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Kim DY, Yun H, You JE, Lee JU, Kang DH, Ryu YS, Koh DI, Jin DH. Inactivation of VRK1 sensitizes ovarian cancer to PARP inhibition through regulating DNA-PK stability. Exp Cell Res 2024; 438:114036. [PMID: 38614421 DOI: 10.1016/j.yexcr.2024.114036] [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: 11/27/2023] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 04/15/2024]
Abstract
Ovarian cancer is the leading cause of gynecologic cancer death. Among the most innovative anti-cancer approaches, the genetic concept of synthetic lethality is that mutations in multiple genes work synergistically to effect cell death. Previous studies found that although vaccinia-related kinase-1 (VRK1) associates with DNA damage repair proteins, its underlying mechanisms remain unclear. Here, we found high VRK1 expression in ovarian tumors, and that VRK1 depletion can significantly promote apoptosis and cell cycle arrest. The effect of VRK1 knockdown on apoptosis was manifested by increased DNA damage, genomic instability, and apoptosis, and also blocked non-homologous end joining (NHEJ) by destabilizing DNA-PK. Further, we verified that VRK1 depletion enhanced sensitivity to a PARP inhibitor (PARPi), olaparib, promoting apoptosis through DNA damage, especially in ovarian cancer cell lines with high VRK1 expression. Proteins implicated in DNA damage responses are suitable targets for the development of new anti-cancer therapeutic strategies, and their combination could represent an alternative form of synthetic lethality. Therefore, normal protective DNA damage responses are impaired by combining olaparib with elimination of VRK1 and could be used to reduce drug dose and its associated toxicity. In summary, VRK1 represents both a potential biomarker for PARPi sensitivity, and a new DDR-associated therapeutic target, in ovarian cancer.
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Affiliation(s)
- Do Yeon Kim
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea; Department of Pharmacology, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Hyeseon Yun
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea; Department of Pharmacology, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Ji-Eun You
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea; Department of Pharmacology, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Ji-U Lee
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea
| | - Dong-Hee Kang
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea; Department of Pharmacology, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Yea Seong Ryu
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea
| | - Dong-In Koh
- Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea
| | - Dong-Hoon Jin
- Department of Convergence Medicine, Asan Institute for Life Science, Asan Medical Center, Seoul 05505, Republic of Korea; Department of Pharmacology, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea.
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2
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Rajendra E, Grande D, Mason B, Di Marcantonio D, Armstrong L, Hewitt G, Elinati E, Galbiati A, Boulton SJ, Heald RA, Smith GCM, Robinson HMR. Quantitative, titratable and high-throughput reporter assays to measure DNA double strand break repair activity in cells. Nucleic Acids Res 2024; 52:1736-1752. [PMID: 38109306 PMCID: PMC10899754 DOI: 10.1093/nar/gkad1196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023] Open
Abstract
Repair of DNA damage is essential for the maintenance of genome stability and cell viability. DNA double strand breaks (DSBs) constitute a toxic class of DNA lesion and multiple cellular pathways exist to mediate their repair. Robust and titratable assays of cellular DSB repair (DSBR) are important to functionally interrogate the integrity and efficiency of these mechanisms in disease models as well as in response to genetic or pharmacological perturbations. Several variants of DSBR reporters are available, however these are often limited by throughput or restricted to specific cellular models. Here, we describe the generation and validation of a suite of extrachromosomal reporter assays that can efficiently measure the major DSBR pathways of homologous recombination (HR), classical nonhomologous end joining (cNHEJ), microhomology-mediated end joining (MMEJ) and single strand annealing (SSA). We demonstrate that these assays can be adapted to a high-throughput screening format and that they are sensitive to pharmacological modulation, thus providing mechanistic and quantitative insights into compound potency, selectivity, and on-target specificity. We propose that these reporter assays can serve as tools to dissect the interplay of DSBR pathway networks in cells and will have broad implications for studies of DSBR mechanisms in basic research and drug discovery.
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Affiliation(s)
- Eeson Rajendra
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Diego Grande
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Bethany Mason
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | | - Lucy Armstrong
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | | - Elias Elinati
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | | | - Simon J Boulton
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | - Robert A Heald
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
| | - Graeme C M Smith
- Artios Pharma Ltd, Babraham Research Campus, Cambridge CB22 3FH, UK
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3
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Amritha PP, Shah JM. Essential role of the BRCA2B gene in somatic homologous recombination in Arabidopsis thaliana. BIOTECHNOLOGIA 2023; 104:371-380. [PMID: 38213474 PMCID: PMC10777725 DOI: 10.5114/bta.2023.132773] [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: 01/30/2023] [Revised: 06/15/2023] [Accepted: 08/29/2023] [Indexed: 01/13/2024] Open
Abstract
Constant exposure to various environmental and endogenous stresses can cause structural DNA damage, resulting in genome instability. Higher eukaryotic cells deploy conserved DNA repair systems, which include various DNA repair pathways, to maintain genome stability. Homologous recombination (HR), one of these repair pathways, involves multiple proteins. BRCA2, one of the proteins in the HR pathway, is of substantial research interest in humans because it is an oncogene. However, the study of this gene is limited due to the lack of availability of homozygous BRCA2-knockout mutants in mammals, which results in embryonic lethality. Arabidopsis thaliana has two copies of the BRCA2 homologs: BRCA2A and BRCA2B . Therefore, the single mutants remain nonlethal and fertile in Arabidopsis. The BRCA2A homolog, which plays a significant role in the HR pathway of germline cells and during the defense response, is well-studied in Arabidopsis. Our study focuses on the functional characterization of the BRCA2B homolog in the somatic cells of Arabidopsis, using the homozygous ΔBRCA2B mutant line. The phenotypic differences of ΔBRCA2B mutants were characterized and compared with wild Arabidopsis plants. The role of BRCA2B in spontaneous somatic HR (SHR) was studied using the ΔBRCA2B-gus detector line. ΔBRCA2B plants have a 6.3-fold lower SHR frequency than the control detector plants. Expression of four other HR pathway genes, including BRE, BRCC36A, RAD50, and RAD54, was significantly reduced in ΔBRCA2B mutants. Thus, our findings convey that the BRCA2B homolog plays an important role in maintaining spontaneous SHR rates and has a direct or indirect regulatory effect on the expression of other HR-related genes.
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Affiliation(s)
| | - Jasmine M. Shah
- Department of Plant Science, Central University of Kerala, Kasaragod, Kerala, India
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4
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Lavi ES, Lin ZP, Ratner ES. Gene expression of non-homologous end-joining pathways in the prognosis of ovarian cancer. iScience 2023; 26:107934. [PMID: 37810216 PMCID: PMC10558711 DOI: 10.1016/j.isci.2023.107934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/04/2023] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
Ovarian cancer is the deadliest gynecologic malignancy in women, with a 46% five-year overall survival rate. The objective of the study was to investigate the effects of non-homologous end-joining (NHEJ) genes on clinical outcomes of ovarian cancer patients. To determine if these genes act as prognostic biomarkers of mortality and disease progression, the expression profiles of 48 NHEJ-associated genes were analyzed using an array of statistical and machine learning techniques: logistic regression models, decision trees, naive-Bayes, two sample t-tests, support vector machines, hierarchical clustering, principal component analysis, and neural networks. In this process, the correlation of genes with patient survival and disease progression and recurrence was noted. Also, multiple features from the gene set were found to have significant predictive capabilities. APTX, BRCA1, PAXX, LIG1, and TP53 were identified as most important out of all the candidate genes for predicting clinical outcomes of ovarian cancer patients.
