S Schrump
- Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1201
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University, New York, NY 10016
| | - Lilit Atanesyan
- Department of Oncogenetics, MRC Holland, Amsterdam 1057, the Netherlands
| | - Jan Smout
- Department of Oncogenetics, MRC Holland, Amsterdam 1057, the Netherlands
| | - Suvi Savola
- Department of Oncogenetics, MRC Holland, Amsterdam 1057, the Netherlands
| | - Kavita Y Sarin
- Department of Dermatology, Stanford University Medical Center, Stanford, CA 94305
| | - Hassan Abolhassani
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17165, Sweden
| | - Lennart Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17165, Sweden
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17165, Sweden
| | - Carlotta Giorgi
- Department of Medical Sciences, Laboratory for Technologies of Advanced Therapies, University of Ferrara, Ferrara 44121, Italy
| | - Paolo Pinton
- Department of Medical Sciences, Laboratory for Technologies of Advanced Therapies, University of Ferrara, Ferrara 44121, Italy
| | - Haining Yang
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
| | - Michele Carbone
- Thoracic Oncology, University of Hawaii Cancer Center, Honolulu, HI 96816
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Huang X, Dai Z, Zeng B, Xiao X, Zahid KR, Lin X, Liu T, Zeng T. KIN17 functions in DNA damage repair and chemosensitivity by modulating RAD51 in hepatocellular carcinoma. Hum Cell 2024:10.1007/s13577-024-01096-5. [PMID: 38935235 DOI: 10.1007/s13577-024-01096-5] [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: 04/10/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
The limited response of hepatocellular carcinoma (HCC) to chemotherapy drugs has always been a bottleneck in therapy. DNA damage repair is a major reason for chemoresistance. Previous studies have confirmed that KIN17 affects chemosensitivity. In this study, we examined the impact of KIN17 on chemotherapy response and DNA repair in HCC cells treated with oxaliplatin (L-OHP). We evaluated the expression and biological roles of KIN17 in HCC using bioinformatic analysis. The correlation between KIN17 and RAD51, particularly their nuclear expression levels, was evaluated using immunofluorescence, immunoblotting after nucleocytoplasmic separation in HCC cells, and immunohistochemistry of mouse xenograft tumors and human HCC tissues. The results indicated a significant increase in KIN17 expression in HCC tissues compared to normal tissues. The GSEA analysis revealed that upregulation of KIN17 was significantly associated with DNA damage repair. Knockdown of KIN17 led to increased DNA damage and reduced cellular survival after exposure to L-OHP. On the other hand, overexpression of KIN17 was linked to decreased DNA damage and improved cell survival following L-OHP treatment. Further experiments indicated that KIN17 affects the expression of RAD51, particularly in the nucleus. KIN17 plays a crucial role in influencing the sensitivity of HCC to chemotherapy by triggering the DNA repair response. Increased expression of KIN17 is associated with a poor prognosis for HCC patients, indicating that KIN17 could serve as a prognostic marker and therapeutic target for HCC.
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Affiliation(s)
- Xueran Huang
- Department of Medical Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, P. R. China
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, Guangdong, P. R. China
| | - Zichang Dai
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Biyun Zeng
- School of Medical Technology, Guangdong Medical University, Dongguan, 523808, Guangdong, P. R. China
| | - Xiangyan Xiao
- Department of Medical Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, P. R. China
| | - Kashif Rafiq Zahid
- Department of Radiation Oncology, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Xiaocong Lin
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Zhanjiang, 524023, Guangdong, P. R. China.
| | - Tiancai Liu
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, Guangdong, P. R. China.
| | - Tao Zeng
- Department of Medical Laboratory, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, P. R. China.
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de Baumont AC, Cadore NA, Pedrotti LG, Curzel GD, Schuch JB, Bessel M, Bordignon C, Rosa ML, Macedo GDS, Rosa DD. Germline rare variants in HER2-positive breast cancer predisposition: a systematic review and meta-analysis. Front Oncol 2024; 14:1395970. [PMID: 38978731 PMCID: PMC11228612 DOI: 10.3389/fonc.2024.1395970] [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: 03/04/2024] [Accepted: 06/04/2024] [Indexed: 07/10/2024] Open
Abstract
Introduction Approximately 10% of breast cancer (BC) cases result from hereditary causes. Genetic testing has been widely implemented in BC care to determine hereditary cancer syndromes and personalized medicine. Thus, identification of individuals carrying germline pathogenic variants could be useful to provide appropriate prophylactic or screening measures for each BC subtype, however, there are few formal recommendations for genetic testing in this sense so far. In this study, we assessed rare germline variants in a specific group of genes in order to determine the association with human epidermal growth factor 2 enriched (HER2+) BC phenotype through a systematic review and meta-analysis comparing subtypes overexpressing HER2 with other clinically recognized subtypes of BC. This review was registered with PROSPERO (ID: CRD42023447571). Methods We conducted an online literature search in PubMed (MEDLINE), Scopus, and EMBASE databases. We included original studies that investigated germline variants in HER2+ BC patients and selected the studies that reported only rare and/or pathogenic germline variants. We assessed the risk of bias and quality of the studies using the Joanna Briggs Institute Critical Appraisal checklists and the Modified Newcastle-Ottawa Scale for Genetic Studies, respectively. Considering hormone receptor and HER2 expression status, we compared gene-based risks initially in HR-HER2-, HR+HER2-, HR+HER2+, and HR-HER2+ groups, conducting separate meta-analyses using the random effects model for each comparison, and within them for each gene. Results Of the total 36 studies describing germline variants, 11 studies provided information on the prevalence of variants in the different clinically relevant BC subtypes and allowed comparisons. Germline variants within eight genes showed significant differences when meta-analyzed between the BC groups: BRCA1, BRCA2, TP53, ATM, CHEK2, PALB2, RAD51C, and BARD1. Notably, TP53, ATM, and CHEK2 germline variants were identified as predisposing factors for HER2+ subtypes, whereas BRCA1, BRCA2, PALB2, RAD51C, and BARD1 germline variants were associated with a predisposition to low HER2 expression. Main concerns about bias and quality assessment were the lack of confounding factors control; and comparability or outcome assessment, respectively. Discussion Our findings underscore the connection between germline variants and differential expression of the HER2 protein and BC subtypes. Systematic review registration https://www.crd.york.ac.uk/PROSPERO, identifier CRD42023447571.
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Affiliation(s)
| | - Nathan Araujo Cadore
- Responsabilidade Social, Hospital Moinhos de Vento, Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | | | - Marina Bessel
- Responsabilidade Social, Hospital Moinhos de Vento, Porto Alegre, RS, Brazil
| | - Cláudia Bordignon
- Responsabilidade Social, Hospital Moinhos de Vento, Porto Alegre, RS, Brazil
| | - Mahira Lopes Rosa
- Responsabilidade Social, Hospital Moinhos de Vento, Porto Alegre, RS, Brazil
| | | | - Daniela Dornelles Rosa
- Responsabilidade Social, Hospital Moinhos de Vento, Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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5
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Pavani R, Tripathi V, Vrtis KB, Zong D, Chari R, Callen E, Pankajam AV, Zhen G, Matos-Rodrigues G, Yang J, Wu S, Reginato G, Wu W, Cejka P, Walter JC, Nussenzweig A. Structure and repair of replication-coupled DNA breaks. Science 2024:eado3867. [PMID: 38900911 DOI: 10.1126/science.ado3867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024]
Abstract
Using CRISPR/Cas9 nicking enzymes, we examine the interaction between the replication machinery and single strand breaks, one of the most common forms of endogenous DNA damage. We show that replication fork collapse at leading strand nicks generates resected single-ended double-strand breaks (seDSBs) that are repaired by homologous recombination (HR). If these seDSBs are not promptly repaired, arrival of adjacent forks creates double ended DSBs (deDSBs), which could drive genomic scarring in HR-deficient cancers. deDSBs can also be generated directly when the replication fork bypasses lagging strand nicks. Unlike deDSBs produced independently of replication, end-resection at nick-induced se/deDSBs is BRCA1-independent. Nevertheless, BRCA1 antagonizes 53BP1 suppression of RAD51 filament formation. These results highlight unique mechanisms that maintain replication fork stability.
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Affiliation(s)
- Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Veenu Tripathi
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Kyle B Vrtis
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
| | - Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Raj Chari
- Genome Modification Core, Frederick National Lab for Cancer Research, Frederick, MD, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ajith V Pankajam
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gang Zhen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Jiajie Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Shuheng Wu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Giordano Reginato
- Institute for Research in Biomedicine, Universita della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, 6500, Switzerland
| | - Wei Wu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Petr Cejka
- Institute for Research in Biomedicine, Universita della Svizzera italiana (USI), Faculty of Biomedical Sciences, Bellinzona, 6500, Switzerland
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Blavatnik Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard University, Boston, MA, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
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Cui X, Zhang C, Fu C, Hu J, Li T, Li L. YY1 is involved in homologous recombination inhibition at guanine quadruplex sites in human cells. Nucleic Acids Res 2024:gkae502. [PMID: 38869071 DOI: 10.1093/nar/gkae502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/14/2024] Open
Abstract
Homologous recombination (HR) is a key process for repairing DNA double strand breaks and for promoting genetic diversity. However, HR occurs unevenly across the genome, and certain genomic features can influence its activity. One such feature is the presence of guanine quadruplexes (G4s), stable secondary structures widely distributed throughout the genome. These G4s play essential roles in gene transcription and genome stability regulation. Especially, elevated G4 levels in cells deficient in the Bloom syndrome helicase (BLM) significantly enhance HR at G4 sites, potentially threatening genome stability. Here, we investigated the role of G4-binding protein Yin Yang-1 (YY1) in modulating HR at G4 sites in human cells. Our results show that YY1's binding to G4 structures suppresses sister chromatid exchange after BLM knockdown, and YY1's chromatin occupancy negatively correlates with the overall HR rate observed across the genome. By limiting RAD51 homolog 1 (RAD51) access, YY1 preferentially binds to essential genomic regions, shielding them from excessive HR. Our findings unveil a novel role of YY1-G4 interaction, revealing novel insights into cellular mechanisms involved in HR regulation.
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Affiliation(s)
- Xinyu Cui
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chengwen Zhang
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunqing Fu
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinglei Hu
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tengjiao Li
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin Li
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, Shanghai 200240, China
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7
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Zhong C, Wang H, Yuan X, He Y, Cong J, Yang R, Ma W, Gao L, Gao C, Cui Y, Wu J, Tan R, Pu D. The crucial role of HFM1 in regulating FUS ubiquitination and localization for oocyte meiosis prophase I progression in mice. Biol Res 2024; 57:36. [PMID: 38822414 PMCID: PMC11140966 DOI: 10.1186/s40659-024-00518-w] [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: 02/04/2024] [Accepted: 05/16/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Helicase for meiosis 1 (HFM1), a putative DNA helicase expressed in germ-line cells, has been reported to be closely associated with premature ovarian insufficiency (POI). However, the underlying molecular mechanism has not been clearly elucidated. The aim of this study was to investigate the function of HFM1 in the first meiotic prophase of mouse oocytes. RESULTS The results suggested that the deficiency of HFM1 resulting in increased apoptosis and depletion of oocytes in mice, while the oocytes were arrested in the pachytene stage of the first meiotic prophase. In addition, impaired DNA double-strand break repair and disrupted synapsis were observed in the absence of HFM1. Further investigation revealed that knockout of HFM1 promoted ubiquitination and degradation of FUS protein mediated by FBXW11. Additionally, the depletion of HFM1 altered the intranuclear localization of FUS and regulated meiotic- and oocyte development-related genes in oocytes by modulating the expression of BRCA1. CONCLUSIONS These findings elaborated that the critical role of HFM1 in orchestrating the regulation of DNA double-strand break repair and synapsis to ensure meiosis procession and primordial follicle formation. This study provided insights into the pathogenesis of POI and highlighted the importance of HFM1 in maintaining proper meiotic function in mouse oocytes.
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Affiliation(s)
- Chenyi Zhong
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center of Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Huiyuan Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Xiong Yuan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Yuheng He
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Jing Cong
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Rui Yang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Wenjie Ma
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Li Gao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Chao Gao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Yugui Cui
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Jie Wu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China.
| | - Rongrong Tan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China.
| | - Danhua Pu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China.
