1
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Olvera-León R, Zhang F, Offord V, Zhao Y, Tan HK, Gupta P, Pal T, Robles-Espinoza CD, Arriaga-González FG, Matsuyama LSAS, Delage E, Dicks E, Ezquina S, Rowlands CF, Turnbull C, Pharoah P, Perry JRB, Jasin M, Waters AJ, Adams DJ. High-resolution functional mapping of RAD51C by saturation genome editing. Cell 2024; 187:5719-5734.e19. [PMID: 39299233 DOI: 10.1016/j.cell.2024.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/29/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
Abstract
Pathogenic variants in RAD51C confer an elevated risk of breast and ovarian cancer, while individuals homozygous for specific RAD51C alleles may develop Fanconi anemia. Using saturation genome editing (SGE), we functionally assess 9,188 unique variants, including >99.5% of all possible coding sequence single-nucleotide alterations. By computing changes in variant abundance and Gaussian mixture modeling (GMM), we functionally classify 3,094 variants to be disruptive and use clinical truth sets to reveal an accuracy/concordance of variant classification >99.9%. Cell fitness was the primary assay readout allowing us to observe a phenomenon where specific missense variants exhibit distinct depletion kinetics potentially suggesting that they represent hypomorphic alleles. We further explored our exhaustive functional map, revealing critical residues on the RAD51C structure and resolving variants found in cancer-segregating kindred. Furthermore, through interrogation of UK Biobank and a large multi-center ovarian cancer cohort, we find significant associations between SGE-depleted variants and cancer diagnoses.
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Affiliation(s)
- Rebeca Olvera-León
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro, Querétaro, Mexico
| | - Fang Zhang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA; Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Victoria Offord
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Yajie Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, UK
| | - Hong Kee Tan
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Prashant Gupta
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Tuya Pal
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center (VUMC)/Vanderbilt-Ingram Cancer Center (VICC), Nashville, TN, USA
| | - Carla Daniela Robles-Espinoza
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro, Querétaro, Mexico
| | - Fernanda G Arriaga-González
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro, Querétaro, Mexico
| | | | - Erwan Delage
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ed Dicks
- Department of Public Health and Primary Care, University of Cambridge, Robinson Way, Cambridge, UK
| | - Suzana Ezquina
- Department of Public Health and Primary Care, University of Cambridge, Robinson Way, Cambridge, UK
| | - Charlie F Rowlands
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; National Cancer Registration and Analysis Service, National Health Service (NHS) England, London, UK; Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Paul Pharoah
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, UK
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew J Waters
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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2
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Tomaszowski KH, Chen Y, Roy S, Harris M, Zhang J, Tsai CL, Schlacher K. Diet induced mitochondrial DNA replication instability in Rad51c mutant mice drives sex-bias in anemia of inflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.21.613572. [PMID: 39345482 PMCID: PMC11430050 DOI: 10.1101/2024.09.21.613572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Anemia of inflammation (AI) is a common comorbidity associated with obesity, diabetes, cardiac disease, aging, and during anti-cancer therapies. Mounting evidence illustrates that males are disproportionally affected by AI, but not why. Here we demonstrate a molecular cause for a sex-bias in inflammation. The data shows that mitochondrial DNA (mtDNA) instability induced by dietary stress causes anemia associated with inflamed macrophages and improper iron recycling in mice. These phenotypes are enhanced in mice with mutations in Fanco/Rad51c , which predisposes to the progeroid disease Fanconi Anemia. The data reveals a striking sex-bias whereby females are protected. We find that estrogen acts as a mitochondrial antioxidant that reduces diet-induced oxidative stress, mtDNA replication instability and the distinctively mtDNA-dependent unphosphorylated STAT1 response. Consequently, treatment of male Rad51c mutant mice with estrogen or mitochondrial antioxidants suppresses the inflammation-induced anemia. Collectively, this study uncovers estrogen-responsive mtDNA replication instability as a cause for sex-specific inflammatory responses and molecular driver for AI.
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3
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Akita M, Girvan P, Spirek M, Novacek J, Rueda D, Prokop Z, Krejci L. Mechanism of BCDX2-mediated RAD51 nucleation on short ssDNA stretches and fork DNA. Nucleic Acids Res 2024:gkae770. [PMID: 39268578 DOI: 10.1093/nar/gkae770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 08/20/2024] [Accepted: 08/26/2024] [Indexed: 09/17/2024] Open
Abstract
Homologous recombination (HR) factors are crucial for DSB repair and processing stalled replication forks. RAD51 paralogs, including RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3, have emerged as essential tumour suppressors, forming two subcomplexes, BCDX2 and CX3. Mutations in these genes are associated with cancer susceptibility and Fanconi anaemia, yet their biochemical activities remain unclear. This study reveals a linear arrangement of BCDX2 subunits compared to the RAD51 ring. BCDX2 shows a strong affinity towards single-stranded DNA (ssDNA) via unique binding mechanism compared to RAD51, and a contribution of DX2 subunits in binding branched DNA substrates. We demonstrate that BCDX2 facilitates RAD51 loading on ssDNA by suppressing the cooperative requirement of RAD51 binding to DNA and stabilizing the filament. Notably, BCDX2 also promotes RAD51 loading on short ssDNA and reversed replication fork substrates. Moreover, while mutants defective in ssDNA binding retain the ability to bind branched DNA substrates, they still facilitate RAD51 loading onto reversed replication forks. Our study provides mechanistic insights into how the BCDX2 complex stimulates the formation of BRCA2-independent RAD51 filaments on short stretches of ssDNA present at ssDNA gaps or stalled replication forks, highlighting its role in genome maintenance and DNA repair.
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Affiliation(s)
- Masaki Akita
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Paul Girvan
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Mario Spirek
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Jiri Novacek
- Cryo-Electron Microscopy and Tomography Core Facility, Central European Institute of Technology, Brno, Czech Republic
| | - David Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Single Molecule Imaging Group, MRC-London Institute of Medical Sciences, London, UK
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St Anne's University Hospital, Brno, Czech Republic
| | - Lumir Krejci
- Department of Biology and National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
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4
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Chauhan AS, Jhujh SS, Stewart GS. E3 ligases: a ubiquitous link between DNA repair, DNA replication and human disease. Biochem J 2024; 481:923-944. [PMID: 38985307 PMCID: PMC11346458 DOI: 10.1042/bcj20240124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 07/11/2024]
Abstract
Maintenance of genome stability is of paramount importance for the survival of an organism. However, genomic integrity is constantly being challenged by various endogenous and exogenous processes that damage DNA. Therefore, cells are heavily reliant on DNA repair pathways that have evolved to deal with every type of genotoxic insult that threatens to compromise genome stability. Notably, inherited mutations in genes encoding proteins involved in these protective pathways trigger the onset of disease that is driven by chromosome instability e.g. neurodevelopmental abnormalities, neurodegeneration, premature ageing, immunodeficiency and cancer development. The ability of cells to regulate the recruitment of specific DNA repair proteins to sites of DNA damage is extremely complex but is primarily mediated by protein post-translational modifications (PTMs). Ubiquitylation is one such PTM, which controls genome stability by regulating protein localisation, protein turnover, protein-protein interactions and intra-cellular signalling. Over the past two decades, numerous ubiquitin (Ub) E3 ligases have been identified to play a crucial role not only in the initiation of DNA replication and DNA damage repair but also in the efficient termination of these processes. In this review, we discuss our current understanding of how different Ub E3 ligases (RNF168, TRAIP, HUWE1, TRIP12, FANCL, BRCA1, RFWD3) function to regulate DNA repair and replication and the pathological consequences arising from inheriting deleterious mutations that compromise the Ub-dependent DNA damage response.
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Affiliation(s)
- Anoop S. Chauhan
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Satpal S. Jhujh
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Grant S. Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
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5
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Skubitz KM, Murugan P. RAD51C and MYST3 Mutations in a Case of Desmoid-Type Fibromatosis With No Mutation in CTNNB1 or APC. Cureus 2024; 16:e55496. [PMID: 38571839 PMCID: PMC10990071 DOI: 10.7759/cureus.55496] [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] [Accepted: 03/04/2024] [Indexed: 04/05/2024] Open
Abstract
Most cases of desmoid-type fibromatosis (DTF) exhibit a mutation in APC or CTNNB1. We report a case of mesenteric DTF in which no mutation in APC or CTNNB1 was found, but a germline variant of uncertain significance (VUS) in RAD51C and a subclonal mutation in MYST3 were identified. Whether these genetic changes are important in DTF in this case, or whether genetically conventional DTF cells were present at a density below detection is unknown; it will be of interest to see results in further studies of wild-type APC/CTNNB1 cases.
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Affiliation(s)
| | - Paari Murugan
- Laboratory Medicine and Pathology, University of Minnesota, MInneapolis, USA
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6
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Lin K, Chang YC, Billmann M, Ward HN, Le K, Hassan AZ, Bhojoo U, Chan K, Costanzo M, Moffat J, Boone C, Bielinsky AK, Myers CL. A scalable platform for efficient CRISPR-Cas9 chemical-genetic screens of DNA damage-inducing compounds. Sci Rep 2024; 14:2508. [PMID: 38291084 PMCID: PMC10828508 DOI: 10.1038/s41598-024-51735-y] [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: 09/20/2023] [Accepted: 01/09/2024] [Indexed: 02/01/2024] Open
Abstract
Current approaches to define chemical-genetic interactions (CGIs) in human cell lines are resource-intensive. We designed a scalable chemical-genetic screening platform by generating a DNA damage response (DDR)-focused custom sgRNA library targeting 1011 genes with 3033 sgRNAs. We performed five proof-of-principle compound screens and found that the compounds' known modes-of-action (MoA) were enriched among the compounds' CGIs. These scalable screens recapitulated expected CGIs at a comparable signal-to-noise ratio (SNR) relative to genome-wide screens. Furthermore, time-resolved CGIs, captured by sequencing screens at various time points, suggested an unexpected, late interstrand-crosslinking (ICL) repair pathway response to camptothecin-induced DNA damage. Our approach can facilitate screening compounds at scale with 20-fold fewer resources than commonly used genome-wide libraries and produce biologically informative CGI profiles.
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Affiliation(s)
- Kevin Lin
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Ya-Chu Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Maximilian Billmann
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Khoi Le
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Arshia Z Hassan
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Urvi Bhojoo
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Katherine Chan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael Costanzo
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Institute for Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
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7
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Hughes T, Rose AM. The emergence of Fanconi anaemia type S: a phenotypic spectrum of biallelic BRCA1 mutations. Front Oncol 2023; 13:1278004. [PMID: 38146508 PMCID: PMC10749362 DOI: 10.3389/fonc.2023.1278004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/23/2023] [Indexed: 12/27/2023] Open
Abstract
BRCA1 is involved in the Fanconi anaemia (FA) pathway, which coordinates repair of DNA interstrand cross-links. FA is a rare genetic disorder characterised by bone marrow failure, cancer predisposition and congenital abnormalities, caused by biallelic mutations affecting proteins in the FA pathway. Germline monoallelic pathogenic BRCA1 mutations are known to be associated with hereditary breast/ovarian cancer, however biallelic mutations of BRCA1 were long predicted to be incompatible with embryonic viability, hence BRCA1 was not considered to be a canonical FA gene. Despite this, several patients with biallelic pathogenic BRCA1 mutations and FA-like phenotypes have been identified - defining a new FA type (FA-S) and designating BRCA1 as an FA gene. This report presents a scoping review of the cases of biallelic BRCA1 mutations identified to date, discusses the functional effects of the mutations identified, and proposes a phenotypic spectrum of BRCA1 mutations based upon available clinical and genetic data. We report that this FA-S cohort phenotype includes short stature, microcephaly, facial dysmorphisms, hypo/hyperpigmented lesions, intellectual disability, chromosomal sensitivity to crosslinking agents and predisposition to breast/ovarian cancer and/or childhood cancers, with some patients exhibiting sensitivity to chemotherapy. Unlike most other types of FA, FA-S patients lack bone marrow failure.
