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Cortes DRE, Stapleton MC, Schwab KE, West D, Coulson NW, O’Donnell MG, Christodoulou AG, Powers RW, Wu YL. Modeling normal mouse uterine contraction and placental perfusion with non-invasive longitudinal dynamic contrast enhancement MRI. PLoS One 2024; 19:e0303957. [PMID: 38950083 PMCID: PMC11216620 DOI: 10.1371/journal.pone.0303957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 05/05/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND The placenta is a transient organ critical for fetal development. Disruptions of normal placental functions can impact health throughout an individual's entire life. Although being recognized by the NIH Human Placenta Project as an important organ, the placenta remains understudied, partly because of a lack of non-invasive tools for longitudinally evaluation for key aspects of placental functionalities. OBJECTIVE Our goal is to create a non-invasive preclinical imaging pipeline that can longitudinally probe murine placental health in vivo. We use advanced imaging processing schemes to establish functional biomarkers for non-invasive longitudinal evaluation of placental development. METHODOLOGY We implement dynamic contrast enhancement magnetic resonance imaging (DCE-MRI) and analysis pipeline to quantify uterine contraction and placental perfusion dynamics. We use optic flow and time-frequency analysis to quantify and characterize contraction-related placental motion. Our novel imaging and analysis pipeline uses subcutaneous administration of gadolinium for steepest slope-based perfusion evaluation, enabling non-invasive longitudinal monitoring. RESULTS We demonstrate that the placenta exhibits spatially asymmetric contractile motion that develops from E14.5 to E17.5. Additionally, we see that placental perfusion, perfusion delivery rate, and substrate delivery all increase from E14.5 to E17.5, with the High Perfusion Chamber (HPC) leading the placental changes that occur from E14.5 to E17.5. DISCUSSION We advance the placental perfusion chamber paradigm with a novel, physiologically based threshold model for chamber localization and demonstrate spatially varying placental chambers using multiple functional metrics that assess mouse placental development and remodeling throughout gestation. CONCLUSION Our pipeline enables the non-invasive, longitudinal assessment of multiple placenta functions from a single imaging session. Our pipeline serves as a key toolbox for advancing research in mouse models of placental disease and disorder.
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Affiliation(s)
- Devin Raine Everaldo Cortes
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Margaret C. Stapleton
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Kristina E. Schwab
- Rangos Research Center Animal Imaging Core, Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States of America
| | - Dalton West
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Noah W. Coulson
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States of America
| | | | - Anthony G. Christodoulou
- Department of Radiological Sciences and Engineering, University of California, Los Angeles, California, United States of America
| | - Robert W. Powers
- Magee-Womens Research Institute, Pittsburgh, PA, United States of America
| | - Yijen L. Wu
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, United States of America
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States of America
- Rangos Research Center Animal Imaging Core, Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States of America
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2
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Cortes DRE, Stapleton MC, Schwab KE, West D, Coulson NW, O'Donnell MG, Powers RW, Wu YL. Modeling Normal Mouse Uterine Contraction and Placental Perfusion with Non-invasive Longitudinal Dynamic Contrast Enhancement MRI. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.577398. [PMID: 38352563 PMCID: PMC10862875 DOI: 10.1101/2024.01.31.577398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
The placenta is a transient organ critical for fetal development. Disruptions of normal placental functions can impact health throughout an individual's entire life. Although being recognized by the NIH Human Placenta Project as an important organ, the placenta remains understudied, partly because of a lack of non-invasive tools for longitudinally evaluation for key aspects of placental functionalities. Non-invasive imaging that can longitudinally probe murine placental health in vivo are critical to understanding placental development throughout pregnancy. We developed advanced imaging processing schemes to establish functional biomarkers for non-invasive longitudinal evaluation of placental development. We developed a dynamic contrast enhancement magnetic resonance imaging (DCE-MRI) pipeline combined with advanced image process methods to model uterine contraction and placental perfusion dynamics. Our novel imaging pipeline uses subcutaneous administration of gadolinium for steepest-slope based perfusion evaluation. This enables non-invasive longitudinal monitoring. Additionally, we advance the placental perfusion chamber paradigm with a novel physiologically-based threshold model for chamber localization and demonstrate spatially varying placental chambers using multiple functional metrics that assess mouse placental development and continuing remodeling throughout gestation. Lastly, using optic flow to quantify placental motions arisen from uterine contractions in conjunction with time-frequency analysis, we demonstrated that the placenta exhibited asymmetric contractile motion.
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Affiliation(s)
- Devin Raine Everaldo Cortes
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA
- Rangos Research Center Animal Imaging Core, Children's Hospital of Pittsburgh, PA
| | - Margaret C Stapleton
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA
- Rangos Research Center Animal Imaging Core, Children's Hospital of Pittsburgh, PA
| | - Kristina E Schwab
- Rangos Research Center Animal Imaging Core, Children's Hospital of Pittsburgh, PA
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA
| | - Dalton West
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA
| | - Noah W Coulson
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA
| | | | | | - Yijen L Wu
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA
- Rangos Research Center Animal Imaging Core, Children's Hospital of Pittsburgh, PA
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA
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3
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Huth EA, Zhao X, Owen N, Luna PN, Vogel I, Dorf ILH, Joss S, Clayton-Smith J, Parker MJ, Louw JJ, Gewillig M, Breckpot J, Kraus A, Sasaki E, Kini U, Burgess T, Tan TY, Armstrong R, Neas K, Ferrero GB, Brusco A, Kerstjens-Frederikse WS, Rankin J, Helvaty LR, Landis BJ, Geddes GC, McBride KL, Ware SM, Shaw CA, Lalani SR, Rosenfeld JA, Scott DA. Clinical exome sequencing efficacy and phenotypic expansions involving anomalous pulmonary venous return. Eur J Hum Genet 2023; 31:1430-1439. [PMID: 37673932 PMCID: PMC10689790 DOI: 10.1038/s41431-023-01451-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/08/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023] Open
Abstract
Anomalous pulmonary venous return (APVR) frequently occurs with other congenital heart defects (CHDs) or extra-cardiac anomalies. While some genetic causes have been identified, the optimal approach to genetic testing in individuals with APVR remains uncertain, and the etiology of most cases of APVR is unclear. Here, we analyzed molecular data from 49 individuals to determine the diagnostic yield of clinical exome sequencing (ES) for non-isolated APVR. A definitive or probable diagnosis was made for 8 of those individuals yielding a diagnostic efficacy rate of 16.3%. We then analyzed molecular data from 62 individuals with APVR accrued from three databases to identify novel APVR genes. Based on data from this analysis, published case reports, mouse models, and/or similarity to known APVR genes as revealed by a machine learning algorithm, we identified 3 genes-EFTUD2, NAA15, and NKX2-1-for which there is sufficient evidence to support phenotypic expansion to include APVR. We also provide evidence that 3 recurrent copy number variants contribute to the development of APVR: proximal 1q21.1 microdeletions involving RBM8A and PDZK1, recurrent BP1-BP2 15q11.2 deletions, and central 22q11.2 deletions involving CRKL. Our results suggest that ES and chromosomal microarray analysis (or genome sequencing) should be considered for individuals with non-isolated APVR for whom a genetic etiology has not been identified, and that genetic testing to identify an independent genetic etiology of APVR is not warranted in individuals with EFTUD2-, NAA15-, and NKX2-1-related disorders.
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Affiliation(s)
- Emily A Huth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, USA
| | - Nichole Owen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, USA
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ida Vogel
- Department of Clinical Medicine, Aarhus University, 8000, Aarhus, C, Denmark
| | - Inger L H Dorf
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Shelagh Joss
- West of Scotland Genomics Service, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK
| | - Jill Clayton-Smith
- Manchester Centre For Genomic Medicine, Manchester University Hospitals, Manchester, M13 9WL, UK
- University of Manchester, Manchester, M13 9PL, UK
| | - Michael J Parker
- Department of Clinical Genetics, Sheffield, Children's Hospital, UK
| | - Jacoba J Louw
- Pediatric Cardiology Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Marc Gewillig
- Department of Cardiovascular Sciences KU Leuven, Leuven, Belgium
- Pediatric Cardiology University Hospitals Leuven, Leuven, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals Leuven, Catholic University, Leuven, Belgium
| | - Alison Kraus
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, LS7 4SA, UK
| | - Erina Sasaki
- Oxford Centre for Genomic Medicine, Oxford University Hospital, Oxford, OX3 7HE, UK
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospital, Oxford, OX3 7HE, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | - Trent Burgess
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Ruth Armstrong
- East Anglian Medical Genetics Service, Addenbrooke's Treatment Centre, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | | | - Giovanni B Ferrero
- Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
- Città della Salute e della Scienza University Hospital, Torino, Italy
| | | | | | | | | | - Gabrielle C Geddes
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kim L McBride
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, OH, USA
| | - Stephanie M Ware
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.
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4
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Wang B, Irizar H, Thygesen JH, Zartaloudi E, Austin-Zimmerman I, Bhat A, Harju-Seppänen J, Pain O, Bass N, Gkofa V, Alizadeh BZ, van Amelsvoort T, Arranz MJ, Bender S, Cahn W, Stella Calafato M, Crespo-Facorro B, Di Forti M, Giegling I, de Haan L, Hall J, Hall MH, van Haren N, Iyegbe C, Kahn RS, Kravariti E, Lawrie SM, Lin K, Luykx JJ, Mata I, McDonald C, McIntosh AM, Murray RM, Picchioni M, Powell J, Prata DP, Rujescu D, Rutten BPF, Shaikh M, Simons CJP, Toulopoulou T, Weisbrod M, van Winkel R, Kuchenbaecker K, McQuillin A, Bramon E. Psychosis Endophenotypes: A Gene-Set-Specific Polygenic Risk Score Analysis. Schizophr Bull 2023; 49:1625-1636. [PMID: 37582581 PMCID: PMC10686343 DOI: 10.1093/schbul/sbad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
BACKGROUND AND HYPOTHESIS Endophenotypes can help to bridge the gap between psychosis and its genetic predispositions, but their underlying mechanisms remain largely unknown. This study aims to identify biological mechanisms that are relevant to the endophenotypes for psychosis, by partitioning polygenic risk scores into specific gene sets and testing their associations with endophenotypes. STUDY DESIGN We computed polygenic risk scores for schizophrenia and bipolar disorder restricted to brain-related gene sets retrieved from public databases and previous publications. Three hundred and seventy-eight gene-set-specific polygenic risk scores were generated for 4506 participants. Seven endophenotypes were also measured in the sample. Linear mixed-effects models were fitted to test associations between each endophenotype and each gene-set-specific polygenic risk score. STUDY RESULTS After correction for multiple testing, we found that a reduced P300 amplitude was associated with a higher schizophrenia polygenic risk score of the forebrain regionalization gene set (mean difference per SD increase in the polygenic risk score: -1.15 µV; 95% CI: -1.70 to -0.59 µV; P = 6 × 10-5). The schizophrenia polygenic risk score of forebrain regionalization also explained more variance of the P300 amplitude (R2 = 0.032) than other polygenic risk scores, including the genome-wide polygenic risk scores. CONCLUSIONS Our finding on reduced P300 amplitudes suggests that certain genetic variants alter early brain development thereby increasing schizophrenia risk years later. Gene-set-specific polygenic risk scores are a useful tool to elucidate biological mechanisms of psychosis and endophenotypes, offering leads for experimental validation in cellular and animal models.
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Affiliation(s)
- Baihan Wang
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Haritz Irizar
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Johan H Thygesen
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
- Institute of Health Informatics, University College London, London, UK
| | - Eirini Zartaloudi
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
| | - Isabelle Austin-Zimmerman
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Anjali Bhat
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
| | - Jasmine Harju-Seppänen
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
| | - Oliver Pain
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Nick Bass
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
| | - Vasiliki Gkofa
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
| | - Behrooz Z Alizadeh
- University of Groningen, University Medical Center Groningen, University Center for Psychiatry, Rob Giel Research Center, Groningen, The Netherlands
- Department of Epidemiology, University Medical Center Groningen, Groningen, The Netherlands
| | - Therese van Amelsvoort
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Maria J Arranz
- Fundació Docència i Recerca Mutua Terrassa, Terrassa, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Institut de Recerca Biomédica Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Stephan Bender
- Department of Child and Adolescent Psychiatry, Psychosomatic Medicine and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Wiepke Cahn
- Department of Psychiatry, Brain Centre Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Altrecht, General Mental Health Care, Utrecht, The Netherlands
| | - Maria Stella Calafato
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
| | - Benedicto Crespo-Facorro
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Sevilla, Spain
- Department of Psychiatry, University Hospital Virgen del Rocio, School of Medicine, University of Sevilla–IBiS, Sevilla, Spain
| | - Marta Di Forti
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | | | - Ina Giegling
- Comprehensive Centers for Clinical Neurosciences and Mental Health (C3NMH), Medical University of Vienna, Austria
| | - Lieuwe de Haan
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Arkin, Institute for Mental Health, Amsterdam, The Netherlands
| | - Jeremy Hall
- Neuroscience and Mental Health Innovation Institute, School of Medicine, Cardiff University, Hadyn Ellis Building, Mandy Road, Cardiff, UK
| | - Mei-Hua Hall
- Psychosis Neurobiology Laboratory, Harvard Medical School, McLean Hospital, Belmont, MA, USA
| | - Neeltje van Haren
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Sophia’s Children Hospital, Rotterdam, The Netherlands
| | - Conrad Iyegbe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - René S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eugenia Kravariti
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Stephen M Lawrie
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jurjen J Luykx
- Department of Psychiatry, Brain Centre Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ignacio Mata
- Fundacion Argibide, Pamplona, Spain
- CIBERSAM, Centro Investigación Biomédica en Red Salud Mental, Madrid, Spain
| | - Colm McDonald
- The Centre for Neuroimaging & Cognitive Genomics (NICOG) and NCBES Galway Neuroscience Centre, University of Galway, Galway, Ireland
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Robin M Murray
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | | | - Marco Picchioni
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- St Magnus Hospital, Surrey, UK
| | - John Powell
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
| | - Diana P Prata
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- Instituto de Biofísica e Engenharia Biomédica, Faculdade de Ciencias da Universidade de Lisboa, Portugal
| | - Dan Rujescu
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Division of General Psychiatry, Medical University of Vienna, Austria
| | - Bart P F Rutten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Madiha Shaikh
- North East London Foundation Trust, London, UK
- Research Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | - Claudia J P Simons
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Center, Maastricht, The Netherlands
- GGzE Institute for Mental Health Care, Eindhoven, The Netherlands
| | - Timothea Toulopoulou
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- Interdisciplinary Program in Neuroscience, Aysel Sabuncu Brain Research Center, Bilkent University, Ankara, Türkiye
- National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara, Türkiye
- Department of Psychology, Bilkent University, Ankara, Türkiye
- School of Medicine, Department of Psychiatry, National and Kapodistrian University of Athens, Athens, Greece
- Department of Psychiatry and Behavioral Health System, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Matthias Weisbrod
- Department of General Psychiatry, Center of Psychosocial Medicine, University of Heidelberg, Germany
- SRH Klinikum, Karlsbad-Langensteinbach, Germany
| | - Ruud van Winkel
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Center, Maastricht, The Netherlands
- KU Leuven, Department of Neuroscience, Research Group Psychiatry, Leuven, Belgium
| | - Karoline Kuchenbaecker
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
- UCL Genetics Institute, Division of Biosciences, University College London, London, UK
| | - Andrew McQuillin
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
| | - Elvira Bramon
- Department of Mental Health Neuroscience, Division of Psychiatry, University College London, London, UK
- Institute of Cognitive Neuroscience, University College London, London, UK
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5
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Weeks EM, Ulirsch JC, Cheng NY, Trippe BL, Fine RS, Miao J, Patwardhan TA, Kanai M, Nasser J, Fulco CP, Tashman KC, Aguet F, Li T, Ordovas-Montanes J, Smillie CS, Biton M, Shalek AK, Ananthakrishnan AN, Xavier RJ, Regev A, Gupta RM, Lage K, Ardlie KG, Hirschhorn JN, Lander ES, Engreitz JM, Finucane HK. Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases. Nat Genet 2023; 55:1267-1276. [PMID: 37443254 PMCID: PMC10836580 DOI: 10.1038/s41588-023-01443-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 06/09/2023] [Indexed: 07/15/2023]
Abstract
Genome-wide association studies (GWASs) are a valuable tool for understanding the biology of complex human traits and diseases, but associated variants rarely point directly to causal genes. In the present study, we introduce a new method, polygenic priority score (PoPS), that learns trait-relevant gene features, such as cell-type-specific expression, to prioritize genes at GWAS loci. Using a large evaluation set of genes with fine-mapped coding variants, we show that PoPS and the closest gene individually outperform other gene prioritization methods, but observe the best overall performance by combining PoPS with orthogonal methods. Using this combined approach, we prioritize 10,642 unique gene-trait pairs across 113 complex traits and diseases with high precision, finding not only well-established gene-trait relationships but nominating new genes at unresolved loci, such as LGR4 for estimated glomerular filtration rate and CCR7 for deep vein thrombosis. Overall, we demonstrate that PoPS provides a powerful addition to the gene prioritization toolbox.
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Affiliation(s)
- Elle M Weeks
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Jacob C Ulirsch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
- Artificial Intelligence Laboratory, Illumina, Inc., San Diego, CA, USA
| | | | - Brian L Trippe
- Program in Computational & Systems Biology, MIT, Cambridge, MA, USA
- Computer Science & Artificial Intelligence Lab, MIT, Cambridge, MA, USA
| | - Rebecca S Fine
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Vertex Pharmaceuticals Incorporated, Boston, MA, USA
| | - Jenkai Miao
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Tejal A Patwardhan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Masahiro Kanai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, MGH, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Joseph Nasser
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Bristol Myers Squibb, Cambridge, MA, USA
| | | | | | - Taibo Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MD-PhD Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jose Ordovas-Montanes
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Program in Immunology, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Christopher S Smillie
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Computational & Systems Biology, MIT, Cambridge, MA, USA
| | - Moshe Biton
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, MGH, Boston, MA, USA
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Department of Chemistry, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Ragon Institute of MGH, MMIT, Cambridge, MA, USA
| | - Ashwin N Ananthakrishnan
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, MGH, Boston, MA, USA
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, MGH, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, MIT, Cambridge, MA, USA
- Genentech, San Francisco, CA, USA
| | - Rajat M Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Cardiovascular Medicine and Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kasper Lage
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Surgery, MGH, Boston, MA, USA
| | - Kristin G Ardlie
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Joel N Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, MIT, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Jesse M Engreitz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- BASE Initiative, Betty Irene Moore Children's Heart Center, Lucile Packard Children's Hospital, Stanford University School of Medicine, Stanford, CA, USA
| | - Hilary K Finucane
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, MGH, Boston, MA, USA.
