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Gupta N, Waas B, Austin D, De Mazière AM, Kujala P, Stockwell AD, Li T, Yaspan BL, Klumperman J, Scales SJ. Apolipoprotein L1 (APOL1) renal risk variant-mediated podocyte cytotoxicity depends on African haplotype and surface expression. Sci Rep 2024; 14:3765. [PMID: 38355600 PMCID: PMC10866943 DOI: 10.1038/s41598-024-53298-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
Homozygous Apolipoprotein L1 (APOL1) variants G1 and G2 cause APOL1-mediated kidney disease, purportedly acting as surface cation channels in podocytes. APOL1-G0 exhibits various single nucleotide polymorphisms, most commonly haplotype E150K, M228I and R255K ("KIK"; the Reference Sequence is "EMR"), whereas variants G1 and G2 are mostly found in a single "African" haplotype background ("EIK"). Several labs reported cytotoxicity with risk variants G1 and G2 in KIK or EIK background haplotypes, but used HEK-293 cells and did not verify equal surface expression. To see if haplotype matters in a more relevant cell type, we induced APOL1-G0, G1 and G2 EIK, KIK and EMR at comparable surface levels in immortalized podocytes. G1 and G2 risk variants (but not G0) caused dose-dependent podocyte death within 48h only in their native African EIK haplotype and correlated with K+ conductance (thallium FLIPR). We ruled out differences in localization and trafficking, except for possibly greater surface clustering of cytotoxic haplotypes. APOL1 surface expression was required, since Brefeldin A rescued cytotoxicity; and cytoplasmic isoforms vB3 and vC were not cytotoxic. Thus, APOL1-EIK risk variants kill podocytes in a dose and haplotype-dependent manner (as in HEK-293 cells), whereas unlike in HEK-293 cells the KIK risk variants did not.
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Affiliation(s)
- Nidhi Gupta
- Department of Discovery Immunology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Bridget Waas
- Department of Discovery Immunology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Daniel Austin
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ann M De Mazière
- Section of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pekka Kujala
- Section of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Amy D Stockwell
- Department of Human Genetics, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Tianbo Li
- Department of Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Brian L Yaspan
- Department of Human Genetics, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Judith Klumperman
- Section of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Suzie J Scales
- Department of Discovery Immunology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
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2
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Leavy OC, Goemans AF, Stockwell AD, Allen RJ, Guillen-Guio B, Hernandez-Beeftink T, Adegunsoye A, Booth HL, Cullinan P, Fahy WA, Fingerlin TE, Virk HS, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, Kaminski N, Ma SF, McAnulty RJ, Sheng XR, Millar AB, Molina-Molina M, Navaratnam V, Neighbors M, Parfrey H, Saini G, Sayers I, Strek ME, Tobin MD, Whyte MK, Zhang Y, Maher TM, Molyneaux PL, Oldham JM, Yaspan BL, Flores C, Martinez F, Reynolds CJ, Schwartz DA, Noth I, Jenkins RG, Wain LV. Genome-wide SNP-sex interaction analysis of susceptibility to idiopathic pulmonary fibrosis. medRxiv 2024:2024.01.12.24301204. [PMID: 38293162 PMCID: PMC10827242 DOI: 10.1101/2024.01.12.24301204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a chronic lung condition that is more prevalent in males than females. The reasons for this are not fully understood, with differing environmental exposures due to historically sex-biased occupations, or diagnostic bias, being possible explanations. To date, over 20 independent genetic variants have been identified to be associated with IPF susceptibility, but these have been discovered when combining males and females. Our aim was to test for the presence of sex-specific associations with IPF susceptibility and assess whether there is a need to consider sex-specific effects when evaluating genetic risk in clinical prediction models for IPF. Methods We performed genome-wide single nucleotide polymorphism (SNP)-by-sex interaction studies of IPF risk in six independent IPF case-control studies and combined them using inverse-variance weighted fixed effect meta-analysis. In total, 4,561 cases (1,280 females and 2,281 males) and 23,500 controls (8,360 females and 14,528 males) of European genetic ancestry were analysed. We used polygenic risk scores (PRS) to assess differences in genetic risk prediction between males and females. Findings Three independent genetic association signals were identified. All showed a consistent direction of effect across all individual IPF studies and an opposite direction of effect in IPF susceptibility between females and males. None had been previously identified in IPF susceptibility genome-wide association studies (GWAS). The predictive accuracy of the PRSs were similar between males and females, regardless of whether using combined or sex-specific GWAS results. Interpretation We prioritised three genetic variants whose effect on IPF risk may be modified by sex, however these require further study. We found no evidence that the predictive accuracy of common SNP-based PRSs varies significantly between males and females.
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Affiliation(s)
- Olivia C Leavy
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Anne F Goemans
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | | | - Richard J Allen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | | | | | | | | | - Ian P Hall
- University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | | | | | - Richard B Hubbard
- University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | | | | | | | | | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Vidya Navaratnam
- Department of Respiratory Medicine, Sir Charles Gardiner Hospital, Perth, Australia
- Centre for Respiratory Research, University of Western Australia, Perth, Australia
| | | | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | | | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | | | - Martin D Tobin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | - Toby M Maher
- NIHR Imperial Biomedical Research Unit, National Heart and Lung Institute, Imperial College London, London, UK
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, USA
| | - Philip L Molyneaux
- National Institute for Health Research Respiratory Clinical Research Facility, Royal Brompton Hospital, London, UK
- NIHR Imperial Biomedical Research Unit, National Heart and Lung Institute, Imperial College London, London, UK
| | | | | | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnologico y de Energias Renovables, Santa Cruz de Tenerife, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | | | | | | | - Imre Noth
- University of Virginia, Virginia, USA
| | - R Gisli Jenkins
- NIHR Imperial Biomedical Research Unit, National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
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3
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Guillen-Guio B, Paynton ML, Allen RJ, Chin DP, Donoghue LJ, Stockwell A, Leavy OC, Hernandez-Beeftink T, Reynolds C, Cullinan P, Martinez F, Booth HL, Fahy WA, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Sayers I, Tobin MD, Whyte MK, Adegunsoye A, Kaminski N, Ma SF, Strek ME, Zhang Y, Fingerlin TE, Molina-Molina M, Neighbors M, Sheng XR, Oldham JM, Maher TM, Molyneaux PL, Flores C, Noth I, Schwartz DA, Yaspan BL, Jenkins RG, Wain LV, Hollox EJ. Association study of human leukocyte antigen variants and idiopathic pulmonary fibrosis. ERJ Open Res 2024; 10:00553-2023. [PMID: 38375425 PMCID: PMC10875457 DOI: 10.1183/23120541.00553-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/05/2023] [Indexed: 02/21/2024] Open
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial pneumonia marked by progressive lung fibrosis and a poor prognosis. Recent studies have highlighted the potential role of infection in the pathogenesis of IPF, and a prior association of the HLA-DQB1 gene with idiopathic fibrotic interstitial pneumonia (including IPF) has been reported. Owing to the important role that the human leukocyte antigen (HLA) region plays in the immune response, here we evaluated if HLA genetic variation was associated specifically with IPF risk. Methods We performed a meta-analysis of associations of the HLA region with IPF risk in individuals of European ancestry from seven independent case-control studies of IPF (comprising 5159 cases and 27 459 controls, including a prior study of fibrotic interstitial pneumonia). Single nucleotide polymorphisms, classical HLA alleles and amino acids were analysed and signals meeting a region-wide association threshold of p<4.5×10-4 and a posterior probability of replication >90% were considered significant. We sought to replicate the previously reported HLA-DQB1 association in the subset of studies independent of the original report. Results The meta-analysis of all seven studies identified four significant independent single nucleotide polymorphisms associated with IPF risk. However, none met the posterior probability for replication criterion. The HLA-DQB1 association was not replicated in the independent IPF studies. Conclusion Variation in the HLA region was not consistently associated with risk in studies of IPF. However, this does not preclude the possibility that other genomic regions linked to the immune response may be involved in the aetiology of IPF.
