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Jadav R, Weiland F, Noordermeer SM, Carroll T, Gao Y, Wang J, Zhou H, Lamoliatte F, Toth R, Macartney T, Brown F, Hastie CJ, Alabert C, van Attikum H, Zenke F, Masson JY, Rouse J. Chemo-Phosphoproteomic Profiling with ATR Inhibitors Berzosertib and Gartisertib Uncovers New Biomarkers and DNA Damage Response Regulators. Mol Cell Proteomics 2024; 23:100802. [PMID: 38880245 PMCID: PMC11338954 DOI: 10.1016/j.mcpro.2024.100802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 06/04/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024] Open
Abstract
The ATR kinase protects cells against DNA damage and replication stress and represents a promising anti-cancer drug target. The ATR inhibitors (ATRi) berzosertib and gartisertib are both in clinical trials for the treatment of advanced solid tumors as monotherapy or in combination with genotoxic agents. We carried out quantitative phospho-proteomic screening for ATR biomarkers that are highly sensitive to berzosertib and gartisertib, using an optimized mass spectrometry pipeline. Screening identified a range of novel ATR-dependent phosphorylation events, which were grouped into three broad classes: (i) targets whose phosphorylation is highly sensitive to ATRi and which could be the next generation of ATR biomarkers; (ii) proteins with known genome maintenance roles not previously known to be regulated by ATR; (iii) novel targets whose cellular roles are unclear. Class iii targets represent candidate DNA damage response proteins and, with this in mind, proteins in this class were subjected to secondary screening for recruitment to DNA damage sites. We show that one of the proteins recruited, SCAF1, interacts with RNAPII in a phospho-dependent manner and recruitment requires PARP activity and interaction with RNAPII. We also show that SCAF1 deficiency partly rescues RAD51 loading in cells lacking the BRCA1 tumor suppressor. Taken together these data reveal potential new ATR biomarkers and new genome maintenance factors.
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Affiliation(s)
- Rathan Jadav
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Florian Weiland
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Sylvie M Noordermeer
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands; Department of Genetics, Oncode Institute, Utrecht, The Netherlands
| | - Thomas Carroll
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Yuandi Gao
- CHU de Quebec Research Center, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec Cit, Quebec, Canada
| | - Jianming Wang
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Houjiang Zhou
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Fiona Brown
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - C James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Constance Alabert
- Division of Molecular, Cell and Developmental Biology, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Frank Zenke
- EMD Serono, Research Unit Oncology, Billerica, Massachusetts, USA
| | - Jean-Yves Masson
- CHU de Quebec Research Center, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec Cit, Quebec, Canada
| | - John Rouse
- MRC Protein Phosphorylation and Ubiquitylation Unit and School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK.
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Töpf A, Cox D, Zaharieva IT, Di Leo V, Sarparanta J, Jonson PH, Sealy IM, Smolnikov A, White RJ, Vihola A, Savarese M, Merteroglu M, Wali N, Laricchia KM, Venturini C, Vroling B, Stenton SL, Cummings BB, Harris E, Marini-Bettolo C, Diaz-Manera J, Henderson M, Barresi R, Duff J, England EM, Patrick J, Al-Husayni S, Biancalana V, Beggs AH, Bodi I, Bommireddipalli S, Bönnemann CG, Cairns A, Chiew MT, Claeys KG, Cooper ST, Davis MR, Donkervoort S, Erasmus CE, Fassad MR, Genetti CA, Grosmann C, Jungbluth H, Kamsteeg EJ, Lornage X, Löscher WN, Malfatti E, Manzur A, Martí P, Mongini TE, Muelas N, Nishikawa A, O'Donnell-Luria A, Ogonuki N, O'Grady GL, O'Heir E, Paquay S, Phadke R, Pletcher BA, Romero NB, Schouten M, Shah S, Smuts I, Sznajer Y, Tasca G, Taylor RW, Tuite A, Van den Bergh P, VanNoy G, Voermans NC, Wanschitz JV, Wraige E, Yoshimura K, Oates EC, Nakagawa O, Nishino I, Laporte J, Vilchez JJ, MacArthur DG, Sarkozy A, Cordell HJ, Udd B, Busch-Nentwich EM, Muntoni F, Straub V. Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy. Nat Genet 2024; 56:395-407. [PMID: 38429495 PMCID: PMC10937387 DOI: 10.1038/s41588-023-01651-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 12/19/2023] [Indexed: 03/03/2024]
Abstract
In digenic inheritance, pathogenic variants in two genes must be inherited together to cause disease. Only very few examples of digenic inheritance have been described in the neuromuscular disease field. Here we show that predicted deleterious variants in SRPK3, encoding the X-linked serine/argenine protein kinase 3, lead to a progressive early onset skeletal muscle myopathy only when in combination with heterozygous variants in the TTN gene. The co-occurrence of predicted deleterious SRPK3/TTN variants was not seen among 76,702 healthy male individuals, and statistical modeling strongly supported digenic inheritance as the best-fitting model. Furthermore, double-mutant zebrafish (srpk3-/-; ttn.1+/-) replicated the myopathic phenotype and showed myofibrillar disorganization. Transcriptome data suggest that the interaction of srpk3 and ttn.1 in zebrafish occurs at a post-transcriptional level. We propose that digenic inheritance of deleterious changes impacting both the protein kinase SRPK3 and the giant muscle protein titin causes a skeletal myopathy and might serve as a model for other genetic diseases.
