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Amid A, Liu S, Babbs C, Higgs DR. Haemoglobin Bart's Hydrops Fetalis: Charting the Past and Envisioning the Future. Blood 2024:blood.2023023692. [PMID: 38457773 DOI: 10.1182/blood.2023023692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/10/2024] Open
Abstract
Haemoglobin Bart's hydrops fetalis syndrome (BHFS) represents the most severe form of α-thalassaemia, arising from deletion of the duplicated α-globin genes from both alleles. The absence of α-globin leads to the formation of non-functional haemoglobin Bart's (γ4) or haemoglobin H (HbH: β4) resulting in severe anaemia, tissue hypoxia, and, in some cases, variable congenital or neurocognitive abnormalities. BHFS is the most common cause of hydrops fetalis in Southeast Asia; however, owing to global migration, the burden of this condition is increasing worldwide. With the availability of intensive perinatal care and intrauterine transfusions, an increasing number of patients survive with this condition. The current approach to long-term management of survivors involves regular blood transfusions and iron chelation, a task made challenging by the need for intensified transfusions to suppress the production of non-functional HbH-containing erythrocytes. While our knowledge of outcomes of this condition is evolving, it seems, in comparison to individuals with transfusion-dependent β-thalassaemia, those with BHFS may face an elevated risk of complications arising from chronic anaemia and hypoxia, ongoing haemolysis, iron overload, and from their respective treatments. Although stem cell transplantation remains a viable option for a select few, it is not without potential side effects. Looking ahead, potential advancements in the form of genetic engineering and innovative therapeutic approaches, such as the reactivation of embryonic α-like globin gene expression, hold promise for furthering the treatment of this condition. Prevention remains a crucial aspect of care, particularly in areas with high prevalence or limited resources.
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Affiliation(s)
- Ali Amid
- BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Siyu Liu
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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Blayney JW, Francis H, Rampasekova A, Camellato B, Mitchell L, Stolper R, Cornell L, Babbs C, Boeke JD, Higgs DR, Kassouf M. Super-enhancers include classical enhancers and facilitators to fully activate gene expression. Cell 2023; 186:5826-5839.e18. [PMID: 38101409 PMCID: PMC10858684 DOI: 10.1016/j.cell.2023.11.030] [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: 08/08/2022] [Revised: 07/06/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
Super-enhancers are compound regulatory elements that control expression of key cell identity genes. They recruit high levels of tissue-specific transcription factors and co-activators such as the Mediator complex and contact target gene promoters with high frequency. Most super-enhancers contain multiple constituent regulatory elements, but it is unclear whether these elements have distinct roles in activating target gene expression. Here, by rebuilding the endogenous multipartite α-globin super-enhancer, we show that it contains bioinformatically equivalent but functionally distinct element types: classical enhancers and facilitator elements. Facilitators have no intrinsic enhancer activity, yet in their absence, classical enhancers are unable to fully upregulate their target genes. Without facilitators, classical enhancers exhibit reduced Mediator recruitment, enhancer RNA transcription, and enhancer-promoter interactions. Facilitators are interchangeable but display functional hierarchy based on their position within a multipartite enhancer. Facilitators thus play an important role in potentiating the activity of classical enhancers and ensuring robust activation of target genes.
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Affiliation(s)
- Joseph W Blayney
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Helena Francis
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Alexandra Rampasekova
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Brendan Camellato
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Leslie Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Rosa Stolper
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Lucy Cornell
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA.
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK; Chinese Academy of Medical Sciences Oxford Institute, Oxford OX3 7BN, UK.
| | - Mira Kassouf
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
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Pagnamenta AT, Camps C, Giacopuzzi E, Taylor JM, Hashim M, Calpena E, Kaisaki PJ, Hashimoto A, Yu J, Sanders E, Schwessinger R, Hughes JR, Lunter G, Dreau H, Ferla M, Lange L, Kesim Y, Ragoussis V, Vavoulis DV, Allroggen H, Ansorge O, Babbs C, Banka S, Baños-Piñero B, Beeson D, Ben-Ami T, Bennett DL, Bento C, Blair E, Brasch-Andersen C, Bull KR, Cario H, Cilliers D, Conti V, Davies EG, Dhalla F, Dacal BD, Dong Y, Dunford JE, Guerrini R, Harris AL, Hartley J, Hollander G, Javaid K, Kane M, Kelly D, Kelly D, Knight SJL, Kreins AY, Kvikstad EM, Langman CB, Lester T, Lines KE, Lord SR, Lu X, Mansour S, Manzur A, Maroofian R, Marsden B, Mason J, McGowan SJ, Mei D, Mlcochova H, Murakami Y, Németh AH, Okoli S, Ormondroyd E, Ousager LB, Palace J, Patel SY, Pentony MM, Pugh C, Rad A, Ramesh A, Riva SG, Roberts I, Roy N, Salminen O, Schilling KD, Scott C, Sen A, Smith C, Stevenson M, Thakker RV, Twigg SRF, Uhlig HH, van Wijk R, Vona B, Wall S, Wang J, Watkins H, Zak J, Schuh AH, Kini U, Wilkie AOM, Popitsch N, Taylor JC. Structural and non-coding variants increase the diagnostic yield of clinical whole genome sequencing for rare diseases. Genome Med 2023; 15:94. [PMID: 37946251 PMCID: PMC10636885 DOI: 10.1186/s13073-023-01240-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Whole genome sequencing is increasingly being used for the diagnosis of patients with rare diseases. However, the diagnostic yields of many studies, particularly those conducted in a healthcare setting, are often disappointingly low, at 25-30%. This is in part because although entire genomes are sequenced, analysis is often confined to in silico gene panels or coding regions of the genome. METHODS We undertook WGS on a cohort of 122 unrelated rare disease patients and their relatives (300 genomes) who had been pre-screened by gene panels or arrays. Patients were recruited from a broad spectrum of clinical specialties. We applied a bioinformatics pipeline that would allow comprehensive analysis of all variant types. We combined established bioinformatics tools for phenotypic and genomic analysis with our novel algorithms (SVRare, ALTSPLICE and GREEN-DB) to detect and annotate structural, splice site and non-coding variants. RESULTS Our diagnostic yield was 43/122 cases (35%), although 47/122 cases (39%) were considered solved when considering novel candidate genes with supporting functional data into account. Structural, splice site and deep intronic variants contributed to 20/47 (43%) of our solved cases. Five genes that are novel, or were novel at the time of discovery, were identified, whilst a further three genes are putative novel disease genes with evidence of causality. We identified variants of uncertain significance in a further fourteen candidate genes. The phenotypic spectrum associated with RMND1 was expanded to include polymicrogyria. Two patients with secondary findings in FBN1 and KCNQ1 were confirmed to have previously unidentified Marfan and long QT syndromes, respectively, and were referred for further clinical interventions. Clinical diagnoses were changed in six patients and treatment adjustments made for eight individuals, which for five patients was considered life-saving. CONCLUSIONS Genome sequencing is increasingly being considered as a first-line genetic test in routine clinical settings and can make a substantial contribution to rapidly identifying a causal aetiology for many patients, shortening their diagnostic odyssey. We have demonstrated that structural, splice site and intronic variants make a significant contribution to diagnostic yield and that comprehensive analysis of the entire genome is essential to maximise the value of clinical genome sequencing.
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Affiliation(s)
- Alistair T Pagnamenta
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Carme Camps
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Edoardo Giacopuzzi
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Human Technopole, Viale Rita Levi Montalcini 1, 20157, Milan, Italy
| | - John M Taylor
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Mona Hashim
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Eduardo Calpena
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Pamela J Kaisaki
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Akiko Hashimoto
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Jing Yu
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Edward Sanders
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Ron Schwessinger
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Jim R Hughes
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Gerton Lunter
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- University Medical Center Groningen, Groningen University, PO Box 72, 9700 AB, Groningen, The Netherlands
| | - Helene Dreau
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Matteo Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Lukas Lange
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Yesim Kesim
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Vassilis Ragoussis
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Dimitrios V Vavoulis
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Holger Allroggen
- Neurosciences Department, UHCW NHS Trust, Clifford Bridge Road, Coventry, CV2 2DX, UK
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK
| | - Benito Baños-Piñero
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - David Beeson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Tal Ben-Ami
- Pediatric Hematology-Oncology Unit, Kaplan Medical Center, Rehovot, Israel
| | - David L Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Celeste Bento
- Hematology Department, Hospitais da Universidade de Coimbra, Coimbra, Portugal
| | - Edward Blair
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Charlotte Brasch-Andersen
- Department of Clinical Genetics, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Katherine R Bull
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Holger Cario
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Eythstrasse 24, 89075, Ulm, Germany
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Valerio Conti
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - E Graham Davies
- Department of Immunology, Great Ormond Street Hospital for Children NHS Trust and UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research, 2Nd Floor, 20C Guilford Street, London, WC1N 1DZ, UK
| | - Fatima Dhalla
- Department of Paediatrics, Institute of Developmental and Regenerative Medicine, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive, Oxford, OX3 7TY, UK
| | - Beatriz Diez Dacal
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Yin Dong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - James E Dunford
- Oxford NIHR Musculoskeletal BRC and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Old Road, Oxford, OX3 7HE, UK
| | - Renzo Guerrini
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - Adrian L Harris
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Jane Hartley
- Liver Unit, Birmingham Women's & Children's Hospital and University of Birmingham, Steelhouse Lane, Birmingham, B4 6NH, UK
| | - Georg Hollander
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Kassim Javaid
- Oxford NIHR Musculoskeletal BRC and Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Nuffield Orthopaedic Centre, Old Road, Oxford, OX3 7HE, UK
| | - Maureen Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Pharmacy Hall North, Room 731, 20 N. Pine Street, Baltimore, MD, 21201, USA
| | - Deirdre Kelly
- Liver Unit, Birmingham Women's & Children's Hospital and University of Birmingham, Steelhouse Lane, Birmingham, B4 6NH, UK
| | - Dominic Kelly
- Children's Hospital, OUH NHS Foundation Trust, NIHR Oxford BRC, Headley Way, Oxford, OX3 9DU, UK
| | - Samantha J L Knight
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Alexandra Y Kreins
- Department of Immunology, Great Ormond Street Hospital for Children NHS Trust and UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research, 2Nd Floor, 20C Guilford Street, London, WC1N 1DZ, UK
| | - Erika M Kvikstad
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Craig B Langman
- Feinberg School of Medicine, Northwestern University, 211 E Chicago Avenue, Chicago, IL, MS37, USA
| | - Tracy Lester
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Kate E Lines
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Simon R Lord
- Early Phase Clinical Trials Unit, Department of Oncology, University of Oxford, Cancer and Haematology Centre, Level 2 Administration Area, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Xin Lu
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Sahar Mansour
- St George's University Hospitals NHS Foundation Trust, Blackshore Road, Tooting, London, SW17 0QT, UK
| | - Adnan Manzur
- MRC Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, WC1N 3BG, UK
| | - Brian Marsden
- Nuffield Department of Medicine, Kennedy Institute, University of Oxford, Oxford, OX3 7BN, UK
| | - Joanne Mason
- Yourgene Health Headquarters, Skelton House, Lloyd Street North, Manchester Science Park, Manchester, M15 6SH, UK
| | - Simon J McGowan
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Davide Mei
- Neuroscience Department, Meyer Children's Hospital IRCCS, Viale Pieraccini 24, 50139, Florence, Italy
| | - Hana Mlcochova
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Yoshiko Murakami
- Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Steven Okoli
- Imperial College NHS Trust, Department of Haematology, Hammersmith Hospital, Du Cane Road, London, W12 0HS, UK
| | - Elizabeth Ormondroyd
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Level 6 West Wing, Oxford, OX3 9DU, JR, UK
| | - Lilian Bomme Ousager
- Department of Clinical Genetics, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jacqueline Palace
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Smita Y Patel
- Clinical Immunology, John Radcliffe Hospital, Level 4A, Oxford, OX3 9DU, UK
| | - Melissa M Pentony
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Chris Pugh
- Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
| | - Aboulfazl Rad
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany
| | - Archana Ramesh
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Simone G Riva
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Irene Roberts
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Noémi Roy
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Level 4, Haematology, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Outi Salminen
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Kyleen D Schilling
- Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Avenue, Chicago, IL, 60611, USA
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Arjune Sen
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Conrad Smith
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Old Road, Oxford, OX3 7LE, UK
| | - Mark Stevenson
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Rajesh V Thakker
- University of Oxford, Academic Endocrine Unit, OCDEM, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Stephen R F Twigg
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Holm H Uhlig
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Paediatrics, University of Oxford, Level 2, Children's Hospital, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Richard van Wijk
- UMC Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Barbara Vona
- Department of Otolaryngology-Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Heinrich-Düker-Weg 12, 37073, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Steven Wall
- Oxford Craniofacial Unit, John Radcliffe Hospital, Level LG1, West Wing, Oxford, OX3 9DU, UK
| | - Jing Wang
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, UK
| | - Hugh Watkins
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- University of Oxford, Level 6 West Wing, Oxford, OX3 9DU, JR, UK
| | - Jaroslav Zak
- Nuffield Department of Clinical Medicine, Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
- Department of Immunology and Microbiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anna H Schuh
- Department of Oncology, Oxford Molecular Diagnostics Centre, University of Oxford, Level 4, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Usha Kini
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7LE, UK
| | - Andrew O M Wilkie
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Niko Popitsch
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter(VBC), Dr.-Bohr-Gasse 9, 1030, Vienna, Austria
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7BN, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK.