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Affiliation(s)
- Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
- Joint first authors
| | - Megan L. Paynton
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Joint first authors
| | - Richard J. Allen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Daniel P.W. Chin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | - Olivia C. Leavy
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Carl Reynolds
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Paul Cullinan
- National Heart & Lung Institute, Imperial College London, London, UK
| | | | - Helen L. Booth
- University College Hospital, University College London, London, UK
| | | | - Ian P. Hall
- School of Medicine, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | - Simon P. Hart
- Hull York Medical School, University of Hull, Hull, UK
| | - Mike R. Hill
- MRC Population Health Unit, University of Oxford, Oxford, UK
| | - Nik Hirani
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Richard B. Hubbard
- School of Medicine, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | - Ann B. Millar
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Vidya Navaratnam
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD, Australia
| | | | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | - Gauri Saini
- School of Medicine, University of Nottingham, Nottingham, UK
| | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Martin D. Tobin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Moira K.B. Whyte
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | | | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shwu-Fan Ma
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Mary E. Strek
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tasha E. Fingerlin
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, USA
| | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, UK
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, USA
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas’ NHS Foundation Trust, London, UK
| | - Carlos Flores
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnologico y de Energias Renovables, Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Imre Noth
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | | | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V. Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
- Joint senior authors
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Joint senior authors
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Stockwell AD, Chang MC, Mahajan A, Forrest W, Anegondi N, Pendergrass RK, Selvaraj S, Reeder J, Wei E, Iglesias VA, Creps NM, Macri L, Neeranjan AN, van der Brug MP, Scales SJ, McCarthy MI, Yaspan BL. Multi-ancestry GWAS analysis identifies two novel loci associated with diabetic eye disease and highlights APOL1 as a high risk locus in patients with diabetic macular edema. PLoS Genet 2023; 19:e1010609. [PMID: 37585454 PMCID: PMC10461827 DOI: 10.1371/journal.pgen.1010609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/28/2023] [Accepted: 06/11/2023] [Indexed: 08/18/2023] Open
Abstract
Diabetic retinopathy (DR) is a common complication of diabetes. Approximately 20% of DR patients have diabetic macular edema (DME) characterized by fluid leakage into the retina. There is a genetic component to DR and DME risk, but few replicable loci. Because not all DR cases have DME, we focused on DME to increase power, and conducted a multi-ancestry GWAS to assess DME risk in a total of 1,502 DME patients and 5,603 non-DME controls in discovery and replication datasets. Two loci reached GWAS significance (p<5x10-8). The strongest association was rs2239785, (K150E) in APOL1. The second finding was rs10402468, which co-localized to PLVAP and ANKLE1 in vascular / endothelium tissues. We conducted multiple sensitivity analyses to establish that the associations were specific to DME status and did not reflect diabetes status or other diabetic complications. Here we report two novel loci for risk of DME which replicated in multiple clinical trial and biobank derived datasets. One of these loci, containing the gene APOL1, is a risk factor in African American DME and DKD patients, indicating that this locus plays a broader role in diabetic complications for multiple ancestries. Trial Registration: NCT00473330, NCT00473382, NCT03622580, NCT03622593, NCT04108156.
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Affiliation(s)
| | | | - Anubha Mahajan
- Genentech, San Francisco, California, United States of America
| | - William Forrest
- Genentech, San Francisco, California, United States of America
| | - Neha Anegondi
- Genentech, San Francisco, California, United States of America
| | | | - Suresh Selvaraj
- Genentech, San Francisco, California, United States of America
| | - Jens Reeder
- Genentech, San Francisco, California, United States of America
| | - Eric Wei
- Genentech, San Francisco, California, United States of America
| | | | | | - Laura Macri
- Character Biosciences, San Francisco, California, United States of America
| | | | | | - Suzie J. Scales
- Genentech, San Francisco, California, United States of America
| | | | - Brian L. Yaspan
- Genentech, San Francisco, California, United States of America
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5
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Guillen-Guio B, Paynton ML, Allen RJ, Chin DP, Donoghue LJ, Stockwell A, Leavy OC, Hernandez-Beeftink T, Reynolds C, Cullinan P, Martinez F, Booth HL, Fahy WA, Hall IP, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Sayers I, Tobin MD, Whyte MKB, Adegunsoye A, Kaminski N, Shwu-Fan M, Strek ME, Zhang Y, Fingerlin TE, Molina-Molina M, Neighbors M, Sheng XR, Oldham JM, Maher TM, Molyneaux PL, Flores C, Noth I, Schwartz DA, Yaspan BL, Jenkins RG, Wain LV, Hollox EJ. Association study of human leukocyte antigen (HLA) variants and idiopathic pulmonary fibrosis. medRxiv 2023:2023.07.20.23292940. [PMID: 37546732 PMCID: PMC10402235 DOI: 10.1101/2023.07.20.23292940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial pneumonia marked by progressive lung fibrosis and a poor prognosis. Recent studies have highlighted the potential role of infection in the pathogenesis of IPF and a prior association of the HLA-DQB1 gene with idiopathic fibrotic interstitial pneumonia (including IPF) has been reported. Due to the important role that the Human Leukocyte Antigen (HLA) region plays in the immune response, here we evaluated if HLA genetic variation was associated specifically with IPF risk. Methods We performed a meta-analysis of associations of the HLA region with IPF risk in individuals of European ancestry from seven independent case-control studies of IPF (comprising a total of 5,159 cases and 27,459 controls, including the prior study of fibrotic interstitial pneumonia). Single nucleotide polymorphisms, classical HLA alleles and amino acids were analysed and signals meeting a region-wide association threshold p<4.5×10-4 and a posterior probability of replication >90% were considered significant. We sought to replicate the previously reported HLA-DQB1 association in the subset of studies independent of the original report. Results The meta-analysis of all seven studies identified four significant independent single nucleotide polymorphisms associated with IPF risk. However, none met the posterior probability for replication criterion. The HLA-DQB1 association was not replicated in the independent IPF studies. Conclusion Variation in the HLA region was not consistently associated with risk in studies of IPF. However, this does not preclude the possibility that other genomic regions linked to the immune response may be involved in the aetiology of IPF.