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Affiliation(s)
- Tirion Hughes
- University of Oxford Medical School, Oxford, United Kingdom
| | - Anna M. Rose
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
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8
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Guh CL, Lei KH, Chen YA, Jiang YZ, Chang HY, Liaw H, Li HW, Yen HY, Chi P. RAD51 paralogs synergize with RAD51 to protect reversed forks from cellular nucleases. Nucleic Acids Res 2023; 51:11717-11731. [PMID: 37843130 PMCID: PMC10681713 DOI: 10.1093/nar/gkad856] [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: 04/14/2023] [Revised: 09/12/2023] [Accepted: 09/23/2023] [Indexed: 10/17/2023] Open
Abstract
Fork reversal is a conserved mechanism to prevent stalled replication forks from collapsing. Formation and protection of reversed forks are two crucial steps in ensuring fork integrity and stability. Five RAD51 paralogs, namely, RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3, which share sequence and structural similarity to the recombinase RAD51, play poorly defined mechanistic roles in these processes. Here, using purified BCDX2 (RAD51BCD-XRCC2) and CX3 (RAD51C-XRCC3) complexes and in vitro reconstituted biochemical systems, we mechanistically dissect their functions in forming and protecting reversed forks. We show that both RAD51 paralog complexes lack fork reversal activities. Whereas CX3 exhibits modest fork protection activity, BCDX2 significantly synergizes with RAD51 to protect DNA against attack by the nucleases MRE11 and EXO1. DNA protection is contingent upon the ability of RAD51 to form a functional nucleoprotein filament on DNA. Collectively, our results provide evidence for a hitherto unknown function of RAD51 paralogs in synergizing with RAD51 nucleoprotein filament to prevent degradation of stressed replication forks.
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Affiliation(s)
- Chia-Lun Guh
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Kai-Hang Lei
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Yi-An Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yi-Zhen Jiang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Hao-Yen Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yung Yen
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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9
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Szakal B, Branzei D. Hot on RAD51C: structure and functions of RAD51C-XRCC3. Mol Oncol 2023; 17:1950-1952. [PMID: 37681281 PMCID: PMC10552886 DOI: 10.1002/1878-0261.13518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/09/2023] Open
Abstract
A new study by Longo, Roy et al. has solved the structure of the RAD51C-XRCC3 (CX3) heterodimer with a bound ATP analog, identifying two main structural interfaces and defining separable replication fork stability roles. One function relates to the ability of RAD51C to bind and assemble CX3 on nascent DNA, with an impact on the ability of forks to restart upon replication stress. The other relates to effective CX3 heterodimer formation, required for 5' RAD51 filament capping, with effects on RAD51 filament disassembly, fork protection and influencing the persistence of reversed forks.
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Affiliation(s)
- Barnabas Szakal
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Dana Branzei
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM‐CNR)PaviaItaly
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10
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Longo MA, Roy S, Chen Y, Tomaszowski KH, Arvai AS, Pepper JT, Boisvert RA, Kunnimalaiyaan S, Keshvani C, Schild D, Bacolla A, Williams GJ, Tainer JA, Schlacher K. RAD51C-XRCC3 structure and cancer patient mutations define DNA replication roles. Nat Commun 2023; 14:4445. [PMID: 37488098 PMCID: PMC10366140 DOI: 10.1038/s41467-023-40096-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023] Open
Abstract
RAD51C is an enigmatic predisposition gene for breast, ovarian, and prostate cancer. Currently, missing structural and related functional understanding limits patient mutation interpretation to homology-directed repair (HDR) function analysis. Here we report the RAD51C-XRCC3 (CX3) X-ray co-crystal structure with bound ATP analog and define separable RAD51C replication stability roles informed by its three-dimensional structure, assembly, and unappreciated polymerization motif. Mapping of cancer patient mutations as a functional guide confirms ATP-binding matching RAD51 recombinase, yet highlights distinct CX3 interfaces. Analyses of CRISPR/Cas9-edited human cells with RAD51C mutations combined with single-molecule, single-cell and biophysics measurements uncover discrete CX3 regions for DNA replication fork protection, restart and reversal, accomplished by separable functions in DNA binding and implied 5' RAD51 filament capping. Collective findings establish CX3 as a cancer-relevant replication stress response complex, show how HDR-proficient variants could contribute to tumor development, and identify regions to aid functional testing and classification of cancer mutations.
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Affiliation(s)
- Michael A Longo
- Department of Molecular & Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Sunetra Roy
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yue Chen
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | - Andrew S Arvai
- The Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jordan T Pepper
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rebecca A Boisvert
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | - Caezanne Keshvani
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - David Schild
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Albino Bacolla
- Department of Molecular & Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Gareth J Williams
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - John A Tainer
- Department of Molecular & Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX, USA.
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA.
| | - Katharina Schlacher
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA.
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11
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Rawal Y, Jia L, Meir A, Zhou S, Kaur H, Ruben EA, Kwon Y, Bernstein KA, Jasin M, Taylor AB, Burma S, Hromas R, Mazin AV, Zhao W, Zhou D, Wasmuth EV, Greene EC, Sung P, Olsen SK. Structural insights into BCDX2 complex function in homologous recombination. Nature 2023; 619:640-649. [PMID: 37344589 PMCID: PMC10712684 DOI: 10.1038/s41586-023-06219-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023]
Abstract
Homologous recombination (HR) fulfils a pivotal role in the repair of DNA double-strand breaks and collapsed replication forks1. HR depends on the products of several paralogues of RAD51, including the tetrameric complex of RAD51B, RAD51C, RAD51D and XRCC2 (BCDX2)2. BCDX2 functions as a mediator of nucleoprotein filament assembly by RAD51 and single-stranded DNA (ssDNA) during HR, but its mechanism remains undefined. Here we report cryogenic electron microscopy reconstructions of human BCDX2 in apo and ssDNA-bound states. The structures reveal how the amino-terminal domains of RAD51B, RAD51C and RAD51D participate in inter-subunit interactions that underpin complex formation and ssDNA-binding specificity. Single-molecule DNA curtain analysis yields insights into how BCDX2 enhances RAD51-ssDNA nucleoprotein filament assembly. Moreover, our cryogenic electron microscopy and functional analyses explain how RAD51C alterations found in patients with cancer3-6 inactivate DNA binding and the HR mediator activity of BCDX2. Our findings shed light on the role of BCDX2 in HR and provide a foundation for understanding how pathogenic alterations in BCDX2 impact genome repair.
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Affiliation(s)
- Yashpal Rawal
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Lijia Jia
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Aviv Meir
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Shuo Zhou
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Hardeep Kaur
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Eliza A Ruben
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Youngho Kwon
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Kara A Bernstein
- Department of Biochemistry & Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander B Taylor
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Sandeep Burma
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Robert Hromas
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Alexander V Mazin
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Weixing Zhao
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Daohong Zhou
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Elizabeth V Wasmuth
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
| | - Patrick Sung
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Shaun K Olsen
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA.
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12
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Greenhough LA, Liang CC, Belan O, Kunzelmann S, Maslen S, Rodrigo-Brenni MC, Anand R, Skehel M, Boulton SJ, West SC. Structure and function of the RAD51B-RAD51C-RAD51D-XRCC2 tumour suppressor. Nature 2023; 619:650-657. [PMID: 37344587 PMCID: PMC7614784 DOI: 10.1038/s41586-023-06179-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/08/2023] [Indexed: 06/23/2023]
Abstract
Homologous recombination is a fundamental process of life. It is required for the protection and restart of broken replication forks, the repair of chromosome breaks and the exchange of genetic material during meiosis. Individuals with mutations in key recombination genes, such as BRCA2 (also known as FANCD1), or the RAD51 paralogues RAD51B, RAD51C (also known as FANCO), RAD51D, XRCC2 (also known as FANCU) and XRCC3, are predisposed to breast, ovarian and prostate cancers1-10 and the cancer-prone syndrome Fanconi anaemia11-13. The BRCA2 tumour suppressor protein-the product of BRCA2-is well characterized, but the cellular functions of the RAD51 paralogues remain unclear. Genetic knockouts display growth defects, reduced RAD51 focus formation, spontaneous chromosome abnormalities, sensitivity to PARP inhibitors and replication fork defects14,15, but the precise molecular roles of RAD51 paralogues in fork stability, DNA repair and cancer avoidance remain unknown. Here we used cryo-electron microscopy, AlphaFold2 modelling and structural proteomics to determine the structure of the RAD51B-RAD51C-RAD51D-XRCC2 complex (BCDX2), revealing that RAD51C-RAD51D-XRCC2 mimics three RAD51 protomers aligned within a nucleoprotein filament, whereas RAD51B is highly dynamic. Biochemical and single-molecule analyses showed that BCDX2 stimulates the nucleation and extension of RAD51 filaments-which are essential for recombinational DNA repair-in reactions that depend on the coupled ATPase activities of RAD51B and RAD51C. Our studies demonstrate that BCDX2 orchestrates RAD51 assembly on single stranded DNA for replication fork protection and double strand break repair, in reactions that are critical for tumour avoidance.
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Affiliation(s)
| | | | - Ondrej Belan
- The Francis Crick Institute, London, UK
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
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13
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Zemet R, Du H, Gambin T, Lupski JR, Liu P, Stankiewicz P. SNV/indel hypermutator phenotype in biallelic RAD51C variant: Fanconi anemia. Hum Genet 2023; 142:721-733. [PMID: 37031326 PMCID: PMC10996436 DOI: 10.1007/s00439-023-02550-4] [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: 02/25/2023] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving RAD51C. Interestingly, the trio exome sequencing analysis also detected eight apparent de novo mosaic variants with variant allele fraction (VAF) ranging between 11.5 and 37%. Here, using whole genome sequencing and a 'home-brew' variant filtering pipeline and DeepMosaic module, we investigated the number and signature of de novo heterozygous and mosaic variants and the hypothesis of a rare phenomenon of hypermutation. Eight-hundred-thirty apparent de novo SNVs and 21 de novo indels had VAFs below 37.41% and were considered postzygotic somatic mosaic variants. The VAFs showed a bimodal distribution, with one component having an average VAF of 25% (range: 18.7-37.41%) (n = 446), representing potential postzygotic first mitotic events, and the other component with an average VAF of 12.5% (range 9.55-18.69%) (n = 384), describing potential second mitotic events. No increased rate of CNV formation was observed. The mutational pattern analysis for somatic single base substitution showed SBS40, SBS5, and SBS3 as the top recognized signatures. SBS3 is a known signature associated with homologous recombination-based DNA damage repair error. Our data demonstrate that biallelic RAD51C variants show evidence for defective genomic DNA damage repair and thereby result in a hypermutator phenotype with the accumulation of postzygotic de novo mutations, at least in the prenatal period. This 'genome hypermutator phenomenon' might contribute to the observed hematological manifestations and the predisposition to tumors in patients with FA. We propose that other FA groups should be investigated for genome-wide de novo variants.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Baylor Genetics, Houston, TX, USA.
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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14
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Tomaszowski KH, Roy S, Guerrero C, Shukla P, Keshvani C, Chen Y, Ott M, Wu X, Zhang J, DiNardo CD, Schindler D, Schlacher K. Hypomorphic Brca2 and Rad51c double mutant mice display Fanconi anemia, cancer and polygenic replication stress. Nat Commun 2023; 14:1333. [PMID: 36906610 PMCID: PMC10008622 DOI: 10.1038/s41467-023-36933-y] [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: 02/26/2021] [Accepted: 02/10/2023] [Indexed: 03/13/2023] Open
Abstract
The prototypic cancer-predisposition disease Fanconi Anemia (FA) is identified by biallelic mutations in any one of twenty-three FANC genes. Puzzlingly, inactivation of one Fanc gene alone in mice fails to faithfully model the pleiotropic human disease without additional external stress. Here we find that FA patients frequently display FANC co-mutations. Combining exemplary homozygous hypomorphic Brca2/Fancd1 and Rad51c/Fanco mutations in mice phenocopies human FA with bone marrow failure, rapid death by cancer, cellular cancer-drug hypersensitivity and severe replication instability. These grave phenotypes contrast the unremarkable phenotypes seen in mice with single gene-function inactivation, revealing an unexpected synergism between Fanc mutations. Beyond FA, breast cancer-genome analysis confirms that polygenic FANC tumor-mutations correlate with lower survival, expanding our understanding of FANC genes beyond an epistatic FA-pathway. Collectively, the data establish a polygenic replication stress concept as a testable principle, whereby co-occurrence of a distinct second gene mutation amplifies and drives endogenous replication stress, genome instability and disease.
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Affiliation(s)
- Karl-Heinz Tomaszowski
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Sunetra Roy
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Carolina Guerrero
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Poojan Shukla
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Caezaan Keshvani
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Yue Chen
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Martina Ott
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Xiaogang Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Courtney D DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Detlev Schindler
- Institut fuer Humangenetik, University of Wuerzburg, Wuerzburg, Germany
| | - Katharina Schlacher
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA.
