1
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Wu S, Yao X, Sun W, Jiang K, Hao J. Exploration of poly (ADP-ribose) polymerase inhibitor resistance in the treatment of BRCA1/2-mutated cancer. Genes Chromosomes Cancer 2024; 63:e23243. [PMID: 38747337 DOI: 10.1002/gcc.23243] [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: 04/08/2024] [Accepted: 04/19/2024] [Indexed: 05/21/2024] Open
Abstract
Breast cancer susceptibility 1/2 (BRCA1/2) genes play a crucial role in DNA damage repair, yet mutations in these genes increase the susceptibility to tumorigenesis. Exploiting the synthetic lethality mechanism between BRCA1/2 mutations and poly(ADP-ribose) polymerase (PARP) inhibition has led to the development and clinical approval of PARP inhibitor (PARPi), representing a milestone in targeted therapy for BRCA1/2 mutant tumors. This approach has paved the way for leveraging synthetic lethality in tumor treatment strategies. Despite the initial success of PARPis, resistance to these agents diminishes their efficacy in BRCA1/2-mutant tumors. Investigations into PARPi resistance have identified replication fork stability and homologous recombination repair as key factors sensitive to PARPis. Additionally, studies suggest that replication gaps may also confer sensitivity to PARPis. Moreover, emerging evidence indicates a correlation between PARPi resistance and cisplatin resistance, suggesting a potential overlap in the mechanisms underlying resistance to both agents. Given these findings, it is imperative to explore the interplay between replication gaps and PARPi resistance, particularly in the context of platinum resistance. Understanding the impact of replication gaps on PARPi resistance may offer insights into novel therapeutic strategies to overcome resistance mechanisms and enhance the efficacy of targeted therapies in BRCA1/2-mutant tumors.
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Affiliation(s)
- Shuyi Wu
- School of Life Sciences, Zhejiang Chinese Medicine University, HangZhou, China
| | - Xuanjie Yao
- The Fourth Clinical Medical College, Zhejiang Chinese Medicine University, HangZhou, China
| | - Weiwei Sun
- School of Life Sciences, Zhejiang Chinese Medicine University, HangZhou, China
| | - Kaitao Jiang
- School of Life Sciences, Zhejiang Chinese Medicine University, HangZhou, China
| | - Jie Hao
- School of Life Sciences, Zhejiang Chinese Medicine University, HangZhou, China
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2
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Biller M, Kabir S, Boado C, Nipper S, Saffa A, Tal A, Allen S, Sasanuma H, Dréau D, Vaziri C, Tomida J. REV7-p53 interaction inhibits ATM-mediated DNA damage signaling. Cell Cycle 2024; 23:339-352. [PMID: 38557443 PMCID: PMC11174130 DOI: 10.1080/15384101.2024.2333227] [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: 10/10/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
REV7 is an abundant, multifunctional protein that is a known factor in cell cycle regulation and in several key DNA repair pathways including Trans-Lesion Synthesis (TLS), the Fanconi Anemia (FA) pathway, and DNA Double-Strand Break (DSB) repair pathway choice. Thus far, no direct role has been studied for REV7 in the DNA damage response (DDR) signaling pathway. Here we describe a novel function for REV7 in DSB-induced p53 signaling. We show that REV7 binds directly to p53 to block ATM-dependent p53 Ser15 phosphorylation. We also report that REV7 is involved in the destabilization of p53. These findings affirm REV7's participation in fundamental cell cycle and DNA repair pathways. Furthermore, they highlight REV7 as a critical factor for the integration of multiple processes that determine viability and genome stability.
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Affiliation(s)
- Megan Biller
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Sara Kabir
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Chkylle Boado
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Sarah Nipper
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Alexandra Saffa
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Ariella Tal
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Sydney Allen
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Hiroyuki Sasanuma
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Didier Dréau
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Junya Tomida
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
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3
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Davidge B, McDermott SM, Carnes J, Lewis I, Tracy M, Stuart KD. Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2023; 29:1591-1609. [PMID: 37474258 PMCID: PMC10578492 DOI: 10.1261/rna.079691.123] [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: 04/19/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life-cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multiprotein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing, and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations, most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the zinc fingers (ZFs), an intrinsically disordered region (IDR), and several within or near the carboxy-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing, whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.
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Affiliation(s)
- Brittney Davidge
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Jason Carnes
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Isaac Lewis
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Maxwell Tracy
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Kenneth D Stuart
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
- Department of Global Health, University of Washington, Seattle, Washington 98195, USA
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4
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Simpson D, Ling J, Jing Y, Adamson B. Mapping the Genetic Interaction Network of PARP inhibitor Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553986. [PMID: 37645833 PMCID: PMC10462155 DOI: 10.1101/2023.08.19.553986] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Genetic interactions have long informed our understanding of the coordinated proteins and pathways that respond to DNA damage in mammalian cells, but systematic interrogation of the genetic network underlying that system has yet to be achieved. Towards this goal, we measured 147,153 pairwise interactions among genes implicated in PARP inhibitor (PARPi) response. Evaluating genetic interactions at this scale, with and without exposure to PARPi, revealed hierarchical organization of the pathways and complexes that maintain genome stability during normal growth and defined changes that occur upon accumulation of DNA lesions due to cytotoxic doses of PARPi. We uncovered unexpected relationships among DNA repair genes, including context-specific buffering interactions between the minimally characterized AUNIP and BRCA1-A complex genes. Our work thus establishes a foundation for mapping differential genetic interactions in mammalian cells and provides a comprehensive resource for future studies of DNA repair and PARP inhibitors.
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Affiliation(s)
- Danny Simpson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Jia Ling
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Yangwode Jing
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Britt Adamson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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5
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Bhin J, Paes Dias M, Gogola E, Rolfs F, Piersma SR, de Bruijn R, de Ruiter JR, van den Broek B, Duarte AA, Sol W, van der Heijden I, Andronikou C, Kaiponen TS, Bakker L, Lieftink C, Morris B, Beijersbergen RL, van de Ven M, Jimenez CR, Wessels LFA, Rottenberg S, Jonkers J. Multi-omics analysis reveals distinct non-reversion mechanisms of PARPi resistance in BRCA1- versus BRCA2-deficient mammary tumors. Cell Rep 2023; 42:112538. [PMID: 37209095 DOI: 10.1016/j.celrep.2023.112538] [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: 09/06/2022] [Revised: 03/16/2023] [Accepted: 05/03/2023] [Indexed: 05/22/2023] Open
Abstract
BRCA1 and BRCA2 both function in DNA double-strand break repair by homologous recombination (HR). Due to their HR defect, BRCA1/2-deficient cancers are sensitive to poly(ADP-ribose) polymerase inhibitors (PARPis), but they eventually acquire resistance. Preclinical studies yielded several PARPi resistance mechanisms that do not involve BRCA1/2 reactivation, but their relevance in the clinic remains elusive. To investigate which BRCA1/2-independent mechanisms drive spontaneous resistance in vivo, we combine molecular profiling with functional analysis of HR of matched PARPi-naive and PARPi-resistant mouse mammary tumors harboring large intragenic deletions that prevent reactivation of BRCA1/2. We observe restoration of HR in 62% of PARPi-resistant BRCA1-deficient tumors but none in the PARPi-resistant BRCA2-deficient tumors. Moreover, we find that 53BP1 loss is the prevalent resistance mechanism in HR-proficient BRCA1-deficient tumors, whereas resistance in BRCA2-deficient tumors is mainly induced by PARG loss. Furthermore, combined multi-omics analysis identifies additional genes and pathways potentially involved in modulating PARPi response.
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Affiliation(s)
- Jinhyuk Bhin
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Department of Biomedical System Informatics, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Mariana Paes Dias
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ewa Gogola
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Frank Rolfs
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; OncoProteomics Laboratory, Department Medical Oncology, Amsterdam UMC, 1081HV Amsterdam, the Netherlands
| | - Sander R Piersma
- OncoProteomics Laboratory, Department Medical Oncology, Amsterdam UMC, 1081HV Amsterdam, the Netherlands
| | - Roebi de Bruijn
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Julian R de Ruiter
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Bram van den Broek
- Division of Cell Biology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Alexandra A Duarte
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Wendy Sol
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ingrid van der Heijden
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Christina Andronikou
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088 Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Taina S Kaiponen
- Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088 Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Lara Bakker
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Cor Lieftink
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Ben Morris
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging, Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Connie R Jimenez
- OncoProteomics Laboratory, Department Medical Oncology, Amsterdam UMC, 1081HV Amsterdam, the Netherlands
| | - Lodewyk F A Wessels
- Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands.
| | - Sven Rottenberg
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Cancer Therapy Resistance Cluster and Bern Center for Precision Medicine, Department for Biomedical Research, University of Bern, 3088 Bern, Switzerland; Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands.
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6
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Carnie CJ, Armstrong L, Sebesta M, Ariza A, Wang X, Graham E, Zhu K, Ahel D. ERCC6L2 mitigates replication stress and promotes centromere stability. Cell Rep 2023; 42:112329. [PMID: 37014751 DOI: 10.1016/j.celrep.2023.112329] [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: 06/23/2022] [Revised: 01/26/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Structurally complex genomic regions, such as centromeres, are inherently difficult to duplicate. The mechanism behind centromere inheritance is not well understood, and one of the key questions relates to the reassembly of centromeric chromatin following DNA replication. Here, we define ERCC6L2 as a key regulator of this process. ERCC6L2 accumulates at centromeres and promotes deposition of core centromeric factors. Interestingly, ERCC6L2-/- cells show unrestrained replication of centromeric DNA, likely caused by the erosion of centromeric chromatin. Beyond centromeres, ERCC6L2 facilitates replication at genomic repeats and non-canonical DNA structures. Notably, ERCC6L2 interacts with the DNA-clamp PCNA through an atypical peptide, presented here in a co-crystal structure. Finally, ERCC6L2 also restricts DNA end resection, acting independently of the 53BP1-REV7-Shieldin complex. We propose a mechanistic model, which reconciles seemingly distinct functions of ERCC6L2 in DNA repair and DNA replication. These findings provide a molecular context for studies linking ERCC6L2 to human disease.
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Affiliation(s)
| | - Lucy Armstrong
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Marek Sebesta
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Antonio Ariza
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Xiaomeng Wang
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Emily Graham
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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7
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Davidge B, McDermott SM, Carnes J, Lewis I, Tracy M, Stuart KD. Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA Editing Catalytic Complexes in Trypanosoma brucei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537538. [PMID: 37131796 PMCID: PMC10153193 DOI: 10.1101/2023.04.19.537538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multi-protein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the ZFs, an intrinsically disordered region (IDR) and several within or near the C-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.