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Affiliation(s)
- Beatriz Guillen-Guio
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Megan L. Paynton
- Department of Population Health Sciences, University of Leicester, UK
| | - Richard J. Allen
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Daniel P.W. Chin
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | - Olivia C. Leavy
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Tamara Hernandez-Beeftink
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | | | | | | | | | - Ian P. Hall
- University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | | | | | - Richard B. Hubbard
- University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham, UK
| | | | | | - Vidya Navaratnam
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
- Queensland Lung Transplant Service, The Prince Charles Hospital, Brisbane, QLD, Australia
| | | | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK
| | | | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Martin D. Tobin
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | | | | | | | | | | | | | | | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, UK
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, USA
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | - Carlos Flores
- Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnologico y de Energias Renovables, Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Imre Noth
- University of Virginia, Virginia, USA
| | | | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V. Wain
- Department of Population Health Sciences, University of Leicester, UK
- NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, UK
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6
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Orozco LD, Owen LA, Hofmann J, Stockwell AD, Tao J, Haller S, Mukundan VT, Clarke C, Lund J, Sridhar A, Mayba O, Barr JL, Zavala RA, Graves EC, Zhang C, Husami N, Finley R, Au E, Lillvis JH, Farkas MH, Shakoor A, Sherva R, Kim IK, Kaminker JS, Townsend MJ, Farrer LA, Yaspan BL, Chen HH, DeAngelis MM. A systems biology approach uncovers novel disease mechanisms in age-related macular degeneration. Cell Genom 2023; 3:100302. [PMID: 37388919 PMCID: PMC10300496 DOI: 10.1016/j.xgen.2023.100302] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/21/2023] [Accepted: 03/22/2023] [Indexed: 07/01/2023]
Abstract
Age-related macular degeneration (AMD) is a leading cause of blindness, affecting 200 million people worldwide. To identify genes that could be targeted for treatment, we created a molecular atlas at different stages of AMD. Our resource is comprised of RNA sequencing (RNA-seq) and DNA methylation microarrays from bulk macular retinal pigment epithelium (RPE)/choroid of clinically phenotyped normal and AMD donor eyes (n = 85), single-nucleus RNA-seq (164,399 cells), and single-nucleus assay for transposase-accessible chromatin (ATAC)-seq (125,822 cells) from the retina, RPE, and choroid of 6 AMD and 7 control donors. We identified 23 genome-wide significant loci differentially methylated in AMD, over 1,000 differentially expressed genes across different disease stages, and an AMD Müller state distinct from normal or gliosis. Chromatin accessibility peaks in genome-wide association study (GWAS) loci revealed putative causal genes for AMD, including HTRA1 and C6orf223. Our systems biology approach uncovered molecular mechanisms underlying AMD, including regulators of WNT signaling, FRZB and TLE2, as mechanistic players in disease.
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Affiliation(s)
- Luz D. Orozco
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Leah A. Owen
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Obstetrics and Gynecology, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Jeffrey Hofmann
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Amy D. Stockwell
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Jianhua Tao
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Susan Haller
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Vineeth T. Mukundan
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Christine Clarke
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Jessica Lund
- Departments of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, USA
| | - Akshayalakshmi Sridhar
- Department of Human Pathobiology & OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Oleg Mayba
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Julie L. Barr
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Rylee A. Zavala
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Elijah C. Graves
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Charles Zhang
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Nadine Husami
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Robert Finley
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - Elizabeth Au
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
| | - John H. Lillvis
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
| | - Michael H. Farkas
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Veterans Administration Western New York Healthcare System, Buffalo, NY 14212, USA
| | - Akbar Shakoor
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
| | - Richard Sherva
- Department of Medicine, Biomedical Genetics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ivana K. Kim
- Retina Service, Massachusetts Eye & Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Joshua S. Kaminker
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Michael J. Townsend
- Department of Human Pathobiology & OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Lindsay A. Farrer
- Department of Medicine, Biomedical Genetics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Brian L. Yaspan
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Hsu-Hsin Chen
- Department of Human Pathobiology & OMNI Reverse Translation, Genentech, South San Francisco, CA 94080, USA
| | - Margaret M. DeAngelis
- Department of Ophthalmology and Visual Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Population Health Sciences, University of Utah School of Medicine, The University of Utah, Salt Lake City, UT 84132, USA
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, University at Buffalo, Buffalo, NY 14203, USA
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7
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Oldham JM, Allen RJ, Lorenzo-Salazar JM, Molyneaux PL, Ma SF, Joseph C, Kim JS, Guillen-Guio B, Hernández-Beeftink T, Kropski JA, Huang Y, Lee CT, Adegunsoye A, Pugashetti JV, Linderholm AL, Vo V, Strek ME, Jou J, Muñoz-Barrera A, Rubio-Rodriguez LA, Hubbard R, Hirani N, Whyte MKB, Hart S, Nicholson AG, Lancaster L, Parfrey H, Rassl D, Wallace W, Valenzi E, Zhang Y, Mychaleckyj J, Stockwell A, Kaminski N, Wolters PJ, Molina-Molina M, Banovich NE, Fahy WA, Martinez FJ, Hall IP, Tobin MD, Maher TM, Blackwell TS, Yaspan BL, Jenkins RG, Flores C, Wain LV, Noth I. PCSK6 and Survival in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2023; 207:1515-1524. [PMID: 36780644 PMCID: PMC10263132 DOI: 10.1164/rccm.202205-0845oc] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 02/13/2023] [Indexed: 02/15/2023] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is a devastating disease characterized by limited treatment options and high mortality. A better understanding of the molecular drivers of IPF progression is needed. Objectives: To identify and validate molecular determinants of IPF survival. Methods: A staged genome-wide association study was performed using paired genomic and survival data. Stage I cases were drawn from centers across the United States and Europe and stage II cases from Vanderbilt University. Cox proportional hazards regression was used to identify gene variants associated with differential transplantation-free survival (TFS). Stage I variants with nominal significance (P < 5 × 10-5) were advanced for stage II testing and meta-analyzed to identify those reaching genome-wide significance (P < 5 × 10-8). Downstream analyses were performed for genes and proteins associated with variants reaching genome-wide significance. Measurements and Main Results: After quality controls, 1,481 stage I cases and 397 stage II cases were included in the analysis. After filtering, 9,075,629 variants were tested in stage I, with 158 meeting advancement criteria. Four variants associated with TFS with consistent effect direction were identified in stage II, including one in an intron of PCSK6 (proprotein convertase subtilisin/kexin type 6) reaching genome-wide significance (hazard ratio, 4.11 [95% confidence interval, 2.54-6.67]; P = 9.45 × 10-9). PCSK6 protein was highly expressed in IPF lung parenchyma. PCSK6 lung staining intensity, peripheral blood gene expression, and plasma concentration were associated with reduced TFS. Conclusions: We identified four novel variants associated with IPF survival, including one in PCSK6 that reached genome-wide significance. Downstream analyses suggested that PCSK6 protein plays a potentially important role in IPF progression.
