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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] [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: 03/29/2021] [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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2
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Schoenmakers E, Marelli F, Jørgensen HF, Visser WE, Moran C, Groeneweg S, Avalos C, Jurgens SJ, Figg N, Finigan A, Wali N, Agostini M, Wardle-Jones H, Lyons G, Rusk R, Gopalan D, Twiss P, Visser JJ, Goddard M, Nashef SAM, Heijmen R, Clift P, Sinha S, Pirruccello JP, Ellinor PT, Busch-Nentwich EM, Ramirez-Solis R, Murphy MP, Persani L, Bennett M, Chatterjee K. Selenoprotein deficiency disorder predisposes to aortic aneurysm formation. Nat Commun 2023; 14:7994. [PMID: 38042913 PMCID: PMC10693596 DOI: 10.1038/s41467-023-43851-6] [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: 02/06/2023] [Accepted: 11/22/2023] [Indexed: 12/04/2023] Open
Abstract
Aortic aneurysms, which may dissect or rupture acutely and be lethal, can be a part of multisystem disorders that have a heritable basis. We report four patients with deficiency of selenocysteine-containing proteins due to selenocysteine Insertion Sequence Binding Protein 2 (SECISBP2) mutations who show early-onset, progressive, aneurysmal dilatation of the ascending aorta due to cystic medial necrosis. Zebrafish and male mice with global or vascular smooth muscle cell (VSMC)-targeted disruption of Secisbp2 respectively show similar aortopathy. Aortas from patients and animal models exhibit raised cellular reactive oxygen species, oxidative DNA damage and VSMC apoptosis. Antioxidant exposure or chelation of iron prevents oxidative damage in patient's cells and aortopathy in the zebrafish model. Our observations suggest a key role for oxidative stress and cell death, including via ferroptosis, in mediating aortic degeneration.
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Affiliation(s)
- Erik Schoenmakers
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Federica Marelli
- Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano IRCCS, 20149, Milano, Italy
| | - Helle F Jørgensen
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, UK
| | - W Edward Visser
- Department of Internal Medicine and Rotterdam Thyroid Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Carla Moran
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Stefan Groeneweg
- Department of Internal Medicine and Rotterdam Thyroid Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Carolina Avalos
- Department of Paediatric Endocrinology, Clinica Alemana de Santiago, Vitacura, Chile
| | - Sean J Jurgens
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Nichola Figg
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, UK
| | - Alison Finigan
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, UK
| | - Neha Wali
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Maura Agostini
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | | | - Greta Lyons
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Rosemary Rusk
- Department of Cardiology, Addenbrookes Hospital, Cambridge, UK
| | - Deepa Gopalan
- Department of Radiology, Addenbrookes Hospital, Cambridge, UK
| | - Philip Twiss
- Cambridge Genomics Laboratory, Addenbrookes Hospital, Cambridge, UK
| | - Jacob J Visser
- Department of Radiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Martin Goddard
- Department of Pathology, Royal Papworth Hospital, Cambridge, UK
| | - Samer A M Nashef
- Department of Cardiothoracic Surgery, Royal Papworth Hospital, Cambridge, UK
| | - Robin Heijmen
- Department of Cardiothoracic Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul Clift
- Department of Cardiology, Queen Elizabeth Hospital, Birmingham, UK
| | - Sanjay Sinha
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, UK
| | - James P Pirruccello
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Cardiology, University of California San Francisco, San Francisco, CA, USA
| | - Patrick T Ellinor
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Demoulas Center for Cardiac Arrhythmias, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Luca Persani
- Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano IRCCS, 20149, Milano, Italy
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, 20100, Milano, Italy
| | - Martin Bennett
- Section of Cardiorespiratory Medicine, University of Cambridge, Cambridge, UK
| | - Krishna Chatterjee
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
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Lawson M, Cureton N, Ros S, Cheraghchi-Bashi A, Urosevic J, D'Arcy S, Delpuech O, DuPont M, Fisher DI, Gangl ET, Lewis H, Trueman D, Wali N, Williamson SC, Moss J, Montaudon E, Derrien H, Marangoni E, Miragaia RJ, Gagrica S, Morentin-Gutierrez P, Moss TA, Maglennon G, Sutton D, Polanski R, Rosen A, Cairns J, Zhang P, Sánchez-Guixé M, Serra V, Critchlow SE, Scott JS, Lindemann JP, Barry ST, Klinowska T, Morrow CJ, S Carnevalli L. The Next-Generation Oral Selective Estrogen Receptor Degrader Camizestrant (AZD9833) Suppresses ER+ Breast Cancer Growth and Overcomes Endocrine and CDK4/6 Inhibitor Resistance. Cancer Res 2023; 83:3989-4004. [PMID: 37725704 PMCID: PMC10690091 DOI: 10.1158/0008-5472.can-23-0694] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/11/2023] [Accepted: 09/15/2023] [Indexed: 09/21/2023]
Abstract
Oral selective estrogen receptor degraders (SERD) could become the backbone of endocrine therapy (ET) for estrogen receptor-positive (ER+) breast cancer, as they achieve greater inhibition of ER-driven cancers than current ETs and overcome key resistance mechanisms. In this study, we evaluated the preclinical pharmacology and efficacy of the next-generation oral SERD camizestrant (AZD9833) and assessed ER-co-targeting strategies by combining camizestrant with CDK4/6 inhibitors (CDK4/6i) and PI3K/AKT/mTOR-targeted therapy in models of progression on CDK4/6i and/or ET. Camizestrant demonstrated robust and selective ER degradation, modulated ER-regulated gene expression, and induced complete ER antagonism and significant antiproliferation activity in ESR1 wild-type (ESR1wt) and mutant (ESR1m) breast cancer cell lines and patient-derived xenograft (PDX) models. Camizestrant also delivered strong antitumor activity in fulvestrant-resistant ESR1wt and ESR1m PDX models. Evaluation of camizestrant in combination with CDK4/6i (palbociclib or abemaciclib) in CDK4/6-naive and -resistant models, as well as in combination with PI3Kαi (alpelisib), mTORi (everolimus), or AKTi (capivasertib), indicated that camizestrant was active with CDK4/6i or PI3K/AKT/mTORi and that antitumor activity was further increased by the triple combination. The response was observed independently of PI3K pathway mutation status. Overall, camizestrant shows strong and broad antitumor activity in ER+ breast cancer as a monotherapy and when combined with CDK4/6i and PI3K/AKT/mTORi. SIGNIFICANCE Camizestrant, a next-generation oral SERD, shows promise in preclinical models of ER+ breast cancer alone and in combination with CDK4/6 and PI3K/AKT/mTOR inhibitors to address endocrine resistance, a current barrier to treatment.