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Affiliation(s)
- Brittney Davidge
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Jason Carnes
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Isaac Lewis
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Maxwell Tracy
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Kenneth D Stuart
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
- Department of Pediatrics, University of Washington, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
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8
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Du Z, Zhang F, Liu L, Shen H, Liu T, Jin J, Yu N, Wan Z, Wang H, Hu X, Chen Y, Cai J. LncRNA ANRIL promotes HR repair through regulating PARP1 expression by sponging miR-7-5p in lung cancer. BMC Cancer 2023; 23:130. [PMID: 36755223 PMCID: PMC9906921 DOI: 10.1186/s12885-023-10593-z] [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: 08/21/2022] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Radiotherapy is an important treatment for lung cancer, mainly by triggering DNA double-strand breaks to induce cell death. Blocking DNA damage repair can increase the radiosensitivity of tumor cells. Recent studies have identified long noncoding RNAs as key regulators in DNA damage repair. The lncRNA ANRIL was previously shown to be involved in homologous recombination (HR) repair, but its specific mechanism has not been fully elucidated. METHODS The downstream interacting miRNAs of ANRIL were predicted according to miRanda software. Fluorescence quantitative PCR was used to detect the expression levels of ANRIL and candidate miRNAs. Clone formation experiment and cell viability assays detect cell viability after ionizing radiation. Apoptosis assay was used to detect the apoptosis of cells after 8 h of ionizing radiation. Western blot analysis and immunofluorescence assays verified the protein expression levels of the downstream target molecule PARP1 of miR-7-5p and key molecules in the HR pathway. Fluorescent reporter gene experiments were used to verify the interaction between ANRIL and miR-7-5p and between miR-7-5p and PARP1. RESULTS Bioinformatics analysis and qPCR validation suggested that miR-7-5p might be a downstream molecule of ANRIL. The expression of miR-7-5p was up-regulated after knockdown of ANRIL, and the expression of miR-7-5p was down-regulated after overexpression of ANRIL. Meanwhile, there was a negative correlation between ANRIL and miR-7-5p expression changes before and after ionizing radiation. The luciferase reporter gene assay confirmed the existence of ANRIL binding site with miR-7-5p, and found that transfection of miR-7-5p inhibitor can reduce the radiation sensitivity of ANRIL-KD cells. A downstream target molecule of miR-7-5p related to HR repair, PARP1, was screened through website prediction. Subsequently, it was confirmed by Western blot and luciferase reporter assays that miR-7-5p could down-regulate the expression of PARP1, and there was a miR-7-5p binding site on the 3'UTR of PARP1 mRNA. This suggests that ANRIL may act as a competitive endogenous RNA to bind miR-7-5p and upregulate the expression of PARP1. Western blot and immunofluorescence staining were used to detect the expression changes of HR repair factors in ANRIL-KD cells after ionizing radiation, and it was found that knockdown of ANRIL can inhibit the expression of PARP1, BRCA1 and Rad51, hinder radiation-induced HR repair, and eventually result in resensitizing ANRIL-KD cells to ionizing radiation. CONCLUSIONS Our findings provide evidence that ANRIL targets the miR-7-5p/PARP1 axis to exert its regulatory effect on HR repair, suggesting that altering ANRIL expression may be a promising strategy to overcome radiation resistance.
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Affiliation(s)
- Zhipeng Du
- grid.268099.c0000 0001 0348 3990School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, Zhejiang P. R. China
| | - Fangxiao Zhang
- grid.268099.c0000 0001 0348 3990School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, Zhejiang P. R. China
| | - Lei Liu
- grid.417279.eDepartment of Oncology, General Hospital of Central Theater Command of Chinese People’s Liberation Army, Wuhan, Hubei P. R. China
| | - Hui Shen
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, P. R. China
| | - Tingting Liu
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, P. R. China
| | - Jing Jin
- grid.216417.70000 0001 0379 7164Department of Occupational and Environment Health, Xiangya School of Public Health, Central South University, Changsha, Hunan P. R. China
| | - Nanxi Yu
- grid.268099.c0000 0001 0348 3990School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, Zhejiang P. R. China
| | - Zhijie Wan
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, P. R. China
| | - Hang Wang
- grid.73113.370000 0004 0369 1660Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, P. R. China
| | - Xuguang Hu
- Department of Gastrointestinal Surgery, Changhai Hospital, Shanghai, P. R. China.
| | - Yuanyuan Chen
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, P. R. China. .,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, Zhejiang, P. R. China.
| | - Jianming Cai
- School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, Zhejiang, P. R. China. .,Department of Oncology, General Hospital of Central Theater Command of Chinese People's Liberation Army, Wuhan, Hubei, P. R. China. .,Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, Shanghai, P. R. China.
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9
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McPherson KS, Rizzo AA, Erlandsen H, Chatterjee N, Walker GC, Korzhnev DM. Evolution of Rev7 interactions in eukaryotic TLS DNA polymerase Polζ. J Biol Chem 2023; 299:102859. [PMID: 36592930 PMCID: PMC9926120 DOI: 10.1016/j.jbc.2022.102859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 01/01/2023] Open
Abstract
Translesion synthesis (TLS) DNA polymerase Polζ is crucial for the bypass replication over sites of DNA damage. The Rev7 subunit of Polζ is a HORMA (Hop1, Rev7, Mad2) protein that facilitates recruitment of Polζ to the replication fork via interactions with the catalytic subunit Rev3 and the translesion synthesis scaffold protein Rev1. Human Rev7 (hRev7) interacts with two Rev7-binding motifs (RBMs) of hRev3 by a mechanism conserved among HORMA proteins whereby the safety-belt loop of hRev7 closes on the top of the ligand. The two copies of hRev7 tethered by the two hRev3-RBMs form a symmetric head-to-head dimer through the canonical HORMA dimerization interface. Recent cryo-EM structures reveal that Saccharomyces cerevisiae Polζ (scPolζ) also includes two copies of scRev7 bound to distinct regions of scRev3. Surprisingly, the HORMA dimerization interface is not conserved in scRev7, with the two scRev7 protomers forming an asymmetric head-to-tail dimer with a much smaller interface than the hRev7 dimer. Here, we validated the two adjacent RBM motifs in scRev3, which bind scRev7 with affinities that differ by two orders of magnitude and confirmed the 2:1 stoichiometry of the scRev7:Rev3 complex in solution. However, our biophysical studies reveal that scRev7 does not form dimers in solution either on its own accord or when tethered by the two RBMs in scRev3. These findings imply that the scRev7 dimer observed in the cryo-EM structures is induced by scRev7 interactions with other Polζ subunits and that Rev7 homodimerization via the HORMA interface is a mechanism that emerged later in evolution.
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Affiliation(s)
- Kerry Silva McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Alessandro A Rizzo
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Heidi Erlandsen
- Center for Open Research Resources & Equipment, University of Connecticut, Storrs, Connecticut, USA
| | - Nimrat Chatterjee
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA
| | - Graham C Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA.
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10
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DNA Damage Response Mechanisms in Head and Neck Cancer: Significant Implications for Therapy and Survival. Int J Mol Sci 2023; 24:ijms24032760. [PMID: 36769087 PMCID: PMC9917521 DOI: 10.3390/ijms24032760] [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: 12/28/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Head and neck cancer (HNC) is a term collectively used to describe a heterogeneous group of tumors that arise in the oral cavity, larynx, nasopharynx, oropharynx, and hypopharynx, and represents the sixth most common type of malignancy worldwide. Despite advances in multimodality treatment, the disease has a recurrence rate of around 50%, and the prognosis of metastatic patients remains poor. HNCs are characterized by a high degree of genomic instability, which involves a vicious circle of accumulating DNA damage, defective DNA damage repair (DDR), and replication stress. Nonetheless, the damage that is induced on tumor cells by chemo and radiotherapy relies on defective DDR processes for a successful response to treatment, and may play an important role in the development of novel and more effective therapies. This review summarizes the current knowledge on the genes and proteins that appear to be deregulated in DDR pathways, their implication in HNC pathogenesis, and the rationale behind targeting these genes and pathways for the development of new therapies. We give particular emphasis on the therapeutic targets that have shown promising results at the pre-clinical stage and on those that have so far been associated with a therapeutic advantage in the clinical setting.
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11
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Rass E, Willaume S, Bertrand P. 53BP1: Keeping It under Control, Even at a Distance from DNA Damage. Genes (Basel) 2022; 13:genes13122390. [PMID: 36553657 PMCID: PMC9778356 DOI: 10.3390/genes13122390] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Double-strand breaks (DSBs) are toxic lesions that can be generated by exposure to genotoxic agents or during physiological processes, such as during V(D)J recombination. The repair of these DSBs is crucial to prevent genomic instability and to maintain cellular homeostasis. Two main pathways participate in repairing DSBs, namely, non-homologous end joining (NHEJ) and homologous recombination (HR). The P53-binding protein 1 (53BP1) plays a pivotal role in the choice of DSB repair mechanism, promotes checkpoint activation and preserves genome stability upon DSBs. By preventing DSB end resection, 53BP1 promotes NHEJ over HR. Nonetheless, the balance between DSB repair pathways remains crucial, as unscheduled NHEJ or HR events at different phases of the cell cycle may lead to genomic instability. Therefore, the recruitment of 53BP1 to chromatin is tightly regulated and has been widely studied. However, less is known about the mechanism regulating 53BP1 recruitment at a distance from the DNA damage. The present review focuses on the mechanism of 53BP1 recruitment to damage and on recent studies describing novel mechanisms keeping 53BP1 at a distance from DSBs.
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Affiliation(s)
- Emilie Rass
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Correspondence:
| | - Simon Willaume
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
| | - Pascale Bertrand
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
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12
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CCAR2 functions downstream of the Shieldin complex to promote double-strand break end-joining. Proc Natl Acad Sci U S A 2022; 119:e2214935119. [PMID: 36442094 PMCID: PMC9894118 DOI: 10.1073/pnas.2214935119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The 53BP1-RIF1 pathway restricts the resection of DNA double-strand breaks (DSBs) and promotes blunt end-ligation by non-homologous end joining (NHEJ) repair. The Shieldin complex is a downstream effector of the 53BP1-RIF1 pathway. Here, we identify a component of this pathway, CCAR2/DBC1, which is also required for restriction of DNA end-resection. CCAR2 co-immunoprecipitates with the Shieldin complex, and knockout of CCAR2 in a BRCA1-deficient cell line results in elevated DSB end-resection, RAD51 loading, and PARP inhibitor (PARPi) resistance. Knockout of CCAR2 is epistatic with knockout of other Shieldin proteins. The S1-like RNA-binding domain of CCAR2 is required for its interaction with the Shieldin complex and for suppression of DSB end-resection. CCAR2 functions downstream of the Shieldin complex, and CCAR2 knockout cells have delayed resolution of Shieldin complex foci. Forkhead-associated (FHA)-dependent targeting of CCAR2 to DSB sites re-sensitized BRCA1-/-SHLD2-/- cells to PARPi. Taken together, CCAR2 is a functional component of the 53BP1-RIF1 pathway, promotes the refill of resected DSBs, and suppresses homologous recombination.