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8
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Kyriukha Y, Watkins MB, Redington JM, Dastvan R, Uversky VN, Hopkins JB, Pozzi N, Korolev S. The strand exchange domain of tumor suppressor PALB2 is intrinsically disordered and promotes oligomerization-dependent DNA compaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.01.543259. [PMID: 37333393 PMCID: PMC10274692 DOI: 10.1101/2023.06.01.543259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The Partner and Localizer of BRCA2 (PALB2) is a scaffold protein that links BRCA1 with BRCA2 to initiate homologous recombination (HR). PALB2 interaction with DNA strongly enhances HR efficiency in cells. The PALB2 DNA-binding domain (PALB2-DBD) supports strand exchange, a complex multistep reaction conducted by only a few proteins such as RecA-like recombinases and Rad52. Using bioinformatics analysis, small-angle X-ray scattering, circular dichroism, and electron paramagnetic spectroscopy, we determined that PALB2-DBD is an intrinsically disordered region (IDR) forming compact molten globule-like dimer. IDRs contribute to oligomerization synergistically with the coiled-coil interaction. Using confocal single-molecule FRET we demonstrated that PALB2-DBD compacts single-stranded DNA even in the absence of DNA secondary structures. The compaction is bimodal, oligomerization-dependent, and is driven by IDRs, suggesting a novel strand exchange mechanism. Intrinsically disordered proteins (IDPs) are prevalent in the human proteome. Novel DNA binding properties of PALB2-DBD and the complexity of strand exchange mechanism significantly expands the functional repertoire of IDPs. Multivalent interactions and bioinformatics analysis suggest that PALB2 function is likely to depend on formation of protein-nucleic acids condensates. Similar intrinsically disordered DBDs may use chaperone-like mechanism to aid formation and resolution of DNA and RNA multichain intermediates during DNA replication, repair and recombination.
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Affiliation(s)
- Yevhenii Kyriukha
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Maxwell B Watkins
- The Biophysics Collaborative Access Team (BioCat), Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL
| | - Jennifer M Redington
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Reza Dastvan
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCat), Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
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9
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Schreuder A, Wendel TJ, Dorresteijn CGV, Noordermeer SM. (Single-stranded DNA) gaps in understanding BRCAness. Trends Genet 2024:S0168-9525(24)00100-8. [PMID: 38789375 DOI: 10.1016/j.tig.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024]
Abstract
The tumour-suppressive roles of BRCA1 and 2 have been attributed to three seemingly distinct functions - homologous recombination, replication fork protection, and single-stranded (ss)DNA gap suppression - and their relative importance is under debate. In this review, we examine the origin and resolution of ssDNA gaps and discuss the recent advances in understanding the role of BRCA1/2 in gap suppression. There are ample data showing that gap accumulation in BRCA1/2-deficient cells is linked to genomic instability and chemosensitivity. However, it remains unclear whether there is a causative role and the function of BRCA1/2 in gap suppression cannot unambiguously be dissected from their other functions. We therefore conclude that the three functions of BRCA1 and 2 are closely intertwined and not mutually exclusive.
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Affiliation(s)
- Anne Schreuder
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Tiemen J Wendel
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Carlo G V Dorresteijn
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | - Sylvie M Noordermeer
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
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10
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Salas-Lloret D, García-Rodríguez N, Soto-Hidalgo E, González-Vinceiro L, Espejo-Serrano C, Giebel L, Mateos-Martín ML, de Ru AH, van Veelen PA, Huertas P, Vertegaal ACO, González-Prieto R. BRCA1/BARD1 ubiquitinates PCNA in unperturbed conditions to promote continuous DNA synthesis. Nat Commun 2024; 15:4292. [PMID: 38769345 PMCID: PMC11106271 DOI: 10.1038/s41467-024-48427-6] [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: 08/03/2023] [Accepted: 04/30/2024] [Indexed: 05/22/2024] Open
Abstract
Deficiencies in the BRCA1 tumor suppressor gene are the main cause of hereditary breast and ovarian cancer. BRCA1 is involved in the Homologous Recombination DNA repair pathway and, together with BARD1, forms a heterodimer with ubiquitin E3 activity. The relevance of the BRCA1/BARD1 ubiquitin E3 activity for tumor suppression and DNA repair remains controversial. Here, we observe that the BRCA1/BARD1 ubiquitin E3 activity is not required for Homologous Recombination or resistance to Olaparib. Using TULIP2 methodology, which enables the direct identification of E3-specific ubiquitination substrates, we identify substrates for BRCA1/BARD1. We find that PCNA is ubiquitinated by BRCA1/BARD1 in unperturbed conditions independently of RAD18. PCNA ubiquitination by BRCA1/BARD1 avoids the formation of ssDNA gaps during DNA replication and promotes continuous DNA synthesis. These results provide additional insight about the importance of BRCA1/BARD1 E3 activity in Homologous Recombination.
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Grants
- KWF-KIG 11367/2017-2 KWF Kankerbestrijding (Dutch Cancer Society)
- EMERGIA20_00276 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)
- EMERGIA21_00057 Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)
- 310913 EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))
- MICIU/AEI/10.13039/501100011033 and by European Union NextGenerationEU/PRTR - Grants: CNS2022-135216 ; MICIU/AEI/10.13039/501100011033 and by European Union : PID2021-122361NA-I00
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Affiliation(s)
- Daniel Salas-Lloret
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Néstor García-Rodríguez
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Emily Soto-Hidalgo
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Lourdes González-Vinceiro
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Carmen Espejo-Serrano
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Lisanne Giebel
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - María Luisa Mateos-Martín
- Institute of Biomedicine of Seville, IBiS/Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Proteomics Facility, Sevilla, Spain
| | - Arnoud H de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pablo Huertas
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands.
- Andalusian Centre for Regenerative Medicine and Molecular Biology (CABIMER), Universidad de Sevilla-CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Sevilla, Spain.
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain.
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11
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Uhrig ME, Sharma N, Maxwell P, Selemenakis P, Mazin AV, Wiese C. Disparate requirements for RAD54L in replication fork reversal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.26.550704. [PMID: 37546955 PMCID: PMC10402051 DOI: 10.1101/2023.07.26.550704] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
RAD54L is a DNA motor protein with multiple roles in homologous recombination DNA repair (HR). In vitro , RAD54L was shown to also catalyze the reversal and restoration of model replication forks. In cells, however, little is known about how RAD54L may regulate the dynamics of DNA replication. Here, we show that RAD54L restrains the progression of replication forks and functions as a fork remodeler in human cells. Analogous to HLTF, SMARCAL1, and FBH1, and consistent with a role in fork reversal, RAD54L decelerates fork progression in response to replication stress and suppresses the formation of replication-associated ssDNA gaps. Interestingly, loss of RAD54L prevents nascent strand DNA degradation in both BRCA1/2- and 53BP1-deficient cells, suggesting that RAD54L functions in both pathways of RAD51-mediated replication fork reversal. In the HLTF/SMARCAL1 pathway, RAD54L is critical, but its ability to catalyze branch migration is dispensable, indicative of its function downstream of HLTF/SMARCAL1. Conversely, in the FBH1 pathway, branch migration activity of RAD54L is essential, and FBH1 engagement is dependent on its concerted action with RAD54L. Collectively, our results reveal disparate requirements for RAD54L in two distinct RAD51-mediated fork reversal pathways, positing its potential as a future therapeutic target.
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12
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Hosen MB, Kawasumi R, Hirota K. Dominant roles of BRCA1 in cellular tolerance to a chain-terminating nucleoside analog, alovudine. DNA Repair (Amst) 2024; 137:103668. [PMID: 38460389 DOI: 10.1016/j.dnarep.2024.103668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024]
Abstract
Alovudine is a chain-terminating nucleoside analog (CTNA) that is frequently used as an antiviral and anticancer agent. Generally, CTNAs inhibit DNA replication after their incorporation into nascent DNA during DNA synthesis by suppressing subsequent polymerization, which restricts the proliferation of viruses and cancer cells. Alovudine is a thymidine analog used as an antiviral drug. However, the mechanisms underlying the removal of alovudine and DNA damage tolerance pathways involved in cellular resistance to alovudine remain unclear. Here, we explored the DNA damage tolerance pathways responsible for cellular tolerance to alovudine and found that BRCA1-deficient cells exhibited the highest sensitivity to alovudine. Moreover, alovudine interfered with DNA replication in two distinct mechanisms: first: alovudine incorporated at the end of nascent DNA interfered with subsequent DNA synthesis; second: DNA replication stalled on the alovudine-incorporated template strand. Additionally, BRCA1 facilitated the removal of the incorporated alovudine from nascent DNA, and BRCA1-mediated homologous recombination (HR) contributed to the progressive replication on the alovudine-incorporated template. Thus, we have elucidated the previously unappreciated mechanism of alovudine-mediated inhibition of DNA replication and the role of BRCA1 in cellular tolerance to alovudine.
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Affiliation(s)
- Md Bayejid Hosen
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Ryotaro Kawasumi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.
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13
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Elango R, Nilavar N, Li AG, Duffey EE, Jiang Y, Nguyen D, Abakir A, Willis NA, Houseley J, Scully R. Two-ended recombination at a Flp-nickase-broken replication fork. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588130. [PMID: 38645103 PMCID: PMC11030319 DOI: 10.1101/2024.04.10.588130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Collision of a replication fork with a DNA nick is thought to generate a one-ended break, fostering genomic instability. Collision of the opposing converging fork with the nick could, in principle, form a second DNA end, enabling conservative repair by homologous recombination (HR). To study mechanisms of nickase-induced HR, we developed the Flp recombinase "step arrest" nickase in mammalian cells. Flp-nickase-induced HR entails two-ended, BRCA2/RAD51-dependent short tract gene conversion (STGC), BRCA2/RAD51-independent long tract gene conversion, and discoordinated two-ended invasions. HR induced by a replication-independent break and by the Flp-nickase differ in their dependence on BRCA1 . To determine the origin of the second DNA end during Flp-nickase-induced STGC, we blocked the opposing fork using a site-specific Tus/ Ter replication fork barrier. Flp-nickase-induced STGC remained robust and two-ended. Thus, collision of a single replication fork with a Flp-nick can trigger two-ended HR, possibly reflecting replicative bypass of lagging strand nicks. This response may limit genomic instability during replication of a nicked DNA template.
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14
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Sheng X, Xia Z, Yang H, Hu R. The ubiquitin codes in cellular stress responses. Protein Cell 2024; 15:157-190. [PMID: 37470788 PMCID: PMC10903993 DOI: 10.1093/procel/pwad045] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
Ubiquitination/ubiquitylation, one of the most fundamental post-translational modifications, regulates almost every critical cellular process in eukaryotes. Emerging evidence has shown that essential components of numerous biological processes undergo ubiquitination in mammalian cells upon exposure to diverse stresses, from exogenous factors to cellular reactions, causing a dazzling variety of functional consequences. Various forms of ubiquitin signals generated by ubiquitylation events in specific milieus, known as ubiquitin codes, constitute an intrinsic part of myriad cellular stress responses. These ubiquitination events, leading to proteolytic turnover of the substrates or just switch in functionality, initiate, regulate, or supervise multiple cellular stress-associated responses, supporting adaptation, homeostasis recovery, and survival of the stressed cells. In this review, we attempted to summarize the crucial roles of ubiquitination in response to different environmental and intracellular stresses, while discussing how stresses modulate the ubiquitin system. This review also updates the most recent advances in understanding ubiquitination machinery as well as different stress responses and discusses some important questions that may warrant future investigation.
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Affiliation(s)
- Xiangpeng Sheng
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
- State Key Laboratory of Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhixiong Xia
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hanting Yang
- Department of Neurology, State Key Laboratory of Medical Neurobiology, Institute for Translational Brain Research, MOE Frontiers Center for Brain Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ronggui Hu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
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15
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Zhu Y, Tang S, Yuan Q, Fu J, He J, Liu Z, Zhao X, Li Y, Zhao Y, Zhang Y, Zhang X, Zhang Y, Zhu Y, Wang W, Zheng B, Wu R, Wu T, Yang S, Qiu X, Shen S, Hu J, Chen L, Wang Y, Wang H, Gao D, Chen L. Integrated characterization of hepatobiliary tumor organoids provides a potential landscape of pharmacogenomic interactions. Cell Rep Med 2024; 5:101375. [PMID: 38278146 PMCID: PMC10897507 DOI: 10.1016/j.xcrm.2023.101375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 08/20/2023] [Accepted: 12/15/2023] [Indexed: 01/28/2024]
Abstract
Despite considerable efforts to identify human liver cancer genomic alterations that might unveil druggable targets, the systematic translation of multiomics data remains challenging. Here, we report success in long-term culture of 64 patient-derived hepatobiliary tumor organoids (PDHOs) from a Chinese population. A divergent response to 265 metabolism- and epigenetics-related chemicals and 36 anti-cancer drugs is observed. Integration of the whole genome, transcriptome, chromatin accessibility profiles, and drug sensitivity results of 64 clinically relevant drugs defines over 32,000 genome-drug interactions. RUNX1 promoter mutation is associated with an increase in chromatin accessibility and a concomitant gene expression increase, promoting a cluster of drugs preferentially sensitive in hepatobiliary tumors. These results not only provide an annotated PDHO biobank of human liver cancer but also suggest a systematic approach for obtaining a comprehensive understanding of the gene-regulatory network of liver cancer, advancing the applications of potential personalized medicine.