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4
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Martell DJ, Merens HE, Caulier A, Fiorini C, Ulirsch JC, Ietswaart R, Choquet K, Graziadei G, Brancaleoni V, Cappellini MD, Scott C, Roberts N, Proven M, Roy NBA, Babbs C, Higgs DR, Sankaran VG, Churchman LS. RNA polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation. Dev Cell 2023; 58:2112-2127.e4. [PMID: 37586368 PMCID: PMC10615711 DOI: 10.1016/j.devcel.2023.07.018] [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: 03/14/2023] [Revised: 05/23/2023] [Accepted: 07/25/2023] [Indexed: 08/18/2023]
Abstract
Controlled release of promoter-proximal paused RNA polymerase II (RNA Pol II) is crucial for gene regulation. However, studying RNA Pol II pausing is challenging, as pause-release factors are almost all essential. In this study, we identified heterozygous loss-of-function mutations in SUPT5H, which encodes SPT5, in individuals with β-thalassemia. During erythropoiesis in healthy human cells, cell cycle genes were highly paused as cells transition from progenitors to precursors. When the pathogenic mutations were recapitulated by SUPT5H editing, RNA Pol II pause release was globally disrupted, and as cells began transitioning from progenitors to precursors, differentiation was delayed, accompanied by a transient lag in erythroid-specific gene expression and cell cycle kinetics. Despite this delay, cells terminally differentiate, and cell cycle phase distributions normalize. Therefore, hindering pause release perturbs proliferation and differentiation dynamics at a key transition during erythropoiesis, identifying a role for RNA Pol II pausing in temporally coordinating the cell cycle and erythroid differentiation.
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Affiliation(s)
- Danya J Martell
- Department of Genetics, Harvard University, Boston, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hope E Merens
- Department of Genetics, Harvard University, Boston, MA, USA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Karine Choquet
- Department of Genetics, Harvard University, Boston, MA, USA
| | - Giovanna Graziadei
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Valentina Brancaleoni
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Maria Domenica Cappellini
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Melanie Proven
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Noémi B A Roy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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5
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Preston AE, Frost JN, Badat M, Teh M, Armitage AE, Norfo R, Wideman SK, Hanifi M, White N, Roy N, Ghesquiere B, Babbs C, Kassouf M, Davies J, Hughes JR, Beagrie R, Higgs DR, Drakesmith H. Ancient genomic linkage couples metabolism with erythroid development. bioRxiv 2023:2023.09.25.558944. [PMID: 37808769 PMCID: PMC10557585 DOI: 10.1101/2023.09.25.558944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Generation of mature cells from progenitors requires tight coupling of differentiation and metabolism. During erythropoiesis, erythroblasts are required to massively upregulate globin synthesis then clear extraneous material and enucleate to produce erythrocytes1-3. Nprl3 has remained in synteny with the α-globin genes for >500 million years4, and harbours the majority of the α-globin enhancers5. Nprl3 is a highly conserved inhibitor of mTORC1, which controls cellular metabolism. However, whether Nprl3 itself serves an erythroid role is unknown. Here, we show that Nprl3 is a key regulator of erythroid metabolism. Using Nprl3-deficient fetal liver and adult competitive bone marrow - fetal liver chimeras, we show that NprI3 is required for sufficient erythropoiesis. Loss of Nprl3 elevates mTORC1 signalling, suppresses autophagy and disrupts erythroblast glycolysis and redox control. Human CD34+ progenitors lacking NPRL3 produce fewer enucleated cells and demonstrate dysregulated mTORC1 signalling in response to nutrient availability and erythropoietin. Finally, we show that the α-globin enhancers upregulate NprI3 expression, and that this activity is necessary for optimal erythropoiesis. Therefore, the anciently conserved linkage of NprI3, α-globin and their associated enhancers has enabled coupling of metabolic and developmental control in erythroid cells. This may enable erythropoiesis to adapt to fluctuating nutritional and environmental conditions.
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Affiliation(s)
- Alexandra E Preston
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Joe N Frost
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Mohsin Badat
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Megan Teh
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Andrew E Armitage
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ruggiero Norfo
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Sarah K Wideman
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Muhammad Hanifi
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Natasha White
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Noémi Roy
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Bart Ghesquiere
- Metabolomics Expertise Center, VIB Center for Cancer Biology, 3000 Leuven, Belgium
- Metabolomics Expertise Center, Department of Oncology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Mira Kassouf
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - James Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Rob Beagrie
- Chromatin and Disease Group, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
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6
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Babbs C. The incredible ULK improves β-thalassemia. Blood 2023; 142:862-863. [PMID: 37676694 DOI: 10.1182/blood.2023021369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
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7
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Tillotson R, Yan K, Ruston J, DeYoung T, Córdova A, Turcotte-Cardin V, Yee Y, Taylor C, Visuvanathan S, Babbs C, Ivakine EA, Sled JG, Nieman BJ, Picketts DJ, Justice MJ. A new mouse model of ATR-X syndrome carrying a common patient mutation exhibits neurological and morphological defects. Hum Mol Genet 2023; 32:2485-2501. [PMID: 37171606 PMCID: PMC10360390 DOI: 10.1093/hmg/ddad075] [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: 01/24/2023] [Revised: 03/18/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023] Open
Abstract
ATRX is a chromatin remodelling ATPase that is involved in transcriptional regulation, DNA damage repair and heterochromatin maintenance. It has been widely studied for its role in ALT-positive cancers, but its role in neurological function remains elusive. Hypomorphic mutations in the X-linked ATRX gene cause a rare form of intellectual disability combined with alpha-thalassemia called ATR-X syndrome in hemizygous males. Clinical features also include facial dysmorphism, microcephaly, short stature, musculoskeletal defects and genital abnormalities. As complete deletion of ATRX in mice results in early embryonic lethality, the field has largely relied on conditional knockout models to assess the role of ATRX in multiple tissues. Given that null alleles are not found in patients, a more patient-relevant model was needed. Here, we have produced and characterized the first patient mutation knock-in model of ATR-X syndrome, carrying the most common causative mutation, R246C. This is one of a cluster of missense mutations located in the chromatin-binding domain and disrupts its function. The knock-in mice recapitulate several aspects of the patient disorder, including craniofacial defects, microcephaly, reduced body size and impaired neurological function. They provide a powerful model for understanding the molecular mechanisms underlying ATR-X syndrome and testing potential therapeutic strategies.
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Affiliation(s)
- Rebekah Tillotson
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital/Headley Way, Oxford OX3 9DS, UK
| | - Keqin Yan
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Julie Ruston
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Taylor DeYoung
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
| | - Alex Córdova
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Valérie Turcotte-Cardin
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Cellular & Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Yohan Yee
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Christine Taylor
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Shagana Visuvanathan
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Christian Babbs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital/Headley Way, Oxford OX3 9DS, UK
| | - Evgueni A Ivakine
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - John G Sled
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Translational Medicine Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
| | - Brian J Nieman
- Mouse Imaging Centre, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Translational Medicine Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Cellular & Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Monica J Justice
- Genetics and Genome Biology Program, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada
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8
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Martell DJ, Merens HE, Fiorini C, Caulier A, Ulirsch JC, Ietswaart R, Choquet K, Graziadei G, Brancaleoni V, Cappellini MD, Scott C, Roberts N, Proven M, Roy NB, Babbs C, Higgs DR, Sankaran VG, Churchman LS. RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation. medRxiv 2023:2023.03.03.23286760. [PMID: 36945604 PMCID: PMC10029049 DOI: 10.1101/2023.03.03.23286760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The controlled release of promoter-proximal paused RNA polymerase II (Pol II) into productive elongation is a major step in gene regulation. However, functional analysis of Pol II pausing is difficult because factors that regulate pause release are almost all essential. In this study, we identified heterozygous loss-of-function mutations in SUPT5H , which encodes SPT5, in individuals with β-thalassemia unlinked to HBB mutations. During erythropoiesis in healthy human cells, cell cycle genes were highly paused at the transition from progenitors to precursors. When the pathogenic mutations were recapitulated by SUPT5H editing, Pol II pause release was globally disrupted, and the transition from progenitors to precursors was delayed, marked by a transient lag in erythroid-specific gene expression and cell cycle kinetics. Despite this delay, cells terminally differentiate, and cell cycle phase distributions normalize. Therefore, hindering pause release perturbs proliferation and differentiation dynamics at a key transition during erythropoiesis, revealing a role for Pol II pausing in the temporal coordination between the cell cycle and differentiation.
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Affiliation(s)
- Danya J Martell
- Harvard University, Department of Genetics, Boston, MA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Hope E Merens
- Harvard University, Department of Genetics, Boston, MA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | - Giovanna Graziadei
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Valentina Brancaleoni
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Maria Domenica Cappellini
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Melanie Proven
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Noémi Ba Roy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
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9
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Jeziorska DM, Tunnacliffe EAJ, Brown JM, Ayyub H, Sloane-Stanley J, Sharpe JA, Lagerholm BC, Babbs C, Smith AJH, Buckle VJ, Higgs DR. On-microscope staging of live cells reveals changes in the dynamics of transcriptional bursting during differentiation. Nat Commun 2022; 13:6641. [PMID: 36333299 PMCID: PMC9636426 DOI: 10.1038/s41467-022-33977-4] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Determining the mechanisms by which genes are switched on and off during development is a key aim of current biomedical research. Gene transcription has been widely observed to occur in a discontinuous fashion, with short bursts of activity interspersed with periods of inactivity. It is currently not known if or how this dynamic behaviour changes as mammalian cells differentiate. To investigate this, using an on-microscope analysis, we monitored mouse α-globin transcription in live cells throughout erythropoiesis. We find that changes in the overall levels of α-globin transcription are most closely associated with changes in the fraction of time a gene spends in the active transcriptional state. We identify differences in the patterns of transcriptional bursting throughout differentiation, with maximal transcriptional activity occurring in the mid-phase of differentiation. Early in differentiation, we observe increased fluctuation in transcriptional activity whereas at the peak of gene expression, in early erythroblasts, transcription is relatively stable. Later during differentiation as α-globin expression declines, we again observe more variability in transcription within individual cells. We propose that the observed changes in transcriptional behaviour may reflect changes in the stability of active transcriptional compartments as gene expression is regulated during differentiation.