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13
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Kloeber JA, Lou Z. Critical DNA damaging pathways in tumorigenesis. Semin Cancer Biol 2022; 85:164-184. [PMID: 33905873 PMCID: PMC8542061 DOI: 10.1016/j.semcancer.2021.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/22/2022]
Abstract
The acquisition of DNA damage is an early driving event in tumorigenesis. Premalignant lesions show activated DNA damage responses and inactivation of DNA damage checkpoints promotes malignant transformation. However, DNA damage is also a targetable vulnerability in cancer cells. This requires a detailed understanding of the cellular and molecular mechanisms governing DNA integrity. Here, we review current work on DNA damage in tumorigenesis. We discuss DNA double strand break repair, how repair pathways contribute to tumorigenesis, and how double strand breaks are linked to the tumor microenvironment. Next, we discuss the role of oncogenes in promoting DNA damage through replication stress. Finally, we discuss our current understanding on DNA damage in micronuclei and discuss therapies targeting these DNA damage pathways.
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Affiliation(s)
- Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA; Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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14
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Paniagua I, Tayeh Z, Falcone M, Hernández Pérez S, Cerutti A, Jacobs JJL. MAD2L2 promotes replication fork protection and recovery in a shieldin-independent and REV3L-dependent manner. Nat Commun 2022; 13:5167. [PMID: 36075897 PMCID: PMC9458726 DOI: 10.1038/s41467-022-32861-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
Protection of stalled replication forks is essential to prevent genome instability, a major driving force of tumorigenesis. Several key regulators of DNA double-stranded break (DSB) repair, including 53BP1 and RIF1, have been implicated in fork protection. MAD2L2, also known as REV7, plays an important role downstream of 53BP1/RIF1 by counteracting resection at DSBs in the recently discovered shieldin complex. The ability to bind and counteract resection at exposed DNA ends at DSBs makes MAD2L2/shieldin a prime candidate for also suppressing nucleolytic processing at stalled replication forks. However, the function of MAD2L2/shieldin outside of DNA repair is unknown. Here we address this by using genetic and single-molecule analyses and find that MAD2L2 is required for protecting and restarting stalled replication forks. MAD2L2 loss leads to uncontrolled MRE11-dependent resection of stalled forks and single-stranded DNA accumulation, which causes irreparable genomic damage. Unexpectedly, MAD2L2 limits resection at stalled forks independently of shieldin, since fork protection remained unaffected by shieldin loss. Instead, MAD2L2 cooperates with the DNA polymerases REV3L and REV1 to promote fork stability. Thus, MAD2L2 suppresses aberrant nucleolytic processing both at DSBs and stalled replication forks by differentially engaging shieldin and REV1/REV3L, respectively. MAD2L2 – as a member of the shieldin complex - counteracts resection during DNA repair. Here the authors demonstrate that MAD2L2 protects stalled replication forks from excessive resection, in a shieldin-independent and REV3L-dependent manner.
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Affiliation(s)
- Inés Paniagua
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Zainab Tayeh
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Mattia Falcone
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Santiago Hernández Pérez
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Aurora Cerutti
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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15
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CHAMP1 binds to REV7/FANCV and promotes homologous recombination repair. Cell Rep 2022; 40:111297. [PMID: 36044844 PMCID: PMC9472291 DOI: 10.1016/j.celrep.2022.111297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/13/2022] [Accepted: 08/09/2022] [Indexed: 11/22/2022] Open
Abstract
A critical determinant of DNA repair pathway choice is REV7, an adaptor that binds to various DNA repair proteins through its C-terminal seatbelt domain. The REV7 seatbelt binds to either REV3, activating translesion synthesis, or to SHLD3, activating non-homologous end joining (NHEJ) repair. Recent studies have identified another REV7 seatbelt-binding protein, CHAMP1 (chromosome alignment-maintaining phosphoprotein 1), though its possible role in DNA repair is unknown. Here, we show that binding of CHAMP1 to REV7 activates homologous recombination (HR) repair. Mechanistically, CHAMP1 binds directly to REV7 and reduces the level of the Shieldin complex, causing an increase in double-strand break end resection. CHAMP1 also interacts with POGZ in a heterochromatin complex further promoting HR repair. Importantly, in human tumors, CHAMP1 overexpression promotes HR, confers poly (ADP-ribose) polymerase inhibitor resistance, and correlates with poor prognosis. Thus, by binding to either SHLD3 or CHAMP1 through its seatbelt, the REV7 protein can promote either NHEJ or HR repair, respectively. Feng et al. demonstrate that CHAMP1 promotes homologous recombination by binding to REV7 and reducing the level of the Shieldin complex, causing an increase in double-strand break end resection. CHAMP1 and POGZ form a complex to further promote HR. Upregulation of CHAMP1 expression is a mechanism of acquired PARP inhibitor resistance.
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16
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Chen BR, Sleckman BP. The regulation of DNA end resection by chromatin response to DNA double strand breaks. Front Cell Dev Biol 2022; 10:932633. [PMID: 35912102 PMCID: PMC9335370 DOI: 10.3389/fcell.2022.932633] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
DNA double-strand breaks (DSBs) constantly arise upon exposure to genotoxic agents and during physiological processes. The timely repair of DSBs is important for not only the completion of the cellular functions involving DSBs as intermediates, but also the maintenance of genome stability. There are two major pathways dedicated to DSB repair: homologous recombination (HR) and non-homologous end joining (NHEJ). The decision of deploying HR or NHEJ to repair DSBs largely depends on the structures of broken DNA ends. DNA ends resected to generate extensive single-strand DNA (ssDNA) overhangs are repaired by HR, while those remaining blunt or minimally processed can be repaired by NHEJ. As the generation and repair of DSB occurs within the context of chromatin, the resection of broken DNA ends is also profoundly affected by the state of chromatin flanking DSBs. Here we review how DNA end resection can be regulated by histone modifications, chromatin remodeling, and the presence of ssDNA structure through altering the accessibility to chromatin and the activity of pro- and anti-resection proteins.
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Affiliation(s)
- Bo-Ruei Chen
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
- *Correspondence: Bo-Ruei Chen,
| | - Barry P. Sleckman
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
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17
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Chen Z, Tyler JK. The Chromatin Landscape Channels DNA Double-Strand Breaks to Distinct Repair Pathways. Front Cell Dev Biol 2022; 10:909696. [PMID: 35757003 PMCID: PMC9213757 DOI: 10.3389/fcell.2022.909696] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/17/2022] [Indexed: 12/24/2022] Open
Abstract
DNA double-strand breaks (DSBs), the most deleterious DNA lesions, are primarily repaired by two pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ), the choice of which is largely dependent on cell cycle phase and the local chromatin landscape. Recent studies have revealed that post-translational modifications on histones play pivotal roles in regulating DSB repair pathways including repair pathway choice. In this review, we present our current understanding of how these DSB repair pathways are employed in various chromatin landscapes to safeguard genomic integrity. We place an emphasis on the impact of different histone post-translational modifications, characteristic of euchromatin or heterochromatin regions, on DSB repair pathway choice. We discuss the potential roles of damage-induced chromatin modifications in the maintenance of genome and epigenome integrity. Finally, we discuss how RNA transcripts from the vicinity of DSBs at actively transcribed regions also regulate DSB repair pathway choice.
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Affiliation(s)
- Zulong Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, United States
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, United States
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18
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Vincendeau E, Wei W, Zhang X, Planchais C, Yu W, Lenden-Hasse H, Cokelaer T, Pipoli da Fonseca J, Mouquet H, Adams DJ, Alt FW, Jackson SP, Balmus G, Lescale C, Deriano L. SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination. Nat Commun 2022; 13:3707. [PMID: 35764636 PMCID: PMC9240092 DOI: 10.1038/s41467-022-31287-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 06/13/2022] [Indexed: 11/21/2022] Open
Abstract
SHLD1 is part of the Shieldin (SHLD) complex, which acts downstream of 53BP1 to counteract DNA double-strand break (DSB) end resection and promote DNA repair via non-homologous end-joining (NHEJ). While 53BP1 is essential for immunoglobulin heavy chain class switch recombination (CSR), long-range V(D)J recombination and repair of RAG-induced DSBs in XLF-deficient cells, the function of SHLD during these processes remains elusive. Here we report that SHLD1 is dispensable for lymphocyte development and RAG-mediated V(D)J recombination, even in the absence of XLF. By contrast, SHLD1 is essential for restricting resection at AID-induced DSB ends in both NHEJ-proficient and NHEJ-deficient B cells, providing an end-protection mechanism that permits productive CSR by NHEJ and alternative end-joining. Finally, we show that this SHLD1 function is required for orientation-specific joining of AID-initiated DSBs. Our data thus suggest that 53BP1 promotes V(D)J recombination and CSR through two distinct mechanisms: SHLD-independent synapsis of V(D)J segments and switch regions within chromatin, and SHLD-dependent protection of AID-DSB ends against resection.
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Affiliation(s)
- Estelle Vincendeau
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Wenming Wei
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Xuefei Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China
| | - Cyril Planchais
- Institut Pasteur, Université de Paris, INSERM U1222, Laboratory of Humoral Immunology, 75015, Paris, France
| | - Wei Yu
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Hélène Lenden-Hasse
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques, 75015, Paris, France
- Institut Pasteur, Hub de Bioinformatique et Biostatistique, Département de Biologie Computationnelle, 75015, Paris, France
| | - Juliana Pipoli da Fonseca
- Institut Pasteur, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques, 75015, Paris, France
| | - Hugo Mouquet
- Institut Pasteur, Université de Paris, INSERM U1222, Laboratory of Humoral Immunology, 75015, Paris, France
| | - David J Adams
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Stephen P Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Gabriel Balmus
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Chloé Lescale
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France.
| | - Ludovic Deriano
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France.