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Affiliation(s)
- Ethan S. Lavi
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Z. Ping Lin
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Elena S. Ratner
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA
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5
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Matos‐Rodrigues G, Barroca V, Muhammad A, Dardillac E, Allouch A, Koundrioukoff S, Lewandowski D, Despras E, Guirouilh‐Barbat J, Frappart L, Kannouche P, Dupaigne P, Le Cam E, Perfettini J, Romeo P, Debatisse M, Jasin M, Livera G, Martini E, Lopez BS. In vivo reduction of RAD51-mediated homologous recombination triggers aging but impairs oncogenesis. EMBO J 2023; 42:e110844. [PMID: 37661798 PMCID: PMC10577633 DOI: 10.15252/embj.2022110844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/06/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023] Open
Abstract
Homologous recombination (HR) is a prominent DNA repair pathway maintaining genome integrity. Mutations in many HR genes lead to cancer predisposition. Paradoxically, the implication of the pivotal HR factor RAD51 on cancer development remains puzzling. Particularly, no RAD51 mouse models are available to address the role of RAD51 in aging and carcinogenesis in vivo. We engineered a mouse model with an inducible dominant-negative form of RAD51 (SMRad51) that suppresses RAD51-mediated HR without stimulating alternative mutagenic repair pathways. We found that in vivo expression of SMRad51 led to replicative stress, systemic inflammation, progenitor exhaustion, premature aging and reduced lifespan, but did not trigger tumorigenesis. Expressing SMRAD51 in a breast cancer predisposition mouse model (PyMT) decreased the number and the size of tumors, revealing an anti-tumor activity of SMRAD51. We propose that these in vivo phenotypes result from chronic endogenous replication stress caused by HR decrease, which preferentially targets progenitors and tumor cells. Our work underlines the importance of RAD51 activity for progenitor cell homeostasis, preventing aging and more generally for the balance between cancer and aging.
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Affiliation(s)
- Gabriel Matos‐Rodrigues
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut CochinEquipe Labellisée Ligue Contre le CancerParisFrance
- Université de Paris and Université Paris‐Saclay, Laboratory of Development of the Gonads, IRCM/IBFJ CEA, UMR Genetic Stability Stem Cells and RadiationFontenay aux RosesFrance
| | - Vilma Barroca
- Université de Paris and Université Paris‐Saclay, Inserm, IRCM/IBFJ CEAUMR Genetic Stability Stem Cells and RadiationFontenay aux RosesFrance
| | - Ali‐Akbar Muhammad
- Genome Maintenance and Molecular Microscopy UMR8126 CNRSUniversité Paris‐Sud, Université Paris‐Saclay, Gustave RoussyVillejuif CedexFrance
| | - Elodie Dardillac
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut CochinEquipe Labellisée Ligue Contre le CancerParisFrance
| | - Awatef Allouch
- Cell Death and Aging Team, INSERM U1030, Laboratory of Molecular RadiotherapyUniversity Paris‐Sud and Gustave RoussyVillejuifFrance
| | - Stephane Koundrioukoff
- CNRS UMR8200 Sorbonne UniversitésUPMC UniversityParisFrance
- Institut Gustave RoussyVillejuifFrance
| | - Daniel Lewandowski
- Université de Paris and Université Paris‐Saclay, Inserm, IRCM/IBFJ CEAUMR Genetic Stability Stem Cells and RadiationFontenay aux RosesFrance
| | - Emmanuelle Despras
- CNRS UMR8200, Laboratory of Genetic Instability and OncogenesisUniversity Paris‐Sud and Gustave RoussyVillejuifFrance
| | - Josée Guirouilh‐Barbat
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut CochinEquipe Labellisée Ligue Contre le CancerParisFrance
| | - Lucien Frappart
- Leibniz Institute on Aging‐Fritz Lipmann InstituteJenaGermany
| | - Patricia Kannouche
- CNRS UMR8200, Laboratory of Genetic Instability and OncogenesisUniversity Paris‐Sud and Gustave RoussyVillejuifFrance
| | - Pauline Dupaigne
- Genome Maintenance and Molecular Microscopy UMR8126 CNRSUniversité Paris‐Sud, Université Paris‐Saclay, Gustave RoussyVillejuif CedexFrance
| | - Eric Le Cam
- Genome Maintenance and Molecular Microscopy UMR8126 CNRSUniversité Paris‐Sud, Université Paris‐Saclay, Gustave RoussyVillejuif CedexFrance
| | - Jean‐Luc Perfettini
- Cell Death and Aging Team, INSERM U1030, Laboratory of Molecular RadiotherapyUniversity Paris‐Sud and Gustave RoussyVillejuifFrance
| | - Paul‐Henri Romeo
- Université de Paris and Université Paris‐Saclay, Inserm, IRCM/IBFJ CEAUMR Genetic Stability Stem Cells and RadiationFontenay aux RosesFrance
| | - Michelle Debatisse
- CNRS UMR8200 Sorbonne UniversitésUPMC UniversityParisFrance
- Institut Gustave RoussyVillejuifFrance
| | - Maria Jasin
- Developmental Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Gabriel Livera
- Université de Paris and Université Paris‐Saclay, Laboratory of Development of the Gonads, IRCM/IBFJ CEA, UMR Genetic Stability Stem Cells and RadiationFontenay aux RosesFrance
| | - Emmanuelle Martini
- Université de Paris and Université Paris‐Saclay, Laboratory of Development of the Gonads, IRCM/IBFJ CEA, UMR Genetic Stability Stem Cells and RadiationFontenay aux RosesFrance
| | - Bernard S Lopez
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut CochinEquipe Labellisée Ligue Contre le CancerParisFrance
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6
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Ribeiro JH, Altinisik N, Rajan N, Verslegers M, Baatout S, Gopalakrishnan J, Quintens R. DNA damage and repair: underlying mechanisms leading to microcephaly. Front Cell Dev Biol 2023; 11:1268565. [PMID: 37881689 PMCID: PMC10597653 DOI: 10.3389/fcell.2023.1268565] [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: 07/28/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023] Open
Abstract
DNA-damaging agents and endogenous DNA damage constantly harm genome integrity. Under genotoxic stress conditions, the DNA damage response (DDR) machinery is crucial in repairing lesions and preventing mutations in the basic structure of the DNA. Different repair pathways are implicated in the resolution of such lesions. For instance, the non-homologous DNA end joining and homologous recombination pathways are central cellular mechanisms by which eukaryotic cells maintain genome integrity. However, defects in these pathways are often associated with neurological disorders, indicating the pivotal role of DDR in normal brain development. Moreover, the brain is the most sensitive organ affected by DNA-damaging agents compared to other tissues during the prenatal period. The accumulation of lesions is believed to induce cell death, reduce proliferation and premature differentiation of neural stem and progenitor cells, and reduce brain size (microcephaly). Microcephaly is mainly caused by genetic mutations, especially genes encoding proteins involved in centrosomes and DNA repair pathways. However, it can also be induced by exposure to ionizing radiation and intrauterine infections such as the Zika virus. This review explains mammalian cortical development and the major DNA repair pathways that may lead to microcephaly when impaired. Next, we discuss the mechanisms and possible exposures leading to DNA damage and p53 hyperactivation culminating in microcephaly.
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Affiliation(s)
- Jessica Honorato Ribeiro
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Nazlican Altinisik
- Laboratory for Centrosome and Cytoskeleton Biology, Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Nicholas Rajan
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Mieke Verslegers
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
- Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jay Gopalakrishnan
- Laboratory for Centrosome and Cytoskeleton Biology, Institute of Human Genetics, University Hospital, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Roel Quintens
- Radiobiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
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7
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Sahu S, Sullivan TL, Mitrophanov AY, Galloux M, Nousome D, Southon E, Caylor D, Mishra AP, Evans CN, Clapp ME, Burkett S, Malys T, Chari R, Biswas K, Sharan SK. Saturation genome editing of 11 codons and exon 13 of BRCA2 coupled with chemotherapeutic drug response accurately determines pathogenicity of variants. PLoS Genet 2023; 19:e1010940. [PMID: 37713444 PMCID: PMC10529611 DOI: 10.1371/journal.pgen.1010940] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 09/27/2023] [Accepted: 08/28/2023] [Indexed: 09/17/2023] Open
Abstract
The unknown pathogenicity of a significant number of variants found in cancer-related genes is attributed to limited epidemiological data, resulting in their classification as variant of uncertain significance (VUS). To date, Breast Cancer gene-2 (BRCA2) has the highest number of VUSs, which has necessitated the development of several robust functional assays to determine their functional significance. Here we report the use of a humanized-mouse embryonic stem cell (mESC) line expressing a single copy of the human BRCA2 for a CRISPR-Cas9-based high-throughput functional assay. As a proof-of-principle, we have saturated 11 codons encoded by BRCA2 exons 3, 18, 19 and all possible single-nucleotide variants in exon 13 and multiplexed these variants for their functional categorization. Specifically, we used a pool of 180-mer single-stranded donor DNA to generate all possible combination of variants. Using a high throughput sequencing-based approach, we show a significant drop in the frequency of non-functional variants, whereas functional variants are enriched in the pool of the cells. We further demonstrate the response of these variants to the DNA-damaging agents, cisplatin and olaparib, allowing us to use cellular survival and drug response as parameters for variant classification. Using this approach, we have categorized 599 BRCA2 variants including 93-single nucleotide variants (SNVs) across the 11 codons, of which 28 are reported in ClinVar. We also functionally categorized 252 SNVs from exon 13 into 188 functional and 60 non-functional variants, demonstrating that saturation genome editing (SGE) coupled with drug sensitivity assays can enhance functional annotation of BRCA2 VUS.