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Affiliation(s)
- Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Jose M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Shwu-Fan Ma
- Division of Pulmonary and Critical Care Medicine and
| | | | - John S. Kim
- Division of Pulmonary and Critical Care Medicine and
| | - Beatriz Guillen-Guio
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Tamara Hernández-Beeftink
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario de Gran Canaria Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - Jonathan A. Kropski
- Division of Pulmonary and Critical Care Medicine, Vanderbilt University, Nashville, Tennessee
| | - Yong Huang
- Division of Pulmonary and Critical Care Medicine and
| | - Cathryn T. Lee
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Janelle Vu Pugashetti
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Angela L. Linderholm
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Vivian Vo
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis, Davis, California
| | - Mary E. Strek
- Section of Pulmonary and Critical Care Medicine, University of Chicago, Chicago, Illinois
| | - Jonathan Jou
- Department of Surgery, College of Medicine, University of Illinois, Peoria, Illinois
| | - Adrian Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodriguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Richard Hubbard
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, United Kingdom
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Nik Hirani
- Medical Research Council Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Moira K. B. Whyte
- Medical Research Council Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon Hart
- Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, United Kingdom
| | - Andrew G. Nicholson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Lisa Lancaster
- Division of Pulmonary and Critical Care Medicine, Vanderbilt University, Nashville, Tennessee
| | - Helen Parfrey
- Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Doris Rassl
- Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital, Cambridge, United Kingdom
| | - William Wallace
- Medical Research Council Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Eleanor Valenzi
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Josyf Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | | | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, School of Medicine, Yale University, New Haven, Connecticut
| | - Paul J. Wolters
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, San Francisco, California
| | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge, Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | | | - William A. Fahy
- Discovery Medicine, GlaxoSmithKline, Stevenage, United Kingdom
| | | | - Ian P. Hall
- Division of Respiratory Medicine and
- National Institute for Health Research, Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, California; and
| | - Timothy S. Blackwell
- Division of Pulmonary and Critical Care Medicine, Vanderbilt University, Nashville, Tennessee
| | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield Hospitals, Guy’s and St. Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine and
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8
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Chang D, Hammer C, Holweg CTJ, Selvaraj S, Rathore N, McCarthy MI, Yaspan BL, Choy DF. A genome-wide association study of chronic spontaneous urticaria risk and heterogeneity. J Allergy Clin Immunol 2023; 151:1351-1356. [PMID: 36343773 DOI: 10.1016/j.jaci.2022.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Chronic spontaneous urticaria (CSU) is a dermatologic condition characterized by spontaneous, pruritic hives and/or angioedema that persists for 6 weeks or longer with no identifiable trigger. Antihistamines and second-line therapies such as omalizumab are effective for some CSU patients, but others remain symptomatic, with significant impact on quality of life. This variable response to treatment and autoantibody levels across patients highlight clinically heterogeneous subgroups. OBJECTIVE We aimed to highlight pathways involved in CSU by investigating the genetics of CSU risk and subgroups. METHODS We performed a genome-wide association study (GWAS) of 679 CSU patients and 4446 controls and a GWAS of chronic urticaria (CU)-index, which measures IgG autoantibodies levels, by comparing 447 CU index-low to 183 CU index-high patients. We also tested whether polygenic scores for autoimmune-related disorders were associated with CSU risk and CU index. RESULTS We identified 2 loci significantly associated with disease risk. The strongest association mapped to position 56 of HLA-DQA1 (P = 1.69 × 10-9), where the arginine residue was associated with increased risk (odds ratio = 1.64). The second association signal colocalized with expression-quantitative trait loci for ITPKB in whole blood (Pcolocalization = .997). The arginine residue at position 56 of HLA-DQA1 was also associated with increased risk of CU index-high (P = 6.15 × 10-5, odds ratio = 1.86), while the ITKPB association was not (P = .64). Polygenic scores for 3 autoimmune-related disorders (hypothyroidism, type 1 diabetes, and vitiligo) were associated with CSU risk and CU index (P < 2.34 × 10-3, odds ratio > 1.72). CONCLUSION A GWAS of CSU identified 2 genome-wide significant loci, highlighting the shared genetics between CU index and autoimmune disorders.
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Affiliation(s)
- Diana Chang
- Department of Human Genetics, Genentech Inc, South San Francisco, Calif.
| | - Christian Hammer
- Department of Human Genetics, Genentech Inc, South San Francisco, Calif; Department of Cancer Immunology, Genentech Inc, South San Francisco, Calif
| | | | - Suresh Selvaraj
- Department of Biosample and Repository Management, Genentech Inc, South San Francisco, Calif
| | - Nisha Rathore
- Biomarker Discovery OMNI, Genentech Inc, South San Francisco, Calif
| | - Mark I McCarthy
- Department of Human Genetics, Genentech Inc, South San Francisco, Calif
| | - Brian L Yaspan
- Department of Human Genetics, Genentech Inc, South San Francisco, Calif
| | - David F Choy
- Biomarker Discovery OMNI, Genentech Inc, South San Francisco, Calif
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9
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Donoghue LJ, Stockwell AD, Neighbors M, Sheng RX, Prabhakaran R, Wolters PJ, Lancaster LH, Kropski JA, Blackwell TS, McCarthy MI, Yaspan BL. Identification of a Genetic Susceptibility Locus for Idiopathic Pulmonary Fibrosis in the 16p Subtelomere Using Whole Genome Sequencing. Am J Respir Crit Care Med 2023; 207:941-944. [PMID: 36603154 PMCID: PMC10111979 DOI: 10.1164/rccm.202206-1139le] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
| | - Amy D Stockwell
- Genentech Inc, 7412, South San Francisco, California, United States
| | | | - Rebecca X Sheng
- Genentech Inc, 7412, South San Francisco, California, United States
| | | | - Paul J Wolters
- University of California, Medicine/CVRI, San Francisco, California, United States
| | - Lisa H Lancaster
- Vanderbilt University Medical Center, 12328, Nashville, Tennessee, United States
| | - Jonathan A Kropski
- Vanderbilt University Medical Center, 12328, Medicine, Nashville, Tennessee, United States
| | - Timothy S Blackwell
- Vanderbilt University Medical Center, 12328, Medicine, Nashville, Tennessee, United States
| | - Mark I McCarthy
- Genentech Inc, 7412, South San Francisco, California, United States
| | - Brian L Yaspan
- Genentech Inc, 7412, South San Francisco, California, United States;
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10
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Kim S, Stockwell A, Qin H, Gao SS, Sagolla M, Stoilov I, Wuster A, Lai P, Yaspan BL, Jeanne M. Rare CIDEC coding variants enriched in age-related macular degeneration patients with small low-luminance deficit cause lipid droplet and fat storage defects. PLoS One 2023; 18:e0280484. [PMID: 37079518 PMCID: PMC10118094 DOI: 10.1371/journal.pone.0280484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/05/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND The basis of Age-related macular degeneration (AMD) genetic risk has been well documented; however, few studies have looked at genetic biomarkers of disease progression or treatment response within advanced AMD patients. Here we report the first genome-wide analysis of genetic determinants of low-luminance vision deficit (LLD), which is seen as predictive of visual acuity loss and anti-VEGF treatment response in neovascular AMD patients. METHODS AMD patients were separated into small- and large-LLD groups for comparison and whole genome sequencing was performed. Genetic determinants of LLD were assessed by common and rare variant genetic analysis. Follow-up functional analysis of rare coding variants identified by the burden test was then performed in vitro. RESULTS We identified four coding variants in the CIDEC gene. These rare variants were only present in patients with a small LLD, which has been previously shown to indicate better prognosis and better anti-VEGF treatment response. Our in vitro functional characterization of these CIDEC alleles revealed that all decrease the binding affinity between CIDEC and the lipid droplet fusion effectors PLIN1, RAB8A and AS160. The rare CIDEC alleles all cause a hypomorphic defect in lipid droplet fusion and enlargement, resulting in a decreased fat storage capability in adipocytes. CONCLUSIONS As we did not detect CIDEC expression in the ocular tissue affected by AMD, our results suggest that the CIDEC variants do not play a direct role in the eye and influence low-luminance vision deficit via an indirect and systemic effect related to fat storage capacity.
