1
|
Oakley J, Hill M, Giess A, Tanguy M, Elgar G. Long read sequencing characterises a novel structural variant, revealing underactive AKR1C1 with overactive AKR1C2 as a possible cause of severe chronic fatigue. J Transl Med 2023; 21:825. [PMID: 37978513 PMCID: PMC10655400 DOI: 10.1186/s12967-023-04711-5] [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: 09/04/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Causative genetic variants cannot yet be found for many disorders with a clear heritable component, including chronic fatigue disorders like myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). These conditions may involve genes in difficult-to-align genomic regions that are refractory to short read approaches. Structural variants in these regions can be particularly hard to detect or define with short reads, yet may account for a significant number of cases. Long read sequencing can overcome these difficulties but so far little data is available regarding the specific analytical challenges inherent in such regions, which need to be taken into account to ensure that variants are correctly identified. Research into chronic fatigue disorders faces the additional challenge that the heterogeneous patient populations likely encompass multiple aetiologies with overlapping symptoms, rather than a single disease entity, such that each individual abnormality may lack statistical significance within a larger sample. Better delineation of patient subgroups is needed to target research and treatment. METHODS We use nanopore sequencing in a case of unexplained severe fatigue to identify and fully characterise a large inversion in a highly homologous region spanning the AKR1C gene locus, which was indicated but could not be resolved by short-read sequencing. We then use GC-MS/MS serum steroid analysis to investigate the functional consequences. RESULTS Several commonly used bioinformatics tools are confounded by the homology but a combined approach including visual inspection allows the variant to be accurately resolved. The DNA inversion appears to increase the expression of AKR1C2 while limiting AKR1C1 activity, resulting in a relative increase of inhibitory GABAergic neurosteroids and impaired progesterone metabolism which could suppress neuronal activity and interfere with cellular function in a wide range of tissues. CONCLUSIONS This study provides an example of how long read sequencing can improve diagnostic yield in research and clinical care, and highlights some of the analytical challenges presented by regions containing tandem arrays of genes. It also proposes a novel gene associated with a novel disease aetiology that may be an underlying cause of complex chronic fatigue. It reveals biomarkers that could now be assessed in a larger cohort, potentially identifying a subset of patients who might respond to treatments suggested by the aetiology.
Collapse
Affiliation(s)
| | - Martin Hill
- Department of Steroids and Proteofactors, Institute of Endocrinology, Národni 8, 11694, Prague, Czech Republic
| | - Adam Giess
- Scientific Research and Development, Genomics England, London, UK
| | - Mélanie Tanguy
- Scientific Research and Development, Genomics England, London, UK
| | - Greg Elgar
- Scientific Research and Development, Genomics England, London, UK.
| |
Collapse
|
2
|
Wei W, Schon KR, Elgar G, Orioli A, Tanguy M, Giess A, Tischkowitz M, Caulfield MJ, Chinnery PF. Nuclear-embedded mitochondrial DNA sequences in 66,083 human genomes. Nature 2022; 611:105-114. [PMID: 36198798 PMCID: PMC9630118 DOI: 10.1038/s41586-022-05288-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 08/29/2022] [Indexed: 02/02/2023]
Abstract
DNA transfer from cytoplasmic organelles to the cell nucleus is a legacy of the endosymbiotic event-the majority of nuclear-mitochondrial segments (NUMTs) are thought to be ancient, preceding human speciation1-3. Here we analyse whole-genome sequences from 66,083 people-including 12,509 people with cancer-and demonstrate the ongoing transfer of mitochondrial DNA into the nucleus, contributing to a complex NUMT landscape. More than 99% of individuals had at least one of 1,637 different NUMTs, with 1 in 8 individuals having an ultra-rare NUMT that is present in less than 0.1% of the population. More than 90% of the extant NUMTs that we evaluated inserted into the nuclear genome after humans diverged from apes. Once embedded, the sequences were no longer under the evolutionary constraint seen within the mitochondrion, and NUMT-specific mutations had a different mutational signature to mitochondrial DNA. De novo NUMTs were observed in the germline once in every 104 births and once in every 103 cancers. NUMTs preferentially involved non-coding mitochondrial DNA, linking transcription and replication to their origin, with nuclear insertion involving multiple mechanisms including double-strand break repair associated with PR domain zinc-finger protein 9 (PRDM9) binding. The frequency of tumour-specific NUMTs differed between cancers, including a probably causal insertion in a myxoid liposarcoma. We found evidence of selection against NUMTs on the basis of size and genomic location, shaping a highly heterogenous and dynamic human NUMT landscape.
Collapse
Affiliation(s)
- Wei Wei
- Department of Clinical Neuroscience, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Katherine R Schon
- Department of Clinical Neuroscience, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Marc Tischkowitz
- Academic Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Mark J Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Patrick F Chinnery
- Department of Clinical Neuroscience, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
| |
Collapse
|
3
|
Kousathanas A, Pairo-Castineira E, Rawlik K, Stuckey A, Odhams CA, Walker S, Russell CD, Malinauskas T, Wu Y, Millar J, Shen X, Elliott KS, Griffiths F, Oosthuyzen W, Morrice K, Keating S, Wang B, Rhodes D, Klaric L, Zechner M, Parkinson N, Siddiq A, Goddard P, Donovan S, Maslove D, Nichol A, Semple MG, Zainy T, Maleady-Crowe F, Todd L, Salehi S, Knight J, Elgar G, Chan G, Arumugam P, Patch C, Rendon A, Bentley D, Kingsley C, Kosmicki JA, Horowitz JE, Baras A, Abecasis GR, Ferreira MAR, Justice A, Mirshahi T, Oetjens M, Rader DJ, Ritchie MD, Verma A, Fowler TA, Shankar-Hari M, Summers C, Hinds C, Horby P, Ling L, McAuley D, Montgomery H, Openshaw PJM, Elliott P, Walsh T, Tenesa A, Fawkes A, Murphy L, Rowan K, Ponting CP, Vitart V, Wilson JF, Yang J, Bretherick AD, Scott RH, Hendry SC, Moutsianas L, Law A, Caulfield MJ, Baillie JK. Whole-genome sequencing reveals host factors underlying critical COVID-19. Nature 2022; 607:97-103. [PMID: 35255492 PMCID: PMC9259496 DOI: 10.1038/s41586-022-04576-6] [Citation(s) in RCA: 139] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2-4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.
Collapse
Affiliation(s)
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Clark D Russell
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Tomas Malinauskas
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Xia Shen
- Biostatistics Group, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | | | | | | | - Kirstie Morrice
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Sean Keating
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Bo Wang
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Marie Zechner
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Nick Parkinson
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | - David Maslove
- Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Alistair Nichol
- Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland
| | - Malcolm G Semple
- NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Respiratory Medicine and Institute in the Park, Alder Hey Children's Hospital and University of Liverpool, Liverpool, UK
| | | | | | | | | | - Julian Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tom A Fowler
- Genomics England, London, UK
- Test and Trace, the Health Security Agency, Department of Health and Social Care, London, UK
| | - Manu Shankar-Hari
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Charles Hinds
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Peter Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Danny McAuley
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Intensive Care Medicine, Royal Victoria Hospital, Belfast, UK
| | | | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust: London, London, UK
| | | | - Timothy Walsh
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Angie Fawkes
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Kathy Rowan
- Intensive Care National Audit and Research Centre, London, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Andrew D Bretherick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Richard H Scott
- Genomics England, London, UK
- Great Ormond Street Hospital, London, UK
| | | | | | - Andy Law
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Mark J Caulfield
- Genomics England, London, UK.
- William Harvey Research Institute, Queen Mary University of London, London, UK.
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, UK.
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.
- Centre for Inflammation Research, The Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK.
| |
Collapse
|
4
|
Polubothu S, Zecchin D, Al-Olabi L, Lionarons DA, Harland M, Horswell S, Thomas AC, Hunt L, Wlodarchak N, Aguilera P, Brand S, Bryant D, Carrera C, Chen H, Elgar G, Harwood CA, Howell M, Larue L, Loughlin S, MacDonald J, Malvehy J, Barberan SM, da Silva VM, Molina M, Morrogh D, Moulding D, Nsengimana J, Pittman A, Puig-Butillé JA, Parmar K, Sebire NJ, Scherer S, Stadnik P, Stanier P, Tell G, Waelchli R, Zarrei M, Puig S, Bataille V, Xing Y, Healy E, Moore GE, Di WL, Newton-Bishop J, Downward J, Kinsler VA. Inherited duplications of PPP2R3B predispose to nevi and melanoma via a C21orf91-driven proliferative phenotype. Genet Med 2021; 23:1636-1647. [PMID: 34145395 PMCID: PMC8460442 DOI: 10.1038/s41436-021-01204-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/13/2020] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 01/16/2023] Open
Abstract
PURPOSE Much of the heredity of melanoma remains unexplained. We sought predisposing germline copy-number variants using a rare disease approach. METHODS Whole-genome copy-number findings in patients with melanoma predisposition syndrome congenital melanocytic nevus were extrapolated to a sporadic melanoma cohort. Functional effects of duplications in PPP2R3B were investigated using immunohistochemistry, transcriptomics, and stable inducible cellular models, themselves characterized using RNAseq, quantitative real-time polymerase chain reaction (qRT-PCR), reverse phase protein arrays, immunoblotting, RNA interference, immunocytochemistry, proliferation, and migration assays. RESULTS We identify here a previously unreported genetic susceptibility to melanoma and melanocytic nevi, familial duplications of gene PPP2R3B. This encodes PR70, a regulatory unit of critical phosphatase PP2A. Duplications increase expression of PR70 in human nevus, and increased expression in melanoma tissue correlates with survival via a nonimmunological mechanism. PPP2R3B overexpression induces pigment cell switching toward proliferation and away from migration. Importantly, this is independent of the known microphthalmia-associated transcription factor (MITF)-controlled switch, instead driven by C21orf91. Finally, C21orf91 is demonstrated to be downstream of MITF as well as PR70. CONCLUSION This work confirms the power of a rare disease approach, identifying a previously unreported copy-number change predisposing to melanocytic neoplasia, and discovers C21orf91 as a potentially targetable hub in the control of phenotype switching.
Collapse
Affiliation(s)
- Satyamaanasa Polubothu
- Mosaicism and Precision Medicine Laboratory, Francis Crick Institute, London, UK
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
- Paediatric Dermatology, Great Ormond Street Hospital for Children, London, UK
| | - Davide Zecchin
- Mosaicism and Precision Medicine Laboratory, Francis Crick Institute, London, UK
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Lara Al-Olabi
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | | | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, Cancer Research UK Clinical Centre at Leeds, St James's University Hospital, Leeds, UK
| | - Stuart Horswell
- Bioinformatics and Biostatistics, Francis Crick Institute, London, UK
| | - Anna C Thomas
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Lilian Hunt
- Advanced Sequencing Facility, Francis Crick Institute, London, UK
| | - Nathan Wlodarchak
- McArdle Laboratory, Department of Oncology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Paula Aguilera
- Department of Dermatology, Hospital Clínic de Barcelona (Melanoma Unit), University of Barcelona, IDIBAPS, Barcelona & CIBERER, Barcelona, Spain
| | - Sarah Brand
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Dale Bryant
- Mosaicism and Precision Medicine Laboratory, Francis Crick Institute, London, UK
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Cristina Carrera
- Department of Dermatology, Hospital Clínic de Barcelona (Melanoma Unit), University of Barcelona, IDIBAPS, Barcelona & CIBERER, Barcelona, Spain
| | - Hui Chen
- McArdle Laboratory, Department of Oncology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Greg Elgar
- Advanced Sequencing Facility, Francis Crick Institute, London, UK
| | - Catherine A Harwood
- Centre for Cell Biology and Cutaneous Research, Blizzard Institute, Barts, London, UK
| | - Michael Howell
- High Throughput Screening Facility, Francis Crick Institute, London, UK
| | - Lionel Larue
- Centre de Recherche, Developmental Genetics of Melanocytes, Institut Curie, Orsay, France
| | - Sam Loughlin
- North East Thames Regional Genetics Laboratory Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jeff MacDonald
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Josep Malvehy
- Department of Dermatology, Hospital Clínic de Barcelona (Melanoma Unit), University of Barcelona, IDIBAPS, Barcelona & CIBERER, Barcelona, Spain
| | - Sara Martin Barberan
- Mosaicism and Precision Medicine Laboratory, Francis Crick Institute, London, UK
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Vanessa Martins da Silva
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
- Department of Dermatology, Hospital Clínic de Barcelona (Melanoma Unit), University of Barcelona, IDIBAPS, Barcelona & CIBERER, Barcelona, Spain
| | - Miriam Molina
- Oncogene Biology Laboratory, Francis Crick Institute, London, UK
| | - Deborah Morrogh
- North East Thames Regional Genetics Laboratory Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Dale Moulding
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Jérémie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, Cancer Research UK Clinical Centre at Leeds, St James's University Hospital, Leeds, UK
| | - Alan Pittman
- Bioinformatics, St George's University of London, London, UK
| | - Joan-Anton Puig-Butillé
- Department of Dermatology, Hospital Clínic de Barcelona (Melanoma Unit), University of Barcelona, IDIBAPS, Barcelona & CIBERER, Barcelona, Spain
| | - Kiran Parmar
- Department of Twin Research and Genetic Epidemiology, King's College London, South Wing Block D, London, UK
| | - Neil J Sebire
- Department of Histopathology, Great Ormond Street Hospital for Children, London, UK
| | - Stephen Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Paulina Stadnik
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Philip Stanier
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Gemma Tell
- McArdle Laboratory, Department of Oncology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Regula Waelchli
- Paediatric Dermatology, Great Ormond Street Hospital for Children, London, UK
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Susana Puig
- Department of Dermatology, Hospital Clínic de Barcelona (Melanoma Unit), University of Barcelona, IDIBAPS, Barcelona & CIBERER, Barcelona, Spain
| | | | - Yongna Xing
- McArdle Laboratory, Department of Oncology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Eugene Healy
- Department of Dermatology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Gudrun E Moore
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK
| | - Wei-Li Di
- Infection, Immunity and Inflammation Programme, Immunobiology Section, UCL GOS Institute of Child Health, London, UK
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, Cancer Research UK Clinical Centre at Leeds, St James's University Hospital, Leeds, UK
| | - Julian Downward
- Oncogene Biology Laboratory, Francis Crick Institute, London, UK
| | - Veronica A Kinsler
- Mosaicism and Precision Medicine Laboratory, Francis Crick Institute, London, UK.