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6
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Du B, Xiao X, Wang H, Li W, Xia Z, Yang P, Huang SK, Yuan R, Liu J, Han M, Zou Y, Zhu J, He D, Lyu J, Jin X, Xu X, Wang J, Yang H, Xiao L, Liu X, Kristiansen K. Evaluation of the Impact of BaP Exposure on the Gut Microbiota and Allergic Responses in an OVA-Sensitized Mouse Model. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:67004. [PMID: 37267060 DOI: 10.1289/ehp11874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
BACKGROUND Exposure to environmental pollutants, including benzo[a]pyrene (BaP), has been implicated in allergic diseases and intestinal microbiota homeostasis, but the environment-microbiota-immunity triangular relationship and to what extent BaP-induced remodeling of the gut microbiota contributes to intestinal allergic inflammation remain to be established. OBJECTIVES We investigated the impact of BaP on intestinal allergic inflammation and examined the relationship between this effect and gut microbiota dysbiosis. We explored the potential ability of intestinal bacteria to degrade BaP and alleviate cytotoxicity as a detoxification strategy to counteract the effects of BaP exposure. METHODS We combined microbiome shotgun metagenomics with animal histological and intestinal allergic inflammatory responses to assess the effects of BaP (50μg/mouse per day) in a 23-d toxicity test in antigen-induced allergic female mice. In addition, genome annotation, quantitative analysis of BaP, and in vitro cytotoxicity-tests using CaCo-2 cells were conducted to infer the role of intestinal bacteria in BaP detoxification. RESULTS BaP exposure impacted the taxonomic composition and the functional potential of the gut microbiota and aggravated antigen-induced intestinal allergic inflammatory responses. The level of inflammatory cytokines correlated with the abundance of specific bacterial taxa, including Lachnospiraceae bacterium 28-4 and Alistipes inops. We identified 614 bacteria harboring genes implicated in the degradation of BaP, and 4 of these bacterial strains were shown to significantly reduce the cytotoxicity of BaP to CaCo-2 cells in vitro. DISCUSSION Using allergic female mice as a model, we investigated the relationship between BaP, microbiota, and host immune reactions, highlighting the role of gut bacteria in BaP-aggravated allergic reactions. Our findings offer novel insight toward establishing the causal relationship between BaP exposure and the occurrence of allergic disorders. Identifying gut bacteria that degrade BaP may provide new strategies for ameliorating BaP cytotoxicity. https://doi.org/10.1289/EHP11874.
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Affiliation(s)
- Beibei Du
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Xiaojun Xiao
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Huailing Wang
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Wenxi Li
- BGI-Shenzhen, Shenzhen, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | | | - Pingchang Yang
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, China
- National Institute of Environmental Health Sciences, National Health Research Institutes, Taiwan, China
| | - Shau-Ku Huang
- National Institute of Environmental Health Sciences, National Health Research Institutes, Taiwan, China
- Department of Allergy, Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Department of Medicine, Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ruyi Yuan
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Jie Liu
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Mo Han
- BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
| | | | | | | | - Xin Jin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
| | | | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
| | - Liang Xiao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, China
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
| | - Xiaoyu Liu
- State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen Key Laboratory of Allergy and Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao, China
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7
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Sarver DC, Xu C, Velez LM, Aja S, Jaffe AE, Seldin MM, Reeves RH, Wong GW. Dysregulated systemic metabolism in a Down syndrome mouse model. Mol Metab 2023; 68:101666. [PMID: 36587842 PMCID: PMC9841171 DOI: 10.1016/j.molmet.2022.101666] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/14/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVE Trisomy 21 is one of the most complex genetic perturbations compatible with postnatal survival. Dosage imbalance arising from the triplication of genes on human chromosome 21 (Hsa21) affects multiple organ systems. Much of Down syndrome (DS) research, however, has focused on addressing how aneuploidy dysregulates CNS function leading to cognitive deficit. Although obesity, diabetes, and associated sequelae such as fatty liver and dyslipidemia are well documented in the DS population, only limited studies have been conducted to determine how gene dosage imbalance affects whole-body metabolism. Here, we conduct a comprehensive and systematic analysis of key metabolic parameters across different physiological states in the Ts65Dn trisomic mouse model of DS. METHODS Ts65Dn mice and euploid littermates were subjected to comprehensive metabolic phenotyping under basal (chow-fed) state and the pathophysiological state of obesity induced by a high-fat diet (HFD). RNA sequencing of liver, skeletal muscle, and two major fat depots were conducted to determine the impact of aneuploidy on tissue transcriptome. Pathway enrichments, gene-centrality, and key driver estimates were performed to provide insights into tissue autonomous and non-autonomous mechanisms contributing to the dysregulation of systemic metabolism. RESULTS Under the basal state, chow-fed Ts65Dn mice of both sexes had elevated locomotor activity and energy expenditure, reduced fasting serum cholesterol levels, and mild glucose intolerance. Sexually dimorphic deterioration in metabolic homeostasis became apparent when mice were challenged with a high-fat diet. While obese Ts65Dn mice of both sexes exhibited dyslipidemia, male mice also showed impaired systemic insulin sensitivity, reduced mitochondrial activity, and elevated fibrotic and inflammatory gene signatures in the liver and adipose tissue. Systems-level analysis highlighted conserved pathways and potential endocrine drivers of adipose-liver crosstalk that contribute to dysregulated glucose and lipid metabolism. CONCLUSIONS A combined alteration in the expression of trisomic and disomic genes in peripheral tissues contribute to metabolic dysregulations in Ts65Dn mice. These data lay the groundwork for understanding the impact of aneuploidy on in vivo metabolism.
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Affiliation(s)
- Dylan C Sarver
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cheng Xu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leandro M Velez
- Department of Biological Chemistry, University of California, Irvine, Irvine, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, USA
| | - Susan Aja
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew E Jaffe
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; The Lieber Institute for Brain Development, Baltimore, MD, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Marcus M Seldin
- Department of Biological Chemistry, University of California, Irvine, Irvine, USA; Center for Epigenetics and Metabolism, University of California Irvine, Irvine, USA
| | - Roger H Reeves
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - G William Wong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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8
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Libiseller-Egger J, Phelan JE, Attia ZI, Benavente ED, Campino S, Friedman PA, Lopez-Jimenez F, Leon DA, Clark TG. Deep learning-derived cardiovascular age shares a genetic basis with other cardiac phenotypes. Sci Rep 2022; 12:22625. [PMID: 36587059 PMCID: PMC9805465 DOI: 10.1038/s41598-022-27254-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/28/2022] [Indexed: 01/01/2023] Open
Abstract
Artificial intelligence (AI)-based approaches can now use electrocardiograms (ECGs) to provide expert-level performance in detecting heart abnormalities and diagnosing disease. Additionally, patient age predicted from ECGs by AI models has shown great potential as a biomarker for cardiovascular age, where recent work has found its deviation from chronological age ("delta age") to be associated with mortality and co-morbidities. However, despite being crucial for understanding underlying individual risk, the genetic underpinning of delta age is unknown. In this work we performed a genome-wide association study using UK Biobank data (n=34,432) and identified eight loci associated with delta age ([Formula: see text]), including genes linked to cardiovascular disease (CVD) (e.g. SCN5A) and (heart) muscle development (e.g. TTN). Our results indicate that the genetic basis of cardiovascular ageing is predominantly determined by genes directly involved with the cardiovascular system rather than those connected to more general mechanisms of ageing. Our insights inform the epidemiology of CVD, with implications for preventative and precision medicine.
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Affiliation(s)
- Julian Libiseller-Egger
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Zachi I Attia
- Department of Cardiovascular Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Laboratory of Experimental Cardiology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Paul A Friedman
- Department of Cardiovascular Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | | | - David A Leon
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- Department of Community Medicine, UiT the Arctic University of Norway, Tromsø, Norway
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
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9
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Genome Editing and Myocardial Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1396:53-73. [PMID: 36454459 DOI: 10.1007/978-981-19-5642-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Congenital heart disease (CHD) has a strong genetic etiology, making it a likely candidate for therapeutic intervention using genetic editing. Complex genetics involving an orchestrated series of genetic events and over 400 genes are responsible for myocardial development. Cooperation is required from a vast series of genetic networks, and mutations in such can lead to CHD and cardiovascular abnormalities, affecting up to 1% of all live births. Genome editing technologies are becoming better studied and with time and improved logistics, CHD could be a prime therapeutic target. Syndromic, nonsyndromic, and cases of familial inheritance all involve identifiable causative mutations and thus have the potential for genome editing therapy. Mouse models are well-suited to study and predict clinical outcome. This review summarizes the anatomical and genetic timeline of myocardial development in both mice and humans, the potential of gene editing in typical CHD categories, as well as the use of mice thus far in reproducing models of human CHD and correcting the mutations that create them.
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10
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Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder. Nat Commun 2022; 13:6463. [PMID: 36309498 PMCID: PMC9617891 DOI: 10.1038/s41467-022-34112-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 10/13/2022] [Indexed: 02/06/2023] Open
Abstract
Defining different genetic subtypes of autism spectrum disorder (ASD) can enable the prediction of developmental outcomes. Based on minor physical and major congenital anomalies, we categorize 325 Canadian children with ASD into dysmorphic and nondysmorphic subgroups. We develop a method for calculating a patient-level, genome-wide rare variant score (GRVS) from whole-genome sequencing (WGS) data. GRVS is a sum of the number of variants in morphology-associated coding and non-coding regions, weighted by their effect sizes. Probands with dysmorphic ASD have a significantly higher GRVS compared to those with nondysmorphic ASD (P = 0.03). Using the polygenic transmission disequilibrium test, we observe an over-transmission of ASD-associated common variants in nondysmorphic ASD probands (P = 2.9 × 10-3). These findings replicate using WGS data from 442 ASD probands with accompanying morphology data from the Simons Simplex Collection. Our results provide support for an alternative genomic classification of ASD subgroups using morphology data, which may inform intervention protocols.
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11
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Identifying genes targeted by disease-associated non-coding SNPs with a protein knowledge graph. PLoS One 2022; 17:e0271395. [PMID: 35830458 PMCID: PMC9278741 DOI: 10.1371/journal.pone.0271395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/29/2022] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified many single nucleotide polymorphisms (SNPs) that play important roles in the genetic heritability of traits and diseases. With most of these SNPs located on the non-coding part of the genome, it is currently assumed that these SNPs influence the expression of nearby genes on the genome. However, identifying which genes are targeted by these disease-associated SNPs remains challenging. In the past, protein knowledge graphs have often been used to identify genes that are associated with disease, also referred to as “disease genes”. Here, we explore whether protein knowledge graphs can be used to identify genes that are targeted by disease-associated non-coding SNPs by testing and comparing the performance of six existing methods for a protein knowledge graph, four of which were developed for disease gene identification. We compare our performance against two baselines: (1) an existing state-of-the-art method that is based on guilt-by-association, and (2) the leading assumption that SNPs target the nearest gene on the genome. We test these methods with four reference sets, three of which were obtained by different means. Furthermore, we combine methods to investigate whether their combination improves performance. We find that protein knowledge graphs that include predicate information perform comparable to the current state of the art, achieving an area under the receiver operating characteristic curve (AUC) of 79.6% on average across all four reference sets. Protein knowledge graphs that lack predicate information perform comparable to our other baseline (genetic distance) which achieved an AUC of 75.7% across all four reference sets. Combining multiple methods improved performance to 84.9% AUC. We conclude that methods for a protein knowledge graph can be used to identify which genes are targeted by disease-associated non-coding SNPs.
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12
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Coleman CS, Stanley BA, Lang CH. Enrichment of Newly Synthesized Proteins following treatment of C2C12 Myotubes with Endotoxin and Interferon-γ. Inflammation 2022; 45:1313-1331. [PMID: 35028803 PMCID: PMC9106851 DOI: 10.1007/s10753-022-01622-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 11/28/2022]
Abstract
Inflammation in muscle induces the synthesis of mediators that can impair protein synthesis and enhance proteolysis, and when sustained lead to muscle atrophy. Furthermore, muscle-derived mediators that are secreted may participate in disrupting the function of other peripheral organs. Selective identification of newly synthesized proteins can provide insight on biological processes that depend on the continued synthesis of specific proteins to maintain homeostasis as well as those proteins that are up- or down-regulated in response to inflammation. We used puromycin-associated nascent chain proteomics (PUNCH-P) to characterize new protein synthesis in C2C12 myotubes and changes resulting from their exposure to the inflammatory mediators lipopolysaccharide (LPS) and interferon (IFN)-γ for either a short (4 h) or prolonged (16 h) time period. We identified sequences of nascent polypeptide chains belonging to a total of 1523 proteins and report their detection from three independent samples of each condition at each time point. The identified nascent proteins correspond to approximately 15% of presently known proteins in C2C12 myotubes and are enriched in specific cellular components and pathways. A subset of these proteins was identified only in treated samples and has functional characteristics consistent with the synthesis of specific new proteins in response to LPS/IFNγ. Thus, the identification of proteins from their nascent polypeptide chains provides a resource to analyze the role of new synthesis of proteins in both protein homeostasis and in proteome responses to stimuli in C2C12 myotubes. Our results reveal a profile of actively translating proteins for specific cellular components and biological processes in normal C2C12 myotubes and a different enrichment of proteins in response to LPS/IFNγ. Collectively, our data disclose a highly interconnected network that integrates the regulation of cellular proteostasis and reveal a diverse immune response to inflammation in muscle which may underlie the concomitantly observed atrophy and be important in inter-organ communication.
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Affiliation(s)
- Catherine S Coleman
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Bruce A Stanley
- Section of Research Resources, Penn State College of Medicine, Hershey, PA, 17033, USA
| | - Charles H Lang
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, 17033, USA.
- Department of Surgery, Penn State College of Medicine, Hershey, PA, 17033, USA.
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13
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Comparative systeomics to elucidate physiological differences between CHO and SP2/0 cell lines. Sci Rep 2022; 12:3280. [PMID: 35228567 PMCID: PMC8885639 DOI: 10.1038/s41598-022-06886-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 02/03/2022] [Indexed: 12/14/2022] Open
Abstract
Omics-based tools were coupled with bioinformatics for a systeomics analysis of two biopharma cell types: Chinese hamster ovary (M-CHO and CHO-K1) and SP2/0. Exponential and stationary phase samples revealed more than 10,000 transcripts and 6000 proteins across these two manufacturing cell lines. A statistical comparison of transcriptomics and proteomics data identified downregulated genes involved in protein folding, protein synthesis and protein metabolism, including PPIA-cyclophilin A, HSPD1, and EIF3K, in M-CHO compared to SP2/0 while cell cycle and actin cytoskeleton genes were reduced in SP2/0. KEGG pathway comparisons revealed glycerolipids, glycosphingolipids, ABC transporters, calcium signaling, cell adhesion, and secretion pathways depleted in M-CHO while retinol metabolism was upregulated. KEGG and IPA also indicated apoptosis, RNA degradation, and proteosomes enriched in CHO stationary phase. Alternatively, gene ontology analysis revealed an underrepresentation in ion and potassium channel activities, membrane proteins, and secretory granules including Stxbpt2, Syt1, Syt9, and Cma1 proteins in M-CHO. Additional enrichment strategies involving ultracentrifugation, biotinylation, and hydrazide chemistry identified over 4000 potential CHO membrane and secretory proteins, yet many secretory and membrane proteins were still depleted. This systeomics pipeline has revealed bottlenecks and potential opportunities for cell line engineering in CHO and SP2/0 to improve their production capabilities.
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14
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Shukla R, Yadav AK, Sote WO, Junior MC, Singh TR. Systems biology and big data analytics. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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15
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Satooka H, Matsui M, Ichioka S, Nakamura Y, Hirata T. The ERM protein moesin regulates natural killer cell homeostasis in vivo. Cell Immunol 2021; 371:104456. [PMID: 34798556 DOI: 10.1016/j.cellimm.2021.104456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/15/2021] [Accepted: 11/04/2021] [Indexed: 12/14/2022]
Abstract
Moesin is a member of the ezrin-radixin-moesin (ERM) family of proteins that link plasma membrane proteins with actin filaments in the cell cortex. Hemizygous mutations in the X-linked moesin gene are associated with primary immunodeficiency with T and B cell lymphopenia, which also affects natural killer (NK) cells in most cases. We previously showed that moesin deficiency in mice substantially affects lymphocyte homeostasis, but its impact on NK cells remains unexplored. Here, we found that in moesin-deficient mice, NK cells were decreased in the peripheral blood and bone marrow but increased in the spleen. Analysis of female heterozygous mice showed a selective advantage for moesin-expressing NK cells in the blood. Moesin-deficient NK cells exhibited increased cell death and impaired signaling in response to IL-15, suggesting that moesin regulates NK cell survival through IL-15-mediated signaling. Our findings thus identify moesin as an NK cell homeostasis regulator in vivo.
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Affiliation(s)
- Hiroki Satooka
- Department of Fundamental Biosciences, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan.
| | - Makoto Matsui
- Department of Fundamental Biosciences, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan.
| | - Satoko Ichioka
- Department of Fundamental Biosciences, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan.
| | - Yuzuki Nakamura
- Department of Fundamental Biosciences, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan.
| | - Takako Hirata
- Department of Fundamental Biosciences, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan.
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16
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Scarpa JR, Jiang P, Gao VD, Vitaterna MH, Turek FW, Kasarskis A. NREM delta power and AD-relevant tauopathy are associated with shared cortical gene networks. Sci Rep 2021; 11:7797. [PMID: 33833255 PMCID: PMC8032807 DOI: 10.1038/s41598-021-86255-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/27/2020] [Indexed: 02/01/2023] Open
Abstract
Reduced NREM sleep in humans is associated with AD neuropathology. Recent work has demonstrated a reduction in NREM sleep in preclinical AD, pointing to its potential utility as an early marker of dementia. We test the hypothesis that reduced NREM delta power and increased tauopathy are associated with shared underlying cortical molecular networks in preclinical AD. We integrate multi-omics data from two extensive public resources, a human Alzheimer's disease cohort from the Mount Sinai Brain Bank (N = 125) reflecting AD progression and a (C57BL/6J × 129S1/SvImJ) F2 mouse population in which NREM delta power was measured (N = 98). Two cortical gene networks, including a CLOCK-dependent circadian network, are associated with NREM delta power and AD tauopathy progression. These networks were validated in independent mouse and human cohorts. Identifying gene networks related to preclinical AD elucidate possible mechanisms associated with the early disease phase and potential targets to alter the disease course.
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Affiliation(s)
- Joseph R Scarpa
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Peng Jiang
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL, 60208, USA
| | - Vance D Gao
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL, 60208, USA
| | - Martha H Vitaterna
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL, 60208, USA
| | - Fred W Turek
- Center for Sleep and Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL, 60208, USA
| | - Andrew Kasarskis
- Icahn Institute for Genomics and Multiscale Biology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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17
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Bhat A, Irizar H, Thygesen JH, Kuchenbaecker K, Pain O, Adams RA, Zartaloudi E, Harju-Seppänen J, Austin-Zimmerman I, Wang B, Muir R, Summerfelt A, Du XM, Bruce H, O'Donnell P, Srivastava DP, Friston K, Hong LE, Hall MH, Bramon E. Transcriptome-wide association study reveals two genes that influence mismatch negativity. Cell Rep 2021; 34:108868. [PMID: 33730571 PMCID: PMC7972991 DOI: 10.1016/j.celrep.2021.108868] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/09/2020] [Accepted: 02/24/2021] [Indexed: 01/22/2023] Open
Abstract
Mismatch negativity (MMN) is a differential electrophysiological response measuring cortical adaptability to unpredictable stimuli. MMN is consistently attenuated in patients with psychosis. However, the genetics of MMN are uncharted, limiting the validation of MMN as a psychosis endophenotype. Here, we perform a transcriptome-wide association study of 728 individuals, which reveals 2 genes (FAM89A and ENGASE) whose expression in cortical tissues is associated with MMN. Enrichment analyses of neurodevelopmental expression signatures show that genes associated with MMN tend to be overexpressed in the frontal cortex during prenatal development but are significantly downregulated in adulthood. Endophenotype ranking value calculations comparing MMN and three other candidate psychosis endophenotypes (lateral ventricular volume and two auditory-verbal learning measures) find MMN to be considerably superior. These results yield promising insights into sensory processing in the cortex and endorse the notion of MMN as a psychosis endophenotype.