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Affiliation(s)
- Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Teresa L. Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Alexander Y. Mitrophanov
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland, United States of America
| | | | - Darryl Nousome
- CCR Bioinformatics Resource, Leidos Biomedical Sciences, Inc. Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Dylan Caylor
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Arun Prakash Mishra
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Christine N. Evans
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Michelle E. Clapp
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Sandra Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Tyler Malys
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, Maryland, United States of America
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Shyam K. Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
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8
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Pikkusaari S, Tumiati M, Virtanen A, Oikkonen J, Li Y, Perez-Villatoro F, Muranen T, Salko M, Huhtinen K, Kanerva A, Koskela H, Tapper J, Koivisto-Korander R, Joutsiniemi T, Haltia UM, Lassus H, Hautaniemi S, Färkkilä A, Hynninen J, Hietanen S, Carpén O, Kauppi L. Functional Homologous Recombination Assay on FFPE Specimens of Advanced High-Grade Serous Ovarian Cancer Predicts Clinical Outcomes. Clin Cancer Res 2023; 29:3110-3123. [PMID: 36805632 PMCID: PMC10425726 DOI: 10.1158/1078-0432.ccr-22-3156] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/29/2022] [Accepted: 02/15/2023] [Indexed: 02/22/2023]
Abstract
PURPOSE Deficiency in homologous recombination (HR) repair of DNA damage is characteristic of many high-grade serous ovarian cancers (HGSC). It is imperative to identify patients with homologous recombination-deficient (HRD) tumors as they are most likely to benefit from platinum-based chemotherapy and PARP inhibitors (PARPi). Existing methods measure historical, not necessarily current HRD and/or require high tumor cell content, which is not achievable for many patients. We set out to develop a clinically feasible assay for identifying functionally HRD tumors that can predict clinical outcomes. EXPERIMENTAL DESIGN We quantified RAD51, a key HR protein, in immunostained formalin-fixed, paraffin-embedded (FFPE) tumor samples obtained from chemotherapy-naïve and neoadjuvant chemotherapy (NACT)-treated HGSC patients. We defined cutoffs for functional HRD separately for these sample types, classified the patients accordingly as HRD or HR-proficient, and analyzed correlations with clinical outcomes. From the same specimens, genomics-based HRD estimates (HR gene mutations, genomic signatures, and genomic scars) were also determined, and compared with functional HR (fHR) status. RESULTS fHR status significantly predicted several clinical outcomes, including progression-free survival (PFS) and overall survival (OS), when determined from chemo-naïve (PFS, P < 0.0001; OS, P < 0.0001) as well as NACT-treated (PFS, P < 0.0001; OS, P = 0.0033) tumor specimens. The fHR test also identified as HRD those PARPi-at-recurrence-treated patients with longer OS (P = 0.0188). CONCLUSIONS We developed an fHR assay performed on routine FFPE specimens, obtained from either chemo-naïve or NACT-treated HGSC patients, that can significantly predict real-world platinum-based chemotherapy and PARPi response. See related commentary by Garg and Oza, p. 2957.
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Affiliation(s)
- Sanna Pikkusaari
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Manuela Tumiati
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anni Virtanen
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Jaana Oikkonen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Yilin Li
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Fernando Perez-Villatoro
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Taru Muranen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matilda Salko
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaisa Huhtinen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Kanerva
- Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Heidi Koskela
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Johanna Tapper
- Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | | | - Titta Joutsiniemi
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Ulla-Maija Haltia
- Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Heini Lassus
- Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anniina Färkkilä
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN digital precision cancer medicine flagship, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Sakari Hietanen
- Department of Obstetrics and Gynecology, Turku University Hospital, Turku, Finland
| | - Olli Carpén
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pathology, University of Helsinki and HUS Diagnostic Center, Helsinki University Hospital, Helsinki, Finland
| | - Liisa Kauppi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN digital precision cancer medicine flagship, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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9
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Li Y, Chen Z, Peng J, Yuan C, Yan S, Yang N, Li P, Kong B. The splicing factor SNRPB promotes ovarian cancer progression through regulating aberrant exon skipping of POLA1 and BRCA2. Oncogene 2023:10.1038/s41388-023-02763-x. [PMID: 37391593 DOI: 10.1038/s41388-023-02763-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/08/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023]
Abstract
Splicing factors play a crucial role in the initiation and development of various human cancers. SNRPB, a core spliceosome component, regulates pre-mRNA alternative splicing. However, its function and underlying mechanism in ovarian cancer remain unclear. This study identified SNRPB as a critical driver of ovarian cancer through TCGA and CPTAC database analysis. SNRPB was highly upregulated in fresh frozen ovarian cancer tissues compared with normal fallopian tubes. Immunohistochemistry revealed that SNRPB expression was increased in formalin-fixed, paraffin-embedded ovarian cancer sections and was positively correlated with a poor prognosis for ovarian cancer. Functionally, SNRPB knockdown suppressed ovarian cancer cell proliferation and invasion, and overexpression exerted opposite effects. SNRPB expression increased after cisplatin treatment, and silencing SNRPB sensitized ovarian cancer cells to cisplatin. KEGG pathway analysis revealed that the differentially expressed genes (DEGs) were mainly enriched in DNA replication and homologous recombination, and almost all DEGs related to DNA replication and homologous recombination were downregulated after SNRPB knockdown according to RNA-seq. Exon 3 skipping of the DEGs DNA polymerase alpha 1 (POLA1) and BRCA2 was induced by SNRPB silencing. Exon 3 skipping of POLA1 yielded premature termination codons and led to nonsense-mediated RNA decay (NMD); exon 3 skipping of BRCA2 led to loss of the PALB2 binding domain, which is necessary for homologous recombination, and increased ovarian cancer cell cisplatin sensitivity. POLA1 or BRCA2 knockdown partially impaired the increased malignancy of SNRPB-overexpressing ovarian cancer cells. Moreover, miR-654-5p was found to reduce SNRPB mRNA expression by directly binding to the SNRPB 3'-UTR. Overall, SNRPB was identified as an important oncogenic driver that promotes ovarian cancer progression by repressing exon 3 skipping of POLA1 and BRCA2. Thus, SNRPB is a potential treatment target and prognostic marker for ovarian cancer.
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Affiliation(s)
- Yingwei Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China.
- Medical Integration and Practice Center, Cheeloo College of Medicine, Shandong University, Ji'nan 250012, Shandong Province, China.
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China.
| | - Zhongshao Chen
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Jiali Peng
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Cunzhong Yuan
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Shi Yan
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Ning Yang
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Peng Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, 107 Wenhua Xi Road, Ji'nan 250012, Shandong Province, China.
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Ji'nan 250012, Shandong Province, China.
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10
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Thomas M, Dubacq C, Rabut E, Lopez BS, Guirouilh-Barbat J. Noncanonical Roles of RAD51. Cells 2023; 12:cells12081169. [PMID: 37190078 DOI: 10.3390/cells12081169] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Homologous recombination (HR), an evolutionary conserved pathway, plays a paramount role(s) in genome plasticity. The pivotal HR step is the strand invasion/exchange of double-stranded DNA by a homologous single-stranded DNA (ssDNA) covered by RAD51. Thus, RAD51 plays a prime role in HR through this canonical catalytic strand invasion/exchange activity. The mutations in many HR genes cause oncogenesis. Surprisingly, despite its central role in HR, the invalidation of RAD51 is not classified as being cancer prone, constituting the "RAD51 paradox". This suggests that RAD51 exercises other noncanonical roles that are independent of its catalytic strand invasion/exchange function. For example, the binding of RAD51 on ssDNA prevents nonconservative mutagenic DNA repair, which is independent of its strand exchange activity but relies on its ssDNA occupancy. At the arrested replication forks, RAD51 plays several noncanonical roles in the formation, protection, and management of fork reversal, allowing for the resumption of replication. RAD51 also exhibits noncanonical roles in RNA-mediated processes. Finally, RAD51 pathogenic variants have been described in the congenital mirror movement syndrome, revealing an unexpected role in brain development. In this review, we present and discuss the different noncanonical roles of RAD51, whose presence does not automatically result in an HR event, revealing the multiple faces of this prominent actor in genomic plasticity.