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Affiliation(s)
- Yanjing Zhu
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China; National Center for Liver Cancer, Shanghai 200438, China
| | - Shijie Tang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Qiuyue Yuan
- CEMS, NCMIS, HCMS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China; School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Fu
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Juan He
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhuang Liu
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofang Zhao
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yunguang Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Zhao
- Institute of Metabolism and Integrative Biology and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yani Zhang
- Institute of Metabolism and Integrative Biology and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoyu Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yangqianwen Zhang
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Yiqin Zhu
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wenwen Wang
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Bo Zheng
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Rui Wu
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China; Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Tong Wu
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Shuai Yang
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xinyao Qiu
- Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Siyun Shen
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Ji Hu
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China
| | - Luonan Chen
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 330106, China; Guangdong Institute of Intelligence Science and Technology, Hengqin, Zhuhai, Guangdong 519031, China.
| | - Yong Wang
- CEMS, NCMIS, HCMS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China; School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China; West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China; Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of the Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou 330106, China.
| | - Hongyang Wang
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China; National Center for Liver Cancer, Shanghai 200438, China; Institute of Metabolism and Integrative Biology and School of Life Sciences, Fudan University, Shanghai 200438, China; Shanghai Key Laboratory of Hepatobiliary Tumor Biology, Shanghai 200438, China.
| | - Dong Gao
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Lei Chen
- The International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, China; National Center for Liver Cancer, Shanghai 200438, China; Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer, Ministry of Education, Shanghai 200438, China.
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16
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Tsukada K, Jones SE, Bannister J, Durin MA, Vendrell I, Fawkes M, Fischer R, Kessler BM, Chapman JR, Blackford AN. BLM and BRCA1-BARD1 coordinate complementary mechanisms of joint DNA molecule resolution. Mol Cell 2024; 84:640-658.e10. [PMID: 38266639 DOI: 10.1016/j.molcel.2023.12.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 10/10/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The Bloom syndrome helicase BLM interacts with topoisomerase IIIα (TOP3A), RMI1, and RMI2 to form the BTR complex, which dissolves double Holliday junctions and DNA replication intermediates to promote sister chromatid disjunction before cell division. In its absence, structure-specific nucleases like the SMX complex (comprising SLX1-SLX4, MUS81-EME1, and XPF-ERCC1) can cleave joint DNA molecules instead, but cells deficient in both BTR and SMX are not viable. Here, we identify a negative genetic interaction between BLM loss and deficiency in the BRCA1-BARD1 tumor suppressor complex. We show that this is due to a previously overlooked role for BARD1 in recruiting SLX4 to resolve DNA intermediates left unprocessed by BLM in the preceding interphase. Consequently, cells with defective BLM and BRCA1-BARD1 accumulate catastrophic levels of chromosome breakage and micronucleation, leading to cell death. Thus, we reveal mechanistic insights into SLX4 recruitment to DNA lesions, with potential clinical implications for treating BRCA1-deficient tumors.
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Affiliation(s)
- Kaima Tsukada
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Samuel E Jones
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Julius Bannister
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Mary-Anne Durin
- MRC Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Matthew Fawkes
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - J Ross Chapman
- MRC Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
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17
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van de Kooij B, Schreuder A, Pavani R, Garzero V, Uruci S, Wendel TJ, van Hoeck A, San Martin Alonso M, Everts M, Koerse D, Callen E, Boom J, Mei H, Cuppen E, Luijsterburg MS, van Vugt MATM, Nussenzweig A, van Attikum H, Noordermeer SM. EXO1 protects BRCA1-deficient cells against toxic DNA lesions. Mol Cell 2024; 84:659-674.e7. [PMID: 38266640 DOI: 10.1016/j.molcel.2023.12.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/14/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Inactivating mutations in the BRCA1 and BRCA2 genes impair DNA double-strand break (DSB) repair by homologous recombination (HR), leading to chromosomal instability and cancer. Importantly, BRCA1/2 deficiency also causes therapeutically targetable vulnerabilities. Here, we identify the dependency on the end resection factor EXO1 as a key vulnerability of BRCA1-deficient cells. EXO1 deficiency generates poly(ADP-ribose)-decorated DNA lesions during S phase that associate with unresolved DSBs and genomic instability in BRCA1-deficient but not in wild-type or BRCA2-deficient cells. Our data indicate that BRCA1/EXO1 double-deficient cells accumulate DSBs due to impaired repair by single-strand annealing (SSA) on top of their HR defect. In contrast, BRCA2-deficient cells retain SSA activity in the absence of EXO1 and hence tolerate EXO1 loss. Consistent with a dependency on EXO1-mediated SSA, we find that BRCA1-mutated tumors show elevated EXO1 expression and increased SSA-associated genomic scars compared with BRCA1-proficient tumors. Overall, our findings uncover EXO1 as a promising therapeutic target for BRCA1-deficient tumors.
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Affiliation(s)
- Bert van de Kooij
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Department of Medical Oncology, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Anne Schreuder
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Veronica Garzero
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Sidrit Uruci
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Tiemen J Wendel
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Arne van Hoeck
- Oncode Institute, Utrecht 3521 AL, the Netherlands; Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht 3584 CG, the Netherlands
| | - Marta San Martin Alonso
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands
| | - Marieke Everts
- Department of Medical Oncology, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Dana Koerse
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jasper Boom
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Edwin Cuppen
- Oncode Institute, Utrecht 3521 AL, the Netherlands; Centre for Molecular Medicine, University Medical Centre Utrecht, Utrecht 3584 CG, the Netherlands; Hartwig Medical Foundation, Amsterdam 1098 XH, the Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands.
| | - Sylvie M Noordermeer
- Department of Human Genetics, Leiden University Medical Centre, Leiden 2333 ZC, the Netherlands; Oncode Institute, Utrecht 3521 AL, the Netherlands.
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Horan TS, Ascenção CFR, Mellor C, Wang M, Smolka MB, Cohen PE. The DNA helicase FANCJ (BRIP1) functions in double strand break repair processing, but not crossover formation during prophase I of meiosis in male mice. PLoS Genet 2024; 20:e1011175. [PMID: 38377115 PMCID: PMC10906868 DOI: 10.1371/journal.pgen.1011175] [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: 11/16/2023] [Revised: 03/01/2024] [Accepted: 02/07/2024] [Indexed: 02/22/2024] Open
Abstract
Meiotic recombination between homologous chromosomes is initiated by the formation of hundreds of programmed double-strand breaks (DSBs). Approximately 10% of these DSBs result in crossovers (COs), sites of physical DNA exchange between homologs that are critical to correct chromosome segregation. Virtually all COs are formed by coordinated efforts of the MSH4/MSH5 and MLH1/MLH3 heterodimers, the latter representing the defining marks of CO sites. The regulation of CO number and position is poorly understood, but undoubtedly requires the coordinated action of multiple repair pathways. In a previous report, we found gene-trap disruption of the DNA helicase, FANCJ (BRIP1/BACH1), elicited elevated numbers of MLH1 foci and chiasmata. In somatic cells, FANCJ interacts with numerous DNA repair proteins including MLH1, and we hypothesized that FANCJ functions with MLH1 to regulate the major CO pathway. To further elucidate the meiotic function of FANCJ, we produced three new Fancj mutant mouse lines via CRISPR/Cas9 gene editing: a full-gene deletion, truncation of the N-terminal Helicase domain, and a C-terminal dual-tagged allele. We also generated an antibody against the C-terminus of the mouse FANCJ protein. Surprisingly, none of our Fancj mutants show any change in either MLH1 focus counts during pachynema or total CO number at diakinesis of prophase I. We find evidence that FANCJ and MLH1 do not interact in meiosis; further, FANCJ does not co-localize with MSH4, MLH1, or MLH3 in meiosis. Instead, FANCJ co-localizes with BRCA1 and TOPBP1, forming discrete foci along the chromosome cores beginning in early meiotic prophase I and densely localized to unsynapsed chromosome axes in late zygonema and to the XY chromosomes in early pachynema. Fancj mutants also exhibit a subtle persistence of DSBs in pachynema. Collectively, these data indicate a role for FANCJ in early DSB repair, but they rule out a role for FANCJ in MLH1-mediated CO events.
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Affiliation(s)
- Tegan S. Horan
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, New York, United States of America
| | - Carolline F. R. Ascenção
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, New York, United States of America
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Christopher Mellor
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Meng Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Marcus B. Smolka
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, New York, United States of America
- Weill Institute for Cell and Molecular Biology, Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Paula E. Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, New York, United States of America
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19
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Ito M, Fujita Y, Shinohara A. Positive and negative regulators of RAD51/DMC1 in homologous recombination and DNA replication. DNA Repair (Amst) 2024; 134:103613. [PMID: 38142595 DOI: 10.1016/j.dnarep.2023.103613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/10/2023] [Accepted: 12/10/2023] [Indexed: 12/26/2023]
Abstract
RAD51 recombinase plays a central role in homologous recombination (HR) by forming a nucleoprotein filament on single-stranded DNA (ssDNA) to catalyze homology search and strand exchange between the ssDNA and a homologous double-stranded DNA (dsDNA). The catalytic activity of RAD51 assembled on ssDNA is critical for the DNA-homology-mediated repair of DNA double-strand breaks in somatic and meiotic cells and restarting stalled replication forks during DNA replication. The RAD51-ssDNA complex also plays a structural role in protecting the regressed/reversed replication fork. Two types of regulators control RAD51 filament formation, stability, and dynamics, namely positive regulators, including mediators, and negative regulators, so-called remodelers. The appropriate balance of action by the two regulators assures genome stability. This review describes the roles of positive and negative RAD51 regulators in HR and DNA replication and its meiosis-specific homolog DMC1 in meiotic recombination. We also provide future study directions for a comprehensive understanding of RAD51/DMC1-mediated regulation in maintaining and inheriting genome integrity.
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Affiliation(s)
- Masaru Ito
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
| | - Yurika Fujita
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
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20
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Randall MP, Egolf LE, Vaksman Z, Samanta M, Tsang M, Groff D, Evans JP, Rokita JL, Layeghifard M, Shlien A, Maris JM, Diskin SJ, Bosse KR. BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma. J Natl Cancer Inst 2024; 116:138-148. [PMID: 37688570 PMCID: PMC10777668 DOI: 10.1093/jnci/djad182] [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: 03/10/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND High-risk neuroblastoma is a complex genetic disease that is lethal in more than 50% of patients despite intense multimodal therapy. Through genome-wide association studies (GWAS) and next-generation sequencing, we have identified common single nucleotide polymorphisms and rare, pathogenic or likely pathogenic germline loss-of-function variants in BARD1 enriched in neuroblastoma patients. The functional implications of these findings remain poorly understood. METHODS We correlated BARD1 genotype with expression in normal tissues and neuroblastomas, along with the burden of DNA damage in tumors. To validate the functional consequences of germline pathogenic or likely pathogenic BARD1 variants, we used CRISPR-Cas9 to generate isogenic neuroblastoma (IMR-5) and control (RPE1) cellular models harboring heterozygous BARD1 loss-of-function variants (R112*, R150*, E287fs, and Q564*) and quantified genomic instability in these cells via next-generation sequencing and with functional assays measuring the efficiency of DNA repair. RESULTS Both common and rare neuroblastoma-associated BARD1 germline variants were associated with lower levels of BARD1 mRNA and an increased burden of DNA damage. Using isogenic heterozygous BARD1 loss-of-function variant cellular models, we functionally validated this association with inefficient DNA repair. BARD1 loss-of-function variant isogenic cells exhibited reduced efficiency in repairing Cas9-induced DNA damage, ineffective RAD51 focus formation at DNA double-strand break sites, and enhanced sensitivity to cisplatin and poly (ADP-ribose) polymerase (PARP) inhibition both in vitro and in vivo. CONCLUSIONS Taken together, we demonstrate that germline BARD1 variants disrupt DNA repair fidelity. This is a fundamental molecular mechanism contributing to neuroblastoma initiation that may have important therapeutic implications.