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Affiliation(s)
- Anjali Bhat
- Division of Psychiatry, University College London, London, UK; Wellcome Centre for Human Neuroimaging, University College London, London, UK; Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK; Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK.
| | - Haritz Irizar
- Division of Psychiatry, University College London, London, UK
| | | | - Karoline Kuchenbaecker
- Division of Psychiatry, University College London, London, UK; UCL Genetics Institute, University College London, London, UK
| | - Oliver Pain
- Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Rick A Adams
- Division of Psychiatry, University College London, London, UK; Institute of Cognitive Neuroscience, University College London, London, UK
| | | | - Jasmine Harju-Seppänen
- Division of Psychiatry, University College London, London, UK; Department of Clinical, Educational and Health Psychology, University College London, London, UK
| | | | - Baihan Wang
- Division of Psychiatry, University College London, London, UK
| | - Rebecca Muir
- Division of Psychiatry, University College London, London, UK
| | - Ann Summerfelt
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland, Baltimore, MD, USA
| | - Xiaoming Michael Du
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland, Baltimore, MD, USA
| | - Heather Bruce
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland, Baltimore, MD, USA
| | - Patricio O'Donnell
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland, Baltimore, MD, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Takeda Pharmaceuticals, Cambridge, MA, USA
| | - Deepak P Srivastava
- Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK; Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK; MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Karl Friston
- Wellcome Centre for Human Neuroimaging, University College London, London, UK
| | - L Elliot Hong
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland, Baltimore, MD, USA
| | - Mei-Hua Hall
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA; Psychosis Neurobiology Laboratory, McLean Hospital, Belmont, MA, USA
| | - Elvira Bramon
- Division of Psychiatry, University College London, London, UK; Institute of Cognitive Neuroscience, University College London, London, UK; Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK; Camden and Islington NHS Foundation Trust, London, UK.
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18
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Chen M, Wang W, Song W, Qian W, Lin GN. Integrative Analysis Identified Key Schizophrenia Risk Factors from an Abnormal Behavior Mouse Gene Set. Life (Basel) 2021; 11:172. [PMID: 33672431 PMCID: PMC7927082 DOI: 10.3390/life11020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/10/2021] [Accepted: 02/20/2021] [Indexed: 01/12/2023] Open
Abstract
Schizophrenia (SCZ) is a severe chronic psychiatric illness with heterogeneous symptoms. However, the pathogenesis of SCZ is unclear, and the number of well-defined SCZ risk factors is limited. We hypothesized that an abnormal behavior (AB) gene set verified by mouse model experiments can be used to better understand SCZ risks. In this work, we carried out an integrative bioinformatics analysis to study two types of risk genes that are either differentially expressed (DEGs) in the case-control study data or carry reported SCZ genetic variants (MUTs). Next, we used RNA-Seq expression data from the hippocampus (HIPPO) and dorsolateral prefrontal cortex (DLPFC) to define the key genes affected by different types (DEGs and MUTs) in different brain regions (DLPFC and HIPPO): DLPFC-kDEG, DLPFC-kMUT, HIPPO-kDEG, and HIPPO-kMUT. The four hub genes (SHANK1, SHANK2, DLG4, and NLGN3) of the biological functionally enriched terms were strongly linked to SCZ via gene co-expression network analysis. Then, we observed that specific spatial expressions of DLPFC-kMUT and HIPPO-kMUT were convergent in the early stages and divergent in the later stages of development. In addition, all four types of key genes showed significantly larger average protein-protein interaction degrees than the background. Comparing the different cell types, the expression of four types of key genes showed specificity in different dimensions. Together, our results offer new insights into potential risk factors and help us understand the complexity and regional heterogeneity of SCZ.
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Affiliation(s)
- Miao Chen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (M.C.); (W.W.); (W.S.); (W.Q.)
| | - Weidi Wang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (M.C.); (W.W.); (W.S.); (W.Q.)
| | - Weicheng Song
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (M.C.); (W.W.); (W.S.); (W.Q.)
| | - Wei Qian
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (M.C.); (W.W.); (W.S.); (W.Q.)
| | - Guan Ning Lin
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (M.C.); (W.W.); (W.S.); (W.Q.)
- Engineering Research Center of Digital Medicine and Clinical Translational, Ministry of Education of China, Shanghai 200030, China
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19
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Hall LS, Medway CW, Pain O, Pardiñas AF, Rees EG, Escott-Price V, Pocklington A, Bray NJ, Holmans PA, Walters JTR, Owen MJ, O'Donovan MC. A transcriptome-wide association study implicates specific pre- and post-synaptic abnormalities in schizophrenia. Hum Mol Genet 2020; 29:159-167. [PMID: 31691811 PMCID: PMC7416679 DOI: 10.1093/hmg/ddz253] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/31/2019] [Accepted: 09/02/2019] [Indexed: 12/25/2022] Open
Abstract
Schizophrenia is a complex highly heritable disorder. Genome-wide association studies (GWAS) have identified multiple loci that influence the risk of developing schizophrenia, although the causal variants driving these associations and their impacts on specific genes are largely unknown. We identify a significant correlation between schizophrenia risk and expression at 89 genes in the dorsolateral prefrontal cortex (P ≤ 9.43 × 10-6), including 20 novel genes. Genes whose expression correlate with schizophrenia were enriched for those involved in abnormal CNS synaptic transmission (PFDR = 0.02) and antigen processing and presentation of peptide antigen via MHC class I (PFDR = 0.02). Within the CNS synaptic transmission set, we identify individual significant candidate genes to which we assign direction of expression changes in schizophrenia. The findings provide strong candidates for experimentally probing the molecular basis of synaptic pathology in schizophrenia.
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Affiliation(s)
- Lynsey S Hall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Christopher W Medway
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Oliver Pain
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK.,Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Elliott G Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Andrew Pocklington
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Nicholas J Bray
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Peter A Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
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20
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Filipek-Górniok B, Habicher J, Ledin J, Kjellén L. Heparan Sulfate Biosynthesis in Zebrafish. J Histochem Cytochem 2020; 69:49-60. [PMID: 33216642 DOI: 10.1369/0022155420973980] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The biosynthesis of heparan sulfate (HS) proteoglycans occurs in the Golgi compartment of cells and will determine the sulfation pattern of HS chains, which in turn will have a large impact on the biological activity of the proteoglycans. Earlier studies in mice have demonstrated the importance of HS for embryonic development. In this review, the enzymes participating in zebrafish HS biosynthesis, along with a description of enzyme mutants available for functional studies, are presented. The consequences of the zebrafish genome duplication and maternal transcript contribution are briefly discussed as are the possibilities of CRISPR/Cas9 methodologies to use the zebrafish model system for studies of biosynthesis as well as proteoglycan biology.
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Affiliation(s)
- Beata Filipek-Górniok
- Department of Organismal Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Judith Habicher
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Johan Ledin
- Department of Organismal Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lena Kjellén
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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21
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Reiss RA, Lowe TC, Sena JA, Makhnin O, Connick MC, Illescas PE, Davis CF. Bio-activating ultrafine grain titanium: RNA sequencing reveals enhanced mechano-activation of osteoconduction on nanostructured substrates. PLoS One 2020; 15:e0237463. [PMID: 32970688 PMCID: PMC7514099 DOI: 10.1371/journal.pone.0237463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/27/2020] [Indexed: 02/02/2023] Open
Abstract
Titanium is essentially absent from biological systems yet reliably integrates into bone. To achieve osseointegration, titanium must activate biological processes without entering cells, defining it as a bio-activating material. Nanostructuring bulk titanium reduces grain size, increases strength, and improves other quantifiable physical properties, including cytocompatibility. The biological processes activated by increasing grain boundary availability were detected with total RNA-sequencing in mouse pre-osteoblasts grown for 72 hours on nanometrically smooth substrates of either coarse grain or nanostructured ultrafine grain titanium. The average grain boundary length under cells on the conventional coarse grain substrates is 273.0 μm, compared to 70,881.5 μm for cells adhered to the nanostructured ultrafine grain substrates; a 260-fold difference. Cells on both substrates exhibit similar expression profiles for genes whose products are critical for mechanosensation and transduction of cues that trigger osteoconduction. Biological process Gene Ontology term enrichment analysis of differentially expressed genes reveals that cell cycle, chromatin modification, telomere maintenance, and RNA metabolism processes are upregulated on ultrafine grain titanium. Processes related to immune response, including apoptosis, are downregulated. Tumor-suppressor genes are upregulated while tumor-promoting genes are downregulated. Upregulation of genes involved in chromatin remodeling and downregulation of genes under the control of the peripheral circadian clock implicate both processes in the transduction of mechanosensory information. Non-coding RNAs may also play a role in the response. Merging transcriptomics with well-established mechanobiology principles generates a unified model to explain the bio-activating properties of titanium. The modulation of processes is accomplished through chromatin remodeling in which the nucleus responds like a rheostat to grain boundary concentration. This convergence of biological and materials science reveals a pathway toward understanding the biotic-abiotic interface and will inform the development of effective bio-activating and bio-inactivating materials.
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Affiliation(s)
- Rebecca A. Reiss
- Biology Department, New Mexico Institution of Mining and Technology, Socorro, New Mexico, United States of America
| | - Terry C. Lowe
- George S. Ansell Department of Metallurgical and Materials Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Johnny A. Sena
- National Center for Genome Resources, Santa Fe, New Mexico, United States of America
| | - Oleg Makhnin
- Mathematics Department, New Mexico Institute of Mining and Technology, Socorro, New Mexico, United States of America
| | - Melanie C. Connick
- Biology Department, New Mexico Institution of Mining and Technology, Socorro, New Mexico, United States of America
| | - Patrick E. Illescas
- Biology Department, New Mexico Institution of Mining and Technology, Socorro, New Mexico, United States of America
| | - Casey F. Davis
- George S. Ansell Department of Metallurgical and Materials Engineering, Colorado School of Mines, Golden, Colorado, United States of America
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22
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Grama S, Willcocks I, Hubert JJ, Pardiñas AF, Legge SE, Bracher-Smith M, Menzies GE, Hall LS, Pocklington AJ, Anney RJL, Bray NJ, Escott-Price V, Caseras X. Polygenic risk for schizophrenia and subcortical brain anatomy in the UK Biobank cohort. Transl Psychiatry 2020; 10:309. [PMID: 32908133 PMCID: PMC7481214 DOI: 10.1038/s41398-020-00940-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/07/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
Research has shown differences in subcortical brain volumes between participants with schizophrenia and healthy controls. However, none of these differences have been found to associate with schizophrenia polygenic risk. Here, in a large sample (n = 14,701) of unaffected participants from the UK Biobank, we test whether schizophrenia polygenic risk scores (PRS) limited to specific gene-sets predict subcortical brain volumes. We compare associations with schizophrenia PRS at the whole genome level ('genomic', including all SNPs associated with the disorder at a p-value threshold < 0.05) with 'genic' PRS (based on SNPs in the vicinity of known genes), 'intergenic' PRS (based on the remaining SNPs), and genic PRS limited to SNPs within 7 gene-sets previously found to be enriched for genetic association with schizophrenia ('abnormal behaviour,' 'abnormal long-term potentiation,' 'abnormal nervous system electrophysiology,' 'FMRP targets,' '5HT2C channels,' 'CaV2 channels' and 'loss-of-function intolerant genes'). We observe a negative association between the 'abnormal behaviour' gene-set PRS and volume of the right thalamus that survived correction for multiple testing (ß = -0.031, pFDR = 0.005) and was robust to different schizophrenia PRS p-value thresholds. In contrast, the only association with genomic PRS surviving correction for multiple testing was for right pallidum, which was observed using a schizophrenia PRS p-value threshold < 0.01 (ß = -0.032, p = 0.0003, pFDR = 0.02), but not when using other PRS P-value thresholds. We conclude that schizophrenia PRS limited to functional gene sets may provide a better means of capturing differences in subcortical brain volume than whole genome PRS approaches.
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Affiliation(s)
- Steluta Grama
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, CF10 3AT, UK
| | - Isabella Willcocks
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, CF10 3AT, UK
| | - John J Hubert
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, CF10 3AT, UK
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, CF10 3AT, UK
| | - Sophie E Legge
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, CF10 3AT, UK
| | - Matthew Bracher-Smith
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, CF10 3AT, UK
| | - Georgina E Menzies
- UK Dementia Research Institute, Cardiff University, Cardiff, CF10 3AT, UK
| | - Lynsey S Hall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, CF10 3AT, UK
| | - Andrew J Pocklington
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, CF10 3AT, UK
| | - Richard J L Anney
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, CF10 3AT, UK
| | - Nicholas J Bray
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, CF10 3AT, UK
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, CF10 3AT, UK
- UK Dementia Research Institute, Cardiff University, Cardiff, CF10 3AT, UK
| | - Xavier Caseras
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, CF10 3AT, UK.
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23
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North HL, Caminade P, Severac D, Belkhir K, Smadja CM. The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190540. [PMID: 32654648 PMCID: PMC7423270 DOI: 10.1098/rstb.2019.0540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2020] [Indexed: 12/24/2022] Open
Abstract
Reinforcement has the potential to generate strong reproductive isolation through the evolution of barrier traits as a response to selection against maladaptive hybridization, but the genetic changes associated with this process remain largely unexplored. Building upon the increasing evidence for a role of structural variants in adaptation and speciation, we addressed the role of copy-number variation in the reinforcement of sexual isolation evidenced between the two European subspecies of the house mouse. We characterized copy-number divergence between populations of Mus musculus musculus that display assortative mate choice, and those that do not, using whole-genome resequencing data. Updating methods to detect deletions and tandem duplications (collectively: copy-number variants, CNVs) in Pool-Seq data, we developed an analytical pipeline dedicated to identifying genomic regions showing the expected pattern of copy-number displacement under a reinforcement scenario. This strategy allowed us to detect 1824 deletions and seven tandem duplications that showed extreme differences in frequency between behavioural classes across replicate comparisons. A subset of 480 deletions and four tandem duplications were specifically associated with the derived trait of assortative mate choice. These 'Choosiness-associated' CNVs occur in hundreds of genes. Consistent with our hypothesis, such genes included olfactory receptors potentially involved in the olfactory-based assortative mate choice in this system as well as one gene, Sp110, that is known to show patterns of differential expression between behavioural classes in an organ used in mate choice-the vomeronasal organ. These results demonstrate that fine-scale structural changes are common and highly variable within species, despite being under-studied, and may be important targets of reinforcing selection in this system and others. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Henry L. North
- Institut des Sciences de l'Evolution (UMR 5554 CNRS, IRD, EPHE, Université de Montpellier), Université de Montpellier, Campus Triolet, Place Eugène Bataillon, 34095 Montpellier, France
| | - Pierre Caminade
- Institut des Sciences de l'Evolution (UMR 5554 CNRS, IRD, EPHE, Université de Montpellier), Université de Montpellier, Campus Triolet, Place Eugène Bataillon, 34095 Montpellier, France
| | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094 Montpellier Cedex 5, France
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution (UMR 5554 CNRS, IRD, EPHE, Université de Montpellier), Université de Montpellier, Campus Triolet, Place Eugène Bataillon, 34095 Montpellier, France
| | - Carole M. Smadja
- Institut des Sciences de l'Evolution (UMR 5554 CNRS, IRD, EPHE, Université de Montpellier), Université de Montpellier, Campus Triolet, Place Eugène Bataillon, 34095 Montpellier, France
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24
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Edwards JJ, Rouillard AD, Fernandez NF, Wang Z, Lachmann A, Shankaran SS, Bisgrove BW, Demarest B, Turan N, Srivastava D, Bernstein D, Deanfield J, Giardini A, Porter G, Kim R, Roberts AE, Newburger JW, Goldmuntz E, Brueckner M, Lifton RP, Seidman CE, Chung WK, Tristani-Firouzi M, Yost HJ, Ma'ayan A, Gelb BD. Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects. JACC Basic Transl Sci 2020; 5:376-386. [PMID: 32368696 PMCID: PMC7188873 DOI: 10.1016/j.jacbts.2020.01.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/30/2022]
Abstract
Combining CHD phenotype–driven gene set enrichment and CRISPR knockdown screening in zebrafish is an effective approach to identifying novel CHD genes. Mutations affecting genes coding for the WAVE2 protein complex and small GTPase-mediated signaling are associated with LVOTO lesions. WAVE2 complex genes brk1, nckap1, and wasf2 and regulators of small GTPase signaling cul3a and racgap1 are critical to zebrafish heart development.
Genetic variants are the primary driver of congenital heart disease (CHD) pathogenesis. However, our ability to identify causative variants is limited. To identify causal CHD genes that are associated with specific molecular functions, the study used prior knowledge to filter de novo variants from 2,881 probands with sporadic severe CHD. This approach enabled the authors to identify an association between left ventricular outflow tract obstruction lesions and genes associated with the WAVE2 complex and regulation of small GTPase-mediated signal transduction. Using CRISPR zebrafish knockdowns, the study confirmed that WAVE2 complex proteins brk1, nckap1, and wasf2 and the regulators of small GTPase signaling cul3a and racgap1 are critical to cardiac development.
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Key Words
- CHD, congenital heart disease
- CORUM, Comprehensive Resource of Mammalian Protein Complexes
- CRISPR, clustered regularly interspaced short palindromic repeats
- CTD, conotruncal defect
- GOBP, Gene Ontology biological processes
- HHE, high heart expression
- HLHS, hypoplastic left heart syndrome
- HTX, heterotaxy
- LVOTO, left ventricular outflow tract obstruction
- MGI, Mouse Genome Informatics
- PCGC, Pediatric Cardiac Genomics Consortium
- PPI, protein-protein interaction
- congenital heart disease
- systems biology
- translational genomics
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Affiliation(s)
- Jonathan J Edwards
- Department of Pediatrics, Division of Pediatric Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Andrew D Rouillard
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nicolas F Fernandez
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zichen Wang
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alexander Lachmann
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sunita S Shankaran
- Department of Molecular Physiology and Biophysics, Vanderbilt School of Medicine, Nashville, Tennessee
| | - Brent W Bisgrove
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah
| | - Bradley Demarest
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, California
| | - Daniel Bernstein
- Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - John Deanfield
- Department of Cardiology, Great Ormond Street Hospital, University College London, London, United Kingdom
| | - Alessandro Giardini
- Department of Cardiology, Great Ormond Street Hospital, University College London, London, United Kingdom
| | - George Porter
- Department of Pediatrics, University of Rochester Medical Center, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Richard Kim
- Section of Cardiothoracic Surgery, Keck School of Medicine of USC, University of Southern California, Los Angeles, California
| | - Amy E Roberts
- Department of Cardiology, Children's Hospital Boston, Boston, Massachusetts
| | - Jane W Newburger
- Department of Cardiology, Children's Hospital Boston, Boston, Massachusetts
| | - Elizabeth Goldmuntz
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Martina Brueckner
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut.,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts.,Cardiovascular Division, Brigham and Women's Hospital, Harvard University, Boston, Massachusetts
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York.,Department of Medicine, Columbia University Medical Center, New York, New York
| | - Martin Tristani-Firouzi
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - H Joseph Yost
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, LINCS-BD2K DCIC, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
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25
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Novel Approaches for Identifying the Molecular Background of Schizophrenia. Cells 2020; 9:cells9010246. [PMID: 31963710 PMCID: PMC7017322 DOI: 10.3390/cells9010246] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/06/2020] [Accepted: 01/16/2020] [Indexed: 12/20/2022] Open
Abstract
Recent advances in psychiatric genetics have led to the discovery of dozens of genomic loci associated with schizophrenia. However, a gap exists between the detection of genetic associations and understanding the underlying molecular mechanisms. This review describes the basic approaches used in the so-called post-GWAS studies to generate biological interpretation of the existing population genetic data, including both molecular (creation and analysis of knockout animals, exploration of the transcriptional effects of common variants in human brain cells) and computational (fine-mapping of causal variability, gene set enrichment analysis, partitioned heritability analysis) methods. The results of the crucial studies, in which these approaches were used to uncover the molecular and neurobiological basis of the disease, are also reported.
