1
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Carnie CJ, Acampora AC, Bader AS, Erdenebat C, Zhao S, Bitensky E, van den Heuvel D, Parnas A, Gupta V, D'Alessandro G, Sczaniecka-Clift M, Weickert P, Aygenli F, Götz MJ, Cordes J, Esain-Garcia I, Melidis L, Wondergem AP, Lam S, Robles MS, Balasubramanian S, Adar S, Luijsterburg MS, Jackson SP, Stingele J. Transcription-coupled repair of DNA-protein cross-links depends on CSA and CSB. Nat Cell Biol 2024:10.1038/s41556-024-01391-1. [PMID: 38600235 DOI: 10.1038/s41556-024-01391-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 02/29/2024] [Indexed: 04/12/2024]
Abstract
Covalent DNA-protein cross-links (DPCs) are toxic DNA lesions that block replication and require repair by multiple pathways. Whether transcription blockage contributes to the toxicity of DPCs and how cells respond when RNA polymerases stall at DPCs is unknown. Here we find that DPC formation arrests transcription and induces ubiquitylation and degradation of RNA polymerase II. Using genetic screens and a method for the genome-wide mapping of DNA-protein adducts, DPC sequencing, we discover that Cockayne syndrome (CS) proteins CSB and CSA provide resistance to DPC-inducing agents by promoting DPC repair in actively transcribed genes. Consequently, CSB- or CSA-deficient cells fail to efficiently restart transcription after induction of DPCs. In contrast, nucleotide excision repair factors that act downstream of CSB and CSA at ultraviolet light-induced DNA lesions are dispensable. Our study describes a transcription-coupled DPC repair pathway and suggests that defects in this pathway may contribute to the unique neurological features of CS.
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Affiliation(s)
- Christopher J Carnie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Aleida C Acampora
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Aldo S Bader
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chimeg Erdenebat
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shubo Zhao
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Elnatan Bitensky
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Avital Parnas
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Giuseppina D'Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Pedro Weickert
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fatih Aygenli
- Institute of Medical Psychology and Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian J Götz
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacqueline Cordes
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Isabel Esain-Garcia
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Larry Melidis
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Annelotte P Wondergem
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Maria S Robles
- Institute of Medical Psychology and Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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2
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Adams DJ, Barlas B, McIntyre RE, Salguero I, van der Weyden L, Barros A, Vicente JR, Karimpour N, Haider A, Ranzani M, Turner G, Thompson NA, Harle V, Olvera-León R, Robles-Espinoza CD, Speak AO, Geisler N, Weninger WJ, Geyer SH, Hewinson J, Karp NA, Fu B, Yang F, Kozik Z, Choudhary J, Yu L, van Ruiten MS, Rowland BD, Lelliott CJ, Del Castillo Velasco-Herrera M, Verstraten R, Bruckner L, Henssen AG, Rooimans MA, de Lange J, Mohun TJ, Arends MJ, Kentistou KA, Coelho PA, Zhao Y, Zecchini H, Perry JRB, Jackson SP, Balmus G. Genetic determinants of micronucleus formation in vivo. Nature 2024; 627:130-136. [PMID: 38355793 PMCID: PMC10917660 DOI: 10.1038/s41586-023-07009-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/21/2023] [Indexed: 02/16/2024]
Abstract
Genomic instability arising from defective responses to DNA damage1 or mitotic chromosomal imbalances2 can lead to the sequestration of DNA in aberrant extranuclear structures called micronuclei (MN). Although MN are a hallmark of ageing and diseases associated with genomic instability, the catalogue of genetic players that regulate the generation of MN remains to be determined. Here we analyse 997 mouse mutant lines, revealing 145 genes whose loss significantly increases (n = 71) or decreases (n = 74) MN formation, including many genes whose orthologues are linked to human disease. We found that mice null for Dscc1, which showed the most significant increase in MN, also displayed a range of phenotypes characteristic of patients with cohesinopathy disorders. After validating the DSCC1-associated MN instability phenotype in human cells, we used genome-wide CRISPR-Cas9 screening to define synthetic lethal and synthetic rescue interactors. We found that the loss of SIRT1 can rescue phenotypes associated with DSCC1 loss in a manner paralleling restoration of protein acetylation of SMC3. Our study reveals factors involved in maintaining genomic stability and shows how this information can be used to identify mechanisms that are relevant to human disease biology1.
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Affiliation(s)
- D J Adams
- Wellcome Sanger Institute, Cambridge, UK.
| | - B Barlas
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - I Salguero
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - A Barros
- Wellcome Sanger Institute, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - J R Vicente
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - N Karimpour
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - A Haider
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - M Ranzani
- Wellcome Sanger Institute, Cambridge, UK
| | - G Turner
- Wellcome Sanger Institute, Cambridge, UK
| | | | - V Harle
- Wellcome Sanger Institute, Cambridge, UK
| | | | - C D Robles-Espinoza
- Wellcome Sanger Institute, Cambridge, UK
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, México
| | - A O Speak
- Wellcome Sanger Institute, Cambridge, UK
| | - N Geisler
- Wellcome Sanger Institute, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W J Weninger
- Division of Anatomy, MIC, Medical University of Vienna, Wien, Austria
| | - S H Geyer
- Division of Anatomy, MIC, Medical University of Vienna, Wien, Austria
| | - J Hewinson
- Wellcome Sanger Institute, Cambridge, UK
| | - N A Karp
- Wellcome Sanger Institute, Cambridge, UK
| | - B Fu
- Wellcome Sanger Institute, Cambridge, UK
| | - F Yang
- Wellcome Sanger Institute, Cambridge, UK
| | - Z Kozik
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - J Choudhary
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - L Yu
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - M S van Ruiten
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - B D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - L Bruckner
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - A G Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M A Rooimans
- Department of Human Genetics, Section of Oncogenetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - J de Lange
- Department of Human Genetics, Section of Oncogenetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - T J Mohun
- Division of Developmental Biology, MRC, National Institute for Medical Research, London, UK
| | - M J Arends
- Division of Pathology, Cancer Research UK Scotland Centre, Institute of Genetics & Cancer The University of Edinburgh, Edinburgh, UK
| | - K A Kentistou
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - P A Coelho
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Y Zhao
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - H Zecchini
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - J R B Perry
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - S P Jackson
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - G Balmus
- Wellcome Sanger Institute, Cambridge, UK.
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK.
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Department of Molecular Neuroscience, Transylvanian Institute of Neuroscience, Cluj-Napoca, Romania.
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3
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D’Alessandro G, Morales-Juarez DA, Richards SL, Nitiss KC, Serrano-Benitez A, Wang J, Thomas JC, Gupta V, Voigt A, Belotserkovskaya R, Goh CG, Bowden AR, Galanty Y, Beli P, Nitiss JL, Zagnoli-Vieira G, Jackson SP. RAD54L2 counters TOP2-DNA adducts to promote genome stability. Sci Adv 2023; 9:eadl2108. [PMID: 38055822 PMCID: PMC10699776 DOI: 10.1126/sciadv.adl2108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
The catalytic cycle of topoisomerase 2 (TOP2) enzymes proceeds via a transient DNA double-strand break (DSB) intermediate termed the TOP2 cleavage complex (TOP2cc), in which the TOP2 protein is covalently bound to DNA. Anticancer agents such as etoposide operate by stabilizing TOP2ccs, ultimately generating genotoxic TOP2-DNA protein cross-links that require processing and repair. Here, we identify RAD54 like 2 (RAD54L2) as a factor promoting TOP2cc resolution. We demonstrate that RAD54L2 acts through a novel mechanism together with zinc finger protein associated with tyrosyl-DNA phosphodiesterase 2 (TDP2) and TOP2 (ZATT/ZNF451) and independent of TDP2. Our work suggests a model wherein RAD54L2 recognizes sumoylated TOP2 and, using its ATPase activity, promotes TOP2cc resolution and prevents DSB exposure. These findings suggest RAD54L2-mediated TOP2cc resolution as a potential mechanism for cancer therapy resistance and highlight RAD54L2 as an attractive candidate for drug discovery.
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Affiliation(s)
- Giuseppina D’Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Sean L. Richards
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Juanjuan Wang
- Institute of Molecular Biology (IMB), Chromatin Biology & Proteomics, Mainz, Germany
| | - John C. Thomas
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Andrea Voigt
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Rimma Belotserkovskaya
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chen Gang Goh
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anne Ramsay Bowden
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Yaron Galanty
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Chromatin Biology & Proteomics, Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | | | - Guido Zagnoli-Vieira
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Stephen P. Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
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4
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Fang TSZ, Sun Y, Pearce AC, Eleuteri S, Kemp M, Luckhurst CA, Williams R, Mills R, Almond S, Burzynski L, Márkus NM, Lelliott CJ, Karp NA, Adams DJ, Jackson SP, Zhao JF, Ganley IG, Thompson PW, Balmus G, Simon DK. Knockout or inhibition of USP30 protects dopaminergic neurons in a Parkinson's disease mouse model. Nat Commun 2023; 14:7295. [PMID: 37957154 PMCID: PMC10643470 DOI: 10.1038/s41467-023-42876-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
Mutations in SNCA, the gene encoding α-synuclein (αSyn), cause familial Parkinson's disease (PD) and aberrant αSyn is a key pathological hallmark of idiopathic PD. This α-synucleinopathy leads to mitochondrial dysfunction, which may drive dopaminergic neurodegeneration. PARKIN and PINK1, mutated in autosomal recessive PD, regulate the preferential autophagic clearance of dysfunctional mitochondria ("mitophagy") by inducing ubiquitylation of mitochondrial proteins, a process counteracted by deubiquitylation via USP30. Here we show that loss of USP30 in Usp30 knockout mice protects against behavioral deficits and leads to increased mitophagy, decreased phospho-S129 αSyn, and attenuation of SN dopaminergic neuronal loss induced by αSyn. These observations were recapitulated with a potent, selective, brain-penetrant USP30 inhibitor, MTX115325, with good drug-like properties. These data strongly support further study of USP30 inhibition as a potential disease-modifying therapy for PD.
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Affiliation(s)
- Tracy-Shi Zhang Fang
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
| | - Yu Sun
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH, UK
| | - Andrew C Pearce
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Simona Eleuteri
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Mark Kemp
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Christopher A Luckhurst
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Rachel Williams
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Ross Mills
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Sarah Almond
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Laura Burzynski
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | - Nóra M Márkus
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
| | | | | | | | - Stephen P Jackson
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0RE, UK
| | - Jin-Feng Zhao
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Ian G Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Paul W Thompson
- Mission Therapeutics Ltd. Glenn Berge Building, Babraham Research Campus, Cambridge, CB22 3FH, UK.
| | - Gabriel Balmus
- UK Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0AH, UK.
- Department of Molecular Neuroscience, Transylvanian Institute of Neuroscience, 400191, Cluj-Napoca, Romania.
| | - David K Simon
- Department of Neurology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
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5
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Serrano‐Benitez A, Wells SE, Drummond‐Clarke L, Russo LC, Thomas JC, Leal GA, Farrow M, Edgerton JM, Balasubramanian S, Yang M, Frezza C, Gautam A, Brazina J, Burdova K, Hoch NC, Jackson SP, Caldecott KW. Unrepaired base excision repair intermediates in template DNA strands trigger replication fork collapse and PARP inhibitor sensitivity. EMBO J 2023; 42:e113190. [PMID: 37492888 PMCID: PMC10505916 DOI: 10.15252/embj.2022113190] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/17/2023] [Accepted: 07/07/2023] [Indexed: 07/27/2023] Open
Abstract
DNA single-strand breaks (SSBs) disrupt DNA replication and induce chromosome breakage. However, whether SSBs induce chromosome breakage when present behind replication forks or ahead of replication forks is unclear. To address this question, we exploited an exquisite sensitivity of SSB repair-defective human cells lacking PARP activity or XRCC1 to the thymidine analogue 5-chloro-2'-deoxyuridine (CldU). We show that incubation with CldU in these cells results in chromosome breakage, sister chromatid exchange, and cytotoxicity by a mechanism that depends on the S phase activity of uracil DNA glycosylase (UNG). Importantly, we show that CldU incorporation in one cell cycle is cytotoxic only during the following cell cycle, when it is present in template DNA. In agreement with this, while UNG induces SSBs both in nascent strands behind replication forks and in template strands ahead of replication forks, only the latter trigger fork collapse and chromosome breakage. Finally, we show that BRCA-defective cells are hypersensitive to CldU, either alone and/or in combination with PARP inhibitor, suggesting that CldU may have clinical utility.