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15
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Pillonetto DV, Piovezan BZ, Nichele S, Lima ACM, Pasquini R, Pereira NF, Bonfim C. Investigation of mutations in Fanconi anemia genes and malignancy predisposition in Brazilian patients. Int J Lab Hematol 2023; 45:82-89. [PMID: 36333938 DOI: 10.1111/ijlh.13986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022]
Abstract
INTRODUCTION This study proposed to identify Fanconi anemia (FA) mutations in Brazilian patients and to investigate their impact on clinical manifestations and malignancies onset. METHODS A total of 116 patients were screened for nine mutations in FANCA, FANCC, FANCG. Those with no mutations were investigated by multiplex ligation-dependent probe amplification (MLPA) and Sanger sequencing for FANCA, FANCC, FANCE, FANCF, FANCG, FANCD1/BRCA2. RESULTS Genetic subtype was identified in 107/116 (78 FA-A, 8 FA-C, 13 FA-G, 8 FA-E), with only one mutation in 1/116, and no mutations in 9/116 patients. Before hematopoietic cell transplantation (HCT), malignancies were detected in 16/116 patients (14/78 FA-A, 01/08 FA-C, 01/08 FA-E), and 12 of them were hematological. Observed to expected ratio (O/E) of hematologic malignancy was 303.7 (95% CI = 148.6-458.7). CONCLUSION This study allowed the identification of biallelic mutations in 91.4% of patients. FANCG and FANCC mutations had significantly earlier bone marrow failure onset, and FANCG severe cytopenia at diagnosis. Despite the inherent limitations of the small number of malignancy events in each genetic subtype, the hematologic malignancies O/E ratio was very high. Cumulative incidence of malignancy before HCT was higher in the third and fourth decades of life, considering HCT and death as competing risks. The cumulative incidence of HCT increased during the first decade, competing with malignancy development.
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Affiliation(s)
| | - Bruno Zagonel Piovezan
- Immunogenetic's Laboratory - Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Samantha Nichele
- Bone Marrow Transplantation Service, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Ricardo Pasquini
- Bone Marrow Transplantation Service, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Noemi Farah Pereira
- Immunogenetic's Laboratory - Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil
| | - Carmem Bonfim
- Bone Marrow Transplantation Service, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Brazil.,Faculdades Pequeno Principe, Instituto de Pesquisa Pele Pequeno Principe, Curitiba, Brazil
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16
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Rashid MU, Muhammad N, Shehzad U, Khan FA, Loya A, Hamann U. Prevalence of FANCM germline variants in BRCA1/2 negative breast and/or ovarian cancer patients from Pakistan. Fam Cancer 2023; 22:31-41. [PMID: 35802266 DOI: 10.1007/s10689-022-00304-1] [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: 01/28/2022] [Accepted: 06/18/2022] [Indexed: 01/12/2023]
Abstract
The Fanconi anemia complementation group M (FANCM) gene is a potential candidate for breast/ovarian cancer susceptibility in European populations. Here, we examined the contribution of FANCM germline variants to hereditary breast and/or ovarian cancer in Pakistan. Comprehensive FANCM variant screening was performed in 201 BRCA1 and BRCA2 (BRCA1/2) negative Pakistani patients with and without triple-negative breast cancer (TNBC) and/or ovarian cancer, using denaturing high-performance liquid chromatography analysis (DHPLC) followed by DNA sequencing. Novel variants were tested for their potential effect on protein function using in silico tools. Reverse transcription (RT)-PCR analysis of RNA extracted from one deletion/insertion (delins) variant (p.K1780delinsNGIT) carrier and three non-carriers was performed to evaluate the impact of this variant on splicing. Furthermore, potentially functional variants were evaluated in 200 healthy female controls. A missense variant (p.V1857M) was identified in a 50-year-old TNBC patient with a family history of breast cancer. It was also identified in the index patient´s daughter, who was diagnosed with osteosarcoma at 15 years of age. Further, one delins variant (p.K1780delinsNGIT) was identified in a 45-year-old non-TNBC patient, but not detected in her brother, who was diagnosed with Hodgkin's lymphoma at 38 years of age. Based on in silico and RNA analyses, p.V1857M and p.K1780delinsNGIT were predicted as variants of uncertain significance (VUS), respectively. Both variants were absent in 200 healthy controls. Our findings suggest a marginal contribution of FANCM variants to hereditary breast/ovarian cancer in Pakistan, which need to be confirmed in larger studies.
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Affiliation(s)
- Muhammad Usman Rashid
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7A, Block R3, Johar Town, Lahore, 54000, Punjab, Pakistan.
| | - Noor Muhammad
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7A, Block R3, Johar Town, Lahore, 54000, Punjab, Pakistan
| | - Umara Shehzad
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7A, Block R3, Johar Town, Lahore, 54000, Punjab, Pakistan
| | - Faiz Ali Khan
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), 7A, Block R3, Johar Town, Lahore, 54000, Punjab, Pakistan
| | - Asif Loya
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
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17
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Bonfiglio F, Lasorsa VA, Cantalupo S, D'Alterio G, Aievola V, Boccia A, Ardito M, Furini S, Renieri A, Morini M, Stainczyk S, Westermann F, Paolella G, Eva A, Iolascon A, Capasso M. Inherited rare variants in homologous recombination and neurodevelopmental genes are associated with increased risk of neuroblastoma. EBioMedicine 2022; 87:104395. [PMID: 36493725 PMCID: PMC9732128 DOI: 10.1016/j.ebiom.2022.104395] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the most common solid extracranial paediatric tumour. Genome-wide association studies have driven the discovery of common risk variants, but no large study has investigated the contribution of rare variants to NB susceptibility. Here, we conducted a whole-exome sequencing (WES) of 664 NB cases and 822 controls and used independent validation datasets to identify genes with rare risk variants and involved pathways. METHODS WES was performed at 50× depth and variants were jointly called in cases and controls. We developed two models to identify mutations with high clinical impact (P/LP model) and to discover less penetrant risk mutations affecting non-canonical cancer pathways (RPV model). We performed a gene-level collapsing test using Firth's logistic regression in 242 selected cancer predisposition genes (CPGs) and a gene-sets burden analysis of biologically-informed pathways. FINDINGS Twelve percent of patients carried P/LP variants in CPGs and showed a significant enrichment (P = 2.3 × 10-4) compared to controls (6%). We identified P/LP variants in 45 CPGs enriched in homologous recombination (HR) pathway. The most P/LP enriched genes in NB were BRCA1, ALK and RAD51C. Additionally, we found higher RPV burden in gene-sets of neuron differentiation, neural tube development and synapse assembly, and in gene-sets associated with neurodevelopmental disorders (NDD). INTERPRETATION The high fraction of NB patients with P/LP variants indicates the need of genetic counselling. Furthermore, inherited rare variants predispose to NB development by affecting mechanisms related to HR and neurodevelopmental processes, and demonstrate that NDD genes are altered in NB at the germline level. FUNDING Associazione Italiana per la Ricerca sul Cancro, Fondazione Italiana per la Lotta al Neuroblastoma, Associazione Oncologia Pediatrica e Neuroblastoma, Regione Campania, Associazione Giulio Adelfio onlus, and Italian Health Ministry.
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Affiliation(s)
- Ferdinando Bonfiglio
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Chemical, Materials and Production Engineering, University of Naples Federico II, Naples, Italy
| | - Vito Alessandro Lasorsa
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Sueva Cantalupo
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Giuseppe D'Alterio
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,European School of Medical Medicine, University of Milan, Milan, Italy
| | - Vincenzo Aievola
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Angelo Boccia
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy
| | - Martina Ardito
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessandra Renieri
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Martina Morini
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Sabine Stainczyk
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Frank Westermann
- Hopp-Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany,Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Giovanni Paolella
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Alessandra Eva
- Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Achille Iolascon
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Mario Capasso
- CEINGE Biotecnologie Avanzate s.c.ar.l., Naples, Italy,Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy,Corresponding author. Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, Via Gaetano Salvatore 486, 80145 Napoli, Italy.
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18
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Franca MM, Condezo YB, Elzaiat M, Felipe-Medina N, Sánchez-Sáez F, Muñoz S, Sainz-Urruela R, Martín-Hervás MR, García-Valiente R, Sánchez-Martín MA, Astudillo A, Mendez J, Llano E, Veitia RA, Mendonca BB, Pendás AM. A truncating variant of RAD51B associated with primary ovarian insufficiency provides insights into its meiotic and somatic functions. Cell Death Differ 2022; 29:2347-2361. [PMID: 35624308 PMCID: PMC9751091 DOI: 10.1038/s41418-022-01021-z] [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: 10/28/2021] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 01/31/2023] Open
Abstract
Primary ovarian insufficiency (POI) causes female infertility by abolishing normal ovarian function. Although its genetic etiology has been extensively investigated, most POI cases remain unexplained. Using whole-exome sequencing, we identified a homozygous variant in RAD51B -(c.92delT) in two sisters with POI. In vitro studies revealed that this variant leads to translation reinitiation at methionine 64. Here, we show that this is a pathogenic hypomorphic variant in a mouse model. Rad51bc.92delT/c.92delT mice exhibited meiotic DNA repair defects due to RAD51 and HSF2BP/BMRE1 accumulation in the chromosome axes leading to a reduction in the number of crossovers. Interestingly, the interaction of RAD51B-c.92delT with RAD51C and with its newly identified interactors RAD51 and HELQ was abrogated or diminished. Repair of mitomycin-C-induced chromosomal aberrations was impaired in RAD51B/Rad51b-c.92delT human and mouse somatic cells in vitro and in explanted mouse bone marrow cells. Accordingly, Rad51b-c.92delT variant reduced replication fork progression of patient-derived lymphoblastoid cell lines and pluripotent reprogramming efficiency of primary mouse embryonic fibroblasts. Finally, Rad51bc.92delT/c.92delT mice displayed increased incidence of pituitary gland hyperplasia. These results provide new mechanistic insights into the role of RAD51B not only in meiosis but in the maintenance of somatic genome stability.
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Affiliation(s)
- Monica M Franca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42 and SELA, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brasil
- Section of Endocrinology Diabetes and Metabolism, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Yazmine B Condezo
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Maëva Elzaiat
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Natalia Felipe-Medina
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Fernando Sánchez-Sáez
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Sergio Muñoz
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Raquel Sainz-Urruela
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - M Rosario Martín-Hervás
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Rodrigo García-Valiente
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
| | - Manuel A Sánchez-Martín
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
- Transgenic Facility, Nucleus platform, Universidad de Salamanca, Salamanca, Spain
| | | | - Juan Mendez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, E-28029, Madrid, Spain
| | - Elena Llano
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain
- Departamento de Fisiología y Farmacología, Universidad de Salamanca, Salamanca, Spain
| | - Reiner A Veitia
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France.
- Université Paris-Saclay and Institut François Jacob, Comissariat à l'Energie Atomique, Gif-sur-Yvette, France.
| | - Berenice B Mendonca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular/LIM42 and SELA, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, Brasil.
| | - Alberto M Pendás
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Salamanca, Spain.
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19
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Cytogenetics in Fanconi Anemia: The Importance of Follow-Up and the Search for New Biomarkers of Genomic Instability. Int J Mol Sci 2022; 23:ijms232214119. [PMID: 36430597 PMCID: PMC9699043 DOI: 10.3390/ijms232214119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Fanconi Anemia (FA) is a disease characterized by genomic instability, increased sensitivity to DNA cross-linking agents, and the presence of clonal chromosomal abnormalities. This genomic instability can compromise the bone marrow (BM) and confer a high cancer risk to the patients, particularly in the development of Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML). The diagnosis of FA patients is complex and cannot be based only on clinical features at presentation. The gold standard diagnostic assay for these patients is cytogenetic analysis, revealing chromosomal breaks induced by DNA cross-linking agents. Clonal chromosome abnormalities, such as the ones involving chromosomes 1q, 3q, and 7, are also common features in FA patients and are associated with progressive BM failure and/or a pre-leukemia condition. In this review, we discuss the cytogenetic methods and their application in diagnosis, stratification of the patients into distinct prognostic groups, and the clinical follow-up of FA patients. These methods have been invaluable for the understanding of FA pathogenesis and identifying novel disease biomarkers. Additional evidence is required to determine the association of these biomarkers with prognosis and cancer risk, and their potential as druggable targets for FA therapy.