- Genetics and Genomic Medicine, UCL GOS Institute of Child Health, London, UK.
- Paediatric Dermatology, Great Ormond Street Hospital for Children, London, UK.
| |
Collapse
|
5
|
Pagnamenta AT, Kaiyrzhanov R, Zou Y, Da'as SI, Maroofian R, Donkervoort S, Dominik N, Lauffer M, Ferla MP, Orioli A, Giess A, Tucci A, Beetz C, Sedghi M, Ansari B, Barresi R, Basiri K, Cortese A, Elgar G, Fernandez-Garcia MA, Yip J, Foley AR, Gutowski N, Jungbluth H, Lassche S, Lavin T, Marcelis C, Marks P, Marini-Bettolo C, Medne L, Moslemi AR, Sarkozy A, Reilly MM, Muntoni F, Millan F, Muraresku CC, Need AC, Nemeth AH, Neuhaus SB, Norwood F, O'Donnell M, O'Driscoll M, Rankin J, Yum SW, Zolkipli-Cunningham Z, Brusius I, Wunderlich G, Karakaya M, Wirth B, Fakhro KA, Tajsharghi H, Bönnemann CG, Taylor JC, Houlden H. An ancestral 10-bp repeat expansion in VWA1 causes recessive hereditary motor neuropathy. Brain 2021; 144:584-600. [PMID: 33559681 PMCID: PMC8263055 DOI: 10.1093/brain/awaa420] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/16/2020] [Accepted: 10/15/2020] [Indexed: 01/26/2023] Open
Abstract
The extracellular matrix comprises a network of macromolecules such as collagens, proteoglycans and glycoproteins. VWA1 (von Willebrand factor A domain containing 1) encodes a component of the extracellular matrix that interacts with perlecan/collagen VI, appears to be involved in stabilizing extracellular matrix structures, and demonstrates high expression levels in tibial nerve. Vwa1-deficient mice manifest with abnormal peripheral nerve structure/function; however, VWA1 variants have not previously been associated with human disease. By interrogating the genome sequences of 74 180 individuals from the 100K Genomes Project in combination with international gene-matching efforts and targeted sequencing, we identified 17 individuals from 15 families with an autosomal-recessive, non-length dependent, hereditary motor neuropathy and rare biallelic variants in VWA1. A single disease-associated allele p.(G25Rfs*74), a 10-bp repeat expansion, was observed in 14/15 families and was homozygous in 10/15. Given an allele frequency in European populations approaching 1/1000, the seven unrelated homozygote individuals ascertained from the 100K Genomes Project represents a substantial enrichment above expected. Haplotype analysis identified a shared 220 kb region suggesting that this founder mutation arose >7000 years ago. A wide age-range of patients (6-83 years) helped delineate the clinical phenotype over time. The commonest disease presentation in the cohort was an early-onset (mean 2.0 ± 1.4 years) non-length-dependent axonal hereditary motor neuropathy, confirmed on electrophysiology, which will have to be differentiated from other predominantly or pure motor neuropathies and neuronopathies. Because of slow disease progression, ambulation was largely preserved. Neurophysiology, muscle histopathology, and muscle MRI findings typically revealed clear neurogenic changes with single isolated cases displaying additional myopathic process. We speculate that a few findings of myopathic changes might be secondary to chronic denervation rather than indicating an additional myopathic disease process. Duplex reverse transcription polymerase chain reaction and immunoblotting using patient fibroblasts revealed that the founder allele results in partial nonsense mediated decay and an absence of detectable protein. CRISPR and morpholino vwa1 modelling in zebrafish demonstrated reductions in motor neuron axonal growth, synaptic formation in the skeletal muscles and locomotive behaviour. In summary, we estimate that biallelic variants in VWA1 may be responsible for up to 1% of unexplained hereditary motor neuropathy cases in Europeans. The detailed clinical characterization provided here will facilitate targeted testing on suitable patient cohorts. This novel disease gene may have previously evaded detection because of high GC content, consequential low coverage and computational difficulties associated with robustly detecting repeat-expansions. Reviewing previously unsolved exomes using lower QC filters may generate further diagnoses.
Collapse
Affiliation(s)
- Alistair T Pagnamenta
- NIHR Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Yaqun Zou
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, National Institutes of Health, Bethesda, MD, USA
| | - Sahar I Da'as
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, National Institutes of Health, Bethesda, MD, USA
| | - Natalia Dominik
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Marlen Lauffer
- Institute of Human Genetics, Center for Molecular Medicine Cologne (CMMC), Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Matteo P Ferla
- NIHR Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andrea Orioli
- William Harvey Research Institute, Queen Mary University of London, London, UK
- Genomics England, London, UK
| | - Adam Giess
- William Harvey Research Institute, Queen Mary University of London, London, UK
- Genomics England, London, UK
| | - Arianna Tucci
- William Harvey Research Institute, Queen Mary University of London, London, UK
- Genomics England, London, UK
| | | | - Maryam Sedghi
- Medical Genetics Laboratory, Alzahra University Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Behnaz Ansari
- Department of Neurology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rita Barresi
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Keivan Basiri
- Department of Neurology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Andrea Cortese
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Greg Elgar
- William Harvey Research Institute, Queen Mary University of London, London, UK
- Genomics England, London, UK
| | - Miguel A Fernandez-Garcia
- Department of Paediatric Neurology - Neuromuscular Service, Evelina Children's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Janice Yip
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas Gutowski
- Department of Neurology, Royal Devon and Exeter NHS Trust, Exeter, UK
| | - Heinz Jungbluth
- Department of Paediatric Neurology - Neuromuscular Service, Evelina Children's Hospital, Guy's & St Thomas' NHS Foundation Trust, London, UK
- Randall Division of Cell and Molecular Biophysics Muscle Signalling Section, King's College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Saskia Lassche
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Tim Lavin
- Department of Neurology, Salford Royal NHS Foundation Trust, Manchester, UK
| | - Carlo Marcelis
- Department of Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Peter Marks
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - Chiara Marini-Bettolo
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - Livija Medne
- Divisions of Neurology and Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ali-Reza Moslemi
- Department of Pathology, University of Gothenburg, Sahlgrenska University Hospital, Sweden
| | - Anna Sarkozy
- The Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, and Great Ormond Street Hospital Trust, London, UK
| | - Mary M Reilly
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| | - Francesco Muntoni
- The Dubowitz Neuromuscular Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, and Great Ormond Street Hospital Trust, London, UK
| | | | - Colleen C Muraresku
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, PA, USA
| | - Anna C Need
- William Harvey Research Institute, Queen Mary University of London, London, UK
- Genomics England, London, UK
| | - Andrea H Nemeth
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Sarah B Neuhaus
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, National Institutes of Health, Bethesda, MD, USA
| | - Fiona Norwood
- Department of Neurology, King's College Hospital, London, UK
| | - Marie O'Donnell
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - Mary O'Driscoll
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - Julia Rankin
- Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Trust, Exeter, UK
| | - Sabrina W Yum
- Division of Pediatric Neurology, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Zarazuela Zolkipli-Cunningham
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA, USA
| | - Isabell Brusius
- Institute of Human Genetics, Center for Molecular Medicine Cologne (CMMC), Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Gilbert Wunderlich
- Department of Neurology, Center for Rare Diseases Cologne, University Hospital Cologne, Cologne, Germany
| | - Mert Karakaya
- Institute of Human Genetics, Center for Molecular Medicine Cologne (CMMC), Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne (CMMC), Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, Doha, Qatar
| | - Homa Tajsharghi
- School of Health Science, Division Biomedicine and Translational Medicine, University of Skovde, Sweden
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, NINDS, National Institutes of Health, Bethesda, MD, USA
| | - Jenny C Taylor
- NIHR Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, UK
| |
Collapse
|
6
|
Tolchin D, Yeager JP, Prasad P, Dorrani N, Russi AS, Martinez-Agosto JA, Haseeb A, Angelozzi M, Santen G, Ruivenkamp C, Mercimek-Andrews S, Depienne C, Kuechler A, Mikat B, Ludecke HJ, Bilan F, Le Guyader G, Gilbert-Dussardier B, Keren B, Heide S, Haye D, Van Esch H, Keldermans L, Ortiz D, Lancaster E, Krantz ID, Krock BL, Pechter KB, Arkader A, Medne L, DeChene ET, Calpena E, Melistaccio G, Wilkie AO, Suri M, Foulds N, Begtrup A, Henderson LB, Forster C, Reed P, McDonald MT, McConkie-Rosell A, Thevenon J, Le Tanno P, Coutton C, Tsai AC, Stewart S, Maver A, Gorazd R, Pichon O, Nizon M, Cogné B, Isidor B, Martin-Coignard D, Stoeva R, Lefebvre V, Le Caignec C, Ambrose J, Bleda M, Boardman-Pretty F, Boissiere J, Boustred C, Caulfield M, Chan G, Craig C, Daugherty L, de Burca A, Devereau A, Elgar G, Foulger R, Fowler T, Furió-Tarí P, Hackett J, Halai D, Holman J, Hubbard T, Kasperaviciute D, Kayikci M, Lahnstein L, Lawson K, Leigh S, Leong I, Lopez F, Maleady-Crowe F, Mason J, McDonagh E, Moutsianas L, Mueller M, Need A, Odhams C, Patch C, Perez-Gil D, Polychronopoulos D, Pullinger J, Rahim T, Rendon A, Rogers T, Ryten M, Savage K, Scott R, Siddiq A, Sieghart A, Smedley D, Smith K, Sosinsky A, Spooner W, Stevens H, Stuckey A, Thomas E, Thompson S, Tregidgo C, Tucci A, Walsh E, Watters S, Welland M, Williams E, Witkowska K, Wood S, Zarowiecki M. De Novo SOX6 Variants Cause a Neurodevelopmental Syndrome Associated with ADHD, Craniosynostosis, and Osteochondromas. Am J Hum Genet 2020; 106:830-845. [PMID: 32442410 DOI: 10.1016/j.ajhg.2020.04.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/24/2020] [Indexed: 12/21/2022] Open
Abstract
SOX6 belongs to a family of 20 SRY-related HMG-box-containing (SOX) genes that encode transcription factors controlling cell fate and differentiation in many developmental and adult processes. For SOX6, these processes include, but are not limited to, neurogenesis and skeletogenesis. Variants in half of the SOX genes have been shown to cause severe developmental and adult syndromes, referred to as SOXopathies. We here provide evidence that SOX6 variants also cause a SOXopathy. Using clinical and genetic data, we identify 19 individuals harboring various types of SOX6 alterations and exhibiting developmental delay and/or intellectual disability; the individuals are from 17 unrelated families. Additional, inconstant features include attention-deficit/hyperactivity disorder (ADHD), autism, mild facial dysmorphism, craniosynostosis, and multiple osteochondromas. All variants are heterozygous. Fourteen are de novo, one is inherited from a mosaic father, and four offspring from two families have a paternally inherited variant. Intragenic microdeletions, balanced structural rearrangements, frameshifts, and nonsense variants are predicted to inactivate the SOX6 variant allele. Four missense variants occur in residues and protein regions highly conserved evolutionarily. These variants are not detected in the gnomAD control cohort, and the amino acid substitutions are predicted to be damaging. Two of these variants are located in the HMG domain and abolish SOX6 transcriptional activity in vitro. No clear genotype-phenotype correlations are found. Taken together, these findings concur that SOX6 haploinsufficiency leads to a neurodevelopmental SOXopathy that often includes ADHD and abnormal skeletal and other features.
Collapse
|
7
|
Gabryšová L, Alvarez-Martinez M, Luisier R, Cox LS, Sodenkamp J, Hosking C, Pérez-Mazliah D, Whicher C, Kannan Y, Potempa K, Wu X, Bhaw L, Wende H, Sieweke MH, Elgar G, Wilson M, Briscoe J, Metzis V, Langhorne J, Luscombe NM, O'Garra A. Publisher Correction: c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4 + T cells. Nat Immunol 2019; 20:374. [PMID: 30733606 DOI: 10.1038/s41590-019-0331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article initially published, the Supplementary Data file was an incorrect version. The correct version is now provided. The error has been corrected in the HTML and PDF version of the article.