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Hyung D, Mallon AM, Kyung DS, Cho SY, Seong JK. TarGo: network based target gene selection system for human disease related mouse models. Lab Anim Res 2019; 35:23. [PMID: 32257911 PMCID: PMC7081697 DOI: 10.1186/s42826-019-0023-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 10/21/2019] [Indexed: 11/25/2022] Open
Abstract
Genetically engineered mouse models are used in high-throughput phenotyping screens to understand genotype-phenotype associations and their relevance to human diseases. However, not all mutant mouse lines with detectable phenotypes are associated with human diseases. Here, we propose the “Target gene selection system for Genetically engineered mouse models” (TarGo). Using a combination of human disease descriptions, network topology, and genotype-phenotype correlations, novel genes that are potentially related to human diseases are suggested. We constructed a gene interaction network using protein-protein interactions, molecular pathways, and co-expression data. Several repositories for human disease signatures were used to obtain information on human disease-related genes. We calculated disease- or phenotype-specific gene ranks using network topology and disease signatures. In conclusion, TarGo provides many novel features for gene function prediction.
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Affiliation(s)
- Daejin Hyung
- 1National Cancer Center, 323 Ilsan-ro, Goyang-si, Kyeonggi-do 10408 Republic of Korea
| | - Ann-Marie Mallon
- 2MRC Harwell Institute, Mammalian Genetics Unit, Oxfordshire, OX11 0RD UK
| | - Dong Soo Kyung
- 3Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Plus Program for Creative Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826 Republic of Korea.,4Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, 08826 Republic of Korea.,5Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX institute, Seoul National University, Seoul, 08826 Republic of Korea
| | - Soo Young Cho
- 1National Cancer Center, 323 Ilsan-ro, Goyang-si, Kyeonggi-do 10408 Republic of Korea.,4Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, 08826 Republic of Korea
| | - Je Kyung Seong
- 3Laboratory of Developmental Biology and Genomics, Research Institute for Veterinary Science, and BK21 Plus Program for Creative Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, 08826 Republic of Korea.,4Korea Mouse Phenotyping Center (KMPC), Seoul National University, Seoul, 08826 Republic of Korea.,5Interdisciplinary Program for Bioinformatics, Program for Cancer Biology and BIO-MAX institute, Seoul National University, Seoul, 08826 Republic of Korea
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Alshahrani M, Hoehndorf R. Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes. Bioinformatics 2019; 34:i901-i907. [PMID: 30423077 PMCID: PMC6129260 DOI: 10.1093/bioinformatics/bty559] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Motivation In the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease’s (or patient’s) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse. Results We developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprised of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network. Availability and implementation https://github.com/bio-ontology-research-group/SmuDGE
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Affiliation(s)
- Mona Alshahrani
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Robert Hoehndorf
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Gurumurthy CB, O'Brien AR, Quadros RM, Adams J, Alcaide P, Ayabe S, Ballard J, Batra SK, Beauchamp MC, Becker KA, Bernas G, Brough D, Carrillo-Salinas F, Chan W, Chen H, Dawson R, DeMambro V, D'Hont J, Dibb KM, Eudy JD, Gan L, Gao J, Gonzales A, Guntur AR, Guo H, Harms DW, Harrington A, Hentges KE, Humphreys N, Imai S, Ishii H, Iwama M, Jonasch E, Karolak M, Keavney B, Khin NC, Konno M, Kotani Y, Kunihiro Y, Lakshmanan I, Larochelle C, Lawrence CB, Li L, Lindner V, Liu XD, Lopez-Castejon G, Loudon A, Lowe J, Jerome-Majewska LA, Matsusaka T, Miura H, Miyasaka Y, Morpurgo B, Motyl K, Nabeshima YI, Nakade K, Nakashiba T, Nakashima K, Obata Y, Ogiwara S, Ouellet M, Oxburgh L, Piltz S, Pinz I, Ponnusamy MP, Ray D, Redder RJ, Rosen CJ, Ross N, Ruhe MT, Ryzhova L, Salvador AM, Alam SS, Sedlacek R, Sharma K, Smith C, Staes K, Starrs L, Sugiyama F, Takahashi S, Tanaka T, Trafford AW, Uno Y, Vanhoutte L, Vanrockeghem F, Willis BJ, Wright CS, Yamauchi Y, Yi X, Yoshimi K, Zhang X, Zhang Y, Ohtsuka M, Das S, Garry DJ, Hochepied T, Thomas P, Parker-Thornburg J, Adamson AD, Yoshiki A, Schmouth JF, Golovko A, Thompson WR, Lloyd KCK, Wood JA, Cowan M, Mashimo T, Mizuno S, Zhu H, Kasparek P, Liaw L, Miano JM, Burgio G. Reproducibility of CRISPR-Cas9 methods for generation of conditional mouse alleles: a multi-center evaluation. Genome Biol 2019; 20:171. [PMID: 31446895 PMCID: PMC6709553 DOI: 10.1186/s13059-019-1776-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/27/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND CRISPR-Cas9 gene-editing technology has facilitated the generation of knockout mice, providing an alternative to cumbersome and time-consuming traditional embryonic stem cell-based methods. An earlier study reported up to 16% efficiency in generating conditional knockout (cKO or floxed) alleles by microinjection of 2 single guide RNAs (sgRNA) and 2 single-stranded oligonucleotides as donors (referred herein as "two-donor floxing" method). RESULTS We re-evaluate the two-donor method from a consortium of 20 laboratories across the world. The dataset constitutes 56 genetic loci, 17,887 zygotes, and 1718 live-born mice, of which only 15 (0.87%) mice contain cKO alleles. We subject the dataset to statistical analyses and a machine learning algorithm, which reveals that none of the factors analyzed was predictive for the success of this method. We test some of the newer methods that use one-donor DNA on 18 loci for which the two-donor approach failed to produce cKO alleles. We find that the one-donor methods are 10- to 20-fold more efficient than the two-donor approach. CONCLUSION We propose that the two-donor method lacks efficiency because it relies on two simultaneous recombination events in cis, an outcome that is dwarfed by pervasive accompanying undesired editing events. The methods that use one-donor DNA are fairly efficient as they rely on only one recombination event, and the probability of correct insertion of the donor cassette without unanticipated mutational events is much higher. Therefore, one-donor methods offer higher efficiencies for the routine generation of cKO animal models.
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Affiliation(s)
- Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA.
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Aidan R O'Brien
- Transformational Bioinformatics, Health and Biosecurity Business Unit, CSIRO, North Ryde, Australia
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - John Adams
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Pilar Alcaide
- Department of Immunology, Tufts University School of Medicine, Boston, USA
| | - Shinya Ayabe
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Johnathan Ballard
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Marie-Claude Beauchamp
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Kathleen A Becker
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Guillaume Bernas
- Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - David Brough
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | | | - Wesley Chan
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Hanying Chen
- School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
| | - Ruby Dawson
- South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | - Victoria DeMambro
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Jinke D'Hont
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Katharine M Dibb
- Unit of Cardiac Physiology, School of Medical Sciences, Manchester Academic Health Science Center, University of Manchester, Manchester, UK
| | - James D Eudy
- High-Throughput DNA Sequencing and Genotyping Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, USA
| | - Lin Gan
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Jing Gao
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Amy Gonzales
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Anyonya R Guntur
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Huiping Guo
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Donald W Harms
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Anne Harrington
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Kathryn E Hentges
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Neil Humphreys
- Transgenic Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Shiho Imai
- Department of Basic Medicine, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Hideshi Ishii
- Department of Medical Data Science, Osaka University Graduate School of Medicine, Suita, Japan
| | - Mizuho Iwama
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Eric Jonasch
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michelle Karolak
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Bernard Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and Manchester Heart Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Nay-Chi Khin
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Masamitsu Konno
- Department of Frontier Science for Cancer and Chemotherapy, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yuko Kotani
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yayoi Kunihiro
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Catherine Larochelle
- Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - Catherine B Lawrence
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, UK
| | - Lin Li
- Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Volkhard Lindner
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Xian-De Liu
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gloria Lopez-Castejon
- Manchester Collaborative Centre for Inflammation Research (MCCIR), School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Andrew Loudon
- Centre for Biological Timing, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jenna Lowe
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Loydie A Jerome-Majewska
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Taiji Matsusaka
- Department of Basic Medicine, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Hiromi Miura
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, 259-1193, Japan
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Yoshiki Miyasaka
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Benjamin Morpurgo
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - Katherine Motyl
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Yo-Ichi Nabeshima
- Laboratory of Molecular Life Science, Foundation for Biomedical Research and Innovation, Kobe, Japan
| | - Koji Nakade
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | | | - Kenichi Nakashima
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Yuichi Obata
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Sanae Ogiwara
- Department of Laboratory Animal Science, Support Center for Medical Research and Education, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Mariette Ouellet
- Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - Leif Oxburgh
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
- Basic and Clinical Research, The Rogosin Institute, New York, USA
| | - Sandra Piltz
- South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | - Ilka Pinz
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Moorthy P Ponnusamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - David Ray
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX37LE, UK
| | - Ronald J Redder
- High-Throughput DNA Sequencing and Genotyping Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, USA
| | - Clifford J Rosen
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Nikki Ross
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Mark T Ruhe
- Mouse Biology Program, University of California, Davis, USA
| | - Larisa Ryzhova
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Ane M Salvador
- Department of Immunology, Tufts University School of Medicine, Boston, USA
| | - Sabrina Shameen Alam
- Departments of Anatomy and Cell Biology, Human Genetics and Pediatrics, Research Institute McGill University Health Center (RI-MUHC), Montreal, Canada
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Karan Sharma
- College of Osteopathic Medicine, Marian University, Indianapolis, IN, 46222, USA
| | - Chad Smith
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katrien Staes
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Lora Starrs
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan
| | - Tomohiro Tanaka
- Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Andrew W Trafford
- Unit of Cardiac Physiology, School of Medical Sciences, Manchester Academic Health Science Center, University of Manchester, Manchester, UK
| | - Yoshihiro Uno
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Leen Vanhoutte
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Frederique Vanrockeghem
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Christian S Wright
- School of Health and Human Sciences, Department of Physical Therapy, Indiana University, Indianapolis, IN, 46202, USA
| | - Yuko Yamauchi
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Xin Yi
- School of Health and Human Sciences, Department of Physical Therapy, Indiana University, Indianapolis, IN, 46202, USA
| | - Kazuto Yoshimi
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Xuesong Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yu Zhang
- Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Masato Ohtsuka
- Center for Matrix Biology and Medicine, Graduate School of Medicine, Tokai University, Isehara, Kanagawa, 259-1193, Japan
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, School of Medicine, Tokai University, 143, Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Satyabrata Das
- Lillehei Heart Institute Regenerative Medicine and Sciences Program, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Garry
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, USA
- Department of Surgery, School of Medicine, University of California, Davis, Davis, USA
| | - Tino Hochepied
- Transgenic Mouse Core Facility, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Paul Thomas
- South Australian Health & Medical Research Institute and Department of Medicine, University of Adelaide, Adelaide, Australia
| | | | - Antony D Adamson
- Transgenic Unit Core Facility, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Atsushi Yoshiki
- RIKEN BioResource Research Center, Tsukuba, Ibaraki, 305-0074, Japan
| | - Jean-Francois Schmouth
- Transgenesis and Animal Modeling Core Facility, Centre de Recherche du Centre Hospitalier Universitaire de Montreal (CRCHUM), Montreal, Canada
| | - Andrei Golovko
- Texas A&M Institute for Genomic Medicine (TIGM), Texas A&M University, College Station, TX, 77843, USA
| | - William R Thompson
- School of Health and Human Sciences, Department of Physical Therapy, Indiana University, Indianapolis, IN, 46202, USA
| | - K C Kent Lloyd
- Mouse Biology Program, University of California, Davis, USA
- Department of Surgery, School of Medicine, University of California, Davis, Davis, USA
| | - Joshua A Wood
- Mouse Biology Program, University of California, Davis, USA
| | - Mitra Cowan
- McGill Integrated Core for Animal Modeling (MICAM), Montreal, Canada
| | - Tomoji Mashimo
- The Institute of Experimental Animal Sciences, Osaka University Graduate School of Medicine, Suita, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, University of Tsukuba, Tsukuba, Japan
| | - Hao Zhu
- Children's Research Institute Mouse Genome Engineering Core, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Petr Kasparek
- Laboratory of Transgenic Models of Diseases and Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lucy Liaw
- Maine Medical Center Research Institute (MMCRI), Scarborough, ME, USA
| | - Joseph M Miano
- University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Gaetan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, Australia.
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Gokhman D, Kelman G, Amartely A, Gershon G, Tsur S, Carmel L. Gene ORGANizer: linking genes to the organs they affect. Nucleic Acids Res 2019; 45:W138-W145. [PMID: 28444223 PMCID: PMC5570240 DOI: 10.1093/nar/gkx302] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/14/2017] [Indexed: 12/16/2022] Open
Abstract
One of the biggest challenges in studying how genes work is understanding their effect on the physiology and anatomy of the body. Existing tools try to address this using indirect features, such as expression levels and biochemical pathways. Here, we present Gene ORGANizer (geneorganizer.huji.ac.il), a phenotype-based tool that directly links human genes to the body parts they affect. It is built upon an exhaustive curated database that links >7000 genes to ∼150 anatomical parts using >150 000 gene-organ associations. The tool offers user-friendly platforms to analyze the anatomical effects of individual genes, and identify trends within groups of genes. We demonstrate how Gene ORGANizer can be used to make new discoveries, showing that chromosome X is enriched with genes affecting facial features, that positive selection targets genes with more constrained phenotypic effects, and more. We expect Gene ORGANizer to be useful in a variety of evolutionary, medical and molecular studies aimed at understanding the phenotypic effects of genes.
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Affiliation(s)
- David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Guy Kelman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Adir Amartely
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Guy Gershon
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Shira Tsur
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.,Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
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30
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Ando T, Kato R, Honda H. Identification of an early cell fate regulator by detecting dynamics in transcriptional heterogeneity and co-regulation during astrocyte differentiation. NPJ Syst Biol Appl 2019; 5:18. [PMID: 31098297 PMCID: PMC6506553 DOI: 10.1038/s41540-019-0095-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 04/16/2019] [Indexed: 01/19/2023] Open
Abstract
There are an increasing number of reports that characterize the temporal behavior of gene expression at the single-cell level during cell differentiation. Despite accumulation of data describing the heterogeneity of biological responses, the dynamics of gene expression heterogeneity and its regulation during the differentiation process have not been studied systematically. To understand transcriptional heterogeneity during astrocyte differentiation, we analyzed single-cell transcriptional data from cells representing the different stages of astrocyte differentiation. When we compared the transcriptional variability of co-expressed genes between the undifferentiated and differentiated states, we found that there was significant increase in transcriptional variability in the undifferentiated state. The genes showing large changes in both "variability" and "correlation" between neural stem cells (NSCs) and astrocytes were found to be functionally involved in astrocyte differentiation. We determined that these genes are potentially regulated by Ascl1, a previously known oscillatory gene in NSCs. Pharmacological blockade of Ntsr2, which is transcriptionally co-regulated with Ascl1, showed that Ntsr2 may play an important role in the differentiation from NSCs to astrocytes. This study shows the importance of characterizing transcriptional heterogeneity and rearrangement of the co-regulation network between different cell states. It also highlights the potential for identifying novel regulators of cell differentiation that will further increase our understanding of the molecular mechanisms underlying the differentiation process.
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Affiliation(s)
- Tatsuya Ando
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Aichi Japan
| | - Ryuji Kato
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi Japan
- Division of Micro-Nano Mechatronics, Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Hiroyuki Honda
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Aichi Japan
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31
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Chan AJS, Cytrynbaum C, Hoang N, Ambrozewicz PM, Weksberg R, Drmic I, Ritzema A, Schachar R, Walker S, Uddin M, Zarrei M, Yuen RKC, Scherer SW. Expanding the neurodevelopmental phenotypes of individuals with de novo KMT2A variants. NPJ Genom Med 2019; 4:9. [PMID: 31044088 PMCID: PMC6486600 DOI: 10.1038/s41525-019-0083-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/20/2019] [Indexed: 01/07/2023] Open
Abstract
De novo loss-of-function (LoF) variants in the KMT2A gene are associated with Wiedemann-Steiner Syndrome (WSS). Recently, de novo KMT2A variants have been identified in sequencing studies of cohorts of individuals with neurodevelopmental disorders (NDDs). However, most of these studies lack the detailed clinical information required to determine whether those individuals have isolated NDDs or WSS (i.e. syndromic NDDs). We performed thorough clinical and neurodevelopmental phenotyping on six individuals with de novo KMT2A variants. From these data, we found that all six patients met clinical criteria for WSS and we further define the neurodevelopmental phenotypes associated with KMT2A variants and WSS. In particular, we identified a subtype of Autism Spectrum Disorder (ASD) in five individuals, characterized by marked rigid, repetitive and inflexible behaviours, emotional dysregulation, externalizing behaviours, but relative social motivation. To further explore the clinical spectrum associated with KMT2A variants, we also conducted a meta-analysis of individuals with KMT2A variants reported in the published literature. We found that de novo LoF or missense variants in KMT2A were significantly more prevalent than predicted by a previously established statistical model of de novo mutation rate for KMT2A. Our genotype-phenotype findings better define the clinical spectrum associated with KMT2A variants and suggest that individuals with de novo LoF and missense variants likely have a clinically unrecognized diagnosis of WSS, rather than isolated NDD or ASD alone. This highlights the importance of a clinical genetic and neurodevelopmental assessment for individuals with such variants in KMT2A.