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Affiliation(s)
- D. M. Jeziorska
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK ,Present Address: Nucleome Therapeutics Ltd., BioEscalator, The Innovation Building, Old Road Campus, Oxford, OX3 7FZ UK
| | - E. A. J. Tunnacliffe
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - J. M. Brown
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - H. Ayyub
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - J. Sloane-Stanley
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - J. A. Sharpe
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - B. C. Lagerholm
- grid.4991.50000 0004 1936 8948Wolfson Imaging Centre, MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK ,grid.4991.50000 0004 1936 8948Present Address: The Kennedy Institute Of Rheumatology, University of Oxford, Old Road Campus, Oxford, OX3 7FY UK
| | - C. Babbs
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - A. J. H. Smith
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK ,grid.4305.20000 0004 1936 7988Present Address: MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU UK
| | - V. J. Buckle
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK
| | - D. R. Higgs
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute for Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS UK ,grid.4991.50000 0004 1936 8948Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford, OX3 7BN UK
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10
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Scott C, Bartolovic K, Clark SA, Waithe D, Hill QA, Okoli S, Renella R, Ryan K, Cahill MR, Higgs DR, Roy NBA, Buckle V, Roberts I, Babbs C. Functional impairment of erythropoiesis in Congenital Dyserythropoietic Anaemia type I arises at the progenitor level. Br J Haematol 2022; 198:e10-e14. [PMID: 35417566 DOI: 10.1111/bjh.18167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Kerol Bartolovic
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sally-Ann Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Dominic Waithe
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, Oxford, UK
| | | | - Steven Okoli
- Imperial College, The Commonwealth Building, Hammersmith Hospital, London, UK
| | - Raffaele Renella
- Pediatric Hematology-Oncology Research Laboratory, CHUV-UNIL, Lausanne, Switzerland
| | - Kate Ryan
- Department of Haematology, Manchester Royal Infirmary, Manchester, UK
| | - Mary R Cahill
- Department of Haematology, Cork University Hospital, Cork, Ireland
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Noémi B A Roy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - Veronica Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, Children's Hospital, John Radcliffe Hospital, and MRC WIMM, University of Oxford, Oxford, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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11
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Francis HS, Harold CL, Beagrie RA, King AJ, Gosden ME, Blayney JW, Jeziorska DM, Babbs C, Higgs DR, Kassouf MT. Scalable in vitro production of defined mouse erythroblasts. PLoS One 2022; 17:e0261950. [PMID: 34995303 PMCID: PMC8741028 DOI: 10.1371/journal.pone.0261950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 12/14/2021] [Indexed: 01/23/2023] Open
Abstract
Mouse embryonic stem cells (mESCs) can be manipulated in vitro to recapitulate the process of erythropoiesis, during which multipotent cells undergo lineage specification, differentiation and maturation to produce erythroid cells. Although useful for identifying specific progenitors and precursors, this system has not been fully exploited as a source of cells to analyse erythropoiesis. Here, we establish a protocol in which characterised erythroblasts can be isolated in a scalable manner from differentiated embryoid bodies (EBs). Using transcriptional and epigenetic analysis, we demonstrate that this system faithfully recapitulates normal primitive erythropoiesis and fully reproduces the effects of natural and engineered mutations seen in primary cells obtained from mouse models. We anticipate this system to be of great value in reducing the time and costs of generating and maintaining mouse lines in a number of research scenarios.
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Affiliation(s)
- Helena S. Francis
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Caroline L. Harold
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Robert A. Beagrie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew J. King
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew E. Gosden
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Joseph W. Blayney
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Danuta M. Jeziorska
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Douglas R. Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Mira T. Kassouf
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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12
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Scott C, Downes DJ, Brown JM, Beagrie R, Olijnik AA, Gosden M, Schwessinger R, Fisher CA, Rose A, Ferguson DJP, Johnson E, Hill QA, Okoli S, Renella R, Ryan K, Brand M, Hughes J, Roy NBA, Higgs DR, Babbs C, Buckle VJ. Recapitulation of erythropoiesis in congenital dyserythropoietic anaemia type I (CDA-I) identifies defects in differentiation and nucleolar abnormalities. Haematologica 2021; 106:2960-2970. [PMID: 33121234 PMCID: PMC8561284 DOI: 10.3324/haematol.2020.260158] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/17/2020] [Indexed: 11/19/2022] Open
Abstract
The investigation of inherited disorders of erythropoiesis has elucidated many of the principles underlying the production of normal red blood cells and how this is perturbed in human disease. Congenital Dyserythropoietic Anaemia type 1 (CDA-I) is a rare form of anaemia caused by mutations in two genes of unknown function: CDAN1 and CDIN1 (previously called C15orf41), whilst in some cases, the underlying genetic abnormality is completely unknown. Consequently, the pathways affected in CDA-I remain to be discovered. To enable detailed analysis of this rare disorder we have validated a culture system which recapitulates all of the cardinal haematological features of CDA-I, including the formation of the pathognomonic 'spongy' heterochromatin seen by electron microscopy. Using a variety of cell and molecular biological approaches we discovered that erythroid cells in this condition show a delay during terminal erythroid differentiation, associated with increased proliferation and widespread changes in chromatin accessibility. We also show that the proteins encoded by CDAN1 and CDIN1 are enriched in nucleoli which are structurally and functionally abnormal in CDA-I. Together these findings provide important pointers to the pathways affected in CDA-I which for the first time can now be pursued in the tractable culture system utilised here.
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Affiliation(s)
- Caroline Scott
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford.
| | - Damien J Downes
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - Jill M Brown
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - Robert Beagrie
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | | | - Matthew Gosden
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - Ron Schwessinger
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | | | - Anna Rose
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - David J P Ferguson
- Ultrastructural Morphology Group, NDCLS, John Radcliffe Hospital, Oxford
| | - Errin Johnson
- Sir William Dunn School of Pathology, Oxford University, Oxford
| | | | - Steven Okoli
- Imperial College, The Commonwealth Building, The Hammersmith Hospital, Du Cane Rd, London
| | - Raffaele Renella
- Pediatric Hematology-Oncology Research Laboratory, CHUV-UNIL Lausanne Switzerland
| | - Kate Ryan
- Department of Haematology, Manchester Royal Infirmary, Oxford Rd, Manchester
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa
| | - Jim Hughes
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - Noemi B A Roy
- Department of Haematology, Oxford University Hospitals NHS Trust, Churchill Hospital, Old Rd, Headington, and NIHR Biomedical Research Centre, Oxford
| | - Douglas R Higgs
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - Christian Babbs
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - Veronica J Buckle
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford.
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13
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King AJ, Songdej D, Downes DJ, Beagrie RA, Liu S, Buckley M, Hua P, Suciu MC, Marieke Oudelaar A, Hanssen LLP, Jeziorska D, Roberts N, Carpenter SJ, Francis H, Telenius J, Olijnik AA, Sharpe JA, Sloane-Stanley J, Eglinton J, Kassouf MT, Orkin SH, Pennacchio LA, Davies JOJ, Hughes JR, Higgs DR, Babbs C. Reactivation of a developmentally silenced embryonic globin gene. Nat Commun 2021; 12:4439. [PMID: 34290235 PMCID: PMC8295333 DOI: 10.1038/s41467-021-24402-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 09/04/2020] [Accepted: 06/12/2021] [Indexed: 12/26/2022] Open
Abstract
The α- and β-globin loci harbor developmentally expressed genes, which are silenced throughout post-natal life. Reactivation of these genes may offer therapeutic approaches for the hemoglobinopathies, the most common single gene disorders. Here, we address mechanisms regulating the embryonically expressed α-like globin, termed ζ-globin. We show that in embryonic erythroid cells, the ζ-gene lies within a ~65 kb sub-TAD (topologically associating domain) of open, acetylated chromatin and interacts with the α-globin super-enhancer. By contrast, in adult erythroid cells, the ζ-gene is packaged within a small (~10 kb) sub-domain of hypoacetylated, facultative heterochromatin within the acetylated sub-TAD and that it no longer interacts with its enhancers. The ζ-gene can be partially re-activated by acetylation and inhibition of histone de-acetylases. In addition to suggesting therapies for severe α-thalassemia, these findings illustrate the general principles by which reactivation of developmental genes may rescue abnormalities arising from mutations in their adult paralogues.
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Affiliation(s)
- Andrew J King
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Duantida Songdej
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Division of Hematology/Oncology, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Robert A Beagrie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Siyu Liu
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Megan Buckley
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Peng Hua
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Maria C Suciu
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Lars L P Hanssen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Danuta Jeziorska
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stephanie J Carpenter
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Helena Francis
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jelena Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Aude-Anais Olijnik
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jacqueline A Sharpe
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jacqueline Sloane-Stanley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jennifer Eglinton
- National Haemoglobinopathy Reference Laboratory, Department of Haematology, Level 4, John Radcliffe Hospital, Oxford, UK
| | - Mira T Kassouf
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stuart H Orkin
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA
| | - Len A Pennacchio
- Functional Genomics Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
| | - James O J Davies
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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14
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Roy NBA, Zaal AI, Hall G, Wilkinson N, Proven M, McGowan S, Hipkiss R, Buckle V, Kavirayani A, Babbs C. Majeed syndrome: description of a novel mutation and therapeutic response to bisphosphonates and IL-1 blockade with anakinra. Rheumatology (Oxford) 2020; 59:448-451. [PMID: 31377798 PMCID: PMC7571481 DOI: 10.1093/rheumatology/kez317] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2019] [Indexed: 11/12/2022] Open
Affiliation(s)
- Noémi B A Roy
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust.,Oxford BRC Haematology Theme, University of Oxford
| | - Ahmad I Zaal
- Paediatric Rheumatology, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford.,Children's Hospital, Damascus University, Damascus, Syria
| | - Georgina Hall
- Paediatric Haematology/Oncology Unit, Oxford University Hospitals, Oxford
| | - Nick Wilkinson
- Paediatric Rheumatology, Evelina Children's Hospital, Guy's and St Thomas' NHS Foundation Trust, London
| | - Melanie Proven
- Molecular Haematology Laboratory, Oxford University Hospitals NHS Foundation Trust
| | - Simon McGowan
- Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford
| | - Ria Hipkiss
- Molecular Haematology Laboratory, Oxford University Hospitals NHS Foundation Trust
| | - Veronica Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Akhila Kavirayani
- Paediatric Rheumatology, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford
| | - Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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15
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Olijnik AA, Roy NBA, Scott C, Marsh JA, Brown J, Lauschke K, Ask K, Roberts N, Downes DJ, Brolih S, Johnson E, Xella B, Proven M, Hipkiss R, Ryan K, Frisk P, Mäkk J, Stattin ELM, Sadasivam N, McIlwaine L, Hill QA, Renella R, Hughes JR, Gibbons RJ, Groth A, McHugh PJ, Higgs DR, Buckle VJ, Babbs C. Genetic and functional insights into CDA-I prevalence and pathogenesis. J Med Genet 2020; 58:185-195. [PMID: 32518175 DOI: 10.1136/jmedgenet-2020-106880] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/05/2020] [Accepted: 04/02/2020] [Indexed: 01/30/2023]
Abstract
BACKGROUND Congenital dyserythropoietic anaemia type I (CDA-I) is a hereditary anaemia caused by biallelic mutations in the widely expressed genes CDAN1 and C15orf41. Little is understood about either protein and it is unclear in which cellular pathways they participate. METHODS Genetic analysis of a cohort of patients with CDA-I identifies novel pathogenic variants in both known causative genes. We analyse the mutation distribution and the predicted structural positioning of amino acids affected in Codanin-1, the protein encoded by CDAN1. Using western blotting, immunoprecipitation and immunofluorescence, we determine the effect of particular mutations on both proteins and interrogate protein interaction, stability and subcellular localisation. RESULTS We identify six novel CDAN1 mutations and one novel mutation in C15orf41 and uncover evidence of further genetic heterogeneity in CDA-I. Additionally, population genetics suggests that CDA-I is more common than currently predicted. Mutations are enriched in six clusters in Codanin-1 and tend to affect buried residues. Many missense and in-frame mutations do not destabilise the entire protein. Rather C15orf41 relies on Codanin-1 for stability and both proteins, which are enriched in the nucleolus, interact to form an obligate complex in cells. CONCLUSION Stability and interaction data suggest that C15orf41 may be the key determinant of CDA-I and offer insight into the mechanism underlying this disease. Both proteins share a common pathway likely to be present in a wide variety of cell types; however, nucleolar enrichment may provide a clue as to the erythroid specific nature of CDA-I. The surprisingly high predicted incidence of CDA-I suggests that better ascertainment would lead to improved patient care.