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Affiliation(s)
- Almudena Serrano‐Benitez
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- The Wellcome and Cancer Research UK Gurdon Institute and Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Sophie E Wells
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Lylah Drummond‐Clarke
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Lilian C Russo
- Departament of Biochemistry, Chemistry InstituteUniversity of São PauloSão PauloBrazil
| | - John Christopher Thomas
- The Wellcome and Cancer Research UK Gurdon Institute and Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Giovanna A Leal
- Departament of Biochemistry, Chemistry InstituteUniversity of São PauloSão PauloBrazil
| | - Mark Farrow
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | | | - Shankar Balasubramanian
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Ming Yang
- CECAD Research Center, Faculty of MedicineUniversity Hospital CologneCologneGermany
| | - Christian Frezza
- CECAD Research Center, Faculty of MedicineUniversity Hospital CologneCologneGermany
| | - Amit Gautam
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Jan Brazina
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Kamila Burdova
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Nicolas C Hoch
- Departament of Biochemistry, Chemistry InstituteUniversity of São PauloSão PauloBrazil
| | - Stephen P Jackson
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- The Wellcome and Cancer Research UK Gurdon Institute and Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
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6
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Kaisinger LR, Kentistou KA, Stankovic S, Gardner EJ, Day FR, Zhao Y, Mörseburg A, Carnie CJ, Zagnoli-Vieira G, Puddu F, Jackson SP, O’Rahilly S, Farooqi IS, Dearden L, Pantaleão LC, Ozanne SE, Ong KK, Perry JR. Large-scale exome sequence analysis identifies sex- and age-specific determinants of obesity. Cell Genom 2023; 3:100362. [PMID: 37601970 PMCID: PMC10435378 DOI: 10.1016/j.xgen.2023.100362] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/15/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023]
Abstract
Obesity contributes substantially to the global burden of disease and has a significant heritable component. Recent large-scale exome sequencing studies identified several genes in which rare, protein-coding variants have large effects on adult body mass index (BMI). Here we extended such work by performing sex-stratified associations in the UK Biobank study (N∼420,000). We identified genes in which rare heterozygous loss-of-function increases adult BMI in women (DIDO1, PTPRG, and SLC12A5) and in men (SLTM), with effect sizes up to ∼8 kg/m2. This is complemented by analyses implicating rare variants in OBSCN and MADD for recalled childhood adiposity. The known functions of these genes, as well as findings of common variant genome-wide pathway enrichment analyses, suggest a role for neuron death, apoptosis, and DNA damage response mechanisms in the susceptibility to obesity across the life-course. These findings highlight the importance of considering sex-specific and life-course effects in the genetic regulation of obesity.
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Affiliation(s)
- Lena R. Kaisinger
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Katherine A. Kentistou
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Stasa Stankovic
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Eugene J. Gardner
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Felix R. Day
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Yajie Zhao
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Alexander Mörseburg
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Christopher J. Carnie
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Cancer Research UK Cambridge Institute, Li Ka Shing Building, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Guido Zagnoli-Vieira
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Fabio Puddu
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Stephen P. Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Cancer Research UK Cambridge Institute, Li Ka Shing Building, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
| | - Stephen O’Rahilly
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - I. Sadaf Farooqi
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Laura Dearden
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Lucas C. Pantaleão
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Susan E. Ozanne
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Ken K. Ong
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - John R.B. Perry
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
- MRC Metabolic Diseases Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
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7
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Awwad SW, Serrano-Benitez A, Thomas JC, Gupta V, Jackson SP. Revolutionizing DNA repair research and cancer therapy with CRISPR-Cas screens. Nat Rev Mol Cell Biol 2023; 24:477-494. [PMID: 36781955 DOI: 10.1038/s41580-022-00571-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 02/15/2023]
Abstract
All organisms possess molecular mechanisms that govern DNA repair and associated DNA damage response (DDR) processes. Owing to their relevance to human disease, most notably cancer, these mechanisms have been studied extensively, yet new DNA repair and/or DDR factors and functional interactions between them are still being uncovered. The emergence of CRISPR technologies and CRISPR-based genetic screens has enabled genome-scale analyses of gene-gene and gene-drug interactions, thereby providing new insights into cellular processes in distinct DDR-deficiency genetic backgrounds and conditions. In this Review, we discuss the mechanistic basis of CRISPR-Cas genetic screening approaches and describe how they have contributed to our understanding of DNA repair and DDR pathways. We discuss how DNA repair pathways are regulated, and identify and characterize crosstalk between them. We also highlight the impacts of CRISPR-based studies in identifying novel strategies for cancer therapy, and in understanding, overcoming and even exploiting cancer-drug resistance, for example in the contexts of PARP inhibition, homologous recombination deficiencies and/or replication stress. Lastly, we present the DDR CRISPR screen (DDRcs) portal , in which we have collected and reanalysed data from CRISPR screen studies and provide a tool for systematically exploring them.
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Affiliation(s)
- Samah W Awwad
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - John C Thomas
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
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8
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Morales-Juarez DA, Jackson SP. Clinical prospects of WRN inhibition as a treatment for MSI tumours. NPJ Precis Oncol 2022; 6:85. [DOI: 10.1038/s41698-022-00319-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022] Open
Abstract
AbstractThe discovery of synthetic lethal interactions with genetic deficiencies in cancers has highlighted several candidate targets for drug development, with variable clinical success. Recent work has unveiled a promising synthetic lethal interaction between inactivation/inhibition of the WRN DNA helicase and tumours with microsatellite instability, a phenotype that arises from DNA mismatch repair deficiency. While these and further studies have highlighted the therapeutic potential of WRN inhibitors, compounds with properties suitable for clinical exploitation remain to be described. Furthermore, the complexities of MSI development and its relationship to cancer evolution pose challenges for clinical prospects. Here, we discuss possible paths of MSI tumour development, the viability of WRN inhibition as a strategy in different scenarios, and the necessary conditions to create a roadmap towards successful implementation of WRN inhibitors in the clinic.
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9
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Sun D, Llora Batlle O, van den Ameele J, Thomas JC, He P, Lim K, Tang W, Xu C, Meyer KB, Teichmann SA, Marioni JC, Jackson SP, Brand AH, Rawlins EL. SOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling. EMBO J 2022; 41:e111338. [PMID: 36121125 PMCID: PMC9627674 DOI: 10.15252/embj.2022111338] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 12/01/2022] Open
Abstract
The balance between self-renewal and differentiation in human foetal lung epithelial progenitors controls the size and function of the adult organ. Moreover, progenitor cell gene regulation networks are employed by both regenerating and malignant lung cells, where modulators of their effects could potentially be of therapeutic value. Details of the molecular networks controlling human lung progenitor self-renewal remain unknown. We performed the first CRISPRi screen in primary human lung organoids to identify transcription factors controlling progenitor self-renewal. We show that SOX9 promotes proliferation of lung progenitors and inhibits precocious airway differentiation. Moreover, by identifying direct transcriptional targets using Targeted DamID, we place SOX9 at the centre of a transcriptional network, which amplifies WNT and RTK signalling to stabilise the progenitor cell state. In addition, the proof-of-principle CRISPRi screen and Targeted DamID tools establish a new workflow for using primary human organoids to elucidate detailed functional mechanisms underlying normal development and disease.
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Affiliation(s)
- Dawei Sun
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Oriol Llora Batlle
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Jelle van den Ameele
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
- Present address:
Department of Clinical Neurosciences and MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - John C Thomas
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Peng He
- Wellcome Sanger InstituteCambridgeUK
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Kyungtae Lim
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Walfred Tang
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Chufan Xu
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Present address:
Department of Anaesthesiology and Surgical Intensive Care Unit, Xinhua HospitalShanghai Jiaotong University School of MedicineShanghaiChina
| | | | - Sarah A Teichmann
- Wellcome Sanger InstituteCambridgeUK
- Department of Physics/Cavendish LaboratoryUniversity of CambridgeCambridgeUK
| | - John C Marioni
- Wellcome Sanger InstituteCambridgeUK
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)CambridgeUK
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
| | - Stephen P Jackson
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Andrea H Brand
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Emma L Rawlins
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
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10
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Jackson SP. Abstract PL06-03: Exploiting genome instability for new cancer therapies: PARP inhibitors and beyond. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-pl06-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
As DNA is frequently subject to a wide array of molecularly distinct forms of damage, life has evolved multiple DNA repair and associated processes, collectively termed the DNA-damage response (DDR). The importance of DNA repair and other DDR mechanisms is underlined by their deregulation or loss causing cancer and various human genetic disorders. Work in my laboratory aims to decipher DDR mechanisms, particularly those triggered by DNA double-strand breaks. In my talk, I will begin by briefly summarising past work by me and my collaborators that led to the world's first registered DDR enzyme inhibitor drug - the PARP inhibitor olaparib/Lynparza. I will then describe some of our recent work using CRISPR-Cas9 genetic screens to discover new DDR factors/regulators, identify potential new avenues for anti-cancer therapy, and help us understand how cancer cells can evolve resistance to DNA-damaging chemotherapies, PARP inhibitors or other DDR enzyme inhibitors.
Citation Format: Stephen P. Jackson. Exploiting genome instability for new cancer therapies: PARP inhibitors and beyond [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr PL06-03.
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11
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Abstract
The DNA damage response (DDR) fulfils essential roles to preserve genome integrity. Targeting the DDR in tumors has had remarkable success over the last decade, exemplified by the licensing of PARP inhibitors for cancer therapy. Recent studies suggest that the application of DDR inhibitors impacts on cellular innate and adaptive immune responses, wherein key DNA repair factors have roles in limiting chronic inflammatory signaling. Antitumor immunity plays an emerging part in cancer therapy, and extensive efforts have led to the development of immune checkpoint inhibitors overcoming immune suppressive signals in tumors. Here, we review the current understanding of the molecular mechanisms underlying DNA damage-triggered immune responses, including cytosolic DNA sensing via the cGAS/STING pathway. We highlight the implications of DDR components for therapeutic outcomes of immune checkpoint inhibitors or their use as biomarkers. Finally, we discuss the rationale for novel combinations of DDR inhibitors with antagonists of immune checkpoints and current hindrances limiting their broader therapeutic applications.
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Affiliation(s)
- Domenic Pilger
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Leonard W Seymour
- Department of Oncology, University of Oxford, Oxford, Oxford OX3 7DQ, United Kingdom
| | - Stephen P Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
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12
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Herzog M, Alonso-Perez E, Salguero I, Warringer J, Adams D, Jackson SP, Puddu F. Mutagenic mechanisms of cancer-associated DNA polymerase ϵ alleles. Nucleic Acids Res 2021; 49:3919-3931. [PMID: 33764464 PMCID: PMC8053093 DOI: 10.1093/nar/gkab160] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/03/2021] [Indexed: 01/08/2023] Open
Abstract
A single amino acid residue change in the exonuclease domain of human DNA polymerase ϵ, P286R, is associated with the development of colorectal cancers, and has been shown to impart a mutator phenotype. The corresponding Pol ϵ allele in the yeast Saccharomyces cerevisiae (pol2-P301R), was found to drive greater mutagenesis than an entirely exonuclease-deficient Pol ϵ (pol2-4), an unexpected phenotype of ultra-mutagenesis. By studying the impact on mutation frequency, type, replication-strand bias, and sequence context, we show that ultra-mutagenesis is commonly observed in yeast cells carrying a range of cancer-associated Pol ϵ exonuclease domain alleles. Similarities between mutations generated by these alleles and those generated in pol2-4 cells indicate a shared mechanism of mutagenesis that yields a mutation pattern similar to cancer Signature 14. Comparison of POL2 ultra-mutator with pol2-M644G, a mutant in the polymerase domain decreasing Pol ϵ fidelity, revealed unexpected analogies in the sequence context and strand bias of mutations. Analysis of mutational patterns unique to exonuclease domain mutant cells suggests that backtracking of the polymerase, when the mismatched primer end cannot be accommodated in the proofreading domain, results in the observed insertions and T>A mutations in specific sequence contexts.