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20
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Testis-expressed gene 11 inhibits cisplatin-induced DNA damage and contributes to chemoresistance in testicular germ cell tumor. Sci Rep 2022; 12:18423. [PMID: 36319719 PMCID: PMC9626550 DOI: 10.1038/s41598-022-21856-3] [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: 03/18/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022] Open
Abstract
Testicular germ cell tumor (TGCT) is a rare cancer but the most common tumor among adolescent and young adult males. Patients with advanced TGCT often exhibit a worse prognosis due to the acquisition of therapeutic resistance. Cisplatin-based chemotherapy is a standard treatment for advanced TGCTs initially sensitive to cisplatin, as exemplified by embryonal carcinoma. The acquisition of cisplatin resistance, however, could be a fatal obstacle for TGCT management. To identify cisplatin resistance-related genes, we performed transcriptome analysis for cisplatin-resistant TGCT cells compared to parental cells. In two types of cisplatin-resistant TGCT cell models that we established from patient-derived TGCT cells, and from the NEC8 cell line, we found that mRNA levels of the high-mobility-group nucleosome-binding gene HMGN5 and meiosis-related gene TEX11 were remarkably upregulated compared to those in the corresponding parental cells. We showed that either HMGN5 or TEX11 knockdown substantially reduced the viability of cisplatin-resistant TGCT cells in the presence of cisplatin. Notably, TEX11 silencing in cisplatin-resistant TGCT cells increased the level of cleaved PARP1 protein, and the percentage of double-strand break marker γH2AX-positive cells. We further demonstrated the therapeutic efficiency of TEX11-specific siRNA on in vivo xenograft models derived from cisplatin-resistant patient-derived TGCT cells. Taken together, the present study provides a potential insight into a mechanism of cisplatin resistance via TEX11-dependent pathways that inhibit apoptosis and DNA damage. We expect that our findings can be applied to the improvement of cisplatin-based chemotherapy for TGCT, particularly for TEX11-overexpressing tumor.
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21
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Prakash R, Rawal Y, Sullivan MR, Grundy MK, Bret H, Mihalevic MJ, Rein HL, Baird JM, Darrah K, Zhang F, Wang R, Traina TA, Radke MR, Kaufmann SH, Swisher EM, Guérois R, Modesti M, Sung P, Jasin M, Bernstein KA. Homologous recombination-deficient mutation cluster in tumor suppressor RAD51C identified by comprehensive analysis of cancer variants. Proc Natl Acad Sci U S A 2022; 119:e2202727119. [PMID: 36099300 PMCID: PMC9499524 DOI: 10.1073/pnas.2202727119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/09/2022] [Indexed: 01/05/2023] Open
Abstract
Mutations in homologous recombination (HR) genes, including BRCA1, BRCA2, and the RAD51 paralog RAD51C, predispose to tumorigenesis and sensitize cancers to DNA-damaging agents and poly(ADP ribose) polymerase inhibitors. However, ∼800 missense variants of unknown significance have been identified for RAD51C alone, impairing cancer risk assessment and therapeutic strategies. Here, we interrogated >50 RAD51C missense variants, finding that mutations in residues conserved with RAD51 strongly predicted HR deficiency and disrupted interactions with other RAD51 paralogs. A cluster of mutations was identified in and around the Walker A box that led to impairments in HR, interactions with three other RAD51 paralogs, binding to single-stranded DNA, and ATP hydrolysis. We generated structural models of the two RAD51 paralog complexes containing RAD51C, RAD51B-RAD51C-RAD51D-XRCC2 and RAD51C-XRCC3. Together with our functional and biochemical analyses, the structural models predict ATP binding at the interface of RAD51C interactions with other RAD51 paralogs, similar to interactions between monomers in RAD51 filaments, and explain the failure of RAD51C variants in binding multiple paralogs. Ovarian cancer patients with variants in this cluster showed exceptionally long survival, which may be relevant to the reversion potential of the variants. This comprehensive analysis provides a framework for RAD51C variant classification. Importantly, it also provides insight into the functioning of the RAD51 paralog complexes.
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Affiliation(s)
- Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Yashpal Rawal
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Meghan R. Sullivan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - McKenzie K. Grundy
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Hélène Bret
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, 91198 France
| | - Michael J. Mihalevic
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Hayley L. Rein
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Jared M. Baird
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Kristie Darrah
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Fang Zhang
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853
| | - Raymond Wang
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Tiffany A. Traina
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Marc R. Radke
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, WA 98195
| | - Scott H. Kaufmann
- Departments of Oncology and Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905
| | - Elizabeth M. Swisher
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, WA 98195
| | - Raphaël Guérois
- Institute for Integrative Biology of the Cell, Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, 91198 France
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS, INSERM, Institut Paoli-Calmettes, Aix-Marseille Université, Marseille, 13273 France
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Kara A. Bernstein
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
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22
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Astore C, Zhou H, Ilkowski B, Forness J, Skolnick J. LeMeDISCO is a computational method for large-scale prediction & molecular interpretation of disease comorbidity. Commun Biol 2022; 5:870. [PMID: 36008469 PMCID: PMC9411158 DOI: 10.1038/s42003-022-03816-9] [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] [Received: 09/30/2021] [Accepted: 08/08/2022] [Indexed: 11/09/2022] Open
Abstract
To understand the origin of disease comorbidity and to identify the essential proteins and pathways underlying comorbid diseases, we developed LeMeDISCO (Large-Scale Molecular Interpretation of Disease Comorbidity), an algorithm that predicts disease comorbidities from shared mode of action proteins predicted by the artificial intelligence-based MEDICASCY algorithm. LeMeDISCO was applied to predict the occurrence of comorbid diseases for 3608 distinct diseases. Benchmarking shows that LeMeDISCO has much better comorbidity recall than the two molecular methods XD-score (44.5% vs. 6.4%) and the SAB score (68.6% vs. 8.0%). Its performance is somewhat comparable to the phenotype method-based Symptom Similarity Score, 63.7% vs. 100%, but LeMeDISCO works for far more cases and its large comorbidity recall is attributed to shared proteins that can help provide an understanding of the molecular mechanism(s) underlying disease comorbidity. The LeMeDISCO web server is available for academic users at: http://sites.gatech.edu/cssb/LeMeDISCO .
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Affiliation(s)
- Courtney Astore
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Hongyi Zhou
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Bartosz Ilkowski
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jessica Forness
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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23
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Fiesco-Roa MÓ, García-de Teresa B, Leal-Anaya P, van ‘t Hek R, Wegman-Ostrosky T, Frías S, Rodríguez A. Fanconi anemia and dyskeratosis congenita/telomere biology disorders: Two inherited bone marrow failure syndromes with genomic instability. Front Oncol 2022; 12:949435. [PMID: 36091172 PMCID: PMC9453478 DOI: 10.3389/fonc.2022.949435] [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] [Received: 05/20/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFS) are a complex and heterogeneous group of genetic diseases. To date, at least 13 IBMFS have been characterized. Their pathophysiology is associated with germline pathogenic variants in genes that affect hematopoiesis. A couple of these diseases also have genomic instability, Fanconi anemia due to DNA damage repair deficiency and dyskeratosis congenita/telomere biology disorders as a result of an alteration in telomere maintenance. Patients can have extramedullary manifestations, including cancer and functional or structural physical abnormalities. Furthermore, the phenotypic spectrum varies from cryptic features to patients with significantly evident manifestations. These diseases require a high index of suspicion and should be considered in any patient with abnormal hematopoiesis, even if extramedullary manifestations are not evident. This review describes the disrupted cellular processes that lead to the affected maintenance of the genome structure, contrasting the dysmorphological and oncological phenotypes of Fanconi anemia and dyskeratosis congenita/telomere biology disorders. Through a dysmorphological analysis, we describe the phenotypic features that allow to make the differential diagnosis and the early identification of patients, even before the onset of hematological or oncological manifestations. From the oncological perspective, we analyzed the spectrum and risks of cancers in patients and carriers.
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Affiliation(s)
- Moisés Ó. Fiesco-Roa
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México, Mexico
- Maestría y Doctorado en Ciencias Médicas, Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Ciudad de México, Mexico
| | | | - Paula Leal-Anaya
- Departamento de Genética Humana, Instituto Nacional de Pediatría, Ciudad de México, Mexico
| | - Renée van ‘t Hek
- Facultad de Medicina, Universidad Nacional Autoínoma de Meíxico (UNAM), Ciudad Universitaria, Ciudad de México, Mexico
| | - Talia Wegman-Ostrosky
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México, Mexico
| | - Sara Frías
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, Ciudad de México, Mexico
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
- *Correspondence: Alfredo Rodríguez, ; Sara Frías,
| | - Alfredo Rodríguez
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
- Unidad de Genética de la Nutrición, Instituto Nacional de Pediatría, Ciudad de México, Mexico
- *Correspondence: Alfredo Rodríguez, ; Sara Frías,
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24
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Dokal I, Tummala H, Vulliamy T. Inherited bone marrow failure in the pediatric patient. Blood 2022; 140:556-570. [PMID: 35605178 PMCID: PMC9373017 DOI: 10.1182/blood.2020006481] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/17/2020] [Indexed: 12/05/2022] Open
Abstract
Inherited bone marrow (BM) failure syndromes are a diverse group of disorders characterized by BM failure, usually in association with ≥1 extrahematopoietic abnormalities. BM failure, which can involve ≥1 cell lineages, often presents in the pediatric age group. Furthermore, some children initially labeled as having idiopathic aplastic anemia or myelodysplasia represent cryptic cases of inherited BM failure. Significant advances in the genetics of these syndromes have been made, identifying more than 100 disease genes, giving insights into normal hematopoiesis and how it is disrupted in patients with BM failure. They have also provided important information on fundamental biological pathways, including DNA repair: Fanconi anemia (FA) genes; telomere maintenance: dyskeratosis congenita (DC) genes; and ribosome biogenesis: Shwachman-Diamond syndrome and Diamond-Blackfan anemia genes. In addition, because these disorders are usually associated with extrahematopoietic abnormalities and increased risk of cancer, they have provided insights into human development and cancer. In the clinic, genetic tests stemming from the recent advances facilitate diagnosis, especially when clinical features are insufficient to accurately classify a disorder. Hematopoietic stem cell transplantation using fludarabine-based protocols has significantly improved outcomes, particularly in patients with FA or DC. Management of some other complications, such as cancer, remains a challenge. Recent studies have suggested the possibility of new and potentially more efficacious therapies, including a renewed focus on hematopoietic gene therapy and drugs [transforming growth factor-β inhibitors for FA and PAPD5, a human poly(A) polymerase, inhibitors for DC] that target disease-specific defects.
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Affiliation(s)
- Inderjeet Dokal
- Centre for Genomics and Child Health, Blizard Institute, London, United Kingdom; and
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Barts Health National Health Service (NHS) Trust, London, United Kingdom
| | - Hemanth Tummala
- Centre for Genomics and Child Health, Blizard Institute, London, United Kingdom; and
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Barts Health National Health Service (NHS) Trust, London, United Kingdom
| | - Tom Vulliamy
- Centre for Genomics and Child Health, Blizard Institute, London, United Kingdom; and
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Barts Health National Health Service (NHS) Trust, London, United Kingdom
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25
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Hater N, Iwaniuk KM, Leifeld C, Grüten P, Wiek C, Raba K, Zhang F, Fischer JC, Andreassen PR, Hanenberg H, Trompeter HI. Identification of new RAD51D-regulating microRNAs that also emerge as potent inhibitors of the Fanconi anemia/homologous recombination pathways. Hum Mol Genet 2022; 31:4241-4254. [PMID: 35904444 PMCID: PMC9759333 DOI: 10.1093/hmg/ddac177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/28/2022] [Accepted: 07/27/2022] [Indexed: 01/21/2023] Open
Abstract
The Fanconi anemia (FA) and homologous recombination (HR) pathways, which partially overlap and include RAD51 and its paralogs, are key for the repair of different types of DNA damage, such as DNA interstrand crosslinks. First, to broadly assess the impact of microRNA-mediated regulation, we examined microRNA expression profiles in five isogenic fibroblast cell pairs, either deficient in DNA repair due to germline mutations in FANCA, FANCB, FANCC, FANCI or BRIP1/FANCJ or proficient due to correction with retroviral vectors. In each pair, we observed lower abundance of specific microRNAs in the FA-deficient cells. From the list of microRNAs, we experimentally confirmed the effects of miR-141-3p and miR-369-3p targeting RAD51B and miR-15a-5p, miR-494-3p as well as miR-544a targeting RAD51D. However, by western blotting, only RAD51D protein was reduced by a mixture of its regulating microRNAs. Gene ontology analyses and identification of additional FA/HR factors as targets of miR-15a-5p, miR-494-3p and miR-544a strongly suggested the widespread influence of these microRNAs on HR. Interestingly, only miR-494-3p directly reduced RAD51 foci formation, while a mixture of miR-15a-5p, miR-494-3p and miR-544a strongly reduced HR activity in green fluorescent protein (GFP) repair assays. In summary, by successfully employing this novel loss- and gain-of-function strategy, we have identified new microRNAs strongly inhibiting HR in mammalian cells. Understanding and modulating such miRNA regulation of DNA repair genes/pathways might help to overcome the reduced repair capacity of FA patients with biallelic hypomorphic mutations or help to engineer synthetic lethality strategies for patients with mutations in cancer-associated FA/HR genes.