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Affiliation(s)
- Michael P Randall
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura E Egolf
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Zalman Vaksman
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Current affiliation: New York Genome Center, New York, NY
| | - Minu Samanta
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthew Tsang
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - David Groff
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - J Perry Evans
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Current affiliation: Genomics and Data Sciences, Spark Therapeutics, Philadelphia, PA
| | - Jo Lynne Rokita
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mehdi Layeghifard
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Adam Shlien
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Sharon J Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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21
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Wynen F, Krautstrunk J, Müller LM, Graf V, Brinkmann V, Fritz G. Cisplatin-induced DNA crosslinks trigger neurotoxicity in C. elegans. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119591. [PMID: 37730131 DOI: 10.1016/j.bbamcr.2023.119591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023]
Abstract
The anticancer drug cisplatin (CisPt) injures post-mitotic neuronal cells, leading to neuropathy. Furthermore, CisPt triggers cell death in replicating cells. Here, we aim to unravel the relevance of different types of CisPt-induced DNA lesions for evoking neurotoxicity. To this end, we comparatively analyzed wild-type and loss of function mutants of C. elegans lacking key players of specific DNA repair pathways. Deficiency in ercc-1, which is essential for nucleotide excision repair (NER) and interstrand crosslink (ICL) repair, revealed the most pronounced enhancement in CisPt-induced neurotoxicity with respect to the functionality of post-mitotic chemosensory AWA neurons, without inducing neuronal cell death. Potentiation of CisPt-triggered neurotoxicity in ercc-1 mutants was accompanied by complex alterations in both basal and CisPt-stimulated mRNA expression of genes involved in the regulation of neurotransmission, including cat-4, tph-1, mod-1, glr-1, unc-30 and eat-18. Moreover, xpf-1, csb-1, csb-1;xpc-1 and msh-6 mutants were significantly more sensitive to CisPt-induced neurotoxicity than the wild-type, whereas xpc-1, msh-2, brc-1 and dog-1 mutants did not distinguish from the wild-type. The majority of DNA repair mutants also revealed increased basal germline apoptosis, which was analyzed for control. Yet, only xpc-1, xpc-1;csb-1 and dog-1 mutants showed elevated apoptosis in the germline following CisPt treatment. To conclude, we provide evidence that neurotoxicity, including sensory neurotoxicity, is triggered by CisPt-induced DNA intra- and interstrand crosslinks that are subject of repair by NER and ICL repair. We hypothesize that especially ERCC1/XPF, CSB and MSH6-related DNA repair protects from chemotherapy-induced neuropathy in the context of CisPt-based anticancer therapy.
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Affiliation(s)
- Fabian Wynen
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute of Toxicology, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Johannes Krautstrunk
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute of Toxicology, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Lisa Marie Müller
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute of Toxicology, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Viktoria Graf
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute of Toxicology, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Vanessa Brinkmann
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute of Toxicology, Moorenstraße 5, 40225 Düsseldorf, Germany.
| | - Gerhard Fritz
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute of Toxicology, Moorenstraße 5, 40225 Düsseldorf, Germany.
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22
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Ahmad T, Kawasumi R, Taniguchi T, Abe T, Terada K, Tsuda M, Shimizu N, Tsurimoto T, Takeda S, Hirota K. The proofreading exonuclease of leading-strand DNA polymerase epsilon prevents replication fork collapse at broken template strands. Nucleic Acids Res 2023; 51:12288-12302. [PMID: 37944988 PMCID: PMC10711444 DOI: 10.1093/nar/gkad999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/03/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023] Open
Abstract
Leading-strand DNA replication by polymerase epsilon (Polϵ) across single-strand breaks (SSBs) causes single-ended double-strand breaks (seDSBs), which are repaired via homology-directed repair (HDR) and suppressed by fork reversal (FR). Although previous studies identified many molecules required for hydroxyurea-induced FR, FR at seDSBs is poorly understood. Here, we identified molecules that specifically mediate FR at seDSBs. Because FR at seDSBs requires poly(ADP ribose)polymerase 1 (PARP1), we hypothesized that seDSB/FR-associated molecules would increase tolerance to camptothecin (CPT) but not the PARP inhibitor olaparib, even though both anti-cancer agents generate seDSBs. Indeed, we uncovered that Polϵ exonuclease and CTF18, a Polϵ cofactor, increased tolerance to CPT but not olaparib. To explore potential functional interactions between Polϵ exonuclease, CTF18, and PARP1, we created exonuclease-deficient POLE1exo-/-, CTF18-/-, PARP1-/-, CTF18-/-/POLE1exo-/-, PARP1-/-/POLE1exo-/-, and CTF18-/-/PARP1-/- cells. Epistasis analysis indicated that Polϵ exonuclease and CTF18 were interdependent and required PARP1 for CPT tolerance. Remarkably, POLE1exo-/- and HDR-deficient BRCA1-/- cells exhibited similar CPT sensitivity. Moreover, combining POLE1exo-/- with BRCA1-/- mutations synergistically increased CPT sensitivity. In conclusion, the newly identified PARP1-CTF18-Polϵ exonuclease axis and HDR act independently to prevent fork collapse at seDSBs. Olaparib inhibits this axis, explaining the pronounced cytotoxic effects of olaparib on HDR-deficient cells.
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Affiliation(s)
- Tasnim Ahmad
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Ryotaro Kawasumi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Tomoya Taniguchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Takuya Abe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Kazuhiro Terada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki 210-9501, Japan
| | - Naoto Shimizu
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Toshiki Tsurimoto
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shunichi Takeda
- Shenzhen University, School of Medicine, Shenzhen, Guangdong 518060, China
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
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23
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Abstract
PURPOSE The transcription factor NF-E2-related factor 2 (NRF2) is a master regulator widely involved in essential cellular functions such as DNA repair. By clarifying the upstream and downstream links of NRF2 to DNA damage repair, we hope that attention will be drawn to the utilization of NRF2 as a target for cancer therapy. METHODS Query and summarize relevant literature on the role of NRF2 in direct repair, BER, NER, MMR, HR, and NHEJ in pubmed. Make pictures of Roles of NRF2 in DNA Damage Repair and tables of antioxidant response elements (AREs) of DNA repair genes. Analyze the mutation frequency of NFE2L2 in different types of cancer using cBioPortal online tools. By using TCGA, GTEx and GO databases, analyze the correlation between NFE2L2 mutations and DNA repair systems as well as the degree of changes in DNA repair systems as malignant tumors progress. RESULTS NRF2 plays roles in maintaining the integrity of the genome by repairing DNA damage, regulating the cell cycle, and acting as an antioxidant. And, it possibly plays roles in double stranded break (DSB) pathway selection following ionizing radiation (IR) damage. Whether pathways such as RNA modification, ncRNA, and protein post-translational modification affect the regulation of NRF2 on DNA repair is still to be determined. The overall mutation frequency of the NFE2L2 gene in esophageal carcinoma, lung cancer, and penile cancer is the highest. Genes (50 of 58) that are negatively correlated with clinical staging are positively correlated with NFE2L2 mutations or NFE2L2 expression levels. CONCLUSION NRF2 participates in a variety of DNA repair pathways and plays important roles in maintaining genome stability. NRF2 is a potential target for cancer treatment.
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Affiliation(s)
- Jiale Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
| | - Chang Xu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China.
| | - Qiang Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China.
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24
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Ronson GE, Starowicz K, Anthony EJ, Piberger AL, Clarke LC, Garvin AJ, Beggs AD, Whalley CM, Edmonds MJ, Beesley JFJ, Morris JR. Mechanisms of synthetic lethality between BRCA1/2 and 53BP1 deficiencies and DNA polymerase theta targeting. Nat Commun 2023; 14:7834. [PMID: 38030626 PMCID: PMC10687250 DOI: 10.1038/s41467-023-43677-2] [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: 01/31/2022] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
A synthetic lethal relationship exists between disruption of polymerase theta (Polθ), and loss of either 53BP1 or homologous recombination (HR) proteins, including BRCA1; however, the mechanistic basis of these observations are unclear. Here we reveal two distinct mechanisms of Polθ synthetic lethality, identifying dual influences of 1) whether Polθ is lost or inhibited, and 2) the underlying susceptible genotype. Firstly, we find that the sensitivity of BRCA1/2- and 53BP1-deficient cells to Polθ loss, and 53BP1-deficient cells to Polθ inhibition (ART558) requires RAD52, and appropriate reduction of RAD52 can ameliorate these phenotypes. We show that in the absence of Polθ, RAD52 accumulations suppress ssDNA gap-filling in G2/M and encourage MRE11 nuclease accumulation. In contrast, the survival of BRCA1-deficient cells treated with Polθ inhibitor are not restored by RAD52 suppression, and ssDNA gap-filling is prevented by the chemically inhibited polymerase itself. These data define an additional role for Polθ, reveal the mechanism underlying synthetic lethality between 53BP1, BRCA1/2 and Polθ loss, and indicate genotype-dependent Polθ inhibitor mechanisms.
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Affiliation(s)
- George E Ronson
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Katarzyna Starowicz
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Adthera Bio, Lyndon House, 62 Hagley Road, Birmingham, B16 8PE, UK
| | - Elizabeth J Anthony
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ann Liza Piberger
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Lucy C Clarke
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- West Midlands Regional Genetics Laboratory, Birmingham Women's Hospital, Mindelsohn Way, Birmingham, B15 2TG, UK
| | - Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- University of Leeds, Leeds, UK
| | - Andrew D Beggs
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Genomics Birmingham, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Celina M Whalley
- Genomics Birmingham, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Matthew J Edmonds
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Certara Insight, Danebrook Court, Oxford Office Village, Kidlington, Oxfordshire, OX5 1LQ, UK
| | - James F J Beesley
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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25
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Fang L, Sun Y, Dong M, Yang M, Hao J, Li J, Zhang H, He N, Du L, Xu C. RMI1 facilitates repair of ionizing radiation-induced DNA damage and maintenance of genomic stability. Cell Death Discov 2023; 9:426. [PMID: 38007566 PMCID: PMC10676437 DOI: 10.1038/s41420-023-01726-1] [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: 07/05/2023] [Revised: 11/08/2023] [Accepted: 11/15/2023] [Indexed: 11/27/2023] Open
Abstract
Ionizing radiation (IR) causes a wide variety of DNA lesions, of which DNA double-stranded breaks (DSBs) are the most deleterious. Homologous recombination (HR) is a crucial route responsible for repairing DSBs. RecQ-mediated genome instability protein 1 (RMI1) is a member of an evolutionarily conserved Bloom syndrome complex, which prevents and resolves aberrant recombination products during HR, thereby promoting genome stability. However, little is known about the role of RMI1 in regulating the cellular response to IR. This study aimed to understand the cellular functions and molecular mechanisms by which RMI1 maintains genomic stability after IR exposure. Here, we showed IR upregulated the RMI1 protein level and induced RMI1 relocation to the DNA damage sites. We also demonstrated that the loss of RMI1 in cells resulted in enhanced levels of DNA damage, sustained cell cycle arrest, and impaired HR repair after IR, leading to reduced cell viability and elevated genome instability. Taken together, our results highlighted the direct roles of RMI1 in response to DNA damage induced by IR and implied that RMI1 might be a new genome safeguard molecule to radiation-induced damage.
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Affiliation(s)
- Lianying Fang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
- School of Preventive Medicine Sciences, Institute of Radiation Medicine, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Yuxiao Sun
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
| | - Mingxin Dong
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
| | - Mengmeng Yang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
| | - Jianxiu Hao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
| | - Jiale Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
| | - Huanteng Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
| | - Ningning He
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China.
| | - Liqing Du
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China.
| | - Chang Xu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China.
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26
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Wang Z, Castillo-González CM, Zhao C, Tong CY, Li C, Zhong S, Liu Z, Xie K, Zhu J, Wu Z, Peng X, Jacob Y, Michaels SD, Jacobsen SE, Zhang X. H3.1K27me1 loss confers Arabidopsis resistance to Geminivirus by sequestering DNA repair proteins onto host genome. Nat Commun 2023; 14:7484. [PMID: 37980416 PMCID: PMC10657422 DOI: 10.1038/s41467-023-43311-1] [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: 10/05/2022] [Accepted: 11/06/2023] [Indexed: 11/20/2023] Open
Abstract
The H3 methyltransferases ATXR5 and ATXR6 deposit H3.1K27me1 to heterochromatin to prevent genomic instability and transposon re-activation. Here, we report that atxr5 atxr6 mutants display robust resistance to Geminivirus. The viral resistance is correlated with activation of DNA repair pathways, but not with transposon re-activation or heterochromatin amplification. We identify RAD51 and RPA1A as partners of virus-encoded Rep protein. The two DNA repair proteins show increased binding to heterochromatic regions and defense-related genes in atxr5 atxr6 vs wild-type plants. Consequently, the proteins have reduced binding to viral DNA in the mutant, thus hampering viral amplification. Additionally, RAD51 recruitment to the host genome arise via BRCA1, HOP2, and CYCB1;1, and this recruitment is essential for viral resistance in atxr5 atxr6. Thus, Geminiviruses adapt to healthy plants by hijacking DNA repair pathways, whereas the unstable genome, triggered by reduced H3.1K27me1, could retain DNA repairing proteins to suppress viral amplification in atxr5 atxr6.