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Affiliation(s)
- Mandy Lawson
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Natalie Cureton
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Susana Ros
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | | | - Jelena Urosevic
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Sophie D'Arcy
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Oona Delpuech
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Michelle DuPont
- Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts
| | - David I. Fisher
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Eric T. Gangl
- Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts
| | - Hilary Lewis
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Dawn Trueman
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Neha Wali
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | | | - Jennifer Moss
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | | | | | | | | | - Sladjana Gagrica
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | | | - Thomas A. Moss
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Gareth Maglennon
- Clinical Pharmacology and Safety Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Daniel Sutton
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Radoslaw Polanski
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Alan Rosen
- Research and Early Development, Oncology R&D, AstraZeneca, Waltham, Massachusetts
| | - Jonathan Cairns
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Pei Zhang
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Mònica Sánchez-Guixé
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Susan E. Critchlow
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - James S. Scott
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | | | - Simon T. Barry
- The Discovery Centre, Biomedical Campus, AstraZeneca, Cambridge, United Kingdom
| | - Teresa Klinowska
- Late Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
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4
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Kuczynski EA, Morlino G, Peter A, Coenen‐Stass AML, Moss JI, Wali N, Delpuech O, Reddy A, Solanki A, Sinclair C, Calado DP, Carnevalli LS. A preclinical model of peripheral T-cell lymphoma GATA3 reveals DNA damage response pathway vulnerability. EMBO Mol Med 2022; 14:e15816. [PMID: 35510955 PMCID: PMC9174882 DOI: 10.15252/emmm.202215816] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 11/20/2022] Open
Abstract
Peripheral T-cell lymphoma (PTCL) represents a rare group of heterogeneous diseases in urgent need of effective treatments. A scarcity of disease-relevant preclinical models hinders research advances. Here, we isolated a novel mouse (m)PTCL by serially transplanting a lymphoma from a germinal center B-cell hyperplasia model (Cγ1-Cre Blimp1fl/fl ) through immune-competent mice. Lymphoma cells were identified as clonal TCRβ+ T-helper cells expressing T-follicular helper markers. We also observed coincident B-cell activation and development of a de novo B-cell lymphoma in the model, reminiscent of B-cell activation/lymphomagenesis found in human PTCL. Molecular profiling linked the mPTCL to the high-risk "GATA3" subtype of PTCL, showing GATA3 and Th2 gene expression, PI3K/mTOR pathway enrichment, hyperactivated MYC, and genome instability. Exome sequencing identified a human-relevant oncogenic β-catenin mutation possibly involved in T-cell lymphomagenesis. Prolonged treatment responses were achieved in vivo by targeting ATR in the DNA damage response (DDR), a result corroborated in PTCL cell lines. This work provides mechanistic insight into the molecular and immunological drivers of T-cell lymphomagenesis and proposes DDR inhibition as an effective and readily translatable therapy in PTCL.
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Affiliation(s)
| | - Giulia Morlino
- Immunity & Cancer LaboratoryFrancis Crick InstituteLondonUK
- Present address:
Benevolent AILondonUK
| | | | - Anna M L Coenen‐Stass
- Oncology R&DAstraZenecaCambridgeUK
- Present address:
Translational MedicineMerck Healthcare KGaADarmstadtGermany
| | | | - Neha Wali
- Oncology R&DAstraZenecaCambridgeUK
- Present address:
LGC Genomics DivisionCambridgeUK
| | | | | | | | - Charles Sinclair
- Oncology R&DAstraZenecaCambridgeUK
- Present address:
Flagship PioneeringCambridgeMAUSA
| | - Dinis P Calado
- Immunity & Cancer LaboratoryFrancis Crick InstituteLondonUK
- Peter Gorer Department of ImmunobiologySchool of Immunology & Microbial SciencesLondonUK
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5
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Wali N, Merteroglu M, White RJ, Busch-Nentwich EM. Total Nucleic Acid Extraction from Single Zebrafish Embryos for Genotyping and RNA-seq. Bio Protoc 2022; 12:e4284. [PMID: 35118175 PMCID: PMC8769753 DOI: 10.21769/bioprotoc.4284] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/04/2021] [Accepted: 10/21/2021] [Indexed: 04/25/2024] Open
Abstract
RNA sequencing allows for the quantification of the transcriptome of embryos to investigate transcriptional responses to various perturbations (e.g., mutations, infections, drug treatments). Previous protocols either lack the option to genotype individual samples, or are laborious and therefore difficult to do at a large scale. We have developed a protocol to extract total nucleic acid from individual zebrafish embryos. Individual embryos are lysed in 96-well plates and nucleic acid is extracted using SPRI beads. The total nucleic acid can be genotyped and then DNase I treated to produce RNA samples for sequencing. This protocol allows for processing large numbers of individual samples, with the ability to genotype each sample, which makes it possible to undertake transcriptomic analysis on mutants at timepoints before the phenotype is visible. Graphic abstract: Extraction of total nucleic acid from individual zebrafish embryos for genotyping and RNA-seq.
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Affiliation(s)
- Neha Wali
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Munise Merteroglu
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Richard J. White
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Elisabeth M. Busch-Nentwich
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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6
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Carnevalli LS, Taylor MA, King M, Coenen-Stass AML, Hughes AM, Bell S, Proia TA, Wang Y, Ramos-Montoya A, Wali N, Carroll D, Singh M, Moschetta M, Gutierrez PM, Gardelli C, Critchlow SE, Klinowska T, Fawell SE, Barry ST. Macrophage Activation Status Rather than Repolarization Is Associated with Enhanced Checkpoint Activity in Combination with PI3Kγ Inhibition. Mol Cancer Ther 2021; 20:1080-1091. [PMID: 33785652 DOI: 10.1158/1535-7163.mct-20-0961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/08/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022]
Abstract
Suppressive myeloid cells mediate resistance to immune checkpoint blockade. PI3Kγ inhibition can target suppressive macrophages, and enhance efficacy of immune checkpoint inhibitors. However, how PI3Kγ inhibitors function in different tumor microenvironments (TME) to activate specific immune cells is underexplored. The effect of the novel PI3Kγ inhibitor AZD3458 was assessed in preclinical models. AZD3458 enhanced antitumor activity of immune checkpoint inhibitors in 4T1, CT26, and MC38 syngeneic models, increasing CD8+ T-cell activation status. Immune and TME biomarker analysis of MC38 tumors revealed that AZD3458 monotherapy or combination treatment did not repolarize the phenotype of tumor-associated macrophage cells but induced gene signatures associated with LPS and type II INF activation. The activation biomarkers were present across tumor macrophages that appear phenotypically heterogenous. AZD3458 alone or in combination with PD-1-blocking antibodies promoted an increase in antigen-presenting (MHCII+) and cytotoxic (iNOS+)-activated macrophages, as well as dendritic cell activation. AZD3458 reduced IL-10 secretion and signaling in primary human macrophages and murine tumor-associated macrophages, but did not strongly regulate IL-12 as observed in other studies. Therefore, rather than polarizing tumor macrophages, PI3Kγ inhibition with AZD3458 promotes a cytotoxic switch of macrophages into antigen-presenting activated macrophages, resulting in CD8 T-cell-mediated antitumor activity with immune checkpoint inhibitors associated with tumor and peripheral immune activation.