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Affiliation(s)
- Ada J. S. Chan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
| | - Cheryl Cytrynbaum
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON Canada
| | - Ny Hoang
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON Canada
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON Canada
| | - Patricia M. Ambrozewicz
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON Canada
- Department of Psychology, The Hospital for Sick Children, Toronto, ON Canada
| | - Rosanna Weksberg
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Institute of Medical Science, University of Toronto, Toronto, ON Canada
- Department of Paediatrics, University of Toronto, Toronto, ON Canada
| | - Irene Drmic
- Ron Joyce Children’s Health Centre, Hamilton Health Services, Hamilton, ON Canada
| | - Anne Ritzema
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON Canada
- Department of Psychology, The Hospital for Sick Children, Toronto, ON Canada
| | - Russell Schachar
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON Canada
- Department of Psychiatry, University of Toronto, Toronto, ON Canada
| | - Susan Walker
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Mohammed Uddin
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mehdi Zarrei
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Ryan K. C. Yuen
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Stephen W. Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Institute of Medical Science, University of Toronto, Toronto, ON Canada
- McLaughin Centre, University of Toronto, Toronto, ON Canada
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32
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Bentley AR, Sung YJ, Brown MR, Winkler TW, Kraja AT, Ntalla I, Schwander K, Chasman DI, Lim E, Deng X, Guo X, Liu J, Lu Y, Cheng CY, Sim X, Vojinovic D, Huffman JE, Musani SK, Li C, Feitosa MF, Richard MA, Noordam R, Baker J, Chen G, Aschard H, Bartz TM, Ding J, Dorajoo R, Manning AK, Rankinen T, Smith AV, Tajuddin SM, Zhao W, Graff M, Alver M, Boissel M, Chai JF, Chen X, Divers J, Evangelou E, Gao C, Goel A, Hagemeijer Y, Harris SE, Hartwig FP, He M, Horimoto ARVR, Hsu FC, Hung YJ, Jackson AU, Kasturiratne A, Komulainen P, Kühnel B, Leander K, Lin KH, Luan J, Lyytikäinen LP, Matoba N, Nolte IM, Pietzner M, Prins B, Riaz M, Robino A, Said MA, Schupf N, Scott RA, Sofer T, Stancáková A, Takeuchi F, Tayo BO, van der Most PJ, Varga TV, Wang TD, Wang Y, Ware EB, Wen W, Xiang YB, Yanek LR, Zhang W, Zhao JH, Adeyemo A, Afaq S, Amin N, Amini M, Arking DE, Arzumanyan Z, Aung T, Ballantyne C, Barr RG, Bielak LF, Boerwinkle E, Bottinger EP, Broeckel U, Brown M, Cade BE, Campbell A, Canouil M, Charumathi S, Chen YDI, Christensen K, Concas MP, Connell JM, de Las Fuentes L, de Silva HJ, de Vries PS, Doumatey A, Duan Q, Eaton CB, Eppinga RN, Faul JD, Floyd JS, Forouhi NG, Forrester T, Friedlander Y, Gandin I, Gao H, Ghanbari M, Gharib SA, Gigante B, Giulianini F, Grabe HJ, Gu CC, Harris TB, Heikkinen S, Heng CK, Hirata M, Hixson JE, Ikram MA, Jia Y, Joehanes R, Johnson C, Jonas JB, Justice AE, Katsuya T, Khor CC, Kilpeläinen TO, Koh WP, Kolcic I, Kooperberg C, Krieger JE, Kritchevsky SB, Kubo M, Kuusisto J, Lakka TA, Langefeld CD, Langenberg C, Launer LJ, Lehne B, Lewis CE, Li Y, Liang J, Lin S, Liu CT, Liu J, Liu K, Loh M, Lohman KK, Louie T, Luzzi A, Mägi R, Mahajan A, Manichaikul AW, McKenzie CA, Meitinger T, Metspalu A, Milaneschi Y, Milani L, Mohlke KL, Momozawa Y, Morris AP, Murray AD, Nalls MA, Nauck M, Nelson CP, North KE, O'Connell JR, Palmer ND, Papanicolau GJ, Pedersen NL, Peters A, Peyser PA, Polasek O, Poulter N, Raitakari OT, Reiner AP, Renström F, Rice TK, Rich SS, Robinson JG, Rose LM, Rosendaal FR, Rudan I, Schmidt CO, Schreiner PJ, Scott WR, Sever P, Shi Y, Sidney S, Sims M, Smith JA, Snieder H, Starr JM, Strauch K, Stringham HM, Tan NYQ, Tang H, Taylor KD, Teo YY, Tham YC, Tiemeier H, Turner ST, Uitterlinden AG, van Heemst D, Waldenberger M, Wang H, Wang L, Wang L, Wei WB, Williams CA, Wilson G, Wojczynski MK, Yao J, Young K, Yu C, Yuan JM, Zhou J, Zonderman AB, Becker DM, Boehnke M, Bowden DW, Chambers JC, Cooper RS, de Faire U, Deary IJ, Elliott P, Esko T, Farrall M, Franks PW, Freedman BI, Froguel P, Gasparini P, Gieger C, Horta BL, Juang JMJ, Kamatani Y, Kammerer CM, Kato N, Kooner JS, Laakso M, Laurie CC, Lee IT, Lehtimäki T, Magnusson PKE, Oldehinkel AJ, Penninx BWJH, Pereira AC, Rauramaa R, Redline S, Samani NJ, Scott J, Shu XO, van der Harst P, Wagenknecht LE, Wang JS, Wang YX, Wareham NJ, Watkins H, Weir DR, Wickremasinghe AR, Wu T, Zeggini E, Zheng W, Bouchard C, Evans MK, Gudnason V, Kardia SLR, Liu Y, Psaty BM, Ridker PM, van Dam RM, Mook-Kanamori DO, Fornage M, Province MA, Kelly TN, Fox ER, Hayward C, van Duijn CM, Tai ES, Wong TY, Loos RJF, Franceschini N, Rotter JI, Zhu X, Bierut LJ, Gauderman WJ, Rice K, Munroe PB, Morrison AC, Rao DC, Rotimi CN, Cupples LA. Multi-ancestry genome-wide gene-smoking interaction study of 387,272 individuals identifies new loci associated with serum lipids. Nat Genet 2019; 51:636-648. [PMID: 30926973 PMCID: PMC6467258 DOI: 10.1038/s41588-019-0378-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/07/2019] [Indexed: 12/08/2022]
Abstract
The concentrations of high- and low-density-lipoprotein cholesterol and triglycerides are influenced by smoking, but it is unknown whether genetic associations with lipids may be modified by smoking. We conducted a multi-ancestry genome-wide gene-smoking interaction study in 133,805 individuals with follow-up in an additional 253,467 individuals. Combined meta-analyses identified 13 new loci associated with lipids, some of which were detected only because association differed by smoking status. Additionally, we demonstrate the importance of including diverse populations, particularly in studies of interactions with lifestyle factors, where genomic and lifestyle differences by ancestry may contribute to novel findings.
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Affiliation(s)
- Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, USA.
| | - Yun J Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael R Brown
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Aldi T Kraja
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ioanna Ntalla
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Karen Schwander
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Elise Lim
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Xuan Deng
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jingmin Liu
- Women's Health Initiative Clinical Coordinating Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Yingchang Lu
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Centre for Quantitative Medicine, Academic Medicine Research Institute, Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jennifer E Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Solomon K Musani
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Changwei Li
- Epidemiology and Biostatistics, University of Georgia at Athens College of Public Health, Athens, GA, USA
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Melissa A Richard
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Raymond Noordam
- Internal Medicine, Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jenna Baker
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Hugues Aschard
- Centre de Bioinformatique, Biostatistique, et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Biostatistics, University of Washington, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jingzhong Ding
- Center on Diabetes, Obesity, and Metabolism, Gerontology and Geriatric Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Alisa K Manning
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Albert V Smith
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Salman M Tajuddin
- Health Disparities Research Section, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, US National Institutes of Health, Baltimore, MD, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maris Alver
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mathilde Boissel
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Jin Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Xu Chen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jasmin Divers
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Chuan Gao
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Anuj Goel
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yanick Hagemeijer
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, the Netherlands
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | - Fernando P Hartwig
- Postgraduate Programme in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Meian He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Andrea R V R Horimoto
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Fang-Chi Hsu
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Yi-Jen Hung
- Endocrinology and Metabolism, Tri-Service General Hospital, Taipei, Taiwan
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Pirjo Komulainen
- Foundation for Research in Health, Exercise, and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Brigitte Kühnel
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Karin Leander
- Unit of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Keng-Hung Lin
- Ophthalmology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jian'an Luan
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Technology, Tampere University, Tampere, Finland
| | - Nana Matoba
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ilja M Nolte
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
| | - Maik Pietzner
- DZHK (German Centre for Cardiovascular Health), Partner Site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Bram Prins
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Muhammad Riaz
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Antonietta Robino
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | - M Abdullah Said
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, the Netherlands
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Robert A Scott
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Alena Stancáková
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Bamidele O Tayo
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
| | - Peter J van der Most
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
| | - Tibor V Varga
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden
| | - Tzung-Dau Wang
- Cardiovascular Center, National Taiwan University Hospital, Taipei, Taiwan
- National Taiwan University College of Medicine, Taipei, Taiwan
- Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yajuan Wang
- Department of Population Quantitative and Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Erin B Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yong-Bing Xiang
- SKLORG and Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lisa R Yanek
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Weihua Zhang
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK
- Department of Cardiology, Ealing Hospital, Middlesex, UK
| | - Jing Hua Zhao
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Saima Afaq
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK
| | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marzyeh Amini
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
| | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zorayr Arzumanyan
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Christie Ballantyne
- Section of Cardiovascular Research, Baylor College of Medicine, Houston, TX, USA
- Houston Methodist Debakey Heart and Vascular Center, Houston, TX, USA
| | - R Graham Barr
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Erwin P Bottinger
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ulrich Broeckel
- Section of Genomic Pediatrics, Departments of Pediatrics, Medicine, and Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Morris Brown
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Mickaël Canouil
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Sabanayagam Charumathi
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Centre for Quantitative Medicine, Academic Medicine Research Institute, Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kaare Christensen
- Danish Aging Research Center, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Maria Pina Concas
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
| | - John M Connell
- Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Lisa de Las Fuentes
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - H Janaka de Silva
- Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Qing Duan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charles B Eaton
- Department of Family Medicine and Epidemiology, Alpert Medical School of Brown University, Providence, RI, USA
| | - Ruben N Eppinga
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, the Netherlands
| | - Jessica D Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Nita G Forouhi
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Terrence Forrester
- UWI Solutions for Developing Countries, University of the West Indies, Kingston, Jamaica
| | - Yechiel Friedlander
- Braun School of Public Health, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Ilaria Gandin
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - He Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Bruna Gigante
- Unit of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - C Charles Gu
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, US National Institutes of Health, Bethesda, MD, USA
| | - Sami Heikkinen
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Chew-Kiat Heng
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Makoto Hirata
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Minato-ku, Japan
| | - James E Hixson
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Yucheng Jia
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Roby Joehanes
- Hebrew SeniorLife, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Craig Johnson
- Collaborative Health Studies Coordinating Center, University of Washington, Seattle, WA, USA
| | - Jost Bruno Jonas
- Department of Ophthalmology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- Beijing Institute of Ophthalmology, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing Tongren Eye Center, Capital Medical University, Beijing, China
| | - Anne E Justice
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Geriatric and General Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Woon-Puay Koh
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Ivana Kolcic
- Department of Public Health, Department of Medicine, University of Split, Split, Croatia
| | - Charles Kooperberg
- Fred Hutchinson Cancer Research Center, University of Washington School of Public Health, Seattle, WA, USA
| | - Jose E Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Stephen B Kritchevsky
- Sticht Center for Healthy Aging and Alzheimer's Prevention, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Johanna Kuusisto
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Timo A Lakka
- Foundation for Research in Health, Exercise, and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Claudia Langenberg
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, US National Institutes of Health, Bethesda, MD, USA
| | - Benjamin Lehne
- Institute of Clinical Sciences, Department of Molecular Sciences, Imperial College, London, UK
| | - Cora E Lewis
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yize Li
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jingjing Liang
- Department of Population Quantitative and Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Shiow Lin
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kiang Liu
- Epidemiology, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marie Loh
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology, and Research, Singapore, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Kurt K Lohman
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Anna Luzzi
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Colin A McKenzie
- Tropical Metabolism Research Unit, Caribbean Institute for Health Research, University of the West Indies, Mona, Jamaica
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
- Technische Universität München, Munich, Germany
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands
| | - Lili Milani
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Andrew P Morris
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Alison D Murray
- Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - Mike A Nalls
- Data Tecnica International, Glen Echo, MD, USA
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Matthias Nauck
- DZHK (German Centre for Cardiovascular Health), Partner Site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeffrey R O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - George J Papanicolau
- Epidemiology Branch, Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Epidemiology, Faculty of Medicine, Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig Maximilian University, Munich, Germany
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Ozren Polasek
- Department of Public Health, Department of Medicine, University of Split, Split, Croatia
- Psychiatric Hospital 'Sveti Ivan', Zagreb, Croatia
- Gen-info, Ltd, Zagreb, Croatia
| | - Neil Poulter
- School of Public Health, Imperial College, London, UK
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Alex P Reiner
- Fred Hutchinson Cancer Research Center, University of Washington School of Public Health, Seattle, WA, USA
| | - Frida Renström
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden
- Department of Biobank Research, Umeå University, Umeå, Sweden
| | - Treva K Rice
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jennifer G Robinson
- Department of Epidemiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Frits R Rosendaal
- Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Carsten O Schmidt
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Pamela J Schreiner
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - William R Scott
- Institute of Clinical Sciences, Department of Molecular Sciences, Imperial College, London, UK
- National Heart and Lung Institute, Imperial College, London, UK
| | - Peter Sever
- National Heart and Lung Institute, Imperial College, London, UK
| | - Yuan Shi
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Stephen Sidney
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Mario Sims
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Harold Snieder
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, UK
| | - Konstantin Strauch
- Genetic Epidemiology, Faculty of Medicine, Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig Maximilian University, Munich, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Heather M Stringham
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas Y Q Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Hua Tang
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Yih Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Social and Behavioral Sciences, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Stephen T Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Diana van Heemst
- Internal Medicine, Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Heming Wang
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Lan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Wen Bin Wei
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Christine A Williams
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Gregory Wilson
- Jackson Heart Study, School of Public Health, Jackson State University, Jackson, MS, USA
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kristin Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caizheng Yu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jian-Min Yuan
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, USA
| | - Alan B Zonderman
- Behavioral Epidemiology Section, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, US National Institutes of Health, Baltimore, MD, USA
| | - Diane M Becker
- Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Donald W Bowden
- Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK
- Department of Cardiology, Ealing Hospital, Middlesex, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Imperial College Healthcare NHS Trust, London, UK
| | - Richard S Cooper
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
| | - Ulf de Faire
- Unit of Cardiovascular Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Psychology, University of Edinburgh, Edinburgh, UK
| | - Paul Elliott
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK
| | - Tõnu Esko
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Martin Farrall
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul W Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
- OCDEM, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Barry I Freedman
- Nephrology, Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Philippe Froguel
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
- Department of Genomics of Common Disease, Imperial College, London, UK
| | - Paolo Gasparini
- Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', Trieste, Italy
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Bernardo L Horta
- Postgraduate Programme in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Jyh-Ming Jimmy Juang
- National Taiwan University College of Medicine, Taipei, Taiwan
- Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Candace M Kammerer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jaspal S Kooner
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK
- Department of Cardiology, Ealing Hospital, Middlesex, UK
- National Heart and Lung Institute, Imperial College, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - I-Te Lee
- Endocrinology and Metabolism, Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Technology, Tampere University, Tampere, Finland
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Albertine J Oldehinkel
- University of Groningen, University Medical Center Groningen, Department of Psychiatry, Groningen, the Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Vrije Universiteit, Amsterdam, the Netherlands
| | - Alexandre C Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Rainer Rauramaa
- Foundation for Research in Health, Exercise, and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - James Scott
- National Heart and Lung Institute, Imperial College, London, UK
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Pim van der Harst
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Lynne E Wagenknecht
- Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jun-Sing Wang
- Endocrinology and Metabolism, Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ya Xing Wang
- Beijing Institute of Ophthalmology, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing Tongren Eye Center, Capital Medical University, Beijing, China
| | - Nicholas J Wareham
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David R Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | | | - Tangchun Wu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Eleftheria Zeggini
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
- Institute of Translational Genomics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Michele K Evans
- Health Disparities Research Section, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, US National Institutes of Health, Baltimore, MD, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Yongmei Liu
- Public Health Sciences, Epidemiology and Prevention, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Dennis O Mook-Kanamori
- Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Public Health and Primary Care, Leiden University Medical Center, Leiden, the Netherlands
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Tanika N Kelly
- Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Ervin R Fox
- Cardiology, Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiaofeng Zhu
- Department of Population Quantitative and Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Laura J Bierut
- Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - W James Gauderman
- Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Patricia B Munroe
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- NIHR Barts Cardiovascular Biomedical Research Centre, Queen Mary University of London, London, UK
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dabeeru C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, USA.
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
- Framingham Heart Study, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD, USA.
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Genetic variants differentially associated with rheumatoid arthritis and systemic lupus erythematosus reveal the disease-specific biology. Sci Rep 2019; 9:2739. [PMID: 30804378 PMCID: PMC6390106 DOI: 10.1038/s41598-019-39132-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/18/2019] [Indexed: 12/29/2022] Open
Abstract
Two rheumatic autoimmune diseases, rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), have distinct clinical features despite their genetic similarities. We hypothesized that disease-specific variants exclusively associated with only one disease could contribute to disease-specific phenotypes. We calculated the strength of disease specificity for each variant in each disease against the other disease using summary association statistics reported in the largest genome-wide association studies of RA and SLE. Most of highly disease-specific associations were explained by non-coding variants that were significantly enriched within regulatory regions (enhancers or H3K4me3 histone modification marks) in specific cell or organ types. (e.g., In RA, regulatory T primary cells, CD4+ memory T primary cells, thymus and lung; In SLE, CD19+ B primary cells, mobilized CD34+ primary cells, regulatory T primary cells and monocytes). Consistently, genes in the disease-specific loci were significantly involved in T cell- and B cell-related gene sets in RA and SLE. In summary, this study identified disease-specific variants between RA and SLE, and provided statistical evidence for disease-specific cell types, organ and gene sets that may drive the disease-specific phenotypes.
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Clifford H, Dulneva A, Ponting CP, Haerty W, Becker EBE. A gene expression signature in developing Purkinje cells predicts autism and intellectual disability co-morbidity status. Sci Rep 2019; 9:485. [PMID: 30679692 PMCID: PMC6346046 DOI: 10.1038/s41598-018-37284-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 11/16/2018] [Indexed: 11/09/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disease whose underpinning molecular mechanisms and neural substrates are subject to intense scrutiny. Interestingly, the cerebellum has emerged as one of the key brain regions affected in ASD. However, the genetic and molecular mechanisms that link the cerebellum to ASD, particularly during development, remain poorly understood. To gain insight into the genetic and molecular mechanisms that might link the cerebellum to ASD, we analysed the transcriptome dynamics of a developing cell population highly enriched for Purkinje cells of the mouse cerebellum across multiple timepoints. We identified a single cluster of genes whose expression is positively correlated with development and which is enriched for genes associated with ASD. This ASD-associated gene cluster was specific to developing Purkinje cells and not detected in the mouse neocortex during the same developmental period, in which we identified a distinct temporally regulated ASD gene module. Furthermore, the composition of ASD risk genes within the two distinct clusters was significantly different in their association with intellectual disability (ID), consistent with the existence of genetically and spatiotemporally distinct endophenotypes of ASD. Together, our findings define a specific cluster of ASD genes that is enriched in developing PCs and predicts co-morbidity status.
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Affiliation(s)
- Harry Clifford
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Anna Dulneva
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Chris P Ponting
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom
| | - Wilfried Haerty
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom. .,Earlham Institute, Norwich Research Park, Norwich, NR4 7UG, United Kingdom.
| | - Esther B E Becker
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, United Kingdom.