Collapse
Affiliation(s)
- Leona Gabryšová
- The Francis Crick Institute, Laboratory of Immunoregulation and Infection, London, UK
| | | | - Raphaëlle Luisier
- The Francis Crick Institute, Computational Biology Laboratory, London, UK
| | - Luke S Cox
- The Francis Crick Institute, Laboratory of Immunoregulation and Infection, London, UK
| | - Jan Sodenkamp
- The Francis Crick Institute, Malaria Laboratory, London, UK
| | | | | | - Charlotte Whicher
- The Francis Crick Institute, Laboratory of Immunoregulation and Infection, London, UK
| | - Yashaswini Kannan
- The Francis Crick Institute, Helminth Immunology Laboratory, London, UK
| | - Krzysztof Potempa
- The Francis Crick Institute, Laboratory of Immunoregulation and Infection, London, UK
| | - Xuemei Wu
- The Francis Crick Institute, Laboratory of Immunoregulation and Infection, London, UK
| | - Leena Bhaw
- The Francis Crick Institute, Advanced Sequencing Facility Laboratory, London, UK
| | - Hagen Wende
- Heidelberg University, Institute of Pharmacology, Heidelberg, Germany
| | - Michael H Sieweke
- Aix Marseille University, CNRS, INSERM, CIML, Marseille, France.,Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), Berlin, Germany
| | - Greg Elgar
- The Francis Crick Institute, Advanced Sequencing Facility Laboratory, London, UK
| | - Mark Wilson
- The Francis Crick Institute, Helminth Immunology Laboratory, London, UK
| | - James Briscoe
- The Francis Crick Institute, Developmental Dynamics Laboratory, London, UK
| | - Vicki Metzis
- The Francis Crick Institute, Developmental Dynamics Laboratory, London, UK
| | - Jean Langhorne
- The Francis Crick Institute, Malaria Laboratory, London, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, Computational Biology Laboratory, London, UK.,UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anne O'Garra
- The Francis Crick Institute, Laboratory of Immunoregulation and Infection, London, UK. .,National Heart and Lung Institute, Imperial College London, London, UK.
| |
Collapse
|
8
|
Abah SE, Burté F, Marquet S, Brown BJ, Akinkunmi F, Oyinloye G, Afolabi NK, Omokhodion S, Lagunju I, Shokunbi WA, Wahlgren M, Dessein H, Argiro L, Dessein AJ, Noyvert B, Hunt L, Elgar G, Sodeinde O, Holder AA, Fernandez-Reyes D. Low plasma haptoglobin is a risk factor for life-threatening childhood severe malarial anemia and not an exclusive consequence of hemolysis. Sci Rep 2018; 8:17527. [PMID: 30510258 PMCID: PMC6277387 DOI: 10.1038/s41598-018-35944-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 04/23/2018] [Accepted: 09/21/2018] [Indexed: 12/21/2022] Open
Abstract
Severe Malarial Anemia (SMA), a life-threatening childhood Plasmodium falciparum malaria syndrome requiring urgent blood transfusion, exhibits inflammatory and hemolytic pathology. Differentiating between hypo-haptoglobinemia due to hemolysis or that of genetic origin is key to understand SMA pathogenesis. We hypothesized that while malaria-induced hypo-haptoglobinemia should reverse at recovery, that of genetic etiology should not. We carried-out a case-control study of children living under hyper-endemic holoendemic malaria burden in the sub-Saharan metropolis of Ibadan, Nigeria. We show that hypo-haptoglobinemia is a risk factor for childhood SMA and not solely due to intravascular hemolysis from underlying schizogony. In children presenting with SMA, hypo-haptoglobinemia remains through convalescence to recovery suggesting a genetic cause. We identified a haptoglobin gene variant, rs12162087 (g.-1203G > A, frequency = 0.67), to be associated with plasma haptoglobin levels (p = 8.5 × 10-6). The Homo-Var:(AA) is associated with high plasma haptoglobin while the reference Homo-Ref:(GG) is associated with hypo-haptoglobinemia (p = 2.3 × 10-6). The variant is associated with SMA, with the most support for a risk effect for Homo-Ref genotype. Our insights on regulatory haptoglobin genotypes and hypo-haptoglobinemia suggest that haptoglobin screening could be part of risk-assessment algorithms to prevent rapid disease progression towards SMA in regions with no-access to urgent blood transfusion where SMA accounts for high childhood mortality rates.
Collapse
Affiliation(s)
- Samuel Eneọjọ Abah
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom
| | - Florence Burté
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom
| | - Sandrine Marquet
- Aix-Marseille University, Inserm GIMP, Labex ParaFrap, Marseille, 13385, France.,Aix-Marseille University, Inserm Laboratoire TAGC/U1090, Marseille, 13288, France
| | - Biobele J Brown
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria.,Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Francis Akinkunmi
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Gbeminiyi Oyinloye
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria.,Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Nathaniel K Afolabi
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria.,Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Samuel Omokhodion
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria.,Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Ikeoluwa Lagunju
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria.,Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Wuraola A Shokunbi
- Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria.,Department of Haematology, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Mats Wahlgren
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hélia Dessein
- Aix-Marseille University, Inserm GIMP, Labex ParaFrap, Marseille, 13385, France
| | - Laurent Argiro
- Aix-Marseille University, Inserm GIMP, Labex ParaFrap, Marseille, 13385, France
| | - Alain J Dessein
- Aix-Marseille University, Inserm GIMP, Labex ParaFrap, Marseille, 13385, France
| | - Boris Noyvert
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom
| | - Lilian Hunt
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom
| | - Greg Elgar
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom
| | - Olugbemiro Sodeinde
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria.,Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria.,Department of Computer Science, Faculty of Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Anthony A Holder
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, United Kingdom
| | - Delmiro Fernandez-Reyes
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria. .,Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria. .,Department of Computer Science, Faculty of Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
| |
Collapse
|
9
|
Gabryšová L, Alvarez-Martinez M, Luisier R, Cox LS, Sodenkamp J, Hosking C, Pérez-Mazliah D, Whicher C, Kannan Y, Potempa K, Wu X, Bhaw L, Wende H, Sieweke MH, Elgar G, Wilson M, Briscoe J, Metzis V, Langhorne J, Luscombe NM, O'Garra A. c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4 + T cells. Nat Immunol 2018; 19:497-507. [PMID: 29662170 PMCID: PMC5988041 DOI: 10.1038/s41590-018-0083-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [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: 01/29/2018] [Accepted: 03/08/2018] [Indexed: 12/17/2022]
Abstract
The transcription factor c-Maf induces the anti-inflammatory cytokine IL-10 in CD4+ T cells in vitro. However, the global effects of c-Maf on diverse immune responses in vivo are unknown. Here we found that c-Maf regulated IL-10 production in CD4+ T cells in disease models involving the TH1 subset of helper T cells (malaria), TH2 cells (allergy) and TH17 cells (autoimmunity) in vivo. Although mice with c-Maf deficiency targeted to T cells showed greater pathology in TH1 and TH2 responses, TH17 cell-mediated pathology was reduced in this context, with an accompanying decrease in TH17 cells and increase in Foxp3+ regulatory T cells. Bivariate genomic footprinting elucidated the c-Maf transcription-factor network, including enhanced activity of NFAT; this led to the identification and validation of c-Maf as a negative regulator of IL-2. The decreased expression of the gene encoding the transcription factor RORγt (Rorc) that resulted from c-Maf deficiency was dependent on IL-2, which explained the in vivo observations. Thus, c-Maf is a positive and negative regulator of the expression of cytokine-encoding genes, with context-specific effects that allow each immune response to occur in a controlled yet effective manner.
Collapse
Affiliation(s)
- Leona Gabryšová
- The Francis Crick Institute, Laboratory of Immunoregulation and Infection, London, UK
| | | | - Raphaëlle Luisier
- The Francis Crick Institute, Computational Biology Laboratory, London, UK
| | - Luke S Cox
- The Francis Crick Institute, Laboratory of Immunoregulation and Infection, London, UK
| | - Jan Sodenkamp
- The Francis Crick Institute, Malaria Laboratory, London, UK
| | | | | | - Charlotte Whicher
- The Francis Crick Institute, Laboratory of Immunoregulation and Infection, London, UK
| | - Yashaswini Kannan
- The Francis Crick Institute, Helminth Immunology Laboratory, London, UK
| | - Krzysztof Potempa
- The Francis Crick Institute, Laboratory of Immunoregulation and Infection, London, UK
| | - Xuemei Wu
- The Francis Crick Institute, Laboratory of Immunoregulation and Infection, London, UK
| | - Leena Bhaw
- The Francis Crick Institute, Advanced Sequencing Facility Laboratory, London, UK
| | - Hagen Wende
- Heidelberg University, Institute of Pharmacology, Heidelberg, Germany
| | - Michael H Sieweke
- Aix Marseille University, CNRS, INSERM, CIML, Marseille, France
- Max-Delbrück-Centrum für Molekulare Medizin in der Helmholtzgemeinschaft (MDC), Berlin, Germany
| | - Greg Elgar
- The Francis Crick Institute, Advanced Sequencing Facility Laboratory, London, UK
| | - Mark Wilson
- The Francis Crick Institute, Helminth Immunology Laboratory, London, UK
| | - James Briscoe
- The Francis Crick Institute, Developmental Dynamics Laboratory, London, UK
| | - Vicki Metzis
- The Francis Crick Institute, Developmental Dynamics Laboratory, London, UK
| | - Jean Langhorne
- The Francis Crick Institute, Malaria Laboratory, London, UK
| | - Nicholas M Luscombe
- The Francis Crick Institute, Computational Biology Laboratory, London, UK
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anne O'Garra
- The Francis Crick Institute, Laboratory of Immunoregulation and Infection, London, UK.
- National Heart and Lung Institute, Imperial College London, London, UK.
| |
Collapse
|
10
|
Turajlic S, Xu H, Litchfield K, Rowan A, Horswell S, Chambers T, O'Brien T, Lopez JI, Watkins TBK, Nicol D, Stares M, Challacombe B, Hazell S, Chandra A, Mitchell TJ, Au L, Eichler-Jonsson C, Jabbar F, Soultati A, Chowdhury S, Rudman S, Lynch J, Fernando A, Stamp G, Nye E, Stewart A, Xing W, Smith JC, Escudero M, Huffman A, Matthews N, Elgar G, Phillimore B, Costa M, Begum S, Ward S, Salm M, Boeing S, Fisher R, Spain L, Navas C, Grönroos E, Hobor S, Sharma S, Aurangzeb I, Lall S, Polson A, Varia M, Horsfield C, Fotiadis N, Pickering L, Schwarz RF, Silva B, Herrero J, Luscombe NM, Jamal-Hanjani M, Rosenthal R, Birkbak NJ, Wilson GA, Pipek O, Ribli D, Krzystanek M, Csabai I, Szallasi Z, Gore M, McGranahan N, Van Loo P, Campbell P, Larkin J, Swanton C. Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal. Cell 2018; 173:595-610.e11. [PMID: 29656894 PMCID: PMC5938372 DOI: 10.1016/j.cell.2018.03.043] [Citation(s) in RCA: 390] [Impact Index Per Article: 65.0] [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: 09/15/2017] [Revised: 01/12/2018] [Accepted: 03/19/2018] [Indexed: 02/07/2023]
Abstract
The evolutionary features of clear-cell renal cell carcinoma (ccRCC) have not been systematically studied to date. We analyzed 1,206 primary tumor regions from 101 patients recruited into the multi-center prospective study, TRACERx Renal. We observe up to 30 driver events per tumor and show that subclonal diversification is associated with known prognostic parameters. By resolving the patterns of driver event ordering, co-occurrence, and mutual exclusivity at clone level, we show the deterministic nature of clonal evolution. ccRCC can be grouped into seven evolutionary subtypes, ranging from tumors characterized by early fixation of multiple mutational and copy number drivers and rapid metastases to highly branched tumors with >10 subclonal drivers and extensive parallel evolution associated with attenuated progression. We identify genetic diversity and chromosomal complexity as determinants of patient outcome. Our insights reconcile the variable clinical behavior of ccRCC and suggest evolutionary potential as a biomarker for both intervention and surveillance.