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Affiliation(s)
| | - Molly A Taylor
- Bioscience, Early Oncology, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Matthew King
- Bioscience, Early Oncology, R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Adina M Hughes
- Bioscience, Early Oncology, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Sigourney Bell
- Bioscience, Early Oncology, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Theresa A Proia
- Early Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Yanjun Wang
- Early Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Neha Wali
- Bioscience, Early Oncology, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Danielle Carroll
- Translational Medicine, Oncology, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Maneesh Singh
- Early Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | - Michele Moschetta
- Early Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Cristina Gardelli
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, AstraZeneca, Gothenburg, Sweden
| | - Susan E Critchlow
- Bioscience, Early Oncology, R&D, AstraZeneca, Cambridge, United Kingdom
| | - Teresa Klinowska
- Late Development, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Simon T Barry
- Bioscience, Early Oncology, R&D, AstraZeneca, Cambridge, United Kingdom.
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7
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Sánchez-González R, Ramis A, Nofrarías M, Wali N, Valle R, Pérez M, Perlas A, Majó N. Infectivity and pathobiology of H7N1 and H5N8 high pathogenicity avian influenza viruses for pigeons ( Columba livia var. domestica). Avian Pathol 2020; 50:98-106. [PMID: 33034513 DOI: 10.1080/03079457.2020.1832197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Avian influenza (AI) is one of the most important viral diseases in poultry, wildlife and humans. Available data indicate that pigeons play a minimum role in the epidemiology of AI. However, a degree of variation exists in the susceptibility of pigeons to highly pathogenic AI viruses (HPAIVs), especially since the emergence of the goose/Guangdong H5 lineage. Here, the pathogenesis of H5N8 HPAIV in comparison with a H7N1 HPAIV and the role of pigeons in the epidemiology of these viruses were evaluated. Local and urban pigeons (Columba livia var. domestica) were intranasally inoculated with 105 ELD50 of A/goose/Spain/IA17CR02699/2017 (H5N8) or A/Chicken/Italy/5093/1999 (H7N1) and monitored during 14 days. Several pigeons inoculated with H5N8 or H7N1 seroconverted. However, clinical signs, mortality, microscopic lesions and viral antigen were only detected in a local pigeon inoculated with H5N8 HPAIV. This pigeon presented prostration and neurological signs that correlated with the presence of large areas of necrosis and widespread AIV antigen in the central nervous system, indicating that the fatal outcome was associated with neurological dysfunction. Viral RNA in swabs was detected in some pigeons inoculated with H7N1 and H5N8, but it was inconsistent, short-term and at low titres. The present study demonstrates that the majority of pigeons were resistant to H5N8 and H7N1 HPAIVs, despite several pigeons developing asymptomatic infections. The limited viral shedding indicates a minimum role of pigeons as amplifiers of HPAIVs, regardless of the viral lineage, and suggests that this species may represent a low risk for environmental contamination. RESEARCH HIGHLIGHTS H7N1 and H5N8 HPAIVs can produce subclinical infections in pigeons. The mortality caused by H5N8 HPAIV in one pigeon was associated with neurological dysfunction. Pigeons represent a low risk for environmental contamination by HPAIVs.
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Affiliation(s)
- R Sánchez-González
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Bellaterra, España
| | - A Ramis
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Bellaterra, España.,Departament de Sanitat i Anatomia Birds, Universitat Autònoma de Barcelona, Bellaterra, España
| | - M Nofrarías
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Bellaterra, España
| | - N Wali
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Bellaterra, España
| | - R Valle
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Bellaterra, España
| | - M Pérez
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Bellaterra, España
| | - A Perlas
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Bellaterra, España
| | - N Majó
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Bellaterra, España.,Departament de Sanitat i Anatomia Birds, Universitat Autònoma de Barcelona, Bellaterra, España
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8
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Sánchez-González R, Ramis A, Nofrarías M, Wali N, Valle R, Pérez M, Perlas A, Majó N. Experimental infection of domestic geese ( Anser anser var. domesticus) with H5N8 Gs/GD and H7N1 highly pathogenic avian influenza viruses. Avian Pathol 2020; 49:642-657. [PMID: 32795171 DOI: 10.1080/03079457.2020.1809635] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Prior to the emergence of the Asian-origin H5 Goose/Guangdong/1/96 (Gs/GD) lineage, highly pathogenic avian influenza viruses (HPAIV) had rarely caused high mortalities in domestic geese. In 2016/2017 European epidemics, H5N8 Gs/GD clade 2.3.4.4 Group B produced an unprecedented number of outbreaks in waterfowl holdings. In this study, the pathogenesis of H5N8 HPAIV in comparison with H7N1 HPAIV, and the role of domestic geese in the epidemiology of these viruses, were evaluated. Local and commercial geese (Anser anser var. domesticus) were intranasally inoculated with 105 ELD50 of A/goose/Spain/IA17CR02699/2017 (H5N8) or A/Chicken/Italy/5093/1999 (H7N1) and monitored daily during 15 days. H5N8 was highly virulent to domestic geese, reaching 100% mortality by 10 days post-infection. Systemic microscopic necrotizing lesions associated with widespread AIV-antigen were detected by IHC techniques, the central nervous system being the most severely affected. High viral loads, measured by qRT-PCR, were present in all samples collected: oral and cloacal swabs, plasma tissues, and moderate levels in pool water. Domestic geese were also susceptible to H7N1 infection, as demonstrated by seroconversion and detection of viral RNA in tissues and plasma in some geese, but all lacked clinical signs. Viral shedding was confirmed in only some geese and was restricted to the oral route, but levels were high and still detected at the end of the study. Overall, H7N1 presents a lower lethality and shedding than H5N8 in geese; however, the viral shedding indicates that these species could play a role in the epidemiology of Gs/GD and other lineages of HPAIVs. RESEARCH HIGHLIGHTS H5N8 Gs/GD clade 2.3.4.4 Group B is highly virulent to domestic geese. The severity of H5N8 is associated with multisystemic replication. H7N1 can infect domestic geese but is avirulent to this species. Domestic geese could play a role in the epidemiology of Gs/GD HPAIVs.