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Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways. mSphere 2018; 3:3/5/e00445-18. [PMID: 30355668 PMCID: PMC6200987 DOI: 10.1128/msphere.00445-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The transcriptional profiles of related pathogens and their responses to host-induced stresses underpin their pathogenicity. Expression differences between related pathogens during host interaction can indicate when and how these genes contribute to virulence, ultimately informing new and improved treatment strategies for those diseases. In this paper, we compare the transcriptional profiles of five isolates representing four lineages of C. gattii in rich media. Our analyses identified key processes, including those involving cell capsule, ergosterol production, and melanin, that are differentially expressed between lineages, and we found that VGII has the most distinct profile in terms of numbers of differentially expressed genes. All lineages have also undergone subfunctionalization for several paralogs, including capsule biosynthesis and attachment genes. Most genes appeared downregulated during coincubation with macrophages, with the largest decrease observed for capsule attachment genes, which appeared to be coordinated with a stress response, as all lineages also upregulated oxidative stress response genes. Furthermore, VGII upregulated many genes that are linked to ergosterol biosynthesis and switched from expression of the laccase LAC1 to expression of LAC2 ex vivo. Finally, we saw a pronounced increase in the FosB/Jun/Egr1 regulatory proteins at early time points in bone marrow-derived macrophages, marking a role in the host response to C. gattii. This work highlights the dynamic roles of key C. gattii virulence genes in response to macrophages. Cryptococcus gattii is a pathogenic yeast of humans and other animals which causes disease predominantly in immunocompetent hosts. Infection begins when aerosolized yeast or spores enter the body, triggering an immune response, including engulfment by macrophages. To understand the early transcriptional signals in both the yeast and its mammalian host, we performed a time-course dual-transcriptome sequencing (RNA-seq) experiment for four lineages of C. gattii (lineages VGI to IV) interacting with mouse macrophages at 1, 3, and 6 h postinfection. Comparisons of in vitro to ex vivo gene expression levels indicated that lineage VGII is transcriptionally divergent from non-VGII lineages, including differential expression of genes involved in capsule synthesis, capsule attachment, and ergosterol production. Several paralogous genes demonstrated subfunctionalization between lineages, including upregulation of capsule biosynthesis-related gene CAP2 and downregulation of CAP1 in VGIII. Isolates also compensate for lineage-specific gene losses by overexpression of genetically similar paralogs, including overexpression of capsule gene CAS3 in VGIV, which have lost the CAS31 gene. Differential expression of one in five C. gattii genes was detected following coincubation with mouse macrophages; all isolates showed high induction of oxidative-reduction functions and downregulation of capsule attachment genes. We also found that VGII switches expression of two laccase paralogs (from LAC1 to LAC2) during coincubation of macrophages. Finally, we found that mouse macrophages respond to all four lineages of C. gattii by upregulating FosB/Jun/Egr1 regulatory proteins at early time points. This report highlights the evolutionary breadth of expression profiles among the lineages of C. gattii and the diversity of transcriptional responses at this host-pathogen interface. IMPORTANCE The transcriptional profiles of related pathogens and their responses to host-induced stresses underpin their pathogenicity. Expression differences between related pathogens during host interaction can indicate when and how these genes contribute to virulence, ultimately informing new and improved treatment strategies for those diseases. In this paper, we compare the transcriptional profiles of five isolates representing four lineages of C. gattii in rich media. Our analyses identified key processes, including those involving cell capsule, ergosterol production, and melanin, that are differentially expressed between lineages, and we found that VGII has the most distinct profile in terms of numbers of differentially expressed genes. All lineages have also undergone subfunctionalization for several paralogs, including capsule biosynthesis and attachment genes. Most genes appeared downregulated during coincubation with macrophages, with the largest decrease observed for capsule attachment genes, which appeared to be coordinated with a stress response, as all lineages also upregulated oxidative stress response genes. Furthermore, VGII upregulated many genes that are linked to ergosterol biosynthesis and switched from expression of the laccase LAC1 to expression of LAC2 ex vivo. Finally, we saw a pronounced increase in the FosB/Jun/Egr1 regulatory proteins at early time points in bone marrow-derived macrophages, marking a role in the host response to C. gattii. This work highlights the dynamic roles of key C. gattii virulence genes in response to macrophages.
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Chen C, Chen D, Xue H, Liu X, Zhang T, Tang S, Li W, Xu X. IDGenetics: a comprehensive database for genes and mutations of intellectual disability related disorders. Neurosci Lett 2018; 685:96-101. [PMID: 30144540 DOI: 10.1016/j.neulet.2018.08.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/22/2018] [Accepted: 08/21/2018] [Indexed: 11/19/2022]
Abstract
Intellectual disability (ID) is one of the most prevalent chronic developmental brain disorders or phenotype of syndromic ID, affecting nearly 1-2% of the general population worldwide. Over recent decades, tremendous effort and high-throughput platforms have been devised to explore the complex heterogeneity, numerous genes and variants have been associated with the ID, especially de novo mutations and copy number variants. An organized resource containing the increasing genetic data is imperative to assist ID research. In this study, the integrative and annotated intellectual disability database has been developed, named 'IDGenetics', which contains known information about ID, including 815 genes and 17102 variants associated with 918 clinical diseases (3001 clinical phenotype) collected from 3822 publications and ID-related databases. Furthermore, in-depth data mining was performed to obtain an understanding of each entry, including functional annotation, gene/disease/phenotype network establishment and overlap analysis focusing on comorbidity. 1478 candidate genes (483 high-confidence and 995 low-confidence) were collected and prioritized by adopting the annotations of 12 functional prediction tools and algorithm. In addition, IDGenetics database provides concise search methods, convenient browsing functions, intuitive graphical displays and constantly updated features. IDGenetics will be a valuable and integrative resource for deciphering the genetic and functional architecture of ID and the improvement of clinical diagnosis, intervention and treatment.
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Affiliation(s)
- Chong Chen
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, 325000, China
| | - Denghui Chen
- Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Huangqi Xue
- Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xinting Liu
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325035, China
| | - Tao Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325035, China
| | - Shaohua Tang
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, 325000, China; Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Wei Li
- Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China.
| | - Xueqin Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, 325000, China.
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Pardiñas AF, Holmans P, Pocklington AJ, Escott-Price V, Ripke S, Carrera N, Legge SE, Bishop S, Cameron D, Hamshere ML, Han J, Hubbard L, Lynham A, Mantripragada K, Rees E, MacCabe JH, McCarroll SA, Baune BT, Breen G, Byrne EM, Dannlowski U, Eley TC, Hayward C, Martin NG, McIntosh AM, Plomin R, Porteous DJ, Wray NR, Caballero A, Geschwind DH, Huckins LM, Ruderfer DM, Santiago E, Sklar P, Stahl EA, Won H, Agerbo E, Als TD, Andreassen OA, Bækvad-Hansen M, Mortensen PB, Pedersen CB, Børglum AD, Bybjerg-Grauholm J, Djurovic S, Durmishi N, Pedersen MG, Golimbet V, Grove J, Hougaard DM, Mattheisen M, Molden E, Mors O, Nordentoft M, Pejovic-Milovancevic M, Sigurdsson E, Silagadze T, Hansen CS, Stefansson K, Stefansson H, Steinberg S, Tosato S, Werge T, Collier DA, Rujescu D, Kirov G, Owen MJ, O'Donovan MC, Walters JTR. Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Nat Genet 2018; 50:381-389. [PMID: 29483656 PMCID: PMC5918692 DOI: 10.1038/s41588-018-0059-2] [Citation(s) in RCA: 962] [Impact Index Per Article: 160.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/07/2018] [Indexed: 12/13/2022]
Abstract
Schizophrenia is a debilitating psychiatric condition often associated with poor quality of life and decreased life expectancy. Lack of progress in improving treatment outcomes has been attributed to limited knowledge of the underlying biology, although large-scale genomic studies have begun to provide insights. We report a new genome-wide association study of schizophrenia (11,260 cases and 24,542 controls), and through meta-analysis with existing data we identify 50 novel associated loci and 145 loci in total. Through integrating genomic fine-mapping with brain expression and chromosome conformation data, we identify candidate causal genes within 33 loci. We also show for the first time that the common variant association signal is highly enriched among genes that are under strong selective pressures. These findings provide new insights into the biology and genetic architecture of schizophrenia, highlight the importance of mutation-intolerant genes and suggest a mechanism by which common risk variants persist in the population.
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Affiliation(s)
- Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Andrew J Pocklington
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry and Psychotherapy, Charité, Campus Mitte, Berlin, Germany
| | - Noa Carrera
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Sophie E Legge
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Sophie Bishop
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Darren Cameron
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Marian L Hamshere
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Jun Han
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Leon Hubbard
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Amy Lynham
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Kiran Mantripragada
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - James H MacCabe
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bernhard T Baune
- Discipline of Psychiatry, University of Adelaide, Adelaide, South Australia, Australia
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR Biomedical Research Centre for Mental Health, Maudsley Hospital and Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Enda M Byrne
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Udo Dannlowski
- Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - Thalia C Eley
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Caroline Hayward
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Nicholas G Martin
- School of Psychology, University of Queensland, Brisbane, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Robert Plomin
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - David J Porteous
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Naomi R Wray
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología. Facultad de Biología, Universidad de Vigo, Vigo, Spain
| | - Daniel H Geschwind
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laura M Huckins
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Douglas M Ruderfer
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Enrique Santiago
- Departamento de Biología Funcional. Facultad de Biología, Universidad de Oviedo, Oviedo, Spain
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eli A Stahl
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hyejung Won
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Esben Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Thomas D Als
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Ole A Andreassen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Preben Bo Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Carsten Bøcker Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Srdjan Djurovic
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Naser Durmishi
- Department of Child and Adolescent Psychiatry, University Clinic of Psychiatry, Skopje, Macedonia
| | - Marianne Giørtz Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Vera Golimbet
- Department of Clinical Genetics, Mental Health Research Center, Moscow, Russia
| | - Jakob Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Manuel Mattheisen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Espen Molden
- Center for Psychopharmacology, Diakonhjemmet Hospital, Oslo, Norway
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Teimuraz Silagadze
- Department of Psychiatry and Drug Addiction, Tbilisi State Medical University (TSMU), Tbilisi, Georgia
| | - Christine Søholm Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | | | | | | | - Sarah Tosato
- Section of Psychiatry, Department of Public Health and Community Medicine, University of Verona, Verona, Italy
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - David A Collier
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Discovery Neuroscience Research, Eli Lilly and Company, Lilly Research Laboratories, Windlesham, UK
| | - Dan Rujescu
- Department of Psychiatry, University of Halle, Halle, Germany
- Department of Psychiatry, University of Munich, Munich, Germany
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
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Wallqvist A, Wang H, Zavaljevski N, Memišević V, Kwon K, Pieper R, Rajagopala SV, Reifman J. Mechanisms of action of Coxiella burnetii effectors inferred from host-pathogen protein interactions. PLoS One 2017; 12:e0188071. [PMID: 29176882 PMCID: PMC5703456 DOI: 10.1371/journal.pone.0188071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/31/2017] [Indexed: 02/06/2023] Open
Abstract
Coxiella burnetii is an obligate Gram-negative intracellular pathogen and the etiological agent of Q fever. Successful infection requires a functional Type IV secretion system, which translocates more than 100 effector proteins into the host cytosol to establish the infection, restructure the intracellular host environment, and create a parasitophorous vacuole where the replicating bacteria reside. We used yeast two-hybrid (Y2H) screening of 33 selected C. burnetii effectors against whole genome human and murine proteome libraries to generate a map of potential host-pathogen protein-protein interactions (PPIs). We detected 273 unique interactions between 20 pathogen and 247 human proteins, and 157 between 17 pathogen and 137 murine proteins. We used orthology to combine the data and create a single host-pathogen interaction network containing 415 unique interactions between 25 C. burnetii and 363 human proteins. We further performed complementary pairwise Y2H testing of 43 out of 91 C. burnetii-human interactions involving five pathogen proteins. We used the combined data to 1) perform enrichment analyses of target host cellular processes and pathways, 2) examine effectors with known infection phenotypes, and 3) infer potential mechanisms of action for four effectors with uncharacterized functions. The host-pathogen interaction profiles supported known Coxiella phenotypes, such as adapting cell morphology through cytoskeletal re-arrangements, protein processing and trafficking, organelle generation, cholesterol processing, innate immune modulation, and interactions with the ubiquitin and proteasome pathways. The generated dataset of PPIs-the largest collection of unbiased Coxiella host-pathogen interactions to date-represents a rich source of information with respect to secreted pathogen effector proteins and their interactions with human host proteins.
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Affiliation(s)
- Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Hao Wang
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Nela Zavaljevski
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Vesna Memišević
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
| | - Keehwan Kwon
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Rembert Pieper
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America
- * E-mail:
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Krupke DM, Begley DA, Sundberg JP, Richardson JE, Neuhauser SB, Bult CJ. The Mouse Tumor Biology Database: A Comprehensive Resource for Mouse Models of Human Cancer. Cancer Res 2017; 77:e67-e70. [PMID: 29092943 DOI: 10.1158/0008-5472.can-17-0584] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/16/2017] [Accepted: 08/07/2017] [Indexed: 01/28/2023]
Abstract
Research using laboratory mice has led to fundamental insights into the molecular genetic processes that govern cancer initiation, progression, and treatment response. Although thousands of scientific articles have been published about mouse models of human cancer, collating information and data for a specific model is hampered by the fact that many authors do not adhere to existing annotation standards when describing models. The interpretation of experimental results in mouse models can also be confounded when researchers do not factor in the effect of genetic background on tumor biology. The Mouse Tumor Biology (MTB) database is an expertly curated, comprehensive compendium of mouse models of human cancer. Through the enforcement of nomenclature and related annotation standards, MTB supports aggregation of data about a cancer model from diverse sources and assessment of how genetic background of a mouse strain influences the biological properties of a specific tumor type and model utility. Cancer Res; 77(21); e67-70. ©2017 AACR.
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Siriboonpiputtana T, Zeisig BB, Zarowiecki M, Fung TK, Mallardo M, Tsai CT, Lau PNI, Hoang QC, Veiga P, Barnes J, Lynn C, Wilson A, Lenhard B, So CWE. Transcriptional memory of cells of origin overrides β-catenin requirement of MLL cancer stem cells. EMBO J 2017; 36:3139-3155. [PMID: 28978671 PMCID: PMC5666593 DOI: 10.15252/embj.201797994] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 08/23/2017] [Accepted: 08/25/2017] [Indexed: 01/03/2023] Open
Abstract
While β-catenin has been demonstrated as an essential molecule and therapeutic target for various cancer stem cells (CSCs) including those driven by MLL fusions, here we show that transcriptional memory from cells of origin predicts AML patient survival and allows β-catenin-independent transformation in MLL-CSCs derived from hematopoietic stem cell (HSC)-enriched LSK population but not myeloid-granulocyte progenitors. Mechanistically, β-catenin regulates expression of downstream targets of a key transcriptional memory gene, Hoxa9 that is highly enriched in LSK-derived MLL-CSCs and helps sustain leukemic self-renewal. Suppression of Hoxa9 sensitizes LSK-derived MLL-CSCs to β-catenin inhibition resulting in abolishment of CSC transcriptional program and transformation ability. In addition, further molecular and functional analyses identified Prmt1 as a key common downstream mediator for β-catenin/Hoxa9 functions in LSK-derived MLL-CSCs. Together, these findings not only uncover an unexpectedly important role of cells of origin transcriptional memory in regulating CSC self-renewal, but also reveal a novel molecular network mediated by β-catenin/Hoxa9/Prmt1 in governing leukemic self-renewal.
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MESH Headings
- Animals
- Antigens, Ly/genetics
- Antigens, Ly/metabolism
- Cell Proliferation
- Cell Survival
- Disease Models, Animal
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Hematopoietic Stem Cells/metabolism
- Hematopoietic Stem Cells/pathology
- Homeodomain Proteins/antagonists & inhibitors
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Protein-Arginine N-Methyltransferases/genetics
- Protein-Arginine N-Methyltransferases/metabolism
- Proto-Oncogene Proteins c-kit/genetics
- Proto-Oncogene Proteins c-kit/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Signal Transduction
- Survival Analysis
- Transcription, Genetic
- beta Catenin/genetics
- beta Catenin/metabolism
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Affiliation(s)
- Teerapong Siriboonpiputtana
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Bernd B Zeisig
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Magdalena Zarowiecki
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Tsz Kan Fung
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Maria Mallardo
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Chiou-Tsun Tsai
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Priscilla Nga Ieng Lau
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Quoc Chinh Hoang
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Pedro Veiga
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Jo Barnes
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Claire Lynn
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Amanda Wilson
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
| | - Boris Lenhard
- Faculty of Medicine, Institute of Clinical Sciences, Imperial College London, London, UK
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, UK
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Chi Wai Eric So
- Department of Haematological Medicine, Division of Cancer Studies, Leukemia and Stem Cell Biology Team, King's College London, London, UK
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41
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Li AH, Hanchard NA, Furthner D, Fernbach S, Azamian M, Nicosia A, Rosenfeld J, Muzny D, D'Alessandro LCA, Morris S, Jhangiani S, Parekh DR, Franklin WJ, Lewin M, Towbin JA, Penny DJ, Fraser CD, Martin JF, Eng C, Lupski JR, Gibbs RA, Boerwinkle E, Belmont JW. Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns. Genome Med 2017; 9:95. [PMID: 29089047 PMCID: PMC5664429 DOI: 10.1186/s13073-017-0482-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 10/12/2017] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Left-sided lesions (LSLs) account for an important fraction of severe congenital cardiovascular malformations (CVMs). The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes. METHODS Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF), and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs. RESULTS Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1) as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2). We also identified two genes (DNAH5, OFD1) with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95% confidence interval 2.5-6.5). CONCLUSIONS Our analytical strategy highlights the utility of bioinformatic resources, including human disease records and model organism phenotyping, in novel gene discovery for rare human disease. The results underscore the extensive genetic heterogeneity underlying non-syndromic LSLs, and posit potential novel candidate genes and complex modes of inheritance in this important group of birth defects.
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Affiliation(s)
- Alexander H Li
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Dieter Furthner
- Department of Paediatrics, Children's Hospital, Krankenhausstr. 26-30, 4020, Linz, Austria
| | - Susan Fernbach
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mahshid Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Annarita Nicosia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Shaine Morris
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Dhaval R Parekh
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Wayne J Franklin
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Mark Lewin
- Division of Cardiology, Seattle Children's Hospital, Seattle, WA, USA
| | - Jeffrey A Towbin
- Pediatric Cardiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Daniel J Penny
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Charles D Fraser
- Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - James F Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, and the Texas Heart Institute, Houston, TX, USA
| | - Christine Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA. .,, 5200 Illumina Way, San Diego, CA, USA.
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42
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Sandor C, Beer NL, Webber C. Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network. PLoS Comput Biol 2017; 13:e1005816. [PMID: 29059180 PMCID: PMC5667928 DOI: 10.1371/journal.pcbi.1005816] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 11/02/2017] [Accepted: 10/11/2017] [Indexed: 12/14/2022] Open
Abstract
Type 2 Diabetes (T2D) constitutes a global health burden. Efforts to uncover predisposing genetic variation have been considerable, yet detailed knowledge of the underlying pathogenesis remains poor. Here, we constructed a T2D phenotypic-linkage network (T2D-PLN), by integrating diverse gene functional information that highlight genes, which when disrupted in mice, elicit similar T2D-relevant phenotypes. Sensitising the network to T2D-relevant phenotypes enabled significant functional convergence to be detected between genes implicated in monogenic or syndromic diabetes and genes lying within genomic regions associated with T2D common risk. We extended these analyses to a recent multiethnic T2D case-control exome of 12,940 individuals that found no evidence of T2D risk association for rare frequency variants outside of previously known T2D risk loci. Examining associations involving protein-truncating variants (PTV), most at low population frequencies, the T2D-PLN was able to identify a convergent set of biological pathways that were perturbed within four of five independent T2D case/control ethnic sets of 2000 to 5000 exomes each. These same pathways were found to be over-represented among both known monogenic or syndromic diabetes genes and genes within T2D-associated common risk loci. Our study demonstrates convergent biology amongst variants representing different classes of T2D genetic risk. Although convergence was observed at the pathway level, few of the contributing genes were found in common between different cohorts or variant classes, most notably between the exome variant sets which suggests that future rare variant studies may be better focusing their power onto a single population of recent common ancestry.