Collapse
Affiliation(s)
- Samra Turajlic
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Units, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Hang Xu
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Kevin Litchfield
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Andrew Rowan
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, the Francis Crick Institute, London NW1 1AT, UK
| | - Tim Chambers
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Tim O'Brien
- Urology Centre, Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Jose I Lopez
- Department of Pathology, Cruces University Hospital, Biocruces Institute, University of the Basque Country, Barakaldo, Spain
| | - Thomas B K Watkins
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - David Nicol
- Department of Urology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Mark Stares
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Ben Challacombe
- Urology Centre, Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Steve Hazell
- Department of Pathology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Ashish Chandra
- Department of Pathology, Guy's and St. Thomas' NHS Foundation Trust, London SE1 7EH, UK
| | - Thomas J Mitchell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK; Department of Surgery, Addenbrooke's Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Lewis Au
- Renal and Skin Units, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Claudia Eichler-Jonsson
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Faiz Jabbar
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Aspasia Soultati
- Department of Medical Oncology, Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Simon Chowdhury
- Department of Medical Oncology, Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Sarah Rudman
- Department of Medical Oncology, Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Joanna Lynch
- Renal and Skin Units, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Archana Fernando
- Urology Centre, Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Gordon Stamp
- Experimental Histopathology Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Emma Nye
- Experimental Histopathology Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Aengus Stewart
- Department of Bioinformatics and Biostatistics, the Francis Crick Institute, London NW1 1AT, UK
| | - Wei Xing
- Department of Scientific Computing, the Francis Crick Institute, London NW1 1AT, UK
| | - Jonathan C Smith
- Department of Scientific Computing, the Francis Crick Institute, London NW1 1AT, UK
| | - Mickael Escudero
- Department of Bioinformatics and Biostatistics, the Francis Crick Institute, London NW1 1AT, UK
| | - Adam Huffman
- Department of Scientific Computing, the Francis Crick Institute, London NW1 1AT, UK
| | - Nik Matthews
- Advanced Sequencing Facility, the Francis Crick Institute, London NW1 1AT, UK
| | - Greg Elgar
- Advanced Sequencing Facility, the Francis Crick Institute, London NW1 1AT, UK
| | - Ben Phillimore
- Advanced Sequencing Facility, the Francis Crick Institute, London NW1 1AT, UK
| | - Marta Costa
- Advanced Sequencing Facility, the Francis Crick Institute, London NW1 1AT, UK
| | - Sharmin Begum
- Advanced Sequencing Facility, the Francis Crick Institute, London NW1 1AT, UK
| | - Sophia Ward
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Advanced Sequencing Facility, the Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK
| | - Max Salm
- Department of Bioinformatics and Biostatistics, the Francis Crick Institute, London NW1 1AT, UK
| | - Stefan Boeing
- Department of Bioinformatics and Biostatistics, the Francis Crick Institute, London NW1 1AT, UK
| | - Rosalie Fisher
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Lavinia Spain
- Renal and Skin Units, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Carolina Navas
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Eva Grönroos
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Sebastijan Hobor
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Sarkhara Sharma
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Ismaeel Aurangzeb
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Sharanpreet Lall
- Department of Medical Oncology, Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Alexander Polson
- Department of Pathology, Guy's and St. Thomas' NHS Foundation Trust, London SE1 7EH, UK
| | - Mary Varia
- Department of Pathology, Guy's and St. Thomas' NHS Foundation Trust, London SE1 7EH, UK
| | - Catherine Horsfield
- Department of Pathology, Guy's and St. Thomas' NHS Foundation Trust, London SE1 7EH, UK
| | - Nicos Fotiadis
- Department of Radiology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lisa Pickering
- Renal and Skin Units, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Bruno Silva
- Department of Scientific Computing, the Francis Crick Institute, London NW1 1AT, UK
| | - Javier Herrero
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Nick M Luscombe
- Bioinformatics and Computational Biology Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK
| | - Rachel Rosenthal
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK
| | - Nicolai J Birkbak
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK
| | - Gareth A Wilson
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK
| | - Orsolya Pipek
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dezso Ribli
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Marcin Krzystanek
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Istvan Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Zoltan Szallasi
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs Lyngby 2800, Denmark; Computational Health Informatics Program, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Martin Gore
- Renal and Skin Units, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Peter Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - James Larkin
- Renal and Skin Units, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK.
| |
Collapse
|
11
|
Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, Marafioti T, Kirkizlar E, Watkins TBK, McGranahan N, Ward S, Martinson L, Riley J, Fraioli F, Al Bakir M, Grönroos E, Zambrana F, Endozo R, Bi WL, Fennessy FM, Sponer N, Johnson D, Laycock J, Shafi S, Czyzewska-Khan J, Rowan A, Chambers T, Matthews N, Turajlic S, Hiley C, Lee SM, Forster MD, Ahmad T, Falzon M, Borg E, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Hafez D, Naik A, Ganguly A, Kareht S, Shah R, Joseph L, Quinn AM, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Oukrif D, Akarca AU, Hartley JA, Lowe HL, Lock S, Iles N, Bell H, Ngai Y, Elgar G, Szallasi Z, Schwarz RF, Herrero J, Stewart A, Quezada SA, Peggs KS, Van Loo P, Dive C, Lin CJ, Rabinowitz M, Aerts HJWL, Hackshaw A, Shaw JA, Zimmermann BG, Swanton C. Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 2018; 554:264. [PMID: 29258292 DOI: 10.1038/nature25161] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This corrects the article DOI: 10.1038/nature22364.
Collapse
|
12
|
Moss CF, Dalla Rosa I, Hunt LE, Yasukawa T, Young R, Jones AWE, Reddy K, Desai R, Virtue S, Elgar G, Voshol P, Taylor MS, Holt IJ, Reijns MAM, Spinazzola A. Aberrant ribonucleotide incorporation and multiple deletions in mitochondrial DNA of the murine MPV17 disease model. Nucleic Acids Res 2018; 45:12808-12815. [PMID: 29106596 PMCID: PMC5728394 DOI: 10.1093/nar/gkx1009] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/17/2017] [Indexed: 12/24/2022] Open
Abstract
All DNA polymerases misincorporate ribonucleotides despite their preference for deoxyribonucleotides, and analysis of cultured cells indicates that mammalian mitochondrial DNA (mtDNA) tolerates such replication errors. However, it is not clear to what extent misincorporation occurs in tissues, or whether this plays a role in human disease. Here, we show that mtDNA of solid tissues contains many more embedded ribonucleotides than that of cultured cells, consistent with the high ratio of ribonucleotide to deoxynucleotide triphosphates in tissues, and that riboadenosines account for three-quarters of them. The pattern of embedded ribonucleotides changes in a mouse model of Mpv17 deficiency, which displays a marked increase in rGMPs in mtDNA. However, while the mitochondrial dGTP is low in the Mpv17−/− liver, the brain shows no change in the overall dGTP pool, leading us to suggest that Mpv17 determines the local concentration or quality of dGTP. Embedded rGMPs are expected to distort the mtDNA and impede its replication, and elevated rGMP incorporation is associated with early-onset mtDNA depletion in liver and late-onset multiple deletions in brain of Mpv17−/− mice. These findings suggest aberrant ribonucleotide incorporation is a primary mtDNA abnormality that can result in pathology.
Collapse
Affiliation(s)
| | - Ilaria Dalla Rosa
- MRC Laboratory, Mill Hill, London NW7 1AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London NW3 2PF, UK
| | - Lilian E Hunt
- Advanced Sequencing Facility, Francis Crick Institute, London NW1 1AT, UK
| | | | - Robert Young
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Aleck W E Jones
- MRC Laboratory, Mill Hill, London NW7 1AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London NW3 2PF, UK
| | - Kaalak Reddy
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Radha Desai
- MRC Laboratory, Mill Hill, London NW7 1AA, UK
| | - Sam Virtue
- MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Greg Elgar
- Advanced Sequencing Facility, Francis Crick Institute, London NW1 1AT, UK
| | - Peter Voshol
- MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Martin S Taylor
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ian J Holt
- MRC Laboratory, Mill Hill, London NW7 1AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London NW3 2PF, UK.,Biodonostia Health Research Institute, 20014 San Sebastián, Spain and IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Martin A M Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Antonella Spinazzola
- MRC Laboratory, Mill Hill, London NW7 1AA, UK.,Department of Clinical Neurosciences, Institute of Neurology, Royal Free Campus, University College London NW3 2PF, UK.,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| |
Collapse
|
13
|
Abstract
SummaryIn mammalian blood coagulation 5 proteases, factor VII (FVII), factor IX (FIX), factor X (FX), protein C (PC) and prothrombin act with two cofactors factor V and factor VIII to control the generation of fibrin. Biochemical evidence and molecular cloning data have previously indicated that blood coagulation involving tissue factor, prothrombin and fibrinogen is present in all vertebrates. Using degenerate RT-PCR we have isolated and characterized novel cDNAs with sequence identity to the blood coagulation serine proteases and cofactors from chicken and the puffer fish (Fugu rubripes). Sequence alignments, phylogenetic and comparative sequence analysis all support the existence of the Gla-EGF1-EGF2-SP domain serine proteases FVII, FIX, FX, PC and the A1-A2-B-A3-C1-C2 domain protein cofactors FV and FVIII in these species. These results strongly suggest that the blood coagulation network is present in all jawed vertebrates and evolved before the divergence of tetrapods and teleosts over 430 million years ago; and that vertebrate blood coagulation may have benefited from two rounds of gene or whole genome duplication. Sequences identified in Fugu coding for additional FVII-like, FIX-like and PC-like sequences support the possibility of further tandem and large-scale duplications in teleosts. Comparative sequence analyses of amino acid residues in the active site region suggest these additional sequences have evolved new and as yet unknown functions.Supplementary information to this article available at both http://europium.csc.mrc.ac.uk and www.thrombosis-online.com
Collapse
|
14
|
Elgar G. Editorial. Brief Funct Genomics 2017; 16:319. [PMID: 29140479 DOI: 10.1093/bfgp/elx039] [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] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
15
|
Fischer JC, Ambroise B, Elgar G. Chromosome architecture at the Sox21 locus. Mech Dev 2017. [DOI: 10.1016/j.mod.2017.04.378] [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: 11/24/2022]
|
16
|
Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, Marafioti T, Kirkizlar E, Watkins TBK, McGranahan N, Ward S, Martinson L, Riley J, Fraioli F, Al Bakir M, Grönroos E, Zambrana F, Endozo R, Bi WL, Fennessy FM, Sponer N, Johnson D, Laycock J, Shafi S, Czyzewska-Khan J, Rowan A, Chambers T, Matthews N, Turajlic S, Hiley C, Lee SM, Forster MD, Ahmad T, Falzon M, Borg E, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Hafez D, Naik A, Ganguly A, Kareht S, Shah R, Joseph L, Marie Quinn A, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Oukrif D, Akarca AU, Hartley JA, Lowe HL, Lock S, Iles N, Bell H, Ngai Y, Elgar G, Szallasi Z, Schwarz RF, Herrero J, Stewart A, Quezada SA, Peggs KS, Van Loo P, Dive C, Lin CJ, Rabinowitz M, Aerts HJWL, Hackshaw A, Shaw JA, Zimmermann BG, Swanton C. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 2017; 545:446-451. [PMID: 28445469 PMCID: PMC5812436 DOI: 10.1038/nature22364] [Citation(s) in RCA: 1092] [Impact Index Per Article: 156.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/13/2017] [Indexed: 12/13/2022]
Abstract
The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies.
Collapse
MESH Headings
- Biopsy/methods
- Carcinoma, Non-Small-Cell Lung/blood
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/surgery
- Cell Lineage/genetics
- Cell Tracking
- Clone Cells/metabolism
- Clone Cells/pathology
- DNA Mutational Analysis
- DNA, Neoplasm/blood
- DNA, Neoplasm/genetics
- Disease Progression
- Drug Resistance, Neoplasm/genetics
- Early Detection of Cancer/methods
- Evolution, Molecular
- Humans
- Limit of Detection
- Lung Neoplasms/blood
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lung Neoplasms/surgery
- Multiplex Polymerase Chain Reaction
- Neoplasm Metastasis/diagnosis
- Neoplasm Metastasis/genetics
- Neoplasm Metastasis/pathology
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/pathology
- Postoperative Care/methods
- Reproducibility of Results
- Tumor Burden
Collapse
Affiliation(s)
- Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gareth A Wilson
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Tudor Constantin
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Raheleh Salari
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - John Le Quesne
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - David A Moore
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Teresa Marafioti
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - Eser Kirkizlar
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Thomas B K Watkins
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Luke Martinson
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Joan Riley
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Francesco Fraioli
- Department of Nuclear Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
| | - Maise Al Bakir
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eva Grönroos
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Francisco Zambrana
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Raymondo Endozo
- Department of Nuclear Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
| | - Wenya Linda Bi
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fiona M Fennessy
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicole Sponer
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Diana Johnson
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Joanne Laycock
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Seema Shafi
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Justyna Czyzewska-Khan
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Andrew Rowan
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tim Chambers
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nik Matthews
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Tumour Profiling Unit Genomics Facility, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Samra Turajlic
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Crispin Hiley
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Siow Ming Lee
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Martin D Forster
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Tanya Ahmad
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Mary Falzon
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - Elaine Borg
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - David Lawrence
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Martin Hayward
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Shyam Kolvekar
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Nikolaos Panagiotopoulos
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Sam M Janes
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Respiratory Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, Rayne Building, University College London, 5 University Street, London WC1E 6JF, UK
| | - Ricky Thakrar
- Department of Respiratory Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Asia Ahmed
- Department of Radiology, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Fiona Blackhall
- Institute of Cancer Studies, University of Manchester, Oxford Road, Manchester M13 9PL, UK
- The Christie Hospital, Manchester M20 4BX, UK
| | | | - Dina Hafez
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Ashwini Naik
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Apratim Ganguly
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Stephanie Kareht
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Rajesh Shah
- Department of Cardiothoracic Surgery, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Leena Joseph
- Department of Pathology, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Anne Marie Quinn
- Department of Pathology, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Phil A Crosbie
- North West Lung Centre, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Babu Naidu
- Department of Thoracic Surgery, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK. University College London Hospitals NHS Foundation Trust, London, UK
| | - Gary Middleton
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Gerald Langman
- Department of Cellular Pathology, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Simon Trotter
- Department of Cellular Pathology, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Marianne Nicolson
- Department of Medical Oncology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Hardy Remmen
- Department of Cardiothoracic Surgery, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZD, UK
| | - Keith Kerr
- Department of Pathology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZD, UK
| | - Mahendran Chetty
- Department of Respiratory Medicine, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Lesley Gomersall
- Department of Radiology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Dean A Fennell
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Apostolos Nakas
- Department of Thoracic Surgery, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Sridhar Rathinam
- Department of Thoracic Surgery, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Girija Anand
- Department of Radiotherapy, North Middlesex University Hospital, London N18 1QX, UK
| | - Sajid Khan
- Department of Respiratory Medicine, Royal Free Hospital, Pond Street, London NW3 2QG, UK
- Department of Respiratory Medicine, Barnet and Chase Farm Hospitals, Wellhouse Lane, Barnet EN5 3DJ, UK
| | - Peter Russell
- Department of Respiratory Medicine, The Princess Alexandra Hospital, Hamstel Road, Harlow CM20 1QX, UK
| | - Veni Ezhil
- Department of Clinical Oncology, St.Luke's Cancer Centre, Royal Surrey County Hospital, Guildford GU2 7XX, UK
| | - Babikir Ismail
- Department of Pathology, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Melanie Irvin-Sellers
- Department of Respiratory Medicine, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Vineet Prakash
- Department of Radiology, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Jason F Lester
- Department of Clinical Oncology, Velindre Hospital, Cardiff CF14 2TL, UK
| | | | - Richard Attanoos
- Department of Cellular Pathology, University Hospital of Wales and Cardiff University, Heath Park, Cardiff, UK
| | - Haydn Adams
- Department of Radiology, University Hospital Llandough, Cardiff CF64 2XX, UK
| | - Helen Davies
- Department of Respiratory Medicine, University Hospital Llandough, Cardiff CF64 2XX, UK
| | - Dahmane Oukrif
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Ayse U Akarca
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - John A Hartley
- University College London Experimental Cancer Medicine Centre GCLP Facility, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Helen L Lowe
- University College London Experimental Cancer Medicine Centre GCLP Facility, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Sara Lock
- Department of Respiratory Medicine, The Whittington Hospital NHS Trust, London, N19 5NF, UK
| | - Natasha Iles
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Harriet Bell
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Yenting Ngai
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Greg Elgar
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Zoltan Szallasi
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Aengus Stewart
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Karl S Peggs
- Cancer Immunology Unit, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Research Department of Haematology, University College Cancer Institute, London WC1E 6DD, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Human Genetics, University of Leuven, B-3000 Leuven, Belgium
| | - Caroline Dive
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - C Jimmy Lin
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | | | - Hugo J W L Aerts
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215-5450, USA
| | - Allan Hackshaw
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Jacqui A Shaw
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| |
Collapse
|
17
|
Abstract
Morphological evolution is driven both by coding sequence variation and by changes in regulatory sequences. However, how cis-regulatory modules (CRMs) evolve to generate entirely novel expression domains is largely unknown. Here, we reconstruct the evolutionary history of a lens enhancer located within a CRM that not only predates the lens, a vertebrate innovation, but bilaterian animals in general. Alignments of orthologous sequences from different deuterostomes sub-divide the CRM into a deeply conserved core and a more divergent flanking region. We demonstrate that all deuterostome flanking regions, including invertebrate sequences, activate gene expression in the zebrafish lens through the same ancient cluster of activator sites. However, levels of gene expression vary between species due to the presence of repressor motifs in flanking region and core. These repressor motifs are responsible for the relatively weak enhancer activity of tetrapod flanking regions. Ray-finned fish, however, have gained two additional lineage-specific activator motifs which in combination with the ancient cluster of activators and the core constitute a potent lens enhancer. The exploitation and modification of existing regulatory potential in flanking regions but not in the highly conserved core might represent a more general model for the emergence of novel regulatory functions in complex CRMs.