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Affiliation(s)
- Aude-Anais Olijnik
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Noémi B A Roy
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,NIHR Oxford Biomedical Research Centre and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - Caroline Scott
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jill Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Karin Lauschke
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Katrine Ask
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Eli Lilly Danmark, Herlev, Denmark
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sanja Brolih
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Errin Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Barbara Xella
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Melanie Proven
- Molecular Haematology Laboratory, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ria Hipkiss
- Molecular Haematology Laboratory, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Kate Ryan
- Haematology Department, Manchester University NHS Foundation Trust, Manchester, UK
| | - Per Frisk
- Department of Women's and Children's Health, Uppsala University and Uppsala University Childrens' Hospital, Uppsala, Sweden
| | - Johan Mäkk
- Centre for Health Development, Västmanland Region, Uppsala University, Uppsala, Sweden
| | | | - Nandini Sadasivam
- Haematology Department, Manchester University NHS Foundation Trust, Manchester, UK
| | - Louisa McIlwaine
- Department of Haematology, NHS Trust Greater Glasgow and Clyde, Glasgow, UK
| | - Quentin A Hill
- Department of Haematology, St James's University Hospital, Leeds, UK
| | - Raffaele Renella
- Pediatric Hematology-Oncology Laboratory, Lausanne University Hospital and University of Lausanne, Lausanne, VD, Switzerland
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,The Novo Nordisk Center for Protein Research (CPR), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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16
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Babbs C, Brown J, Horsley SW, Slater J, Maifoshie E, Kumar S, Ooijevaar P, Kriek M, Dixon-McIver A, Harteveld CL, Traeger-Synodinos J, Wilkie AOM, Higgs DR, Buckle VJ. ATR-16 syndrome: mechanisms linking monosomy to phenotype. J Med Genet 2020; 57:414-421. [PMID: 32005695 PMCID: PMC7279195 DOI: 10.1136/jmedgenet-2019-106528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 08/28/2019] [Revised: 11/29/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022]
Abstract
Background Deletions removing 100s–1000s kb of DNA, and variable numbers of poorly characterised genes, are often found in patients with a wide range of developmental abnormalities. In such cases, understanding the contribution of the deletion to an individual’s clinical phenotype is challenging. Methods Here, as an example of this common phenomenon, we analysed 41 patients with simple deletions of ~177 to ~2000 kb affecting one allele of the well-characterised, gene dense, distal region of chromosome 16 (16p13.3), referred to as ATR-16 syndrome. We characterised deletion extents and screened for genetic background effects, telomere position effect and compensatory upregulation of hemizygous genes. Results We find the risk of developmental and neurological abnormalities arises from much smaller distal chromosome 16 deletions (~400 kb) than previously reported. Beyond this, the severity of ATR-16 syndrome increases with deletion size, but there is no evidence that critical regions determine the developmental abnormalities associated with this disorder. Surprisingly, we find no evidence of telomere position effect or compensatory upregulation of hemizygous genes; however, genetic background effects substantially modify phenotypic abnormalities. Conclusions Using ATR-16 as a general model of disorders caused by CNVs, we show the degree to which individuals with contiguous gene syndromes are affected is not simply related to the number of genes deleted but depends on their genetic background. We also show there is no critical region defining the degree of phenotypic abnormalities in ATR-16 syndrome and this has important implications for genetic counselling.
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Affiliation(s)
- Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jill Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sharon W Horsley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Joanne Slater
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Evie Maifoshie
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Paul Ooijevaar
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Kriek
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Cornelis L Harteveld
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Traeger-Synodinos
- Department of Medical Genetics, National and Kapodistrian University of Athens, Athens, Greece
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Craniofacial Unit, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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17
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Abstract
Congenital dyserythropoietic anaemia type I (CDA-I) is one of a heterogeneous group of inherited anaemias characterised by ineffective erythropoiesis. CDA-I is caused by bi-allelic mutations in either CDAN1 or C15orf41 and, to date, 56 causative mutations have been documented. The diagnostic pathway is reviewed and the utility of genetic testing in reducing the time taken to reach an accurate molecular diagnosis and avoiding bone marrow aspiration, where possible, is described. The management of CDA-I patients is discussed, highlighting both general and specific measures which impact on disease progression. The use of interferon alpha and careful management of iron overload are reviewed and suggest the most favourable outcomes are achieved when CDA-I patients are managed with a holistic and multidisciplinary approach. Finally, the current understanding of the molecular and cellular pathogenesis of CDA-I is presented, highlighting critical questions likely to lead to improved therapy for this disease.
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Affiliation(s)
- Noémi B. A. Roy
- MRC Molecular Haematology UnitMRC Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics CentreJohn Radcliffe HospitalOxfordUK
- Oxford University Hospitals NHS Foundation TrustJohn Radcliffe HospitalOxfordUK
| | - Christian Babbs
- MRC Molecular Haematology UnitMRC Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
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18
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Moazen M, Marghoub A, Babbs C, Pauws E, Herring SW, Fagan MJ. Biomechanics of craniofacial development in mice. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.16.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | - Erwin Pauws
- University College LondonLondonUnited Kingdom
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19
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Marghoub A, Libby J, Babbs C, Ventikos Y, Fagan MJ, Moazen M. Characterizing and Modeling Bone Formation during Mouse Calvarial Development. Phys Rev Lett 2019; 122:048103. [PMID: 30768286 DOI: 10.1103/physrevlett.122.048103] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/06/2018] [Indexed: 06/09/2023]
Abstract
The newborn mammalian cranial vault consists of five flat bones that are joined together along their edges by soft fibrous tissues called sutures. Early fusion of these sutures leads to a medical condition known as craniosynostosis. The mechanobiology of normal and craniosynostotic skull growth is not well understood. In a series of previous studies, we characterized and modeled radial expansion of normal and craniosynostotic (Crouzon) mice. Here, we describe a new modeling algorithm to simulate bone formation at the sutures in normal and craniosynostotic mice. Our results demonstrate that our modeling approach is capable of predicting the observed ex vivo pattern of bone formation at the sutures in the aforementioned mice. The same approach can be used to model different calvarial reconstruction in children with craniosynostosis to assist in the management of this complex condition.
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Affiliation(s)
- Arsalan Marghoub
- Department of Mechanical Engineering, University College London, Torrington Place, London, WC1E 7JE, United Kingdom
| | - Joseph Libby
- Medical and Biological Engineering, School of Engineering and Computer Science, University of Hull, Hull, HU6 7RX, United Kingdom
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
| | - Yiannis Ventikos
- Department of Mechanical Engineering, University College London, Torrington Place, London, WC1E 7JE, United Kingdom
| | - Michael J Fagan
- Medical and Biological Engineering, School of Engineering and Computer Science, University of Hull, Hull, HU6 7RX, United Kingdom
| | - Mehran Moazen
- Department of Mechanical Engineering, University College London, Torrington Place, London, WC1E 7JE, United Kingdom
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20
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Brown JM, Roberts NA, Graham B, Waithe D, Lagerholm C, Telenius JM, De Ornellas S, Oudelaar AM, Scott C, Szczerbal I, Babbs C, Kassouf MT, Hughes JR, Higgs DR, Buckle VJ. A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions. Nat Commun 2018; 9:3849. [PMID: 30242161 PMCID: PMC6155075 DOI: 10.1038/s41467-018-06248-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 08/24/2018] [Indexed: 11/08/2022] Open
Abstract
Self-interacting chromatin domains encompass genes and their cis-regulatory elements; however, the three-dimensional form a domain takes, whether this relies on enhancer-promoter interactions, and the processes necessary to mediate the formation and maintenance of such domains, remain unclear. To examine these questions, here we use a combination of high-resolution chromosome conformation capture, a non-denaturing form of fluorescence in situ hybridisation and super-resolution imaging to study a 70 kb domain encompassing the mouse α-globin regulatory locus. We show that this region forms an erythroid-specific, decompacted, self-interacting domain, delimited by frequently apposed CTCF/cohesin binding sites early in terminal erythroid differentiation, and does not require transcriptional elongation for maintenance of the domain structure. Formation of this domain does not rely on interactions between the α-globin genes and their major enhancers, suggesting a transcription-independent mechanism for establishment of the domain. However, absence of the major enhancers does alter internal domain interactions. Formation of a loop domain therefore appears to be a mechanistic process that occurs irrespective of the specific interactions within.
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Affiliation(s)
- Jill M Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Nigel A Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Bryony Graham
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Dominic Waithe
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, Oxford, OX3 9DS, UK
| | - Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, Oxford, OX3 9DS, UK
| | - Jelena M Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Sara De Ornellas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Caroline Scott
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Izabela Szczerbal
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Mira T Kassouf
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK.
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21
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Moir-Meyer G, Cheong PL, Olijnik AA, Brown J, Knight S, King A, Kurita R, Nakamura Y, Gibbons RJ, Higgs DR, Buckle VJ, Babbs C. Robust CRISPR/Cas9 Genome Editing of the HUDEP-2 Erythroid Precursor Line Using Plasmids and Single-Stranded Oligonucleotide Donors. Methods Protoc 2018; 1:E28. [PMID: 31164570 PMCID: PMC6481050 DOI: 10.3390/mps1030028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/13/2018] [Accepted: 07/23/2018] [Indexed: 12/23/2022] Open
Abstract
The study of cellular processes and gene regulation in terminal erythroid development has been greatly facilitated by the generation of an immortalised erythroid cell line derived from Human Umbilical Derived Erythroid Precursors, termed HUDEP-2 cells. The ability to efficiently genome edit HUDEP-2 cells and make clonal lines hugely expands their utility as the insertion of clinically relevant mutations allows study of potentially every genetic disease affecting red blood cell development. Additionally, insertion of sequences encoding short protein tags such as Strep, FLAG and Myc permits study of protein behaviour in the normal and disease state. This approach is useful to augment the analysis of patient cells as large cell numbers are obtainable with the additional benefit that the need for specific antibodies may be circumvented. This approach is likely to lead to insights into disease mechanisms and provide reagents to allow drug discovery. HUDEP-2 cells provide a favourable alternative to the existing immortalised erythroleukemia lines as their karyotype is much less abnormal. These cells also provide sufficient material for a broad range of analyses as it is possible to generate in vitro-differentiated erythroblasts in numbers 4-7 fold higher than starting cell numbers within 9-12 days of culture. Here we describe an efficient, robust and reproducible plasmid-based methodology to introduce short (<20 bp) DNA sequences into the genome of HUDEP-2 cells using the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 Cas9 system combined with single-stranded oligodeoxynucleotide (ssODN) donors. This protocol produces genetically modified lines in ~30 days and could also be used to generate knock-out and knock-in mutations.