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Affiliation(s)
- Mareike Herzog
- The Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- The Wellcome Sanger Institute, Hinxton CB10 1HH, UK
| | - Elisa Alonso-Perez
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9 C, 413 90, Göteborg, Sweden
| | - Israel Salguero
- The Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9 C, 413 90, Göteborg, Sweden
| | | | - Stephen P Jackson
- The Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Fabio Puddu
- The Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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13
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Thompson NA, Ranzani M, van der Weyden L, Iyer V, Offord V, Droop A, Behan F, Gonçalves E, Speak A, Iorio F, Hewinson J, Harle V, Robertson H, Anderson E, Fu B, Yang F, Zagnoli-Vieira G, Chapman P, Del Castillo Velasco-Herrera M, Garnett MJ, Jackson SP, Adams DJ. Combinatorial CRISPR screen identifies fitness effects of gene paralogues. Nat Commun 2021; 12:1302. [PMID: 33637726 PMCID: PMC7910459 DOI: 10.1038/s41467-021-21478-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
Genetic redundancy has evolved as a way for human cells to survive the loss of genes that are single copy and essential in other organisms, but also allows tumours to survive despite having highly rearranged genomes. In this study we CRISPR screen 1191 gene pairs, including paralogues and known and predicted synthetic lethal interactions to identify 105 gene combinations whose co-disruption results in a loss of cellular fitness. 27 pairs influence fitness across multiple cell lines including the paralogues FAM50A/FAM50B, two genes of unknown function. Silencing of FAM50B occurs across a range of tumour types and in this context disruption of FAM50A reduces cellular fitness whilst promoting micronucleus formation and extensive perturbation of transcriptional programmes. Our studies reveal the fitness effects of FAM50A/FAM50B in cancer cells.
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Affiliation(s)
- Nicola A Thompson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Marco Ranzani
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Vivek Iyer
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Victoria Offord
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Alastair Droop
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Fiona Behan
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Emanuel Gonçalves
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Anneliese Speak
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Francesco Iorio
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Human Technopole, Milano, Italy
| | - James Hewinson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Victoria Harle
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Holly Robertson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Beiyuan Fu
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Phil Chapman
- Cancer Research UK, Manchester Institute, Manchester, UK
| | | | - Mathew J Garnett
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - David J Adams
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
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14
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Webber M, Jackson SP, Moon JC, Captur G. Myocardial Fibrosis in Heart Failure: Anti-Fibrotic Therapies and the Role of Cardiovascular Magnetic Resonance in Drug Trials. Cardiol Ther 2020; 9:363-376. [PMID: 32862327 PMCID: PMC7584719 DOI: 10.1007/s40119-020-00199-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Indexed: 12/14/2022] Open
Abstract
All heart muscle diseases that cause chronic heart failure finally converge into one dreaded pathological process that is myocardial fibrosis. Myocardial fibrosis predicts major adverse cardiovascular events and death, yet we are still missing the targeted therapies capable of halting and/or reversing its progression. Fundamentally it is a problem of disproportionate extracellular collagen accumulation that is part of normal myocardial ageing and accentuated in certain disease states. In this article we discuss the role of cardiovascular magnetic resonance (CMR) imaging biomarkers to track fibrosis and collate results from the most promising animal and human trials of anti-fibrotic therapies to date. We underscore the ever-growing role of CMR in determining the efficacy of such drugs and encourage future trialists to turn to CMR when designing their surrogate study endpoints.
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Affiliation(s)
- Matthew Webber
- UCL MRC Unit for Lifelong Health and Ageing, University College London, Fitzrovia, London, WC1E 7HB, UK
- Cardiology Department, Centre for Inherited Heart Muscle Conditions, The Royal Free Hospital, Pond Street, Hampstead, London, NW3 2QG, UK
- UCL Institute of Cardiovascular Science, University College London, Gower Street, London, WC1E 6BT, UK
| | - Stephen P Jackson
- Department of Biochemistry, The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK
| | - James C Moon
- UCL Institute of Cardiovascular Science, University College London, Gower Street, London, WC1E 6BT, UK
- Cardiovascular Magnetic Resonance Unit, Barts Heart Centre, West Smithfield, London, UK
| | - Gabriella Captur
- UCL MRC Unit for Lifelong Health and Ageing, University College London, Fitzrovia, London, WC1E 7HB, UK.
- Cardiology Department, Centre for Inherited Heart Muscle Conditions, The Royal Free Hospital, Pond Street, Hampstead, London, NW3 2QG, UK.
- UCL Institute of Cardiovascular Science, University College London, Gower Street, London, WC1E 6BT, UK.
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15
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Abstract
The acquisition of mutations plays critical roles in adaptation, evolution, senescence, and tumorigenesis. Massive genome sequencing has allowed extraction of specific features of many mutational landscapes but it remains difficult to retrospectively determine the mechanistic origin(s), selective forces, and trajectories of transient or persistent mutations and genome rearrangements. Here, we conducted a prospective reciprocal approach to inactivate 13 single or multiple evolutionary conserved genes involved in distinct genome maintenance processes and characterize de novo mutations in 274 diploid Saccharomyces cerevisiae mutation accumulation lines. This approach revealed the diversity, complexity, and ultimate uniqueness of mutational landscapes, differently composed of base substitutions, small insertions/deletions (InDels), structural variants, and/or ploidy variations. Several landscapes parallel the repertoire of mutational signatures in human cancers while others are either novel or composites of subsignatures resulting from distinct DNA damage lesions. Notably, the increase of base substitutions in the homologous recombination-deficient Rad51 mutant, specifically dependent on the Polζ translesion polymerase, yields COSMIC signature 3 observed in BRCA1/BRCA2-mutant breast cancer tumors. Furthermore, "mutome" analyses in highly polymorphic diploids and single-cell bottleneck lineages revealed a diverse spectrum of loss-of-heterozygosity (LOH) signatures characterized by interstitial and terminal chromosomal events resulting from interhomolog mitotic cross-overs. Following the appearance of heterozygous mutations, the strong stimulation of LOHs in the rad27/FEN1 and tsa1/PRDX1 backgrounds leads to fixation of homozygous mutations or their loss along the lineage. Overall, these mutomes and their trajectories provide a mechanistic framework to understand the origin and dynamics of genome variations that accumulate during clonal evolution.
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Affiliation(s)
- Sophie Loeillet
- Institut Curie, Paris Sciences et Lettres Research University, CNRS, UMR3244, 75248 Paris Cedex 05, France
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, CNRS, UMR3244, 75248 Paris Cedex 05, France
| | - Mareike Herzog
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, Cambridge CB2 1QN, United Kingdom
| | - Fabio Puddu
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, Cambridge CB2 1QN, United Kingdom
| | - Patricia Legoix
- ICGex NGS Platform, Institut Curie, 75248 Paris Cedex 05, France
| | - Sylvain Baulande
- ICGex NGS Platform, Institut Curie, 75248 Paris Cedex 05, France
| | - Stephen P Jackson
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, Cambridge CB2 1QN, United Kingdom
| | - Alain G Nicolas
- Institut Curie, Paris Sciences et Lettres Research University, CNRS, UMR3244, 75248 Paris Cedex 05, France;
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, CNRS, UMR3244, 75248 Paris Cedex 05, France
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16
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Berquez M, Gadsby JR, Festa BP, Butler R, Jackson SP, Berno V, Luciani A, Devuyst O, Gallop JL. The phosphoinositide 3-kinase inhibitor alpelisib restores actin organization and improves proximal tubule dysfunction in vitro and in a mouse model of Lowe syndrome and Dent disease. Kidney Int 2020; 98:883-896. [PMID: 32919786 PMCID: PMC7550850 DOI: 10.1016/j.kint.2020.05.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 05/01/2020] [Accepted: 05/15/2020] [Indexed: 12/19/2022]
Abstract
Loss-of-function mutations in the OCRL gene, which encodes the phosphatidylinositol [PI] 4,5-bisphosphate [PI(4,5)P2] 5-phosphatase OCRL, cause defective endocytosis and proximal tubule dysfunction in Lowe syndrome and Dent disease 2. The defect is due to increased levels of PI(4,5)P2 and aberrant actin polymerization, blocking endosomal trafficking. PI 3-phosphate [PI(3)P] has been recently identified as a coactivator with PI(4,5)P2 in the actin pathway. Here, we tested the hypothesis that phosphoinositide 3-kinase (PI3K) inhibitors may rescue the endocytic defect imparted by OCRL loss, by rebalancing phosphoinositide signals to the actin machinery. The broad-range PI3K inhibitor copanlisib and class IA p110α PI3K inhibitor alpelisib reduced aberrant actin polymerization in OCRL-deficient human kidney cells in vitro. Levels of PI 3,4,5-trisphosphate, PI(4,5)P2 and PI(3)P were all reduced with alpelisib treatment, and siRNA knockdown of the PI3K catalytic subunit p110α phenocopied the actin phenotype. In a humanized OcrlY/- mouse model, alpelisib reduced endosomal actin staining while restoring stress fiber architecture and levels of megalin at the plasma membrane of proximal tubule cells, reflected by improved endocytic uptake of low molecular weight proteins in vivo. Thus, our findings support the link between phosphoinositide lipids, actin polymerization and endocytic trafficking in the proximal tubule and represent a proof-of-concept for repurposing alpelisib in Lowe syndrome/Dent disease 2.
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Affiliation(s)
- Marine Berquez
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Jonathan R Gadsby
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Richard Butler
- Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Stephen P Jackson
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Valeria Berno
- Experimental Imaging Center, ALEMBIC, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland.
| | - Jennifer L Gallop
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
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17
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Ochi T, Quarantotti V, Lin H, Jullien J, Rosa E Silva I, Boselli F, Barnabas DD, Johnson CM, McLaughlin SH, Freund SMV, Blackford AN, Kimata Y, Goldstein RE, Jackson SP, Blundell TL, Dutcher SK, Gergely F, van Breugel M. CCDC61/VFL3 Is a Paralog of SAS6 and Promotes Ciliary Functions. Structure 2020; 28:674-689.e11. [PMID: 32375023 PMCID: PMC7267773 DOI: 10.1016/j.str.2020.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 10/25/2019] [Revised: 02/24/2020] [Accepted: 04/11/2020] [Indexed: 01/08/2023]
Abstract
Centrioles are cylindrical assemblies whose peripheral microtubule array displays a 9-fold rotational symmetry that is established by the scaffolding protein SAS6. Centriole symmetry can be broken by centriole-associated structures, such as the striated fibers in Chlamydomonas that are important for ciliary function. The conserved protein CCDC61/VFL3 is involved in this process, but its exact role is unclear. Here, we show that CCDC61 is a paralog of SAS6. Crystal structures of CCDC61 demonstrate that it contains two homodimerization interfaces that are similar to those found in SAS6, but result in the formation of linear filaments rather than rings. Furthermore, we show that CCDC61 binds microtubules and that residues involved in CCDC61 microtubule binding are important for ciliary function in Chlamydomonas. Together, our findings suggest that CCDC61 and SAS6 functionally diverged from a common ancestor while retaining the ability to scaffold the assembly of basal body-associated structures or centrioles, respectively.
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Affiliation(s)
- Takashi Ochi
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Valentina Quarantotti
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Huawen Lin
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Jerome Jullien
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; CRTI, INSERM, UNIV Nantes, Nantes, France
| | - Ivan Rosa E Silva
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Francesco Boselli
- DAMTP, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Deepak D Barnabas
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher M Johnson
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephen H McLaughlin
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stefan M V Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Yuu Kimata
- Department of Genetics, University of Cambridge, Cambridge CB4 1AR, UK; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Raymond E Goldstein
- DAMTP, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Stephen P Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Susan K Dutcher
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, St Louis, MO 63110, USA
| | - Fanni Gergely
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Mark van Breugel
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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18
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Bowden AR, Morales-Juarez DA, Sczaniecka-Clift M, Agudo MM, Lukashchuk N, Thomas JC, Jackson SP. Parallel CRISPR-Cas9 screens clarify impacts of p53 on screen performance. eLife 2020; 9:e55325. [PMID: 32441252 PMCID: PMC7244323 DOI: 10.7554/elife.55325] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/23/2020] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas9 genome engineering has revolutionised high-throughput functional genomic screens. However, recent work has raised concerns regarding the performance of CRISPR-Cas9 screens using TP53 wild-type human cells due to a p53-mediated DNA damage response (DDR) limiting the efficiency of generating viable edited cells. To directly assess the impact of cellular p53 status on CRISPR-Cas9 screen performance, we carried out parallel CRISPR-Cas9 screens in wild-type and TP53 knockout human retinal pigment epithelial cells using a focused dual guide RNA library targeting 852 DDR-associated genes. Our work demonstrates that although functional p53 status negatively affects identification of significantly depleted genes, optimal screen design can nevertheless enable robust screen performance. Through analysis of our own and published screen data, we highlight key factors for successful screens in both wild-type and p53-deficient cells.