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Affiliation(s)
- Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Dan Cox
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Irina T Zaharieva
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
| | - Valeria Di Leo
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Jaakko Sarparanta
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Per Harald Jonson
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Ian M Sealy
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Andrei Smolnikov
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Richard J White
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Anna Vihola
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Neuromuscular Research Centre, Tampere University and University Hospital, Tampere, Finland
| | - Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Munise Merteroglu
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Laboratory of Angiogenesis and Cancer Metabolism, Department of Biology, University of Padua, Padua, Italy
| | - Neha Wali
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Cristina Venturini
- Division of Infection and Immunity, University College London, London, UK
| | | | - Sarah L Stenton
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Beryl B Cummings
- Laboratory of Angiogenesis and Cancer Metabolism, Department of Biology, University of Padua, Padua, Italy
| | - Elizabeth Harris
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Northern Genetics Service, Institute of Genetics Medicine, Newcastle upon Tyne, UK
| | - Chiara Marini-Bettolo
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Jordi Diaz-Manera
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Matt Henderson
- Muscle Immunoanalysis Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Jennifer Duff
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Eleina M England
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jane Patrick
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sundos Al-Husayni
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Valerie Biancalana
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Inserm U1258, Cnrs UMR7104, Université de Strasbourg, Illkirch, France
| | - Alan H Beggs
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Istvan Bodi
- Department of Clinical Neuropathology, King's College Hospital NHS Foundation Trust, London, UK
| | - Shobhana Bommireddipalli
- Kids Neuroscience Centre, the Children's Hospital at Westmead, the University of Sydney and the Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Anita Cairns
- Neurosciences Department, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Mei-Ting Chiew
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Perth, Western Australia, Australia
| | - Kristl G Claeys
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
- Laboratory for Muscle Diseases and Neuropathies, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Sandra T Cooper
- Kids Neuroscience Centre, the Children's Hospital at Westmead, the University of Sydney and the Children's Medical Research Institute, Westmead, New South Wales, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Perth, Western Australia, Australia
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Corrie E Erasmus
- Department of Paediatric Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, Amalia Children's Hospital, Nijmegen, The Netherlands
| | - Mahmoud R Fassad
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Casie A Genetti
- The Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carla Grosmann
- Department of Neurology, Rady Children's Hospital University of California San Diego, San Diego, CA, USA
| | - Heinz Jungbluth
- Department of Paediatric Neurology, Neuromuscular Service, Evelina's Children Hospital, Guy's & St. Thomas' Hospital NHS Foundation Trust, London, UK
- Randall Centre for Cell and Molecular Biophysics, Muscle Signalling Section, Faculty of Life Sciences and Medicine (FoLSM), King's College London, London, UK
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Xavière Lornage
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Inserm U1258, Cnrs UMR7104, Université de Strasbourg, Illkirch, France
| | - Wolfgang N Löscher
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Edoardo Malfatti
- APHP, Neuromuscular Reference Center Nord-Est-Ile-de-France, Henri Mondor Hospital, Université Paris Est, U955, INSERM, Creteil, France
| | - Adnan Manzur
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
| | - Pilar Martí
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Neuromuscular Research Group, IIS La Fe, Valencia, Spain
| | - Tiziana E Mongini
- Department of Neurosciences Rita Levi Montalcini, Università degli Studi di Torino, Torino, Italy
| | - Nuria Muelas
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Neuromuscular Research Group, IIS La Fe, Valencia, Spain
- Department of Medicine, Universitat de Valencia, Valencia, Spain
- Neuromuscular Diseases Unit, Neurology Department, Hospital Universitari I Politècnic La Fe, Valencia, Spain
| | - Atsuko Nishikawa
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | | | - Gina L O'Grady
- Starship Children's Health, Auckland District Health Board, Auckland, New Zealand
| | - Emily O'Heir
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stéphanie Paquay
- Cliniques Universitaires St-Luc, Centre de Référence Neuromusculaire, Université de Louvain, Brussels, Belgium
| | - Rahul Phadke
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
| | - Beth A Pletcher
- Division of Clinical Genetics, Department of Pediatrics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Norma B Romero
- Neuromuscular Morphology Unit, Myology Institute, Sorbonne Université, Centre de Référence de Pathologie Neuromusculaire Nord/Est/Ile-de-France (APHP), GH Pitié-Salpêtrière, Paris, France
| | - Meyke Schouten
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Snehal Shah
- Department of Neurology, Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Izelle Smuts
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Yves Sznajer
- Center for Human Genetic, Cliniques Universitaires Saint Luc, UCLouvain, Brussels, Belgium
| | - Giorgio Tasca
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Allysa Tuite
- Division of Clinical Genetics, Department of Pediatrics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Peter Van den Bergh
- Cliniques Universitaires St-Luc, Centre de Référence Neuromusculaire, Université de Louvain, Brussels, Belgium
| | - Grace VanNoy
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicol C Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Julia V Wanschitz
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Elizabeth Wraige
- Evelina's Children Hospital, Guy's & St. Thomas' Hospital NHS Foundation Trust, London, UK
| | | | - Emily C Oates
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Osamu Nakagawa
- Department of Molecular Physiology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Jocelyn Laporte
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Inserm U1258, Cnrs UMR7104, Université de Strasbourg, Illkirch, France
| | - Juan J Vilchez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Neuromuscular Research Group, IIS La Fe, Valencia, Spain
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Anna Sarkozy
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
| | - Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Bjarne Udd
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Neuromuscular Research Centre, Tampere University and University Hospital, Tampere, Finland
| | - Elisabeth M Busch-Nentwich
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Hospital, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, UCL & Great Ormond Street Hospital Trust, London, UK
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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