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Affiliation(s)
- Nina Hater
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Katharina M Iwaniuk
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Carina Leifeld
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Pia Grüten
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Constanze Wiek
- Department of Otorhinolaryngology & Head/Neck Surgery, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Katharina Raba
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Fan Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Johannes C Fischer
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Hans-Ingo Trompeter
- To whom correspondence should be addressed. Tel: +49 211 8118751; Fax: +49 211 8119109;
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26
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Minigene Splicing Assays Identify 20 Spliceogenic Variants of the Breast/Ovarian Cancer Susceptibility Gene RAD51C. Cancers (Basel) 2022; 14:cancers14122960. [PMID: 35740625 PMCID: PMC9221245 DOI: 10.3390/cancers14122960] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
RAD51C loss-of-function variants are associated with an increased risk of breast and ovarian cancers. Likewise, splicing disruptions are a frequent mechanism of gene inactivation. Taking advantage of a previous splicing-reporter minigene with exons 2-8 (mgR51C_ex2-8), we proceeded to check its impact on the splicing of candidate ClinVar variants. A total of 141 RAD51C variants at the intron/exon boundaries were analyzed with MaxEntScan. Twenty variants were selected and genetically engineered into the wild-type minigene. All the variants disrupted splicing, and 18 induced major splicing anomalies without any trace or minimal amounts (<2.4%) of the minigene full-length (FL) transcript. Twenty-seven transcripts (including the wild-type and r.904A FL transcripts) were identified by fluorescent fragment electrophoresis; of these, 14 were predicted to truncate the RAD51C protein, 3 kept the reading frame, and 8 minor isoforms (1.1−4.7% of the overall expression) could not be characterized. Finally, we performed a tentative interpretation of the variants according to an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme, classifying 16 variants as likely pathogenic. Minigene assays have been proven as valuable tools for the initial characterization of potential spliceogenic variants. Hence, minigene mgR51C_ex2-8 provided useful splicing data for 40 RAD51C variants.
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27
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Villalona-Calero MA, Diaz JP, Duan W, Diaz Z, Schroeder ED, Aparo S, Gatcliffe T, Albrecht F, Venkatappa S, Guardiola V, Garrido S, Rubens M, DeZarraga F, Vuong H. Pembrolizumab activity in patients with Fanconi anemia repair pathway competent and deficient tumors. Biomark Res 2022; 10:39. [PMID: 35658948 PMCID: PMC9164357 DOI: 10.1186/s40364-022-00386-0] [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] [Received: 02/17/2022] [Accepted: 05/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background Given the observed antitumor activity of immune-checkpoint-inhibitors in patients with mismatch-repair deficient (MSI-H) tumors, we hypothesized that deficiency in homologous-recombination-repair (HRR) can also influence susceptibility. Methods Patients with disease progression on standard of care and for whom pembrolizumab had no FDA approved indication received pembrolizumab. Patients with MSI-H tumors were excluded. Objectives included immune-related objective response rate (iORR), progression-free survival (PFS) and 20-weeks-PFS. Pembrolizumab was given every 3 weeks and scans performed every six. We evaluated a triple-stain (FANCD2foci/DAPI/Ki67) functional assay of the Fanconi Anemia (FA) pathway: FATSI, in treated patients’ archived tumors. The two-stage sample size of 20/39 patients evaluated an expected iORR≥20% in the whole population vs. the null hypothesis of an iORR≤5%, based on an assumed iORR≥40% in patients with functional FA deficiency, and < 10% in patients with intact HRR. An expansion cohort of MSI stable endometrial cancer (MS-EC) followed. Exploratory stool microbiome analyses in selected patients were performed. Results Fifty-two patients (45F,7M;50-evaluable) were enrolled. For the 39 in the two-stage cohort, response evaluation showed 2CR,5PR,11SD,21PD (iORR-18%). FATSI tumor analyses showed 29 competent (+) and 10 deficient (−). 2PR,9SD,17PD,1NE occurred among the FATSI+ (iORR-7%) and 2CR,3PR,2SD,3PD among the FATSI(−) patients (iORR-50%). mPFS and 20w-PFS were 43 days and 21% in FATSI+, versus 202 days and 70% in FATSI(−) patients. One PR occurred in the MS-EC expansion cohort. Conclusions Pembrolizumab has meaningful antitumor activity in malignancies with no current FDA approved indications and FA functional deficiency. The results support further evaluation of FATSI as a discriminatory biomarker for population-selected studies. Supplementary Information The online version contains supplementary material available at 10.1186/s40364-022-00386-0.
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28
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Athar F, Templeman NM. C. elegans as a model organism to study female reproductive health. Comp Biochem Physiol A Mol Integr Physiol 2022; 266:111152. [PMID: 35032657 DOI: 10.1016/j.cbpa.2022.111152] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 12/17/2022]
Abstract
Female reproductive health has been historically understudied and underfunded. Here, we present the advantages of using a free-living nematode, Caenorhabditis elegans, as an animal system to study fundamental aspects of female reproductive health. C. elegans is a powerful high-throughput model organism that shares key genetic and physiological similarities with humans. In this review, we highlight areas of pressing medical and biological importance in the 21st century within the context of female reproductive health. These include the decline in female reproductive capacity with increasing chronological age, reproductive dysfunction arising from toxic environmental insults, and cancers of the reproductive system. C. elegans has been instrumental in uncovering mechanistic insights underlying these processes, and has been valuable for developing and testing therapeutics to combat them. Adopting a convenient model organism such as C. elegans for studying reproductive health will encourage further research into this field, and broaden opportunities for making advancements into evolutionarily conserved mechanisms that control reproductive function.
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Affiliation(s)
- Faria Athar
- Department of Biology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Nicole M Templeman
- Department of Biology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada.
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29
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Lim BWX, Li N, Rowley SM, Thompson ER, McInerny S, Zethoven M, Scott RJ, Devereux L, Sloan EK, James PA, Campbell IG. Integration of tumour sequencing and case-control data to assess pathogenicity of RAD51C missense variants in familial breast cancer. NPJ Breast Cancer 2022; 8:10. [PMID: 35039523 PMCID: PMC8763908 DOI: 10.1038/s41523-021-00373-y] [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] [Received: 03/23/2021] [Accepted: 12/06/2021] [Indexed: 11/09/2022] Open
Abstract
While protein-truncating variants in RAD51C have been shown to predispose to triple-negative (TN) breast cancer (BC) and ovarian cancer, little is known about the pathogenicity of missense (MS) variants. The frequency of rare RAD51C MS variants was assessed in the BEACCON study of 5734 familial BC cases and 14,382 population controls, and findings were integrated with tumour sequencing data from 21 cases carrying a candidate variant. Collectively, a significant enrichment of rare MS variants was detected in cases (MAF < 0.001, OR 1.57, 95% CI 1.00-2.44, p = 0.05), particularly for variants with a REVEL score >0.5 (OR 3.95, 95% CI 1.40-12.01, p = 0.006). Sequencing of 21 tumours from 20 heterozygous and 1 homozygous carriers of nine candidate MS variants identified four cases with biallelic inactivation through loss of the wild-type allele, while six lost the variant allele and ten that remained heterozygous. Biallelic loss of the wild-type alleles corresponded strongly with ER- and TN breast tumours, high homologous recombination deficiency scores and mutational signature 3. Using this approach, the p.Gly264Ser variant, which was previously suspected to be pathogenic based on small case-control analyses and loss of activity in in vitro functional assays, was shown to be benign with similar prevalence in cases and controls and seven out of eight tumours showing no biallelic inactivation or characteristic mutational signature. Conversely, evaluation of case-control findings and tumour sequencing data identified p.Ile144Thr, p.Arg212His, p.Gln143Arg and p.Gly114Arg as variants warranting further investigation.
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Affiliation(s)
- Belle W X Lim
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Drug Delivery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
| | - Na Li
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.,Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Simone M Rowley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Ella R Thompson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.,Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Simone McInerny
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Magnus Zethoven
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Bioinformatics Consulting Core, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Rodney J Scott
- Discipline of Medical Genetics and Centre for Information-Based Medicine, The University of Newcastle and Hunter Medical Research Institute, Newcastle, NSW, Australia.,Division of Molecular Medicine, Pathology North, Newcastle, NSW, Australia
| | - Lisa Devereux
- Lifepool, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Erica K Sloan
- Drug Delivery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia.,Peter MacCallum Cancer Centre Division of Surgery, Melbourne, VIC, Australia
| | - Paul A James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.,Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia. .,Lifepool, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. .,Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
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30
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Boni J, Idani A, Roca C, Feliubadaló L, Tomiak E, Weber E, Foulkes WD, Orthwein A, El Haffaf Z, Lazaro C, Rivera B. A decade of RAD51C and RAD51D germline variants in cancer. Hum Mutat 2021; 43:285-298. [PMID: 34923718 DOI: 10.1002/humu.24319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 11/12/2022]
Abstract
Defects in DNA repair genes have been extensively associated with cancer susceptibility. Germline pathogenic variants (GPV) in genes involved in homologous recombination repair pathways predispose to cancers arising mainly in the breast and ovary, but also other tissues. The RAD51 paralogs RAD51C and RAD51D were included in this group 10 years ago when germline variants were associated with non-BRCA1/2 familial ovarian cancer. Here, we have reviewed the landscape of RAD51C and RAD51D germline variants in cancer reported in the literature during the last decade, integrating this list with variants identified by in-house patient screening. A comprehensive catalog of 341 variants that have been classified applying ACMG/AMP criteria has been generated pinpointing the existence of recurrent variants in both genes. Recurrent variants have been extensively discussed compiling data on population frequencies and functional characterization if available, highlighting variants that have not been fully characterized yet to properly establish their pathogenicity. Finally, we have complemented this data with relevant information regarding the conservation of mutated residues among RAD51 paralogs and modeling of putative hotspot areas, which contributes to generating an exhaustive update on these two cancer predisposition genes.
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Affiliation(s)
- Jacopo Boni
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Aida Idani
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Carla Roca
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Eva Tomiak
- Department of Genetics, University of Ottawa, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Evan Weber
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Quebec, Montreal, Canada
| | - William D Foulkes
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Quebec, Montreal, Canada.,Gerald Bronfman Department of Oncology, McGill University Montreal, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University Montreal, Montreal, Quebec, Canada.,Cancer Research Axis, Lady Davis Institute, Jewish General Hospital, Quebec, Montreal, Canada
| | - Alexandre Orthwein
- Gerald Bronfman Department of Oncology, McGill University Montreal, Montreal, Quebec, Canada.,Cancer Research Axis, Lady Davis Institute, Jewish General Hospital, Quebec, Montreal, Canada
| | - Zaki El Haffaf
- Division of Genetics, Department of Medicine, Research Center, Centre Hospitalier de l'Université de Montréal (CRCHUM), Quebec, Montreal, Canada
| | - Conxi Lazaro
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Barbara Rivera
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain.,Gerald Bronfman Department of Oncology, McGill University Montreal, Montreal, Quebec, Canada.,Cancer Research Axis, Lady Davis Institute, Jewish General Hospital, Quebec, Montreal, Canada
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31
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Luzwick JW, Dombi E, Boisvert RA, Roy S, Park S, Kunnimalaiyaan S, Goffart S, Schindler D, Schlacher K. MRE11-dependent instability in mitochondrial DNA fork protection activates a cGAS immune signaling pathway. SCIENCE ADVANCES 2021; 7:eabf9441. [PMID: 34910513 PMCID: PMC8673762 DOI: 10.1126/sciadv.abf9441] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Mitochondrial DNA (mtDNA) instability activates cGAS-dependent innate immune signaling by unknown mechanisms. Here, we find that Fanconi anemia suppressor genes are acting in the mitochondria to protect mtDNA replication forks from instability. Specifically, Fanconi anemia patient cells show a loss of nascent mtDNA through MRE11 nuclease degradation. In contrast to DNA replication fork stability, which requires pathway activation by FANCD2-FANCI monoubiquitination and upstream FANC core complex genes, mitochondrial replication fork protection does not, revealing a mechanistic and genetic separation between mitochondrial and nuclear genome stability pathways. The degraded mtDNA causes hyperactivation of cGAS-dependent immune signaling resembling the unphosphorylated ISG3 response. Chemical inhibition of MRE11 suppresses this innate immune signaling, identifying MRE11 as a nuclease responsible for activating the mtDNA-dependent cGAS/STING response. Collective results establish a previously unknown molecular pathway for mtDNA replication stability and reveal a molecular handle to control mtDNA-dependent cGAS activation by inhibiting MRE11 nuclease.
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Affiliation(s)
- Jessica W. Luzwick
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Eszter Dombi
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Rebecca A. Boisvert
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Sunetra Roy
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Soyoung Park
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Detlev Schindler
- Institut für Humangenetik, University of Würzburg, Würzburg, Germany
| | - Katharina Schlacher
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
- Corresponding author.