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Affiliation(s)
- Anne Ramsay Bowden
- Wellcome/Cancer Research UK Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | - David A Morales-Juarez
- Wellcome/Cancer Research UK Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | | | - Maria Martin Agudo
- Wellcome/Cancer Research UK Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | - Natalia Lukashchuk
- Wellcome/Cancer Research UK Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | - John Christopher Thomas
- Wellcome/Cancer Research UK Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
| | - Stephen P Jackson
- Wellcome/Cancer Research UK Gurdon Institute, University of CambridgeCambridgeUnited Kingdom
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19
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Lowe DJ, Herzog M, Mosler T, Cohen H, Felton S, Beli P, Raj K, Galanty Y, Jackson SP. Chronic irradiation of human cells reduces histone levels and deregulates gene expression. Sci Rep 2020; 10:2200. [PMID: 32042076 PMCID: PMC7010678 DOI: 10.1038/s41598-020-59163-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/24/2020] [Indexed: 01/10/2023] Open
Abstract
Over the past decades, there have been huge advances in understanding cellular responses to ionising radiation (IR) and DNA damage. These studies, however, were mostly executed with cell lines and mice using single or multiple acute doses of radiation. Hence, relatively little is known about how continuous exposure to low dose ionising radiation affects normal cells and organisms, even though our cells are constantly exposed to low levels of radiation. We addressed this issue by examining the consequences of exposing human primary cells to continuous ionising γ-radiation delivered at 6-20 mGy/h. Although these dose rates are estimated to inflict fewer than a single DNA double-strand break (DSB) per hour per cell, they still caused dose-dependent reductions in cell proliferation and increased cellular senescence. We concomitantly observed histone protein levels to reduce by up to 40%, which in contrast to previous observations, was not mainly due to protein degradation but instead correlated with reduced histone gene expression. Histone reductions were accompanied by enlarged nuclear size paralleled by an increase in global transcription, including that of pro-inflammatory genes. Thus, chronic irradiation, even at low dose-rates, can induce cell senescence and alter gene expression via a hitherto uncharacterised epigenetic route. These features of chronic radiation represent a new aspect of radiation biology.
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Affiliation(s)
- Donna J Lowe
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire, OX11 0RQ, UK.
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| | - Mareike Herzog
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | | | - Howard Cohen
- Elizabeth House Surgery, Warlingham, Surrey, CR6 9LF, UK
| | - Sarah Felton
- Department of Dermatology, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire, OX11 0RQ, UK
| | - Yaron Galanty
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| | - Stephen P Jackson
- Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
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20
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Belotserkovskaya R, Raga Gil E, Lawrence N, Butler R, Clifford G, Wilson MD, Jackson SP. PALB2 chromatin recruitment restores homologous recombination in BRCA1-deficient cells depleted of 53BP1. Nat Commun 2020; 11:819. [PMID: 32041954 PMCID: PMC7010753 DOI: 10.1038/s41467-020-14563-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 01/17/2020] [Indexed: 02/07/2023] Open
Abstract
Loss of functional BRCA1 protein leads to defects in DNA double-strand break (DSB) repair by homologous recombination (HR) and renders cells hypersensitive to poly (ADP-ribose) polymerase (PARP) inhibitors used to treat BRCA1/2-deficient cancers. However, upon chronic treatment of BRCA1-mutant cells with PARP inhibitors, resistant clones can arise via several mechanisms, including loss of 53BP1 or its downstream co-factors. Defects in the 53BP1 axis partially restore the ability of a BRCA1-deficient cell to form RAD51 filaments at resected DSBs in a PALB2- and BRCA2-dependent manner, and thereby repair DSBs by HR. Here we show that depleting 53BP1 in BRCA1-null cells restores PALB2 accrual at resected DSBs. Moreover, we demonstrate that PALB2 DSB recruitment in BRCA1/53BP1-deficient cells is mediated by an interaction between PALB2's chromatin associated motif (ChAM) and the nucleosome acidic patch region, which in 53BP1-expressing cells is bound by 53BP1's ubiquitin-directed recruitment (UDR) domain.
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Affiliation(s)
- Rimma Belotserkovskaya
- Wellcome Trust CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
| | - Elisenda Raga Gil
- Wellcome Trust CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Nicola Lawrence
- Wellcome Trust CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Richard Butler
- Wellcome Trust CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Gillian Clifford
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK.
| | - Stephen P Jackson
- Wellcome Trust CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
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21
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Salguero I, Belotserkovskaya R, Coates J, Sczaniecka-Clift M, Demir M, Jhujh S, Wilson MD, Jackson SP. MDC1 PST-repeat region promotes histone H2AX-independent chromatin association and DNA damage tolerance. Nat Commun 2019; 10:5191. [PMID: 31729360 PMCID: PMC6858307 DOI: 10.1038/s41467-019-12929-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 10/03/2019] [Indexed: 02/02/2023] Open
Abstract
Histone H2AX and MDC1 are key DNA repair and DNA-damage signalling proteins. When DNA double-strand breaks (DSBs) occur, H2AX is phosphorylated and then recruits MDC1, which in turn serves as a docking platform to promote the localization of other factors, including 53BP1, to DSB sites. Here, by using CRISPR-Cas9 engineered human cell lines, we identify a hitherto unknown, H2AX-independent, function of MDC1 mediated by its PST-repeat region. We show that the PST-repeat region directly interacts with chromatin via the nucleosome acidic patch and mediates DNA damage-independent association of MDC1 with chromatin. We find that this region is largely functionally dispensable when the canonical γH2AX-MDC1 pathway is operative but becomes critical for 53BP1 recruitment to DNA-damage sites and cell survival following DSB induction when H2AX is not available. Consequently, our results suggest a role for MDC1 in activating the DDR in areas of the genome lacking or depleted of H2AX.
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Affiliation(s)
- Israel Salguero
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Rimma Belotserkovskaya
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Julia Coates
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Matylda Sczaniecka-Clift
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Mukerrem Demir
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Satpal Jhujh
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Marcus D Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK
| | - Stephen P Jackson
- Wellcome Trust/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
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22
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Cornwell M, Thomson GJ, Coates J, Belotserkovskaya R, Waddell ID, Jackson SP, Galanty Y. Small-Molecule Inhibition of UBE2T/FANCL-Mediated Ubiquitylation in the Fanconi Anemia Pathway. ACS Chem Biol 2019; 14:2148-2154. [PMID: 31525021 PMCID: PMC6804243 DOI: 10.1021/acschembio.9b00570] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/16/2019] [Indexed: 12/16/2022]
Abstract
The Fanconi anemia pathway orchestrates the repair of DNA interstrand cross-links and stalled replication forks. A key step in this pathway is UBE2T and FANCL-dependent monoubiquitylation of the FANCD2-FANCI complex. The Fanconi anemia pathway represents an attractive therapeutic target, because activation of this pathway has been linked to chemotherapy resistance in several cancers. However, to date, very few selective inhibitors of ubiquitin conjugation pathways are known. By using a high-throughput screen-compatible assay, we have identified a small-molecule inhibitor of UBE2T/FANCL-mediated FANCD2 monoubiquitylation that sensitizes cells to the DNA cross-linking agent, carboplatin.
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Affiliation(s)
- Matthew
J. Cornwell
- The
Wellcome Trust/Cancer Research UK Gurdon Institute and Department
of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Graeme J. Thomson
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, United Kingdom
| | - Julia Coates
- The
Wellcome Trust/Cancer Research UK Gurdon Institute and Department
of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Rimma Belotserkovskaya
- The
Wellcome Trust/Cancer Research UK Gurdon Institute and Department
of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Ian D. Waddell
- Drug
Discovery Unit, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, United Kingdom
| | - Stephen P. Jackson
- The
Wellcome Trust/Cancer Research UK Gurdon Institute and Department
of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Yaron Galanty
- The
Wellcome Trust/Cancer Research UK Gurdon Institute and Department
of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
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23
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Puddu F, Herzog M, Selivanova A, Wang S, Zhu J, Klein-Lavi S, Gordon M, Meirman R, Millan-Zambrano G, Ayestaran I, Salguero I, Sharan R, Li R, Kupiec M, Jackson SP. Genome architecture and stability in the Saccharomyces cerevisiae knockout collection. Nature 2019; 573:416-420. [PMID: 31511699 PMCID: PMC6774800 DOI: 10.1038/s41586-019-1549-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/07/2019] [Indexed: 02/07/2023]
Abstract
Despite major progress in defining the functional roles of genes, a complete understanding of their influences is far from being realized, even in relatively simple organisms. A major milestone in this direction arose via the completion of the yeast Saccharomyces cerevisiae gene-knockout collection (YKOC), which has enabled high-throughput reverse genetics, phenotypic screenings and analyses of synthetic-genetic interactions1-3. Ensuing experimental work has also highlighted some inconsistencies and mistakes in the YKOC, or genome instability events that rebalance the effects of specific knockouts4-6, but a complete overview of these is lacking. The identification and analysis of genes that are required for maintaining genomic stability have traditionally relied on reporter assays and on the study of deletions of individual genes, but whole-genome-sequencing technologies now enable-in principle-the direct observation of genome instability globally and at scale. To exploit this opportunity, we sequenced the whole genomes of nearly all of the 4,732 strains comprising the homozygous diploid YKOC. Here, by extracting information on copy-number variation of tandem and interspersed repetitive DNA elements, we describe-for almost every single non-essential gene-the genomic alterations that are induced by its loss. Analysis of this dataset reveals genes that affect the maintenance of various genomic elements, highlights cross-talks between nuclear and mitochondrial genome stability, and shows how strains have genetically adapted to life in the absence of individual non-essential genes.
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Affiliation(s)
- Fabio Puddu
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Hinxton, UK.
| | - Mareike Herzog
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Alexandra Selivanova
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Siyue Wang
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jin Zhu
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shir Klein-Lavi
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Molly Gordon
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Roi Meirman
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Gonzalo Millan-Zambrano
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Iñigo Ayestaran
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Israel Salguero
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Rong Li
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Martin Kupiec
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Stephen P Jackson
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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24
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Elling U, Woods M, Forment JV, Fu B, Yang F, Ng BL, Vicente JR, Adams DJ, Doe B, Jackson SP, Penninger JM, Balmus G. Derivation and maintenance of mouse haploid embryonic stem cells. Nat Protoc 2019; 14:1991-2014. [PMID: 31160788 PMCID: PMC6997032 DOI: 10.1038/s41596-019-0169-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 03/21/2019] [Indexed: 01/05/2023]
Abstract
Ploidy represents the number of chromosome sets in a cell. Although gametes have a haploid genome (n), most mammalian cells have diploid genomes (2n). The diploid status of most cells correlates with the number of probable alleles for each autosomal gene and makes it difficult to target these genes via mutagenesis techniques. Here, we describe a 7-week protocol for the derivation of mouse haploid embryonic stem cells (hESCs) from female gametes that also outlines how to maintain the cells once derived. We detail additional procedures that can be used with cell lines obtained from the mouse Haplobank, a biobank of >100,000 individual mouse hESC lines with targeted mutations in 16,970 genes. hESCs can spontaneously diploidize and can be maintained in both haploid and diploid states. Mouse hESCs are genomically and karyotypically stable, are innately immortal and isogenic, and can be derived in an array of differentiated cell types; they are thus highly amenable to genetic screens and to defining molecular connectivity pathways.
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Affiliation(s)
- Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Michael Woods
- UK Dementia Research Institute at University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Josep V Forment
- DNA Damage Response Biology, Oncology Innovative Medicines, AstraZeneca, Cambridge, UK
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Cambridge, UK
| | | | - Bee Ling Ng
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Jose R Vicente
- UK Dementia Research Institute at University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - Brendan Doe
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Stephen P Jackson
- The Wellcome Trust CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria.