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Affiliation(s)
- Sehyun Kim
- Department of Neuroscience, Genentech Inc., South San Francisco, California, United States of America
| | - Amy Stockwell
- Department of Human Genetics, Genentech Inc., South San Francisco, California, United States of America
| | - Han Qin
- Department of Neuroscience, Genentech Inc., South San Francisco, California, United States of America
| | - Simon S Gao
- Department of Clinical Imaging, Genentech Inc., South San Francisco, California, United States of America
| | - Meredith Sagolla
- Department of Research Pathology, Genentech Inc., South San Francisco, California, United States of America
| | - Ivaylo Stoilov
- Medical Affairs Ophthalmology, Genentech Inc., South San Francisco, California, United States of America
| | - Arthur Wuster
- Department of Human Genetics, Genentech Inc., South San Francisco, California, United States of America
| | - Phillip Lai
- Early Clinical Development, Genentech Inc., South San Francisco, California, United States of America
| | - Brian L Yaspan
- Department of Human Genetics, Genentech Inc., South San Francisco, California, United States of America
| | - Marion Jeanne
- Department of Neuroscience, Genentech Inc., South San Francisco, California, United States of America
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11
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Chavarria-Smith J, Chiu CPC, Jackman JK, Yin J, Zhang J, Hackney JA, Lin WY, Tyagi T, Sun Y, Tao J, Dunlap D, Morton WD, Ghodge SV, Maun HR, Li H, Hernandez-Barry H, Loyet KM, Chen E, Liu J, Tam C, Yaspan BL, Cai H, Balazs M, Arron JR, Li J, Wittwer AJ, Pappu R, Austin CD, Lee WP, Lazarus RA, Sudhamsu J, Koerber JT, Yi T. Dual antibody inhibition of KLK5 and KLK7 for Netherton syndrome and atopic dermatitis. Sci Transl Med 2022; 14:eabp9159. [PMID: 36516271 DOI: 10.1126/scitranslmed.abp9159] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The epidermis is a barrier that prevents water loss while keeping harmful substances from penetrating the host. The impermeable cornified layer of the stratum corneum is maintained by balancing continuous turnover driven by epidermal basal cell proliferation, suprabasal cell differentiation, and corneal shedding. The epidermal desquamation process is tightly regulated by balance of the activities of serine proteases of the Kallikrein-related peptidases (KLK) family and their cognate inhibitor lymphoepithelial Kazal type-related inhibitor (LEKTI), which is encoded by the serine peptidase inhibitor Kazal type 5 gene. Imbalance of proteolytic activity caused by a deficiency of LEKTI leads to excessive desquamation due to increased activities of KLK5, KLK7, and KLK14 and results in Netherton syndrome (NS), a debilitating condition with an unmet clinical need. Increased activity of KLKs may also be pathological in other dermatoses such as atopic dermatitis (AD). Here, we describe the discovery of inhibitory antibodies against murine KLK5 and KLK7 that could compensate for the deficiency of LEKTI in NS. These antibodies are protective in mouse models of NS and AD and, when combined, promote improved skin barrier integrity and reduced inflammation. To translate these findings, we engineered a humanized bispecific antibody capable of potent inhibition of human KLK5 and KLK7. A crystal structure of KLK5 bound to the inhibitory Fab revealed that the antibody binds distal to its active site and uses a relatively unappreciated allosteric inhibition mechanism. Treatment with the bispecific anti-KLK5/7 antibody represents a promising therapy for clinical development in NS and other inflammatory dermatoses.
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Affiliation(s)
- Joseph Chavarria-Smith
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Cecilia P C Chiu
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Janet K Jackman
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jianping Yin
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Juan Zhang
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason A Hackney
- Department of Bioinformatics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wei-Yu Lin
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tulika Tyagi
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yonglian Sun
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Janet Tao
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Debra Dunlap
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - William D Morton
- Confluence Discovery Technologies Inc., 4320 Duncan Ave, Suite 400, St. Louis, MO 63108, USA
| | - Swapnil V Ghodge
- Departments of Biological Chemistry and Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Henry R Maun
- Departments of Biological Chemistry and Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hong Li
- Department of Protein Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hilda Hernandez-Barry
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kelly M Loyet
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Emily Chen
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - John Liu
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christine Tam
- Department of Biomolecular Resources, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Brian L Yaspan
- Department of Human Genetics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hao Cai
- Department of Preclinical and Translational Pharmacokinetics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mercedesz Balazs
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joseph R Arron
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jing Li
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Arthur J Wittwer
- Confluence Discovery Technologies Inc., 4320 Duncan Ave, Suite 400, St. Louis, MO 63108, USA
| | - Rajita Pappu
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Cary D Austin
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Robert A Lazarus
- Departments of Biological Chemistry and Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jawahar Sudhamsu
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - James T Koerber
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tangsheng Yi
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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12
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Partanen JJ, Häppölä P, Zhou W, Lehisto AA, Ainola M, Sutinen E, Allen RJ, Stockwell AD, Leavy OC, Oldham JM, Guillen-Guio B, Cox NJ, Hirbo JB, Schwartz DA, Fingerlin TE, Flores C, Noth I, Yaspan BL, Jenkins RG, Wain LV, Ripatti S, Pirinen M, Laitinen T, Kaarteenaho R, Myllärniemi M, Daly MJ, Koskela JT. Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics. Cell Genom 2022; 2:100181. [PMID: 36777997 PMCID: PMC9903787 DOI: 10.1016/j.xgen.2022.100181] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/24/2022] [Accepted: 09/07/2022] [Indexed: 04/12/2023]
Abstract
The research of rare and devastating orphan diseases, such as idiopathic pulmonary fibrosis (IPF) has been limited by the rarity of the disease itself. The prognosis is poor-the prevalence of IPF is only approximately four times the incidence, limiting the recruitment of patients to trials and studies of the underlying biology. Global biobanking efforts can dramatically alter the future of IPF research. We describe a large-scale meta-analysis of IPF, with 8,492 patients and 1,355,819 population controls from 13 biobanks around the globe. Finally, we combine this meta-analysis with the largest available meta-analysis of IPF, reaching 11,160 patients and 1,364,410 population controls. We identify seven novel genome-wide significant loci, only one of which would have been identified if the analysis had been limited to European ancestry individuals. We observe notable pleiotropy across IPF susceptibility and severe COVID-19 infection and note an unexplained sex-heterogeneity effect at the strongest IPF locus MUC5B.
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Affiliation(s)
- Juulia J. Partanen
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Paavo Häppölä
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Wei Zhou
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Arto A. Lehisto
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Mari Ainola
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Eva Sutinen
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Olivia C. Leavy
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Justin M. Oldham
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
| | | | - Nancy J. Cox
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jibril B. Hirbo
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Tasha E. Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Carlos Flores
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Samuli Ripatti
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Pirinen
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - International IPF Genetics Consortium
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
- Department of Health Sciences, University of Leicester, Leicester, UK
- Human Genetics, Genentech, South San Francisco, CA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, University of Colorado, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Global Biobank Meta-Analysis Initiative (GBMI)
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
- Department of Health Sciences, University of Leicester, Leicester, UK
- Human Genetics, Genentech, South San Francisco, CA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, University of Colorado, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Tarja Laitinen
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
| | - Riitta Kaarteenaho
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Marjukka Myllärniemi
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Mark J. Daly
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jukka T. Koskela
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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13
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Allen RJ, Stockwell A, Oldham JM, Guillen-Guio B, Schwartz DA, Maher TM, Flores C, Noth I, Yaspan BL, Jenkins RG, Wain LV. Genome-wide association study across five cohorts identifies five novel loci associated with idiopathic pulmonary fibrosis. Thorax 2022; 77:829-833. [PMID: 35688625 PMCID: PMC9329250 DOI: 10.1136/thoraxjnl-2021-218577] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/24/2022] [Indexed: 11/03/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung condition with poor survival times. We previously published a genome-wide meta-analysis of IPF risk across three studies with independent replication of associated variants in two additional studies. To maximise power and to generate more accurate effect size estimates, we performed a genome-wide meta-analysis across all five studies included in the previous IPF risk genome-wide association studies. We used the distribution of effect sizes across the five studies to assess the replicability of the results and identified five robust novel genetic association signals implicating mTOR (mammalian target of rapamycin) signalling, telomere maintenance and spindle assembly genes in IPF risk.