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Affiliation(s)
- Gemma Moir-Meyer
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Pak Leng Cheong
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Aude-Anais Olijnik
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Jill Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Samantha Knight
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford OX3 7BN, UK.
| | - Andrew King
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, 1-1-3 Shibadaimon, Minato-ku, Tokyo 105-8521, Japan.
| | - Yukio Nakamura
- RIKEN BioResource Research Center, Koyadai 3-1-1, Tsukuba 305-0074, Japan.
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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22
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Marghoub A, Libby J, Babbs C, Pauws E, Fagan MJ, Moazen M. Predicting calvarial growth in normal and craniosynostotic mice using a computational approach. J Anat 2018; 232:440-448. [PMID: 29243252 PMCID: PMC5807955 DOI: 10.1111/joa.12764] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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] [Accepted: 11/21/2017] [Indexed: 11/26/2022] Open
Abstract
During postnatal calvarial growth the brain grows gradually and the overlying bones and sutures accommodate that growth until the later juvenile stages. The whole process is coordinated through a complex series of biological, chemical and perhaps mechanical signals between various elements of the craniofacial system. The aim of this study was to investigate to what extent a computational model can accurately predict the calvarial growth in wild-type (WT) and mutant type (MT) Fgfr2C342Y/+ mice displaying bicoronal suture fusion. A series of morphological studies were carried out to quantify the calvarial growth at P3, P10 and P20 in both mouse types. MicroCT images of a P3 specimen were used to develop a finite element model of skull growth to predict the calvarial shape of WT and MT mice at P10. Sensitivity tests were performed and the results compared with ex vivo P10 data. Although the models were sensitive to the choice of input parameters, they predicted the overall skull growth in the WT and MT mice. The models also captured the difference between the ex vivoWT and MT mice. This modelling approach has the potential to be translated to human skull growth and to enhance our understanding of the different reconstruction methods used to manage clinically the different forms of craniosynostosis, and in the long term possibly reduce the number of re-operations in children displaying this condition and thereby enhance their quality of life.
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Affiliation(s)
- Arsalan Marghoub
- Department of Mechanical EngineeringUniversity College LondonLondonUK
| | - Joseph Libby
- Medical and Biological EngineeringSchool of Engineering and Computer ScienceUniversity of HullHullUK
| | - Christian Babbs
- MRC Molecular Haematology UnitMRC Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Erwin Pauws
- Institute of Child HealthGreat Ormond StreetUniversity College LondonLondonUK
| | - Michael J. Fagan
- Medical and Biological EngineeringSchool of Engineering and Computer ScienceUniversity of HullHullUK
| | - Mehran Moazen
- Department of Mechanical EngineeringUniversity College LondonLondonUK
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23
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Abstract
This two part study examined the written communication between psychiatrists and other hospital doctors. In the first part a set of sample letters from a psychiatrist, who had seen a ward referral, was sent to 110 physicians and surgeons. Nearly half expressed a preference for a psychiatrist's letter that was one page long with main points underlined. Clarity of psychiatric diagnosis and opinion and clear treatment/follow-up arrangements were the key items of content. In the second part 100 consecutive referral letters and their replies were assessed; 20% of referral letters did not express the precise reason why psychiatric opinion was sought and many of the psychiatrists' replies did not describe adequately the follow-up arrangements and prognosis. In general the psychiatrist found the referral letters short and lacking in information whereas referring doctors found the brief replies from the psychiatrists preferable because the brief letters contained the key items mentioned in the first part of the study. In addition to these recommendations regarding written communications, this study emphasizes the need for personal discussion between psychiatrists and other hospital doctors; nearly half the doctors in the first part of the study thought this would be essential for good management of the patient.
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Affiliation(s)
- I Leonard
- University Department of Psychiatry, Manchester Royal Infirmary
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24
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Nguyen DT, Voon HPJ, Xella B, Scott C, Clynes D, Babbs C, Ayyub H, Kerry J, Sharpe JA, Sloane-Stanley JA, Butler S, Fisher CA, Gray NE, Jenuwein T, Higgs DR, Gibbons RJ. The chromatin remodelling factor ATRX suppresses R-loops in transcribed telomeric repeats. EMBO Rep 2017; 18:914-928. [PMID: 28487353 DOI: 10.15252/embr.201643078] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [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: 07/20/2016] [Revised: 03/21/2017] [Accepted: 03/27/2017] [Indexed: 02/04/2023] Open
Abstract
ATRX is a chromatin remodelling factor found at a wide range of tandemly repeated sequences including telomeres (TTAGGG)n ATRX mutations are found in nearly all tumours that maintain their telomeres via the alternative lengthening of telomere (ALT) pathway, and ATRX is known to suppress this pathway. Here, we show that recruitment of ATRX to telomeric repeats depends on repeat number, orientation and, critically, on repeat transcription. Importantly, the transcribed telomeric repeats form RNA-DNA hybrids (R-loops) whose abundance correlates with the recruitment of ATRX Here, we show loss of ATRX is also associated with increased R-loop formation. Our data suggest that the presence of ATRX at telomeres may have a central role in suppressing deleterious DNA secondary structures that form at transcribed telomeric repeats, and this may account for the increased DNA damage, stalling of replication and homology-directed repair previously observed upon loss of ATRX function.
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Affiliation(s)
- Diu Tt Nguyen
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Hsiao Phin J Voon
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.,Department of Biochemistry and Molecular Biology, The Biomedicine Discovery Institute, Monash University, Clayton, Vic., Australia
| | - Barbara Xella
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Caroline Scott
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - David Clynes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Christian Babbs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Helena Ayyub
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jon Kerry
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jacqueline A Sharpe
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jackie A Sloane-Stanley
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Sue Butler
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Chris A Fisher
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Nicki E Gray
- Computational Biology Research Group, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Thomas Jenuwein
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
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25
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Songdej D, Babbs C, Higgs DR. An international registry of survivors with Hb Bart's hydrops fetalis syndrome. Blood 2017; 129:1251-1259. [PMID: 28057638 PMCID: PMC5345731 DOI: 10.1182/blood-2016-08-697110] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [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: 08/11/2016] [Accepted: 12/19/2016] [Indexed: 11/20/2022] Open
Abstract
Hemoglobin (Hb) Bart's hydrops fetalis syndrome (BHFS) resulting from α0-thalassemia is considered a universally fatal disorder. However, over the last 3 decades, improvements in intrauterine interventions and perinatal intensive care have resulted in increasing numbers of BHFS survivors. We have initiated an international registry containing information on 69 patients, of which 31 are previously unpublished. In this perspective, we analyze the available clinical information to document the natural history of BHFS. In the future, once we have accrued sufficient cases, we aim to build on this study and provide information to allow counseling of at-risk couples. To date, 39 patients have survived beyond the age of 5 years, 18 of whom are now older than 10 years. Based on the available cases, we find evidence to suggest that intrauterine therapy provides benefits during the perinatal and neonatal period; however, it may not provide additional benefits to long-term growth and neurodevelopmental outcomes. Growth retardation is a major adverse long-term outcome among BHFS patients with ∼40% being severely affected in terms of weight and ∼50% in terms of height. There is also an increased risk of neurodevelopmental delay as we find 20% (11/55) of BHFS survivors suffer from a serious delay of ≥6 months. Most patients in the registry require lifelong transfusion and often have associated congenital abnormalities and comorbidities. This perspective is a first step in gathering information to allow provision of informed counseling on the predicted outcomes of affected babies.
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Affiliation(s)
- Duantida Songdej
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and
- Division of Hematology/Oncology, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Christian Babbs
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and
| | - Douglas R Higgs
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and
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26
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Roy NBA, Wilson EA, Henderson S, Wray K, Babbs C, Okoli S, Atoyebi W, Mixon A, Cahill MR, Carey P, Cullis J, Curtin J, Dreau H, Ferguson DJP, Gibson B, Hall G, Mason J, Morgan M, Proven M, Qureshi A, Sanchez Garcia J, Sirachainan N, Teo J, Tedgård U, Higgs D, Roberts D, Roberts I, Schuh A. A novel 33-Gene targeted resequencing panel provides accurate, clinical-grade diagnosis and improves patient management for rare inherited anaemias. Br J Haematol 2016; 175:318-330. [PMID: 27432187 PMCID: PMC5132128 DOI: 10.1111/bjh.14221] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/08/2016] [Indexed: 01/21/2023]
Abstract
Accurate diagnosis of rare inherited anaemias is challenging, requiring a series of complex and expensive laboratory tests. Targeted next-generation-sequencing (NGS) has been used to investigate these disorders, but the selection of genes on individual panels has been narrow and the validation strategies used have fallen short of the standards required for clinical use. Clinical-grade validation of negative results requires the test to distinguish between lack of adequate sequencing reads at the locations of known mutations and a real absence of mutations. To achieve a clinically-reliable diagnostic test and minimize false-negative results we developed an open-source tool (CoverMi) to accurately determine base-coverage and the 'discoverability' of known mutations for every sample. We validated our 33-gene panel using Sanger sequencing and microarray. Our panel demonstrated 100% specificity and 99·7% sensitivity. We then analysed 57 clinical samples: molecular diagnoses were made in 22/57 (38·6%), corresponding to 32 mutations of which 16 were new. In all cases, accurate molecular diagnosis had a positive impact on clinical management. Using a validated NGS-based platform for routine molecular diagnosis of previously undiagnosed congenital anaemias is feasible in a clinical diagnostic setting, improves precise diagnosis and enhances management and counselling of the patient and their family.
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Affiliation(s)
- Noémi B A Roy
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Edward A Wilson
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - Shirley Henderson
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - Katherine Wray
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Christian Babbs
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Steven Okoli
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Wale Atoyebi
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Avery Mixon
- Division of Pediatric Hematology/Oncology, Children's Hospital at Erlanger, Chattanooga, TN, USA
| | - Mary R Cahill
- Department of Haematology, Cork University Hospital, Cork, Ireland
| | - Peter Carey
- Department of Haematology, The Royal Victoria Infirmary, Newcastle-upon-Tyne, UK
| | - Jonathan Cullis
- Department of Haematology, Salisbury NHS Foundation Trust, Salisbury, UK
| | - Julie Curtin
- Department of Haematology, Sydney Children's Hospitals Network, Westmead, Australia
| | - Helene Dreau
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - David J P Ferguson
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Brenda Gibson
- Department of Paediatric Haematology/Oncology, Royal Hospital for Children, Glasgow, UK
| | - Georgina Hall
- Paediatric Haematology/Oncology Unit, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Joanne Mason
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - Mary Morgan
- Department of Paediatric Haematology-Oncology, University Hospital Southampton, Southampton, UK
| | - Melanie Proven
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
| | - Amrana Qureshi
- Paediatric Haematology/Oncology Unit, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Joaquin Sanchez Garcia
- Laboratorio Diagnóstico UGC de Hematología Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Nongnuch Sirachainan
- Division of Haemato-Oncology, Department of Paediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Juliana Teo
- Department of Haematology, Sydney Children's Hospitals Network, Westmead, Australia
| | - Ulf Tedgård
- Department of Paediatrics, Skåne University Hospital, Lund, Sweden
| | - Doug Higgs
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - David Roberts
- NHS Blood and Transplant, NHSBT - John Radcliffe Hospital, Level 2, Oxford, UK
| | - Irene Roberts
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK.
| | - Anna Schuh
- BRC Blood Theme and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK.