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Affiliation(s)
- Zhen Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX, 77843, USA
| | | | - Changjiang Zhao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Chun-Yip Tong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Songxiao Zhong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Zhiyang Liu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Kaili Xie
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jiaying Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Zhongshou Wu
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xu Peng
- Department of Molecular Physiology, College of Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Yannick Jacob
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Scott D Michaels
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX, 77843, USA.
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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27
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Burdett H, Foglizzo M, Musgrove LJ, Kumar D, Clifford G, Campbell L, Heath GR, Zeqiraj E, Wilson M. BRCA1-BARD1 combines multiple chromatin recognition modules to bridge nascent nucleosomes. Nucleic Acids Res 2023; 51:11080-11103. [PMID: 37823591 PMCID: PMC10639053 DOI: 10.1093/nar/gkad793] [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: 04/06/2023] [Revised: 08/02/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
Chromatin association of the BRCA1-BARD1 heterodimer is critical to promote homologous recombination repair of DNA double-strand breaks (DSBs) in S/G2. How the BRCA1-BARD1 complex interacts with chromatin that contains both damage induced histone H2A ubiquitin and inhibitory H4K20 methylation is not fully understood. We characterised BRCA1-BARD1 binding and enzymatic activity to an array of mono- and di-nucleosome substrates using biochemical, structural and single molecule imaging approaches. We found that the BRCA1-BARD1 complex preferentially interacts and modifies di-nucleosomes over mono-nucleosomes, allowing integration of H2A Lys-15 ubiquitylation signals with other chromatin modifications and features. Using high speed- atomic force microscopy (HS-AFM) to monitor how the BRCA1-BARD1 complex recognises chromatin in real time, we saw a highly dynamic complex that bridges two nucleosomes and associates with the DNA linker region. Bridging is aided by multivalent cross-nucleosome interactions that enhance BRCA1-BARD1 E3 ubiquitin ligase catalytic activity. Multivalent interactions across nucleosomes explain how BRCA1-BARD1 can recognise chromatin that retains partial di-methylation at H4 Lys-20 (H4K20me2), a parental histone mark that blocks BRCA1-BARD1 interaction with nucleosomes, to promote its enzymatic and DNA repair activities.
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Affiliation(s)
- Hayden Burdett
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Martina Foglizzo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Laura J Musgrove
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Dhananjay Kumar
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Gillian Clifford
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Lisa J Campbell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - George R Heath
- Astbury Centre for Structural Molecular Biology, School of Physics & Astronomy and Biomedical Sciences, Faculty of Engineering & Physical Sciences and Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
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28
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Wu Y, Chen S, Shao Y, Su Y, Li Q, Wu J, Zhu J, Wen H, Huang Y, Zheng Z, Chen X, Ju X, Huang S, Wu X, Hu Z. KLF5 Promotes Tumor Progression and Parp Inhibitor Resistance in Ovarian Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304638. [PMID: 37702443 PMCID: PMC10625120 DOI: 10.1002/advs.202304638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/16/2023] [Indexed: 09/14/2023]
Abstract
One major characteristic of tumor cells is the aberrant activation of epigenetic regulatory elements, which remodel the tumor transcriptome and ultimately promote cancer progression and drug resistance. However, the oncogenic functions and mechanisms of ovarian cancer (OC) remain elusive. Here, super-enhancer (SE) regulatory elements that are aberrantly activated in OC are identified and it is found that SEs drive the relative specific expression of the transcription factor KLF5 in OC patients and poly(ADP-ribose) polymerase inhibitor (PARPi)-resistant patients. KLF5 expression is associated with poor outcomes in OC patients and can drive tumor progression in vitro and in vivo. Mechanistically, KLF5 forms a transcriptional complex with EHF and ELF3 and binds to the promoter region of RAD51 to enhance its transcription, strengthening the homologous recombination repair (HRR) pathway. Notably, the combination of suberoylanilide hydroxamic acid (SAHA) and olaparib significantly inhibits tumor growth and metastasis of PARPi-resistant OC cells with high KLF5. In conclusion, it is discovered that SEs-driven KLF5 is a key regulatory factor in OC progression and PARPi resistance; and potential therapeutic strategies for OC patients with PARPi resistance and high KLF5 are identified.
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Affiliation(s)
- Yong Wu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Siyu Chen
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yang Shao
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Ying Su
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Qin Li
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Jiangchun Wu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Jun Zhu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Hao Wen
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Yan Huang
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Zhong Zheng
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Xiaojun Chen
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Xingzhu Ju
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Shenglin Huang
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Xiaohua Wu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Zhixiang Hu
- Department of Gynecologic OncologyFudan University Shanghai Cancer CenterShanghai Key Laboratory of Medical EpigeneticsInternational Co‐laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
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29
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Chen Y, Chen Y, Li Q, Liu H, Han J, Zhang H, Cheng L, Lin G. Short C-terminal Musashi-1 proteins regulate pluripotency states in embryonic stem cells. Cell Rep 2023; 42:113308. [PMID: 37858462 DOI: 10.1016/j.celrep.2023.113308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/04/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
The RNA-binding protein Musashi-1 (MSI1) regulates the proliferation and differentiation of adult stem cells. However, its role in embryonic stem cells (ESCs) and early embryonic development remains poorly understood. Here, we report the presence of short C-terminal MSI1 (MSI1-C) proteins in early mouse embryos and mouse ESCs, but not in human ESCs, under conventional culture conditions. In mouse embryos and mESCs, deletion of MSI1-C together with full-length MSI1 causes early embryonic developmental arrest and pluripotency dissolution. MSI1-C is induced upon naive induction and facilitates hESC naive pluripotency acquisition, elevating the pluripotency of primed hESCs toward a formative-like state. MSI1-C proteins are nuclear localized and bind to RNAs involved in DNA-damage repair (including MLH1, BRCA1, and MSH2), conferring on hESCs better survival in human-mouse interspecies cell competition and prolonged ability to form blastoids. This study identifies MSI1-C as an essential regulator in ESC pluripotency states and early embryonic development.
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Affiliation(s)
- Youwei Chen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China; Clinical Center for Brain and Spinal Cord Research, Medical School, Tongji University, Shanghai, China
| | - Ying Chen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Qianyan Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Huahua Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiazhen Han
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hailin Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Liming Cheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China; Clinical Center for Brain and Spinal Cord Research, Medical School, Tongji University, Shanghai, China.
| | - Gufa Lin
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China; Clinical Center for Brain and Spinal Cord Research, Medical School, Tongji University, Shanghai, China.
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30
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Ito M, Furukohri A, Matsuzaki K, Fujita Y, Toyoda A, Shinohara A. FIGNL1 AAA+ ATPase remodels RAD51 and DMC1 filaments in pre-meiotic DNA replication and meiotic recombination. Nat Commun 2023; 14:6857. [PMID: 37891173 PMCID: PMC10611733 DOI: 10.1038/s41467-023-42576-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
The formation of RAD51/DMC1 filaments on single-stranded (ss)DNAs essential for homology search and strand exchange in DNA double-strand break (DSB) repair is tightly regulated. FIGNL1 AAA+++ ATPase controls RAD51-mediated recombination in human cells. However, its role in gametogenesis remains unsolved. Here, we characterized a germ line-specific conditional knockout (cKO) mouse of FIGNL1. Fignl1 cKO male mice showed defective chromosome synapsis and impaired meiotic DSB repair with the accumulation of RAD51/DMC1 on meiotic chromosomes, supporting a positive role of FIGNL1 in homologous recombination at a post-assembly stage of RAD51/DMC1 filaments. Fignl1 cKO spermatocytes also accumulate RAD51/DMC1 on chromosomes in pre-meiotic S-phase. These RAD51/DMC1 assemblies are independent of meiotic DSB formation. We also showed that purified FIGNL1 dismantles RAD51 filament on double-stranded (ds)DNA as well as ssDNA. These results suggest an additional role of FIGNL1 in limiting the non-productive assembly of RAD51/DMC1 on native dsDNAs during pre-meiotic S-phase and meiotic prophase I.
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Affiliation(s)
- Masaru Ito
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Asako Furukohri
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kenichiro Matsuzaki
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan
| | - Yurika Fujita
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan.
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31
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Liu W, Feng W, Zhang Y, Lei T, Wang X, Qiao T, Chen Z, Song W. RP11-789C1.1 inhibits gastric cancer cell proliferation and accelerates apoptosis via the ATR/CHK1 signaling pathway. Chin Med J (Engl) 2023:00029330-990000000-00827. [PMID: 37882063 DOI: 10.1097/cm9.0000000000002869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) plays an important role in the progression of gastric cancer (GC). Their involvement ranges from genetic regulation to cancer progression. However, the mechanistic roles of RP11-789C1.1 in GC are not fully understood. METHODS We identified the expression of lncRNA RP11-789C1.1 in GC tissues and cell lines by real-time fluorescent quantitative polymerase chain reaction. A series of functional experiments revealed the effect of RP11-789C1.1 on the proliferation of GC cells. In vivo experiments verified the effect of RP11-789C1.1 on the biological behavior of a GC cell line. RNA pull-down unveiled RP11-789C1.1 interacting proteins. Western blot analysis indicated the downstream pathway changes of RP11-789C1.1, and an oxaliplatin dosing experiment disclosed the influence of RP11-789C1.1 on the drug sensitivity of oxaliplatin. RESULTS Our results demonstrated that RP11-789C1.1 inhibited the proliferation of GC cells and promoted the apoptosis of GC cells. Mechanistically, RP11-789C1.1 inhibited checkpoint kinase 1 (CHK1) phosphorylation by binding ataxia-telangiectasia mutated and Rad3 related (ATR), a serine/threonine-specific protein kinase, promoted GC apoptosis, and mediated oxaliplatin sensitivity. CONCLUSION In general, we discovered a tumor suppressor molecule RP11-789C1.1 and confirmed its mechanism of action, providing a theoretical basis for targeted GC therapy.
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Affiliation(s)
- Wenwei Liu
- Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518000, China
| | - Wei Feng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Yongxin Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Tianxiang Lei
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xiaofeng Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Tang Qiao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Zehong Chen
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Wu Song
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
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32
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Wang M, Li W, Tomimatsu N, Yu CH, Ji JH, Alejo S, Witus SR, Alimbetov D, Fitzgerald O, Wu B, Wang Q, Huang Y, Gan Y, Dong F, Kwon Y, Sareddy GR, Curiel TJ, Habib AA, Hromas R, Dos Santos Passos C, Yao T, Ivanov DN, Brzovic PS, Burma S, Klevit RE, Zhao W. Crucial roles of the BRCA1-BARD1 E3 ubiquitin ligase activity in homology-directed DNA repair. Mol Cell 2023; 83:3679-3691.e8. [PMID: 37797621 PMCID: PMC10591799 DOI: 10.1016/j.molcel.2023.09.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/08/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
The tumor-suppressor breast cancer 1 (BRCA1) in complex with BRCA1-associated really interesting new gene (RING) domain 1 (BARD1) is a RING-type ubiquitin E3 ligase that modifies nucleosomal histone and other substrates. The importance of BRCA1-BARD1 E3 activity in tumor suppression remains highly controversial, mainly stemming from studying mutant ligase-deficient BRCA1-BARD1 species that we show here still retain significant ligase activity. Using full-length BRCA1-BARD1, we establish robust BRCA1-BARD1-mediated ubiquitylation with specificity, uncover multiple modes of activity modulation, and construct a truly ligase-null variant and a variant specifically impaired in targeting nucleosomal histones. Cells expressing either of these BRCA1-BARD1 separation-of-function alleles are hypersensitive to DNA-damaging agents. Furthermore, we demonstrate that BRCA1-BARD1 ligase is not only required for DNA resection during homology-directed repair (HDR) but also contributes to later stages for HDR completion. Altogether, our findings reveal crucial, previously unrecognized roles of BRCA1-BARD1 ligase activity in genome repair via HDR, settle prior controversies regarding BRCA1-BARD1 ligase functions, and catalyze new efforts to uncover substrates related to tumor suppression.