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19
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Raina VB, Schoot Uiterkamp M, Vader G. Checkpoint control in meiotic prophase: Idiosyncratic demands require unique characteristics. Curr Top Dev Biol 2022; 151:281-315. [PMID: 36681474 DOI: 10.1016/bs.ctdb.2022.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chromosomal transactions such as replication, recombination and segregation are monitored by cell cycle checkpoint cascades. These checkpoints ensure the proper execution of processes that are needed for faithful genome inheritance from one cell to the next, and across generations. In meiotic prophase, a specialized checkpoint monitors defining events of meiosis: programmed DNA break formation, followed by dedicated repair through recombination based on interhomolog (IH) crossovers. This checkpoint shares molecular characteristics with canonical DNA damage checkpoints active during somatic cell cycles. However, idiosyncratic requirements of meiotic prophase have introduced unique features in this signaling cascade. In this review, we discuss the unique features of the meiotic prophase checkpoint. While being related to canonical DNA damage checkpoint cascades, the meiotic prophase checkpoint also shows similarities with the spindle assembly checkpoint (SAC) that guards chromosome segregation. We highlight these emerging similarities in the signaling logic of the checkpoints that govern meiotic prophase and chromosome segregation, and how thinking of these similarities can help us better understand meiotic prophase control. We also discuss work showing that, when aberrantly expressed, components of the meiotic prophase checkpoint might alter DNA repair fidelity and chromosome segregation in cancer cells. Considering checkpoint function in light of demands imposed by the special characteristics of meiotic prophase helps us understand checkpoint integration into the meiotic cell cycle machinery.
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Affiliation(s)
- Vivek B Raina
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York City, NY, United States
| | - Maud Schoot Uiterkamp
- Center for Reproductive Medicine, Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands; Section of Oncogenetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Gerben Vader
- Center for Reproductive Medicine, Reproductive Biology Laboratory, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands; Section of Oncogenetics, Department of Human Genetics, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands.
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20
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Lei T, Du S, Peng Z, Chen L. Multifaceted regulation and functions of 53BP1 in NHEJ‑mediated DSB repair (Review). Int J Mol Med 2022; 50:90. [PMID: 35583003 PMCID: PMC9162042 DOI: 10.3892/ijmm.2022.5145] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/29/2022] [Indexed: 12/02/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) is crucial for the preservation of genomic integrity and the maintenance of cellular homeostasis. Non-homologous DNA end joining (NHEJ) is the predominant repair mechanism for any type of DNA DSB during the majority of the cell cycle. NHEJ defects regulate tumor sensitivity to ionizing radiation and anti-neoplastic agents, resulting in immunodeficiencies and developmental abnormalities in malignant cells. p53-binding protein 1 (53BP1) is a key mediator involved in DSB repair, which functions to maintain a balance in the repair pathway choices and in preserving genomic stability. 53BP1 promotes DSB repair via NHEJ and antagonizes DNA end overhang resection. At present, novel lines of evidence have revealed the molecular mechanisms underlying the recruitment of 53BP1 and DNA break-responsive effectors to DSB sites, and the promotion of NHEJ-mediated DSB repair via 53BP1, while preventing homologous recombination. In the present review article, recent advances made in the elucidation of the structural and functional characteristics of 53BP1, the mechanisms of 53BP1 recruitment and interaction with the reshaping of the chromatin architecture around DSB sites, the post-transcriptional modifications of 53BP1, and the up- and downstream pathways of 53BP1 are discussed. The present review article also focuses on the application perspectives, current challenges and future directions of 53BP1 research.
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Affiliation(s)
- Tiantian Lei
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Suya Du
- Department of Clinical Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610041, P.R. China
| | - Zhe Peng
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Lin Chen
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
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21
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Lashgari A, Kougnassoukou Tchara PE, Lambert JP, Côté J. New insights into the DNA repair pathway choice with NuA4/TIP60. DNA Repair (Amst) 2022; 113:103315. [PMID: 35278769 DOI: 10.1016/j.dnarep.2022.103315] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 11/03/2022]
Abstract
In eukaryotic cells, DNA double-strand breaks (DSBs) can be repaired through two main pathways, non-homologous end-joining (NHEJ) or homologous recombination (HR). The selection of the repair pathway choice is governed by an antagonistic relationship between repair factors specific to each pathway, in a cell cycle-dependent manner. The molecular mechanisms of this decision implicate post-translational modifications of chromatin surrounding the break. Here, we discuss the recent advances regarding the function of the NuA4/TIP60 histone acetyltransferase/chromatin remodeling complex during DSBs repair. In particular, we emphasise the contribution of NuA4/TIP60 in repair pathway choice, in collaboration with the SAGA acetyltransferase complex, and how they regulate chromatin dynamics, modify non-histone substrates to allow DNA end resection and recombination.
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Affiliation(s)
- Anahita Lashgari
- St-Patrick Research Group in Basic Oncology, Canada; Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada; Department of Molecular Medicine, Big Data Research Center, Université Laval, Quebec, Canada
| | - Pata-Eting Kougnassoukou Tchara
- Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada; Department of Molecular Medicine, Big Data Research Center, Université Laval, Quebec, Canada
| | - Jean-Philippe Lambert
- Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada; Department of Molecular Medicine, Big Data Research Center, Université Laval, Quebec, Canada.
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Canada; Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Quebec City, QC, Canada.
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22
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Kim J, Lee S, Choi J, Baek K, Shim TS, Hyun JK, Park SJ. Shape-Changing DNA-Linked Nanoparticle Films Dictated by Lateral and Vertical Patterns. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2109091. [PMID: 35119767 DOI: 10.1002/adma.202109091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/10/2022] [Indexed: 06/14/2023]
Abstract
The self-assembly of nanoscale building blocks into complex nanostructures with controlled structural anisotropy can open up new opportunities for realizing active nanomaterials exhibiting spatiotemporal structural transformations. Here, a combination of bottom-up DNA-directed self-assembly and top-down photothermal patterning is adopted to fabricate free-standing nanoparticle films with vertical and lateral heterogeneity. This approach involves the construction of multicomponent plasmonic nanoparticle films by DNA-directed layer-by-layer (LbL) self-assembly, followed by on-demand lateral patterning by the direct photothermal writing method. The distinct plasmonic properties of nanospheres and nanorods constituting the multidomain films enable photopatterning in a selective domain with precisely controlled vertical depths. The photopatterned films exhibit complex morphing actions instructed by the lateral and vertical patterns inscribed in the film as well as the information carried in DNA.
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Affiliation(s)
- Jongwook Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
| | - Sunghee Lee
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
| | - Jisu Choi
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
| | - Kyungnae Baek
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
| | - Tae Soup Shim
- Department of Energy Systems Research and Department of Chemical Engineering, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, 16499, South Korea
| | - Jerome Kartham Hyun
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
| | - So-Jung Park
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul, 03760, South Korea
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23
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Feng S, Ma S, Li K, Gao S, Ning S, Shang J, Guo R, Chen Y, Blumenfeld B, Simon I, Li Q, Guo R, Xu D. RIF1-ASF1-mediated high-order chromatin structure safeguards genome integrity. Nat Commun 2022; 13:957. [PMID: 35177609 PMCID: PMC8854732 DOI: 10.1038/s41467-022-28588-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 02/01/2022] [Indexed: 11/12/2022] Open
Abstract
The 53BP1-RIF1 pathway antagonizes resection of DNA broken ends and confers PARP inhibitor sensitivity on BRCA1-mutated tumors. However, it is unclear how this pathway suppresses initiation of resection. Here, we identify ASF1 as a partner of RIF1 via an interacting manner similar to its interactions with histone chaperones CAF-1 and HIRA. ASF1 is recruited to distal chromatin flanking DNA breaks by 53BP1-RIF1 and promotes non-homologous end joining (NHEJ) using its histone chaperone activity. Epistasis analysis shows that ASF1 acts in the same NHEJ pathway as RIF1, but via a parallel pathway with the shieldin complex, which suppresses resection after initiation. Moreover, defects in end resection and homologous recombination (HR) in BRCA1-deficient cells are largely suppressed by ASF1 deficiency. Mechanistically, ASF1 compacts adjacent chromatin by heterochromatinization to protect broken DNA ends from BRCA1-mediated resection. Taken together, our findings identify a RIF1-ASF1 histone chaperone complex that promotes changes in high-order chromatin structure to stimulate the NHEJ pathway for DSB repair. The 53BP1-RIF1 pathway is important for DNA repair. Here, the authors identified the histone chaperone ASF1, which functions as a suppressor of DNA end resection through changing high-order chromatin structure, as a partner of RIF1. This finding links DNA repair and dynamic changes of high-order chromatin structure.
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Affiliation(s)
- Sumin Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Sai Ma
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Kejiao Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Shengxian Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Shaokai Ning
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Jinfeng Shang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Ruiyuan Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Yingying Chen
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Britny Blumenfeld
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, 91120, Israel
| | - Itamar Simon
- Department of Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, 91120, Israel
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Rong Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871, Beijing, China.
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24
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RIF1 acts in DNA repair through phosphopeptide recognition of 53BP1. Mol Cell 2022; 82:1359-1371.e9. [PMID: 35216668 PMCID: PMC8995355 DOI: 10.1016/j.molcel.2022.01.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 12/09/2021] [Accepted: 01/27/2022] [Indexed: 12/14/2022]
Abstract
The chromatin-binding protein 53BP1 promotes DNA repair by orchestrating the recruitment of downstream effectors including PTIP, RIF1, and shieldin to DNA double-strand break sites. While we know how PTIP recognizes 53BP1, the molecular details of RIF1 recruitment to DNA-damage sites remains undefined. Here, we report that RIF1 is a phosphopeptide-binding protein that directly interacts with three phosphorylated 53BP1 epitopes. The RIF1-binding sites on 53BP1 share an essential LxL motif followed by two closely apposed phosphorylated residues. Simultaneous mutation of these sites on 53BP1 abrogates RIF1 accumulation into ionizing-radiation-induced foci, but surprisingly, only fully compromises 53BP1-dependent DNA repair when an alternative mode of shieldin recruitment to DNA-damage sites is also disabled. Intriguingly, this alternative mode of recruitment still depends on RIF1 but does not require its interaction with 53BP1. RIF1 therefore employs phosphopeptide recognition to promote DNA repair but also modifies shieldin action independently of 53BP1 binding.