Collapse
Affiliation(s)
- Stefan Pauls
- Division of Systems Biology, Francis Crick Institute, Mill Hill laboratories, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Debbie K Goode
- Cambridge Institute for Medical Research and the Wellcome Trust/MRC Cambridge Stem Cell Institute, University of Cambridge, Hills Road, Cambridge CB2 OXY, UK
| | - Libero Petrone
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1 E6BT, UK
| | - Paola Oliveri
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1 E6BT, UK
| | - Greg Elgar
- Division of Systems Biology, Francis Crick Institute, Mill Hill laboratories, The Ridgeway, Mill Hill, London NW7 1AA, UK
| |
Collapse
|
18
|
Dalla Rosa I, Cámara Y, Durigon R, Moss CF, Vidoni S, Akman G, Hunt L, Johnson MA, Grocott S, Wang L, Thorburn DR, Hirano M, Poulton J, Taylor RW, Elgar G, Martí R, Voshol P, Holt IJ, Spinazzola A. MPV17 Loss Causes Deoxynucleotide Insufficiency and Slow DNA Replication in Mitochondria. PLoS Genet 2016; 12:e1005779. [PMID: 26760297 PMCID: PMC4711891 DOI: 10.1371/journal.pgen.1005779] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 12/08/2015] [Indexed: 11/21/2022] Open
Abstract
MPV17 is a mitochondrial inner membrane protein whose dysfunction causes mitochondrial DNA abnormalities and disease by an unknown mechanism. Perturbations of deoxynucleoside triphosphate (dNTP) pools are a recognized cause of mitochondrial genomic instability; therefore, we determined DNA copy number and dNTP levels in mitochondria of two models of MPV17 deficiency. In Mpv17 ablated mice, liver mitochondria showed substantial decreases in the levels of dGTP and dTTP and severe mitochondrial DNA depletion, whereas the dNTP pool was not significantly altered in kidney and brain mitochondria that had near normal levels of DNA. The shortage of mitochondrial dNTPs in Mpv17-/- liver slows the DNA replication in the organelle, as evidenced by the elevated level of replication intermediates. Quiescent fibroblasts of MPV17-mutant patients recapitulate key features of the primary affected tissue of the Mpv17-/- mice, displaying virtual absence of the protein, decreased dNTP levels and mitochondrial DNA depletion. Notably, the mitochondrial DNA loss in the patients’ quiescent fibroblasts was prevented and rescued by deoxynucleoside supplementation. Thus, our study establishes dNTP insufficiency in the mitochondria as the cause of mitochondrial DNA depletion in MPV17 deficiency, and identifies deoxynucleoside supplementation as a potential therapeutic strategy for MPV17-related disease. Moreover, changes in the expression of factors involved in mitochondrial deoxynucleotide homeostasis indicate a remodeling of nucleotide metabolism in MPV17 disease models, which suggests mitochondria lacking functional MPV17 have a restricted purine mitochondrial salvage pathway. Mitochondrial DNA depletion syndrome (MDS) is a genetically heterogeneous condition characterized by a decrease of mitochondrial DNA (mtDNA) copy number and decreased activities of respiratory chain enzymes. Depletion of mtDNA has been associated with mutations in several genes, which encode either proteins directly involved in mtDNA replication or factors regulating the homeostasis of the mitochondrial deoxynucleotide pool. However, for some genes the mechanism linking mutations and mtDNA depletion is not known. One such gene is MPV17, whose loss-of-function causes mtDNA abnormalities in human, mouse and yeast. Here we show that MPV17 dysfunction leads to a shortage of the precursors for DNA synthesis in the mitochondria, slowing DNA replication in the organelle. Not only does mtDNA copy number correlate with dNTP pool size in both mouse tissues and human cells, deoxynucleoside supplementation of the growth medium prevents depletion and restores mtDNA copy number in quiescent MPV17-deficient cells. Hence, our study links MPV17 deficiency, insufficiency of mitochondrial dNTPs, and slow replication in mitochondria to depletion of mtDNA manifesting in the human disease, and places MPV17-related disease firmly in the category of mtDNA disorders caused by deoxynucleotide perturbation. The prevention and reversal of mtDNA loss in MPV17 patient-derived cells identifies potential therapeutic strategy for a currently untreatable disease.
Collapse
Affiliation(s)
| | - Yolanda Cámara
- Laboratory of Mitochondrial Disorders, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Catalonia
- Biomedical Network Research Centre on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Sara Vidoni
- MRC Mitochondrial Biology Unit, Wellcome Trust-MRC Building, Cambridge, United Kingdom
| | - Gokhan Akman
- MRC Mill Hill Laboratory, London, United Kingdom
| | - Lilian Hunt
- MRC Mill Hill Laboratory, London, United Kingdom
| | - Mark A. Johnson
- MRC Mitochondrial Biology Unit, Wellcome Trust-MRC Building, Cambridge, United Kingdom
| | - Sarah Grocott
- Mitochondrial Genetics Group, Nuffield Department of Obstetrics and Gynaecology, Women's Centre, The John Radcliffe Hospital, Oxford, United Kingdom
| | - Liya Wang
- Department of Anatomy, Physiology and Biochemistry, The Swedish University of Agricultural Sciences, Biomedical Center, Uppsala, Sweden
| | - David R. Thorburn
- Murdoch Childrens Research Institute and University of Melbourne Department of Paediatrics, Royal Children's Hospital, Flemington Road, Parkville, Victoria, Australia
| | - Michio Hirano
- Department of Neurology, Columbia University Medical Center, New York, New York, United States of America
| | - Joanna Poulton
- Mitochondrial Genetics Group, Nuffield Department of Obstetrics and Gynaecology, Women's Centre, The John Radcliffe Hospital, Oxford, United Kingdom
| | - Robert W. Taylor
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, The Medical School, Newcastle upon Tyne, United Kingdom
| | - Greg Elgar
- MRC Mill Hill Laboratory, London, United Kingdom
| | - Ramon Martí
- Laboratory of Mitochondrial Disorders, Vall d’Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Catalonia
- Biomedical Network Research Centre on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Peter Voshol
- Institute of Metabolic Science, University of Cambridge, Cambridge, United Kingdom
| | - Ian J. Holt
- MRC Mill Hill Laboratory, London, United Kingdom
| | | |
Collapse
|
19
|
Hunt LE, Noyvert B, Bhaw-Rosun L, Sesay AK, Paternoster L, Nohr EA, Davey Smith G, Tommerup N, Sørensen TIA, Elgar G. Complete re-sequencing of a 2Mb topological domain encompassing the FTO/IRXB genes identifies a novel obesity-associated region upstream of IRX5. Genome Med 2015; 7:126. [PMID: 26642925 PMCID: PMC4671217 DOI: 10.1186/s13073-015-0250-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 07/21/2015] [Accepted: 11/17/2015] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Association studies have identified a number of loci that contribute to an increased body mass index (BMI), the strongest of which is in the first intron of the FTO gene on human chromosome 16q12.2. However, this region is both non-coding and under strong linkage disequilibrium, making it recalcitrant to functional interpretation. Furthermore, the FTO gene is located within a complex cis-regulatory landscape defined by a topologically associated domain that includes the IRXB gene cluster, a trio of developmental regulators. Consequently, at least three genes in this interval have been implicated in the aetiology of obesity. METHODS Here, we sequence a 2 Mb region encompassing the FTO, RPGRIP1L and IRXB cluster genes in 284 individuals from a well-characterised study group of Danish men containing extremely overweight young adults and controls. We further replicate our findings both in an expanded male cohort and an independent female study group. Finally, we compare our variant data with a previous study describing IRX3 and FTO interactions in this region. RESULTS We obtain deep coverage across the entire region, allowing accurate and unequivocal determination of almost every single nucleotide polymorphism and short insertion/deletion. As well as confirming previous findings across the interval, we identify a further novel age-dependent association upstream of IRX5 that imposes a similar burden on BMI to the FTO locus. CONCLUSIONS Our findings are consistent with the hypothesis that chromatin architectures play a role in regulating gene expression levels across topological domains while our targeted sequence approach represents a widely applicable methodology for high-resolution analysis of regional variation across candidate genomic loci.
Collapse
Affiliation(s)
- Lilian E Hunt
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Boris Noyvert
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Leena Bhaw-Rosun
- Genomics Facility, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Abdul K Sesay
- Genomics Facility, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol, UK
| | - Ellen A Nohr
- Research Unit for Gynecology and Obstetrics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol, UK
| | - Niels Tommerup
- Willhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, The Faculty of Health Sciences, The University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen N, Denmark
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit (IEU) at the University of Bristol, University of Bristol, Bristol, UK.,The Novo Nordisk Foundation Centre for Basic Metabolic Research, Section on Metabolic genetics, The Faculty of Health and Medical Sciences, University of Copenhagen, DK2100, Copenhagen Ø, Denmark.,Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospitals, The Capital Region, DK2000, Frederiksberg, Denmark
| | - Greg Elgar
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK.
| |
Collapse
|
20
|
Anwar S, Minhas R, Ali S, Lambert N, Kawakami Y, Elgar G, Azam SS, Abbasi AA. Identification and functional characterization of novel transcriptional enhancers involved in regulating human GLI3 expression during early development. Dev Growth Differ 2015; 57:570-80. [PMID: 26464005 PMCID: PMC4609622 DOI: 10.1111/dgd.12239] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/06/2015] [Accepted: 08/25/2015] [Indexed: 12/13/2022]
Abstract
The zinc-finger transcription factor GLI3 acts as a primary transducer of Sonic hedgehog (Shh) signaling in a context-dependent combinatorial fashion. GLI3 participates in the patterning and growth of many organs, including the central nervous system (CNS) and limbs. Previously, we reported a subset of human intronic cis-regulators controlling many known aspects of endogenous Gli3 expression in mouse and zebrafish. Here we demonstrate in a transgenic zebrafish assay the potential of two novel tetrapod-teleost conserved non-coding elements (CNEs) docking within GLI3 intronic intervals (intron 3 and 4) to induce reporter gene expression at known sites of endogenous Gli3 transcription in embryonic domains such as the central nervous system (CNS) and limbs. Interestingly, the cell culture based assays reveal harmony with the context dependent dual nature of intra-GLI3 conserved elements. Furthermore, a transgenic zebrafish assay of previously reported limb-specific GLI3 transcriptional enhancers (previously tested in mice and chicken limb buds) induced reporter gene expression in zebrafish blood precursor cells and notochord instead of fin. These results demonstrate that the appendage-specific activity of a subset of GLI3-associated enhancers might be a tetrapod innovation. Taken together with our recent data, these results suggest that during the course of vertebrate evolution Gli3 expression control acquired a complex cis-regulatory landscape for spatiotemporal patterning of CNS and limbs. Comparative data from fish and mice suggest that the functional aspects of a subset of these cis-regulators have diverged significantly between these two lineages.