- Department of Medical Genetics, Life Science Institute, University of British Columbia, Vancouver, BC, Canada.
| | - Gabriel Balmus
- UK Dementia Research Institute at University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
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25
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Kucab JE, Zou X, Morganella S, Joel M, Nanda AS, Nagy E, Gomez C, Degasperi A, Harris R, Jackson SP, Arlt VM, Phillips DH, Nik-Zainal S. A Compendium of Mutational Signatures of Environmental Agents. Cell 2019; 177:821-836.e16. [PMID: 30982602 PMCID: PMC6506336 DOI: 10.1016/j.cell.2019.03.001] [Citation(s) in RCA: 333] [Impact Index Per Article: 66.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/21/2018] [Accepted: 02/28/2019] [Indexed: 12/21/2022]
Abstract
Whole-genome-sequencing (WGS) of human tumors has revealed distinct mutation patterns that hint at the causative origins of cancer. We examined mutational signatures in 324 WGS human-induced pluripotent stem cells exposed to 79 known or suspected environmental carcinogens. Forty-one yielded characteristic substitution mutational signatures. Some were similar to signatures found in human tumors. Additionally, six agents produced double-substitution signatures and eight produced indel signatures. Investigating mutation asymmetries across genome topography revealed fully functional mismatch and transcription-coupled repair pathways. DNA damage induced by environmental mutagens can be resolved by disparate repair and/or replicative pathways, resulting in an assortment of signature outcomes even for a single agent. This compendium of experimentally induced mutational signatures permits further exploration of roles of environmental agents in cancer etiology and underscores how human stem cell DNA is directly vulnerable to environmental agents. VIDEO ABSTRACT.
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Affiliation(s)
- Jill E Kucab
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - Xueqing Zou
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Madeleine Joel
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - A Scott Nanda
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK
| | - Eszter Nagy
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - Celine Gomez
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Andrea Degasperi
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Rebecca Harris
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Stephen P Jackson
- The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Volker M Arlt
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK
| | - David H Phillips
- Department of Analytical, Environmental and Forensic Sciences, MRC-PHE Centre for Environment and Health, King's College London, 150 Stamford Street, London SE1 9NH, UK.
| | - Serena Nik-Zainal
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge CB2 9NB, UK; MRC Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
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26
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Affiliation(s)
| | - Brian T Weinert
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Chunaram Choudhary
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK.
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27
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Paonessa F, Evans LD, Solanki R, Larrieu D, Wray S, Hardy J, Jackson SP, Livesey FJ. Microtubules Deform the Nuclear Membrane and Disrupt Nucleocytoplasmic Transport in Tau-Mediated Frontotemporal Dementia. Cell Rep 2019; 26:582-593.e5. [PMID: 30650353 PMCID: PMC6335264 DOI: 10.1016/j.celrep.2018.12.085] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/12/2018] [Accepted: 12/18/2018] [Indexed: 02/02/2023] Open
Abstract
The neuronal microtubule-associated protein tau, MAPT, is central to the pathogenesis of many dementias. Autosomal-dominant mutations in MAPT cause inherited frontotemporal dementia (FTD), but the underlying pathogenic mechanisms are unclear. Using human stem cell models of FTD due to MAPT mutations, we find that tau becomes hyperphosphorylated and mislocalizes to cell bodies and dendrites in cortical neurons, recapitulating a key early event in FTD. Mislocalized tau in the cell body leads to abnormal microtubule movements in FTD-MAPT neurons that grossly deform the nuclear membrane. This results in defective nucleocytoplasmic transport, which is corrected by microtubule depolymerization. Neurons in the post-mortem human FTD-MAPT cortex have a high incidence of nuclear invaginations, indicating that tau-mediated nuclear membrane dysfunction is an important pathogenic process in FTD. Defects in nucleocytoplasmic transport in FTD point to important commonalities in the pathogenic mechanisms of tau-mediated dementias and ALS-FTD due to TDP-43 and C9orf72 mutations.
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Affiliation(s)
- Francesco Paonessa
- Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK; Alzheimer's Research UK Stem Cell Research Centre, University of Cambridge, CB2 1QN, UK
| | - Lewis D Evans
- Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK; Alzheimer's Research UK Stem Cell Research Centre, University of Cambridge, CB2 1QN, UK
| | - Ravi Solanki
- Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK; Alzheimer's Research UK Stem Cell Research Centre, University of Cambridge, CB2 1QN, UK
| | - Delphine Larrieu
- Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Selina Wray
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Stephen P Jackson
- Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Frederick J Livesey
- Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK; Alzheimer's Research UK Stem Cell Research Centre, University of Cambridge, CB2 1QN, UK; UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK.
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28
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Balmus G, Pilger D, Coates J, Demir M, Sczaniecka-Clift M, Barros AC, Woods M, Fu B, Yang F, Chen E, Ostermaier M, Stankovic T, Ponstingl H, Herzog M, Yusa K, Martinez FM, Durant ST, Galanty Y, Beli P, Adams DJ, Bradley A, Metzakopian E, Forment JV, Jackson SP. ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks. Nat Commun 2019; 10:87. [PMID: 30622252 PMCID: PMC6325118 DOI: 10.1038/s41467-018-07729-2] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/15/2018] [Indexed: 02/02/2023] Open
Abstract
Mutations in the ATM tumor suppressor gene confer hypersensitivity to DNA-damaging chemotherapeutic agents. To explore genetic resistance mechanisms, we performed genome-wide CRISPR-Cas9 screens in cells treated with the DNA topoisomerase I inhibitor topotecan. Thus, we here establish that inactivating terminal components of the non-homologous end-joining (NHEJ) machinery or of the BRCA1-A complex specifically confer topotecan resistance to ATM-deficient cells. We show that hypersensitivity of ATM-mutant cells to topotecan or the poly-(ADP-ribose) polymerase (PARP) inhibitor olaparib reflects delayed engagement of homologous recombination at DNA-replication-fork associated single-ended double-strand breaks (DSBs), allowing some to be subject to toxic NHEJ. Preventing DSB ligation by NHEJ, or enhancing homologous recombination by BRCA1-A complex disruption, suppresses this toxicity, highlighting a crucial role for ATM in preventing toxic LIG4-mediated chromosome fusions. Notably, suppressor mutations in ATM-mutant backgrounds are different to those in BRCA1-mutant scenarios, suggesting new opportunities for patient stratification and additional therapeutic vulnerabilities for clinical exploitation.
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Affiliation(s)
- Gabriel Balmus
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- UK Dementia Research Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Domenic Pilger
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Julia Coates
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Mukerrem Demir
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Matylda Sczaniecka-Clift
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Ana C Barros
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Michael Woods
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Elisabeth Chen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Hannes Ponstingl
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Mareike Herzog
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Kosuke Yusa
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Francisco Munoz Martinez
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Stephen T Durant
- DNA Damage Response Biology, Bioscience Oncology IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Yaron Galanty
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - David J Adams
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Allan Bradley
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Emmanouil Metzakopian
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- UK Dementia Research Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Josep V Forment
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
- DNA Damage Response Biology, Bioscience Oncology IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK.
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
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29
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Allen F, Crepaldi L, Alsinet C, Strong AJ, Kleshchevnikov V, De Angeli P, Palenikova P, Khodak A, Kiselev V, Kosicki M, Bassett AR, Harding H, Galanty Y, Muñoz-Martínez F, Metzakopian E, Jackson SP, Parts L. Predicting the mutations generated by repair of Cas9-induced double-strand breaks. Nat Biotechnol 2018; 37:nbt.4317. [PMID: 30480667 PMCID: PMC6949135 DOI: 10.1038/nbt.4317] [Citation(s) in RCA: 275] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022]
Abstract
The DNA mutation produced by cellular repair of a CRISPR-Cas9-generated double-strand break determines its phenotypic effect. It is known that the mutational outcomes are not random, but depend on DNA sequence at the targeted location. Here we systematically study the influence of flanking DNA sequence on repair outcome by measuring the edits generated by >40,000 guide RNAs (gRNAs) in synthetic constructs. We performed the experiments in a range of genetic backgrounds and using alternative CRISPR-Cas9 reagents. In total, we gathered data for >109 mutational outcomes. The majority of reproducible mutations are insertions of a single base, short deletions or longer microhomology-mediated deletions. Each gRNA has an individual cell-line-dependent bias toward particular outcomes. We uncover sequence determinants of the mutations produced and use these to derive a predictor of Cas9 editing outcomes. Improved understanding of sequence repair will allow better design of gene editing experiments.
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Affiliation(s)
| | | | | | | | | | | | | | - Anton Khodak
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | | | - Heather Harding
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Yaron Galanty
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Francisco Muñoz-Martínez
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Emmanouil Metzakopian
- Wellcome Sanger Institute, Hinxton, United Kingdom
- UK Dementia Research Institute, Cambridge, United Kingdom
| | - Stephen P. Jackson
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Leopold Parts
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Computer Science, University of Tartu, Tartu, Estonia
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30
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Millan-Zambrano G, Santos-Rosa H, Puddu F, Robson SC, Jackson SP, Kouzarides T. Phosphorylation of Histone H4T80 Triggers DNA Damage Checkpoint Recovery. Mol Cell 2018; 72:625-635.e4. [PMID: 30454561 PMCID: PMC6242705 DOI: 10.1016/j.molcel.2018.09.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/08/2018] [Accepted: 09/18/2018] [Indexed: 11/24/2022]
Abstract
In response to genotoxic stress, cells activate a signaling cascade known as the DNA damage checkpoint (DDC) that leads to a temporary cell cycle arrest and activation of DNA repair mechanisms. Because persistent DDC activation compromises cell viability, this process must be tightly regulated. However, despite its importance, the mechanisms regulating DDC recovery are not completely understood. Here, we identify a DNA-damage-regulated histone modification in Saccharomyces cerevisiae, phosphorylation of H4 threonine 80 (H4T80ph), and show that it triggers checkpoint inactivation. H4T80ph is critical for cell survival to DNA damage, and its absence causes impaired DDC recovery and persistent cell cycle arrest. We show that, in response to genotoxic stress, p21-activated kinase Cla4 phosphorylates H4T80 to recruit Rtt107 to sites of DNA damage. Rtt107 displaces the checkpoint adaptor Rad9, thereby interrupting the checkpoint-signaling cascade. Collectively, our results indicate that H4T80ph regulates DDC recovery.
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Affiliation(s)
- Gonzalo Millan-Zambrano
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
| | - Helena Santos-Rosa
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Fabio Puddu
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Samuel C Robson
- School of Pharmacy and Biomedical Science, University of Portsmouth, White Swan Road, Portsmouth PO1 2DT, UK
| | - Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Tony Kouzarides
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
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31
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Dev H, Chiang TWW, Lescale C, de Krijger I, Martin AG, Pilger D, Coates J, Sczaniecka-Clift M, Wei W, Ostermaier M, Herzog M, Lam J, Shea A, Demir M, Wu Q, Yang F, Fu B, Lai Z, Balmus G, Belotserkovskaya R, Serra V, O'Connor MJ, Bruna A, Beli P, Pellegrini L, Caldas C, Deriano L, Jacobs JJL, Galanty Y, Jackson SP. Shieldin complex promotes DNA end-joining and counters homologous recombination in BRCA1-null cells. Nat Cell Biol 2018; 20:954-965. [PMID: 30022119 PMCID: PMC6145444 DOI: 10.1038/s41556-018-0140-1] [Citation(s) in RCA: 250] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/11/2018] [Indexed: 02/02/2023]
Abstract
BRCA1 deficiencies cause breast, ovarian, prostate and other cancers, and render tumours hypersensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. To understand the resistance mechanisms, we conducted whole-genome CRISPR-Cas9 synthetic-viability/resistance screens in BRCA1-deficient breast cancer cells treated with PARP inhibitors. We identified two previously uncharacterized proteins, C20orf196 and FAM35A, whose inactivation confers strong PARP-inhibitor resistance. Mechanistically, we show that C20orf196 and FAM35A form a complex, 'Shieldin' (SHLD1/2), with FAM35A interacting with single-stranded DNA through its C-terminal oligonucleotide/oligosaccharide-binding fold region. We establish that Shieldin acts as the downstream effector of 53BP1/RIF1/MAD2L2 to promote DNA double-strand break (DSB) end-joining by restricting DSB resection and to counteract homologous recombination by antagonizing BRCA2/RAD51 loading in BRCA1-deficient cells. Notably, Shieldin inactivation further sensitizes BRCA1-deficient cells to cisplatin, suggesting how defining the SHLD1/2 status of BRCA1-deficient tumours might aid patient stratification and yield new treatment opportunities. Highlighting this potential, we document reduced SHLD1/2 expression in human breast cancers displaying intrinsic or acquired PARP-inhibitor resistance.