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Affiliation(s)
- Cynthia Sandor
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Nicola L. Beer
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Caleb Webber
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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43
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Sequence analysis of chromosome 1 revealed different selection patterns between Chinese wild mice and laboratory strains. Mol Genet Genomics 2017. [PMID: 28631230 DOI: 10.1007/s00438-017-1335-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Both natural and artificial selection play a critical role in animals' adaptation to the environment. Detection of the signature of selection in genomic regions can provide insights for understanding the function of specific phenotypes. It is generally assumed that laboratory mice may experience intense artificial selection while wild mice more natural selection. However, the differences of selection signature in the mouse genome and underlying genes between wild and laboratory mice remain unclear. In this study, we used two mouse populations: chromosome 1 (Chr 1) substitution lines (C1SLs) derived from Chinese wild mice and mouse genome project (MGP) sequenced inbred strains and two selection detection statistics: Fst and Tajima's D to identify the signature of selection footprint on Chr 1. For the differentiation between the C1SLs and MGP, 110 candidate selection regions containing 47 protein coding genes were detected. A total of 149 selection regions which encompass 7.215 Mb were identified in the C1SLs by Tajima's D approach. While for the MGP, we identified nearly twice selection regions (243) compared with the C1SLs which accounted for 13.27 Mb Chr 1 sequence. Through functional annotation, we identified several biological processes with significant enrichment including seven genes in the olfactory transduction pathway. In addition, we searched the phenotypes associated with the 47 candidate selection genes identified by Fst. These genes were involved in behavior, growth or body weight, mortality or aging, and immune systems which align well with the phenotypic differences between wild and laboratory mice. Therefore, the findings would be helpful for our understanding of the phenotypic differences between wild and laboratory mice and applications for using this new mouse resource (C1SLs) for further genetics studies.
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44
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Muscle-relevant genes marked by stable H3K4me2/3 profiles and enriched MyoD binding during myogenic differentiation. PLoS One 2017; 12:e0179464. [PMID: 28609469 PMCID: PMC5469484 DOI: 10.1371/journal.pone.0179464] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/29/2017] [Indexed: 11/18/2022] Open
Abstract
Post-translational modifications of histones play a key role in the regulation of gene expression during development and differentiation. Numerous studies have shown the dynamics of combinatorial regulation by transcription factors and histone modifications, in the sense that different combinations lead to distinct expression outcomes. Here, we investigated gene regulation by stable enrichment patterns of histone marks H3K4me2 and H3K4me3 in combination with the chromatin binding of the muscle tissue-specific transcription factor MyoD during myogenic differentiation of C2C12 cells. Using k-means clustering, we found that specific combinations of H3K4me2/3 profiles over and towards the gene body impact on gene expression and marks a subset of genes important for muscle development and differentiation. By further analysis, we found that the muscle key regulator MyoD was significantly enriched on this subset of genes and played a repressive role during myogenic differentiation. Among these genes, we identified the pluripotency gene Patz1, which is repressed during myogenic differentiation through direct binding of MyoD to promoter elements. These results point to the importance of integrating histone modifications and MyoD chromatin binding for coordinated gene activation and repression during myogenic differentiation.
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45
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Aung T, Ozaki M, Lee MC, Schlötzer-Schrehardt U, Thorleifsson G, Mizoguchi T, Igo RP, Haripriya A, Williams SE, Astakhov YS, Orr AC, Burdon KP, Nakano S, Mori K, Abu-Amero K, Hauser M, Li Z, Prakadeeswari G, Bailey JNC, Cherecheanu AP, Kang JH, Nelson S, Hayashi K, Manabe SI, Kazama S, Zarnowski T, Inoue K, Irkec M, Coca-Prados M, Sugiyama K, Järvelä I, Schlottmann P, Lerner SF, Lamari H, Nilgün Y, Bikbov M, Park KH, Cha SC, Yamashiro K, Zenteno JC, Jonas JB, Kumar RS, Perera SA, Chan ASY, Kobakhidze N, George R, Vijaya L, Do T, Edward DP, de Juan Marcos L, Pakravan M, Moghimi S, Ideta R, Bach-Holm D, Kappelgaard P, Wirostko B, Thomas S, Gaston D, Bedard K, Greer WL, Yang Z, Chen X, Huang L, Sang J, Jia H, Jia L, Qiao C, Zhang H, Liu X, Zhao B, Wang YX, Xu L, Leruez S, Reynier P, Chichua G, Tabagari S, Uebe S, Zenkel M, Berner D, Mossböck G, Weisschuh N, Hoja U, Welge-Luessen UC, Mardin C, Founti P, Chatzikyriakidou A, Pappas T, Anastasopoulos E, Lambropoulos A, Ghosh A, Shetty R, Porporato N, Saravanan V, Venkatesh R, Shivkumar C, Kalpana N, Sarangapani S, Kanavi MR, Beni AN, Yazdani S, Lashay A, Naderifar H, Khatibi N, Fea A, Lavia C, Dallorto L, Rolle T, Frezzotti P, Paoli D, Salvi E, Manunta P, Mori Y, Miyata K, Higashide T, Chihara E, Ishiko S, Yoshida A, Yanagi M, Kiuchi Y, Ohashi T, Sakurai T, Sugimoto T, Chuman H, Aihara M, Inatani M, Miyake M, Gotoh N, Matsuda F, Yoshimura N, Ikeda Y, Ueno M, Sotozono C, Jeoung JW, Sagong M, Park KH, Ahn J, Cruz-Aguilar M, Ezzouhairi SM, Rafei A, Chong YF, Ng XY, Goh SR, Chen Y, Yong VHK, Khan MI, Olawoye OO, Ashaye AO, Ugbede I, Onakoya A, Kizor-Akaraiwe N, Teekhasaenee C, Suwan Y, Supakontanasan W, Okeke S, Uche NJ, Asimadu I, Ayub H, Akhtar F, Kosior-Jarecka E, Lukasik U, Lischinsky I, Castro V, Grossmann RP, Sunaric Megevand G, Roy S, Dervan E, Silke E, Rao A, Sahay P, Fornero P, Cuello O, Sivori D, Zompa T, Mills RA, Souzeau E, Mitchell P, Wang JJ, Hewitt AW, Coote M, Crowston JG, Astakhov SY, Akopov EL, Emelyanov A, Vysochinskaya V, Kazakbaeva G, Fayzrakhmanov R, Al-Obeidan SA, Owaidhah O, Aljasim LA, Chowbay B, Foo JN, Soh RQ, Sim KS, Xie Z, Cheong AWO, Mok SQ, Soo HM, Chen XY, Peh SQ, Heng KK, Husain R, Ho SL, Hillmer AM, Cheng CY, Escudero-Domínguez FA, González-Sarmiento R, Martinon-Torres F, Salas A, Pathanapitoon K, Hansapinyo L, Wanichwecharugruang B, Kitnarong N, Sakuntabhai A, Nguyn HX, Nguyn GTT, Nguyn TV, Zenz W, Binder A, Klobassa DS, Hibberd ML, Davila S, Herms S, Nöthen MM, Moebus S, Rautenbach RM, Ziskind A, Carmichael TR, Ramsay M, Álvarez L, García M, González-Iglesias H, Rodríguez-Calvo PP, Fernández-Vega Cueto L, Oguz Ç, Tamcelik N, Atalay E, Batu B, Aktas D, Kasım B, Wilson MR, Coleman AL, Liu Y, Challa P, Herndon L, Kuchtey RW, Kuchtey J, Curtin K, Chaya CJ, Crandall A, Zangwill LM, Wong TY, Nakano M, Kinoshita S, den Hollander AI, Vesti E, Fingert JH, Lee RK, Sit AJ, Shingleton BJ, Wang N, Cusi D, Qamar R, Kraft P, Pericak-Vance MA, Raychaudhuri S, Heegaard S, Kivelä T, Reis A, Kruse FE, Weinreb RN, Pasquale LR, Haines JL, Thorsteinsdottir U, Jonasson F, Allingham RR, Milea D, Ritch R, Kubota T, Tashiro K, Vithana EN, Micheal S, Topouzis F, Craig JE, Dubina M, Sundaresan P, Stefansson K, Wiggs JL, Pasutto F, Khor CC. Genetic association study of exfoliation syndrome identifies a protective rare variant at LOXL1 and five new susceptibility loci. Nat Genet 2017; 49:993-1004. [PMID: 28553957 DOI: 10.1038/ng.3875] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/26/2017] [Indexed: 12/14/2022]
Abstract
Exfoliation syndrome (XFS) is the most common known risk factor for secondary glaucoma and a major cause of blindness worldwide. Variants in two genes, LOXL1 and CACNA1A, have previously been associated with XFS. To further elucidate the genetic basis of XFS, we collected a global sample of XFS cases to refine the association at LOXL1, which previously showed inconsistent results across populations, and to identify new variants associated with XFS. We identified a rare protective allele at LOXL1 (p.Phe407, odds ratio (OR) = 25, P = 2.9 × 10-14) through deep resequencing of XFS cases and controls from nine countries. A genome-wide association study (GWAS) of XFS cases and controls from 24 countries followed by replication in 18 countries identified seven genome-wide significant loci (P < 5 × 10-8). We identified association signals at 13q12 (POMP), 11q23.3 (TMEM136), 6p21 (AGPAT1), 3p24 (RBMS3) and 5q23 (near SEMA6A). These findings provide biological insights into the pathology of XFS and highlight a potential role for naturally occurring rare LOXL1 variants in disease biology.
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Affiliation(s)
- Tin Aung
- Singapore Eye Research Institute, Singapore.,Singapore National Eye Center, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mineo Ozaki
- Ozaki Eye Hospital, Hyuga, Miyazaki, Japan.,Department of Ophthalmology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Mei Chin Lee
- Singapore Eye Research Institute, Singapore.,Academic Clinical Program for Ophthalmology and Visual Sciences, Office of Clinical and Academic Faculty Affairs, Duke-NUS Graduate Medical School, Singapore
| | - Ursula Schlötzer-Schrehardt
- Department of Ophthalmology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | | | - Robert P Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | | | - Susan E Williams
- Division of Ophthalmology, University of the Witwatersrand, Johannesburg, South Africa
| | - Yury S Astakhov
- Department of Ophthalmology, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Andrew C Orr
- Department of Ophthalmology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Kathryn P Burdon
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Satoko Nakano
- Department of Ophthalmology, Oita University Faculty of Medicine, Oita, Japan
| | - Kazuhiko Mori
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Khaled Abu-Amero
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Ophthalmology, College of Medicine, University of Florida, Jacksonville, Florida, USA
| | - Michael Hauser
- Singapore Eye Research Institute, Singapore.,Department of Ophthalmology, Duke University Eye Center, Durham, North Carolina, USA.,Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Zheng Li
- Genome Institute of Singapore, Singapore
| | | | - Jessica N Cooke Bailey
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Alina Popa Cherecheanu
- 'Carol Davila' University of Medicine and Pharmacy, Bucharest, Romania.,Department of Ophthalmology, University Emergency Hospital, Bucharest, Romania
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah Nelson
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | | | | | | | - Tomasz Zarnowski
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University, Lublin, Poland
| | | | - Murat Irkec
- Department of Ophthalmology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - Miguel Coca-Prados
- Fernández-Vega University Institute and Foundation of Ophthalmological Research, University of Oviedo, Oviedo, Spain.,Fernández-Vega Ophthalmological Institute, Oviedo, Spain.,Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kazuhisa Sugiyama
- Department of Ophthalmology, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | | | - S Fabian Lerner
- Fundación para el Estudio del Glaucoma, Buenos Aires, Argentina
| | - Hasnaa Lamari
- Clinique Spécialisée en Ophtalmologie Mohammedia, Mohammedia, Morocco
| | - Yildirim Nilgün
- Department of Ophthalmology, Eskisehir Osmangazi University, Meselik, Eskisehir, Turkey
| | | | - Ki Ho Park
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soon Cheol Cha
- Department of Ophthalmology, Yeungnam University College of Medicine, Daegu, Republic of Korea
| | - Kenji Yamashiro
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Ophthalmology, Otsu Red Cross Hospital, Otsu, Japan
| | - Juan C Zenteno
- Genetics Department, Institute of Ophthalmology 'Conde de Valenciana', Mexico City, Mexico.,Biochemistry Department, Faculty of Medicine, UNAM, Mexico City, Mexico
| | - Jost B Jonas
- Department of Ophthalmology, Medical Faculty Mannheim of the Ruprecht Karls University of Heidelberg, Mannheim, Germany.,Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China
| | | | - Shamira A Perera
- Singapore Eye Research Institute, Singapore.,Singapore National Eye Center, Singapore
| | - Anita S Y Chan
- Singapore Eye Research Institute, Singapore.,Singapore National Eye Center, Singapore.,Academic Clinical Program for Ophthalmology and Visual Sciences, Office of Clinical and Academic Faculty Affairs, Duke-NUS Graduate Medical School, Singapore
| | | | - Ronnie George
- Jadhavbhai Nathamal Singhvi Department of Glaucoma, Medical Research Foundation, Chennai, India
| | - Lingam Vijaya
- Jadhavbhai Nathamal Singhvi Department of Glaucoma, Medical Research Foundation, Chennai, India
| | - Tan Do
- Vietnam National Institute of Ophthalmology, Hanoi, Vietnam
| | - Deepak P Edward
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia.,Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Lourdes de Juan Marcos
- Department of Ophthalmology, University Hospital of Salamanca, Salamanca, Spain.,Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Mohammad Pakravan
- Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sasan Moghimi
- Farabi Eye Hospital, Tehran University Eye Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | | | - Barbara Wirostko
- John A. Moran Eye Center, Department of Ophthalmology, University of Utah, Salt Lake City, Utah, USA
| | - Samuel Thomas
- John A. Moran Eye Center, Department of Ophthalmology, University of Utah, Salt Lake City, Utah, USA
| | - Daniel Gaston
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Karen Bedard
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Wenda L Greer
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Zhenglin Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xueyi Chen
- Department of Ophthalmology, First Affiliated Hospital of Xinjiang Medical University, Urumchi, China
| | - Lulin Huang
- Center for Human Molecular Biology and Genetics, Institute of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China.,Sichuan Translational Research Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Jinghong Sang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China
| | - Hongyan Jia
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China
| | - Liyun Jia
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China.,Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Chunyan Qiao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China
| | - Hui Zhang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China
| | - Xuyang Liu
- Shenzhen Key Laboratory of Ophthalmology, Shenzhen Eye Hospital, Jinan University, Shenzhen, China
| | - Bowen Zhao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China.,Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ya-Xing Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Liang Xu
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China
| | - Stéphanie Leruez
- Département d'Ophtalmologie, Centre Hospitalier Universitaire, Angers, France
| | - Pascal Reynier
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire, Angers, France
| | | | | | - Steffen Uebe
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Matthias Zenkel
- Department of Ophthalmology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Daniel Berner
- Department of Ophthalmology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Georg Mossböck
- Department of Ophthalmology, Medical University Graz, Graz, Austria
| | - Nicole Weisschuh
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Ursula Hoja
- Department of Ophthalmology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ulrich-Christoph Welge-Luessen
- Department of Ophthalmology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christian Mardin
- Department of Ophthalmology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Panayiota Founti
- Department of Ophthalmology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anthi Chatzikyriakidou
- Laboratory of General Biology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Theofanis Pappas
- Department of Ophthalmology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleftherios Anastasopoulos
- Department of Ophthalmology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alexandros Lambropoulos
- Laboratory of General Biology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Arkasubhra Ghosh
- GROW Research Laboratory, Narayana Nethralaya Foundation, Bangalore, India
| | - Rohit Shetty
- Narayana Nethralaya Eye Hospital, Bangalore, India
| | | | - Vijayan Saravanan
- Department of Genetics, Aravind Medical Research Foundation, Madurai, India
| | | | | | | | | | - Mozhgan R Kanavi
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afsaneh Naderi Beni
- Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahin Yazdani
- Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Lashay
- Farabi Eye Hospital, Tehran University Eye Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Homa Naderifar
- Farabi Eye Hospital, Tehran University Eye Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nassim Khatibi
- Farabi Eye Hospital, Tehran University Eye Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Antonio Fea
- Dipartimento di Scienze Chirurgiche, Università di Torino, Turin, Italy
| | - Carlo Lavia
- Dipartimento di Scienze Chirurgiche, Università di Torino, Turin, Italy
| | - Laura Dallorto
- Dipartimento di Scienze Chirurgiche, Università di Torino, Turin, Italy
| | - Teresa Rolle
- Dipartimento di Scienze Chirurgiche, Università di Torino, Turin, Italy
| | - Paolo Frezzotti
- Ophthalmology Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - Daniela Paoli
- Department of Ophthalmology, Monfalcone Hospital, Gorizia, Italy
| | - Erika Salvi
- Department of Health Sciences, University of Milan, Milan, Italy
| | - Paolo Manunta
- Department of Nephrology, University Vita-Salute San Raffaele, Milan, Italy
| | | | | | - Tomomi Higashide
- Department of Ophthalmology, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | | | - Satoshi Ishiko
- Department of Medicine and Engineering Combined Research Institute, Asahikawa Medical University, Asahikawa, Japan
| | - Akitoshi Yoshida
- Department of Ophthalmology, Asahikawa Medical University, Asahikawa, Japan
| | - Masahide Yanagi
- Department of Ophthalmology and Visual Sciences, Hiroshima University, Hiroshima, Japan
| | - Yoshiaki Kiuchi
- Department of Ophthalmology and Visual Sciences, Hiroshima University, Hiroshima, Japan
| | | | | | - Takako Sugimoto
- Department of Ophthalmology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Hideki Chuman
- Department of Ophthalmology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Makoto Aihara
- Department of Ophthalmology, University of Tokyo, Tokyo, Japan
| | - Masaru Inatani
- Department of Ophthalmology, Faculty of Medical Science, University of Fukui, Fukui, Japan
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Norimoto Gotoh
- Center for Genomic Medicine, INSERM U852, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, INSERM U852, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nagahisa Yoshimura
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Tazuke Kofukai Foundation, Medical Research Institute, Kitano Hospital, Osaka, Japan
| | - Yoko Ikeda
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Morio Ueno
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Chie Sotozono
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Jin Wook Jeoung
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Min Sagong
- Department of Ophthalmology, Yeungnam University College of Medicine, Daegu, Republic of Korea
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University Bundang Hospital, Gyeonggi, Republic of Korea
| | - Jeeyun Ahn
- Department of Ophthalmology, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Marisa Cruz-Aguilar
- Genetics Department, Institute of Ophthalmology 'Conde de Valenciana', Mexico City, Mexico
| | - Sidi M Ezzouhairi
- Clinique Spécialisée en Ophtalmologie Mohammedia, Mohammedia, Morocco
| | | | | | - Xiao Yu Ng
- Singapore Eye Research Institute, Singapore
| | | | | | | | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Olusola O Olawoye
- Department of Ophthalmology, College of Medicine, University of Ibadan, Ibadan, Nigeria.,Department of Ophthalmology, University College Hospital, Ibadan, Nigeria
| | - Adeyinka O Ashaye
- Department of Ophthalmology, College of Medicine, University of Ibadan, Ibadan, Nigeria.,Department of Ophthalmology, University College Hospital, Ibadan, Nigeria
| | | | - Adeola Onakoya
- Department of Ophthalmology, University of Lagos, Lagos, Nigeria.,Guinness Eye Centre, Lagos University Teaching Hospital, Lagos, Nigeria
| | - Nkiru Kizor-Akaraiwe
- Department of Ophthalmology, ESUT Teaching Hospital Parklane, Enugu, Nigeria.,Eye Specialists Hospital, Enugu, Nigeria
| | - Chaiwat Teekhasaenee
- Department of Ophthalmology, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Yanin Suwan
- Department of Ophthalmology, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Wasu Supakontanasan
- Department of Ophthalmology, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suhanya Okeke
- Department of Ophthalmology, ESUT Teaching Hospital Parklane, Enugu, Nigeria.,Eye Specialists Hospital, Enugu, Nigeria
| | - Nkechi J Uche
- Eye Specialists Hospital, Enugu, Nigeria.,Department of Ophthalmology, University of Nigeria Teaching Hospital, Ituku-Ozalla, Enugu, Nigeria.,Department of Ophthalmology, College of Medicine, University of Nigeria, Nsukka, Ituku Ozalla Campus, Enugu, Nigeria