Collapse
Affiliation(s)
- Saneela Anwar
- National Center for Bioinformatics, Computational Biology Lab, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Rashid Minhas
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nicholas Lambert
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Greg Elgar
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London, NW7 1AA, UK
| | - Syed Sikandar Azam
- National Center for Bioinformatics, Computational Biology Lab, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| |
Collapse
|
21
|
Grice J, Noyvert B, Doglio L, Elgar G. A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes. PLoS One 2015; 10:e0130413. [PMID: 26131856 PMCID: PMC4489388 DOI: 10.1371/journal.pone.0130413] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/19/2015] [Indexed: 12/17/2022] Open
Abstract
Background Determining the function of regulatory elements is fundamental for our understanding of development, disease and evolution. However, the sequence features that mediate these functions are often unclear and the prediction of tissue-specific expression patterns from sequence alone is non-trivial. Previous functional studies have demonstrated a link between PBX-HOX and MEIS/PREP binding interactions and hindbrain enhancer activity, but the defining grammar of these sites, if any exists, has remained elusive. Results Here, we identify a shared sequence signature (syntax) within a heterogeneous set of conserved vertebrate hindbrain enhancers composed of spatially co-occurring PBX-HOX and MEIS/PREP transcription factor binding motifs. We use this syntax to accurately predict hindbrain enhancers in 89% of cases (67/75 predicted elements) from a set of conserved non-coding elements (CNEs). Furthermore, mutagenesis of the sites abolishes activity or generates ectopic expression, demonstrating their requirement for segmentally restricted enhancer activity in the hindbrain. We refine and use our syntax to predict over 3,000 hindbrain enhancers across the human genome. These sequences tend to be located near developmental transcription factors and are enriched in known hindbrain activating elements, demonstrating the predictive power of this simple model. Conclusion Our findings support the theory that hundreds of CNEs, and perhaps thousands of regions across the human genome, function to coordinate gene expression in the developing hindbrain. We speculate that deeply conserved sequences of this kind contributed to the co-option of new genes into the hindbrain gene regulatory network during early vertebrate evolution by linking patterns of hox expression to downstream genes involved in segmentation and patterning, and evolutionarily newer instances may have continued to contribute to lineage-specific elaboration of the hindbrain.
Collapse
Affiliation(s)
- Joseph Grice
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
| | - Boris Noyvert
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
| | - Laura Doglio
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
| | - Greg Elgar
- The Francis Crick Institute Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
- * E-mail:
| |
Collapse
|
22
|
Minhas R, Pauls S, Ali S, Doglio L, Khan MR, Elgar G, Abbasi AA. Cis-regulatory control of human GLI2 expression in the developing neural tube and limb bud. Dev Dyn 2015; 244:681-92. [DOI: 10.1002/dvdy.24266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/29/2015] [Accepted: 02/16/2015] [Indexed: 11/08/2022] Open
Affiliation(s)
- Rashid Minhas
- National Center for Bioinformatics; Program of Comparative and Evolutionary Genomics; Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad 45320 Pakistan
| | - Stefan Pauls
- Division of Systems Biology; MRC National Institute for Medical Research; The Ridgeway, Mill Hill London NW7 1AA United Kingdom
| | - Shahid Ali
- National Center for Bioinformatics; Program of Comparative and Evolutionary Genomics; Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad 45320 Pakistan
| | - Laura Doglio
- Division of Systems Biology; MRC National Institute for Medical Research; The Ridgeway, Mill Hill London NW7 1AA United Kingdom
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology; National Agricultural Research Center; Park Road Islamabad Pakistan
| | - Greg Elgar
- Division of Systems Biology; MRC National Institute for Medical Research; The Ridgeway, Mill Hill London NW7 1AA United Kingdom
| | - Amir Ali Abbasi
- National Center for Bioinformatics; Program of Comparative and Evolutionary Genomics; Faculty of Biological Sciences; Quaid-i-Azam University; Islamabad 45320 Pakistan
| |
Collapse
|
23
|
De Silva DR, Nichols R, Elgar G. Purifying selection in deeply conserved human enhancers is more consistent than in coding sequences. PLoS One 2014; 9:e103357. [PMID: 25062004 PMCID: PMC4111549 DOI: 10.1371/journal.pone.0103357] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 07/01/2014] [Indexed: 12/30/2022] Open
Abstract
Comparison of polymorphism at synonymous and non-synonymous sites in protein-coding DNA can provide evidence for selective constraint. Non-coding DNA that forms part of the regulatory landscape presents more of a challenge since there is not such a clear-cut distinction between sites under stronger and weaker selective constraint. Here, we consider putative regulatory elements termed Conserved Non-coding Elements (CNEs) defined by their high level of sequence identity across all vertebrates. Some mutations in these regions have been implicated in developmental disorders; we analyse CNE polymorphism data to investigate whether such deleterious effects are widespread in humans. Single nucleotide variants from the HapMap and 1000 Genomes Projects were mapped across nearly 2000 CNEs. In the 1000 Genomes data we find a significant excess of rare derived alleles in CNEs relative to coding sequences; this pattern is absent in HapMap data, apparently obscured by ascertainment bias. The distribution of polymorphism within CNEs is not uniform; we could identify two categories of sites by exploiting deep vertebrate alignments: stretches that are non-variant, and those that have at least one substitution. The conserved category has fewer polymorphic sites and a greater excess of rare derived alleles, which can be explained by a large proportion of sites under strong purifying selection within humans--higher than that for non-synonymous sites in most protein coding regions, and comparable to that at the strongly conserved trans-dev genes. Conversely, the more evolutionarily labile CNE sites have an allele frequency distribution not significantly different from non-synonymous sites. Future studies should exploit genome-wide re-sequencing to obtain better coverage in selected non-coding regions, given the likelihood that mutations in evolutionarily conserved enhancer sequences are deleterious. Discovery pipelines should validate non-coding variants to aid in identifying causal and risk-enhancing variants in complex disorders, in contrast to the current focus on exome sequencing.
Collapse
Affiliation(s)
- Dilrini R. De Silva
- Systems Biology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Richard Nichols
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Greg Elgar
- Systems Biology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
| |
Collapse
|
24
|
Chen WC, Pauls S, Bacha J, Elgar G, Loose M, Shimeld SM. Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity. Dev Biol 2014; 390:261-72. [PMID: 24680932 PMCID: PMC4010673 DOI: 10.1016/j.ydbio.2014.03.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 03/03/2014] [Accepted: 03/19/2014] [Indexed: 01/31/2023]
Abstract
Vertebrate genomes share numerous conserved non-coding elements, many of which function as enhancer elements and are hypothesised to be under evolutionary constraint due to a need to be bound by combinations of sequence-specific transcription factors. In contrast, few such conserved elements can be detected between vertebrates and their closest invertebrate relatives. Despite this lack of sequence identity, cross-species transgenesis has identified some cases where non-coding DNA from invertebrates drives reporter gene expression in transgenic vertebrates in patterns reminiscent of the expression of vertebrate orthologues. Such instances are presumed to reflect the presence of conserved suites of binding sites in the regulatory regions of invertebrate and vertebrate orthologues, such that both regulatory elements can correctly interpret the trans-activating environment. Shuffling of binding sites has been suggested to lie behind loss of sequence conservation; however this has not been experimentally tested. Here we examine the underlying basis of enhancer activity for the Ciona intestinalis βγ-crystallin gene, which drives expression in the lens of transgenic vertebrates despite the Ciona lineage predating the evolution of the lens. We construct an interactive gene regulatory network (GRN) for vertebrate lens development, allowing network interactions to be robustly catalogued and conserved network components and features to be identified. We show that a small number of binding motifs are necessary for Ciona βγ-crystallin expression, and narrow down the likely factors that bind to these motifs. Several of these overlap with the conserved core of the vertebrate lens GRN, implicating these sites in cross species function. However when we test these motifs in a transgenic vertebrate they prove to be dispensable for reporter expression in the lens. These results show that current models depicting cross species enhancer function as dependent on conserved binding sites can be overly simplistic, with sound evolutionary inference requiring detailed dissection of underlying mechanisms. Analysis of binding motifs in a Ciona enhancer that also works in vertebrate lens. Establishment of candidate transcription factors that may regulate this enhancer. Construction of a curated, interactive gene regulatory network of lens development. Public accessibility of this via a dedicated web site. Experimental test of binding motif function in cross species transgenesis.
Collapse
Affiliation(s)
- Wei-Chung Chen
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Stefan Pauls
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Jamil Bacha
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
| | - Greg Elgar
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Matthew Loose
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK.
| | - Sebastian M Shimeld
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
| |
Collapse
|
25
|
Parker HJ, Sauka-Spengler T, Bronner M, Elgar G. A reporter assay in lamprey embryos reveals both functional conservation and elaboration of vertebrate enhancers. PLoS One 2014; 9:e85492. [PMID: 24416417 PMCID: PMC3887057 DOI: 10.1371/journal.pone.0085492] [Citation(s) in RCA: 23] [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: 08/19/2013] [Accepted: 12/05/2013] [Indexed: 11/27/2022] Open
Abstract
The sea lamprey is an important model organism for investigating the evolutionary origins of vertebrates. As more vertebrate genome sequences are obtained, evolutionary developmental biologists are becoming increasingly able to identify putative gene regulatory elements across the breadth of the vertebrate taxa. The identification of these regions makes it possible to address how changes at the genomic level have led to changes in developmental gene regulatory networks and ultimately to the evolution of morphological diversity. Comparative genomics approaches using sea lamprey have already predicted a number of such regulatory elements in the lamprey genome. Functional characterisation of these sequences and other similar elements requires efficient reporter assays in lamprey. In this report, we describe the development of a transient transgenesis method for lamprey embryos. Focusing on conserved non-coding elements (CNEs), we use this method to investigate their functional conservation across the vertebrate subphylum. We find instances of both functional conservation and lineage-specific functional evolution of CNEs across vertebrates, emphasising the utility of functionally testing homologous CNEs in their host species.
Collapse
Affiliation(s)
- Hugo J. Parker
- Division of Systems Biology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Tatjana Sauka-Spengler
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Marianne Bronner
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Greg Elgar
- Division of Systems Biology, Medical Research Council National Institute for Medical Research, London, United Kingdom
- * E-mail:
| |
Collapse
|
26
|
Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SMJ, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet 2013; 45:415-21, 421e1-2. [PMID: 23435085 PMCID: PMC3709584 DOI: 10.1038/ng.2568] [Citation(s) in RCA: 429] [Impact Index Per Article: 39.0] [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: 07/20/2012] [Accepted: 01/31/2013] [Indexed: 12/19/2022]
Abstract
Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ∼500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms.
Collapse
Affiliation(s)
- Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Abstract
A key finding from early genomics research is the remarkable consistency in the number of protein-coding regions across diverse species. This has led many researchers to look to the cis-regulatory elements of genes as the fundamental influence behind evolving gene function and subsequent species diversification. Historically, since these elements are often located in vast intergenic and intronic regions of the genome, their identification has been recalcitrant. Now, with the deluge of whole-genome data from representatives of numerous eukaryotic lineages, various approaches have enabled us to begin to recognize features that characterize regulatory regions of the genome. Here we endeavour to collate these approaches in order to give an overview of the complexities involved in extrapolating regulatory signatures. The resource provided by the escalating richness of whole-genome datasets enables more sophisticated modelling of these regulatory signatures yet at the same time introduces increasing potential for noise. While we are only at the advent of making these discoveries, the next decade promises to be a very exciting and rewarding time for genome researchers.
Collapse
Affiliation(s)
- Debbie K Goode
- Cambridge Institute for Medical Research, Deptartment of Haematology, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | | |
Collapse
|
28
|
Pauls S, Smith SF, Elgar G. Lens development depends on a pair of highly conserved Sox21 regulatory elements. Dev Biol 2012; 365:310-8. [PMID: 22387845 PMCID: PMC3480646 DOI: 10.1016/j.ydbio.2012.02.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 02/16/2012] [Accepted: 02/18/2012] [Indexed: 02/03/2023]
Abstract
Highly conserved non-coding elements (CNEs) linked to genes involved in embryonic development have been hypothesised to correspond to cis-regulatory modules due to their ability to induce tissue-specific expression patterns. However, attempts to prove their requirement for normal development or for the correct expression of the genes they are associated with have yielded conflicting results. Here, we show that CNEs at the vertebrate Sox21 locus are crucial for Sox21 expression in the embryonic lens and that loss of Sox21 function interferes with normal lens development. Using different expression assays in zebrafish we find that two CNEs linked to Sox21 in all vertebrates contain lens enhancers and that their removal from a reporter BAC abolishes lens expression. Furthermore inhibition of Sox21 function after the injection of a sox21b morpholino into zebrafish leads to defects in lens development. These findings identify a direct link between sequence conservation and genomic function of regulatory sequences. In addition to this we provide evidence that putative Sox binding sites in one of the CNEs are essential for induction of lens expression as well as enhancer function in the CNS. Our results show that CNEs identified in pufferfish-mammal whole-genome comparisons are crucial developmental enhancers and hence essential components of gene regulatory networks underlying vertebrate embryogenesis.