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Affiliation(s)
- Meiling Wang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Wenjing Li
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Nozomi Tomimatsu
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Corey H Yu
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Jae-Hoon Ji
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Salvador Alejo
- Department of Obstetrics & Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Samuel R Witus
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Dauren Alimbetov
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - O'Taveon Fitzgerald
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Bo Wu
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Qijing Wang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yuxin Huang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yaqi Gan
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Felix Dong
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Youngho Kwon
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Gangadhara R Sareddy
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Tyler J Curiel
- Geisel School of Medicine at Dartmouth and Department of Medicine, Dartmouth Health, Lebanon, NH 03765, USA
| | - Amyn A Habib
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Robert Hromas
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Carolina Dos Santos Passos
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Dmitri N Ivanov
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Peter S Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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Horan TS, Ascenção CFR, Mellor CA, Wang M, Smolka MB, Cohen PE. The DNA helicase FANCJ (BRIP1) functions in Double Strand Break repair processing, but not crossover formation during Prophase I of meiosis in male mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561296. [PMID: 37873301 PMCID: PMC10592954 DOI: 10.1101/2023.10.06.561296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
During meiotic prophase I, recombination between homologous parental chromosomes is initiated by the formation of hundreds of programmed double-strand breaks (DSBs), each of which must be repaired with absolute fidelity to ensure genome stability of the germline. One outcome of these DSB events is the formation of Crossovers (COs), the sites of physical DNA exchange between homologs that are critical to ensure the correct segregation of parental chromosomes. However, COs account for only a small (~10%) proportion of all DSB repair events; the remaining 90% are repaired as non-crossovers (NCOs), most by synthesis dependent strand annealing. Virtually all COs are formed by coordinated efforts of the MSH4/MSH5 and MLH1/MLH3 heterodimers. The number and positioning of COs is exquisitely controlled via mechanisms that remain poorly understood, but which undoubtedly require the coordinated action of multiple repair pathways downstream of the initiating DSB. In a previous report we found evidence suggesting that the DNA helicase and Fanconi Anemia repair protein, FANCJ (BRIP1/BACH1), functions to regulate meiotic recombination in mouse. A gene-trap disruption of Fancj showed an elevated number of MLH1 foci and COs. FANCJ is known to interact with numerous DNA repair proteins in somatic cell repair contexts, including MLH1, BLM, BRCA1, and TOPBP1, and we hypothesized that FANCJ regulates CO formation through a direct interaction with MLH1 to suppress the major CO pathway. To further elucidate the function of FANCJ in meiosis, we produced three new Fancj mutant mouse lines via CRISPR/Cas9 gene editing: a full-gene deletion, a mutant line lacking the MLH1 interaction site and the N-terminal region of the Helicase domain, and a C-terminal 6xHIS-HA dual-tagged allele of Fancj. We also generated an antibody against the C-terminus of the mouse FANCJ protein. Surprisingly, while Fanconi-like phenotypes are observed within the somatic cell lineages of the full deletion Fancj line, none of the Fancj mutants show any change in either MLH1 focus counts during pachynema or total CO number at diakinesis of prophase I of meiosis. We find evidence that FANCJ and MLH1 do not interact in meiosis; further, FANCJ does not co-localize with MSH4, MLH1, or MLH3 during late prophase I. Instead, FANCJ forms discrete foci along the chromosome cores beginning in early meiotic prophase I, occasionally co-localizing with MSH4, and then becomes densely localized on unsynapsed chromosome axes in late zygonema and to the XY chromosomes in early pachynema. Strikingly, this localization strongly overlaps with BRCA1 and TOPBP1. Fancj mutants also exhibit a subtle persistence of DSBs in pachynema. Collectively, these data suggest a role for FANCJ in early DSB repair events, and possibly in the formation of NCOs, but they rule out a role for FANCJ in MLH1-mediated CO events. Thus, the role of FANCJ in meiotic cells involves different pathways and different interactors to those described in somatic cell lineages.
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Affiliation(s)
- Tegan S Horan
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, NY 14853
| | - Carolline F R Ascenção
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, NY 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | | | - Meng Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853
| | - Marcus B Smolka
- Cornell Reproductive Sciences Center, Cornell University, Ithaca, NY 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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Ayala-Zambrano C, Yuste M, Frias S, Garcia-de-Teresa B, Mendoza L, Azpeitia E, Rodríguez A, Torres L. A Boolean network model of the double-strand break repair pathway choice. J Theor Biol 2023; 573:111608. [PMID: 37595867 DOI: 10.1016/j.jtbi.2023.111608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/20/2023]
Abstract
Double strand break (DSB) repair is critical to maintaining the integrity of the genome. DSB repair deficiency underlies multiple pathologies, including cancer, chromosome instability syndromes, and, potentially, neurodevelopmental defects. DSB repair is mainly handled by two pathways: highly accurate homologous recombination (HR), which requires a sister chromatid for template-based repair, limited to S/G2 phases of the cell cycle, and canonical non-homologous end joining (c-NHEJ), available throughout the cell cycle in which minimum homology is sufficient for highly efficient yet error-prone repair. Some circumstances, such as cancer, require alternative highly mutagenic DSB repair pathways like microhomology-mediated end-joining (MMEJ) and single-strand annealing (SSA), which are triggered to attend to DNA damage. These non-canonical repair alternatives are emerging as prominent drivers of resistance in drug-based tumor therapies. Multiple DSB repair options require tight inter-pathway regulation to prevent unscheduled activities. In addition to this complexity, epigenetic modifications of the histones surrounding the DSB region are emerging as critical regulators of the DSB repair pathway choice. Modeling approaches to understanding DSBs repair pathway choice are advantageous to perform simulations and generate predictions on previously uncharacterized aspects of DSBs response. In this work, we present a Boolean network model of the DSB repair pathway choice that incorporates the knowledge, into a dynamic system, of the inter-pathways regulation involved in DSB repair, i.e., HR, c-NHEJ, SSA, and MMEJ. Our model recapitulates the well-characterized HR activity observed in wild-type cells in response to DSBs. It also recovers clinically relevant behaviors of BRCA1/FANCS mutants, and their corresponding drug resistance mechanisms ascribed to DNA repair gain-of-function pathogenic variants. Since epigenetic modifiers are dynamic and possible druggable targets, we incorporated them into our model to better characterize their involvement in DSB repair. Our model predicted that loss of the TIP60 complex and its corresponding histone acetylation activity leads to activation of SSA in response to DSBs. Our experimental validation showed that TIP60 effectively prevents activation of RAD52, a key SSA executor, and confirms the suitable use of Boolean network modeling for understanding DNA DSB repair.
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Affiliation(s)
- Cecilia Ayala-Zambrano
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - Mariana Yuste
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Sara Frias
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico; Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apartado Postal 70228, Ciudad de México 04510, Mexico
| | | | - Luis Mendoza
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apartado Postal 70228, Ciudad de México 04510, Mexico
| | - Eugenio Azpeitia
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia, Mexico
| | - Alfredo Rodríguez
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Apartado Postal 70228, Ciudad de México 04510, Mexico; Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico.
| | - Leda Torres
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico.
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Kyriukha Y, Watkins MB, Redington JM, Dastvan R, Uversky VN, Hopkins J, Pozzi N, Korolev S. The PALB2 DNA-binding domain is an intrinsically disordered recombinase. RESEARCH SQUARE 2023:rs.3.rs-3235465. [PMID: 37790553 PMCID: PMC10543426 DOI: 10.21203/rs.3.rs-3235465/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The Partner and Localizer of BRCA2 (PALB2) tumor suppressor is a scaffold protein that links BRCA1 with BRCA2 to initiate homologous recombination (HR). PALB2 interaction with DNA strongly enhances HR efficiency. The PALB2 DNA-binding domain (PALB2-DBD) supports DNA strand exchange, a complex multistep reaction supported by only a few protein families such as RecA-like recombinases or Rad52. The mechanisms of PALB2 DNA binding and strand exchange are unknown. We performed circular dichroism, electron paramagnetic spectroscopy, and small-angle X-ray scattering analyses and determined that PALB2-DBD is intrinsically disordered, even when bound to DNA. The intrinsically disordered nature of this domain was further supported by bioinformatics analysis. Intrinsically disordered proteins (IDPs) are prevalent in the human proteome and have many important biological functions. The complexity of the strand exchange reaction significantly expands the functional repertoire of IDPs. The results of confocal single-molecule FRET indicated that PALB2-DBD binding leads to oligomerization-dependent DNA compaction. We hypothesize that PALB2-DBD uses a chaperone-like mechanism to aid formation and resolution of complex DNA and RNA multichain intermediates during DNA replication and repair. Since PALB2-DBD alone or within the full-length PALB2 is predicted to have strong liquid-liquid phase separation (LLPS) potential, protein-nucleic acids condensates are likely to play a role in complex functionality of PALB2-DBD. Similar DNA-binding intrinsically disordered regions may represent a novel class of functional domains that evolved to function in eukaryotic nucleic acid metabolism complexes.
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Affiliation(s)
- Yevhenii Kyriukha
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | | | - Jennifer M Redington
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Reza Dastvan
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Jesse Hopkins
- BioCat, Advanced Photon Source, Argonne National Lab, Argonne, IL
| | - Nicola Pozzi
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
| | - Sergey Korolev
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St Louis, MO
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36
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Park J, Kim JY, Park JW, Kang JY, Oh H, Hahm J, Chae YC, Chakravarti D, Seo S. INHAT subunit SET/TAF-Iβ regulates PRC1-independent H2AK119 mono-ubiquitination via E3 ligase MIB1 in colon cancer. NAR Cancer 2023; 5:zcad050. [PMID: 37746636 PMCID: PMC10516711 DOI: 10.1093/narcan/zcad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/21/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023] Open
Abstract
SET/TAF-Iβ, a subunit of the inhibitor of acetyltransferases (INHAT) complex, exhibits transcriptional repression activity by inhibiting histone acetylation. We find that SET/TAF-Iβ regulates mono-ubiquitination of histone H2A at lysine 119 (H2AK119ub), which is involved in polycomb-mediated transcriptional repression, in HCT116 cells. In this report, we demonstrate that SET/TAF-Iβ acts as an E2 ubiquitin-conjugating enzyme for PRC1-independent H2AK119ub. Furthermore, we identify that MIB1 is the E3 ligase partner for SET/TAF-Iβ using LC-MS/MS and in vitro ubiquitination assays. Transcriptome analysis reveals that SET/TAF-Iβ and MIB1 regulate the expression of genes related to DNA replication and cell cycle progression in HCT116 cells, and knockdown of either protein reduces proliferation of HCT116 cells by impeding cell cycle progression. Together, our study reveals a novel PRC1-independent epigenetic regulatory mechanism for H2AK119ub by SET/TAF-Iβ and MIB1 in colon cancer.
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Affiliation(s)
- Junyoung Park
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ji-Young Kim
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jin Woo Park
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Joo Young Kang
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyein Oh
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ja Young Hahm
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yun-Cheol Chae
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Debabrata Chakravarti
- Division of Reproductive Sciences in Medicine, Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sang Beom Seo
- Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul 06974, Republic of Korea
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37
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Zhou Z, Yang H, Liang X, Zhou T, Zhang T, Yang Y, Wang J, Wang W. C1orf112 teams up with FIGNL1 to facilitate RAD51 filament disassembly and DNA interstrand cross-link repair. Cell Rep 2023; 42:112907. [PMID: 37515771 DOI: 10.1016/j.celrep.2023.112907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/19/2023] [Accepted: 07/14/2023] [Indexed: 07/31/2023] Open
Abstract
The recombinase RAD51 plays a core role in DNA repair by homologous recombination (HR). The assembly and disassembly of RAD51 filament need to be orderly regulated by mediators such as BRCA2 and anti-recombinases. To screen for potential regulators of RAD51, we perform RAD51 proximity proteomics and identify factor C1orf112. We further find that C1orf112 complexed with FIGNL1 facilitates RAD51 filament disassembly in the HR step of Fanconi anemia (FA) pathway. Specifically, C1orf112 physically interacts with FIGNL1 and enhances its protein stability. Meanwhile, the RAD51 filament disassembly activity of FIGNL1 is directly stimulated by C1orf112. BRCA2 directly interacts with C1orf112-FIGNL1 complex and functions upstream of this complex to protect RAD51 filament from premature disassembly. C1orf112- and FIGNL1-deficient cells are primarily sensitive to DNA interstrand cross-link (ICL) agents. Thus, these findings suggest an important function of C1orf112 in RAD51 regulation in the HR step of ICL repair by FA pathway.
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Affiliation(s)
- Zenan Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Han Yang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xinxin Liang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tao Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tao Zhang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yang Yang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
| | - Weibin Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
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Li X, Gao D, Shen F, Chen H, Zhang Z, He C, Gao A, Lang Y, Zhu X, Zhou J, Shang ZF, Ding WQ, Zhu J. Polymerase iota (POLI) confers radioresistance of esophageal squamous cell carcinoma by regulating RAD51 stability and facilitating homologous recombination. Cell Death Discov 2023; 9:291. [PMID: 37558683 PMCID: PMC10412619 DOI: 10.1038/s41420-023-01541-8] [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: 04/13/2023] [Revised: 06/15/2023] [Accepted: 07/03/2023] [Indexed: 08/11/2023] Open
Abstract
Radiotherapy resistance is an important and urgent challenge in the clinical management of esophageal squamous carcinoma (ESCC). However, the factors mediating the ESCC resistance to radiotherapy and its underlying molecular mechanisms are not fully clarified. Our previous studies have demonstrated the critical role of DNA polymerase iota (POLI) in ESCC development and progression, here, we aimed to investigate the involvement of POLI in ESCC radiotherapy resistance and elucidate the underlying molecular mechanism. We found that highly expressed POLI was correlated with shorter overall survival of ESCC patients received radiotherapy. Down-regulation of POLI sensitized ESCC to IR, prolonged γH2AX foci in nuclei and comet tails after IR. HR but not NHEJ repair is inhibited in POLI-deficient ESCC cells. POLI stabilizes RAD51 protein via competitively binding with and blocking the interaction between RAD51 and E3 ligase XIAP and XIAP-mediated ubiquitination. Furthermore, loss of POLI leads to the activation of GAS signaling. Our findings provide novel insight into the role of POLI in the development of radioresistance mediated by stabilizing RAD51 protein in ESCC.