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Affiliation(s)
- R Sánchez-González
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España.,Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - A Ramis
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España.,Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - M Nofrarías
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - N Wali
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - R Valle
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - M Pérez
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - A Perlas
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
| | - N Majó
- IRTA, Centre de Recerca en Sanitat Animal (IRTA-CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España.,Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, España
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9
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Schubert AD, Channah Broner E, Agrawal N, London N, Pearson A, Gupta A, Wali N, Seiwert TY, Wheelan S, Lingen M, Macleod K, Allen H, Chatterjee A, Vassiliki S, Gaykalova D, Hoque MO, Sidransky D, Suresh K, Izumchenko E. Somatic mitochondrial mutation discovery using ultra-deep sequencing of the mitochondrial genome reveals spatial tumor heterogeneity in head and neck squamous cell carcinoma. Cancer Lett 2019; 471:49-60. [PMID: 31830557 DOI: 10.1016/j.canlet.2019.12.006] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022]
Abstract
Mutations in mitochondrial DNA (mtDNA) have been linked to risk, progression, and treatment response of head and neck squamous cell carcinoma (HNSCC). Due to their clonal nature and high copy number, mitochondrial mutations could serve as powerful molecular markers for detection of cancer cells in bodily fluids, surgical margins, biopsies and lymph node (LN) metastasis, especially at sites where tumor involvement is not histologically apparent. Despite a pressing need for high-throughput, cost-effective mtDNA mutation profiling system, current methods for library preparation are still imperfect for detection of low prevalence heteroplasmic mutations. To this end, we have designed an ultra-deep amplicon-based sequencing library preparation approach that covers the entire mitochondrial genome. We sequenced mtDNA in 28 HNSCCs, matched LNs, surgical margins and bodily fluids, and applied multiregional sequencing approach on 14 primary tumors. Our results demonstrate that this quick, sensitive and cost-efficient method allows obtaining a snapshot on the mitochondrial heterogeneity, and can be used for detection of low frequency tumor-associated mtDNA mutations in LNs, sputum and serum specimens. These findings provide the foundation for using mitochondrial sequencing for risk assessment, early detection, and tumor surveillance.
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Affiliation(s)
- Adrian D Schubert
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Esther Channah Broner
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Nishant Agrawal
- Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Nyall London
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Alexander Pearson
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Anuj Gupta
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Neha Wali
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Tanguy Y Seiwert
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Sarah Wheelan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Mark Lingen
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Kay Macleod
- The Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Hailey Allen
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Saloura Vassiliki
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Daria Gaykalova
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Mohammad O Hoque
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - David Sidransky
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Karthik Suresh
- Division of Pulmonary Critical Care Medicine, Johns Hopkins University School of Medicine. Baltimore, MD, USA
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA.
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10
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Collins JE, White RJ, Staudt N, Sealy IM, Packham I, Wali N, Tudor C, Mazzeo C, Green A, Siragher E, Ryder E, White JK, Papatheodoru I, Tang A, Füllgrabe A, Billis K, Geyer SH, Weninger WJ, Galli A, Hemberger M, Stemple DL, Robertson E, Smith JC, Mohun T, Adams DJ, Busch-Nentwich EM. Common and distinct transcriptional signatures of mammalian embryonic lethality. Nat Commun 2019; 10:2792. [PMID: 31243271 PMCID: PMC6594971 DOI: 10.1038/s41467-019-10642-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 07/16/2018] [Accepted: 05/22/2019] [Indexed: 12/20/2022] Open
Abstract
The Deciphering the Mechanisms of Developmental Disorders programme has analysed the morphological and molecular phenotypes of embryonic and perinatal lethal mouse mutant lines in order to investigate the causes of embryonic lethality. Here we show that individual whole-embryo RNA-seq of 73 mouse mutant lines (>1000 transcriptomes) identifies transcriptional events underlying embryonic lethality and associates previously uncharacterised genes with specific pathways and tissues. For example, our data suggest that Hmgxb3 is involved in DNA-damage repair and cell-cycle regulation. Further, we separate embryonic delay signatures from mutant line-specific transcriptional changes by developing a baseline mRNA expression catalogue of wild-type mice during early embryogenesis (4-36 somites). Analysis of transcription outside coding sequence identifies deregulation of repetitive elements in Morc2a mutants and a gene involved in gene-specific splicing. Collectively, this work provides a large scale resource to further our understanding of early embryonic developmental disorders.
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Affiliation(s)
- John E Collins
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Richard J White
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Nicole Staudt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Ian M Sealy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Ian Packham
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Neha Wali
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Catherine Tudor
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Cecilia Mazzeo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Angela Green
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Emma Siragher
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Edward Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Irene Papatheodoru
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Amy Tang
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Stefan H Geyer
- Division of Anatomy, MIC, Medical University of Vienna, Waehringerstr. 13, 1090, Wien, Austria
| | - Wolfgang J Weninger
- Division of Anatomy, MIC, Medical University of Vienna, Waehringerstr. 13, 1090, Wien, Austria
| | - Antonella Galli
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Myriam Hemberger
- The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK
- Departments of Biochemistry & Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Derek L Stemple
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Camena Bioscience, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Elizabeth Robertson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - James C Smith
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Timothy Mohun
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Elisabeth M Busch-Nentwich
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK.
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11
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Dooley CM, Wali N, Sealy IM, White RJ, Stemple DL, Collins JE, Busch-Nentwich EM. The gene regulatory basis of genetic compensation during neural crest induction. PLoS Genet 2019; 15:e1008213. [PMID: 31199790 PMCID: PMC6594659 DOI: 10.1371/journal.pgen.1008213] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 03/25/2019] [Revised: 06/26/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022] Open
Abstract
The neural crest (NC) is a vertebrate-specific cell type that contributes to a wide range of different tissues across all three germ layers. The gene regulatory network (GRN) responsible for the formation of neural crest is conserved across vertebrates. Central to the induction of the NC GRN are AP-2 and SoxE transcription factors. NC induction robustness is ensured through the ability of some of these transcription factors to compensate loss of function of gene family members. However the gene regulatory events underlying compensation are poorly understood. We have used gene knockout and RNA sequencing strategies to dissect NC induction and compensation in zebrafish. We genetically ablate the NC using double mutants of tfap2a;tfap2c or remove specific subsets of the NC with sox10 and mitfa knockouts and characterise genome-wide gene expression levels across multiple time points. We find that compensation through a single wild-type allele of tfap2c is capable of maintaining early NC induction and differentiation in the absence of tfap2a function, but many target genes have abnormal expression levels and therefore show sensitivity to the reduced tfap2 dosage. This separation of morphological and molecular phenotypes identifies a core set of genes required for early NC development. We also identify the 15 somites stage as the peak of the molecular phenotype which strongly diminishes at 24 hpf even as the morphological phenotype becomes more apparent. Using gene knockouts, we associate previously uncharacterised genes with pigment cell development and establish a role for maternal Hippo signalling in melanocyte differentiation. This work extends and refines the NC GRN while also uncovering the transcriptional basis of genetic compensation via paralogues. Embryonic development is an intricate process that requires genes to be active at the right time and place. Organisms have evolved mechanisms that ensure faithful execution of developmental programmes even if genes fail to function. For example, in a process called genetic compensation, one or more genes become activated in response to loss of function of another. In this work we use the zebrafish model to investigate how two related genes, tfap2a and tfap2c, interact to ensure establishment of the neural crest, a vertebrate-specific cell type that contributes to many different tissues. Losing tfap2a activity causes mild morphological defects and losing tfap2c has no visible effect. Yet when both are inactive, embryos are severely abnormal due to lack of neural crest-derived tissues. Here we show that loss of tfap2a triggers upregulation of tfap2c which prevents the loss of neural crest tissue. However, the genes normally regulated by tfap2a respond differently to tfap2c allowing us to identify the first tier of the Ap2 network and new players in neural crest biology. Our work demonstrates that the expression signature of partial, but morphologically sufficient, genetic compensation provides an opportunity to dissect gene regulatory networks.