Collapse
|
29
|
Parker HJ, Piccinelli P, Sauka-Spengler T, Bronner M, Elgar G. Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers. BMC Genomics 2011; 12:637. [PMID: 22208168 PMCID: PMC3261376 DOI: 10.1186/1471-2164-12-637] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 12/30/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene regulation through cis-regulatory elements plays a crucial role in development and disease. A major aim of the post-genomic era is to be able to read the function of cis-regulatory elements through scrutiny of their DNA sequence. Whilst comparative genomics approaches have identified thousands of putative regulatory elements, our knowledge of their mechanism of action is poor and very little progress has been made in systematically de-coding them. RESULTS Here, we identify ancient functional signatures within vertebrate conserved non-coding elements (CNEs) through a combination of phylogenetic footprinting and functional assay, using genomic sequence from the sea lamprey as a reference. We uncover a striking enrichment within vertebrate CNEs for conserved binding-site motifs of the Pbx-Hox hetero-dimer. We further show that these predict reporter gene expression in a segment specific manner in the hindbrain and pharyngeal arches during zebrafish development. CONCLUSIONS These findings evoke an evolutionary scenario in which many CNEs evolved early in the vertebrate lineage to co-ordinate Hox-dependent gene-regulatory interactions that pattern the vertebrate head. In a broader context, our evolutionary analyses reveal that CNEs are composed of tightly linked transcription-factor binding-sites (TFBSs), which can be systematically identified through phylogenetic footprinting approaches. By placing a large number of ancient vertebrate CNEs into a developmental context, our findings promise to have a significant impact on efforts toward de-coding gene-regulatory elements that underlie vertebrate development, and will facilitate building general models of regulatory element evolution.
Collapse
Affiliation(s)
- Hugo J Parker
- Division of Systems Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | | | | | | | | |
Collapse
|
30
|
Abnizova I, Walter K, Te Boekhorst R, Elgar G, Gilks WR. STATISTICAL INFORMATION CHARACTERIZATION OF CONSERVED NON-CODING ELEMENTS IN VERTEBRATES. J Bioinform Comput Biol 2011; 5:533-47. [PMID: 17636860 DOI: 10.1142/s0219720007002898] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 02/23/2007] [Accepted: 02/23/2007] [Indexed: 01/28/2023]
Abstract
Recently, a set of highly conserved non-coding elements (CNEs) has been derived from a comparison between the genomes of the puffer fish, Takifugu or Fugu rubripes, and man. In order to facilitate the identification of these conserved elements in silico, we characterize them by a number of statistical features.We found a pronounced information pattern around CNE borders; although the CNEs themselves are AT rich and have high entropy (complexity), they are flanked by GC-rich regions of low entropy (complexity). We also identified the most abundant motifs within and around of CNEs, and identified those that group around their borders. Like in human promoter regions, the TBP, NF-Y and some other binding motifs are clustered around CNE boundaries, which may suggest a possible transcription regulatory function of CNEs.
Collapse
|
31
|
Goode DK, Callaway HA, Cerda GA, Lewis KE, Elgar G. Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events. Development 2011; 138:879-84. [PMID: 21247963 DOI: 10.1242/dev.055996] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Within the vertebrate lineage, a high proportion of duplicate genes have been retained after whole genome duplication (WGD) events. It has been proposed that many of these duplicate genes became indispensable because the ancestral gene function was divided between them. In addition, novel functions may have evolved, owing to changes in cis-regulatory elements. Functional analysis of the PAX2/5/8 gene subfamily appears to support at least the first part of this hypothesis. The collective role of these genes has been widely retained, but sub-functions have been differentially partitioned between the genes in different vertebrates. Conserved non-coding elements (CNEs) represent an interesting and readily identifiable class of putative cis-regulatory elements that have been conserved from fish to mammals, an evolutionary distance of 450 million years. Within the PAX2/5/8 gene subfamily, PAX2 is associated with the highest number of CNEs. An additional WGD experienced in the teleost lineage led to two copies of pax2, each of which retained a large proportion of these CNEs. Using a reporter gene assay in zebrafish embryos, we have exploited this rich collection of regulatory elements in order to determine whether duplicate CNEs have evolved different functions. Remarkably, we find that even highly conserved sequences exhibit more functional differences than similarities. We also discover that short flanking sequences can have a profound impact on CNE function. Therefore, if CNEs are to be used as candidate enhancers for transgenic studies or for multi-species comparative analyses, it is paramount that the CNEs are accurately delineated.
Collapse
Affiliation(s)
- Debbie K Goode
- Department of Physiology Development & Neuroscience, Anatomy Building, Downing Street, Cambridge, UK
| | | | | | | | | |
Collapse
|
32
|
Cottage A, Edwards YJ, Elgar G. SAND, a new protein family: from nucleic acid to protein structure and function prediction. Comp Funct Genomics 2010; 2:226-35. [PMID: 18628914 PMCID: PMC2447211 DOI: 10.1002/cfg.93] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2001] [Accepted: 06/21/2001] [Indexed: 11/09/2022] Open
Abstract
As a result of genome, EST and cDNA sequencing projects, there are huge numbers of predicted and/or partially characterised protein sequences compared with a relatively small number of proteins with experimentally determined function and structure. Thus, there is a considerable attention focused on the accurate prediction of gene function and structure from sequence by using bioinformatics. In the course of our analysis of genomic sequence from Fugu rubripes, we identified a novel gene, SAND, with significant sequence identity to hypothetical proteins predicted in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, a Drosophila melanogaster gene, and mouse and human cDNAs. Here we identify a further SAND homologue in human and Arabidopsis thaliana by use of standard computational tools. We describe the genomic organisation of SAND in these evolutionarily divergent species and identify sequence homologues from EST database searches confirming the expression of SAND in over 20 different eukaryotes. We confirm the expression of two different SAND paralogues in mammals and determine expression of one SAND in other vertebrates and eukaryotes. Furthermore, we predict structural properties of SAND, and characterise conserved sequence motifs in this protein family.
Collapse
Affiliation(s)
- A Cottage
- UK Human Genome mapping Project Resource Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK
| | | | | |
Collapse
|
33
|
Abstract
Whole genome duplication events are thought to have substantially contributed to organismal complexity, largely via divergent transcriptional regulation. Members of the vertebrate PAX2, PAX5 and PAX8 gene subfamily derived from an ancient class of paired box genes and arose from such whole genome duplication events. These genes are critical in establishing the midbrain-hindbrain boundary, specifying interneuron populations and for eye, ear and kidney development. Also PAX2 has adopted a unique role in pancreas development, whilst PAX5 is essential for early B-cell differentiation. The contribution of PAX258 genes to their collective role has diverged across paralogues and the animal lineages, resulting in a complex wealth of literature. It is now timely to provide a comprehensive comparative overview of these genes and their ancient and divergent roles. We also discuss their fundamental place within gene regulatory networks and the likely influence of cis-regulatory elements over their differential roles during early animal development.
Collapse
Affiliation(s)
- Debbie K Goode
- Queen Mary, University of London, School of Biological and Chemical Sciences, London, United Kingdom
| | | |
Collapse
|
34
|
McEwen GK, Goode DK, Parker HJ, Woolfe A, Callaway H, Elgar G. Early evolution of conserved regulatory sequences associated with development in vertebrates. PLoS Genet 2009; 5:e1000762. [PMID: 20011110 PMCID: PMC2781166 DOI: 10.1371/journal.pgen.1000762] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [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: 07/22/2009] [Accepted: 11/10/2009] [Indexed: 01/22/2023] Open
Abstract
Comparisons between diverse vertebrate genomes have uncovered thousands of highly conserved non-coding sequences, an increasing number of which have been shown to function as enhancers during early development. Despite their extreme conservation over 500 million years from humans to cartilaginous fish, these elements appear to be largely absent in invertebrates, and, to date, there has been little understanding of their mode of action or the evolutionary processes that have modelled them. We have now exploited emerging genomic sequence data for the sea lamprey, Petromyzon marinus, to explore the depth of conservation of this type of element in the earliest diverging extant vertebrate lineage, the jawless fish (agnathans). We searched for conserved non-coding elements (CNEs) at 13 human gene loci and identified lamprey elements associated with all but two of these gene regions. Although markedly shorter and less well conserved than within jawed vertebrates, identified lamprey CNEs are able to drive specific patterns of expression in zebrafish embryos, which are almost identical to those driven by the equivalent human elements. These CNEs are therefore a unique and defining characteristic of all vertebrates. Furthermore, alignment of lamprey and other vertebrate CNEs should permit the identification of persistent sequence signatures that are responsible for common patterns of expression and contribute to the elucidation of the regulatory language in CNEs. Identifying the core regulatory code for development, common to all vertebrates, provides a foundation upon which regulatory networks can be constructed and might also illuminate how large conserved regulatory sequence blocks evolve and become fixed in genomic DNA. Recent comparative analyses of vertebrate genomes has resulted in the identification of highly conserved non-coding sequences near genes that coordinate early development. Many of these sequences can activate gene expression and are thought to be important regulatory elements. Surprisingly, a large set of these long, near-identical sequences is found in every jawed vertebrate, including sharks, yet almost completely absent in non-vertebrates. This study looks for this set of sequences in the lamprey, a representative of our most distant vertebrate relatives, in order to determine when and how such a large set of important non-coding regulatory sequences became established in the genome. Although the lamprey divergence is only a little older than the divergence of cartilaginous fish (including sharks), relatively few, and considerably shorter, conserved non-coding sequences are identifiable. Nevertheless, these shorter lamprey sequences are capable of driving gene expression in a precise spatial pattern in zebrafish embryos in the same way as the equivalent human elements. This analysis has shed light on the emergence of these regulatory sequences during early vertebrate evolution, at a time of whole-genome duplications and considerable morphological variation, consistent with a role for these sequences in directing gene regulatory networks for vertebrate development.
Collapse
Affiliation(s)
- Gayle K. McEwen
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Debbie K. Goode
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Hugo J. Parker
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Adam Woolfe
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Heather Callaway
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Greg Elgar
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- * E-mail:
| |
Collapse
|
35
|
Elgar G. Pan-vertebrate conserved non-coding sequences associated with developmental regulation. Briefings in Functional Genomics and Proteomics 2009; 8:256-65. [DOI: 10.1093/bfgp/elp033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
36
|
Elgar G. What is systems biology? Brief Funct Genomic Proteomic 2008; 7:237-8. [PMID: 18621799 DOI: 10.1093/bfgp/eln036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
37
|
Elgar G, Vavouri T. Tuning in to the signals: noncoding sequence conservation in vertebrate genomes. Trends Genet 2008; 24:344-52. [PMID: 18514361 DOI: 10.1016/j.tig.2008.04.005] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 04/14/2008] [Accepted: 04/14/2008] [Indexed: 01/25/2023]
|
38
|
Abstract
Sequence conservation has traditionally been used as a means to target functional regions of complex genomes. In addition to its use in identifying coding regions of genes, the recent availability of whole genome data for a number of vertebrates has permitted high-resolution analyses of the noncoding "dark matter" of the genome. This has resulted in the identification of a large number of highly conserved sequence elements that appear to be preserved in all bony vertebrates. Further positional analysis of these conserved noncoding elements (CNEs) in the genome demonstrates that they cluster around genes involved in developmental regulation. This chapter describes the identification and characterization of these elements, with particular reference to their composition and organization.
Collapse
Affiliation(s)
- Adam Woolfe
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, United Kingdom
| | | |
Collapse
|
39
|
Lin C, Zhang T, Elgar G, Rawson DM. 122. Initial studies on cryopreservation and gene expression in isolated blastomeres of zebrafish (Danio rerio). Cryobiology 2007. [DOI: 10.1016/j.cryobiol.2007.10.125] [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: 11/24/2022]
|
40
|
Cardoso JCR, de Vet ECJM, Louro B, Elgar G, Clark MS, Power DM. Persistence of duplicated PAC1 receptors in the teleost, Sparus auratus. BMC Evol Biol 2007; 7:221. [PMID: 17997850 PMCID: PMC2245808 DOI: 10.1186/1471-2148-7-221] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [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: 06/06/2007] [Accepted: 11/12/2007] [Indexed: 12/05/2022] Open
Abstract
Background: Duplicated genes are common in vertebrate genomes. Their persistence is assumed to be either a consequence of gain of novel function (neofunctionalisation) or partitioning of the function of the ancestral molecule (sub-functionalisation). Surprisingly few studies have evaluated the extent of such modifications despite the numerous duplicated receptor and ligand genes identified in vertebrate genomes to date. In order to study the importance of function in the maintenance of duplicated genes, sea bream (Sparus auratus) PAC1 receptors, sequence homologues of the mammalian receptor specific for PACAP (Pituitary Adenylate Cyclase-Activating Polypeptide), were studied. These receptors belong to family 2 GPCRs and most of their members are duplicated in teleosts although the reason why both persist in the genome is unknown. Results: Duplicate sea bream PACAP receptor genes (sbPAC1A and sbPAC1B), members of family 2 GPCRs, were isolated and share 77% amino acid sequence identity. RT-PCR with specific primers for each gene revealed that they have a differential tissue distribution which overlaps with the distribution of the single mammalian receptor. Furthermore, in common with mammals, the teleost genes undergo alternative splicing and a PAC1Ahop1 isoform has been characterised. Duplicated orthologous receptors have also been identified in other teleost genomes and their distribution profile suggests that function may be species specific. Functional analysis of the paralogue sbPAC1s in Cos7 cells revealed that they are strongly stimulated in the presence of mammalian PACAP27 and PACAP38 and far less with VIP (Vasoactive Intestinal Peptide). The sbPAC1 receptors are equally stimulated (LOGEC50 values for maximal cAMP production) in the presence of PACAP27 (-8.74 ± 0.29 M and -9.15 ± 0.21 M, respectively for sbPAC1A and sbPAC1B, P > 0.05) and PACAP38 (-8.54 ± 0.18 M and -8.92 ± 0.24 M, respectively for sbPAC1A and sbPAC1B, P > 0.05). Human VIP was found to stimulate sbPAC1A (-7.23 ± 0.20 M) more strongly than sbPAC1B (-6.57 ± 0.14 M, P < 0.05) and human secretin (SCT), which has not so far been identified in fish genomes, caused negligible stimulation of both receptors. Conclusion: The existence of functionally divergent duplicate sbPAC1 receptors is in line with previously proposed theories about the origin and maintenance of duplicated genes. Sea bream PAC1 duplicate receptors resemble the typical mammalian PAC1, and PACAP peptides were found to be more effective than VIP in stimulating cAMP production, although sbPAC1A was more responsive for VIP than sbPAC1B. These results together with the highly divergent pattern of tissue distribution suggest that a process involving neofunctionalisation occurred after receptor duplication within the fish lineage and probably accounts for their persistence in the genome. The characterisation of further duplicated receptors and their ligands should provide insights into the evolution and function of novel protein-protein interactions associated with the vertebrate radiation.