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25
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Bianco PR. OB-fold Families of Genome Guardians: A Universal Theme Constructed From the Small β-barrel Building Block. Front Mol Biosci 2022; 9:784451. [PMID: 35223988 PMCID: PMC8881015 DOI: 10.3389/fmolb.2022.784451] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
The maintenance of genome stability requires the coordinated actions of multiple proteins and protein complexes, that are collectively known as genome guardians. Within this broadly defined family is a subset of proteins that contain oligonucleotide/oligosaccharide-binding folds (OB-fold). While OB-folds are widely associated with binding to single-stranded DNA this view is no longer an accurate depiction of how these domains are utilized. Instead, the core of the OB-fold is modified and adapted to facilitate binding to a variety of DNA substrates (both single- and double-stranded), phospholipids, and proteins, as well as enabling catalytic function to a multi-subunit complex. The flexibility accompanied by distinctive oligomerization states and quaternary structures enables OB-fold genome guardians to maintain the integrity of the genome via a myriad of complex and dynamic, protein-protein; protein-DNA, and protein-lipid interactions in both prokaryotes and eukaryotes.
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Affiliation(s)
- Piero R. Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, United States
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26
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Libri A, Marton T, Deriano L. The (Lack of) DNA Double-Strand Break Repair Pathway Choice During V(D)J Recombination. Front Genet 2022; 12:823943. [PMID: 35082840 PMCID: PMC8785701 DOI: 10.3389/fgene.2021.823943] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 12/13/2021] [Indexed: 01/08/2023] Open
Abstract
DNA double-strand breaks (DSBs) are highly toxic lesions that can be mended via several DNA repair pathways. Multiple factors can influence the choice and the restrictiveness of repair towards a given pathway in order to warrant the maintenance of genome integrity. During V(D)J recombination, RAG-induced DSBs are (almost) exclusively repaired by the non-homologous end-joining (NHEJ) pathway for the benefit of antigen receptor gene diversity. Here, we review the various parameters that constrain repair of RAG-generated DSBs to NHEJ, including the peculiarity of DNA DSB ends generated by the RAG nuclease, the establishment and maintenance of a post-cleavage synaptic complex, and the protection of DNA ends against resection and (micro)homology-directed repair. In this physiological context, we highlight that certain DSBs have limited DNA repair pathway choice options.
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Affiliation(s)
- Alice Libri
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
| | - Timea Marton
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Institut Pasteur, Université de Paris, INSERM U1223, Equipe Labellisée Ligue Contre Le Cancer, Paris, France
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27
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Mirman Z, Sasi NK, King A, Chapman JR, de Lange T. 53BP1-shieldin-dependent DSB processing in BRCA1-deficient cells requires CST-Polα-primase fill-in synthesis. Nat Cell Biol 2022; 24:51-61. [PMID: 35027730 PMCID: PMC8849574 DOI: 10.1038/s41556-021-00812-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/09/2021] [Indexed: 12/19/2022]
Abstract
The efficacy of poly(ADP)-ribose polymerase 1 inhibition (PARPi) in BRCA1-deficient cells depends on 53BP1 and shieldin, which have been proposed to limit single-stranded DNA at double-strand breaks (DSBs) by blocking resection and/or through CST-Polα-primase-mediated fill-in. We show that primase (like 53BP1-shieldin and CST-Polα) promotes radial chromosome formation in PARPi-treated BRCA1-deficient cells and demonstrate shieldin-CST-Polα-primase-dependent incorporation of BrdU at DSBs. In the absence of 53BP1 or shieldin, radial formation in BRCA1-deficient cells was restored by the tethering of CST near DSBs, arguing that in this context, shieldin acts primarily by recruiting CST. Furthermore, a SHLD1 mutant defective in CST binding (SHLD1Δ) was non-functional in BRCA1-deficient cells and its function was restored after reconnecting SHLD1Δ to CST. Interestingly, at dysfunctional telomeres and at DNA breaks in class switch recombination where CST has been implicated, SHLD1Δ was fully functional, perhaps because these DNA ends carry CST recognition sites that afford SHLD1-independent binding of CST. These data establish that in BRCA1-deficient cells, CST-Polα-primase is the major effector of shieldin-dependent DSB processing.
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Affiliation(s)
- Zachary Mirman
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Nanda Kumar Sasi
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA
| | - Ashleigh King
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - J Ross Chapman
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Titia de Lange
- Laboratory for Cell Biology and Genetics, Rockefeller University, New York, NY, USA.
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28
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Understanding and overcoming resistance to PARP inhibitors in cancer therapy. Nat Rev Clin Oncol 2021; 18:773-791. [PMID: 34285417 DOI: 10.1038/s41571-021-00532-x] [Citation(s) in RCA: 202] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 02/07/2023]
Abstract
Developing novel targeted anticancer therapies is a major goal of current research. The use of poly(ADP-ribose) polymerase (PARP) inhibitors in patients with homologous recombination-deficient tumours provides one of the best examples of a targeted therapy that has been successfully translated into the clinic. The success of this approach has so far led to the approval of four different PARP inhibitors for the treatment of several types of cancers and a total of seven different compounds are currently under clinical investigation for various indications. Clinical trials have demonstrated promising response rates among patients receiving PARP inhibitors, although the majority will inevitably develop resistance. Preclinical and clinical data have revealed multiple mechanisms of resistance and current efforts are focused on developing strategies to address this challenge. In this Review, we summarize the diverse processes underlying resistance to PARP inhibitors and discuss the potential strategies that might overcome these mechanisms such as combinations with chemotherapies, targeting the acquired vulnerabilities associated with resistance to PARP inhibitors or suppressing genomic instability.
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29
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Hayward SB, Ciccia A. Towards a CRISPeR understanding of homologous recombination with high-throughput functional genomics. Curr Opin Genet Dev 2021; 71:171-181. [PMID: 34583241 PMCID: PMC8671205 DOI: 10.1016/j.gde.2021.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-dependent genome editing enables the study of genes and mutations on a large scale. Here we review CRISPR-based functional genomics technologies that generate gene knockouts and single nucleotide variants (SNVs) and discuss how their use has provided new important insights into the function of homologous recombination (HR) genes. In particular, we highlight discoveries from CRISPR screens that have contributed to define the response to PARP inhibition in cells deficient for the HR genes BRCA1 and BRCA2, uncover genes whose loss causes synthetic lethality in combination with BRCA1/2 deficiency, and characterize the function of BRCA1/2 SNVs of uncertain clinical significance. Further use of these approaches, combined with next-generation CRISPR-based technologies, will aid to dissect the genetic network of the HR pathway, define the impact of HR mutations on cancer etiology and treatment, and develop novel targeted therapies for HR-deficient tumors.
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Affiliation(s)
- Samuel B Hayward
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, United States.
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30
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Abstract
DNA double-strand breaks (DSBs) are cytotoxic lesions that threaten genome integrity and cell viability. Typically, cells repair DSBs by either nonhomologous end joining (NHEJ) or homologous recombination (HR). The relative use of these two pathways depends on many factors, including cell cycle stage and the nature of the DNA ends. A critical determinant of repair pathway selection is the initiation of 5'→3' nucleolytic degradation of DNA ends, a process referred to as DNA end resection. End resection is essential to create single-stranded DNA overhangs, which serve as the substrate for the Rad51 recombinase to initiate HR and are refractory to NHEJ repair. Here, we review recent insights into the mechanisms of end resection, how it is regulated, and the pathological consequences of its dysregulation.
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Affiliation(s)
- Petr Cejka
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500 Bellinzona, Switzerland; .,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; .,Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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31
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Blasiak J, Szczepańska J, Sobczuk A, Fila M, Pawlowska E. RIF1 Links Replication Timing with Fork Reactivation and DNA Double-Strand Break Repair. Int J Mol Sci 2021; 22:11440. [PMID: 34768871 PMCID: PMC8583789 DOI: 10.3390/ijms222111440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
Replication timing (RT) is a cellular program to coordinate initiation of DNA replication in all origins within the genome. RIF1 (replication timing regulatory factor 1) is a master regulator of RT in human cells. This role of RIF1 is associated with binding G4-quadruplexes and changes in 3D chromatin that may suppress origin activation over a long distance. Many effects of RIF1 in fork reactivation and DNA double-strand (DSB) repair (DSBR) are underlined by its interaction with TP53BP1 (tumor protein p53 binding protein). In G1, RIF1 acts antagonistically to BRCA1 (BRCA1 DNA repair associated), suppressing end resection and homologous recombination repair (HRR) and promoting non-homologous end joining (NHEJ), contributing to DSBR pathway choice. RIF1 is an important element of intra-S-checkpoints to recover damaged replication fork with the involvement of HRR. High-resolution microscopic studies show that RIF1 cooperates with TP53BP1 to preserve 3D structure and epigenetic markers of genomic loci disrupted by DSBs. Apart from TP53BP1, RIF1 interact with many other proteins, including proteins involved in DNA damage response, cell cycle regulation, and chromatin remodeling. As impaired RT, DSBR and fork reactivation are associated with genomic instability, a hallmark of malignant transformation, RIF1 has a diagnostic, prognostic, and therapeutic potential in cancer. Further studies may reveal other aspects of common regulation of RT, DSBR, and fork reactivation by RIF1.
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Affiliation(s)
- Janusz Blasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Joanna Szczepańska
- Department of Pediatric Dentistry, Medical University of Lodz, 92-216 Lodz, Poland;
| | - Anna Sobczuk
- Department of Gynaecology and Obstetrics, Medical University of Lodz, 93-338 Lodz, Poland;
| | - Michal Fila
- Department of Developmental Neurology and Epileptology, Polish Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland;
| | - Elzbieta Pawlowska
- Department of Orthodontics, Medical University of Lodz, 92-217 Lodz, Poland;
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32
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Sanchez A, Lee D, Kim DI, Miller KM. Making Connections: Integrative Signaling Mechanisms Coordinate DNA Break Repair in Chromatin. Front Genet 2021; 12:747734. [PMID: 34659365 PMCID: PMC8514019 DOI: 10.3389/fgene.2021.747734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/31/2021] [Indexed: 01/25/2023] Open
Abstract
DNA double-strand breaks (DSBs) are hazardous to genome integrity and can promote mutations and disease if not handled correctly. Cells respond to these dangers by engaging DNA damage response (DDR) pathways that are able to identify DNA breaks within chromatin leading ultimately to their repair. The recognition and repair of DSBs by the DDR is largely dependent on the ability of DNA damage sensing factors to bind to and interact with nucleic acids, nucleosomes and their modified forms to target these activities to the break site. These contacts orientate and localize factors to lesions within chromatin, allowing signaling and faithful repair of the break to occur. Coordinating these events requires the integration of several signaling and binding events. Studies are revealing an enormously complex array of interactions that contribute to DNA lesion recognition and repair including binding events on DNA, as well as RNA, RNA:DNA hybrids, nucleosomes, histone and non-histone protein post-translational modifications and protein-protein interactions. Here we examine several DDR pathways that highlight and provide prime examples of these emerging concepts. A combination of approaches including genetic, cellular, and structural biology have begun to reveal new insights into the molecular interactions that govern the DDR within chromatin. While many questions remain, a clearer picture has started to emerge for how DNA-templated processes including transcription, replication and DSB repair are coordinated. Multivalent interactions with several biomolecules serve as key signals to recruit and orientate proteins at DNA lesions, which is essential to integrate signaling events and coordinate the DDR within the milieu of the nucleus where competing genome functions take place. Genome architecture, chromatin structure and phase separation have emerged as additional vital regulatory mechanisms that also influence genome integrity pathways including DSB repair. Collectively, recent advancements in the field have not only provided a deeper understanding of these fundamental processes that maintain genome integrity and cellular homeostasis but have also started to identify new strategies to target deficiencies in these pathways that are prevalent in human diseases including cancer.