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Affiliation(s)
| | - Neha Wali
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ian M. Sealy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Richard J. White
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Derek L. Stemple
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - John E. Collins
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elisabeth M. Busch-Nentwich
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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12
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Sanchez R, Nofrarias M, Wali N, Valle R, Pérez M, Majó N, Ramis A. Comparison of the pathobiology of two different highly pathogenic avian influenza strains of different origin in geese. J Comp Pathol 2019. [DOI: 10.1016/j.jcpa.2018.10.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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13
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Khanna S, Graef S, Mussai F, Thomas A, Wali N, Yenidunya BG, Yuan C, Morrow B, Zhang J, Korangy F, Greten TF, Steinberg SM, Stetler-Stevenson M, Middleton G, De Santo C, Hassan R. Tumor-Derived GM-CSF Promotes Granulocyte Immunosuppression in Mesothelioma Patients. Clin Cancer Res 2018; 24:2859-2872. [PMID: 29602801 PMCID: PMC6601632 DOI: 10.1158/1078-0432.ccr-17-3757] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 12/18/2017] [Revised: 02/09/2018] [Accepted: 03/23/2018] [Indexed: 12/12/2022]
Abstract
Purpose: The cross-talk between tumor cells, myeloid cells, and T cells can play a critical role in tumor pathogenesis and response to immunotherapies. Although the etiology of mesothelioma is well understood, the impact of mesothelioma tumor cells on the surrounding immune microenvironment is less well studied. In this study, the effect of the mesothelioma tumor microenvironment on circulating and infiltrating granulocytes and T cells is investigated.Experimental Design: Tumor tissues and peripheral blood from mesothelioma patients were evaluated for presence of granulocytes, which were then tested for their T-cell suppression potential. Different cocultures of granulocytes and/or mesothelioma tumor cells and/or T cells were set up to identify the mechanism of T-cell inhibition.Results: Analysis of human tumors showed that the mesothelioma microenvironment is enriched in infiltrating granulocytes, which inhibit T-cell proliferation and activation. Characterization of the whole blood at diagnosis identified similar, circulating, immunosuppressive CD11b+CD15+HLADR- granulocytes at increased frequency compared with healthy controls. Culture of healthy-donor granulocytes with human mesothelioma cells showed that GM-CSF upregulates NOX2 expression and the release of reactive oxygen species (ROS) from granulocytes, resulting in T-cell suppression. Immunohistochemistry and transcriptomic analysis revealed that a majority of mesothelioma tumors express GM-CSF and that higher GM-CSF expression correlated with clinical progression. Blockade of GM-CSF with neutralizing antibody, or ROS inhibition, restored T-cell proliferation, suggesting that targeting of GM-CSF could be of therapeutic benefit in these patients.Conclusions: Our study presents the mechanism behind the cross-talk between mesothelioma tumors and the immune microenvironment and indicates that targeting GM-CSF could be a novel treatment strategy to augment immunotherapy in patients with mesothelioma. Clin Cancer Res; 24(12); 2859-72. ©2018 AACR.
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Affiliation(s)
- Swati Khanna
- Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Suzanne Graef
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Francis Mussai
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Anish Thomas
- Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Neha Wali
- University of Maryland Baltimore County, Baltimore, Maryland
| | | | - Constance Yuan
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Betsy Morrow
- Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jingli Zhang
- Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Firouzeh Korangy
- Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Tim F Greten
- Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Seth M Steinberg
- Biostatistics and Data Management Section, Office of the Clinical Director, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Maryalice Stetler-Stevenson
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Gary Middleton
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Carmela De Santo
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Raffit Hassan
- Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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14
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Scahill CM, Digby Z, Sealy IM, White RJ, Wali N, Collins JE, Stemple DL, Busch-Nentwich EM. The age of heterozygous telomerase mutant parents influences the adult phenotype of their offspring irrespective of genotype in zebrafish. Wellcome Open Res 2018; 2:77. [PMID: 29568807 PMCID: PMC5840683 DOI: 10.12688/wellcomeopenres.12530.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2017] [Indexed: 12/03/2022] Open
Abstract
Background: Mutations in proteins involved in telomere maintenance lead to a range of human diseases, including dyskeratosis congenita, idiopathic pulmonary fibrosis and cancer. Telomerase functions to add telomeric repeats back onto the ends of chromosomes, however non-canonical roles of components of telomerase have recently been suggested. Methods: Here we use a zebrafish telomerase mutant which harbours a nonsense mutation in
tert to investigate the adult phenotypes of fish derived from heterozygous parents of different ages. Furthermore we use whole genome sequencing data to estimate average telomere lengths. Results: We show that homozygous offspring from older heterozygotes exhibit signs of body wasting at a younger age than those of younger parents, and that offspring of older heterozygous parents weigh less irrespective of genotype. We also demonstrate that
tert homozygous mutant fish have a male sex bias, and that clutches from older parents also have a male sex bias in the heterozygous and wild-type populations. Telomere length analysis reveals that the telomeres of younger heterozygous parents are shorter than those of older heterozygous parents. Conclusions: These data indicate that the phenotypes observed in offspring from older parents cannot be explained by telomere length. Instead we propose that Tert functions outside of telomere length maintenance in an age-dependent manner to influence the adult phenotypes of the next generation.
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Affiliation(s)
| | - Zsofia Digby
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ian M Sealy
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Richard J White
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Neha Wali
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - John E Collins
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Derek L Stemple
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
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15
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White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. A high-resolution mRNA expression time course of embryonic development in zebrafish. eLife 2017; 6. [PMID: 29144233 PMCID: PMC5690287 DOI: 10.7554/elife.30860] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/04/2017] [Indexed: 12/18/2022] Open
Abstract
We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.