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Affiliation(s)
- Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Justin M Oldham
- Department of Internal Medicine, University of California Davis, Davis, USA
| | | | - David A Schwartz
- Center for Genes, Environment and Health, National Jewish Health, Denver, USA,Department of Medicine, University of Colorado Denver, Denver, USA,Department of Immunology, University of Colorado Denver, Denver, USA
| | - Toby M Maher
- National Heart and Lung Institute, Imperial College London, London, UK,Royal Brompton and Harefield Hospitals, London, UK,Division of Pulmonary and Critical Care Medicine, University of Southern California, Los Angeles, USA
| | - Carlos Flores
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain,Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Imre Noth
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, USA
| | | | - R Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK,National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
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14
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Jackman JK, Stockwell A, Choy DF, Xie MM, Lu P, Jia G, Li H, Abbas AR, Bronson PG, Lin WY, Chiu CPC, Maun HR, Roose-Girma M, Tam L, Zhang J, Modrusan Z, Graham RR, Behrens TW, White SR, Naureckas T, Ober C, Ferreira M, Sedlacek R, Wu J, Lee WP, Lazarus RA, Koerber JT, Arron JR, Yaspan BL, Yi T. Genome-wide association study identifies kallikrein 5 in type 2 inflammation-low asthma. J Allergy Clin Immunol 2022; 150:972-978.e7. [PMID: 35487308 DOI: 10.1016/j.jaci.2022.03.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/26/2022] [Accepted: 03/07/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Clinical studies of type 2 (T2) cytokine-related neutralizing antibodies in asthma have identified a substantial subset of patients with low levels of T2 inflammation who do not benefit from T2 cytokine neutralizing antibody treatment. Non type 2 mechanisms are poorly understood in asthma but represent the redefined unmet medical need. OBJECTIVE To gain understanding of the genetic contribution to T2-low asthma. METHODS We utilized an unbiased genome-wide association study (GWAS) of moderate-severe asthma patients stratified by T2 serum biomarker periostin. We also performed additional expression and biological analysis for the top genetic hit. RESULTS This analysis identified a novel protective SNP at chr19q13.41 which is selectively associated with T2-low asthma and establishes KLK5 as the causal gene mediating this association. Heterozygous carriers of the SNP have reduced KLK5 expression. KLK5 is secreted by human bronchial epithelial cells and elevated in asthma bronchial alveolar lavage. T2 cytokines IL-4 and IL-13 downregulate KLK5 in human bronchial epithelial cells. KLK5, dependent on its catalytic function, induces epithelial chemokine/cytokine expression. Lastly, overexpression of KLK5 in airway, or lack of an endogenous KLK5 inhibitor, SPINK5, leads to spontaneous airway neutrophilic inflammation. CONCLUSION Our data identifies KLK5 as the causal gene at a novel locus at chr19q13.41 associated with T2-low asthma.
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Affiliation(s)
- Janet K Jackman
- Department of Immunology Discovery, South San Francisco, Calif
| | - Amy Stockwell
- Department of Human Genetics, South San Francisco, Calif
| | - David F Choy
- Department of Biomarker Discovery OMNI, South San Francisco, Calif
| | - Markus M Xie
- Department of Immunology Discovery, South San Francisco, Calif
| | - Peipei Lu
- Department of Immunology Discovery, South San Francisco, Calif
| | - Guiquan Jia
- Department of Biomarker Discovery OMNI, South San Francisco, Calif
| | - Hong Li
- Department of Protein Chemistry, South San Francisco, Calif
| | - Alexander R Abbas
- Department of Oncology Biomarker Development, South San Francisco, Calif
| | | | - Wei-Yu Lin
- Department of Antibody Engineering, South San Francisco, Calif
| | | | - Henry R Maun
- Department of Early Discovery Biochemistry, South San Francisco, Calif
| | | | - Lucinda Tam
- Department of Molecular Biology, South San Francisco, Calif
| | - Juan Zhang
- Department of Translational Immunology, South San Francisco, Calif
| | - Zora Modrusan
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech Inc, South San Francisco, Calif
| | | | | | - Steven R White
- Department of Medicine, Section of Pulmonary and Critical Care, Chicago, Ill
| | - Ted Naureckas
- Department of Medicine, Section of Pulmonary and Critical Care, Chicago, Ill
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Manuel Ferreira
- QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Herston, Australia
| | - Radislav Sedlacek
- Labortory of Molecular Genetics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Jiansheng Wu
- Department of Protein Chemistry, South San Francisco, Calif
| | - Wyne P Lee
- Department of Translational Immunology, South San Francisco, Calif
| | - Robert A Lazarus
- Department of Early Discovery Biochemistry, South San Francisco, Calif
| | - James T Koerber
- Department of Antibody Engineering, South San Francisco, Calif
| | - Joseph R Arron
- Department of Immunology Discovery, South San Francisco, Calif
| | - Brian L Yaspan
- Department of Human Genetics, South San Francisco, Calif.
| | - Tangsheng Yi
- Department of Immunology Discovery, South San Francisco, Calif.
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15
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Chang D, Hunkapiller J, Bhangale T, Reeder J, Mukhyala K, Tom J, Cowgill A, Vogel J, Forrest WF, Khan Z, Stockwell A, McCarthy MI, Staton TL, Olsson J, Holweg CTJ, Cheung DS, Chen H, Brauer MJ, Graham RR, Behrens T, Wilson MS, Arron JR, Choy DF, Yaspan BL. A whole genome sequencing study of moderate to severe asthma identifies a lung function locus associated with asthma risk. Sci Rep 2022; 12:5574. [PMID: 35368043 PMCID: PMC8976834 DOI: 10.1038/s41598-022-09447-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/23/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractGenome-wide association studies (GWAS) have identified many common variant loci associated with asthma susceptibility, but few studies investigate the genetics underlying moderate-to-severe asthma risk. Here, we present a whole-genome sequencing study comparing 3181 moderate-to-severe asthma patients to 3590 non-asthma controls. We demonstrate that asthma risk is genetically correlated with lung function measures and that this component of asthma risk is orthogonal to the eosinophil genetics that also contribute to disease susceptibility. We find that polygenic scores for reduced lung function are associated with younger asthma age of onset. Genome-wide, seven previously reported common asthma variant loci and one previously reported lung function locus, near THSD4, reach significance. We replicate association of the lung function locus in a recently published GWAS of moderate-to-severe asthma patients. We additionally replicate the association of a previously reported rare (minor allele frequency < 1%) coding variant in IL33 and show significant enrichment of rare variant burden in genes from common variant allergic disease loci. Our findings highlight the contribution of lung function genetics to moderate-to-severe asthma risk, and provide initial rare variant support for associations with moderate-to-severe asthma risk at several candidate genes from common variant loci.