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Affiliation(s)
- Xiaoqing Li
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Dexuan Gao
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Fei Shen
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hengrui Chen
- Department of Radiation Oncology, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Zhuqiang Zhang
- Department of Radiation Medicine, Baotou Medical College, Baotou, China
| | - Chao He
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Aidi Gao
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Yue Lang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Xiaozhong Zhu
- Department of Cardiothoracic Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jundong Zhou
- Suzhou Cancer Center Core Laboratory, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China.
- Department of Radiation Oncology, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China.
| | - Zeng-Fu Shang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China.
| | - Wei-Qun Ding
- Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Ji Zhu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
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Nie C, Zhou XA, Zhou J, Liu Z, Gu Y, Liu W, Zhan J, Li S, Xiong Y, Zhou M, Shen Q, Wang W, Yang E, Wang J. A transcription-independent mechanism determines rapid periodic fluctuations of BRCA1 expression. EMBO J 2023; 42:e111951. [PMID: 37334492 PMCID: PMC10390875 DOI: 10.15252/embj.2022111951] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 04/28/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023] Open
Abstract
BRCA1 expression is highly regulated to prevent genomic instability and tumorigenesis. Dysregulation of BRCA1 expression correlates closely with sporadic basal-like breast cancer and ovarian cancer. The most significant characteristic of BRCA1 regulation is periodic expression fluctuation throughout the cell cycle, which is important for the orderly progression of different DNA repair pathways throughout the various cell cycle phases and for further genomic stability. However, the underlying mechanism driving this phenomenon is poorly understood. Here, we demonstrate that RBM10-mediated RNA alternative splicing coupled to nonsense-mediated mRNA decay (AS-NMD), rather than transcription, determines the periodic fluctuations in G1/S-phase BRCA1 expression. Furthermore, AS-NMD broadly regulates the expression of period genes, such as DNA replication-related genes, in an uneconomical but more rapid manner. In summary, we identified an unexpected posttranscriptional mechanism distinct from canonical processes that mediates the rapid regulation of BRCA1 as well as other period gene expression during the G1/S-phase transition and provided insights into potential targets for cancer therapy.
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Affiliation(s)
- Chen Nie
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijingChina
| | - Xiao Albert Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijingChina
| | - Jiadong Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijingChina
| | - Zelin Liu
- Department of Medical Bioinformatics, Institute of Systems Biomedicine, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
| | - Yangyang Gu
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijingChina
| | - Wanchang Liu
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijingChina
| | - Jun Zhan
- Department of Anatomy, Histology and Embryology, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
| | - Shiwei Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijingChina
| | - Yundong Xiong
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijingChina
| | - Mei Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijingChina
| | - Qinjian Shen
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijingChina
| | - Weibin Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijingChina
| | - Ence Yang
- Department of Medical Bioinformatics, Institute of Systems Biomedicine, School of Basic Medical SciencesPeking University Health Science CenterBeijingChina
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems BiologyPeking University Health Science CenterBeijingChina
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40
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Witus SR, Tuttle LM, Li W, Zelter A, Wang M, Kermoade KE, Wilburn DB, Davis TN, Brzovic PS, Zhao W, Klevit RE. BRCA1/BARD1 intrinsically disordered regions facilitate chromatin recruitment and ubiquitylation. EMBO J 2023; 42:e113565. [PMID: 37305927 PMCID: PMC10390874 DOI: 10.15252/embj.2023113565] [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: 01/19/2023] [Revised: 04/10/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023] Open
Abstract
BRCA1/BARD1 is a tumor suppressor E3 ubiquitin (Ub) ligase with roles in DNA damage repair and in transcriptional regulation. BRCA1/BARD1 RING domains interact with nucleosomes to facilitate mono-ubiquitylation of distinct residues on the C-terminal tail of histone H2A. These enzymatic domains constitute a small fraction of the heterodimer, raising the possibility of functional chromatin interactions involving other regions such as the BARD1 C-terminal domains that bind nucleosomes containing the DNA damage signal H2A K15-Ub and H4 K20me0, or portions of the expansive intrinsically disordered regions found in both subunits. Herein, we reveal novel interactions that support robust H2A ubiquitylation activity mediated through a high-affinity, intrinsically disordered DNA-binding region of BARD1. These interactions support BRCA1/BARD1 recruitment to chromatin and sites of DNA damage in cells and contribute to their survival. We also reveal distinct BRCA1/BARD1 complexes that depend on the presence of H2A K15-Ub, including a complex where a single BARD1 subunit spans adjacent nucleosome units. Our findings identify an extensive network of multivalent BARD1-nucleosome interactions that serve as a platform for BRCA1/BARD1-associated functions on chromatin.
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Affiliation(s)
- Samuel R Witus
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Lisa M Tuttle
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Wenjing Li
- Department of Biochemistry and Structural BiologyUniversity of Texas Health Science Center at San AntonioSan AntonioTXUSA
| | - Alex Zelter
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Meiling Wang
- Department of Biochemistry and Structural BiologyUniversity of Texas Health Science Center at San AntonioSan AntonioTXUSA
| | | | - Damien B Wilburn
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
- Department of Chemistry and BiochemistryThe Ohio State UniversityColumbusOHUSA
| | - Trisha N Davis
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Peter S Brzovic
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Weixing Zhao
- Department of Biochemistry and Structural BiologyUniversity of Texas Health Science Center at San AntonioSan AntonioTXUSA
| | - Rachel E Klevit
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
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Yin S, Liu L, Gan W. PRMT1 and PRMT5: on the road of homologous recombination and non-homologous end joining. GENOME INSTABILITY & DISEASE 2023; 4:197-209. [PMID: 37663901 PMCID: PMC10470524 DOI: 10.1007/s42764-022-00095-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/28/2022] [Indexed: 09/05/2023]
Abstract
DNA double-strand breaks (DSBs) are widely accepted to be the most deleterious form of DNA lesions that pose a severe threat to genome integrity. Two predominant pathways are responsible for repair of DSBs, homologous recombination (HR) and non-homologous end-joining (NHEJ). HR relies on a template to faithfully repair breaks, while NHEJ is a template-independent and error-prone repair mechanism. Multiple layers of regulation have been documented to dictate the balance between HR and NHEJ, such as cell cycle and post-translational modifications (PTMs). Arginine methylation is one of the most common PTMs, which is catalyzed by protein arginine methyltransferases (PRMTs). PRMT1 and PRMT5 are the predominate PRMTs that promote asymmetric dimethylarginine and symmetric dimethylarginine, respectively. They have emerged to be crucial regulators of DNA damage repair. In this review, we summarize current understanding and unaddressed questions of PRMT1 and PRMT5 in regulation of HR and NHEJ, providing insights into their roles in DSB repair pathway choice and the potential of targeting them for cancer therapy.
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Affiliation(s)
- Shasha Yin
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Liu Liu
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Wenjian Gan
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA
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Zhou H, Xie C, Xie Y, He Y, Chen Y, Zhang C, Zhang Y, Zhao Y, Liu H. UBQLN1 deficiency mediates telomere shortening and IPF through interacting with RPA1. PLoS Genet 2023; 19:e1010856. [PMID: 37463174 PMCID: PMC10381042 DOI: 10.1371/journal.pgen.1010856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
Premature telomere shortening is a known factor correlated to idiopathic pulmonary fibrosis (IPF) occurrence, which is a chronic, progressive, age-related disease with high mortality. The etiology of IPF is still unknown. Here, we found that UBQLN1 plays a key role in telomere length maintenance and is potentially relevant to IPF. UBQLN1 involves in DNA replication by interacting with RPA1 and shuttling it off from the replication fork. The deficiency of UBQLN1 retains RPA1 at replication fork, hinders replication and thus causes cell cycle arrest and genome instability. Especially at telomere regions of the genome, where more endogenous replication stress exists because of G rich sequences, UBQLN1 depletion leads to rapid telomere shortening in HeLa cells. It revealed that UBQLN1 depletion also shortens telomere length at mouse lung and accelerates mouse lung fibrosis. In addition, the UBQLN1 expression level in IPF patients is downregulated and correlated to poor prognosis. Altogether, these results uncover a new role of UBQLN1 in ensuring DNA replication and maintaining telomere stability, which may shed light on IPF pathogenesis and prevention.
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Affiliation(s)
- Haoxian Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Department of Cardiology, Guangdong Provincial Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Chen Xie
- Cardiovascular Department, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yujie Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yunru He
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanlian Chen
- Cardiovascular Department, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Canfeng Zhang
- Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yan Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Haiying Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Han D, Wang L, Jiang S, Yang Q. The ubiquitin-proteasome system in breast cancer. Trends Mol Med 2023:S1471-4914(23)00096-5. [PMID: 37328395 DOI: 10.1016/j.molmed.2023.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 06/18/2023]
Abstract
Ubiquitin-proteasome system (UPS) is a selective proteolytic system that is associated with the expression or function of target proteins and participates in various physiological and pathological processes of breast cancer. Inhibitors targeting the 26S proteasome in combination with other drugs have shown promising therapeutic effects in the clinical treatment of breast cancer. Moreover, several inhibitors/stimulators targeting other UPS components are also effective in preclinical studies, but have not yet been applied in the clinical treatment of breast cancer. Therefore, it is vital to comprehensively understand the functions of ubiquitination in breast cancer and to identify potential tumor promoters or tumor suppressors among UPS family members, with the aim of developing more effective and specific inhibitors/stimulators targeting specific components of this system.
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Affiliation(s)
- Dianwen Han
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China
| | - Lijuan Wang
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China
| | - Shan Jiang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China; Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, Shandong 250012, China; Research Institute of Breast Cancer, Shandong University, Jinan, Shandong 250012, China.
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44
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Chen JK, Wiedemann J, Nguyen L, Lin Z, Tahir M, Hui CC, Plikus MV, Andersen B. IRX5 promotes DNA damage repair and activation of hair follicle stem cells. Stem Cell Reports 2023; 18:1227-1243. [PMID: 37084727 PMCID: PMC10202659 DOI: 10.1016/j.stemcr.2023.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/23/2023] Open
Abstract
The molecular mechanisms allowing hair follicles to periodically activate their stem cells (HFSCs) are incompletely characterized. Here, we identify the transcription factor IRX5 as a promoter of HFSC activation. Irx5-/- mice have delayed anagen onset, with increased DNA damage and diminished HFSC proliferation. Open chromatin regions form near cell cycle progression and DNA damage repair genes in Irx5-/- HFSCs. DNA damage repair factor BRCA1 is an IRX5 downstream target. Inhibition of FGF kinase signaling partially rescues the anagen delay in Irx5-/- mice, suggesting that the Irx5-/- HFSC quiescent phenotype is partly due to failure to suppress Fgf18 expression. Interfollicular epidermal stem cells also show decreased proliferation and increased DNA damage in Irx5-/-mice. Consistent with a role for IRX5 as a promoter of DNA damage repair, we find that IRX genes are upregulated in many cancer types and that there is a correlation between IRX5 and BRCA1 expression in breast cancer.
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Affiliation(s)
- Jefferson K Chen
- Departments of Biological Chemistry and Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Julie Wiedemann
- Departments of Biological Chemistry and Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine, Irvine, CA, USA; Mathematical, Computational and Systems Biology (MCSB) Program, University of California, Irvine, Irvine, CA, USA
| | - Ly Nguyen
- Departments of Biological Chemistry and Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Zhongqi Lin
- Departments of Biological Chemistry and Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Mahum Tahir
- Departments of Biological Chemistry and Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Chi-Chung Hui
- Program in Developmental & Stem Cell Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Bogi Andersen
- Departments of Biological Chemistry and Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine, Irvine, CA, USA.