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Affiliation(s)
- Harveer Dev
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
- Academic Urology Group, Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK
| | - Ting-Wei Will Chiang
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chloe Lescale
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Inge de Krijger
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan , Amsterdam, the Netherlands
| | - Alistair G Martin
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Domenic Pilger
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Julia Coates
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Matylda Sczaniecka-Clift
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Wenming Wei
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | | | - Mareike Herzog
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jonathan Lam
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Abigail Shea
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Mukerrem Demir
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Qian Wu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Gabriel Balmus
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Rimma Belotserkovskaya
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Violeta Serra
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Alejandra Bruna
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, Paris, France.
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan , Amsterdam, the Netherlands.
| | - Yaron Galanty
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
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32
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Larrieu D, Viré E, Robson S, Breusegem SY, Kouzarides T, Jackson SP. Inhibition of the acetyltransferase NAT10 normalizes progeric and aging cells by rebalancing the Transportin-1 nuclear import pathway. Sci Signal 2018; 11:eaar5401. [PMID: 29970603 PMCID: PMC6331045 DOI: 10.1126/scisignal.aar5401] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is an incurable premature aging disease. Identifying deregulated biological processes in HGPS might thus help define novel therapeutic strategies. Fibroblasts from HGPS patients display defects in nucleocytoplasmic shuttling of the GTP-bound form of the small GTPase Ran (RanGTP), which leads to abnormal transport of proteins into the nucleus. We report that microtubule stabilization in HGPS cells sequestered the nonclassical nuclear import protein Transportin-1 (TNPO1) in the cytoplasm, thus affecting the nuclear localization of its cargo, including the nuclear pore protein NUP153. Consequently, nuclear Ran, nuclear anchorage of the nucleoporin TPR, and chromatin organization were disrupted, deregulating gene expression and inducing senescence. Inhibiting N-acetyltransferase 10 (NAT10) ameliorated HGPS phenotypes by rebalancing the nuclear to cytoplasmic ratio of TNPO1. This restored nuclear pore complex integrity and nuclear Ran localization, thereby correcting HGPS cellular phenotypes. We observed a similar mechanism in cells from healthy aged individuals. This study identifies a nuclear import pathway affected in aging and underscores the potential for NAT10 inhibition as a possible therapeutic strategy for HGPS and perhaps also for pathologies associated with normal aging.
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Affiliation(s)
- Delphine Larrieu
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN, UK.
| | - Emmanuelle Viré
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN, UK
| | - Samuel Robson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN, UK
| | - Sophia Y Breusegem
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN, UK
| | - Tony Kouzarides
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN, UK
| | - Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, CB2 1QN, UK.
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33
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Velimezi G, Robinson-Garcia L, Muñoz-Martínez F, Wiegant WW, Ferreira da Silva J, Owusu M, Moder M, Wiedner M, Rosenthal SB, Fisch KM, Moffat J, Menche J, van Attikum H, Jackson SP, Loizou JI. Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48. Nat Commun 2018; 9:2280. [PMID: 29891926 PMCID: PMC5996029 DOI: 10.1038/s41467-018-04649-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 05/14/2018] [Indexed: 01/26/2023] Open
Abstract
Defects in DNA repair can cause various genetic diseases with severe pathological phenotypes. Fanconi anemia (FA) is a rare disease characterized by bone marrow failure, developmental abnormalities, and increased cancer risk that is caused by defective repair of DNA interstrand crosslinks (ICLs). Here, we identify the deubiquitylating enzyme USP48 as synthetic viable for FA-gene deficiencies by performing genome-wide loss-of-function screens across a panel of human haploid isogenic FA-defective cells (FANCA, FANCC, FANCG, FANCI, FANCD2). Thus, as compared to FA-defective cells alone, FA-deficient cells additionally lacking USP48 are less sensitive to genotoxic stress induced by ICL agents and display enhanced, BRCA1-dependent, clearance of DNA damage. Consequently, USP48 inactivation reduces chromosomal instability of FA-defective cells. Our results highlight a role for USP48 in controlling DNA repair and suggest it as a potential target that could be therapeutically exploited for FA.
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Affiliation(s)
- Georgia Velimezi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Lydia Robinson-Garcia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Francisco Muñoz-Martínez
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Wouter W Wiegant
- Department of Human Genetics, Leiden University Medical Center, Leiden, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Joana Ferreira da Silva
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Michel Owusu
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Martin Moder
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Marc Wiedner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, 9500 Gilman Drive #0681, La Jolla, CA, 92093, USA
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, 9500 Gilman Drive #0681, La Jolla, CA, 92093, USA
| | - Jason Moffat
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Stephen P Jackson
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria.
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34
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Zou X, Owusu M, Harris R, Jackson SP, Loizou JI, Nik-Zainal S. Validating the concept of mutational signatures with isogenic cell models. Nat Commun 2018; 9:1744. [PMID: 29717121 PMCID: PMC5931590 DOI: 10.1038/s41467-018-04052-8] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 03/29/2018] [Indexed: 12/23/2022] Open
Abstract
The diversity of somatic mutations in human cancers can be decomposed into individual mutational signatures, patterns of mutagenesis that arise because of DNA damage and DNA repair processes that have occurred in cells as they evolved towards malignancy. Correlations between mutational signatures and environmental exposures, enzymatic activities and genetic defects have been described, but human cancers are not ideal experimental systems-the exposures to different mutational processes in a patient's lifetime are uncontrolled and any relationships observed can only be described as an association. Here, we demonstrate the proof-of-principle that it is possible to recreate cancer mutational signatures in vitro using CRISPR-Cas9-based gene-editing experiments in an isogenic human-cell system. We provide experimental and algorithmic methods to discover mutational signatures generated under highly experimentally-controlled conditions. Our in vitro findings strikingly recapitulate in vivo observations of cancer data, fundamentally validating the concept of (particularly) endogenously-arising mutational signatures.
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Affiliation(s)
- Xueqing Zou
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Michel Owusu
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Rebecca Harris
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Stephen P Jackson
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria.
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, CB2 0QQ, UK.
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35
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Balmus G, Larrieu D, Barros AC, Collins C, Abrudan M, Demir M, Geisler NJ, Lelliott CJ, White JK, Karp NA, Atkinson J, Kirton A, Jacobsen M, Clift D, Rodriguez R, Adams DJ, Jackson SP. Targeting of NAT10 enhances healthspan in a mouse model of human accelerated aging syndrome. Nat Commun 2018; 9:1700. [PMID: 29703891 PMCID: PMC5923383 DOI: 10.1038/s41467-018-03770-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 03/12/2018] [Indexed: 02/02/2023] Open
Abstract
Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare, but devastating genetic disease characterized by segmental premature aging, with cardiovascular disease being the main cause of death. Cells from HGPS patients accumulate progerin, a permanently farnesylated, toxic form of Lamin A, disrupting the nuclear shape and chromatin organization, leading to DNA-damage accumulation and senescence. Therapeutic approaches targeting farnesylation or aiming to reduce progerin levels have provided only partial health improvements. Recently, we identified Remodelin, a small-molecule agent that leads to amelioration of HGPS cellular defects through inhibition of the enzyme N-acetyltransferase 10 (NAT10). Here, we show the preclinical data demonstrating that targeting NAT10 in vivo, either via chemical inhibition or genetic depletion, significantly enhances the healthspan in a Lmna G609G HGPS mouse model. Collectively, the data provided here highlights NAT10 as a potential therapeutic target for HGPS.
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Affiliation(s)
- Gabriel Balmus
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Delphine Larrieu
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
- Department of Clinical Biochemistry, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Ana C Barros
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Casey Collins
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Monica Abrudan
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Mukerrem Demir
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Nicola J Geisler
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | | | | - Natasha A Karp
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, CB4 0WG, UK
| | - James Atkinson
- Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, CB2 23AT, UK
| | - Andrea Kirton
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Matt Jacobsen
- Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, CB2 23AT, UK
| | - Dean Clift
- Laboratory of Molecular Biology, Cambridge, CB2 OQH, UK
| | - Raphael Rodriguez
- Institut Curie, PSL Research University, Paris Cedex 05, France
- CNRS UMR3666, 75005, Paris, France
- INSERM U1143, 75005, Paris, France
| | - David J Adams
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
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Herzog M, Puddu F, Coates J, Geisler N, Forment JV, Jackson SP. Detection of functional protein domains by unbiased genome-wide forward genetic screening. Sci Rep 2018; 8:6161. [PMID: 29670134 PMCID: PMC5906580 DOI: 10.1038/s41598-018-24400-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/22/2018] [Indexed: 12/21/2022] Open
Abstract
Establishing genetic and chemo-genetic interactions has played key roles in elucidating mechanisms by which certain chemicals perturb cellular functions. In contrast to gene disruption/depletion strategies to identify mechanisms of drug resistance, searching for point-mutational genetic suppressors that can identify separation- or gain-of-function mutations has been limited. Here, by demonstrating its utility in identifying chemical-genetic suppressors of sensitivity to the DNA topoisomerase I poison camptothecin or the poly(ADP-ribose) polymerase inhibitor olaparib, we detail an approach allowing systematic, large-scale detection of spontaneous or chemically-induced suppressor mutations in yeast or haploid mammalian cells in a short timeframe, and with potential applications in other haploid systems. In addition to applications in molecular biology research, this protocol can be used to identify drug targets and predict drug-resistance mechanisms. Mapping suppressor mutations on the primary or tertiary structures of protein suppressor hits provides insights into functionally relevant protein domains. Importantly, we show that olaparib resistance is linked to missense mutations in the DNA binding regions of PARP1, but not in its catalytic domain. This provides experimental support to the concept of PARP1 trapping on DNA as the prime source of toxicity to PARP inhibitors, and points to a novel olaparib resistance mechanism with potential therapeutic implications.
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Affiliation(s)
- Mareike Herzog
- The Wellcome/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QN, Cambridge, UK
| | - Fabio Puddu
- The Wellcome/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QN, Cambridge, UK
| | - Julia Coates
- The Wellcome/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QN, Cambridge, UK
| | - Nicola Geisler
- The Wellcome/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QN, Cambridge, UK
| | - Josep V Forment
- The Wellcome/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QN, Cambridge, UK.
- AstraZeneca, Oncology DNA damage response group, Hodgkin Building, 310 Cambridge Science Park, Milton Road, CB4 0WG, Cambridge, UK.
| | - Stephen P Jackson
- The Wellcome/CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QN, Cambridge, UK.
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Abstract
More than a decade after a Nobel Prize was awarded for the discovery of the ubiquitin-proteasome system and clinical approval of proteasome and ubiquitin E3 ligase inhibitors, first-generation deubiquitylating enzyme (DUB) inhibitors are now approaching clinical trials. However, although our knowledge of the physiological and pathophysiological roles of DUBs has evolved tremendously, the clinical development of selective DUB inhibitors has been challenging. In this Review, we discuss these issues and highlight recent advances in our understanding of DUB enzymology and biology as well as technological improvements that have contributed to the current interest in DUBs as therapeutic targets in diseases ranging from oncology to neurodegeneration.
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Affiliation(s)
- Jeanine A. Harrigan
- Mission Therapeutics Ltd, Moneta, Babraham Research Campus, Cambridge, CB22 3AT UK
| | - Xavier Jacq
- Mission Therapeutics Ltd, Moneta, Babraham Research Campus, Cambridge, CB22 3AT UK
| | - Niall M. Martin
- Mission Therapeutics Ltd, Moneta, Babraham Research Campus, Cambridge, CB22 3AT UK
- Present Address: and Department of Biochemistry, The Wellcome Trust and Cancer Research UK Gurdon Institute, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QN UK
- Present address: Artios Pharmaceuticals Ltd, Maia, Babraham Research Campus, Cambridge CB22 3AT, UK,
| | - Stephen P. Jackson
- Mission Therapeutics Ltd, Moneta, Babraham Research Campus, Cambridge, CB22 3AT UK
- Present Address: and Department of Biochemistry, The Wellcome Trust and Cancer Research UK Gurdon Institute, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QN UK
- Present address: Artios Pharmaceuticals Ltd, Maia, Babraham Research Campus, Cambridge CB22 3AT, UK,
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38
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Moder M, Velimezi G, Owusu M, Mazouzi A, Wiedner M, Ferreira da Silva J, Robinson-Garcia L, Schischlik F, Slavkovsky R, Kralovics R, Schuster M, Bock C, Ideker T, Jackson SP, Menche J, Loizou JI. Parallel genome-wide screens identify synthetic viable interactions between the BLM helicase complex and Fanconi anemia. Nat Commun 2017; 8:1238. [PMID: 29089570 PMCID: PMC5663702 DOI: 10.1038/s41467-017-01439-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 09/15/2017] [Indexed: 02/08/2023] Open
Abstract
Maintenance of genome integrity via repair of DNA damage is a key biological process required to suppress diseases, including Fanconi anemia (FA). We generated loss-of-function human haploid cells for FA complementation group C (FANCC), a gene encoding a component of the FA core complex, and used genome-wide CRISPR libraries as well as insertional mutagenesis to identify synthetic viable (genetic suppressor) interactions for FA. Here we show that loss of the BLM helicase complex suppresses FANCC phenotypes and we confirm this interaction in cells deficient for FA complementation group I and D2 (FANCI and FANCD2) that function as part of the FA I-D2 complex, indicating that this interaction is not limited to the FA core complex, hence demonstrating that systematic genome-wide screening approaches can be used to reveal genetic viable interactions for DNA repair defects.