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32
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Špírek M, Taylor MRG, Belan O, Boulton SJ, Krejci L. Nucleotide proofreading functions by nematode RAD51 paralogs facilitate optimal RAD51 filament function. Nat Commun 2021; 12:5545. [PMID: 34545070 PMCID: PMC8452638 DOI: 10.1038/s41467-021-25830-x] [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: 09/22/2020] [Accepted: 09/02/2021] [Indexed: 12/30/2022] Open
Abstract
The RAD51 recombinase assembles as helical nucleoprotein filaments on single-stranded DNA (ssDNA) and mediates invasion and strand exchange with homologous duplex DNA (dsDNA) during homologous recombination (HR), as well as protection and restart of stalled replication forks. Strand invasion by RAD51-ssDNA complexes depends on ATP binding. However, RAD51 can bind ssDNA in non-productive ADP-bound or nucleotide-free states, and ATP-RAD51-ssDNA complexes hydrolyse ATP over time. Here, we define unappreciated mechanisms by which the RAD51 paralog complex RFS-1/RIP-1 limits the accumulation of RAD-51-ssDNA complexes with unfavorable nucleotide content. We find RAD51 paralogs promote the turnover of ADP-bound RAD-51 from ssDNA, in striking contrast to their ability to stabilize productive ATP-bound RAD-51 nucleoprotein filaments. In addition, RFS-1/RIP-1 inhibits binding of nucleotide-free RAD-51 to ssDNA. We propose that ‘nucleotide proofreading’ activities of RAD51 paralogs co-operate to ensure the enrichment of active, ATP-bound RAD-51 filaments on ssDNA to promote HR. A RAD51 paralog complex, RFS-1/RIP-1, is shown to control ssDNA binding and dissociation by RAD-51 differentially in the presence and absence of nucleotide cofactors. These nucleotide proofreading activities drive a preferential accumulation of RAD-51-ssDNA complexes with optimal nucleotide content.
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Affiliation(s)
- Mário Špírek
- International Clinical Research Center, St. Anne's University Hospital in Brno, 62500, Brno, Czech Republic.,Department of Biology Masaryk University, 62500, Brno, Czech Republic
| | | | - Ondrej Belan
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,National Centre for Biomolecular Research, Masaryk University, 62500, Brno, Czech Republic
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Lumir Krejci
- International Clinical Research Center, St. Anne's University Hospital in Brno, 62500, Brno, Czech Republic. .,Department of Biology Masaryk University, 62500, Brno, Czech Republic. .,National Centre for Biomolecular Research, Masaryk University, 62500, Brno, Czech Republic.
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33
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van Riet J, van de Werken HJG, Cuppen E, Eskens FALM, Tesselaar M, van Veenendaal LM, Klümpen HJ, Dercksen MW, Valk GD, Lolkema MP, Sleijfer S, Mostert B. The genomic landscape of 85 advanced neuroendocrine neoplasms reveals subtype-heterogeneity and potential therapeutic targets. Nat Commun 2021; 12:4612. [PMID: 34326338 PMCID: PMC8322054 DOI: 10.1038/s41467-021-24812-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
Metastatic and locally-advanced neuroendocrine neoplasms (aNEN) form clinically and genetically heterogeneous malignancies, characterized by distinct prognoses based upon primary tumor localization, functionality, grade, proliferation index and diverse outcomes to treatment. Here, we report the mutational landscape of 85 whole-genome sequenced aNEN. This landscape reveals distinct genomic subpopulations of aNEN based on primary localization and differentiation grade; we observe relatively high tumor mutational burdens (TMB) in neuroendocrine carcinoma (average 5.45 somatic mutations per megabase) with TP53, KRAS, RB1, CSMD3, APC, CSMD1, LRATD2, TRRAP and MYC as major drivers versus an overall low TMB in neuroendocrine tumors (1.09). Furthermore, we observe distinct drivers which are enriched in somatic aberrations in pancreatic (MEN1, ATRX, DAXX, DMD and CREBBP) and midgut-derived neuroendocrine tumors (CDKN1B). Finally, 49% of aNEN patients reveal potential therapeutic targets based upon actionable (and responsive) somatic aberrations within their genome; potentially directing improvements in aNEN treatment strategies.
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Affiliation(s)
- Job van Riet
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands.
- Department of Urology, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, the Netherlands.
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - Ferry A L M Eskens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Margot Tesselaar
- Department of Medical Oncology, Cancer Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Linde M van Veenendaal
- Department of Medical Oncology, Cancer Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Heinz-Josef Klümpen
- Department of Medical Oncology, Amsterdam University Medical Centers, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Marcus W Dercksen
- Department of Internal Medicine, Maxima Medisch Centrum, Veldhoven, The Netherlands
| | - Gerlof D Valk
- Department of Endocrine Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Martijn P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, the Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, the Netherlands
| | - Bianca Mostert
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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34
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Thompson AS, Saba N, McReynolds LJ, Munir S, Ahmed P, Sajjad S, Jones K, Yeager M, Donovan FX, Chandrasekharappa SC, Alter BP, Savage SA, Rehman S. The causes of Fanconi anemia in South Asia and the Middle East: A case series and review of the literature. Mol Genet Genomic Med 2021; 9:e1693. [PMID: 33960719 PMCID: PMC8372062 DOI: 10.1002/mgg3.1693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/16/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
Background Fanconi anemia (FA) is an inherited bone marrow failure syndrome associated with characteristic dysmorphology primarily caused by biallelic pathogenic germline variants in any of 22 different DNA repair genes. There are limited data on the specific molecular causes of FA in different ethnic groups. Methods We performed exome sequencing and copy number variant analyses on 19 patients with FA from 17 families undergoing hematopoietic cell transplantation evaluation in Pakistan. The scientific literature was reviewed, and we curated germline variants reported in patients with FA from South Asia and the Middle East. Results The genetic causes of FA were identified in 14 of the 17 families: seven FANCA, two FANCC, one FANCF, two FANCG, and two FANCL. Homozygous and compound heterozygous variants were present in 12 and two families, respectively. Nine families carried variants previously reported as pathogenic, including two families with the South Asian FANCL founder variant. We also identified five novel likely deleterious variants in FANCA, FANCF, and FANCG in affected patients. Conclusions Our study supports the importance of determining the genomic landscape of FA in diverse populations, in order to improve understanding of FA etiology and assist in the counseling of families.
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Affiliation(s)
- Ashley S Thompson
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nusrat Saba
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Saeeda Munir
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Parvez Ahmed
- Quaid-i-Azam International Hospital, Islamabad, Pakistan
| | - Sumaira Sajjad
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, 20850, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, 20850, USA
| | - Frank X Donovan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sadia Rehman
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
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35
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Matar CF, Bou-Fakhredin R, Russo R, Andolfo I, Iolascon A, Taher AT. Recommendations for pregnancy in Fanconi anemia. Expert Opin Biol Ther 2021; 21:1403-1409. [PMID: 33798394 DOI: 10.1080/14712598.2021.1913119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: Fanconi anemia (FA) is a rare congenital disease that belongs to the family of congenital trilinear bone marrow failure. Most FA patients will suffer bone marrow failure and the main treatment relies on supportive measures or more recently on the use of hematopoietic stem cell transplant. The improvements seen in the management of FA has led women to reach childbearing age and have successful pregnancies. However, these pregnancies are associated with increased complications such as preterm delivery, cesarean delivery, eclampsia and others.Areas covered: This review highlights on the outcome of pregnancies in FA patients reported in the literature along with practical recommendations.Expert opinion: Multidisciplinary efforts are required to optimize the management of pregnancy in FA patients. Moreover, the development of a set of recommendations to optimize the treatment is highly necessary.
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Affiliation(s)
- Charbel F Matar
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rayan Bou-Fakhredin
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Roberta Russo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE Advanced Biotechnology, Naples, Italy
| | - Immacolata Andolfo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE Advanced Biotechnology, Naples, Italy
| | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy.,CEINGE Advanced Biotechnology, Naples, Italy
| | - Ali T Taher
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
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36
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Blombery P, Fox LC, Ryland GL, Thompson ER, Lickiss J, McBean M, Yerneni S, Hughes D, Greenway A, Mechinaud F, Wood EM, Lieschke GJ, Szer J, Barbaro P, Roy J, Wight J, Lynch E, Martyn M, Gaff C, Ritchie D. Utility of clinical comprehensive genomic characterization for diagnostic categorization in patients presenting with hypocellular bone marrow failure syndromes. Haematologica 2021; 106:64-73. [PMID: 32054657 PMCID: PMC7776333 DOI: 10.3324/haematol.2019.237693] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/07/2020] [Indexed: 12/26/2022] Open
Abstract
Bone marrow failure (BMF) related to hypoplasia of hematopoietic elements in the bone marrow is a heterogeneous clinical entity with a broad differential diagnosis including both inherited and acquired causes. Accurate diagnostic categorization is critical to optimal patient care and detection of genomic variants in these patients may provide this important diagnostic and prognostic information. We performed real-time, accredited (ISO15189) comprehensive genomic characterization including targeted sequencing and whole exome sequencing in 115 patients with BMF syndrome (median age 24 years, range 3 months - 81 years). In patients with clinical diagnoses of inherited BMF syndromes, acquired BMF syndromes or clinically unclassifiable BMF we detected variants in 52% (12/23), 53% (25/47) and 56% (25/45) respectively. Genomic characterization resulted in a change of diagnosis in 30/115 (26%) including the identification of germline causes for 3/47 and 16/45 cases with pre-test diagnoses of acquired and clinically unclassifiable BMF respectively. The observed clinical impact of accurate diagnostic categorization included choice to perform allogeneic stem cell transplantation, disease-specific targeted treatments, identification of at-risk family members and influence of sibling allogeneic stem cell donor choice. Multiple novel pathogenic variants and copy number changes were identified in our cohort including in TERT, FANCA, RPS7 and SAMD9. Whole exome sequence analysis facilitated the identification of variants in two genes not typically associated with a primary clinical manifestation of BMF but also demonstrated reduced sensitivity for detecting low level acquired variants. In conclusion, genomic characterization can improve diagnostic categorization of patients presenting with hypoplastic BMF syndromes and should be routinely performed in this group of patients.
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Affiliation(s)
- Piers Blombery
- Clinical Hematology, Peter MacCallum Cancer Center/Royal Melbourne Hospital, Melbourne, Victoria
- University of Melbourne, Melbourne, Victoria
- Department of Pathology, Peter MacCallum Cancer Center, Melbourne, Victoria
| | - Lucy C. Fox
- Department of Pathology, Peter MacCallum Cancer Center, Melbourne, Victoria
- Epworth Healthcare, Melbourne, Victoria
- Transfusion Research Unit, School of Public Health & Preventive Medicine, Monash University, Melbourne, Victoria
| | - Georgina L. Ryland
- Department of Pathology, Peter MacCallum Cancer Center, Melbourne, Victoria
| | - Ella R. Thompson
- University of Melbourne, Melbourne, Victoria
- Department of Pathology, Peter MacCallum Cancer Center, Melbourne, Victoria
| | - Jennifer Lickiss
- Department of Pathology, Peter MacCallum Cancer Center, Melbourne, Victoria
| | - Michelle McBean
- Department of Pathology, Peter MacCallum Cancer Center, Melbourne, Victoria
| | - Satwica Yerneni
- Department of Pathology, Peter MacCallum Cancer Center, Melbourne, Victoria
| | | | | | | | - Erica M. Wood
- Transfusion Research Unit, School of Public Health & Preventive Medicine, Monash University, Melbourne, Victoria
| | - Graham J. Lieschke
- Clinical Hematology, Peter MacCallum Cancer Center/Royal Melbourne Hospital, Melbourne, Victoria
- Australian Regenerative Medicine Institute, Monash University, Melbourne, Victoria
| | - Jeff Szer
- Clinical Hematology, Peter MacCallum Cancer Center/Royal Melbourne Hospital, Melbourne, Victoria
| | - Pasquale Barbaro
- Children’s Health Queensland and University of Queensland, South Brisbane, Queensland
| | - John Roy
- Children’s Health Queensland and University of Queensland, South Brisbane, Queensland
| | - Joel Wight
- Department of Hematology, Austin Health, Melbourne, Victoria
| | - Elly Lynch
- Melbourne Genomics Health Alliance, Melbourne, Victoria
- Victorian Clinical Genetics Service, Melbourne, Victoria
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Melissa Martyn
- Melbourne Genomics Health Alliance, Melbourne, Victoria
- Victorian Clinical Genetics Service, Melbourne, Victoria
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Clara Gaff
- University of Melbourne, Melbourne, Victoria
- Melbourne Genomics Health Alliance, Melbourne, Victoria
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - David Ritchie
- Clinical Hematology, Peter MacCallum Cancer Center/Royal Melbourne Hospital, Melbourne, Victoria
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37
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DNA polymerase ι compensates for Fanconi anemia pathway deficiency by countering DNA replication stress. Proc Natl Acad Sci U S A 2020; 117:33436-33445. [PMID: 33376220 DOI: 10.1073/pnas.2008821117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Fanconi anemia (FA) is caused by defects in cellular responses to DNA crosslinking damage and replication stress. Given the constant occurrence of endogenous DNA damage and replication fork stress, it is unclear why complete deletion of FA genes does not have a major impact on cell proliferation and germ-line FA patients are able to progress through development well into their adulthood. To identify potential cellular mechanisms that compensate for the FA deficiency, we performed dropout screens in FA mutant cells with a whole genome guide RNA library. This uncovered a comprehensive genome-wide profile of FA pathway synthetic lethality, including POLI and CDK4 As little is known of the cellular function of DNA polymerase iota (Pol ι), we focused on its role in the loss-of-function FA knockout mutants. Loss of both FA pathway function and Pol ι leads to synthetic defects in cell proliferation and cell survival, and an increase in DNA damage accumulation. Furthermore, FA-deficient cells depend on the function of Pol ι to resume replication upon replication fork stalling. Our results reveal a critical role for Pol ι in DNA repair and replication fork restart and suggest Pol ι as a target for therapeutic intervention in malignancies carrying an FA gene mutation.