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Affiliation(s)
- Mélissa Thomas
- INSERM U1016, UMR 8104 CNRS, Institut Cochin, Université de Paris Cité, 24 rue du Faubourg St. Jacques, F-75014 Paris, France
| | - Caroline Dubacq
- Institut de Biologie Paris Seine, IBPS, Neuroscience Paris Seine, NPS, INSERM, CNRS, Sorbonne Université, F-75005 Paris, France
| | - Elise Rabut
- INSERM U1016, UMR 8104 CNRS, Institut Cochin, Université de Paris Cité, 24 rue du Faubourg St. Jacques, F-75014 Paris, France
| | - Bernard S Lopez
- INSERM U1016, UMR 8104 CNRS, Institut Cochin, Université de Paris Cité, 24 rue du Faubourg St. Jacques, F-75014 Paris, France
| | - Josée Guirouilh-Barbat
- INSERM U1016, UMR 8104 CNRS, Institut Cochin, Université de Paris Cité, 24 rue du Faubourg St. Jacques, F-75014 Paris, France
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11
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Wang Z, He S, Jiang M, Li X, Chen N. Mechanism Study on Radiosensitization Effect of Curcumin in Bladder Cancer Cells Regulated by Filamin A. Dose Response 2022; 20:15593258221100997. [PMID: 35677349 PMCID: PMC9168873 DOI: 10.1177/15593258221100997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Objective To study the radiosensitization effect of curcumin, a natural product with
anti-inflammatory and anti-cancer properties, in bladder cancer cells and identify the
specific role of FLNA gene in that process. Methods CCK-8 method was initially adopted to identify the proper interventional concentration
of curcumin. T24 bladder cancer cells were subjected to CCK-8, flow cytometry, and
colony formation assay to study the cell biological behaviors under different
interventions. γ-H2AX test was performed to test the level of damage in T24 cells.
RT-qPCR and Western blot were conducted to measure FLNA mRNA and protein levels. Results Low-dose curcumin (10, 20 μM) following X-ray exposure resulted in increased DNA
damage, augmented apoptosis, and reduced proliferation of T24 cells. Certain
radiosensitization was demonstrated when curcumin was applied at 10 μM. Additionally,
elevation of FLNA gene and protein levels was also indicated upon combination
treatment. Conclusion Low-dose curcumin has certain radiosensitization effect in bladder cancer, where FLNA
plays a certain regulatory role.
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Affiliation(s)
- Zhenfan Wang
- Soochow University Affiliated Suzhou Ninth Hospital, Suzhou, China
| | - Shuqing He
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Minjun Jiang
- Soochow University Affiliated Suzhou Ninth Hospital, Suzhou, China
| | - Xue Li
- Soochow University Affiliated Suzhou Ninth Hospital, Suzhou, China
| | - Na Chen
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
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12
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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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13
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Moyret-Lalle C, Prodhomme MK, Burlet D, Kashiwagi A, Petrilli V, Puisieux A, Seimiya H, Tissier A. Role of EMT in the DNA damage response, double-strand break repair pathway choice and its implications in cancer treatment. Cancer Sci 2022; 113:2214-2223. [PMID: 35534984 PMCID: PMC9277259 DOI: 10.1111/cas.15389] [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: 02/01/2022] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 11/30/2022] Open
Abstract
Numerous epithelial–mesenchymal transition (EMT) characteristics have now been demonstrated to participate in tumor development. Indeed, EMT is involved in invasion, acquisition of stem cell properties, and therapy‐associated resistance of cancer cells. Together, these mechanisms offer advantages in adapting to changes in the tumor microenvironment. However, recent findings have shown that EMT‐associated transcription factors (EMT‐TFs) may also be involved in DNA repair. A better understanding of the coordination between the DNA repair pathways and the role played by some EMT‐TFs in the DNA damage response (DDR) should pave the way for new treatments targeting tumor‐specific molecular vulnerabilities, which result in selective destruction of cancer cells. Here we review recent advances, providing novel insights into the role of EMT in the DDR and repair pathways, with a particular focus on the influence of EMT on cellular sensitivity to damage, as well as the implications of these relationships for improving the efficacy of cancer treatments.
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Affiliation(s)
- Caroline Moyret-Lalle
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Lyon, France.,LabEx DEVweCAN, Université de Lyon, Lyon, France
| | - Mélanie K Prodhomme
- Department of Epigenetics & Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Delphine Burlet
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Lyon, France
| | - Ayaka Kashiwagi
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Virginie Petrilli
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Lyon, France
| | - Alain Puisieux
- Institut Curie, Versailles Saint-Quentin-en-Yvelines University, PSL Research University, Paris, France
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Agnès Tissier
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Centre of Lyon, Lyon, France
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14
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Giallongo S, Řeháková D, Biagini T, Lo Re O, Raina P, Lochmanová G, Zdráhal Z, Resnick I, Pata P, Pata I, Mistrík M, de Magalhães JP, Mazza T, Koutná I, Vinciguerra M. Histone Variant macroH2A1.1 Enhances Nonhomologous End Joining-dependent DNA Double-strand-break Repair and Reprogramming Efficiency of Human iPSCs. Stem Cells 2022; 40:35-48. [PMID: 35511867 PMCID: PMC9199840 DOI: 10.1093/stmcls/sxab004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/02/2021] [Indexed: 01/21/2023]
Abstract
DNA damage repair (DDR) is a safeguard for genome integrity maintenance. Increasing DDR efficiency could increase the yield of induced pluripotent stem cells (iPSC) upon reprogramming from somatic cells. The epigenetic mechanisms governing DDR during iPSC reprogramming are not completely understood. Our goal was to evaluate the splicing isoforms of histone variant macroH2A1, macroH2A1.1, and macroH2A1.2, as potential regulators of DDR during iPSC reprogramming. GFP-Trap one-step isolation of mtagGFP-macroH2A1.1 or mtagGFP-macroH2A1.2 fusion proteins from overexpressing human cell lines, followed by liquid chromatography-tandem mass spectrometry analysis, uncovered macroH2A1.1 exclusive interaction with Poly-ADP Ribose Polymerase 1 (PARP1) and X-ray cross-complementing protein 1 (XRCC1). MacroH2A1.1 overexpression in U2OS-GFP reporter cells enhanced specifically nonhomologous end joining (NHEJ) repair pathway, while macroH2A1.1 knock-out (KO) mice showed an impaired DDR capacity. The exclusive interaction of macroH2A1.1, but not macroH2A1.2, with PARP1/XRCC1, was confirmed in human umbilical vein endothelial cells (HUVEC) undergoing reprogramming into iPSC through episomal vectors. In HUVEC, macroH2A1.1 overexpression activated transcriptional programs that enhanced DDR and reprogramming. Consistently, macroH2A1.1 but not macroH2A1.2 overexpression improved iPSC reprogramming. We propose the macroH2A1 splicing isoform macroH2A1.1 as a promising epigenetic target to improve iPSC genome stability and therapeutic potential.