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Affiliation(s)
- Anthony Sanchez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Doohyung Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Dae In Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, United States
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33
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Paiano J, Zolnerowich N, Wu W, Pavani R, Wang C, Li H, Zheng L, Shen B, Sleckman BP, Chen BR, Nussenzweig A. Role of 53BP1 in end protection and DNA synthesis at DNA breaks. Genes Dev 2021; 35:1356-1367. [PMID: 34503990 DOI: 10.1101/gad.348667.121] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/17/2021] [Indexed: 12/20/2022]
Abstract
Double-strand break (DSB) repair choice is greatly influenced by the initial processing of DNA ends. 53BP1 limits the formation of recombinogenic single-strand DNA (ssDNA) in BRCA1-deficient cells, leading to defects in homologous recombination (HR). However, the exact mechanisms by which 53BP1 inhibits DSB resection remain unclear. Previous studies have identified two potential pathways: protection against DNA2/EXO1 exonucleases presumably through the Shieldin (SHLD) complex binding to ssDNA, and localized DNA synthesis through the CTC1-STN1-TEN1 (CST) and DNA polymerase α (Polα) to counteract resection. Using a combinatorial approach of END-seq, SAR-seq, and RPA ChIP-seq, we directly assessed the extent of resection, DNA synthesis, and ssDNA, respectively, at restriction enzyme-induced DSBs. We show that, in the presence of 53BP1, Polα-dependent DNA synthesis reduces the fraction of resected DSBs and the resection lengths in G0/G1, supporting a previous model that fill-in synthesis can limit the extent of resection. However, in the absence of 53BP1, Polα activity is sustained on ssDNA yet does not substantially counter resection. In contrast, EXO1 nuclease activity is essential for hyperresection in the absence of 53BP1. Thus, Polα-mediated fill-in partially limits resection in the presence of 53BP1 but cannot counter extensive hyperresection due to the loss of 53BP1 exonuclease blockade. These data provide the first nucleotide mapping of DNA synthesis at resected DSBs and provide insight into the relationship between fill-in polymerases and resection exonucleases.
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Affiliation(s)
- Jacob Paiano
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nicholas Zolnerowich
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chen Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Hongzhi Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, California 91010, USA.,Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, California 91010, USA.,Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, California 91010, USA.,Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, California 91010, USA
| | - Barry P Sleckman
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Bo-Ruei Chen
- Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA.,O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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34
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MAD2L2 dimerization and TRIP13 control shieldin activity in DNA repair. Nat Commun 2021; 12:5421. [PMID: 34521823 PMCID: PMC8440562 DOI: 10.1038/s41467-021-25724-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/28/2021] [Indexed: 12/13/2022] Open
Abstract
MAD2L2 (REV7) plays an important role in DNA double-strand break repair. As a member of the shieldin complex, consisting of MAD2L2, SHLD1, SHLD2 and SHLD3, it controls DNA repair pathway choice by counteracting DNA end-resection. Here we investigated the requirements for shieldin complex assembly and activity. Besides a dimerization-surface, HORMA-domain protein MAD2L2 has the extraordinary ability to wrap its C-terminus around SHLD3, likely creating a very stable complex. We show that appropriate function of MAD2L2 within shieldin requires its dimerization, mediated by SHLD2 and accelerating MAD2L2-SHLD3 interaction. Dimerization-defective MAD2L2 impairs shieldin assembly and fails to promote NHEJ. Moreover, MAD2L2 dimerization, along with the presence of SHLD3, allows shieldin to interact with the TRIP13 ATPase, known to drive topological switches in HORMA-domain proteins. We find that appropriate levels of TRIP13 are important for proper shieldin (dis)assembly and activity in DNA repair. Together our data provide important insights in the dependencies for shieldin activity.
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McPherson KS, Korzhnev DM. Targeting protein-protein interactions in the DNA damage response pathways for cancer chemotherapy. RSC Chem Biol 2021; 2:1167-1195. [PMID: 34458830 PMCID: PMC8342002 DOI: 10.1039/d1cb00101a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/20/2021] [Indexed: 12/11/2022] Open
Abstract
Cellular DNA damage response (DDR) is an extensive signaling network that orchestrates DNA damage recognition, repair and avoidance, cell cycle progression and cell death. DDR alteration is a hallmark of cancer, with the deficiency in one DDR capability often compensated by a dependency on alternative pathways endowing cancer cells with survival and growth advantage. Targeting these DDR pathways has provided multiple opportunities for the development of cancer therapies. Traditional drug discovery has mainly focused on catalytic inhibitors that block enzyme active sites, which limits the number of potential drug targets within the DDR pathways. This review article describes the emerging approach to the development of cancer therapeutics targeting essential protein-protein interactions (PPIs) in the DDR network. The overall strategy for the structure-based design of small molecule PPI inhibitors is discussed, followed by an overview of the major DNA damage sensing, DNA repair, and DNA damage tolerance pathways with a specific focus on PPI targets for anti-cancer drug design. The existing small molecule inhibitors of DDR PPIs are summarized that selectively kill cancer cells and/or sensitize cancers to front-line genotoxic therapies, and a range of new PPI targets are proposed that may lead to the development of novel chemotherapeutics.
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Affiliation(s)
- Kerry Silva McPherson
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center Farmington CT 06030 USA +1 860 679 3408 +1 860 679 2849
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center Farmington CT 06030 USA +1 860 679 3408 +1 860 679 2849
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Molecular mechanisms of assembly and TRIP13-mediated remodeling of the human Shieldin complex. Proc Natl Acad Sci U S A 2021; 118:2024512118. [PMID: 33597306 PMCID: PMC7923543 DOI: 10.1073/pnas.2024512118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The Shieldin complex, composed of REV7, SHLD1, SHLD2, and SHLD3, protects DNA double-strand breaks (DSBs) to promote nonhomologous end joining. The AAA+ ATPase TRIP13 remodels Shieldin to regulate DNA repair pathway choice. Here we report crystal structures of human SHLD3-REV7 binary and fused SHLD2-SHLD3-REV7 ternary complexes, revealing that assembly of Shieldin requires fused SHLD2-SHLD3 induced conformational heterodimerization of open (O-REV7) and closed (C-REV7) forms of REV7. We also report the cryogenic electron microscopy (cryo-EM) structures of the ATPγS-bound fused SHLD2-SHLD3-REV7-TRIP13 complexes, uncovering the principles underlying the TRIP13-mediated disassembly mechanism of the Shieldin complex. We demonstrate that the N terminus of REV7 inserts into the central channel of TRIP13, setting the stage for pulling the unfolded N-terminal peptide of C-REV7 through the central TRIP13 hexameric channel. The primary interface involves contacts between the safety-belt segment of C-REV7 and a conserved and negatively charged loop of TRIP13. This process is mediated by ATP hydrolysis-triggered rotatory motions of the TRIP13 ATPase, thereby resulting in the disassembly of the Shieldin complex.
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Lei X, Cao K, Chen Y, Shen H, Liu Z, Qin H, Cai J, Gao F, Yang Y. Nuclear Transglutaminase 2 interacts with topoisomerase II⍺ to promote DNA damage repair in lung cancer cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:224. [PMID: 34225780 PMCID: PMC8258933 DOI: 10.1186/s13046-021-02009-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/07/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND To block repairs of DNA damages, especially the DNA double strand break (DSB) repair, can be used to induce cancer cell death. DSB repair depends on a sequential activation of DNA repair factors that may be potentially targeted for clinical cancer therapy. Up to now, many protein components of DSB repair complex remain unclear or poorly characterized. In this study, we discovered that Transglutaminase 2 (TG2) acted as a new component of DSB repair complex. METHODS A bioinformatic analysis was performed to identify DNA damage relative genes from dataset from The Cancer Genome Atlas. Immunofluorescence and confocal microscopy were used to monitor the protein localization and recruitment kinetics. Furthermore, immunoprecipitation and mass spectrometry analysis were performed to determine protein interaction of both full-length and fragments or mutants in distinct domain. In situ lung cancer model was used to study the effects cancer therapy in vivo. RESULTS After DSB induction, cytoplasmic TG2 was extensively mobilized and translocated into nucleus after phosphorylated at T162 site by DNA-PKcs. Nuclear TG2 quickly accumulated at DSB sites and directly interacting with Topoisomerase IIα (TOPOIIα) with its TGase domain to promote DSB repair. TG2 deficient cells lost capacity of DSB repair and become susceptible to ionizing radiation. Specific inhibition of TG2-TOPOIIα interaction by glucosamine also significantly inhibited DSB repair, which increased sensitivity in lung cancer cells and engrafted lung cancers. CONCLUSIONS These findings elucidate new mechanism of TG2 in DSB repair trough directly interacting with TOPOIIα, inhibition of which provided potential target for overcoming cancer resistance.
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Affiliation(s)
- Xiao Lei
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, P.R. China.,Department of Radiation Oncology, The First Medical Center of PLA General Hospital, Beijing, P.R. China
| | - Kun Cao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, P.R. China
| | - Yuanyuan Chen
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, P.R. China
| | - Hui Shen
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, P.R. China
| | - Zhe Liu
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, P.R. China
| | - Hongran Qin
- Department of Nuclear Radiation, Shanghai Pulmonary Hospital, Tongji University, 507, Zhengmin Road, 200433, Shanghai, P.R. China
| | - Jianming Cai
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, P.R. China. .,School of Public Health and Management, Wenzhou Medical University, University Town, Wenzhou, Zhejiang, P.R. China.
| | - Fu Gao
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, P.R. China.
| | - Yanyong Yang
- Department of Radiation Medicine, Faculty of Naval Medicine, Naval Medical University, 800, Xiangyin Road, 200433, Shanghai, P.R. China.