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Affiliation(s)
- Martin Moder
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Georgia Velimezi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Michel Owusu
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Abdelghani Mazouzi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Marc Wiedner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Joana Ferreira da Silva
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Lydia Robinson-Garcia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Fiorella Schischlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Rastislav Slavkovsky
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Trey Ideker
- Department of Medicine, Division of Genetics, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
- The Cancer Cell Map Initiative, La Jolla, CA, 92093, USA
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
| | - Joanna I Loizou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria.
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Henssen AG, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, Still E, Rodríguez-Fos E, Gonzalez S, Puiggròs M, Blackford AN, Mason CE, Stanchina ED, Gönen M, Emde AK, Shah M, Arora K, Reeves C, Socci ND, Perlman E, Antonescu CR, Roberts CW, Steen H, Mullen E, Jackson SP, Torrents D, Weng Z, Armstrong SA, Kentsis A. Abstract 4888: Human PGBD5 DNA transposase promotes site-specific oncogenic mutations in rhabdoid tumors. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genomic rearrangements are a hallmark of childhood solid tumors, but their mutational causes remain poorly understood. Here, we identify the piggyBac transposable element derived 5 (PGBD5) gene as an enzymatically active human DNA transposase expressed in the majority of rhabdoid tumors, a lethal childhood cancer. Using assembly-based whole-genome DNA sequencing, we observed previously unknown somatic genomic rearrangements in primary human rhabdoid tumors. These rearrangements were characterized by deletions and inversions involving PGBD5-specific signal (PSS) sequences at their breakpoints, with some recurrently targeting tumor suppressor genes, leading to their inactivation. PGBD5 was found to be physically associated with human genomic PSS sequences that were also sufficient to mediate PGBD5-induced DNA rearrangements in rhabdoid tumor cells. We found that ectopic expression of PGBD5 in primary human cells was sufficient to promote penetrant cell transformation in vitro and in immunodeficient mice in vivo. This activity required specific catalytic residues in the PGBD5 transposase domain, as well as end-joining DNA repair, and induced distinct structural rearrangements, involving PSS-associated breakpoints, similar to those found in primary human rhabdoid tumors. Thus, PGBD5 defines a distinct class of oncogenic mutators and induces site-specific somatic DNA rearrangements in human cancer.
Citation Format: Anton G. Henssen, Richard Koche, Jiali Zhuang, Eileen Jiang, Casie Reed, Amy Eisenberg, Eric Still, Elias Rodríguez-Fos, Santiago Gonzalez, Montserrat Puiggròs, Andrew N. Blackford, Christopher E. Mason, Elisa de Stanchina, Mithat Gönen, Anne-Katrin Emde, Minita Shah, Kanika Arora, Catherine Reeves, Nicholas D. Socci, Elizabeth Perlman, Cristina R. Antonescu, Charles W. Roberts, Hanno Steen, Elizabeth Mullen, Stephen P. Jackson, David Torrents, Zhiping Weng, Scott A. Armstrong, Alex Kentsis. Human PGBD5 DNA transposase promotes site-specific oncogenic mutations in rhabdoid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4888. doi:10.1158/1538-7445.AM2017-4888
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Affiliation(s)
| | | | - Jiali Zhuang
- 2University of Massachusetts Medical School, Worcester, MA
| | | | - Casie Reed
- 1Mem. Sloan Kettering Cancer Ctr., New York, NY
| | | | - Eric Still
- 1Mem. Sloan Kettering Cancer Ctr., New York, NY
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Zhiping Weng
- 2University of Massachusetts Medical School, Worcester, MA
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40
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Henssen AG, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, Still E, MacArthur IC, Rodríguez-Fos E, Gonzalez S, Puiggròs M, Blackford AN, Mason CE, de Stanchina E, Gönen M, Emde AK, Shah M, Arora K, Reeves C, Socci ND, Perlman E, Antonescu CR, Roberts CWM, Steen H, Mullen E, Jackson SP, Torrents D, Weng Z, Armstrong SA, Kentsis A. PGBD5 promotes site-specific oncogenic mutations in human tumors. Nat Genet 2017; 49:1005-1014. [PMID: 28504702 PMCID: PMC5489359 DOI: 10.1038/ng.3866] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 04/18/2017] [Indexed: 12/25/2022]
Abstract
Genomic rearrangements are a hallmark of human cancers. Here, we identify the piggyBac transposable element derived 5 (PGBD5) gene as encoding an active DNA transposase expressed in the majority of childhood solid tumors, including lethal rhabdoid tumors. Using assembly-based whole-genome DNA sequencing, we found previously undefined genomic rearrangements in human rhabdoid tumors. These rearrangements involved PGBD5-specific signal (PSS) sequences at their breakpoints and recurrently inactivated tumor-suppressor genes. PGBD5 was physically associated with genomic PSS sequences that were also sufficient to mediate PGBD5-induced DNA rearrangements in rhabdoid tumor cells. Ectopic expression of PGBD5 in primary immortalized human cells was sufficient to promote cell transformation in vivo. This activity required specific catalytic residues in the PGBD5 transposase domain as well as end-joining DNA repair and induced structural rearrangements with PSS breakpoints. These results define PGBD5 as an oncogenic mutator and provide a plausible mechanism for site-specific DNA rearrangements in childhood and adult solid tumors.
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Affiliation(s)
- Anton G. Henssen
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard Koche
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jiali Zhuang
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Eileen Jiang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Casie Reed
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amy Eisenberg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Still
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ian C. MacArthur
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elias Rodríguez-Fos
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center (BSC-CNS), Barcelona, Spain
| | - Santiago Gonzalez
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center (BSC-CNS), Barcelona, Spain
| | - Montserrat Puiggròs
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center (BSC-CNS), Barcelona, Spain
| | - Andrew N. Blackford
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Christopher E. Mason
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | | | | | | | - Nicholas D. Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth Perlman
- Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | | | | | - Hanno Steen
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Elizabeth Mullen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stephen P. Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - David Torrents
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center (BSC-CNS), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Scott A. Armstrong
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Blackford AN, Jackson SP. ATM, ATR, and DNA-PK: The Trinity at the Heart of the DNA Damage Response. Mol Cell 2017; 66:801-817. [PMID: 28622525 DOI: 10.1016/j.molcel.2017.05.015] [Citation(s) in RCA: 1120] [Impact Index Per Article: 160.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/28/2017] [Accepted: 05/16/2017] [Indexed: 01/09/2023]
Abstract
In vertebrate cells, the DNA damage response is controlled by three related kinases: ATM, ATR, and DNA-PK. It has been 20 years since the cloning of ATR, the last of the three to be identified. During this time, our understanding of how these kinases regulate DNA repair and associated events has grown profoundly, although major questions remain unanswered. Here, we provide a historical perspective of their discovery and discuss their established functions in sensing and responding to genotoxic stress. We also highlight what is known regarding their structural similarities and common mechanisms of regulation, as well as emerging non-canonical roles and how our knowledge of ATM, ATR, and DNA-PK is being translated to benefit human health.
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Affiliation(s)
- Andrew N Blackford
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
| | - Stephen P Jackson
- Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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Puddu F, Salguero I, Herzog M, Geisler NJ, Costanzo V, Jackson SP. Chromatin determinants impart camptothecin sensitivity. EMBO Rep 2017; 18:1000-1012. [PMID: 28389464 PMCID: PMC5452016 DOI: 10.15252/embr.201643560] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 11/09/2022] Open
Abstract
Camptothecin-induced locking of topoisomerase 1 on DNA generates a physical barrier to replication fork progression and creates topological stress. By allowing replisome rotation, absence of the Tof1/Csm3 complex promotes the conversion of impending topological stress to DNA catenation and causes camptothecin hypersensitivity. Through synthetic viability screening, we discovered that histone H4 K16 deacetylation drives the sensitivity of yeast cells to camptothecin and that inactivation of this pathway by mutating H4 K16 or the genes SIR1-4 suppresses much of the hypersensitivity of tof1∆ strains towards this agent. We show that disruption of rDNA or telomeric silencing does not mediate camptothecin resistance but that disruption of Sir1-dependent chromatin domains is sufficient to suppress camptothecin sensitivity in wild-type and tof1∆ cells. We suggest that topoisomerase 1 inhibition in proximity of these domains causes topological stress that leads to DNA hypercatenation, especially in the absence of the Tof1/Csm3 complex. Finally, we provide evidence of the evolutionarily conservation of this mechanism.
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Affiliation(s)
- Fabio Puddu
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Israel Salguero
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Mareike Herzog
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton Cambridge, UK
| | - Nicola J Geisler
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vincenzo Costanzo
- IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milan, Italy
| | - Stephen P Jackson
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
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Henssen AG, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, Still E, MacArthur IC, Rodríguez-Fos E, Gonzalez S, Puiggròs M, Blackford AN, Mason CE, de Stanchina E, Gönen M, Emde AK, Shah M, Arora K, Reeves C, Socci ND, Perlman E, Antonescu CR, Roberts CWM, Steen H, Mullen E, Jackson SP, Torrents D, Weng Z, Armstrong SA, Kentsis A. PGBD5 promotes site-specific oncogenic mutations in human tumors. Nat Genet 2017. [DOI: 10.1038/ng.3866 [doi]] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Bar DZ, Arlt MF, Brazier JF, Norris WE, Campbell SE, Chines P, Larrieu D, Jackson SP, Collins FS, Glover TW, Gordon LB. A novel somatic mutation achieves partial rescue in a child with Hutchinson-Gilford progeria syndrome. J Med Genet 2017; 54:212-216. [PMID: 27920058 PMCID: PMC5384422 DOI: 10.1136/jmedgenet-2016-104295] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/03/2016] [Accepted: 11/11/2016] [Indexed: 11/04/2022]
Abstract
BACKGROUND Hutchinson-Gilford progeria syndrome (HGPS) is a fatal sporadic autosomal dominant premature ageing disease caused by single base mutations that optimise a cryptic splice site within exon 11 of the LMNA gene. The resultant disease-causing protein, progerin, acts as a dominant negative. Disease severity relies partly on progerin levels. METHODS AND RESULTS We report a novel form of somatic mosaicism, where a child possessed two cell populations with different HGPS disease-producing mutations of the same nucleotide-one producing severe HGPS and one mild HGPS. The proband possessed an intermediate phenotype. The mosaicism was initially discovered when Sanger sequencing showed a c.1968+2T>A mutation in blood DNA and a c.1968+2T>C in DNA from cultured fibroblasts. Deep sequencing of DNA from the proband's blood revealed 4.7% c.1968+2T>C mutation, and 41.3% c.1968+2T>A mutation. CONCLUSIONS We hypothesise that the germline mutation was c.1968+2T>A, but a rescue event occurred during early development, where the somatic mutation from A to C at 1968+2 provided a selective advantage. This type of mosaicism where a partial phenotypic rescue event results from a second but milder disease-causing mutation in the same nucleotide has not been previously characterised for any disease.