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38
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Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Llovet P, Díez-Gómez B, Caloca MJ, Pérez-Segura P, Fraile-Bethencourt E, Colmena M, Carvalho S, Allen J, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. Comprehensive Functional Characterization and Clinical Interpretation of 20 Splice-Site Variants of the RAD51C Gene. Cancers (Basel) 2020; 12:E3771. [PMID: 33333735 PMCID: PMC7765170 DOI: 10.3390/cancers12123771] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/12/2022] Open
Abstract
Hereditary breast and/or ovarian cancer is a highly heterogeneous disease with more than 10 known disease-associated genes. In the framework of the BRIDGES project (Breast Cancer Risk after Diagnostic Gene Sequencing), the RAD51C gene has been sequenced in 60,466 breast cancer patients and 53,461 controls. We aimed at functionally characterizing all the identified genetic variants that are predicted to disrupt the splicing process. Forty RAD51C variants of the intron-exon boundaries were bioinformatically analyzed, 20 of which were selected for splicing functional assays. To test them, a splicing reporter minigene with exons 2 to 8 was designed and constructed. This minigene generated a full-length transcript of the expected size (1062 nucleotides), sequence, and structure (Vector exon V1- RAD51C exons_2-8- Vector exon V2). The 20 candidate variants were genetically engineered into the wild type minigene and functionally assayed in MCF-7 cells. Nineteen variants (95%) impaired splicing, while 18 of them produced severe splicing anomalies. At least 35 transcripts were generated by the mutant minigenes: 16 protein-truncating, 6 in-frame, and 13 minor uncharacterized isoforms. According to ACMG/AMP-based standards, 15 variants could be classified as pathogenic or likely pathogenic variants: c.404G > A, c.405-6T > A, c.571 + 4A > G, c.571 + 5G > A, c.572-1G > T, c.705G > T, c.706-2A > C, c.706-2A > G, c.837 + 2T > C, c.905-3C > G, c.905-2A > C, c.905-2_905-1del, c.965 + 5G > A, c.1026 + 5_1026 + 7del, and c.1026 + 5G > T.
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Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Patricia Llovet
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Beatriz Díez-Gómez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - María José Caloca
- Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain;
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Eugenia Fraile-Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
- Knight Cancer Research Building, 2720 S Moody Ave, Portland, OR 97201, USA
| | - Marta Colmena
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Peter Devilee
- Leiden University Medical Center, Department of Human Genetics, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Maaike P. G. Vreeswijk
- Leiden University Medical Center, Department of Human Genetics, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Eladio A. Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
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TREX2 Exonuclease Causes Spontaneous Mutations and Stress-Induced Replication Fork Defects in Cells Expressing RAD51 K133A. Cell Rep 2020; 33:108543. [PMID: 33357432 PMCID: PMC7896812 DOI: 10.1016/j.celrep.2020.108543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 04/23/2020] [Accepted: 12/01/2020] [Indexed: 01/01/2023] Open
Abstract
DNA damage tolerance (DDT) and homologous recombination (HR) stabilize replication forks (RFs). RAD18/UBC13/three prime repair exonuclease 2 (TREX2)-mediated proliferating cell nuclear antigen (PCNA) ubiquitination is central to DDT, an error-prone lesion bypass pathway. RAD51 is the recombinase for HR. The RAD51 K133A mutation increased spontaneous mutations and stress-induced RF stalls and nascent strand degradation. Here, we report in RAD51K133A cells that this phenotype is reduced by expressing a TREX2 H188A mutation that deletes its exonuclease activity. In RAD51K133A cells, knocking out RAD18 or overexpressing PCNA reduces spontaneous mutations, while expressing ubiquitination-incompetent PCNAK164R increases mutations, indicating DDT as causal. Deleting TREX2 in cells deficient for the RF maintenance proteins poly(ADP-ribose) polymerase 1 (PARP1) or FANCB increased nascent strand degradation that was rescued by TREX2H188A, implying that TREX2 prohibits degradation independent of catalytic activity. A possible explanation for this occurrence is that TREX2H188A associates with UBC13 and ubiquitinates PCNA, suggesting a dual role for TREX2 in RF maintenance.
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Hirsch S, Gieldon L, Sutter C, Dikow N, Schaaf CP. Germline testing for homologous recombination repair genes—opportunities and challenges. Genes Chromosomes Cancer 2020; 60:332-343. [DOI: 10.1002/gcc.22900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- Steffen Hirsch
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ) Heidelberg Germany
| | - Laura Gieldon
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian Sutter
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Nicola Dikow
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
| | - Christian P. Schaaf
- Institute of Human Genetics Heidelberg University Hospital Heidelberg Germany
- Department of Molecular and Human Genetics Baylor College of Medicine Houston Texas
- Jan and Dan Duncan Neurological Research Institute Texas Children's Hospital Houston Texas
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Tan W, Deans AJ. The ubiquitination machinery of the Fanconi Anemia DNA repair pathway. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 163:5-13. [PMID: 33058944 DOI: 10.1016/j.pbiomolbio.2020.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
The Fanconi Anemia (FA) pathway maintains genome stability by preventing DNA damage from occurring when replication is blocked. Central to the FA pathway is the monoubiquitination of FANCI-FANCD2 mediated by a ubiquitin RING-E3 ligase complex called the FA core complex. Genetic mutation in any component of the FA core complex results in defective FANCI-FANCD2 monoubiquitination and phenotypes of DNA damage sensitivity, birth defects, early-onset bone marrow failure and cancer. Here, we discuss the mechanisms of the FA core complex and FANCI-FANCD2 monoubiquitination at sites of blocked replication and review our current understanding of the biological functions of these proteins in replication fork protection.
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Affiliation(s)
- Winnie Tan
- Genome Stability Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, Victoria, 3065, Australia
| | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute of Medical Research, 9 Princes St, Fitzroy, Victoria, 3065, Australia; Department of Medicine, St. Vincent's Health, The University of Melbourne, Australia. https://twitter.com/GenomeStability
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Grundy MK, Buckanovich RJ, Bernstein KA. Regulation and pharmacological targeting of RAD51 in cancer. NAR Cancer 2020; 2:zcaa024. [PMID: 33015624 PMCID: PMC7520849 DOI: 10.1093/narcan/zcaa024] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/25/2020] [Accepted: 09/03/2020] [Indexed: 01/06/2023] Open
Abstract
Regulation of homologous recombination (HR) is central for cancer prevention. However, too little HR can increase cancer incidence, whereas too much HR can drive cancer resistance to therapy. Importantly, therapeutics targeting HR deficiency have demonstrated a profound efficacy in the clinic improving patient outcomes, particularly for breast and ovarian cancer. RAD51 is central to DNA damage repair in the HR pathway. As such, understanding the function and regulation of RAD51 is essential for cancer biology. This review will focus on the role of RAD51 in cancer and beyond and how modulation of its function can be exploited as a cancer therapeutic.
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Affiliation(s)
- McKenzie K Grundy
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ronald J Buckanovich
- Division of Hematology Oncology, Department of Internal Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Kara A Bernstein
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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Yu H, Pan R, Gao T, Wu D, Ying J, Duan S. FANCF hypomethylation is associated with colorectal cancer in Han Chinese. TURKISH JOURNAL OF GASTROENTEROLOGY 2020; 31:558-565. [PMID: 32915143 DOI: 10.5152/tjg.2020.19394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND/AIMS Fanconi anemia complement group F (FANCF) is known to be involved in DNA repair, and the overexpression of FANCF protein leads to cell proliferation and ultimately to cancer. The purpose of this study was to assess whether FANCF methylation was associated with colorectal cancer (CRC). MATERIALS AND METHODS A case-control experiment was conducted to study the association between FANCF methylation and CRC. We used quantitative methylation-specific PCR to measure the FANCF promoter methylation, and the percentage of methylation reference (PMR) to quantify the FANCF promoter methylation level. To investigate the effect of the selected FANCF fragment on gene expression regulation, we also performed a dual-luciferase reporter gene assay. RESULTS The results indicated that FANCF methylation in CRC tumor tissues was significantly lower than that in the nontumor tissues (median PMR: 44.86% vs. 65.77%, p=0.00001). Analysis of receiver-operating characteristic curves showed that FANCF hypomethylation had a diagnostic value for CRC (area under curve [AUC]: 0.670, sensitivity: 55.8%, specificity: 71.7%, p=0.00001). The dual-luciferase reporter assay showed that the FANCF fragment upregulated gene expression (fold change: 1.93, p=0.002). CONCLUSION Research demonstrates for the first time that FANCF hypomethylation is significantly associated with CRC risk. FANCF hypomethylation may ultimately increase the risk of CRC by upregulating the expression of FANCF.
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Affiliation(s)
- Hang Yu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Ranran Pan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Tong Gao
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Dongping Wu
- Department of Medical Oncology, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Zhejiang, China
| | - Jieer Ying
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
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Yadav G, Vashisht M, Yadav V, Shyam R. Molecular Biomarkers for Early Detection and Prevention of Ovarian Cancer-A Gateway for Good Prognosis: A Narrative Review. Int J Prev Med 2020; 11:135. [PMID: 33088463 PMCID: PMC7554434 DOI: 10.4103/ijpvm.ijpvm_75_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/12/2019] [Indexed: 11/13/2022] Open
Abstract
Gynecological cancers are one of the most lethal and deadliest cancers in the world. In India, the prevalence of ovarian cancer accounts for 2.5% to 3%. Despite the availability of improved treatment option along with improved technology, the survival rate of ovarian cancer in the early-stage and the advanced stage is poor. Therefore, due to the heterogeneity of ovarian cancer, to detect it at an early stage and to prevent further mortality turns out to be a big challenge. Researchers are still in the process to identify any single biomarker with good sensitivity and specificity. Various traditional and serum approaches to identify ovarian cancer have been successful in the early stages. The invention of molecular biomarkers such as the use of genomic profiling, DNA methylation, and other approaches have proven to be of higher sensitivity and specificity, which overall affects the prognosis of ovarian cancer. With the use of whole-genome analysis, the detection of possible location of critical tumor suppressor gene (TSGs) in the paired region of chromosomes has been identified, which are associated with BRCA1 and BRCA2 which further makes these novel molecular biomarkers as potential biomarkers. Moreover, studies are required to assess the combined use of traditional, molecular biomarkers that might be useful for enhanced sensitivity and specificity for early detection and prevention of ovarian cancer in early stages which will lead to reduced mortality and good prognosis.