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Ma Y, Mu X, Gao R, Zhang Y, Geng Y, Chen X, Yin X, Li F, He J. Maternal exposure to dibutyl phthalate regulates MSH6 crotonylation to impair homologous recombination in fetal oocytes. JOURNAL OF HAZARDOUS MATERIALS 2023; 455:131540. [PMID: 37167869 DOI: 10.1016/j.jhazmat.2023.131540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/12/2023] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
Homologous recombination (HR) during early oogenesis repairs programmed double-strand breaks (DSBs) to ensure female fertility and offspring health. The exposure of fetal ovaries to endocrine disrupting chemicals (EDCs) can cause reproductive disorders in the adulthood. The EDC dibutyl phthalate (DBP) is widely distributed in flexible plastic products, leading to ubiquitous human exposure. Here, we report that maternal exposure to DBP caused gross aberrations in meiotic prophase I of fetal oocytes, including delayed progression, impaired DNA damage response, uncoupled localization of DMC1 and RAD51, and decreased HR. However, programmed DSBs were efficiently repaired. DBP exposure negatively regulated lysine crotonylation (Kcr) of MSH6. Similar meiotic defects were observed in fetal ovaries with targeted disruption of Msh6, and mutation of K544cr of MSH6 impaired its association with Ku70, thereby promoting non-homologous end joining (NHEJ) and inhibiting HR. Unlike mature F1 females, F2 female mice exhibited premature follicular activation, precocious puberty, and anxiety-like behaviors. Therefore, DBP can influence early meiotic events, and Kcr of MSH6 may regulate preferential induction of HR or NHEJ for DNA repair during meiosis.
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Affiliation(s)
- Yidan Ma
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Xinyi Mu
- Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China; College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Rufei Gao
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Yan Zhang
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Yanqing Geng
- Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China; College of Basic Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xuemei Chen
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Xin Yin
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Fangfang Li
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China
| | - Junlin He
- Department of Health Toxicology, School of Public Health, Chongqing Medical University, Chongqing 400016, PR China; Joint International Research Laboratory of Reproduction & Development, Chongqing Medical University, Chongqing 400016, PR China.
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Chen H, Yang QL, Xu JX, Deng X, Zhang YJ, Liu T, Rots MG, Xu GL, Huang KY. Efficient methods for multiple types of precise gene-editing in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 37310200 DOI: 10.1111/tpj.16265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
Precise gene-editing using CRISPR/Cas9 technology remains a long-standing challenge, especially for genes with low expression and no selectable phenotypes in Chlamydomonas reinhardtii, a classic model for photosynthesis and cilia research. Here, we developed a multi-type and precise genetic manipulation method in which a DNA break was generated by Cas9 nuclease and the repair was mediated using a homologous DNA template. The efficacy of this method was demonstrated for several types of gene editing, including inactivation of two low-expression genes (CrTET1 and CrKU80), the introduction of a FLAG-HA epitope tag into VIPP1, IFT46, CrTET1 and CrKU80 genes, and placing a YFP tag into VIPP1 and IFT46 for live-cell imaging. We also successfully performed a single amino acid substitution for the FLA3, FLA10 and FTSY genes, and documented the attainment of the anticipated phenotypes. Lastly, we demonstrated that precise fragment deletion from the 3'-UTR of MAA7 and VIPP1 resulted in a stable knock-down effect. Overall, our study has established efficient methods for multiple types of precise gene editing in Chlamydomonas, enabling substitution, insertion and deletion at the base resolution, thus improving the potential of this alga in both basic research and industrial applications.
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Affiliation(s)
- Hui Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qing-Lin Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jia-Xi Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yun-Jie Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ting Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Key Laboratory of Medical Epigenetics, Laboratory of Cancer Epigenetics, Institutes of Biomedical Sciences, Medical College of Fudan University, Chinese Academy of Medical Sciences (RU069), Shanghai, China
| | - Kai-Yao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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Xie D, Huang Q, Zhou P. Drug Discovery Targeting Post-Translational Modifications in Response to DNA Damages Induced by Space Radiation. Int J Mol Sci 2023; 24:ijms24087656. [PMID: 37108815 PMCID: PMC10142602 DOI: 10.3390/ijms24087656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
DNA damage in astronauts induced by cosmic radiation poses a major barrier to human space exploration. Cellular responses and repair of the most lethal DNA double-strand breaks (DSBs) are crucial for genomic integrity and cell survival. Post-translational modifications (PTMs), including phosphorylation, ubiquitylation, and SUMOylation, are among the regulatory factors modulating a delicate balance and choice between predominant DSB repair pathways, such as non-homologous end joining (NHEJ) and homologous recombination (HR). In this review, we focused on the engagement of proteins in the DNA damage response (DDR) modulated by phosphorylation and ubiquitylation, including ATM, DNA-PKcs, CtIP, MDM2, and ubiquitin ligases. The involvement and function of acetylation, methylation, PARylation, and their essential proteins were also investigated, providing a repository of candidate targets for DDR regulators. However, there is a lack of radioprotectors in spite of their consideration in the discovery of radiosensitizers. We proposed new perspectives for the research and development of future agents against space radiation by the systematic integration and utilization of evolutionary strategies, including multi-omics analyses, rational computing methods, drug repositioning, and combinations of drugs and targets, which may facilitate the use of radioprotectors in practical applications in human space exploration to combat fatal radiation hazards.
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Affiliation(s)
- Dafei Xie
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology (BKLRB), Beijing Institute of Radiation Medicine, Taiping Road 27th, Haidian District, Beijing 100850, China
| | - Qi Huang
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology (BKLRB), Beijing Institute of Radiation Medicine, Taiping Road 27th, Haidian District, Beijing 100850, China
- Department of Preventive Medicine, School of Public Health, University of South China, Changsheng West Road 28th, Zhengxiang District, Hengyang 421001, China
| | - Pingkun Zhou
- Department of Radiation Biology, Beijing Key Laboratory for Radiobiology (BKLRB), Beijing Institute of Radiation Medicine, Taiping Road 27th, Haidian District, Beijing 100850, China
- Department of Preventive Medicine, School of Public Health, University of South China, Changsheng West Road 28th, Zhengxiang District, Hengyang 421001, China
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Biegała Ł, Gajek A, Marczak A, Rogalska A. Olaparib-Resistant BRCA2MUT Ovarian Cancer Cells with Restored BRCA2 Abrogate Olaparib-Induced DNA Damage and G2/M Arrest Controlled by the ATR/CHK1 Pathway for Survival. Cells 2023; 12:cells12071038. [PMID: 37048111 PMCID: PMC10093185 DOI: 10.3390/cells12071038] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The PARP inhibitor (PARPi) olaparib is currently the drug of choice for serous ovarian cancer (OC), especially in patients with homologous recombination (HR) repair deficiency associated with deleterious BRCA1/2 mutations. Unfortunately, OC patients who fail to respond to PARPi or relapse after treatment have limited therapeutic options. To elucidate olaparib resistance and enhance the efficacy of olaparib, intracellular factors exploited by OC cells to achieve decreased sensitivity to PARPi were examined. An olaparib-resistant OC cell line, PEO1-OR, was established from BRCA2MUT PEO1 cells. The anticancer activity and action of olaparib combined with inhibitors of the ATR/CHK1 pathway (ceralasertib as ATRi, MK-8776 as CHK1i) in olaparib-sensitive and -resistant OC cell lines were evaluated. Whole-exome sequencing revealed that PEO1-OR cells acquire resistance through subclonal enrichment of BRCA2 secondary mutations that restore functional full-length protein. Moreover, PEO1-OR cells upregulate HR repair-promoting factors (BRCA1, BRCA2, RAD51) and PARP1. Olaparib-inducible activation of the ATR/CHK1 pathway and G2/M arrest is abrogated in olaparib-resistant cells. Drug sensitivity assays revealed that PEO1-OR cells are less sensitive to ATRi and CHK1i agents. Combined treatment is less effective in olaparib-resistant cells considering inhibition of metabolic activity, colony formation, survival, accumulation of DNA double-strand breaks, and chromosomal aberrations. However, synergistic antitumor activity between compounds is achievable in PEO1-OR cells. Collectively, olaparib-resistant cells display co-existing HR repair-related mechanisms that confer resistance to olaparib, which may be effectively utilized to resensitize them to PARPi via combination therapy. Importantly, the addition of ATR/CHK1 pathway inhibitors to olaparib has the potential to overcome acquired resistance to PARPi.
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Zhou Y, Xing X, Zhou J, Jiang H, Cen P, Jin C, Zhong Y, Zhou R, Wang J, Tian M, Zhang H. Therapeutic potential of tumor treating fields for malignant brain tumors. Cancer Rep (Hoboken) 2023; 6:e1813. [PMID: 36987739 PMCID: PMC10172187 DOI: 10.1002/cnr2.1813] [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: 01/18/2023] [Revised: 03/02/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND Malignant brain tumors are among the most threatening diseases of the central nervous system, and despite increasingly updated treatments, the prognosis has not been improved. Tumor treating fields (TTFields) are an emerging approach in cancer treatment using intermediate-frequency and low-intensity electric field and can lead to the development of novel therapeutic options. RECENT FINDINGS A series of biological processes induced by TTFields to exert anti-cancer effects have been identified. Recent studies have shown that TTFields can alter the bioelectrical state of macromolecules and organelles involved in cancer biology. Massive alterations in cancer cell proteomics and transcriptomics caused by TTFields were related to cell biological processes as well as multiple organelle structures and activities. This review addresses the mechanisms of TTFields and recent advances in the application of TTFields therapy in malignant brain tumors, especially in glioblastoma (GBM). CONCLUSIONS As a novel therapeutic strategy, TTFields have shown promising results in many clinical trials, especially in GBM, and continue to evolve. A growing number of patients with malignant brain tumors are being enrolled in ongoing clinical studies demonstrating that TTFields-based combination therapies can improve treatment outcomes.
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Affiliation(s)
- Youyou Zhou
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Nuclear Medicine and Molecular Imaging, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Medical Molecular Imaging of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Xiaoqing Xing
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Nuclear Medicine and Molecular Imaging, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Medical Molecular Imaging of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jinyun Zhou
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Nuclear Medicine and Molecular Imaging, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Medical Molecular Imaging of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Han Jiang
- Faculty of Science and Technology, Department of Electrical and Computer Engineering, Biomedical Imaging Laboratory (BIG), University of Macau, Taipa, Macau SAR, China
| | - Peili Cen
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Nuclear Medicine and Molecular Imaging, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Medical Molecular Imaging of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Chentao Jin
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Nuclear Medicine and Molecular Imaging, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Medical Molecular Imaging of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yan Zhong
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Nuclear Medicine and Molecular Imaging, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Medical Molecular Imaging of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Rui Zhou
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Nuclear Medicine and Molecular Imaging, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Medical Molecular Imaging of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Jing Wang
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Nuclear Medicine and Molecular Imaging, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Medical Molecular Imaging of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Mei Tian
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Nuclear Medicine and Molecular Imaging, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Medical Molecular Imaging of Zhejiang Province, Hangzhou, Zhejiang, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Hong Zhang
- Department of Nuclear Medicine and PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Nuclear Medicine and Molecular Imaging, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Medical Molecular Imaging of Zhejiang Province, Hangzhou, Zhejiang, China
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou, Zhejiang, China
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50
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Gillespie MS, Ward CM, Davies CC. DNA Repair and Therapeutic Strategies in Cancer Stem Cells. Cancers (Basel) 2023; 15:1897. [PMID: 36980782 PMCID: PMC10047301 DOI: 10.3390/cancers15061897] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
First-line cancer treatments successfully eradicate the differentiated tumour mass but are comparatively ineffective against cancer stem cells (CSCs), a self-renewing subpopulation thought to be responsible for tumour initiation, metastasis, heterogeneity, and recurrence. CSCs are thus presented as the principal target for elimination during cancer treatment. However, CSCs are challenging to drug target because of numerous intrinsic and extrinsic mechanisms of drug resistance. One such mechanism that remains relatively understudied is the DNA damage response (DDR). CSCs are presumed to possess properties that enable enhanced DNA repair efficiency relative to their highly proliferative bulk progeny, facilitating improved repair of double-strand breaks induced by radiotherapy and most chemotherapeutics. This can occur through multiple mechanisms, including increased expression and splicing fidelity of DNA repair genes, robust activation of cell cycle checkpoints, and elevated homologous recombination-mediated DNA repair. Herein, we summarise the current knowledge concerning improved genome integrity in non-transformed stem cells and CSCs, discuss therapeutic opportunities within the DDR for re-sensitising CSCs to genotoxic stressors, and consider the challenges posed regarding unbiased identification of novel DDR-directed strategies in CSCs. A better understanding of the DDR mediating chemo/radioresistance mechanisms in CSCs could lead to novel therapeutic approaches, thereby enhancing treatment efficacy in cancer patients.
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Affiliation(s)
- Matthew S. Gillespie
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (M.S.G.)
- School of Cancer Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Ciara M. Ward
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (M.S.G.)
| | - Clare C. Davies
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; (M.S.G.)
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