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Affiliation(s)
- Sebastiano Giallongo
- International Clinical Research Center, St. Anne’s University Hospital, Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Daniela Řeháková
- International Clinical Research Center, St. Anne’s University Hospital, Brno, Czech Republic
| | - Tommaso Biagini
- Laboratory of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Oriana Lo Re
- International Clinical Research Center, St. Anne’s University Hospital, Brno, Czech Republic
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna (RIMUV), Varna, Bulgaria
| | - Priyanka Raina
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Gabriela Lochmanová
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Igor Resnick
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna (RIMUV), Varna, Bulgaria
- Program for Hematology, Immunology, BMT and Cell therapy, St. Marina University Hospital, Varna, Bulgaria
- Department of Medical Genetics, Medical University of Varna, Varna, Bulgaria
| | - Pille Pata
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- IVEX Lab, Akadeemia 15, Tallinn, Estonia
| | - Illar Pata
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Martin Mistrík
- Laboratory of Genome Integrity, Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Tommaso Mazza
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna (RIMUV), Varna, Bulgaria
| | - Irena Koutná
- International Clinical Research Center, St. Anne’s University Hospital, Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Manlio Vinciguerra
- International Clinical Research Center, St. Anne’s University Hospital, Brno, Czech Republic
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna (RIMUV), Varna, Bulgaria
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15
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Paprocka R, Wiese-Szadkowska M, Janciauskiene S, Kosmalski T, Kulik M, Helmin-Basa A. Latest developments in metal complexes as anticancer agents. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214307] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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16
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So A, Dardillac E, Muhammad A, Chailleux C, Sesma-Sanz L, Ragu S, Le Cam E, Canitrot Y, Masson J, Dupaigne P, Lopez BS, Guirouilh-Barbat J. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2651-2666. [PMID: 35137208 PMCID: PMC8934640 DOI: 10.1093/nar/gkac073] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/18/2022] [Accepted: 01/25/2022] [Indexed: 11/23/2022] Open
Abstract
Selection of the appropriate DNA double-strand break (DSB) repair pathway is decisive for genetic stability. It is proposed to act according to two steps: 1-canonical nonhomologous end-joining (C-NHEJ) versus resection that generates single-stranded DNA (ssDNA) stretches; 2-on ssDNA, gene conversion (GC) versus nonconservative single-strand annealing (SSA) or alternative end-joining (A-EJ). Here, we addressed the mechanisms by which RAD51 regulates this second step, preventing nonconservative repair in human cells. Silencing RAD51 or BRCA2 stimulated both SSA and A-EJ, but not C-NHEJ, validating the two-step model. Three different RAD51 dominant-negative forms (DN-RAD51s) repressed GC and stimulated SSA/A-EJ. However, a fourth DN-RAD51 repressed SSA/A-EJ, although it efficiently represses GC. In living cells, the three DN-RAD51s that stimulate SSA/A-EJ failed to load efficiently onto damaged chromatin and inhibited the binding of endogenous RAD51, while the fourth DN-RAD51, which inhibits SSA/A-EJ, efficiently loads on damaged chromatin. Therefore, the binding of RAD51 to DNA, rather than its ability to promote GC, is required for SSA/A-EJ inhibition by RAD51. We showed that RAD51 did not limit resection of endonuclease-induced DSBs, but prevented spontaneous and RAD52-induced annealing of complementary ssDNA in vitro. Therefore, RAD51 controls the selection of the DSB repair pathway, protecting genome integrity from nonconservative DSB repair through ssDNA occupancy, independently of the promotion of CG.
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Affiliation(s)
- Ayeong So
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, France
- CNRS UMR 8200, Gustave-Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Elodie Dardillac
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, France
- CNRS UMR 8200, Gustave-Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Ali Muhammad
- Genome Maintenance and Molecular Microscopy UMR 9019 CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | | | - Laura Sesma-Sanz
- Genome Stability Laboratory, CHU de Québec Research Center (Oncology Division), Quebec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Sandrine Ragu
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, France
- CNRS UMR 8200, Gustave-Roussy, Université Paris-Saclay, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Eric Le Cam
- Genome Maintenance and Molecular Microscopy UMR 9019 CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | - Yvan Canitrot
- CBI, CNRS UMR5088, LBCMCP, Toulouse University, Toulouse, France
| | - Jean Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center (Oncology Division), Quebec City, QC, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, QC, Canada
| | - Pauline Dupaigne
- Genome Maintenance and Molecular Microscopy UMR 9019 CNRS, Université Paris-Saclay, Gustave Roussy, F-94805, Villejuif Cedex, France
| | - Bernard S Lopez
- To whom correspondence should be addressed. Tel: +33 1 53 73 27 40;
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17
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Datta A, Biswas K, Sommers JA, Thompson H, Awate S, Nicolae CM, Thakar T, Moldovan GL, Shoemaker RH, Sharan SK, Brosh RM. WRN helicase safeguards deprotected replication forks in BRCA2-mutated cancer cells. Nat Commun 2021; 12:6561. [PMID: 34772932 PMCID: PMC8590011 DOI: 10.1038/s41467-021-26811-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 10/20/2021] [Indexed: 11/08/2022] Open
Abstract
The tumor suppressor BRCA2 protects stalled forks from degradation to maintain genome stability. However, the molecular mechanism(s) whereby unprotected forks are stabilized remains to be fully characterized. Here, we demonstrate that WRN helicase ensures efficient restart and limits excessive degradation of stalled forks in BRCA2-deficient cancer cells. In vitro, WRN ATPase/helicase catalyzes fork restoration and curtails MRE11 nuclease activity on regressed forks. We show that WRN helicase inhibitor traps WRN on chromatin leading to rapid fork stalling and nucleolytic degradation of unprotected forks by MRE11, resulting in MUS81-dependent double-strand breaks, elevated non-homologous end-joining and chromosomal instability. WRN helicase inhibition reduces viability of BRCA2-deficient cells and potentiates cytotoxicity of a poly (ADP)ribose polymerase (PARP) inhibitor. Furthermore, BRCA2-deficient xenograft tumors in mice exhibited increased DNA damage and growth inhibition when treated with WRN helicase inhibitor. This work provides mechanistic insight into stalled fork stabilization by WRN helicase when BRCA2 is deficient.
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Affiliation(s)
- Arindam Datta
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Joshua A Sommers
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Haley Thompson
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Sanket Awate
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Tanay Thakar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Robert H Shoemaker
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Robert M Brosh
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA.
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18
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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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19
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Llorens-Agost M, Ensminger M, Le HP, Gawai A, Liu J, Cruz-García A, Bhetawal S, Wood RD, Heyer WD, Löbrich M. POLθ-mediated end joining is restricted by RAD52 and BRCA2 until the onset of mitosis. Nat Cell Biol 2021; 23:1095-1104. [PMID: 34616022 PMCID: PMC8675436 DOI: 10.1038/s41556-021-00764-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/30/2021] [Indexed: 01/25/2023]
Abstract
BRCA2-mutant cells are defective in homologous recombination, making them vulnerable to the inactivation of other pathways for the repair of DNA double-strand breaks (DSBs). This concept can be clinically exploited but is currently limited due to insufficient knowledge about how DSBs are repaired in the absence of BRCA2. We show that DNA polymerase θ (POLθ)-mediated end joining (TMEJ) repairs DSBs arising during the S phase in BRCA2-deficient cells only after the onset of the ensuing mitosis. This process is regulated by RAD52, whose loss causes the premature usage of TMEJ and the formation of chromosomal fusions. Purified RAD52 and BRCA2 proteins both block the DNA polymerase function of POLθ, suggesting a mechanism explaining their synthetic lethal relationships. We propose that the delay of TMEJ until mitosis ensures the conversion of originally one-ended DSBs into two-ended DSBs. Mitotic chromatin condensation might further serve to juxtapose correct break ends and limit chromosomal fusions.
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Affiliation(s)
- Marta Llorens-Agost
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Michael Ensminger
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Hang Phuong Le
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Anugrah Gawai
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Jie Liu
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Andrés Cruz-García
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Sarita Bhetawal
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Markus Löbrich
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany.
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20
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Le HP, Heyer WD, Liu J. Guardians of the Genome: BRCA2 and Its Partners. Genes (Basel) 2021; 12:genes12081229. [PMID: 34440403 PMCID: PMC8394001 DOI: 10.3390/genes12081229] [Citation(s) in RCA: 19] [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: 06/28/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/28/2022] Open
Abstract
The tumor suppressor BRCA2 functions as a central caretaker of genome stability, and individuals who carry BRCA2 mutations are predisposed to breast, ovarian, and other cancers. Recent research advanced our mechanistic understanding of BRCA2 and its various interaction partners in DNA repair, DNA replication support, and DNA double-strand break repair pathway choice. In this review, we discuss the biochemical and structural properties of BRCA2 and examine how these fundamental properties contribute to DNA repair and replication fork stabilization in living cells. We highlight selected BRCA2 binding partners and discuss their role in BRCA2-mediated homologous recombination and fork protection. Improved mechanistic understanding of how BRCA2 functions in genome stability maintenance can enable experimental evidence-based evaluation of pathogenic BRCA2 mutations and BRCA2 pseudo-revertants to support targeted therapy.