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Zatreanu D, Robinson HMR, Alkhatib O, Boursier M, Finch H, Geo L, Grande D, Grinkevich V, Heald RA, Langdon S, Majithiya J, McWhirter C, Martin NMB, Moore S, Neves J, Rajendra E, Ranzani M, Schaedler T, Stockley M, Wiggins K, Brough R, Sridhar S, Gulati A, Shao N, Badder LM, Novo D, Knight EG, Marlow R, Haider S, Callen E, Hewitt G, Schimmel J, Prevo R, Alli C, Ferdinand A, Bell C, Blencowe P, Bot C, Calder M, Charles M, Curry J, Ekwuru T, Ewings K, Krajewski W, MacDonald E, McCarron H, Pang L, Pedder C, Rigoreau L, Swarbrick M, Wheatley E, Willis S, Wong AC, Nussenzweig A, Tijsterman M, Tutt A, Boulton SJ, Higgins GS, Pettitt SJ, Smith GCM, Lord CJ. Polθ inhibitors elicit BRCA-gene synthetic lethality and target PARP inhibitor resistance. Nat Commun 2021; 12:3636. [PMID: 34140467 PMCID: PMC8211653 DOI: 10.1038/s41467-021-23463-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/30/2021] [Indexed: 02/05/2023] Open
Abstract
To identify approaches to target DNA repair vulnerabilities in cancer, we discovered nanomolar potent, selective, low molecular weight (MW), allosteric inhibitors of the polymerase function of DNA polymerase Polθ, including ART558. ART558 inhibits the major Polθ-mediated DNA repair process, Theta-Mediated End Joining, without targeting Non-Homologous End Joining. In addition, ART558 elicits DNA damage and synthetic lethality in BRCA1- or BRCA2-mutant tumour cells and enhances the effects of a PARP inhibitor. Genetic perturbation screening revealed that defects in the 53BP1/Shieldin complex, which cause PARP inhibitor resistance, result in in vitro and in vivo sensitivity to small molecule Polθ polymerase inhibitors. Mechanistically, ART558 increases biomarkers of single-stranded DNA and synthetic lethality in 53BP1-defective cells whilst the inhibition of DNA nucleases that promote end-resection reversed these effects, implicating these in the synthetic lethal mechanism-of-action. Taken together, these observations describe a drug class that elicits BRCA-gene synthetic lethality and PARP inhibitor synergy, as well as targeting a biomarker-defined mechanism of PARPi-resistance.
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Affiliation(s)
- Diana Zatreanu
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Helen M R Robinson
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Omar Alkhatib
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Marie Boursier
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Harry Finch
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Lerin Geo
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Diego Grande
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Vera Grinkevich
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Robert A Heald
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Sophie Langdon
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Jayesh Majithiya
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Claire McWhirter
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Niall M B Martin
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Shaun Moore
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Joana Neves
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Eeson Rajendra
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Marco Ranzani
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Theresia Schaedler
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Martin Stockley
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Kimberley Wiggins
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
| | - Rachel Brough
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Sandhya Sridhar
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Aditi Gulati
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Nan Shao
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Luned M Badder
- The Breast Cancer Now Research Unit, King's College London, London, UK
| | - Daniela Novo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Eleanor G Knight
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rebecca Marlow
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Research Unit, King's College London, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Joost Schimmel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Remko Prevo
- Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Christina Alli
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Amanda Ferdinand
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Cameron Bell
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Peter Blencowe
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Chris Bot
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Mathew Calder
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Mark Charles
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Jayne Curry
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Tennyson Ekwuru
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Katherine Ewings
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Wojciech Krajewski
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Ellen MacDonald
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Hollie McCarron
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Leon Pang
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Chris Pedder
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Laurent Rigoreau
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Martin Swarbrick
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Ed Wheatley
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Simon Willis
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Ai Ching Wong
- Cancer Research UK, Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, UK
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andrew Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Breast Cancer Now Research Unit, King's College London, London, UK
| | - Simon J Boulton
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK
- The Francis Crick Institute, London, UK
| | - Geoff S Higgins
- Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Stephen J Pettitt
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - Graeme C M Smith
- Artios Pharma, The Glenn Berge Building, Babraham Research Campus, Cambridge, UK.
| | - Christopher J Lord
- CRUK Gene Function Laboratory, The Institute of Cancer Research, London, UK.
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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Clairmont CS, D'Andrea AD. REV7 directs DNA repair pathway choice. Trends Cell Biol 2021; 31:965-978. [PMID: 34147298 DOI: 10.1016/j.tcb.2021.05.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/18/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
REV7 is a small multifunctional protein that participates in multiple DNA repair pathways, most notably translesion DNA synthesis and double-strand break (DSB) repair. While the role of REV7 in translesion synthesis has been known for several decades, its function in DSB repair is a recent discovery. Investigations into the DSB repair function of REV7 have led to the discovery of a new DNA repair complex known as Shieldin. Recent studies have also highlighted the importance of REV7's HORMA domain, an ancient structural motif, in REV7 function and have identified the HORMA regulators, TRIP13 and p31, as novel DNA repair factors. In this review, we discuss these recent findings and their implications for repair pathway choice, at both DSBs and replication forks. We suggest that REV7, in particular the activation state of its HORMA domain, can act as a critical determinant of mutagenic versus error-free repair in multiple contexts.
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Affiliation(s)
- Connor S Clairmont
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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Fanconi anemia proteins participate in a break-induced-replication-like pathway to counter replication stress. Nat Struct Mol Biol 2021; 28:487-500. [PMID: 34117478 DOI: 10.1038/s41594-021-00602-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/30/2021] [Indexed: 11/08/2022]
Abstract
Fanconi anemia (FA) is a devastating hereditary disease characterized by bone marrow failure (BMF) and acute myeloid leukemia (AML). As FA-deficient cells are hypersensitive to DNA interstrand crosslinks (ICLs), ICLs are widely assumed to be the lesions responsible for FA symptoms. Here, we show that FA-mutated cells are hypersensitive to persistent replication stress and that FA proteins play a role in the break-induced-replication (BIR)-like pathway for fork restart. Both the BIR-like pathway and ICL repair share almost identical molecular mechanisms of 53BP1-BRCA1-controlled signaling response, SLX4- and FAN1-mediated fork cleavage and POLD3-dependent DNA synthesis, suggesting that the FA pathway is intrinsically one of the BIR-like pathways. Replication stress not only triggers BMF in FA-deficient mice, but also specifically induces monosomy 7, which is associated with progression to AML in patients with FA, in FA-deficient cells.
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41
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Repair pathway choice for double-strand breaks. Essays Biochem 2021; 64:765-777. [PMID: 32648897 DOI: 10.1042/ebc20200007] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/20/2022]
Abstract
Deoxyribonucleic acid (DNA) is at a constant risk of damage from endogenous substances, environmental radiation, and chemical stressors. DNA double-strand breaks (DSBs) pose a significant threat to genomic integrity and cell survival. There are two major pathways for DSB repair: nonhomologous end-joining (NHEJ) and homologous recombination (HR). The extent of DNA end resection, which determines the length of the 3' single-stranded DNA (ssDNA) overhang, is the primary factor that determines whether repair is carried out via NHEJ or HR. NHEJ, which does not require a 3' ssDNA tail, occurs throughout the cell cycle. 53BP1 and the cofactors PTIP or RIF1-shieldin protect the broken DNA end, inhibit long-range end resection and thus promote NHEJ. In contrast, HR mainly occurs during the S/G2 phase and requires DNA end processing to create a 3' tail that can invade a homologous region, ensuring faithful gene repair. BRCA1 and the cofactors CtIP, EXO1, BLM/DNA2, and the MRE11-RAD50-NBS1 (MRN) complex promote DNA end resection and thus HR. DNA resection is influenced by the cell cycle, the chromatin environment, and the complexity of the DNA end break. Herein, we summarize the key factors involved in repair pathway selection for DSBs and discuss recent related publications.
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42
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de Krijger I, Boersma V, Jacobs JJL. REV7: Jack of many trades. Trends Cell Biol 2021; 31:686-701. [PMID: 33962851 DOI: 10.1016/j.tcb.2021.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/23/2021] [Accepted: 04/08/2021] [Indexed: 01/01/2023]
Abstract
The HORMA domain protein REV7, also known as MAD2L2, interacts with a variety of proteins and thereby contributes to the establishment of different complexes. With doing so, REV7 impacts a diverse range of cellular processes and gained increasing interest as more of its activities became uncovered. REV7 has important roles in translesion synthesis and mitotic progression, and acts as a central component in the recently discovered shieldin complex that operates in DNA double-strand break repair. Here we discuss the roles of REV7 in its various complexes, focusing on its activity in genome integrity maintenance. Moreover, we will describe current insights on REV7 structural features that allow it to be such a versatile protein.
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Affiliation(s)
- Inge de Krijger
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Vera Boersma
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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43
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The dystonia gene THAP1 controls DNA double-strand break repair choice. Mol Cell 2021; 81:2611-2624.e10. [PMID: 33857404 DOI: 10.1016/j.molcel.2021.03.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 02/01/2021] [Accepted: 03/19/2021] [Indexed: 12/26/2022]
Abstract
The Shieldin complex shields double-strand DNA breaks (DSBs) from nucleolytic resection. Curiously, the penultimate Shieldin component, SHLD1, is one of the least abundant mammalian proteins. Here, we report that the transcription factors THAP1, YY1, and HCF1 bind directly to the SHLD1 promoter, where they cooperatively maintain the low basal expression of SHLD1, thereby ensuring a proper balance between end protection and resection during DSB repair. The loss of THAP1-dependent SHLD1 expression confers cross-resistance to poly (ADP-ribose) polymerase (PARP) inhibitor and cisplatin in BRCA1-deficient cells and shorter progression-free survival in ovarian cancer patients. Moreover, the embryonic lethality and PARPi sensitivity of BRCA1-deficient mice is rescued by ablation of SHLD1. Our study uncovers a transcriptional network that directly controls DSB repair choice and suggests a potential link between DNA damage and pathogenic THAP1 mutations, found in patients with the neurodevelopmental movement disorder adult-onset torsion dystonia type 6.
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Saha T, Sundaravinayagam D, Di Virgilio M. Charting a DNA Repair Roadmap for Immunoglobulin Class Switch Recombination. Trends Biochem Sci 2020; 46:184-199. [PMID: 33250286 DOI: 10.1016/j.tibs.2020.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/08/2020] [Accepted: 10/23/2020] [Indexed: 01/18/2023]
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is the process occurring in mature B cells that diversifies the effector component of antibody responses. CSR is initiated by the activity of the B cell-specific enzyme activation-induced cytidine deaminase (AID), which leads to the formation of programmed DNA double-strand breaks (DSBs) at the Ig heavy chain (Igh) locus. Mature B cells use a multilayered and complex regulatory framework to ensure that AID-induced DNA breaks are channeled into productive repair reactions leading to CSR, and to avoid aberrant repair events causing lymphomagenic chromosomal translocations. Here, we review the DNA repair pathways acting on AID-induced DSBs and their functional interplay, with a particular focus on the latest developments in their molecular composition and mechanistic regulation.