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27
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Hay D, Hughes JR, Babbs C, Davies JO, Graham BJ, Hanssen L, Kassouf MT, Marieke Oudelaar AM, Sharpe JA, Suciu MC, Telenius J, Williams R, Rode C, Li PS, Pennacchio LA, Sloane-Stanley JA, Ayyub H, Butler S, Sauka-Spengler T, Gibbons RJ, Smith AJ, Wood WG, Higgs DR. Genetic dissection of the α-globin super-enhancer in vivo. Nat Genet 2016; 48:895-903. [PMID: 27376235 PMCID: PMC5058437 DOI: 10.1038/ng.3605] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [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: 03/02/2016] [Accepted: 06/01/2016] [Indexed: 12/18/2022]
Abstract
Many genes determining cell identity are regulated by clusters of Mediator-bound enhancer elements collectively referred to as super-enhancers. These super-enhancers have been proposed to manifest higher-order properties important in development and disease. Here we report a comprehensive functional dissection of one of the strongest putative super-enhancers in erythroid cells. By generating a series of mouse models, deleting each of the five regulatory elements of the α-globin super-enhancer individually and in informative combinations, we demonstrate that each constituent enhancer seems to act independently and in an additive fashion with respect to hematological phenotype, gene expression, chromatin structure and chromosome conformation, without clear evidence of synergistic or higher-order effects. Our study highlights the importance of functional genetic analyses for the identification of new concepts in transcriptional regulation.
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Affiliation(s)
- Deborah Hay
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Jim R. Hughes
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Christian Babbs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - James O.J. Davies
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Bryony J. Graham
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Lars Hanssen
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Mira T. Kassouf
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | | | - Jacqueline A Sharpe
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Maria C. Suciu
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Jelena Telenius
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Ruth Williams
- Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Christina Rode
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Pik-Shan Li
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Len A. Pennacchio
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California
| | | | - Helena Ayyub
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Sue Butler
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | | | - Richard J. Gibbons
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Andrew J.H. Smith
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - William G. Wood
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Douglas R. Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
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28
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Brackley CA, Brown JM, Waithe D, Babbs C, Davies J, Hughes JR, Buckle VJ, Marenduzzo D. Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models. Genome Biol 2016; 17:59. [PMID: 27036497 PMCID: PMC4815170 DOI: 10.1186/s13059-016-0909-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [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: 11/27/2015] [Accepted: 02/23/2016] [Indexed: 12/20/2022] Open
Abstract
The three-dimensional (3D) organization of chromosomes can be probed using methods like Capture-C. However, it is unclear how such population-level data relate to the organization within a single cell, and the mechanisms leading to the observed interactions are still largely obscure. We present a polymer modeling scheme based on the assumption that chromosome architecture is maintained by protein bridges, which form chromatin loops. To test the model, we perform FISH experiments and compare with Capture-C data. Starting merely from the locations of protein binding sites, our model accurately predicts the experimentally observed chromatin interactions, revealing a population of 3D conformations.
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Affiliation(s)
- Chris A. Brackley
- />SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ UK
| | - Jill M. Brown
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Dominic Waithe
- />Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Christian Babbs
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - James Davies
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Jim R. Hughes
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Veronica J. Buckle
- />MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS UK
| | - Davide Marenduzzo
- />SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh, EH9 3JZ UK
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29
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Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle VJ, Bull K, Cais O, Cario H, Chapel H, Copley RR, Cornall R, Craft J, Dahan K, Davenport EE, Dendrou C, Devuyst O, Fenwick AL, Flint J, Fugger L, Gilbert RD, Goriely A, Green A, Greger IH, Grocock R, Gruszczyk AV, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight JC, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan SJ, McMullin MF, Miller KA, Murray L, Németh AH, Nesbit MA, Nutt D, Ormondroyd E, Oturai AB, Pagnamenta A, Patel SY, Percy M, Petousi N, Piazza P, Piret SE, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins PA, Robson K, Russo A, Sahgal N, van Schouwenburg PA, Schuh A, Silverman E, Simmons A, Sørensen PS, Sweeney E, Taylor J, Thakker RV, Tomlinson I, Trebes A, Twigg SR, Uhlig HH, Vyas P, Vyse T, Wall SA, Watkins H, Whyte MP, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe PJ, Bell JI, Wilkie AO, Bentley D, Donnelly P, McVean G. Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. Nat Genet 2015; 47:717-726. [PMID: 25985138 PMCID: PMC4601524 DOI: 10.1038/ng.3304] [Citation(s) in RCA: 263] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 04/22/2015] [Indexed: 12/12/2022]
Abstract
To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.
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Affiliation(s)
- Jenny C Taylor
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hilary C Martin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stefano Lise
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - John Broxholme
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Andy Rimmer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alexander Kanapin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simon Fiddy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chris Allan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - A Radu Aricescu
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Moustafa Attar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christian Babbs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - David Beeson
- Neurosciences Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Celeste Bento
- Hematology Department, Centro Hospitalar e Universitário de Coimbra, Portugal
| | - Patricia Bignell
- Molecular Haematology Department, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Edward Blair
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Katherine Bull
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, UK
| | - Ondrej Cais
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Holger Cario
- Department of Pediatrics and Adolescent Medicine, University Medical Center, Ulm, Germany
| | - Helen Chapel
- Primary Immunodeficiency Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Richard R Copley
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Richard Cornall
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, UK
| | - Jude Craft
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Karin Dahan
- Centre de Génétique Humaine, Institut de Génétique et de Pathologie, Gosselies, Belgium
- Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Emma E Davenport
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Calliope Dendrou
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Olivier Devuyst
- Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Aimée L Fenwick
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jonathan Flint
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lars Fugger
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rodney D Gilbert
- University Hospital Southampton NHS Foundation Trust, University of Southampton, Southampton, UK
| | - Anne Goriely
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Angie Green
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ingo H Greger
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Anja V Gruszczyk
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Robert Hastings
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Edouard Hatton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Doug Higgs
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Adrian Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chris Holmes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Malcolm Howard
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Linda Hughes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Peter Humburg
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Johnson
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Fredrik Karpe
- Oxford Laboratory for Integrative Physiology, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | | | - Usha Kini
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jonathan Krohn
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Craig Langman
- Kidney Diseases, Feinberg School of Medicine, Northwestern University and the Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Lorne Lonie
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Joshua Luck
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Davis McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simon J McGowan
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Kerry A Miller
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Lisa Murray
- Illumina Cambridge Limited, Saffron Walden, UK
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - M Andrew Nesbit
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - David Nutt
- Centre for Neuropsychopharmacology, Division of Brain Sciences, Imperial College, London, UK
| | - Elizabeth Ormondroyd
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Annette Bang Oturai
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Alistair Pagnamenta
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Smita Y Patel
- Primary Immunodeficiency Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Melanie Percy
- Department of Haematology, Belfast City Hospital, Belfast, UK
| | - Nayia Petousi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sian E Piret
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | | | - Niko Popitsch
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Fiona Powrie
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Chris Pugh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lynn Quek
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Peter A Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Kathryn Robson
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Alexandra Russo
- Department of Pediatrics, University Hospital, Mainz, Germany
| | - Natasha Sahgal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Anna Schuh
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Earl Silverman
- Division of Rheumatology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alison Simmons
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Per Soelberg Sørensen
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Elizabeth Sweeney
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - John Taylor
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Oxford NHS Regional Molecular Genetics Laboratory, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Rajesh V Thakker
- Academic Endocrine Unit, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Ian Tomlinson
- NIHR Comprehensive Biomedical Research Centre, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Amy Trebes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen Rf Twigg
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Tim Vyse
- Division of Genetics, King's College London, Guy's Hospital, London, UK
| | - Steven A Wall
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Michael P Whyte
- Center for Metabolic Bone Disease and Molecular Research, Shriners Hospital for Children, St Louis, Missouri, USA
| | - Lorna Witty
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ben Wright
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chris Yau
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Buck
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | - John I Bell
- Office of the Regius Professor of Medicine, University of Oxford, Oxford, UK
| | - Andrew Om Wilkie
- Clinical Genetics Group, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Gilean McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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Moazen M, Peskett E, Babbs C, Pauws E, Fagan MJ. Mechanical properties of calvarial bones in a mouse model for craniosynostosis. PLoS One 2015; 10:e0125757. [PMID: 25966306 PMCID: PMC4429024 DOI: 10.1371/journal.pone.0125757] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/25/2015] [Indexed: 11/25/2022] Open
Abstract
The mammalian cranial vault largely consists of five flat bones that are joined together along their edges by soft fibrous tissues called sutures. Premature closure of the cranial sutures, craniosynostosis, can lead to serious clinical pathology unless there is surgical intervention. Research into the genetic basis of the disease has led to the development of various animal models that display this condition, e.g. mutant type Fgfr2C342Y/+ mice which display early fusion of the coronal suture (joining the parietal and frontal bones). However, whether the biomechanical properties of the mutant and wild type bones are affected has not been investigated before. Therefore, nanoindentation was used to compare the elastic modulus of cranial bone and sutures in wild type (WT) and Fgfr2C342Y/+mutant type (MT) mice during their postnatal development. Further, the variations in properties with indentation position and plane were assessed. No difference was observed in the elastic modulus of parietal bone between the WT and MT mice at postnatal (P) day 10 and 20. However, the modulus of frontal bone in the MT group was lower than the WT group at both P10 (1.39±0.30 vs. 5.32±0.68 GPa; p<0.05) and P20 (5.57±0.33 vs. 7.14±0.79 GPa; p<0.05). A wide range of values was measured along the coronal sutures for both the WT and MT samples, with no significant difference between the two groups. Findings of this study suggest that the inherent mechanical properties of the frontal bone in the mutant mice were different to the wild type mice from the same genetic background. These differences may reflect variations in the degree of biomechanical adaptation during skull growth, which could have implications for the surgical management of craniosynostosis patients.
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Affiliation(s)
- Mehran Moazen
- Medical and Biological Engineering, School of Engineering, University of Hull, Hull, United Kingdom
- * E-mail:
| | - Emma Peskett
- UCL Institute of Child Health, London, United Kingdom
| | - Christian Babbs
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Erwin Pauws
- UCL Institute of Child Health, London, United Kingdom
| | - Michael J. Fagan
- Medical and Biological Engineering, School of Engineering, University of Hull, Hull, United Kingdom
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Babbs C, Lloyd D, Pagnamenta AT, Twigg SRF, Green J, McGowan SJ, Mirza G, Naples R, Sharma VP, Volpi EV, Buckle VJ, Wall SA, Knight SJL, Parr JR, Wilkie AOM. De novo and rare inherited mutations implicate the transcriptional coregulator TCF20/SPBP in autism spectrum disorder. J Med Genet 2014; 51:737-47. [PMID: 25228304 PMCID: PMC4215269 DOI: 10.1136/jmedgenet-2014-102582] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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] [Indexed: 12/11/2022]
Abstract
BACKGROUND Autism spectrum disorders (ASDs) are common and have a strong genetic basis, yet the cause of ∼70-80% ASDs remains unknown. By clinical cytogenetic testing, we identified a family in which two brothers had ASD, mild intellectual disability and a chromosome 22 pericentric inversion, not detected in either parent, indicating de novo mutation with parental germinal mosaicism. We hypothesised that the rearrangement was causative of their ASD and localised the chromosome 22 breakpoints. METHODS The rearrangement was characterised using fluorescence in situ hybridisation, Southern blotting, inverse PCR and dideoxy-sequencing. Open reading frames and intron/exon boundaries of the two physically disrupted genes identified, TCF20 and TNRC6B, were sequenced in 342 families (260 multiplex and 82 simplex) ascertained by the International Molecular Genetic Study of Autism Consortium (IMGSAC). RESULTS IMGSAC family screening identified a de novo missense mutation of TCF20 in a single case and significant association of a different missense mutation of TCF20 with ASD in three further families. Through exome sequencing in another project, we independently identified a de novo frameshifting mutation of TCF20 in a woman with ASD and moderate intellectual disability. We did not identify a significant association of TNRC6B mutations with ASD. CONCLUSIONS TCF20 encodes a transcriptional coregulator (also termed SPBP) that is structurally and functionally related to RAI1, the critical dosage-sensitive protein implicated in the behavioural phenotypes of the Smith-Magenis and Potocki-Lupski 17p11.2 deletion/duplication syndromes, in which ASD is frequently diagnosed. This study provides the first evidence that mutations in TCF20 are also associated with ASD.