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Affiliation(s)
- Hang Phuong Le
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA; (H.P.L.); (W.-D.H.)
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA; (H.P.L.); (W.-D.H.)
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Jie Liu
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA; (H.P.L.); (W.-D.H.)
- Correspondence: ; Tel.: +1-530-752-3016
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21
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Lee M, Shorthouse D, Mahen R, Hall BA, Venkitaraman AR. Cancer-causing BRCA2 missense mutations disrupt an intracellular protein assembly mechanism to disable genome maintenance. Nucleic Acids Res 2021; 49:5588-5604. [PMID: 33978741 PMCID: PMC8191791 DOI: 10.1093/nar/gkab308] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/11/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer-causing missense mutations in the 3418 amino acid BRCA2 breast and ovarian cancer suppressor protein frequently affect a short (∼340 residue) segment in its carboxyl-terminal domain (DBD). Here, we identify a shared molecular mechanism underlying their pathogenicity. Pathogenic BRCA2 missense mutations cluster in the DBD’s helical domain (HD) and OB1-fold motifs, which engage the partner protein DSS1. Pathogenic - but not benign – DBD mutations weaken or abolish DSS1-BRCA2 assembly, provoking mutant BRCA2 oligomers that are excluded from the cell nucleus, and disable DNA repair by homologous DNA recombination (HDR). DSS1 inhibits the intracellular oligomerization of wildtype, but not mutant, forms of BRCA2. Remarkably, DSS1 expression corrects defective HDR in cells bearing pathogenic BRCA2 missense mutants with weakened, but not absent, DSS1 binding. Our findings identify a DSS1-mediated intracellular protein assembly mechanism that is disrupted by cancer-causing BRCA2 missense mutations, and suggest an approach for its therapeutic correction.
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Affiliation(s)
- Miyoung Lee
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - David Shorthouse
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Robert Mahen
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Benjamin A Hall
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
| | - Ashok R Venkitaraman
- Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK.,The Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599 & Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove 138648, Singapore
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22
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Matos-Rodrigues G, Guirouilh-Barbat J, Martini E, Lopez BS. Homologous recombination, cancer and the 'RAD51 paradox'. NAR Cancer 2021; 3:zcab016. [PMID: 34316706 PMCID: PMC8209977 DOI: 10.1093/narcan/zcab016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 01/22/2023] Open
Abstract
Genetic instability is a hallmark of cancer cells. Homologous recombination (HR) plays key roles in genome stability and variability due to its roles in DNA double-strand break and interstrand crosslink repair, and in the protection and resumption of arrested replication forks. HR deficiency leads to genetic instability, and, as expected, many HR genes are downregulated in cancer cells. The link between HR deficiency and cancer predisposition is exemplified by familial breast and ovarian cancers and by some subgroups of Fanconi anaemia syndromes. Surprisingly, although RAD51 plays a pivotal role in HR, i.e., homology search and in strand exchange with a homologous DNA partner, almost no inactivating mutations of RAD51 have been associated with cancer predisposition; on the contrary, overexpression of RAD51 is associated with a poor prognosis in different types of tumours. Taken together, these data highlight the fact that RAD51 differs from its HR partners with regard to cancer susceptibility and expose what we call the ‘RAD51 paradox’. Here, we catalogue the dysregulations of HR genes in human pathologies, including cancer and Fanconi anaemia or congenital mirror movement syndromes, and we discuss the RAD51 paradox.
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Affiliation(s)
- Gabriel Matos-Rodrigues
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, F-75014, France
| | - Josée Guirouilh-Barbat
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, F-75014, France
| | - Emmanuelle Martini
- Université de Paris and Université Paris-Saclay, Laboratory of Development of the Gonads, IRCM/IBFJ CEA, UMR Genetic Stability, Stem Cells and Radiation, F-92265 Fontenay aux Roses, France
| | - Bernard S Lopez
- Université de Paris, INSERM U1016, UMR 8104 CNRS, Institut Cochin, Equipe Labellisée Ligue Contre le Cancer, F-75014, France
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23
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Michelena J, Pellegrino S, Spegg V, Altmeyer M. Replicated chromatin curtails 53BP1 recruitment in BRCA1-proficient and BRCA1-deficient cells. Life Sci Alliance 2021; 4:4/6/e202101023. [PMID: 33811064 PMCID: PMC8046418 DOI: 10.26508/lsa.202101023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
This study demonstrates how single cell normalization to genome size provides insight into genome function, here in the context of DNA double-strand break repair by 53BP1 versus BRCA1–BARD1. DNA double-strand breaks can be repaired by non-homologous end-joining or homologous recombination. Which pathway is used depends on the balance between the tumor suppressors 53BP1 and BRCA1 and on the availability of an undamaged template DNA for homology-directed repair. How cells switch from a 53BP1-dominated to a BRCA1-governed homologous recombination response as they progress through the cell cycle is incompletely understood. Here we reveal, using high-throughput microscopy and applying single cell normalization to control for increased genome size as cells replicate their DNA, that 53BP1 recruitment to damaged replicated chromatin is inefficient in both BRCA1-proficient and BRCA1-deficient cells. Our results substantiate a dual switch model from a 53BP1-dominated response in unreplicated chromatin to a BRCA1–BARD1–dominated response in replicated chromatin, in which replication-coupled dilution of 53BP1’s binding mark H4K20me2 functionally cooperates with BRCA1–BARD1–mediated suppression of 53BP1 binding. More generally, we suggest that appropriate normalization of single cell data, for example, to DNA content, provides additional layers of information, which can be critical for quantifying and interpreting cellular phenotypes.
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Affiliation(s)
- Jone Michelena
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Stefania Pellegrino
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School (LSZGS), Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School (LSZGS), Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
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24
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Caracciolo D, Riillo C, Di Martino MT, Tagliaferri P, Tassone P. Alternative Non-Homologous End-Joining: Error-Prone DNA Repair as Cancer's Achilles' Heel. Cancers (Basel) 2021; 13:cancers13061392. [PMID: 33808562 PMCID: PMC8003480 DOI: 10.3390/cancers13061392] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Cancer onset and progression lead to a high rate of DNA damage, due to replicative and metabolic stress. To survive in this dangerous condition, cancer cells switch the DNA repair machinery from faithful systems to error-prone pathways, strongly increasing the mutational rate that, in turn, supports the disease progression and drug resistance. Although DNA repair de-regulation boosts genomic instability, it represents, at the same time, a critical cancer vulnerability that can be exploited for synthetic lethality-based therapeutic intervention. We here discuss the role of the error-prone DNA repair, named Alternative Non-Homologous End Joining (Alt-NHEJ), as inducer of genomic instability and as a potential therapeutic target. We portray different strategies to drug Alt-NHEJ and discuss future challenges for selecting patients who could benefit from Alt-NHEJ inhibition, with the aim of precision oncology. Abstract Error-prone DNA repair pathways promote genomic instability which leads to the onset of cancer hallmarks by progressive genetic aberrations in tumor cells. The molecular mechanisms which foster this process remain mostly undefined, and breakthrough advancements are eagerly awaited. In this context, the alternative non-homologous end joining (Alt-NHEJ) pathway is considered a leading actor. Indeed, there is experimental evidence that up-regulation of major Alt-NHEJ components, such as LIG3, PolQ, and PARP1, occurs in different tumors, where they are often associated with disease progression and drug resistance. Moreover, the Alt-NHEJ addiction of cancer cells provides a promising target to be exploited by synthetic lethality approaches for the use of DNA damage response (DDR) inhibitors and even as a sensitizer to checkpoint-inhibitors immunotherapy by increasing the mutational load. In this review, we discuss recent findings highlighting the role of Alt-NHEJ as a promoter of genomic instability and, therefore, as new cancer’s Achilles’ heel to be therapeutically exploited in precision oncology.