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16
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Maun HR, Jackman JK, Choy DF, Loyet KM, Staton TL, Jia G, Dressen A, Hackney JA, Bremer M, Walters BT, Vij R, Chen X, Trivedi NN, Morando A, Lipari MT, Franke Y, Wu X, Zhang J, Liu J, Wu P, Chang D, Orozco LD, Christensen E, Wong M, Corpuz R, Hang JQ, Lutman J, Sukumaran S, Wu Y, Ubhayakar S, Liang X, Schwartz LB, Babina M, Woodruff PG, Fahy JV, Ahuja R, Caughey GH, Kusi A, Dennis MS, Eigenbrot C, Kirchhofer D, Austin CD, Wu LC, Koerber JT, Lee WP, Yaspan BL, Alatsis KR, Arron JR, Lazarus RA, Yi T. An Allosteric Anti-tryptase Antibody for the Treatment of Mast Cell-Mediated Severe Asthma. Cell 2020; 179:417-431.e19. [PMID: 31585081 DOI: 10.1016/j.cell.2019.09.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 07/09/2019] [Accepted: 09/05/2019] [Indexed: 12/18/2022]
Abstract
Severe asthma patients with low type 2 inflammation derive less clinical benefit from therapies targeting type 2 cytokines and represent an unmet need. We show that mast cell tryptase is elevated in severe asthma patients independent of type 2 biomarker status. Active β-tryptase allele count correlates with blood tryptase levels, and asthma patients carrying more active alleles benefit less from anti-IgE treatment. We generated a noncompetitive inhibitory antibody against human β-tryptase, which dissociates active tetramers into inactive monomers. A 2.15 Å crystal structure of a β-tryptase/antibody complex coupled with biochemical studies reveal the molecular basis for allosteric destabilization of small and large interfaces required for tetramerization. This anti-tryptase antibody potently blocks tryptase enzymatic activity in a humanized mouse model, reducing IgE-mediated systemic anaphylaxis, and inhibits airway tryptase in Ascaris-sensitized cynomolgus monkeys with favorable pharmacokinetics. These data provide a foundation for developing anti-tryptase as a clinical therapy for severe asthma.
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Affiliation(s)
- Henry R Maun
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Janet K Jackman
- Department of Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - David F Choy
- Department of Biomarker Discovery OMNI, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kelly M Loyet
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tracy L Staton
- Department of OMNI Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Guiquan Jia
- Department of Biomarker Discovery OMNI, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Amy Dressen
- Department of Human Genetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason A Hackney
- Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Meire Bremer
- Department of OMNI Biomarker Development, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin T Walters
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rajesh Vij
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xiaocheng Chen
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Neil N Trivedi
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Ashley Morando
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Michael T Lipari
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yvonne Franke
- Depratment of Biomolecular Resources, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xiumin Wu
- Department of Translational Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Juan Zhang
- Department of Translational Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - John Liu
- Department of Translational Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ping Wu
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Diana Chang
- Department of Human Genetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Luz D Orozco
- Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Erin Christensen
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Manda Wong
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Racquel Corpuz
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Julie Q Hang
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jeff Lutman
- Department of Preclinical and Translational Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Siddharth Sukumaran
- Department of Preclinical and Translational Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yan Wu
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Savita Ubhayakar
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Xiaorong Liang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Lawrence B Schwartz
- Department of Internal Medicine, Division of Rheumatology, Allergy and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Magda Babina
- Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Prescott G Woodruff
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John V Fahy
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rahul Ahuja
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - George H Caughey
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Veterans Affairs Medical Center, San Francisco, CA 94121, USA
| | - Aija Kusi
- Department of Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mark S Dennis
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Charles Eigenbrot
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Daniel Kirchhofer
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Cary D Austin
- Department of Pathology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Lawren C Wu
- Department of Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - James T Koerber
- Department of Antibody Engineering, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Brian L Yaspan
- Department of Human Genetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kathila R Alatsis
- Department of Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joseph R Arron
- Department of Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Robert A Lazarus
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Tangsheng Yi
- Department of Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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17
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Pollack S, Igo RP, Jensen RA, Christiansen M, Li X, Cheng CY, Ng MCY, Smith AV, Rossin EJ, Segrè AV, Davoudi S, Tan GS, Ida Chen YD, Kuo JZ, Dimitrov LM, Stanwyck LK, Meng W, Hosseini SM, Imamura M, Nousome D, Kim J, Hai Y, Jia Y, Ahn J, Leong A, Shah K, Park KH, Guo X, Ipp E, Taylor KD, Adler SG, Sedor JR, Freedman BI, Lee IT, Sheu WHH, Kubo M, Takahashi A, Hadjadj S, Marre M, Tregouet DA, Mckean-Cowdin R, Varma R, McCarthy MI, Groop L, Ahlqvist E, Lyssenko V, Agardh E, Morris A, Doney ASF, Colhoun HM, Toppila I, Sandholm N, Groop PH, Maeda S, Hanis CL, Penman A, Chen CJ, Hancock H, Mitchell P, Craig JE, Chew EY, Paterson AD, Grassi MA, Palmer C, Bowden DW, Yaspan BL, Siscovick D, Cotch MF, Wang JJ, Burdon KP, Wong TY, Klein BEK, Klein R, Rotter JI, Iyengar SK, Price AL, Sobrin L. Erratum. Multiethnic Genome-Wide Association Study of Diabetic Retinopathy Using Liability Threshold Modeling of Duration of Diabetes and Glycemic Control. Diabetes 2019;68:441-456. Diabetes 2020; 69:1306. [PMID: 32341040 PMCID: PMC7243291 DOI: 10.2337/db20-er06a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Allen RJ, Guillen-Guio B, Oldham JM, Ma SF, Dressen A, Paynton ML, Kraven LM, Obeidat M, Li X, Ng M, Braybrooke R, Molina-Molina M, Hobbs BD, Putman RK, Sakornsakolpat P, Booth HL, Fahy WA, Hart SP, Hill MR, Hirani N, Hubbard RB, McAnulty RJ, Millar AB, Navaratnam V, Oballa E, Parfrey H, Saini G, Whyte MKB, Zhang Y, Kaminski N, Adegunsoye A, Strek ME, Neighbors M, Sheng XR, Gudmundsson G, Gudnason V, Hatabu H, Lederer DJ, Manichaikul A, Newell JD, O’Connor GT, Ortega VE, Xu H, Fingerlin TE, Bossé Y, Hao K, Joubert P, Nickle DC, Sin DD, Timens W, Furniss D, Morris AP, Zondervan KT, Hall IP, Sayers I, Tobin MD, Maher TM, Cho MH, Hunninghake GM, Schwartz DA, Yaspan BL, Molyneaux PL, Flores C, Noth I, Jenkins RG, Wain LV. Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2020; 201:564-574. [PMID: 31710517 PMCID: PMC7047454 DOI: 10.1164/rccm.201905-1017oc] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 11/07/2019] [Indexed: 01/10/2023] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is a complex lung disease characterized by scarring of the lung that is believed to result from an atypical response to injury of the epithelium. Genome-wide association studies have reported signals of association implicating multiple pathways including host defense, telomere maintenance, signaling, and cell-cell adhesion.Objectives: To improve our understanding of factors that increase IPF susceptibility by identifying previously unreported genetic associations.Methods: We conducted genome-wide analyses across three independent studies and meta-analyzed these results to generate the largest genome-wide association study of IPF to date (2,668 IPF cases and 8,591 controls). We performed replication in two independent studies (1,456 IPF cases and 11,874 controls) and functional analyses (including statistical fine-mapping, investigations into gene expression, and testing for enrichment of IPF susceptibility signals in regulatory regions) to determine putatively causal genes. Polygenic risk scores were used to assess the collective effect of variants not reported as associated with IPF.Measurements and Main Results: We identified and replicated three new genome-wide significant (P < 5 × 10-8) signals of association with IPF susceptibility (associated with altered gene expression of KIF15, MAD1L1, and DEPTOR) and confirmed associations at 11 previously reported loci. Polygenic risk score analyses showed that the combined effect of many thousands of as yet unreported IPF susceptibility variants contribute to IPF susceptibility.Conclusions: The observation that decreased DEPTOR expression associates with increased susceptibility to IPF supports recent studies demonstrating the importance of mTOR signaling in lung fibrosis. New signals of association implicating KIF15 and MAD1L1 suggest a possible role of mitotic spindle-assembly genes in IPF susceptibility.