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Affiliation(s)
| | - John E Collins
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Ian M Sealy
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Neha Wali
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Zsofia Digby
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Matthew P Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Anton J Enright
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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16
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Pickering J, Wali N, Towers M. Transcriptional changes in chick wing bud polarization induced by retinoic acid. Dev Dyn 2017; 246:682-690. [PMID: 28681415 PMCID: PMC5601294 DOI: 10.1002/dvdy.24543] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/11/2017] [Accepted: 06/21/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Retinoic acid is implicated in the induction of the gene encoding Sonic hedgehog (Shh) that specifies anteroposterior positional values and promotes growth of the developing limb bud. However, because retinoic acid is involved in limb initiation, it has been difficult to determine if it could have additional roles in anteroposterior patterning. To investigate this, we implanted retinoic acid-soaked beads to the anterior margin of the chick wing bud and performed microarray analyses prior to onset of Shh expression. RESULTS Retinoic acid up-regulates expression of Hoxd11-13 that encode transcription factors implicated in inducing Shh transcription and that are involved in digit development. In our assay, retinoic acid induces Shh transcription and, consequently, a new pattern of digits at a much later stage than anticipated. Retinoic acid represses many anteriorly expressed genes, including Bmp4, Lhx9, Msx2, and Alx4. We provide evidence that retinoic acid influences transcription via induction of dHAND and inhibition of Gli3 to establish a new anteroposterior pre-pattern. We show that transient exposure to retinoic acid can suppress distal development and expedite cells to transcriptionally respond to Shh. CONCLUSIONS Our findings reveal how retinoic acid and Shh signaling could cooperate in anteroposterior patterning of the limb. Developmental Dynamics 246:682-690, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Joseph Pickering
- Bateson CentreDepartment of Biomedical Science, University of SheffieldSheffieldUnited Kingdom
| | - Neha Wali
- Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - Matthew Towers
- Bateson CentreDepartment of Biomedical Science, University of SheffieldSheffieldUnited Kingdom
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17
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Anagnostou V, Smith KN, Forde PM, Niknafs N, Bhattacharya R, White J, Zhang T, Adleff V, Phallen J, Wali N, Hruban C, Guthrie VB, Rodgers K, Naidoo J, Kang H, Sharfman W, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Zahnow CA, Baylin SB, Scharpf RB, Brahmer JR, Karchin R, Pardoll DM, Velculescu VE. Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer. Cancer Discov 2017; 7:264-276. [PMID: 28031159 PMCID: PMC5733805 DOI: 10.1158/2159-8290.cd-16-0828] [Citation(s) in RCA: 640] [Impact Index Per Article: 91.4] [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: 07/26/2016] [Revised: 12/22/2016] [Accepted: 12/27/2016] [Indexed: 02/06/2023]
Abstract
Immune checkpoint inhibitors have shown significant therapeutic responses against tumors containing increased mutation-associated neoantigen load. We have examined the evolving landscape of tumor neoantigens during the emergence of acquired resistance in patients with non-small cell lung cancer after initial response to immune checkpoint blockade with anti-PD-1 or anti-PD-1/anti-CTLA-4 antibodies. Analyses of matched pretreatment and resistant tumors identified genomic changes resulting in loss of 7 to 18 putative mutation-associated neoantigens in resistant clones. Peptides generated from the eliminated neoantigens elicited clonal T-cell expansion in autologous T-cell cultures, suggesting that they generated functional immune responses. Neoantigen loss occurred through elimination of tumor subclones or through deletion of chromosomal regions containing truncal alterations, and was associated with changes in T-cell receptor clonality. These analyses provide insight into the dynamics of mutational landscapes during immune checkpoint blockade and have implications for the development of immune therapies that target tumor neoantigens.Significance: Acquired resistance to immune checkpoint therapy is being recognized more commonly. This work demonstrates for the first time that acquired resistance to immune checkpoint blockade can arise in association with the evolving landscape of mutations, some of which encode tumor neoantigens recognizable by T cells. These observations imply that widening the breadth of neoantigen reactivity may mitigate the development of acquired resistance. Cancer Discov; 7(3); 264-76. ©2017 AACR.See related commentary by Yang, p. 250This article is highlighted in the In This Issue feature, p. 235.
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MESH Headings
- Adult
- Antibodies, Monoclonal/pharmacology
- Antibodies, Monoclonal/therapeutic use
- Antigens, Neoplasm/immunology
- Antineoplastic Agents, Immunological/pharmacology
- Antineoplastic Agents, Immunological/therapeutic use
- CTLA-4 Antigen/genetics
- CTLA-4 Antigen/immunology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/therapy
- Cell Cycle Checkpoints/drug effects
- Cell Cycle Checkpoints/immunology
- Cohort Studies
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/immunology
- Female
- Humans
- Immunotherapy
- Ipilimumab/pharmacology
- Ipilimumab/therapeutic use
- Janus Kinase 1/genetics
- Janus Kinase 2/genetics
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Lung Neoplasms/pathology
- Lung Neoplasms/therapy
- Male
- Middle Aged
- Mutation
- Nivolumab
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Programmed Cell Death 1 Receptor/genetics
- Programmed Cell Death 1 Receptor/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
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Affiliation(s)
- Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kellie N Smith
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Patrick M Forde
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Noushin Niknafs
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Rohit Bhattacharya
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland
| | - James White
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Vilmos Adleff
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jillian Phallen
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Neha Wali
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Carolyn Hruban
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Violeta B Guthrie
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Kristen Rodgers
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jarushka Naidoo
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hyunseok Kang
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - William Sharfman
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christos Georgiades
- Department of Radiology and Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Franco Verde
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peter Illei
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Qing Kay Li
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Edward Gabrielson
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Malcolm V Brock
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Cynthia A Zahnow
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stephen B Baylin
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Robert B Scharpf
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Julie R Brahmer
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rachel Karchin
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Drew M Pardoll
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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18
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Beury DW, Carter KA, Nelson C, Sinha P, Hanson E, Nyandjo M, Fitzgerald PJ, Majeed A, Wali N, Ostrand-Rosenberg S. Myeloid-Derived Suppressor Cell Survival and Function Are Regulated by the Transcription Factor Nrf2. J Immunol 2016; 196:3470-8. [PMID: 26936880 DOI: 10.4049/jimmunol.1501785] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 02/06/2016] [Indexed: 12/30/2022]
Abstract
Tumor-induced myeloid-derived suppressor cells (MDSC) contribute to immune suppression in tumor-bearing individuals and are a major obstacle to effective immunotherapy. Reactive oxygen species (ROS) are one of the mechanisms used by MDSC to suppress T cell activation. Although ROS are toxic to most cells, MDSC survive despite their elevated content and release of ROS. NF erythroid 2-related factor 2 (Nrf2) is a transcription factor that regulates a battery of genes that attenuate oxidative stress. Therefore, we hypothesized that MDSC resistance to ROS may be regulated by Nrf2. To test this hypothesis, we used Nrf2(+/+)and Nrf2(-/-)BALB/c and C57BL/6 mice bearing 4T1 mammary carcinoma and MC38 colon carcinoma, respectively. Nrf2 enhanced MDSC suppressive activity by increasing MDSC production of H2O2, and it increased the quantity of tumor-infiltrating MDSC by reducing their oxidative stress and rate of apoptosis. Nrf2 did not affect circulating levels of MDSC in tumor-bearing mice because the decreased apoptotic rate of tumor-infiltrating MDSC was balanced by a decreased rate of differentiation from bone marrow progenitor cells. These results demonstrate that Nrf2 regulates the generation, survival, and suppressive potency of MDSC, and that a feedback homeostatic mechanism maintains a steady-state level of circulating MDSC in tumor-bearing individuals.