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25
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CRL4A DTL degrades DNA-PKcs to modulate NHEJ repair and induce genomic instability and subsequent malignant transformation. Oncogene 2021; 40:2096-2111. [PMID: 33627782 PMCID: PMC7979543 DOI: 10.1038/s41388-021-01690-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 01/24/2021] [Accepted: 01/29/2021] [Indexed: 01/30/2023]
Abstract
Genomic instability induced by DNA damage and improper DNA damage repair is one of the main causes of malignant transformation and tumorigenesis. DNA double strand breaks (DSBs) are the most detrimental form of DNA damage, and nonhomologous end-joining (NHEJ) mechanisms play dominant and priority roles in initiating DSB repair. A well-studied oncogene, the ubiquitin ligase Cullin 4A (CUL4A), is reported to be recruited to DSB sites in genomic DNA, but whether it regulates NHEJ mechanisms of DSB repair is unclear. Here, we discovered that the CUL4A-DTL ligase complex targeted the DNA-PKcs protein in the NHEJ repair pathway for nuclear degradation. Overexpression of either CUL4A or DTL reduced NHEJ repair efficiency and subsequently increased the accumulation of DSBs. Moreover, we demonstrated that overexpression of either CUL4A or DTL in normal cells led to genomic instability and malignant proliferation. Consistent with the in vitro findings, in human precancerous lesions, CUL4A expression gradually increased with increasing malignant tendency and was negatively correlated with DNA-PKcs and positively correlated with γ-H2AX expression. Collectively, this study provided strong evidence that the CUL4A-DTL axis increases genomic instability and enhances the subsequent malignant transformation of normal cells by inhibiting NHEJ repair. These results also suggested that CUL4A may be a prognostic marker of precancerous lesions and a potential therapeutic target in cancer.
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26
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Eckelmann BJ, Bacolla A, Wang H, Ye Z, Guerrero EN, Jiang W, El-Zein R, Hegde ML, Tomkinson AE, Tainer JA, Mitra S. XRCC1 promotes replication restart, nascent fork degradation and mutagenic DNA repair in BRCA2-deficient cells. NAR Cancer 2020; 2:zcaa013. [PMID: 32776008 PMCID: PMC7397735 DOI: 10.1093/narcan/zcaa013] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/30/2020] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
Homologous recombination/end joining (HR/HEJ)-deficient cancers with BRCA mutations utilize alternative DNA double-strand break repair pathways, particularly alternative non-homologous end joining or microhomology-mediated end joining (alt-EJ/MMEJ) during S and G2 cell cycle phases. Depletion of alt-EJ factors, including XRCC1, PARP1 and POLQ, is synthetically lethal with BRCA2 deficiency; yet, XRCC1 roles in HR-deficient cancers and replication stress are enigmatic. Here, we show that after replication stress, XRCC1 forms an active repair complex with POLQ and MRE11 that supports alt-EJ activity in vitro. BRCA2 limits XRCC1 recruitment and repair complex formation to suppress alt-EJ at stalled forks. Without BRCA2 fork protection, XRCC1 enables cells to complete DNA replication at the expense of increased genome instability by promoting MRE11-dependent fork resection and restart. High XRCC1 and MRE11 gene expression negatively impacts Kaplan–Meier survival curves and hazard ratios for HR-deficient breast cancer patients in The Cancer Genome Atlas. The additive effects of depleting both BRCA2 and XRCC1 indicate distinct pathways for replication restart. Our collective data show that XRCC1-mediated processing contributes to replication fork degradation, replication restart and chromosome aberrations in BRCA2-deficient cells, uncovering new roles of XRCC1 and microhomology-mediated repair mechanisms in HR-deficient cancers, with implications for chemotherapeutic strategies targeting POLQ and PARP activities.
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Affiliation(s)
- Bradley J Eckelmann
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Albino Bacolla
- Departments of Cancer Biology and Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Haibo Wang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Zu Ye
- Departments of Cancer Biology and Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erika N Guerrero
- Gorgas Memorial Institute for Health Studies, Panama City, Panama
| | - Wei Jiang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, 518036, China
| | - Randa El-Zein
- Department of Radiology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Alan E Tomkinson
- Departments of Internal Medicine and Molecular Genetics & Microbiology, and the University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - John A Tainer
- Departments of Cancer Biology and Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
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27
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Malihi PD, Graf RP, Rodriguez A, Ramesh N, Lee J, Sutton R, Jiles R, Ruiz Velasco C, Sei E, Kolatkar A, Logothetis C, Navin NE, Corn P, Aparicio AM, Dittamore R, Hicks J, Kuhn P, Zurita AJ. Single-Cell Circulating Tumor Cell Analysis Reveals Genomic Instability as a Distinctive Feature of Aggressive Prostate Cancer. Clin Cancer Res 2020; 26:4143-4153. [PMID: 32341031 DOI: 10.1158/1078-0432.ccr-19-4100] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/25/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE Aggressive variant prostate cancer (AVPC) represents a clinical subset distinguished by therapy resistance and poor prognosis, linked to combined losses of the tumor suppressor genes (TSG) PTEN, RB1, and TP53. Circulating tumor cells (CTC) provide a minimally invasive opportunity for identification and molecular characterization of AVPC. We aimed to evaluate the incidence and clinical significance of compound (2+)TSG losses and genomic instability in prostate cancer CTC, and to expand the set genomic biomarkers relevant to AVPC. EXPERIMENTAL DESIGN Genomic analysis of chromosomal copy-number alterations (CNA) at single-cell resolution was performed in CTC from patients with and without AVPC before initiating chemotherapy with cabazitaxel or cabazitaxel and carboplatin. We evaluated associations between single-CTC genomics and clinical features, progression-free survival, and overall survival. RESULTS A total of 257 individual CTC were sequenced from 47 patients (1-22 CTC/patient). Twenty patients (42.6%) had concurrent 2+TSG losses in at least one CTC in association with poor survival and increased genomic instability, inferred by high large-scale transitions scores. Higher LST in CTC were independent of CTC enumerated, clinically more indicative of aggressive behavior than co-occurring TSG losses, and molecularly associated with gains in chromosomal regions including PTK2, Myc, and NCOA2; increased androgen receptor expression; and BRCA2 loss. In 57 patients with matched cell-free tumor DNA data, CTC were more frequently detectable and evaluable for CNA analysis (in 73.7% vs. 42.1%, respectively). CONCLUSIONS Our findings suggest that genomic instability in CTC is a hallmark of advanced prostate cancer aggressiveness, and support single-CTC sequencing as a compelling tool to noninvasively characterize cancer heterogeneity.
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Affiliation(s)
- Paymaneh D Malihi
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | | | | | - Naveen Ramesh
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas.,University of Texas Health Graduate School of Biomedical Sciences, Houston, Texas
| | - Jerry Lee
- Epic Sciences, Inc, San Diego, California
| | | | | | - Carmen Ruiz Velasco
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Emi Sei
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anand Kolatkar
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas.,David H. Koch Center for Applied Research of Genitourinary Cancers, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nicholas E Navin
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas.,University of Texas Health Graduate School of Biomedical Sciences, Houston, Texas.,David H. Koch Center for Applied Research of Genitourinary Cancers, University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Corn
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ana M Aparicio
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - James Hicks
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California
| | - Peter Kuhn
- USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California.
| | - Amado J Zurita
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas.
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28
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Barghouth PG, Karabinis P, Venegas A, Oviedo NJ. Poly(ADP-Ribose) Polymerase-3 Regulates Regeneration in Planarians. Int J Mol Sci 2020; 21:E875. [PMID: 32013251 PMCID: PMC7038108 DOI: 10.3390/ijms21030875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/27/2020] [Indexed: 11/20/2022] Open
Abstract
Protein ADP-ribosylation is a reversible post-translational modification (PTM) process that plays fundamental roles in cell signaling. The covalent attachment of ADP ribose polymers is executed by PAR polymerases (PARP) and it is essential for chromatin organization, DNA repair, cell cycle, transcription, and replication, among other critical cellular events. The process of PARylation or polyADP-ribosylation is dynamic and takes place across many tissues undergoing renewal and repair, but the molecular mechanisms regulating this PTM remain mostly unknown. Here, we introduce the use of the planarian Schmidtea mediterranea as a tractable model to study PARylation in the complexity of the adult body that is under constant renewal and is capable of regenerating damaged tissues. We identified the evolutionary conservation of PARP signaling that is expressed in planarian stem cells and differentiated tissues. We also demonstrate that Smed-PARP-3 homolog is required for proper regeneration of tissues in the anterior region of the animal. Furthermore, our results demonstrate, Smed-PARP-3(RNAi) disrupts the timely location of injury-induced cell death near the anterior facing wounds and also affects the regeneration of the central nervous system. Our work reveals novel roles for PARylation in large-scale regeneration and provides a simplified platform to investigate PARP signaling in the complexity of the adult body.