Collapse
Affiliation(s)
- João C R Cardoso
- CCMAR, Molecular and Comparative Endocrinology, University of Algarve, 8005-139 Faro, Portugal.
| | | | | | | | | | | |
Collapse
|
41
|
Woolfe A, Elgar G. Comparative genomics using Fugu reveals insights into regulatory subfunctionalization. Genome Biol 2007; 8:R53. [PMID: 17428329 PMCID: PMC1896008 DOI: 10.1186/gb-2007-8-4-r53] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Revised: 03/06/2007] [Accepted: 04/11/2007] [Indexed: 02/04/2023] Open
Abstract
Fish-mammal genomic alignments were used to compare over 800 conserved non-coding elements that associate with genes that have undergone fish-specific duplication and retention, revealing a pattern of element retention and loss between paralogs indicative of subfunctionalization. Background A major mechanism for the preservation of gene duplicates in the genome is thought to be mediated via loss or modification of cis-regulatory subfunctions between paralogs following duplication (a process known as regulatory subfunctionalization). Despite a number of gene expression studies that support this mechanism, no comprehensive analysis of regulatory subfunctionalization has been undertaken at the level of the distal cis-regulatory modules involved. We have exploited fish-mammal genomic alignments to identify and compare more than 800 conserved non-coding elements (CNEs) that associate with genes that have undergone fish-specific duplication and retention. Results Using the abundance of duplicated genes within the Fugu genome, we selected seven pairs of teleost-specific paralogs involved in early vertebrate development, each containing clusters of CNEs in their vicinity. CNEs present around each Fugu duplicated gene were identified using multiple alignments of orthologous regions between single-copy mammalian orthologs (representing the ancestral locus) and each fish duplicated region in turn. Comparative analysis reveals a pattern of element retention and loss between paralogs indicative of subfunctionalization, the extent of which differs between duplicate pairs. In addition to complete loss of specific regulatory elements, a number of CNEs have been retained in both regions but may be responsible for more subtle levels of subfunctionalization through sequence divergence. Conclusion Comparative analysis of conserved elements between duplicated genes provides a powerful approach for studying regulatory subfunctionalization at the level of the regulatory elements involved.
Collapse
Affiliation(s)
- Adam Woolfe
- School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
- Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, MD 20870, USA
| | - Greg Elgar
- School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| |
Collapse
|
42
|
Ikeda D, Ono Y, Snell P, Edwards YJK, Elgar G, Watabe S. Divergent evolution of the myosin heavy chain gene family in fish and tetrapods: evidence from comparative genomic analysis. Physiol Genomics 2007; 32:1-15. [PMID: 17940200 DOI: 10.1152/physiolgenomics.00278.2006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Myosin heavy chain genes (MYHs) are the most important functional domains of myosins, which are highly conserved throughout evolution. The human genome contains 15 MYHs, whereas the corresponding number in teleost appears to be much higher. Although teleosts comprise more than one-half of all vertebrate species, our knowledge of MYHs in teleosts is rather limited. A comprehensive analysis of the torafugu (Takifugu rubripes) genome database enabled us to detect at least 28 MYHs, almost twice as many as in humans. RT-PCR revealed that at least 16 torafugu MYH representatives (5 fast skeletal, 3 cardiac, 2 slow skeletal, 1 superfast, 2 smooth, and 3 nonmuscle types) are actually transcribed. Among these, MYH(M743-2) and MYH(M5) of fast and slow skeletal types, respectively, are expressed during development of torafugu embryos. Syntenic analysis reveals that torafugu fast skeletal MYHs are distributed across five genomic regions, three of which form clusters. Interestingly, while human fast skeletal MYHs form one cluster, its syntenic region in torafugu is duplicated, although each locus contains just a single MYH in torafugu. The results of the syntenic analysis were further confirmed by corresponding analysis of MYHs based on databases from Tetraodon, zebrafish, and medaka genomes. Phylogenetic analysis suggests that fast skeletal MYHs evolved independently in teleosts and tetrapods after fast skeletal MYHs had diverged from four ancestral MYHs.
Collapse
Affiliation(s)
- Daisuke Ikeda
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
| | | | | | | | | | | |
Collapse
|
43
|
Paparidis Z, Abbasi AA, Malik S, Goode DK, Callaway H, Elgar G, deGraaff E, Lopez-Rios J, Zeller R, Grzeschik KH. Ultraconserved non-coding sequence element controls a subset of spatiotemporal GLI3 expression. Dev Growth Differ 2007; 49:543-53. [PMID: 17661744 DOI: 10.1111/j.1440-169x.2007.00954.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The zinc-finger transcription factor GLI3 acts during vertebrate development in a combinatorial, context-dependent fashion as a primary transducer of sonic hedgehog (SHH) signaling. In humans, mutations affecting this key regulator of development are associated with GLI3-morphopathies, a group of congenital malformations in which forebrain and limb development are preferentially affected. We show that a non-coding element from intron two of GLI3, ultraconserved in mammals and highly conserved in the pufferfish Fugu, is a transcriptional enhancer. In transient transfection assays, it activates reporter gene transcription in human cell cultures expressing endogenous GLI3 but not in GLI3 negative cells. The identified enhancer element is predicted to contain conserved binding sites for transcription factors crucial for developmental steps in which GLI3 is involved. The regulatory potential of this element is conserved and was used to direct tissue-specific expression of a green fluorescent protein reporter gene in zebrafish embryos and of a beta-galactosidase reporter in transgenic mouse embryos. Time, location, and quantity of reporter gene expression are congruent with part of the pattern previously reported for endogenous GLI3 transcription.
Collapse
Affiliation(s)
- Zissis Paparidis
- Institute of Human Genetics, Philipps-University, Bahnhofstrasse 7, D35037 Marburg, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Elgar G. Editorial. Briefings in Functional Genomics and Proteomics 2007. [DOI: 10.1093/bfgp/elm019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
45
|
Woolfe A, Goode DK, Cooke J, Callaway H, Smith S, Snell P, McEwen GK, Elgar G. CONDOR: a database resource of developmentally associated conserved non-coding elements. BMC Dev Biol 2007; 7:100. [PMID: 17760977 PMCID: PMC2020477 DOI: 10.1186/1471-213x-7-100] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2007] [Accepted: 08/30/2007] [Indexed: 12/04/2022]
Abstract
Background Comparative genomics is currently one of the most popular approaches to study the regulatory architecture of vertebrate genomes. Fish-mammal genomic comparisons have proved powerful in identifying conserved non-coding elements likely to be distal cis-regulatory modules such as enhancers, silencers or insulators that control the expression of genes involved in the regulation of early development. The scientific community is showing increasing interest in characterizing the function, evolution and language of these sequences. Despite this, there remains little in the way of user-friendly access to a large dataset of such elements in conjunction with the analysis and the visualization tools needed to study them. Description Here we present CONDOR (COnserved Non-coDing Orthologous Regions) available at: . In an interactive and intuitive way the website displays data on > 6800 non-coding elements associated with over 120 early developmental genes and conserved across vertebrates. The database regularly incorporates results of ongoing in vivo zebrafish enhancer assays of the CNEs carried out in-house, which currently number ~100. Included and highlighted within this set are elements derived from duplication events both at the origin of vertebrates and more recently in the teleost lineage, thus providing valuable data for studying the divergence of regulatory roles between paralogs. CONDOR therefore provides a number of tools and facilities to allow scientists to progress in their own studies on the function and evolution of developmental cis-regulation. Conclusion By providing access to data with an approachable graphics interface, the CONDOR database presents a rich resource for further studies into the regulation and evolution of genes involved in early development.
Collapse
Affiliation(s)
- Adam Woolfe
- School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
- Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, MD 20870, USA
| | - Debbie K Goode
- School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Julie Cooke
- School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Heather Callaway
- School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Sarah Smith
- School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Phil Snell
- School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Gayle K McEwen
- School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
- Genomic Functional Analysis Section, National Human Genome Research Institute, National Institutes of Health, Rockville, MD 20870, USA
| | - Greg Elgar
- School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| |
Collapse
|
46
|
Abbasi AA, Paparidis Z, Malik S, Goode DK, Callaway H, Elgar G, Grzeschik KH. Human GLI3 intragenic conserved non-coding sequences are tissue-specific enhancers. PLoS One 2007; 2:e366. [PMID: 17426814 PMCID: PMC1838922 DOI: 10.1371/journal.pone.0000366] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Accepted: 03/19/2007] [Indexed: 11/19/2022] Open
Abstract
The zinc-finger transcription factor GLI3 is a key regulator of development, acting as a primary transducer of Sonic hedgehog (SHH) signaling in a combinatorial context dependent fashion controlling multiple patterning steps in different tissues/organs. A tight temporal and spatial control of gene expression is indispensable, however, cis-acting sequence elements regulating GLI3 expression have not yet been reported. We show that 11 ancient genomic DNA signatures, conserved from the pufferfish Takifugu (Fugu) rubripes to man, are distributed throughout the introns of human GLI3. They map within larger conserved non-coding elements (CNEs) that are found in the tetrapod lineage. Full length CNEs transiently transfected into human cell cultures acted as cell type specific enhancers of gene transcription. The regulatory potential of these elements is conserved and was exploited to direct tissue specific expression of a reporter gene in zebrafish embryos. Assays of deletion constructs revealed that the human-Fugu conserved sequences within the GLI3 intronic CNEs were essential but not sufficient for full-scale transcriptional activation. The enhancer activity of the CNEs is determined by a combinatorial effect of a core sequence conserved between human and teleosts (Fugu) and flanking tetrapod-specific sequences, suggesting that successive clustering of sequences with regulatory potential around an ancient, highly conserved nucleus might be a possible mechanism for the evolution of cis-acting regulatory elements.
Collapse
Affiliation(s)
- Amir Ali Abbasi
- Institute of Human Genetics, Philipps-University, Marburg, Germany
| | - Zissis Paparidis
- Institute of Human Genetics, Philipps-University, Marburg, Germany
| | - Sajid Malik
- Institute of Human Genetics, Philipps-University, Marburg, Germany
| | - Debbie K. Goode
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Heather Callaway
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Greg Elgar
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Karl-Heinz Grzeschik
- Institute of Human Genetics, Philipps-University, Marburg, Germany
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
47
|
Elgar G. Editorial. Briefings in Functional Genomics and Proteomics 2007. [DOI: 10.1093/bfgp/elm016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
48
|
Vavouri T, Walter K, Gilks WR, Lehner B, Elgar G. Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. Genome Biol 2007; 8:R15. [PMID: 17274809 PMCID: PMC1852409 DOI: 10.1186/gb-2007-8-2-r15] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 10/20/2006] [Accepted: 02/02/2007] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The human genome contains thousands of non-coding sequences that are often more conserved between vertebrate species than protein-coding exons. These highly conserved non-coding elements (CNEs) are associated with genes that coordinate development, and have been proposed to act as transcriptional enhancers. Despite their extreme sequence conservation in vertebrates, sequences homologous to CNEs have not been identified in invertebrates. RESULTS Here we report that nematode genomes contain an alternative set of CNEs that share sequence characteristics, but not identity, with their vertebrate counterparts. CNEs thus represent a very unusual class of sequences that are extremely conserved within specific animal lineages yet are highly divergent between lineages. Nematode CNEs are also associated with developmental regulatory genes, and include well-characterized enhancers and transcription factor binding sites, supporting the proposed function of CNEs as cis-regulatory elements. Most remarkably, 40 of 156 human CNE-associated genes with invertebrate orthologs are also associated with CNEs in both worms and flies. CONCLUSION A core set of genes that regulate development is associated with CNEs across three animal groups (worms, flies and vertebrates). We propose that these CNEs reflect the parallel evolution of alternative enhancers for a common set of developmental regulatory genes in different animal groups. This 're-wiring' of gene regulatory networks containing key developmental coordinators was probably a driving force during the evolution of animal body plans. CNEs may, therefore, represent the genomic traces of these 'hard-wired' core gene regulatory networks that specify the development of each alternative animal body plan.
Collapse
Affiliation(s)
- Tanya Vavouri
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | - Klaudia Walter
- MRC Biostatistics Unit, Institute of Public Health, Cambridge CB2 2SR, UK
| | - Walter R Gilks
- Department of Statistics, University of Leeds, Leeds LS2 9JT, UK
| | - Ben Lehner
- EMBL/CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), UPF, C/Dr. Aiguader 88, Barcelona 08003, Spain
| | - Greg Elgar
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| |
Collapse
|
49
|
Abstract
There is undeniable value in using sequence comparison to identify putative regulatory sequences. However, a recent report has demonstrated that not all regulatory sequences are evolutionarily conserved. Cis-acting sequences around the RET gene, conserved in mammals but not in fish, are able to reproduce patterns of RET expression in zebrafish embryos. It is as yet unclear whether these sequences are 'below the radar' of current sequence alignment tools or whether their functional homology is not sequence based.
Collapse
Affiliation(s)
- Greg Elgar
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
| |
Collapse
|
50
|
Elgar G. Editorial. Briefings in Functional Genomics and Proteomics 2006. [DOI: 10.1093/bfgp/ell037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|