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Affiliation(s)
- Geetanjali Yadav
- Department of Zoology, Baba Math Nath University, Rohtak, Haryana, India
| | - Minakshi Vashisht
- Department of Genetics, Maharishi Dayanand University, Rohtak, Haryana, India
| | - Vipul Yadav
- Department of Public Health Dentistry, Post Graduate Institute of Dental Sciences, Rohtak, Haryana, India
| | - Radhey Shyam
- Department of Public Health Dentistry, Post Graduate Institute of Dental Sciences, Rohtak, Haryana, India
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Frontline Management of Epithelial Ovarian Cancer-Combining Clinical Expertise with Community Practice Collaboration and Cutting-Edge Research. J Clin Med 2020; 9:jcm9092830. [PMID: 32882942 PMCID: PMC7565288 DOI: 10.3390/jcm9092830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 01/19/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is the most common histology of ovarian cancer defined as epithelial cancer derived from the ovaries, fallopian tubes, or primary peritoneum. It is the fifth most common cause of cancer-related death in women in the United States. Because of a lack of effective screening and non-specific symptoms, EOC is typically diagnosed at an advanced stage (FIGO stage III or IV) and approximately one third of patients have malignant ascites at initial presentation. The treatment of ovarian cancer consists of a combination of cytoreductive surgery and systemic chemotherapy. Despite the advances with new cytotoxic and targeted therapies, the five-year survival rate for all-stage EOC in the United States is 48.6%. Delivery of up-to-date guideline care and multidisciplinary team efforts are important drivers of overall survival. In this paper, we review our frontline management of EOC that relies on a multi-disciplinary approach drawing on clinical expertise and collaboration combined with community practice and cutting edge clinical and translational research. By optimizing partnerships through team medicine and clinical research, we combine our cancer center clinical expertise, community practice partnership, and clinical and translational research to understand the biology of this deadly disease, advance therapy and connect our patients with the optimal treatment that offers the best possible outcomes.
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Dillon B, Feben C, Segal D, du Plessis J, Reynders D, Wainwright R, Poole J, Krause A. Endocrine profiling in patients with Fanconi anemia, homozygous for a FANCG founder mutation. Mol Genet Genomic Med 2020; 8:e1351. [PMID: 32529760 PMCID: PMC7434606 DOI: 10.1002/mgg3.1351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/12/2020] [Accepted: 05/19/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Fanconi anemia (FA) is phenotypically diverse, hereditary condition associated with bone marrow failure, multiple physical abnormalities, and an increased susceptibility to the development of malignancies. Less recognized manifestations of FA include endocrine abnormalities. International discourse has highlighted that these abnormalities are widespread among children and adults with FA. To date there has been no systematic study that has evaluated the endocrine abnormalities in a cohort of patients with FA, homozygous for a founder mutation (c.637_643del (p.Tyr213Lysfs*6)) in FANCG. The objectives of the study were to evaluate endocrine gland function in patients with FA of a single FA genotype, and to determine the frequency and nature of endocrine abnormalities in this group. METHODS Cross-sectional, descriptive study of 24 South African patients of African ancestry with FA (homozygous for a FANCG founder mutation). Outcomes measured included growth, pubertal status, growth hormone axis screening, thyroid gland function, glucose and insulin metabolism and bone age (BA). RESULTS Endocrine dysfunction was present in 70.8% (17 of 24), including abnormal insulin-like growth factor 1 (IGF-1)/insulin-like growth factor-binding protein 3 (IGFBP-3) in 25.0% (6 of 24), insulin resistance in 41.7% (10 of 24), abnormal thyroid function in 16.7% (4 of 24) and short stature in 45.8% (11 of 24). No abnormalities of glucose metabolism were identified. Abnormal pubertal status was seen in three males (12.5%). Abnormal BAs were present in 34.8% (8 of 23). CONCLUSION Endocrine abnormalities occur at a high frequency in patients with FA, homozygous for a FANCG founder mutation, similar to other FA cohorts. Our data are specific to FA patients with a single genotype, and therefore provide the first genotype-phenotype information on endocrine abnormalities in South African patients, homozygous for a FANCG founder mutation. Recommendations regarding endocrine screening in this patient subgroup are made, including, but not limited to, baseline testing of thyroid function, fasted insulin and glucose, and IGF-1 and IGFBP-3.
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Affiliation(s)
- Bronwyn Dillon
- Division of Human GeneticsNational Health Laboratory Service and School of PathologyFaculty of Health SciencesThe University of the WitwatersrandJohannesburgGautengSouth Africa
| | - Candice Feben
- Division of Human GeneticsNational Health Laboratory Service and School of PathologyFaculty of Health SciencesThe University of the WitwatersrandJohannesburgGautengSouth Africa
| | - David Segal
- The University of the Witwatersrand and The Wits University Donald Gordon Medical CentreJohannesburgGautengSouth Africa
| | - Johannes du Plessis
- Paediatric Oncology UnitUniversitas Hospital and The University of the Free StateBloemfonteinFree StateSouth Africa
| | - David Reynders
- Paediatric Haematology and Oncology UnitSteve Biko Academic Hospital and The University of PretoriaPretoriaGautengSouth Africa
| | - Rosalind Wainwright
- Department of Paediatric Haematology and OncologyChris Hani Baragwanath Academic Hospital and The University of the WitwatersrandJohannesburgGautengSouth Africa
| | - Janet Poole
- Department of Paediatric Haematology and OncologyCharlotte Maxeke Johannesburg Academic Hospital and The University of the WitwatersrandJohannesburgGautengSouth Africa
| | - Amanda Krause
- Division of Human GeneticsNational Health Laboratory Service and School of PathologyFaculty of Health SciencesThe University of the WitwatersrandJohannesburgGautengSouth Africa
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Sequential role of RAD51 paralog complexes in replication fork remodeling and restart. Nat Commun 2020; 11:3531. [PMID: 32669601 PMCID: PMC7363682 DOI: 10.1038/s41467-020-17324-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 06/16/2020] [Indexed: 12/19/2022] Open
Abstract
Homologous recombination (HR) factors were recently implicated in DNA replication fork remodeling and protection. While maintaining genome stability, HR-mediated fork remodeling promotes cancer chemoresistance, by as-yet elusive mechanisms. Five HR cofactors – the RAD51 paralogs RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3 – recently emerged as crucial tumor suppressors. Albeit extensively characterized in DNA repair, their role in replication has not been addressed systematically. Here, we identify all RAD51 paralogs while screening for modulators of RAD51 recombinase upon replication stress. Single-molecule analysis of fork progression and architecture in isogenic cellular systems shows that the BCDX2 subcomplex restrains fork progression upon stress, promoting fork reversal. Accordingly, BCDX2 primes unscheduled degradation of reversed forks in BRCA2-defective cells, boosting genomic instability. Conversely, the CX3 subcomplex is dispensable for fork reversal, but mediates efficient restart of reversed forks. We propose that RAD51 paralogs sequentially orchestrate clinically relevant transactions at replication forks, cooperatively promoting fork remodeling and restart. Replication stress has been associated with transient remodelling of replication intermediates into reversed forks, followed by efficient fork restart. Here the authors systematically analyse the role of RAD51 paralogs in these transactions, providing insights on the mechanistic role of different complexes of these proteins.
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DNA Repair and Ovarian Carcinogenesis: Impact on Risk, Prognosis and Therapy Outcome. Cancers (Basel) 2020; 12:cancers12071713. [PMID: 32605254 PMCID: PMC7408288 DOI: 10.3390/cancers12071713] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022] Open
Abstract
There is ample evidence for the essential involvement of DNA repair and DNA damage response in the onset of solid malignancies, including ovarian cancer. Indeed, high-penetrance germline mutations in DNA repair genes are important players in familial cancers: BRCA1, BRCA2 mutations or mismatch repair, and polymerase deficiency in colorectal, breast, and ovarian cancers. Recently, some molecular hallmarks (e.g., TP53, KRAS, BRAF, RAD51C/D or PTEN mutations) of ovarian carcinomas were identified. The manuscript overviews the role of DNA repair machinery in ovarian cancer, its risk, prognosis, and therapy outcome. We have attempted to expose molecular hallmarks of ovarian cancer with a focus on DNA repair system and scrutinized genetic, epigenetic, functional, and protein alterations in individual DNA repair pathways (homologous recombination, non-homologous end-joining, DNA mismatch repair, base- and nucleotide-excision repair, and direct repair). We suggest that lack of knowledge particularly in non-homologous end joining repair pathway and the interplay between DNA repair pathways needs to be confronted. The most important genes of the DNA repair system are emphasized and their targeting in ovarian cancer will deserve further attention. The function of those genes, as well as the functional status of the entire DNA repair pathways, should be investigated in detail in the near future.
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49
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Li N, McInerny S, Zethoven M, Cheasley D, Lim BWX, Rowley SM, Devereux L, Grewal N, Ahmadloo S, Byrne D, Lee JEA, Li J, Fox SB, John T, Antill Y, Gorringe KL, James PA, Campbell IG. Combined Tumor Sequencing and Case-Control Analyses of RAD51C in Breast Cancer. J Natl Cancer Inst 2020; 111:1332-1338. [PMID: 30949688 DOI: 10.1093/jnci/djz045] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/07/2019] [Accepted: 04/03/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Loss-of-function variants in RAD51C are associated with familial ovarian cancer, but its role in hereditary breast cancer remains unclear. The aim of this study was to couple breast tumor sequencing with case-control data to clarify the contribution of RAD51C to hereditary breast cancer. METHODS RAD51C was sequenced in 3080 breast cancer index cases that were negative in BRCA1/2 clinical tests and 4840 population-matched cancer-free controls. Pedigree and pathology data were analyzed. Nine breast cancers and one ovarian cancer from RAD51C variant carriers were sequenced to identify biallelic inactivation of RAD51C, copy number variation, mutational signatures, and the spectrum of somatic mutations in breast cancer driver genes. The promoter of RAD51C was analyzed for DNA methylation. RESULTS A statistically significant excess of loss-of-function variants was identified in 3080 cases (0.4%) compared with 2 among 4840 controls (0.04%; odds ratio = 8.67, 95% confidence interval = 1.89 to 80.52, P< .001), with more than half of the carriers having no personal or family history of ovarian cancer. In addition, the association was highly statistically significant among cases with estrogen-negative (P <. 001) or triple-negative cancer (P < .001), but not in estrogen-positive cases. Tumor sequencing from carriers confirmed bi-allelic inactivation in all the triple-negative cases and was associated with high homologous recombination deficiency scores and mutational signature 3 indicating homologous recombination repair deficiency. CONCLUSIONS This study provides evidence that germline loss-of-function variants of RAD51C are associated with hereditary breast cancer, particularly triple-negative type. RAD51C-null breast cancers possess similar genomic and clinical features to BRCA1-null cancers and may also be vulnerable to DNA double-strand break inducing chemotherapies and poly ADP-ribose polymerase inhibitors.
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50
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Rickman KA, Noonan RJ, Lach FP, Sridhar S, Wang AT, Abhyankar A, Huang A, Kelly M, Auerbach AD, Smogorzewska A. Distinct roles of BRCA2 in replication fork protection in response to hydroxyurea and DNA interstrand cross-links. Genes Dev 2020; 34:832-846. [PMID: 32354836 PMCID: PMC7263144 DOI: 10.1101/gad.336446.120] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/01/2020] [Indexed: 02/07/2023]
Abstract
DNA interstrand cross-links (ICLs) are a form of DNA damage that requires the interplay of a number of repair proteins including those of the Fanconi anemia (FA) and the homologous recombination (HR) pathways. Pathogenic variants in the essential gene BRCA2/FANCD1, when monoallelic, predispose to breast and ovarian cancer, and when biallelic, result in a severe subtype of Fanconi anemia. BRCA2 function in the FA pathway is attributed to its role as a mediator of the RAD51 recombinase in HR repair of programmed DNA double-strand breaks (DSB). BRCA2 and RAD51 functions are also required to protect stalled replication forks from nucleolytic degradation during response to hydroxyurea (HU). While RAD51 has been shown to be necessary in the early steps of ICL repair to prevent aberrant nuclease resection, the role of BRCA2 in this process has not been described. Here, based on the analysis of BRCA2 DNA-binding domain (DBD) mutants (c.8488-1G>A and c.8524C>T) discovered in FA patients presenting with atypical FA-like phenotypes, we establish that BRCA2 is necessary for the protection of DNA at ICLs. Cells carrying BRCA2 DBD mutations are sensitive to ICL-inducing agents but resistant to HU treatment consistent with relatively high HR repair in these cells. BRCA2 function at an ICL protects against DNA2-WRN nuclease-helicase complex and not the MRE11 nuclease that is implicated in the resection of HU-induced stalled replication forks. Our results also indicate that unlike the processing at HU-induced stalled forks, the function of the SNF2 translocases (SMARCAL1, ZRANB3, or HLTF), implicated in fork reversal, are not an integral component of the ICL repair, pointing to a different mechanism of fork protection at different DNA lesions.
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Affiliation(s)
- Kimberly A Rickman
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
| | - Raymond J Noonan
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
| | - Sunandini Sridhar
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
| | - Anderson T Wang
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
| | | | - Athena Huang
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
| | - Michael Kelly
- Tufts Medical Center, Boston, Massachusetts 02111, USA
| | - Arleen D Auerbach
- Human Genetics and Hematology, The Rockefeller University, New York, New York 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
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