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Affiliation(s)
- Paul G. Barghouth
- Department of Molecular and Cell Biology, University of California, Merced, CA 95340, USA; (P.G.B.); (P.K.); (A.V.)
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95340, USA
| | - Peter Karabinis
- Department of Molecular and Cell Biology, University of California, Merced, CA 95340, USA; (P.G.B.); (P.K.); (A.V.)
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95340, USA
| | - Andie Venegas
- Department of Molecular and Cell Biology, University of California, Merced, CA 95340, USA; (P.G.B.); (P.K.); (A.V.)
| | - Néstor J. Oviedo
- Department of Molecular and Cell Biology, University of California, Merced, CA 95340, USA; (P.G.B.); (P.K.); (A.V.)
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95340, USA
- Health Sciences Research Institute, University of California, Merced, CA 95340, USA
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Zhang S, Zhong X, Yuan H, Guo Y, Song D, Qi F, Zhu Z, Wang X, Guo Z. Interfering in apoptosis and DNA repair of cancer cells to conquer cisplatin resistance by platinum(iv) prodrugs. Chem Sci 2020. [DOI: 10.1039/d0sc00197j] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Platinum(iv) prodrugs targeting the DNA repair mechanism downregulate myeloid cell leukemia-1 (Mcl-1) and homologous recombination proteins (RAD51, BRCA2), thereby enhancing cytotoxicity against cisplatin-resistant cancer cells.
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Affiliation(s)
- Shuren Zhang
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Chemistry and Biomedicine Innovation Centre
- Nanjing University
- Nanjing 210023
| | - Xuanmeng Zhong
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Chemistry and Biomedicine Innovation Centre
- Nanjing University
- Nanjing 210023
| | - Hao Yuan
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Chemistry and Biomedicine Innovation Centre
- Nanjing University
- Nanjing 210023
| | - Yan Guo
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Chemistry and Biomedicine Innovation Centre
- Nanjing University
- Nanjing 210023
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Chemistry and Biomedicine Innovation Centre
- Nanjing University
- Nanjing 210023
| | - Fen Qi
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Chemistry and Biomedicine Innovation Centre
- Nanjing University
- Nanjing 210023
| | - Zhenzhu Zhu
- School of Food Science and Engineering
- Nanjing University of Finance & Economics
- Nanjing 210023
- P. R. China
| | - Xiaoyong Wang
- State Key Laboratory of Pharmaceutical Biotechnology
- School of Life Sciences
- Nanjing University
- Nanjing 210023
- P. R. China
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Chemistry and Biomedicine Innovation Centre
- Nanjing University
- Nanjing 210023
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30
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Advances in genome editing through control of DNA repair pathways. Nat Cell Biol 2019; 21:1468-1478. [PMID: 31792376 DOI: 10.1038/s41556-019-0425-z] [Citation(s) in RCA: 221] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 10/25/2019] [Indexed: 02/06/2023]
Abstract
Eukaryotic cells deploy overlapping repair pathways to resolve DNA damage. Advancements in genome editing take advantage of these pathways to produce permanent genetic changes. Despite recent improvements, genome editing can produce diverse outcomes that can introduce risks in clinical applications. Although homology-directed repair is attractive for its ability to encode precise edits, it is particularly difficult in human cells. Here we discuss the DNA repair pathways that underlie genome editing and strategies to favour various outcomes.
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31
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Kumar R, Duhamel M, Coutant E, Ben-Nahia E, Mercier R. Antagonism between BRCA2 and FIGL1 regulates homologous recombination. Nucleic Acids Res 2019; 47:5170-5180. [PMID: 30941419 PMCID: PMC6547764 DOI: 10.1093/nar/gkz225] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 03/18/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023] Open
Abstract
Homologous recombination (HR) maintains genome stability by promoting accurate DNA repair. Two recombinases, RAD51 and DMC1, are central to HR repair and form dynamic nucleoprotein filaments in vivo under tight regulation. However, the interplay between positive and negative regulators to control the dynamic assembly/disassembly of RAD51/DMC1 filaments in multicellular eukaryotes remains poorly characterized. Here, we report an antagonism between BRCA2, a well-studied positive mediator of RAD51/DMC1, and FIDGETIN-LIKE-1 (FIGL1), which we previously proposed as a negative regulator of RAD51/DMC1. Through forward genetic screen, we identified a mutation in one of the two Arabidopsis BRCA2 paralogs that suppresses the meiotic phenotypes of figl1. Consistent with the antagonistic roles of BRCA2 and FIGL1, the figl1 mutation in the brca2 background restores RAD51/DMC1 focus formation and homologous chromosome interaction at meiosis, and RAD51 focus formation in somatic cells. This study shows that BRCA2 and FIGL1 have antagonistic effects on the dynamics of RAD51/DMC1-dependent DNA transactions to promote accurate HR repair.
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Affiliation(s)
- Rajeev Kumar
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Marine Duhamel
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Eve Coutant
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Emna Ben-Nahia
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
| | - Raphael Mercier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
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Abstract
Canonical DNA non-homologous end-joining (c-NHEJ) and homologous recombination (HR), the two major DNA double-strand break (DSB) repair pathways, have long been depicted as competitors, fighting a race to rejoin DSBs. In human cells, Ku, an upstream component of NHEJ, is highly abundant and has exquisite end-binding capacity. Emerging evidence has suggested that Ku is the first protein binding most, if not all, DSBs, and creates a block to resection. Although most c-NHEJ proceeds without resection, recent studies have provided strong evidence for a process of resection-dependent c-NHEJ, that repairs a subset of DSBs. HR also repairs a subset of two-ended DSBs in G2 phase and processes one-ended DSBs that arise following replication fork stalling or collapse to promote replication restart. HR also necessitates end-resection. This raises the question of how end-resection takes place despite Ku's avid end-binding capacity. Insight into this enigma has been gained from the analysis of DSBs generated by Spo11 or TOP2, which create protein-bridged DSBs. The progression of repair by HR or NHEJ requires removal of the end-blocking lesions. The MRE11-RAD50-NBS1 (MRN) complex, CtIP and EXO1 play critical roles in this process. Here, we review our current understanding of how resection arises at lesions blocked by covalently bound Spo11 or TOP2 or following Ku binding, which effectively creates a distinct resection-blocking lesion due to its avid end-binding activity and abundance. Our review reveals that Ku plays an active role in determining pathway choice and exposes similarities yet distinctions in the progression of resection that is suited to the optimal repair pathway choice.
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Affiliation(s)
- Atsushi Shibata
- Education and Research Support Center, Graduate School of Medicine, Gunma University, Maebashi, Japan
| | - Penny Jeggo
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN19 RQ, UK
| | - Markus Löbrich
- Radiation Biology and DNA Repair, Darmstadt University of Technology, 64287 Darmstadt, Germany.
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The concerted roles of FANCM and Rad52 in the protection of common fragile sites. Nat Commun 2018; 9:2791. [PMID: 30022024 PMCID: PMC6052092 DOI: 10.1038/s41467-018-05066-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/10/2018] [Indexed: 12/18/2022] Open
Abstract
Common fragile sites (CFSs) are prone to chromosomal breakage and are hotspots for chromosomal rearrangements in cancer cells. We uncovered a novel function of Fanconi anemia (FA) protein FANCM in the protection of CFSs that is independent of the FA core complex and the FANCI–FANCD2 complex. FANCM, along with its binding partners FAAP24 and MHF1/2, is recruited to CFS-derived structure-prone AT-rich sequences, where it suppresses DNA double-strand break (DSB) formation and mitotic recombination in a manner dependent on FANCM translocase activity. Interestingly, we also identified an indispensable function of Rad52 in the repair of DSBs at CFS-derived AT-rich sequences, despite its nonessential function in general homologous recombination (HR) in mammalian cells. Suppression of Rad52 expression in combination with FANCM knockout drastically reduces cell and tumor growth, suggesting a synthetic lethality interaction between these two genes, which offers a potential targeted treatment strategy for FANCM-deficient tumors with Rad52 inhibition. Fanconi anemia core proteins have been linked to common fragile site stability. Here the authors shed light into the role of FANCM in common fragile site protection by suppressing double-strand break formation and mitotic recombination.
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