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Bernkopf M, Abdullah UB, Bush SJ, Wood KA, Ghaffari S, Giannoulatou E, Koelling N, Maher GJ, Thibaut LM, Williams J, Blair EM, Kelly FB, Bloss A, Burkitt-Wright E, Canham N, Deng AT, Dixit A, Eason J, Elmslie F, Gardham A, Hay E, Holder M, Homfray T, Hurst JA, Johnson D, Jones WD, Kini U, Kivuva E, Kumar A, Lees MM, Leitch HG, Morton JEV, Németh AH, Ramachandrappa S, Saunders K, Shears DJ, Side L, Splitt M, Stewart A, Stewart H, Suri M, Clouston P, Davies RW, Wilkie AOM, Goriely A. Personalized recurrence risk assessment following the birth of a child with a pathogenic de novo mutation. Nat Commun 2023; 14:853. [PMID: 36792598 PMCID: PMC9932158 DOI: 10.1038/s41467-023-36606-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
Following the diagnosis of a paediatric disorder caused by an apparently de novo mutation, a recurrence risk of 1-2% is frequently quoted due to the possibility of parental germline mosaicism; but for any specific couple, this figure is usually incorrect. We present a systematic approach to providing individualized recurrence risk. By combining locus-specific sequencing of multiple tissues to detect occult mosaicism with long-read sequencing to determine the parent-of-origin of the mutation, we show that we can stratify the majority of couples into one of seven discrete categories associated with substantially different risks to future offspring. Among 58 families with a single affected offspring (representing 59 de novo mutations in 49 genes), the recurrence risk for 35 (59%) was decreased below 0.1%, but increased owing to parental mixed mosaicism for 5 (9%)-that could be quantified in semen for paternal cases (recurrence risks of 5.6-12.1%). Implementation of this strategy offers the prospect of driving a major transformation in the practice of genetic counselling.
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Affiliation(s)
- Marie Bernkopf
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ummi B Abdullah
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Stephen J Bush
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Katherine A Wood
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sahar Ghaffari
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Nils Koelling
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Geoffrey J Maher
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Loïc M Thibaut
- Centre for Population Genomics, Garvan Institute of Medical Research, UNSW Sydney, Sydney, NSW, Australia
| | - Jonathan Williams
- Oxford Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Edward M Blair
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Fiona Blanco Kelly
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Angela Bloss
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Emma Burkitt-Wright
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, UK
| | - Natalie Canham
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Alexander T Deng
- Clinical Genetics Department, Guy's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Abhijit Dixit
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Jacqueline Eason
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Frances Elmslie
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Alice Gardham
- North West Thames Regional Genetics Service, London North West University Healthcare NHS Trust, Northwick Park Hospital, Harrow, UK
| | - Eleanor Hay
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Muriel Holder
- Clinical Genetics Department, Guy's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Tessa Homfray
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Jane A Hurst
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Diana Johnson
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Wendy D Jones
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Usha Kini
- NIHR Oxford Biomedical Research Centre, Oxford, UK
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Emma Kivuva
- Clinical Genetics, Royal Devon & Exeter Hospital (Heavitree), Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Ajith Kumar
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Melissa M Lees
- North East Thames Regional Genetics Service, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Harry G Leitch
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
- MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Andrea H Németh
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Shwetha Ramachandrappa
- Clinical Genetics Department, Guy's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Katherine Saunders
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Deborah J Shears
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lucy Side
- Wessex Clinical Genetics Service, University Hospital Southampton, Princess Anne Hospital, Southampton, UK
| | - Miranda Splitt
- Northern Genetics Service, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Alison Stewart
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Mohnish Suri
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Penny Clouston
- Oxford Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | | | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anne Goriely
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford, UK.
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Amunugama R, Willcox S, Wu RA, Abdullah UB, El-Sagheer AH, Brown T, McHugh PJ, Griffith JD, Walter JC. Replication Fork Reversal during DNA Interstrand Crosslink Repair Requires CMG Unloading. Cell Rep 2019; 23:3419-3428. [PMID: 29924986 PMCID: PMC6086610 DOI: 10.1016/j.celrep.2018.05.061] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 03/29/2018] [Accepted: 05/17/2018] [Indexed: 01/08/2023] Open
Abstract
DNA interstrand crosslinks (ICLs) are extremely cytotoxic, but the mechanism of their repair remains incompletely understood. Using Xenopus egg extracts, we previously showed that repair of a cisplatin ICL is triggered when two replication forks converge on the lesion. After CDC45/MCM2-7/GINS (CMG) ubiquitylation and unloading by the p97 segregase, FANCI-FANCD2 promotes DNA incisions by XPF-ERCC1, leading to ICL unhooking. Here, we report that, during this cell-free ICL repair reaction, one of the two converged forks undergoes reversal. Fork reversal fails when CMG unloading is inhibited, but it does not require FANCI-FANCD2. After one fork has undergone reversal, the opposing fork that still abuts the ICL undergoes incisions. Our data show that replication fork reversal at an ICL requires replisome disassembly. We present a revised model of ICL repair that involves a reversed fork intermediate.
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Affiliation(s)
- Ravindra Amunugama
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - R Alex Wu
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ummi B Abdullah
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Tom Brown
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Johannes C Walter
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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Abdullah UB, McGouran JF, Brolih S, Ptchelkine D, El-Sagheer AH, Brown T, McHugh PJ. RPA activates the XPF-ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks. EMBO J 2017; 36:2047-2060. [PMID: 28607004 PMCID: PMC5510000 DOI: 10.15252/embj.201796664] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/13/2017] [Accepted: 05/19/2017] [Indexed: 12/11/2022] Open
Abstract
During replication-coupled DNA interstrand crosslink (ICL) repair, the XPF-ERCC1 endonuclease is required for the incisions that release, or "unhook", ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL Here, we report that while purified XPF-ERCC1 incises simple ICL-containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity. Strikingly, the addition of the single-stranded DNA (ssDNA)-binding replication protein A (RPA) selectively restores XPF-ERCC1 endonuclease activity on this structure. The 5'-3' exonuclease SNM1A can load from the XPF-ERCC1-RPA-induced incisions and digest past the crosslink to quantitatively complete the unhooking reaction. We postulate that these collaborative activities of XPF-ERCC1, RPA and SNM1A might explain how ICL unhooking is achieved in vivo.
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Affiliation(s)
- Ummi B Abdullah
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Sanja Brolih
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Denis Ptchelkine
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, UK
| | | | - Tom Brown
- Department of Chemistry, University of Oxford, Oxford, UK.,Department of Oncology, University of Oxford, Oxford, UK
| | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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