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Affiliation(s)
- Christian Babbs
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK NIHR Biomedical Research Centre, Oxford, UK
| | - Deborah Lloyd
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Alistair T Pagnamenta
- NIHR Biomedical Research Centre, Oxford, UK Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stephen R F Twigg
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Joanne Green
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Simon J McGowan
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Ghazala Mirza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rebecca Naples
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Vikram P Sharma
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Emanuela V Volpi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Veronica J Buckle
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Steven A Wall
- Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Samantha J L Knight
- NIHR Biomedical Research Centre, Oxford, UK Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Jeremy R Parr
- Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne, UK
| | - Andrew O M Wilkie
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK NIHR Biomedical Research Centre, Oxford, UK Craniofacial Unit, Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
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Babbs C, Roberts NA, Sanchez-Pulido L, McGowan SJ, Ahmed MR, Brown JM, Sabry MA, Bentley DR, McVean GA, Donnelly P, Gileadi O, Ponting CP, Higgs DR, Buckle VJ. Homozygous mutations in a predicted endonuclease are a novel cause of congenital dyserythropoietic anemia type I. Haematologica 2013; 98:1383-7. [PMID: 23716552 DOI: 10.3324/haematol.2013.089490] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The congenital dyserythropoietic anemias are a heterogeneous group of rare disorders primarily affecting erythropoiesis with characteristic morphological abnormalities and a block in erythroid maturation. Mutations in the CDAN1 gene, which encodes Codanin-1, underlie the majority of congenital dyserythropoietic anemia type I cases. However, no likely pathogenic CDAN1 mutation has been detected in approximately 20% of cases, suggesting the presence of at least one other locus. We used whole genome sequencing and segregation analysis to identify a homozygous T to A transversion (c.533T>A), predicted to lead to a p.L178Q missense substitution in C15ORF41, a gene of unknown function, in a consanguineous pedigree of Middle-Eastern origin. Sequencing C15ORF41 in other CDAN1 mutation-negative congenital dyserythropoietic anemia type I pedigrees identified a homozygous transition (c.281A>G), predicted to lead to a p.Y94C substitution, in two further pedigrees of SouthEast Asian origin. The haplotype surrounding the c.281A>G change suggests a founder effect for this mutation in Pakistan. Detailed sequence similarity searches indicate that C15ORF41 encodes a novel restriction endonuclease that is a member of the Holliday junction resolvase family of proteins.
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Affiliation(s)
- Christian Babbs
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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33
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Twigg SRF, Babbs C, van den Elzen MEP, Goriely A, Taylor S, McGowan SJ, Giannoulatou E, Lonie L, Ragoussis J, Sadighi Akha E, Knight SJL, Zechi-Ceide RM, Hoogeboom JAM, Pober BR, Toriello HV, Wall SA, Rita Passos-Bueno M, Brunner HG, Mathijssen IMJ, Wilkie AOM. Cellular interference in craniofrontonasal syndrome: males mosaic for mutations in the X-linked EFNB1 gene are more severely affected than true hemizygotes. Hum Mol Genet 2013; 22:1654-62. [PMID: 23335590 PMCID: PMC3605834 DOI: 10.1093/hmg/ddt015] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [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] [Indexed: 12/21/2022] Open
Abstract
Craniofrontonasal syndrome (CFNS), an X-linked disorder caused by loss-of-function mutations of EFNB1, exhibits a paradoxical sex reversal in phenotypic severity: females characteristically have frontonasal dysplasia, craniosynostosis and additional minor malformations, but males are usually more mildly affected with hypertelorism as the only feature. X-inactivation is proposed to explain the more severe outcome in heterozygous females, as this leads to functional mosaicism for cells with differing expression of EPHRIN-B1, generating abnormal tissue boundaries—a process that cannot occur in hemizygous males. Apparently challenging this model, males occasionally present with a more severe female-like CFNS phenotype. We hypothesized that such individuals might be mosaic for EFNB1 mutations and investigated this possibility in multiple tissue samples from six sporadically presenting males. Using denaturing high performance liquid chromatography, massively parallel sequencing and multiplex-ligation-dependent probe amplification (MLPA) to increase sensitivity above standard dideoxy sequencing, we identified mosaic mutations of EFNB1 in all cases, comprising three missense changes, two gene deletions and a novel point mutation within the 5′ untranslated region (UTR). Quantification by Pyrosequencing and MLPA demonstrated levels of mutant cells between 15 and 69%. The 5′ UTR variant mutates the stop codon of a small upstream open reading frame that, using a dual-luciferase reporter construct, was demonstrated to exacerbate interference with translation of the wild-type protein. These results demonstrate a more severe outcome in mosaic than in constitutionally deficient males in an X-linked dominant disorder and provide further support for the cellular interference mechanism, normally related to X-inactivation in females.
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Affiliation(s)
- Stephen R F Twigg
- Clinical Genetics, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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34
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Kowalczyk MS, Hughes JR, Babbs C, Sanchez-Pulido L, Szumska D, Sharpe JA, Sloane-Stanley JA, Morriss-Kay GM, Smoot LB, Roberts AE, Watkins H, Bhattacharya S, Gibbons RJ, Ponting CP, Wood WG, Higgs DR. Nprl3 is required for normal development of the cardiovascular system. Mamm Genome 2012; 23:404-15. [PMID: 22538705 DOI: 10.1007/s00335-012-9398-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 03/19/2012] [Indexed: 12/18/2022]
Abstract
C16orf35 is a conserved and widely expressed gene lying adjacent to the human α-globin cluster in all vertebrate species. In-depth sequence analysis shows that C16orf35 (now called NPRL3) is an orthologue of the yeast gene Npr3 (nitrogen permease regulator 3) and, furthermore, is a paralogue of its protein partner Npr2. The yeast Npr2/3 dimeric protein complex senses amino acid starvation and appropriately adjusts cell metabolism via the TOR pathway. Here we have analysed a mouse model in which expression of Nprl3 has been abolished using homologous recombination. The predominant effect on RNA expression appears to involve genes that regulate protein synthesis and cell cycle, consistent with perturbation of the mTOR pathway. Embryos homozygous for this mutation die towards the end of gestation with a range of cardiovascular defects, including outflow tract abnormalities and ventriculoseptal defects consistent with previous observations, showing that perturbation of the mTOR pathway may affect development of the myocardium. NPRL3 is a candidate gene for harbouring mutations in individuals with developmental abnormalities of the cardiovascular system.
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Affiliation(s)
- Monika S Kowalczyk
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK
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35
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Babbs C, Stewart HS, Williams LJ, Connell L, Goriely A, Twigg SRF, Smith K, Lester T, Wilkie AOM. Duplication of the EFNB1 gene in familial hypertelorism: imbalance in ephrin-B1 expression and abnormal phenotypes in humans and mice. Hum Mutat 2011; 32:930-8. [PMID: 21542058 PMCID: PMC3170877 DOI: 10.1002/humu.21521] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [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: 08/02/2010] [Accepted: 04/18/2011] [Indexed: 11/09/2022]
Abstract
Familial hypertelorism, characterized by widely spaced eyes, classically shows autosomal dominant inheritance (Teebi type), but some pedigrees are compatible with X-linkage. No mechanism has been described previously, but clinical similarity has been noted to craniofrontonasal syndrome (CFNS), which is caused by mutations in the X-linked EFNB1 gene. Here we report a family in which females in three generations presented with hypertelorism, but lacked either craniosynostosis or a grooved nasal tip, excluding CFNS. DNA sequencing of EFNB1 was normal, but further analysis revealed a duplication of 937 kb including EFNB1 and two flanking genes: PJA1 and STARD8. We found that the X chromosome bearing the duplication produces ∼1.6-fold more EFNB1 transcript than the normal X chromosome and propose that, in the context of X-inactivation, this difference in expression level of EFNB1 results in abnormal cell sorting leading to hypertelorism. To support this hypothesis, we provide evidence from a mouse model carrying a targeted human EFNB1 cDNA, that abnormal cell sorting occurs in the cranial region. Hence, we propose that X-linked cases resembling Teebi hypertelorism may have a similar mechanism to CFNS, and that cellular mosaicism for different levels of ephrin-B1 (as well as simple presence/absence) leads to craniofacial abnormalities. Hum Mutat 32:1–9, 2011. © 2011 Wiley-Liss, Inc.
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Affiliation(s)
- Christian Babbs
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
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36
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Geraghty J, George R, Babbs C. A questionnaire study assessing overuse injuries in United Kingdom endoscopists and any effect from the introduction of the National Bowel Cancer Screening Program on these injuries. Gastrointest Endosc 2011; 73:1069-70. [PMID: 21521575 DOI: 10.1016/j.gie.2010.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 11/08/2010] [Indexed: 02/08/2023]
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37
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Babbs C, Stewart H, Williams L, Connell L, Goriely A, Twigg S, Smith K, Lester T, Wilkie A. 06-P003 Imbalance in ephrin-b1 expression leads to hypertelorism in humans and mice. Mech Dev 2009. [DOI: 10.1016/j.mod.2009.06.229] [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: 10/20/2022]
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38
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Twigg SRF, Healy C, Babbs C, Sharpe JA, Wood WG, Sharpe PT, Morriss-Kay GM, Wilkie AOM. Skeletal analysis of the Fgfr3(P244R) mouse, a genetic model for the Muenke craniosynostosis syndrome. Dev Dyn 2009; 238:331-42. [PMID: 19086028 DOI: 10.1002/dvdy.21790] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Muenke syndrome, defined by heterozygosity for a Pro250Arg substitution in fibroblast growth factor receptor 3 (FGFR3), is the most common genetic cause of craniosynostosis in humans. We have used gene targeting to introduce the Muenke syndrome mutation (equivalent to P244R) into the murine Fgfr3 gene. A rounded skull and shortened snout (often skewed) with dental malocclusion was observed in a minority of heterozygotes and many homozygotes. Development of this incompletely penetrant skull phenotype was dependent on genetic background and sex, with males more often affected. However, these cranial abnormalities were rarely attributable to craniosynostosis, which was only present in 2/364 mutants; more commonly, we found fusion of the premaxillary and/or zygomatic sutures. We also found decreased cortical thickness and bone mineral densities in long bones. We conclude that although both cranial and long bone development is variably affected by the murine Fgfr3(P244R) mutation, coronal craniosynostosis is not reliably reproduced.
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Affiliation(s)
- Stephen R F Twigg
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
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Freeman G, Quan W, Kemeny A, Babbs C. Chest compression depth measurement during cardiopulmonary resuscitation predicts successful defibrillation. Resuscitation 2008. [DOI: 10.1016/j.resuscitation.2008.03.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Babbs C, Furniss D, Morriss-Kay GM, Wilkie AOM. Polydactyly in the mouse mutant Doublefoot involves altered Gli3 processing and is caused by a large deletion in cis to Indian hedgehog. Mech Dev 2008; 125:517-26. [PMID: 18272352 PMCID: PMC2428104 DOI: 10.1016/j.mod.2008.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 12/21/2007] [Accepted: 01/03/2008] [Indexed: 11/27/2022]
Abstract
The mouse mutant Doublefoot (Dbf) shows preaxial polydactyly with 6–9 triphalangeal digits in all four limbs and additional abnormalities including a broadened skull, hydrocephalus, and a thickened, kinked tail. The autopod undergoes a characteristic expansion between late embryonic day (E) 10.5 and E11.5, following the onset of ectopic Indian hedgehog (Ihh) expression in the entire distal mesenchyme, except for the zone of polarising activity (ZPA), at E10.5. We show here that limb prepattern, as indicated by expression of Gli3 and Hand2 at E9.5 is unaffected by the mutation. As both Sonic hedgehog (Shh) and Ihh expression are present in Dbf limb buds at E10.5, we generated Dbf/+;Shh−/− mutants to analyse the effects of different patterns of Hedgehog activity on the limb phenotype and molecular differentiation. Dbf/+ embryos lacking Shh showed postaxial as well as preaxial polydactyly, and the Ihh expression domain extended posteriorly into the domain in which Shh is normally expressed, indicating loss of ZPA identity. Differences in gene expression patterns in wild type, single and compound mutants were associated with differences in Gli3 processing: an increased ratio of Gli3 activator to Gli3 repressor was observed in the anterior half of Dbf/+ limb buds and in both anterior and posterior halves of compound mutant limb buds at E10.5. To identify the cause of Ihh misregulation in Dbf/+ mutants, we sequenced ∼20 kb of genomic DNA around Ihh but found no pathogenic changes. However, Southern blot analysis revealed a ∼600 kb deletion disrupting or deleting 25 transcripts, starting 50 kb 5′ of Ihh and extending away from the gene. The large deletion interval may explain the wide range of abnormalities in Dbf/+ mutants. However, we did not detect anologous deletions in cases of Laurin–Sandrow syndrome, a human disorder that shows phenotypic similarities to Dbf.