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Affiliation(s)
- Daniel W Beury
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Kayla A Carter
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Cassandra Nelson
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Pratima Sinha
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Erica Hanson
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Maeva Nyandjo
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Phillip J Fitzgerald
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Amry Majeed
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Neha Wali
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
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19
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Bielczyk-Maczyńska E, Lam Hung L, Ferreira L, Fleischmann T, Weis F, Fernández-Pevida A, Harvey SA, Wali N, Warren AJ, Barroso I, Stemple DL, Cvejic A. The Ribosome Biogenesis Protein Nol9 Is Essential for Definitive Hematopoiesis and Pancreas Morphogenesis in Zebrafish. PLoS Genet 2015; 11:e1005677. [PMID: 26624285 PMCID: PMC4666468 DOI: 10.1371/journal.pgen.1005677] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 05/11/2015] [Accepted: 10/26/2015] [Indexed: 12/27/2022] Open
Abstract
Ribosome biogenesis is a ubiquitous and essential process in cells. Defects in ribosome biogenesis and function result in a group of human disorders, collectively known as ribosomopathies. In this study, we describe a zebrafish mutant with a loss-of-function mutation in nol9, a gene that encodes a non-ribosomal protein involved in rRNA processing. nol9sa1022/sa1022 mutants have a defect in 28S rRNA processing. The nol9sa1022/sa1022 larvae display hypoplastic pancreas, liver and intestine and have decreased numbers of hematopoietic stem and progenitor cells (HSPCs), as well as definitive erythrocytes and lymphocytes. In addition, ultrastructural analysis revealed signs of pathological processes occurring in endothelial cells of the caudal vein, emphasizing the complexity of the phenotype observed in nol9sa1022/sa1022 larvae. We further show that both the pancreatic and hematopoietic deficiencies in nol9sa1022/sa1022 embryos were due to impaired cell proliferation of respective progenitor cells. Interestingly, genetic loss of Tp53 rescued the HSPCs but not the pancreatic defects. In contrast, activation of mRNA translation via the mTOR pathway by L-Leucine treatment did not revert the erythroid or pancreatic defects. Together, we present the nol9sa1022/sa1022 mutant, a novel zebrafish ribosomopathy model, which recapitulates key human disease characteristics. The use of this genetically tractable model will enhance our understanding of the tissue-specific mechanisms following impaired ribosome biogenesis in the context of an intact vertebrate.
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Affiliation(s)
- Ewa Bielczyk-Maczyńska
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Laure Lam Hung
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lauren Ferreira
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Tobias Fleischmann
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Félix Weis
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Antonio Fernández-Pevida
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Steven A. Harvey
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Neha Wali
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alan J. Warren
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Inês Barroso
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Derek L. Stemple
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ana Cvejic
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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20
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Patrick J, Wali N, Sealy I, Collins J, Busch-Nentwich E, Stemple D. Zebrafish models of inherited skeletal muscle disorders. Neuromuscul Disord 2015. [DOI: 10.1016/j.nmd.2015.06.264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Collins JE, Wali N, Sealy IM, Morris JA, White RJ, Leonard SR, Jackson DK, Jones MC, Smerdon NC, Zamora J, Dooley CM, Carruthers SN, Barrett JC, Stemple DL, Busch-Nentwich EM. High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping. BMC Genomics 2015; 16:578. [PMID: 26238335 PMCID: PMC4524448 DOI: 10.1186/s12864-015-1788-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/21/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We present a genome-wide messenger RNA (mRNA) sequencing technique that converts small amounts of RNA from many samples into molecular phenotypes. It encompasses all steps from sample preparation to sequence analysis and is applicable to baseline profiling or perturbation measurements. RESULTS Multiplex sequencing of transcript 3' ends identifies differential transcript abundance independent of gene annotation. We show that increasing biological replicate number while maintaining the total amount of sequencing identifies more differentially abundant transcripts. CONCLUSIONS This method can be implemented on polyadenylated RNA from any organism with an annotated reference genome and in any laboratory with access to Illumina sequencing.
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Affiliation(s)
- John E Collins
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Neha Wali
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Ian M Sealy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - James A Morris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Richard J White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Steven R Leonard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - David K Jackson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Matthew C Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Nathalie C Smerdon
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jorge Zamora
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Christopher M Dooley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Samantha N Carruthers
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Derek L Stemple
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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22
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Kettleborough RNW, Busch-Nentwich EM, Harvey SA, Dooley CM, de Bruijn E, van Eeden F, Sealy I, White RJ, Herd C, Nijman IJ, Fényes F, Mehroke S, Scahill C, Gibbons R, Wali N, Carruthers S, Hall A, Yen J, Cuppen E, Stemple DL. A systematic genome-wide analysis of zebrafish protein-coding gene function. Nature 2013; 496:494-7. [PMID: 23594742 PMCID: PMC3743023 DOI: 10.1038/nature11992] [Citation(s) in RCA: 442] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 02/07/2013] [Indexed: 01/11/2023]
Abstract
Since the publication of the human reference genome, the identities of specific genes associated with human diseases are being discovered at a rapid rate. A central problem is that the biological activity of these genes is often unclear. Detailed investigations in model vertebrate organisms, typically mice, have been essential for understanding the activities of many orthologues of these disease-associated genes. Although gene-targeting approaches and phenotype analysis have led to a detailed understanding of nearly 6,000 protein-coding genes, this number falls considerably short of the more than 22,000 mouse protein-coding genes. Similarly, in zebrafish genetics, one-by-one gene studies using positional cloning, insertional mutagenesis, antisense morpholino oligonucleotides, targeted re-sequencing, and zinc finger and TAL endonucleases have made substantial contributions to our understanding of the biological activity of vertebrate genes, but again the number of genes studied falls well short of the more than 26,000 zebrafish protein-coding genes. Importantly, for both mice and zebrafish, none of these strategies are particularly suited to the rapid generation of knockouts in thousands of genes and the assessment of their biological activity. Here we describe an active project that aims to identify and phenotype the disruptive mutations in every zebrafish protein-coding gene, using a well-annotated zebrafish reference genome sequence, high-throughput sequencing and efficient chemical mutagenesis. So far we have identified potentially disruptive mutations in more than 38% of all known zebrafish protein-coding genes. We have developed a multi-allelic phenotyping scheme to efficiently assess the effects of each allele during embryogenesis and have analysed the phenotypic consequences of over 1,000 alleles. All mutant alleles and data are available to the community and our phenotyping scheme is adaptable to phenotypic analysis beyond embryogenesis.