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Affiliation(s)
- Daniel Z Bar
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Joan F Brazier
- Center for Gerontology and Health Care Research, Brown University, Providence, Rhode Island, USA
| | - Wendy E Norris
- Department of Pediatrics, Hasbro Children's Hospital, Providence, Rhode Island, USA
| | - Susan E Campbell
- Center for Gerontology and Health Care Research, Brown University, Providence, Rhode Island, USA
| | - Peter Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Delphine Larrieu
- Department of Biochemistry, The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Stephen P Jackson
- Department of Biochemistry, The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas W Glover
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Leslie B Gordon
- Department of Pediatrics, Hasbro Children's Hospital, Providence, Rhode Island, USA
- Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
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Forment JV, Herzog M, Coates J, Konopka T, Gapp BV, Nijman SM, Adams DJ, Keane TM, Jackson SP. Genome-wide genetic screening with chemically mutagenized haploid embryonic stem cells. Nat Chem Biol 2017; 13:12-14. [PMID: 27820796 PMCID: PMC5164930 DOI: 10.1038/nchembio.2226] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/24/2016] [Indexed: 12/21/2022]
Abstract
In model organisms, classical genetic screening via random mutagenesis provides key insights into the molecular bases of genetic interactions, helping to define synthetic lethality, synthetic viability and drug-resistance mechanisms. The limited genetic tractability of diploid mammalian cells, however, precludes this approach. Here, we demonstrate the feasibility of classical genetic screening in mammalian systems by using haploid cells, chemical mutagenesis and next-generation sequencing, providing a new tool to explore mammalian genetic interactions.
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Affiliation(s)
- Josep V. Forment
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Mareike Herzog
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Julia Coates
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tomasz Konopka
- Ludwig Institute for Cancer Research Ltd. and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bianca V. Gapp
- Ludwig Institute for Cancer Research Ltd. and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sebastian M. Nijman
- Ludwig Institute for Cancer Research Ltd. and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), Vienna, Austria
| | - David J. Adams
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | - Stephen P. Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Biochemistry, University of Cambridge, Cambridge, UK
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
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Brown JS, O'Carrigan B, Jackson SP, Yap TA. Targeting DNA Repair in Cancer: Beyond PARP Inhibitors. Cancer Discov 2017; 7:20-37. [PMID: 28003236 PMCID: PMC5300099 DOI: 10.1158/2159-8290.cd-16-0860] [Citation(s) in RCA: 411] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 01/14/2023]
Abstract
Germline aberrations in critical DNA-repair and DNA damage-response (DDR) genes cause cancer predisposition, whereas various tumors harbor somatic mutations causing defective DDR/DNA repair. The concept of synthetic lethality can be exploited in such malignancies, as exemplified by approval of poly(ADP-ribose) polymerase inhibitors for treating BRCA1/2-mutated ovarian cancers. Herein, we detail how cellular DDR processes engage various proteins that sense DNA damage, initiate signaling pathways to promote cell-cycle checkpoint activation, trigger apoptosis, and coordinate DNA repair. We focus on novel therapeutic strategies targeting promising DDR targets and discuss challenges of patient selection and the development of rational drug combinations. SIGNIFICANCE Various inhibitors of DDR components are in preclinical and clinical development. A thorough understanding of DDR pathway complexities must now be combined with strategies and lessons learned from the successful registration of PARP inhibitors in order to fully exploit the potential of DDR inhibitors and to ensure their long-term clinical success. Cancer Discov; 7(1); 20-37. ©2016 AACR.
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Affiliation(s)
| | | | - Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Timothy A Yap
- Royal Marsden NHS Foundation Trust, London, United Kingdom.
- The Institute of Cancer Research, London, United Kingdom
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Cobb AM, Larrieu D, Warren DT, Liu Y, Srivastava S, Smith AJO, Bowater RP, Jackson SP, Shanahan CM. Prelamin A impairs 53BP1 nuclear entry by mislocalizing NUP153 and disrupting the Ran gradient. Aging Cell 2016; 15:1039-1050. [PMID: 27464478 PMCID: PMC5114580 DOI: 10.1111/acel.12506] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2016] [Indexed: 01/29/2023] Open
Abstract
The nuclear lamina is essential for the proper structure and organization of the nucleus. Deregulation of A-type lamins can compromise genomic stability, alter chromatin organization and cause premature vascular aging. Here, we show that accumulation of the lamin A precursor, prelamin A, inhibits 53BP1 recruitment to sites of DNA damage and increases basal levels of DNA damage in aged vascular smooth muscle cells. We identify that this genome instability arises through defective nuclear import of 53BP1 as a consequence of abnormal topological arrangement of nucleoporin NUP153. We show for the first time that this nucleoporin is important for the nuclear localization of Ran and that the deregulated Ran gradient is likely to be compromising the nuclear import of 53BP1. Importantly, many of the defects associated with prelamin A expression were significantly reduced upon treatment with Remodelin, a small molecule recently reported to reverse deficiencies associated with abnormal nuclear lamina.
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Affiliation(s)
- Andrew M. Cobb
- The James Black CentreKing's College London125 Coldharbour LaneLondonSE5 9NUUK
| | - Delphine Larrieu
- Wellcome Trust/Cancer Research UK Gurdon InstituteThe Henry Wellcome Building of Cancer and Developmental BiologyUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
| | - Derek T. Warren
- The James Black CentreKing's College London125 Coldharbour LaneLondonSE5 9NUUK
| | - Yiwen Liu
- The James Black CentreKing's College London125 Coldharbour LaneLondonSE5 9NUUK
| | - Sonal Srivastava
- The James Black CentreKing's College London125 Coldharbour LaneLondonSE5 9NUUK
| | | | | | - Stephen P. Jackson
- Wellcome Trust/Cancer Research UK Gurdon InstituteThe Henry Wellcome Building of Cancer and Developmental BiologyUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
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Larsson P, Alwis I, Niego B, Sashindranath M, Fogelstrand P, Wu MCL, Glise L, Magnusson M, Daglas M, Bergh N, Jackson SP, Medcalf RL, Jern S. Valproic acid selectively increases vascular endothelial tissue-type plasminogen activator production and reduces thrombus formation in the mouse. J Thromb Haemost 2016; 14:2496-2508. [PMID: 27706906 DOI: 10.1111/jth.13527] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 08/25/2016] [Indexed: 01/04/2023]
Abstract
Essentials Stimulating endogenous fibrinolysis could be a novel antithrombotic strategy. The effect of valproic acid on endothelial tissue plasminogen activator in mice was investigated. Valproic acid increased tissue plasminogen activator expression in vascular endothelium. Valproic acid reduced fibrin deposition and thrombus formation after vascular injury. SUMMARY Background The endogenous fibrinolytic system has rarely been considered as a target to prevent thrombotic disease. Tissue-type plasminogen activator (t-PA) production is potently increased by histone deacetylase (HDAC) inhibitors in endothelial cells in vitro, but whether this translates into increased vascular t-PA production and an enhanced fibrinolytic capacity in vivo is unknown. Objectives To determine whether the HDAC inhibitor valproic acid (VPA) stimulates production of t-PA in the vasculature of mice, and whether VPA pretreatment affects fibrin deposition and clot formation after mechanical vessel injury. Methods Mice were injected with VPA twice daily for up to 5 days. t-PA mRNA, and antigen expression in the mouse aorta and the circulating levels of t-PA were determined. Fibrin and thrombus dynamics after mechanical vessel injury were monitored with intravital confocal microscopy. Potential effects of VPA on platelets and coagulation were investigated. Results and Conclusions We found that VPA treatment increased vascular t-PA production in vivo and, importantly, that VPA administration was associated with reduced fibrin accumulation and smaller thrombi in response to vascular injury, but still was not associated with an increased risk of bleeding. Furthermore, we observed that higher concentrations of VPA were required to stimulate t-PA production in the brain than in the vasculature. Thus, this study shows that VPA can be dosed to selectively manipulate the fibrinolytic system in the vascular compartment and reduce thrombus formation in vivo.
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Affiliation(s)
- P Larsson
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - I Alwis
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - B Niego
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Molecular Neurotrauma and Haemostasis, Central Clinical School, Monash University, Melbourne, Australia
| | - M Sashindranath
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Molecular Neurotrauma and Haemostasis, Central Clinical School, Monash University, Melbourne, Australia
| | - P Fogelstrand
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - M C L Wu
- Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - L Glise
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - M Magnusson
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - M Daglas
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Molecular Neurotrauma and Haemostasis, Central Clinical School, Monash University, Melbourne, Australia
| | - N Bergh
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - S P Jackson
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - R L Medcalf
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Molecular Neurotrauma and Haemostasis, Central Clinical School, Monash University, Melbourne, Australia
| | - S Jern
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Chang HHY, Watanabe G, Gerodimos CA, Ochi T, Blundell TL, Jackson SP, Lieber MR. Different DNA End Configurations Dictate Which NHEJ Components Are Most Important for Joining Efficiency. J Biol Chem 2016; 291:24377-24389. [PMID: 27703001 PMCID: PMC5114395 DOI: 10.1074/jbc.m116.752329] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/26/2016] [Indexed: 02/02/2023] Open
Abstract
The nonhomologous DNA end-joining (NHEJ) pathway is a key mechanism for repairing dsDNA breaks that occur often in eukaryotic cells. In the simplest model, these breaks are first recognized by Ku, which then interacts with other NHEJ proteins to improve their affinity at DNA ends. These include DNA-PKcs and Artemis for trimming the DNA ends; DNA polymerase μ and λ to add nucleotides; and the DNA ligase IV complex to ligate the ends with the additional factors, XRCC4 (X-ray repair cross-complementing protein 4), XLF (XRCC4-like factor/Cernunos), and PAXX (paralog of XRCC4 and XLF). In vivo studies have demonstrated the degrees of importance of these NHEJ proteins in the mechanism of repair of dsDNA breaks, but interpretations can be confounded by other cellular processes. In vitro studies with NHEJ proteins have been performed to evaluate the nucleolytic resection, polymerization, and ligation steps, but a complete system has been elusive. Here we have developed a NHEJ reconstitution system that includes the nuclease, polymerase, and ligase components to evaluate relative NHEJ efficiency and analyze ligated junctional sequences for various types of DNA ends, including blunt, 5' overhangs, and 3' overhangs. We find that different dsDNA end structures have differential dependence on these enzymatic components. The dependence of some end joining on only Ku and XRCC4·DNA ligase IV allows us to formulate a physical model that incorporates nuclease and polymerase components as needed.
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Affiliation(s)
- Howard H Y Chang
- From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and
| | - Go Watanabe
- From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and
| | - Christina A Gerodimos
- From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and
| | - Takashi Ochi
- the Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Tom L Blundell
- the Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Stephen P Jackson
- the Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Michael R Lieber
- From the Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology and the Section of Molecular & Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033 and.
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50
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Balmus G, Barros AC, Wijnhoven PWG, Lescale C, Hasse HL, Boroviak K, le Sage C, Doe B, Speak AO, Galli A, Jacobsen M, Deriano L, Adams DJ, Blackford AN, Jackson SP. Synthetic lethality between PAXX and XLF in mammalian development. Genes Dev 2016; 30:2152-2157. [PMID: 27798842 PMCID: PMC5088564 DOI: 10.1101/gad.290510.116] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/21/2016] [Indexed: 12/14/2022]
Abstract
PAXX was identified recently as a novel nonhomologous end-joining DNA repair factor in human cells. To characterize its physiological roles, we generated Paxx-deficient mice. Like Xlf-/- mice, Paxx-/- mice are viable, grow normally, and are fertile but show mild radiosensitivity. Strikingly, while Paxx loss is epistatic with Ku80, Lig4, and Atm deficiency, Paxx/Xlf double-knockout mice display embryonic lethality associated with genomic instability, cell death in the central nervous system, and an almost complete block in lymphogenesis, phenotypes that closely resemble those of Xrcc4-/- and Lig4-/- mice. Thus, combined loss of Paxx and Xlf is synthetic-lethal in mammals.
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Affiliation(s)
- Gabriel Balmus
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge CB10 1HH, United Kingdom
| | - Ana C Barros
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge CB10 1HH, United Kingdom
| | - Paul W G Wijnhoven
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Chloé Lescale
- Department of Immunology, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Hélène Lenden Hasse
- Department of Immunology, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | | | - Carlos le Sage
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Brendan Doe
- Wellcome Trust Sanger Institute, Cambridge CB10 1HH, United Kingdom
| | | | - Antonella Galli
- Wellcome Trust Sanger Institute, Cambridge CB10 1HH, United Kingdom
| | | | - Ludovic Deriano
- Department of Immunology, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - David J Adams
- Wellcome Trust Sanger Institute, Cambridge CB10 1HH, United Kingdom
| | - Andrew N Blackford
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
- Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Stephen P Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge CB10 1HH, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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