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Affiliation(s)
- Christian Babbs
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
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Paine PA, Rees W, Babbs C, Shaffer JL, Armstrong G, Burnett H, Aziz Q. A patient with impaired gastric motility. Gut 2007; 56:1635-6. [PMID: 17938436 PMCID: PMC2095635 DOI: 10.1136/gut.2007.132522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Affiliation(s)
- P A Paine
- Department of Gostroenterology, Hope Hospital, Salford, UK.
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Babbs C, Heller R, Everman DB, Crocker M, Twigg SRF, Schwartz CE, Giele H, Wilkie AOM. A new locus for split hand/foot malformation with long bone deficiency (SHFLD) at 2q14.2 identified from a chromosome translocation. Hum Genet 2007; 122:191-9. [PMID: 17569090 DOI: 10.1007/s00439-007-0390-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [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: 04/16/2007] [Accepted: 05/18/2007] [Indexed: 10/23/2022]
Abstract
Split hand/foot malformation (SHFM) with long bone deficiency (SHFLD) is a distinct entity in the spectrum of ectrodactylous limb malformations characterised by associated tibial a/hypoplasia. Pedigrees with multiple individuals affected by SHFLD often include non-penetrant intermediate relatives, making genetic mapping difficult. Here we report a sporadic patient with SHFLD who carries a de novo chromosomal translocation t(2;18)(q14.2;p11.2). Characterisation of the breakpoints revealed that neither disrupts any known gene; however, the chromosome 2 breakpoint lies between GLI2 and INHBB, two genes known to be involved in limb development. To investigate whether mutation of a gene in proximity to the chromosome 2 breakpoint underlies the SHFLD, we sought independent evidence of mutations in GLI2, INHBB and two other genes (RALB and FLJ14816) in 44 unrelated patients with SHFM, SHFLD or isolated long bone deficiency. No convincing pathogenic mutations were found, raising the possibility that a long-range cis acting regulatory element may be disrupted by this translocation. The previous description of a translocation with a 2q14.2 breakpoint associated with ectrodactyly, and the mapping of the ectrodactylous Dominant hemimelia mouse mutation to a region of homologous synteny, suggests that 2q14.2 represents a novel locus for SHFLD.
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MESH Headings
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/pathology
- Base Sequence
- Blotting, Southern
- Chromosome Mapping
- Chromosomes, Artificial, Bacterial
- Chromosomes, Human, Pair 2/genetics
- Computational Biology
- DNA Mutational Analysis
- DNA Primers/genetics
- Foot Deformities, Congenital/genetics
- Foot Deformities, Congenital/pathology
- Hand Deformities, Congenital/genetics
- Hand Deformities, Congenital/pathology
- Humans
- In Situ Hybridization, Fluorescence
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Tibia/abnormalities
- Tibia/pathology
- Translocation, Genetic/genetics
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Affiliation(s)
- Christian Babbs
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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Murugesan SV, Babbs C. Early endoscopic sphincterotomy in acute cholecystitis in elderly patients with high surgical risk. Endoscopy 2007; 39:378; author reply 379. [PMID: 17427085 DOI: 10.1055/s-2007-966209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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Chiracharit W, Sun Y, Kumhom P, Chamnongthai K, Babbs C, Delp E. Normal mammogram classification based on a support vector machine utilizing crossed distribution features. Conf Proc IEEE Eng Med Biol Soc 2007; 2004:1581-4. [PMID: 17272001 DOI: 10.1109/iembs.2004.1403481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Automatic classification of normal mammograms, which constitute a majority of screening mammograms, is a new approach to computer-aided diagnosis of breast cancer. This approach may be limited, however, by non-separable "crossed" distributions of features that are extracted from digitized mammograms. This work presents a method of mapping such non-separable input features into a new set of separable features that can be utilized, together with ordinary "uncrossed" features, by a support vector machine (SVM) classifier. The results of the proposed scheme show improved performance with 80% sensitivity and 95% specificity.
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Affiliation(s)
- W Chiracharit
- Department of Electronics and Telecommunication Engineering, King Mongkut's University of Technology, Bangkok, Thailand
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Perlyn CA, DeLeon VB, Babbs C, Govier D, Burell L, Darvann T, Kreiborg S, Morriss-Kay G. The craniofacial phenotype of the Crouzon mouse: analysis of a model for syndromic craniosynostosis using three-dimensional MicroCT. Cleft Palate Craniofac J 2007; 43:740-8. [PMID: 17105336 DOI: 10.1597/05-212] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE To characterize the craniofacial phenotype of a mouse model for Crouzon syndrome by a quantitative analysis of skull morphology in mutant and wild-type mice and to compare the findings with skull features observed in humans with Crouzon syndrome. METHODS MicroCT scans and skeletal preparations were obtained on previously described Fgfr2(C342Y/+) Crouzon mutant mice and wild-type mice at 6 weeks of age. Three-dimensional coordinate data from biologically relevant landmarks on the skulls were collected. Euclidean Distance Matrix Analysis was used to quantify and compare skull shapes using these landmark data. RESULTS Obliteration of bilateral coronal sutures was observed in 80% of skulls, and complete synostosis of the sagittal suture was observed in 70%. In contrast, fewer than 40% of lambdoid sutures were found to be fully fused. In each of the 10 Fgfr2(C342Y/+) mutant mice analyzed, the presphenoid-basisphenoid synchondrosis was fused. Skull height and width were increased in mutant mice, whereas skull length was decreased. Interorbital distance was also increased in Fgfr2(C342Y/+) mice as compared with wild-type littermates. Upper-jaw length was shorter in the Fgfr2(C342Y/+) mutant skulls, as was mandibular length. CONCLUSION Skulls of Fgfr2(C342Y/+) mice differ from normal littermates in a comparable manner with differences between the skulls of humans with Crouzon syndrome and those of unaffected individuals. These findings were consistent across several regions of anatomic interest. Further investigation into the molecular mechanisms underlying the anomalies seen in the Crouzon mouse model is currently under way.
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Affiliation(s)
- Chad A Perlyn
- Division of Plastic Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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Perlyn CA, Babbs C, Ornitz D, Morriss-Kay G. The role of Fgfr2 in craniofacial development: studies from a Crouzon syndrome mouse model. J Am Coll Surg 2005. [DOI: 10.1016/j.jamcollsurg.2005.06.136] [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: 10/25/2022]
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Sun Y, Babbs C, Delp E. SU-FF-I-04: A Comparison of Two Genetic Algorithms for Feature Selection in the Detection of Breast Cancers. Med Phys 2005. [DOI: 10.1118/1.1997484] [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: 11/07/2022] Open
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Twigg SRF, Kan R, Babbs C, Bochukova EG, Robertson SP, Wall SA, Morriss-Kay GM, Wilkie AOM. Mutations of ephrin-B1 (EFNB1), a marker of tissue boundary formation, cause craniofrontonasal syndrome. Proc Natl Acad Sci U S A 2004; 101:8652-7. [PMID: 15166289 PMCID: PMC423250 DOI: 10.1073/pnas.0402819101] [Citation(s) in RCA: 269] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Craniofrontonasal syndrome (CFNS) is an X-linked developmental disorder that shows paradoxically greater severity in heterozygous females than in hemizygous males. Females have frontonasal dysplasia and coronal craniosynostosis (fusion of the coronal sutures); in males, hypertelorism is the only typical manifestation. Here, we show that the classical female CFNS phenotype is caused by heterozygous loss-of-function mutations in EFNB1, which encodes a member of the ephrin family of transmembrane ligands for Eph receptor tyrosine kinases. In mice, the orthologous Efnb1 gene is expressed in the frontonasal neural crest and demarcates the position of the future coronal suture. Although EFNB1 is X-inactivated, we did not observe markedly skewed X-inactivation in either blood or cranial periosteum from females with CFNS, indicating that lack of ephrin-B1 does not compromise cell viability in these tissues. We propose that in heterozygous females, patchwork loss of ephrin-B1 disturbs tissue boundary formation at the developing coronal suture, whereas in males deficient in ephrin-B1, an alternative mechanism maintains the normal boundary. This is the only known mutation in the ephrin/Eph receptor signaling system in humans and provides clues to the biogenesis of craniosynostosis.
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Affiliation(s)
- Stephen R F Twigg
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
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Abstract
Patients with complicated inflammatory bowel disease commonly undergo repeated surgical procedures, often against a background of chronic opiate use. We describe a case in which a postoperative attempt to withdraw opiate analgesia on two separate occasions led to a clinical syndrome strongly suggestive of intestinal obstruction, the signs and symptoms of which settled rapidly on re-introduction of opiates. Small bowel contrast studies indicated a level of obstruction which not only fluctuated, but occurred at an unusual site for mechanical obstruction. In patients with a history of long-standing opiate use, postoperative opiate withdrawal can cause a significant, functional bowel disorder and should be borne in mind in the differential diagnosis of postoperative intestinal obstruction. Patients can be treated effectively with clonidine.
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Affiliation(s)
- C Macutkiewicz
- Department of Surgery, Hope Hospital, Salford M6 8HD, UK
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Powles N, Babbs C, Ficker M, Schimmang T, Maconochie M. Identification and analysis of genes from the mouse otic vesicle and their association with developmental subprocesses through in situ hybridization. Dev Biol 2004; 268:24-38. [PMID: 15031102 DOI: 10.1016/j.ydbio.2003.11.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2002] [Revised: 11/10/2003] [Accepted: 11/19/2003] [Indexed: 10/26/2022]
Abstract
The otic vesicle (otocyst) occupies a pivotal position in inner ear development, bridging the gap between otic placode determination, and morphogenesis of vestibular and auditory compartments. The molecular mechanisms underlying the progressive subdivision of the developing inner ear into different compartments, and the molecular control and execution of the different developmental processes involved, are largely unknown. Since relatively few genes have been implicated in these processes, we have undertaken this study to identify genes involved in these early embryonic stages. We have used cDNA subtractions of mouse otic vesicle against adult liver cDNA, and describe a set of 280 candidate genes. We have also performed otic vesicle RNA hybridizations against DNA chips to not only confirm the efficacy of the library approach, but also to investigate the utility of DNA array alternatives. To begin to dissect potential developmental roles, we investigated the spatial pattern of gene expression for a selected set of 80 genes in developing mouse embryos at mid-gestation by whole-mount in situ hybridization. These data illustrate the compartmentalisation of gene expression in the otic vesicle for the majority of genes tested, and furthermore, implicate many of the genes tested with distinct developmental subprocesses.
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Affiliation(s)
- Nicola Powles
- Mammalian Genetics Unit, Medical Research Council, Harwell, Oxon OX11 0RD, UK
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