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Affiliation(s)
- Ross N W Kettleborough
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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Abstract
Dark-adapted and light-adapted electroretinographic luminance-response functions were recorded from subjects with light or dark fundus pigmentation based on digitized fundus photographs. For dark- and light-adapted electroretinograms, subjects with dark fundi had smaller b-wave amplitudes at all luminance levels. There was no significant difference in b-wave implicit time for the dark-adapted electroretinogram, but there was a significant difference for the light-adapted ERG between the two groups. The results suggest that fundus pigmentation should be considered in the interpretation of electroretinogram results. A possible mechanism for the influence of fundus pigmentation on b-wave amplitude is based on increased resistance associated with melanin.
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Affiliation(s)
- N Wali
- Department of Ophthalmology, Columbus Children's Hospital
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24
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Abstract
Dark-adapted electroretinograms were obtained over a 3.6-log range of stimulus intensities from 17 black and 15 white normal subjects. Subjects were grouped on the basis of light or dark fundus pigmentation, determined from digitized fundus photographs. B-wave amplitudes for each group were fitted by the Naka-Rushton equation, and the measures Vmax, log K, and n were determined. The luminance-response functions revealed that subjects with light fundi had larger b-wave amplitudes at all luminance levels. There was a significant difference between groups for Vmax and n but not for log K. A comparison of b-wave implicit times showed no significant difference between subjects with dark and light fundi. Ancillary tests and multiple regression analysis suggested that the relationship between Vmax and fundus pigmentation could not be attributed to age, gender, refractive error, axial length or intraocular pressure. The results have implications for the collection of normative electroretinographic data and for the interpretation of electroretinogram results.
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Affiliation(s)
- N Wali
- Department of Ophthalmology, Columbus Children's Hospital, Ohio
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25
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Abstract
Utilizing a high intensity photographic flash unit, electroretinograms were recorded from normal adults under fully light adapted conditions over a 5 log unit range of stimulus luminance (-1.35 to 3.34 log cd-s/m2). At lower luminance levels b-wave amplitude increased with increased luminance until it reached a maximum (Vmax of the Naka-Ruston equation) in agreement with previous work. At higher luminance levels, the b-wave amplitude decreased to 33% of Vmax and then plateaued. This previously unreported phenomenon has been named the photopic hill. There was no appreciable change in b-wave amplitude with increased interstimulus intervals from 15 sec to 5 min and luminance-response functions serially recorded for increasing and for decreasing stimulus luminance were very similar. These latter results indicate that the photopic hill is not due to light adaptation. The reason for the photopic hill and possible clinical implications are discussed.
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Affiliation(s)
- N Wali
- Department of Ophthalmology, Children's Hospital, Columbus, Ohio
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Abstract
Contrast sensitivity functions (CSF's) were measured in the amblyopic and dominant eyes of 17 strabismic and 28 anisometropic children and in 19 similar age normal controls. A three-alternative forced-choice procedure was used to measure CSF's with the VCTS 6500. The results revealed reduced contrast sensitivity (CS) in both the amblyopic and dominant eyes of strabismic and anisometropic amblyopes compared to normal controls. Statistically significant intereye correlations of CS at each spatial frequency were found in all groups and in the presence of deep amblyopia, suggesting continued interocular interactions and binocularity. A separate longitudinal study of 7 of the amblyopes showed that, during the course of occlusion therapy, both the amblyopic and the dominant eyes improved in CSF. The results suggest that the amblyopic eye may influence CS in the dominant eye through interocular interactions. This process may serve to minimize CSF differences between the eyes and maximize binocular vision.
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Affiliation(s)
- N Wali
- Ophthalmology Department, Children's Hospital, Columbus, Ohio
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Abstract
To determine the threshold characteristics of optokinetic nystagmus (OKN), contrast thresholds for involuntary OKN were measured for gratings of different spatial frequency to yield an OKN-contrast sensitivity function (OKN-CSF). The OKN-CSF resembled an inverted U-shaped function with temporal-to-nasal and nasal-to-temporal movement yielding similar functions. In addition, when psychophysical CSFs were determined for separate form and movement thresholds, it was discovered that the OKN-CSF approximated the psychophysical-movement CSF rather than the psychophysical-form CSF.
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Affiliation(s)
- L E Leguire
- Department of Ophthalmology, Children's Hospital, Columbus, OH 43205
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Abstract
Normative dark-adapted electroretinograms were recorded simultaneously with a skin electrode and corneal electrode for varying stimulus intensities. The electroretinogram b-wave amplitudes for each electrode were fitted by the Naka-Rushton equation, and the parameters Vmax, K and n were evaluated. A comparison of parameters between the two electrodes showed a significant difference for Vmax and K but not for n. Vmax was approximately eight times smaller and K was 0.3 log unit smaller for the skin electrode than for the corneal electrode. B-wave amplitude and implicit time were also compared between the two electrodes. The b-wave amplitude ratio of the corneal electrode to that of the skin electrode increased with luminance and ranged from 1.83 to 7.68. Overall, b-wave implicit time for the skin electrode was approximately 10 ms shorter than that of the corneal electrode.
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Affiliation(s)
- N Wali
- Department of Ophthalmology, Children's Hospital, Columbus, OH 43205
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Abstract
Serial sectioning for 3-D reconstruction requires a highly skilled and experienced individual to collect ribbons of ultrathin sections on formvar-coated grids, and to handle the grids after section collection. A simple method is described for placing ribbons in an orderly serial fashion on formvar-coated grids, by a microtomist with average experience. Prior to sectioning, a wax ledge is prepared on the sloping edge of a glass knife in order to support a formvar-coated grid held in a horizontal slot cut in the wax. After a ribbon is formed, the water in the trough is slowly withdrawn to allow the ribbon to settle on the grid. The grids are then placed in an easy-to-make plastic chamber so that the formvar does not get ruptured during drying. The chamber can also be used for staining and storage of grids thereafter. Approximately 4000 sections from mudpuppy retinal cells have been successfully collected using this method. Computer 3-D reconstruction of the individual cells has been done.
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Affiliation(s)
- N Wali
- College of Pharmacy, Ohio State University, Columbus 43210
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30
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Abstract
In the three-dimensional reconstruction of neuronal structure, it is imperative that ribbons of semithin or ultrathin sections be obtained. Resin-embedded semithin sections display better structural details than paraffin-embedded sections. The cutting and collecting of long ribbons of resin-embedded semithin sections using a microtome, requires the use of large troughs on glass knives. A simple plastic trough has been described which facilitates the collection of ribbons directly onto a coverslip. As the ribbons are formed, they are floated on a coverslip. The water in the trough is slowly drained through a tubing which is attached to a syringe. The ribbons settle on the coverslip, which is easily removed and placed on a hotplate to dry the sections.
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Affiliation(s)
- N Wali
- Biomedical Engineering and College of Pharmacy, Ohio State University, Columbus
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