| | - Ifeoma Asimadu
- Department of Ophthalmology, ESUT Teaching Hospital Parklane, Enugu, Nigeria
| | - Humaira Ayub
- Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Farah Akhtar
- Pakistan Institute of Ophthalmology, Al-Shifa Trust Eye Hospital, Rawalpindi, Pakistan
| | - Ewa Kosior-Jarecka
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University, Lublin, Poland
| | - Urszula Lukasik
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University, Lublin, Poland
| | | | - Vania Castro
- Universidad Peruana Cayetano Heredia, Hospital Nacional Arzobispo Loayza, Lima, Peru
| | | | - Gordana Sunaric Megevand
- Clinical Research Centre Adolphe de Rothschild, Société Médicale de Beaulieu, Geneva, Switzerland
| | - Sylvain Roy
- Clinical Research Centre Adolphe de Rothschild, Société Médicale de Beaulieu, Geneva, Switzerland
| | - Edward Dervan
- Mater Misericordiae University Hospital, Dublin, Ireland
| | - Eoin Silke
- Mater Misericordiae University Hospital, Dublin, Ireland
| | - Aparna Rao
- Shri Mithu Tulsi, LV Prasad Eye Institute, Bhubaneswar, India
| | - Priti Sahay
- Shri Mithu Tulsi, LV Prasad Eye Institute, Bhubaneswar, India
| | | | | | - Delia Sivori
- Fundación para el Estudio del Glaucoma, Buenos Aires, Argentina
| | - Tamara Zompa
- Centro Oftalmologico Charles, Buenos Aires, Argentina
| | - Richard A Mills
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Paul Mitchell
- Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Jie Jin Wang
- Centre for Vision Research, Department of Ophthalmology and Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia.,Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Michael Coote
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Jonathan G Crowston
- Centre for Eye Research Australia (CERA), University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Sergei Y Astakhov
- Department of Ophthalmology, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Eugeny L Akopov
- Department of Ophthalmology, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Anton Emelyanov
- Department of Ophthalmology, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia.,St. Petersburg Academic University, St. Petersburg, Russia
| | | | | | | | - Saleh A Al-Obeidan
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Ohoud Owaidhah
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | | | - Balram Chowbay
- Clinical Pharmacology, SingHealth, Singapore.,Clinical Pharmacology Laboratory, National Cancer Centre, Singapore.,Office of Clinical Sciences, Duke-NUS Medical School, Singapore
| | - Jia Nee Foo
- Genome Institute of Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | | | | | | | - Shi Qi Mok
- Genome Institute of Singapore, Singapore
| | | | | | - Su Qin Peh
- Genome Institute of Singapore, Singapore
| | | | | | - Su-Ling Ho
- Department of Ophthalmology, Tan Tock Seng Hospital, Singapore
| | | | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore.,Singapore National Eye Center, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Academic Clinical Program for Ophthalmology and Visual Sciences, Office of Clinical and Academic Faculty Affairs, Duke-NUS Graduate Medical School, Singapore
| | | | - Rogelio González-Sarmiento
- Institute for Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Molecular Medicine Unit, Department of Medicine, University of Salamanca, Salamanca, Spain
| | - Frederico Martinon-Torres
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Kessara Pathanapitoon
- Department of Ophthalmology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Linda Hansapinyo
- Department of Ophthalmology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | - Naris Kitnarong
- Department of Ophthalmology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Anavaj Sakuntabhai
- Institut Pasteur, Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Paris, France.,Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France
| | - Hip X Nguyn
- Vietnam National Institute of Ophthalmology, Hanoi, Vietnam
| | | | - Trình V Nguyn
- Vietnam National Institute of Ophthalmology, Hanoi, Vietnam
| | - Werner Zenz
- Department of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Alexander Binder
- Department of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Daniela S Klobassa
- Department of General Pediatrics, Medical University of Graz, Graz, Austria
| | - Martin L Hibberd
- Genome Institute of Singapore, Singapore.,Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Stefan Herms
- Department of Genomics, Life &Brain Center, University of Bonn, Bonn, Germany.,Department of Biomedicine, University of Basel, Basel, Switzerland.,Division of Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Markus M Nöthen
- Department of Genomics, Life &Brain Center, University of Bonn, Bonn, Germany.,Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Susanne Moebus
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, Germany
| | - Robyn M Rautenbach
- Division of Ophthalmology, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Ari Ziskind
- Division of Ophthalmology, Stellenbosch University and Tygerberg Hospital, Cape Town, South Africa
| | - Trevor R Carmichael
- Division of Ophthalmology, University of the Witwatersrand, Johannesburg, South Africa
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lydia Álvarez
- Fernández-Vega University Institute and Foundation of Ophthalmological Research, University of Oviedo, Oviedo, Spain.,Fernández-Vega Ophthalmological Institute, Oviedo, Spain
| | - Montserrat García
- Fernández-Vega University Institute and Foundation of Ophthalmological Research, University of Oviedo, Oviedo, Spain.,Fernández-Vega Ophthalmological Institute, Oviedo, Spain
| | - Héctor González-Iglesias
- Fernández-Vega University Institute and Foundation of Ophthalmological Research, University of Oviedo, Oviedo, Spain.,Fernández-Vega Ophthalmological Institute, Oviedo, Spain
| | - Pedro P Rodríguez-Calvo
- Fernández-Vega University Institute and Foundation of Ophthalmological Research, University of Oviedo, Oviedo, Spain.,Fernández-Vega Ophthalmological Institute, Oviedo, Spain
| | - Luis Fernández-Vega Cueto
- Fernández-Vega University Institute and Foundation of Ophthalmological Research, University of Oviedo, Oviedo, Spain.,Fernández-Vega Ophthalmological Institute, Oviedo, Spain
| | - Çilingir Oguz
- Department of Genetics, Eskisehir Osmangazi University, Meselik, Eskisehir, Turkey
| | - Nevbahar Tamcelik
- Istanbul University Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Eray Atalay
- Singapore Eye Research Institute, Singapore.,Istanbul University Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Bilge Batu
- Istanbul University Cerrahpasa Faculty of Medicine, Istanbul, Turkey
| | - Dilek Aktas
- DAMAGEN Genetic Diagnostic Center, Ankara, Turkey
| | - Burcu Kasım
- Department of Ophthalmology, Hacettepe University, Faculty of Medicine, Ankara, Turkey
| | - M Roy Wilson
- School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Anne L Coleman
- Center for Community Outreach and Policy, Stein Eye Institute, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Center for Biotechnology and Genomic Medicine, James and Jean Culver Discovery Institute, Augusta University, Augusta, Georgia, USA
| | - Pratap Challa
- Department of Ophthalmology, Duke University Eye Center, Durham, North Carolina, USA
| | - Leon Herndon
- Department of Ophthalmology, Duke University Eye Center, Durham, North Carolina, USA
| | - Rachel W Kuchtey
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John Kuchtey
- Vanderbilt Eye Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Karen Curtin
- John A. Moran Eye Center, Department of Ophthalmology, University of Utah, Salt Lake City, Utah, USA
| | - Craig J Chaya
- John A. Moran Eye Center, Department of Ophthalmology, University of Utah, Salt Lake City, Utah, USA
| | - Alan Crandall
- John A. Moran Eye Center, Department of Ophthalmology, University of Utah, Salt Lake City, Utah, USA
| | - Linda M Zangwill
- Hamilton Glaucoma Center, Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, San Diego, California, USA
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore.,Singapore National Eye Center, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Masakazu Nakano
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeru Kinoshita
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Frontier Medical Science and Technology for Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands.,Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Eija Vesti
- Department of Ophthalmology, University of Turku and Turku University Hospital, Turku, Finland
| | - John H Fingert
- Institute for Vision Research, University of Iowa, Iowa City, Iowa, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Richard K Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Arthur J Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Ningli Wang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China.,Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Daniele Cusi
- Institute of Biomedical Technologies, Italian National Research Centre (ITB-CNR), Segrate-Milano, Italy
| | - Raheel Qamar
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan.,Department of Biochemistry, Al-Nafees Medical College and Hospital, Isra University, Islamabad, Pakistan
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Soumya Raychaudhuri
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Institute of Inflammation and Repair, University of Manchester, Manchester, UK.,Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Steffen Heegaard
- Department of Ophthalmology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Department of Pathology, Rigshospitalet, Eye Pathology Section, University of Copenhagen, Copenhagen, Denmark
| | - Tero Kivelä
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - André Reis
- David Tvildiani Medical University, Tbilisi, Georgia
| | - Friedrich E Kruse
- Department of Ophthalmology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Robert N Weinreb
- Hamilton Glaucoma Center, Department of Ophthalmology and Shiley Eye Institute, University of California, San Diego, San Diego, California, USA
| | - Louis R Pasquale
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA.,Institute of Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Fridbert Jonasson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Department of Ophthalmology, Landspitali University Hospital, Reykjavik, Iceland
| | - R Rand Allingham
- Singapore Eye Research Institute, Singapore.,Department of Ophthalmology, Duke University Eye Center, Durham, North Carolina, USA
| | - Dan Milea
- Singapore Eye Research Institute, Singapore.,Singapore National Eye Center, Singapore.,Academic Clinical Program for Ophthalmology and Visual Sciences, Office of Clinical and Academic Faculty Affairs, Duke-NUS Graduate Medical School, Singapore
| | - Robert Ritch
- Einhorn Clinical Research Center, New York Eye and Ear Infirmary of Mount Sinai, New York, New York, USA
| | - Toshiaki Kubota
- Department of Ophthalmology, Oita University Faculty of Medicine, Oita, Japan
| | - Kei Tashiro
- Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Eranga N Vithana
- Singapore Eye Research Institute, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shazia Micheal
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Fotis Topouzis
- Department of Ophthalmology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Michael Dubina
- Department of Ophthalmology, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia.,St. Petersburg Academic University, St. Petersburg, Russia
| | - Periasamy Sundaresan
- Dr. G.Venkataswamy Eye Research Institute, Aravind Medical Research Foundation, Aravind Eye Hospital, Madurai, India
| | - Kari Stefansson
- deCODE Genetics, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Francesca Pasutto
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Chiea Chuen Khor
- Singapore Eye Research Institute, Singapore.,Genome Institute of Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| |
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Wu YL, Lo CW. Diverse application of MRI for mouse phenotyping. Birth Defects Res 2017; 109:758-770. [PMID: 28544650 DOI: 10.1002/bdr2.1051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 04/15/2017] [Indexed: 02/01/2023]
Abstract
Small animal models, particularly mouse models, of human diseases are becoming an indispensable tool for biomedical research. Studies in animal models have provided important insights into the etiology of diseases and accelerated the development of therapeutic strategies. Detailed phenotypic characterization is essential, both for the development of such animal models and mechanistic studies into disease pathogenesis and testing the efficacy of experimental therapeutics. MRI is a versatile and noninvasive imaging modality with excellent penetration depth, tissue coverage, and soft tissue contrast. MRI, being a multi-modal imaging modality, together with proven imaging protocols and availability of good contrast agents, is ideally suited for phenotyping mutant mouse models. Here we describe the applications of MRI for phenotyping structural birth defects involving the brain, heart, and kidney in mice. The versatility of MRI and its ease of use are well suited to meet the rapidly increasing demands for mouse phenotyping in the coming age of functional genomics. Birth Defects Research 109:758-770, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Yijen L Wu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,Rangos Research Center Animal Imaging Core, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function. Sci Rep 2017; 7:45040. [PMID: 28452372 PMCID: PMC5408227 DOI: 10.1038/srep45040] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/20/2017] [Indexed: 12/31/2022] Open
Abstract
HapMap imputed genome-wide association studies (GWAS) have revealed >50 loci at which common variants with minor allele frequency >5% are associated with kidney function. GWAS using more complete reference sets for imputation, such as those from The 1000 Genomes project, promise to identify novel loci that have been missed by previous efforts. To investigate the value of such a more complete variant catalog, we conducted a GWAS meta-analysis of kidney function based on the estimated glomerular filtration rate (eGFR) in 110,517 European ancestry participants using 1000 Genomes imputed data. We identified 10 novel loci with p-value < 5 × 10-8 previously missed by HapMap-based GWAS. Six of these loci (HOXD8, ARL15, PIK3R1, EYA4, ASTN2, and EPB41L3) are tagged by common SNPs unique to the 1000 Genomes reference panel. Using pathway analysis, we identified 39 significant (FDR < 0.05) genes and 127 significantly (FDR < 0.05) enriched gene sets, which were missed by our previous analyses. Among those, the 10 identified novel genes are part of pathways of kidney development, carbohydrate metabolism, cardiac septum development and glucose metabolism. These results highlight the utility of re-imputing from denser reference panels, until whole-genome sequencing becomes feasible in large samples.
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Anderton B, Camarda R, Balakrishnan S, Balakrishnan A, Kohnz RA, Lim L, Evason KJ, Momcilovic O, Kruttwig K, Huang Q, Xu G, Nomura DK, Goga A. MYC-driven inhibition of the glutamate-cysteine ligase promotes glutathione depletion in liver cancer. EMBO Rep 2017; 18:569-585. [PMID: 28219903 PMCID: PMC5376764 DOI: 10.15252/embr.201643068] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 01/08/2017] [Accepted: 01/13/2017] [Indexed: 12/19/2022] Open
Abstract
How MYC reprograms metabolism in primary tumors remains poorly understood. Using integrated gene expression and metabolite profiling, we identify six pathways that are coordinately deregulated in primary MYC-driven liver tumors: glutathione metabolism; glycine, serine, and threonine metabolism; aminoacyl-tRNA biosynthesis; cysteine and methionine metabolism; ABC transporters; and mineral absorption. We then focus our attention on glutathione (GSH) and glutathione disulfide (GSSG), as they are markedly decreased in MYC-driven tumors. We find that fewer glutamine-derived carbons are incorporated into GSH in tumor tissue relative to non-tumor tissue. Expression of GCLC, the rate-limiting enzyme of GSH synthesis, is attenuated by the MYC-induced microRNA miR-18a. Inhibition of miR-18a in vivo leads to increased GCLC protein expression and GSH abundance in tumor tissue. Finally, MYC-driven liver tumors exhibit increased sensitivity to acute oxidative stress. In summary, MYC-dependent attenuation of GCLC by miR-18a contributes to GSH depletion in vivo, and low GSH corresponds with increased sensitivity to oxidative stress in tumors. Our results identify new metabolic pathways deregulated in primary MYC tumors and implicate a role for MYC in regulating a major antioxidant pathway downstream of glutamine.
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Affiliation(s)
- Brittany Anderton
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Roman Camarda
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sanjeev Balakrishnan
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Asha Balakrishnan
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover Medical School, TWINCORE, Center for Experimental and Clinical Infection Research, Hannover, Germany
| | - Rebecca A Kohnz
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Lionel Lim
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kimberley J Evason
- Department of Pathology and Huntsman Cancer Institute, University of Utah, Salt Lake, UT, USA
| | - Olga Momcilovic
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Klaus Kruttwig
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Qiang Huang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Guowang Xu
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Andrei Goga
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
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49
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van de Lagemaat LN, Stanford LE, Pettit CM, Strathdee DJ, Strathdee KE, Elsegood KA, Fricker DG, Croning MDR, Komiyama NH, Grant SGN. Standardized experiments in mutant mice reveal behavioural similarity on 129S5 and C57BL/6J backgrounds. GENES BRAIN AND BEHAVIOR 2017; 16:409-418. [DOI: 10.1111/gbb.12364] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/12/2016] [Accepted: 11/21/2016] [Indexed: 01/27/2023]
Affiliation(s)
- L. N. van de Lagemaat
- Centre for Clinical Brain Sciences, Chancellor's Building; University of Edinburgh; Edinburgh UK
- Genes to Cognition Programme; Wellcome Trust Sanger Institute; Cambridge UK
| | - L. E. Stanford
- Genes to Cognition Programme; Wellcome Trust Sanger Institute; Cambridge UK
| | - C. M. Pettit
- Genes to Cognition Programme; Wellcome Trust Sanger Institute; Cambridge UK
| | - D. J. Strathdee
- Genes to Cognition Programme; Wellcome Trust Sanger Institute; Cambridge UK
- Transgenic Technology Division; CRUK Beatson Institute; Glasgow UK
| | - K. E. Strathdee
- Genes to Cognition Programme; Wellcome Trust Sanger Institute; Cambridge UK
| | - K. A. Elsegood
- Centre for Clinical Brain Sciences, Chancellor's Building; University of Edinburgh; Edinburgh UK
- Genes to Cognition Programme; Wellcome Trust Sanger Institute; Cambridge UK
| | - D. G. Fricker
- Centre for Clinical Brain Sciences, Chancellor's Building; University of Edinburgh; Edinburgh UK
- Genes to Cognition Programme; Wellcome Trust Sanger Institute; Cambridge UK
| | - M. D. R. Croning
- Centre for Clinical Brain Sciences, Chancellor's Building; University of Edinburgh; Edinburgh UK
- Genes to Cognition Programme; Wellcome Trust Sanger Institute; Cambridge UK
| | - N. H. Komiyama
- Centre for Clinical Brain Sciences, Chancellor's Building; University of Edinburgh; Edinburgh UK
- Genes to Cognition Programme; Wellcome Trust Sanger Institute; Cambridge UK
| | - S. G. N. Grant
- Centre for Clinical Brain Sciences, Chancellor's Building; University of Edinburgh; Edinburgh UK
- Genes to Cognition Programme; Wellcome Trust Sanger Institute; Cambridge UK
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50
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Eppig JT, Smith CL, Blake JA, Ringwald M, Kadin JA, Richardson JE, Bult CJ. Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research. Methods Mol Biol 2017; 1488:47-73. [PMID: 27933520 DOI: 10.1007/978-1-4939-6427-7_3] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Mouse Genome Informatics (MGI), resource ( www.informatics.jax.org ) has existed for over 25 years, and over this time its data content, informatics infrastructure, and user interfaces and tools have undergone dramatic changes (Eppig et al., Mamm Genome 26:272-284, 2015). Change has been driven by scientific methodological advances, rapid improvements in computational software, growth in computer hardware capacity, and the ongoing collaborative nature of the mouse genomics community in building resources and sharing data. Here we present an overview of the current data content of MGI, describe its general organization, and provide examples using simple and complex searches, and tools for mining and retrieving sets of data.
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Affiliation(s)
- Janan T Eppig
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
| | - Cynthia L Smith
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Judith A Blake
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Martin Ringwald
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - James A Kadin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | | | - Carol J Bult
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
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