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Affiliation(s)
- Tannishtha Saha
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany
| | - Devakumar Sundaravinayagam
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany.
| | - Michela Di Virgilio
- Laboratory of Genome Diversification and Integrity, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 13125, Germany; Charité-Universitätsmedizin Berlin, Berlin 10117, Germany.
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45
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The molecular basis and disease relevance of non-homologous DNA end joining. Nat Rev Mol Cell Biol 2020; 21:765-781. [PMID: 33077885 DOI: 10.1038/s41580-020-00297-8] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2020] [Indexed: 12/26/2022]
Abstract
Non-homologous DNA end joining (NHEJ) is the predominant repair mechanism of any type of DNA double-strand break (DSB) during most of the cell cycle and is essential for the development of antigen receptors. Defects in NHEJ result in sensitivity to ionizing radiation and loss of lymphocytes. The most critical step of NHEJ is synapsis, or the juxtaposition of the two DNA ends of a DSB, because all subsequent steps rely on it. Recent findings show that, like the end processing step, synapsis can be achieved through several mechanisms. In this Review, we first discuss repair pathway choice between NHEJ and other DSB repair pathways. We then integrate recent insights into the mechanisms of NHEJ synapsis with updates on other steps of NHEJ, such as DNA end processing and ligation. Finally, we discuss NHEJ-related human diseases, including inherited disorders and neoplasia, which arise from rare failures at different NHEJ steps.
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p31 comet promotes homologous recombination by inactivating REV7 through the TRIP13 ATPase. Proc Natl Acad Sci U S A 2020; 117:26795-26803. [PMID: 33051298 PMCID: PMC7604461 DOI: 10.1073/pnas.2008830117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The repair of DNA double strand breaks (DSBs) that arise from external mutagenic agents and routine cellular processes is essential for life. DSBs are repaired by two major pathways, homologous recombination (HR) and classical nonhomologous end joining (C-NHEJ). DSB repair pathway choice is largely dictated at the step of 5'-3' DNA end resection, which is promoted during S phase, in part by BRCA1. Opposing end resection is the 53BP1 protein, which recruits the ssDNA-binding REV7-Shieldin complex to favor C-NHEJ repair. We recently identified TRIP13 as a proresection factor that remodels REV7, causing its dissociation from the Shieldin subunit SHLD3. Here, we identify p31comet, a negative regulator of MAD2 and the spindle assembly checkpoint, as an important mediator of the TRIP13-REV7 interaction. p31comet binds to the REV7-Shieldin complex in cells, promotes REV7 inactivation, and causes PARP inhibitor resistance. p31comet also participates in the extraction of REV7 from the chromatin. Furthermore, p31comet can counteract REV7 function in translesion synthesis (TLS) by releasing it from REV3 in the Pol ζ complex. Finally, p31comet, like TRIP13, is overexpressed in many cancers and this correlates with poor prognosis. Thus, we reveal a key player in the regulation of HR and TLS with significant clinical implications.
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Francica P, Mutlu M, Blomen VA, Oliveira C, Nowicka Z, Trenner A, Gerhards NM, Bouwman P, Stickel E, Hekkelman ML, Lingg L, Klebic I, van de Ven M, de Korte-Grimmerink R, Howald D, Jonkers J, Sartori AA, Fendler W, Chapman JR, Brummelkamp T, Rottenberg S. Functional Radiogenetic Profiling Implicates ERCC6L2 in Non-homologous End Joining. Cell Rep 2020; 32:108068. [PMID: 32846126 DOI: 10.1016/j.celrep.2020.108068] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/27/2020] [Accepted: 08/04/2020] [Indexed: 12/20/2022] Open
Abstract
Using genome-wide radiogenetic profiling, we functionally dissect vulnerabilities of cancer cells to ionizing radiation (IR). We identify ERCC6L2 as a major determinant of IR response, together with classical DNA damage response genes and members of the recently identified shieldin and CTC1-STN1-TEN1 (CST) complexes. We show that ERCC6L2 contributes to non-homologous end joining (NHEJ), and it may exert this function through interactions with SFPQ. In addition to causing radiosensitivity, ERCC6L2 loss restores DNA end resection and partially rescues homologous recombination (HR) in BRCA1-deficient cells. As a consequence, ERCC6L2 deficiency confers resistance to poly (ADP-ribose) polymerase (PARP) inhibition in tumors deficient for both BRCA1 and p53. Moreover, we show that ERCC6L2 mutations are found in human tumors and correlate with a better overall survival in patients treated with radiotherapy (RT); this finding suggests that ERCC6L2 is a predictive biomarker of RT response.
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Affiliation(s)
- Paola Francica
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Merve Mutlu
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Vincent A Blomen
- Division of Biochemistry, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Catarina Oliveira
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Zuzanna Nowicka
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland
| | - Anika Trenner
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Nora M Gerhards
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Peter Bouwman
- Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Elmer Stickel
- Division of Biochemistry, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Maarten L Hekkelman
- Division of Biochemistry, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Lea Lingg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Ismar Klebic
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Marieke van de Ven
- Mouse Clinic for Cancer and Aging Research (MCCA), Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Renske de Korte-Grimmerink
- Mouse Clinic for Cancer and Aging Research (MCCA), Preclinical Intervention Unit, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Denise Howald
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Jos Jonkers
- Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, 92-215 Lodz, Poland; Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - J Ross Chapman
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Thijn Brummelkamp
- Division of Biochemistry, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Oncode Institute, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; Division of Molecular Pathology, the Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Bern Center for Precision Medicine, University of Bern, 3012 Bern, Switzerland.
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Fackrell K, Bobins L, Parul, Tomida J. FAM35A/SHLD2/RINN2: A novel determinant of double strand break repair pathway choice and genome stability in cancer. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:709-715. [PMID: 32306447 DOI: 10.1002/em.22379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 03/29/2020] [Accepted: 04/10/2020] [Indexed: 06/11/2023]
Abstract
FAM35A, alternatively known as SHLD2 and RINN2, was recently characterized as a DNA repair gene, evolutionarily conserved in higher vertebrates. FAM35A is a 53BP1-pathway factor and a component of the Shieldin/RINN complex. Among 53BP1-pathway factors, FAM35A has unique domains: an N-terminal disordered domain and three C-terminal OB-fold domains. These C-terminal domains have homology with the OB-fold domains of the single-stranded DNA binding protein, RPA1. With other 53BP1-pathway factors, FAM35A inhibits DNA end resection. FAM35A defective cell lines are sensitive to DNA double-strand break inducing agents. Concurrent FAM35A and BRCA1 defects in mammalian cell lines cause resistance to PARP inhibitors and camptothecin. The clinical relevance of this interaction is still unknown, but cancer genomics databases indicate that FAM35A is deleted in 6-13% of prostate cancers and in at least one triple negative breast cancer patient-derived BRCA1 defective cell line. From meta-analysis, FAM35A overexpression in patients with triple negative and basal-like breast cancers is associated with poor survival compared to patients with low expression. From this evidence, clarification of FAM35A's function and the related mechanism of chemoresistance is likely to have clinical implications.
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Affiliation(s)
- Kylie Fackrell
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - LoriAnn Bobins
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Parul
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
| | - Junya Tomida
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, USA
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Kamp JA, van Schendel R, Dilweg IW, Tijsterman M. BRCA1-associated structural variations are a consequence of polymerase theta-mediated end-joining. Nat Commun 2020; 11:3615. [PMID: 32680986 PMCID: PMC7368036 DOI: 10.1038/s41467-020-17455-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/01/2020] [Indexed: 12/03/2022] Open
Abstract
Failure to preserve the integrity of the genome is a hallmark of cancer. Recent studies have revealed that loss of the capacity to repair DNA breaks via homologous recombination (HR) results in a mutational profile termed BRCAness. The enzymatic activity that repairs HR substrates in BRCA-deficient conditions to produce this profile is currently unknown. We here show that the mutational landscape of BRCA1 deficiency in C. elegans closely resembles that of BRCA1-deficient tumours. We identify polymerase theta-mediated end-joining (TMEJ) to be responsible: knocking out polq-1 suppresses the accumulation of deletions and tandem duplications in brc-1 and brd-1 animals. We find no additional back-up repair in HR and TMEJ compromised animals; non-homologous end-joining does not affect BRCAness. The notion that TMEJ acts as an alternative to HR, promoting the genome alteration of HR-deficient cells, supports the idea that polymerase theta is a promising therapeutic target for HR-deficient tumours.
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Affiliation(s)
- J A Kamp
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - R van Schendel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - I W Dilweg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - M Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
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Abstract
In the past decade, the study of the major DNA double strand break (DSB) repair pathways, homologous recombination (HR) and classical non-homologous end joining (C-NHEJ), has revealed a vast and intricate network of regulation. The choice between HR and C-NHEJ is largely controlled at the step of DNA end-resection. A pro-C-NHEJ cascade commencing with 53BP1 and culminating in the newly discovered REV7-Shieldin complex impedes end resection and therefore HR. Importantly, loss of any component of this pathway confers PARP inhibitor resistance in BRCA1-deficient cells; hence, their study is of great clinical importance. The newest entrant on the scene of end resection regulation is the ATPase TRIP13 that disables the pro-C-NHEJ cascade by promoting a novel conformational change of the HORMA protein REV7. Here, we tie these new findings and factors with previous research on the regulation of DSB repair and HORMA proteins, and suggest testable hypotheses for how TRIP13 could specifically inactivate REV7-Shieldin to promote HR. We also discuss these biological questions in the context of clinical therapeutics.
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Affiliation(s)
- Prabha Sarangi
- Department of Radiation Oncology, Dana-Farber Cancer Institute , Boston, MA, USA.,Center for DNA Damage and Repair, Dana-Farber Cancer Institute , Boston, MA, USA
| | - Connor S Clairmont
- Department of Radiation Oncology, Dana-Farber Cancer Institute , Boston, MA, USA.,Center for DNA Damage and Repair, Dana-Farber Cancer Institute , Boston, MA, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute , Boston, MA, USA.,Center for DNA Damage and Repair, Dana-Farber Cancer Institute , Boston, MA, USA
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