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Affiliation(s)
- Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | | | - Justin M. Oldham
- Department of Internal Medicine, University of California Davis, Davis, California
| | - Shwu-Fan Ma
- Division of Pulmonary and Critical Care Medicine
| | | | - Megan L. Paynton
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Luke M. Kraven
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Xuan Li
- The University of British Columbia Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Michael Ng
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences
| | - Rebecca Braybrooke
- Division of Epidemiology and Public Health and
- National Institute for Health Research, Nottingham Biomedical Research Centre and
| | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Brian D. Hobbs
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
| | | | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Helen L. Booth
- Department of Thoracic Medicine, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - William A. Fahy
- Discovery Medicine, GlaxoSmithKline, Stevenage, United Kingdom
| | - Simon P. Hart
- Respiratory Research Group, Hull York Medical School, Castle Hill Hospital, Cottingham, United Kingdom
| | - Mike R. Hill
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health
| | - Nik Hirani
- Medical Research Council Centre for Inflammation Research, The University of Edinburgh, Edinburgh, United Kingdom
| | - Richard B. Hubbard
- Division of Epidemiology and Public Health and
- National Institute for Health Research, Nottingham Biomedical Research Centre and
| | - Robin J. McAnulty
- UCL Respiratory Centre for Inflammation and Tissue Repair, University College London, London, United Kingdom
| | - Ann B. Millar
- Academic Respiratory Unit, School of Clinical Sciences, University of Bristol, Bristol, United Kingdom
| | - Vidyia Navaratnam
- Division of Epidemiology and Public Health and
- National Institute for Health Research, Nottingham Biomedical Research Centre and
| | - Eunice Oballa
- Discovery Medicine, GlaxoSmithKline, Stevenage, United Kingdom
| | - Helen Parfrey
- Cambridge Interstitial Lung Disease Service, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Gauri Saini
- Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Moira K. B. Whyte
- Medical Research Council Centre for Inflammation Research, The University of Edinburgh, Edinburgh, United Kingdom
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine and
- Simmons Center for Interstitial Lung Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Ayodeji Adegunsoye
- Section of Pulmonary and Critical Care, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Mary E. Strek
- Section of Pulmonary and Critical Care, Department of Medicine, The University of Chicago, Chicago, Illinois
| | | | | | - Gunnar Gudmundsson
- Department of Respiratory Medicine, Landspital University Hospital, Reykjavik, Iceland
- Faculty of Medicine University of Iceland, Reykjavik, Iceland
| | - Vilmundur Gudnason
- Faculty of Medicine University of Iceland, Reykjavik, Iceland
- Icelandic Heart Association, Kopavogur, Iceland
| | - Hiroto Hatabu
- Department of Radiology, and
- Center for Pulmonary Functional Imaging, Brigham and Women’s Hospital, Boston, Massachusetts
| | - David J. Lederer
- Department of Medicine, College of Physicians and Surgeons and
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Ani Manichaikul
- Center for Public Health Genomics, and
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - John D. Newell
- Division of Cardiovascular and Pulmonary Imaging, Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa
- Department of Radiology, University of Washington, Seattle, Washington
| | - George T. O’Connor
- Department of Medicine, Pulmonary Center, Boston University, Boston, Massachusetts
- NHLBI’s Framingham Heart Study, Framingham, Massachusetts
| | - Victor E. Ortega
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Tasha E. Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colarado
- Department of Biostatistics and Informatics
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Québec, Québec, Canada
| | - Ke Hao
- Department of Genetics and Genomic Sciences and
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec, Université Laval, Québec, Québec, Canada
| | - David C. Nickle
- Merck Research Laboratories, Genetics and Pharmacogenomics, Boston, Massachusetts
| | - Don D. Sin
- The University of British Columbia Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, British Columbia, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wim Timens
- University Medical Center Groningen, University of Groningen, Department of Pathology and Medical Biology and
- Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - Dominic Furniss
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences
| | - Andrew P. Morris
- Wellcome Centre for Human Genetics, and
- Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom
- Division of Musculoskeletal and Dermatological Sciences, University of Manchester, Manchester, United Kingdom
| | - Krina T. Zondervan
- Wellcome Centre for Human Genetics, and
- Oxford Endometriosis Care and Research Centre, Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Ian P. Hall
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
- National Institute for Health Research, Nottingham Biomedical Research Centre and
| | - Ian Sayers
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
- National Institute for Health Research, Nottingham Biomedical Research Centre and
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Toby M. Maher
- National Institute for Health Research Respiratory Clinical Research Facility, Royal Brompton Hospital, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom; and
| | - Michael H. Cho
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
| | - Gary M. Hunninghake
- Division of Pulmonary and Critical Care Medicine
- Center for Pulmonary Functional Imaging, Brigham and Women’s Hospital, Boston, Massachusetts
| | - David A. Schwartz
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colarado
- Department of Medicine, and
- Department of Immunology, University of Colorado Denver, Denver, Colorado
| | | | - Philip L. Molyneaux
- National Institute for Health Research Respiratory Clinical Research Facility, Royal Brompton Hospital, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom; and
| | - Carlos Flores
- Unidad de Investigacion, Hospital Universitario Ntra. Sra. de Candelaria and
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto Tecnológico y de Energías Renovables, S.A., Santa Cruz de Tenerife, Spain
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine
| | - R. Gisli Jenkins
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
- National Institute for Health Research, Nottingham Biomedical Research Centre and
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
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Maun HR, Jackman JK, Choy DF, Loyet KM, Staton TL, Jia G, Dressen A, Hackney JA, Bremer M, Walters BT, Vij R, Chen X, Trivedi NN, Morando A, Lipari MT, Franke Y, Wu X, Zhang J, Liu J, Wu P, Chang D, Orozco LD, Christensen E, Wong M, Corpuz R, Hang JQ, Lutman J, Sukumaran S, Wu Y, Ubhayakar S, Liang X, Schwartz LB, Babina M, Woodruff PG, Fahy JV, Ahuja R, Caughey GH, Kusi A, Dennis MS, Eigenbrot C, Kirchhofer D, Austin CD, Wu LC, Koerber JT, Lee WP, Yaspan BL, Alatsis KR, Arron JR, Lazarus RA, Yi T. An Allosteric Anti-tryptase Antibody for the Treatment of Mast Cell-Mediated Severe Asthma. Cell 2020; 180:406. [PMID: 31978350 DOI: 10.1016/j.cell.2020.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Ley B, Torgerson DG, Oldham JM, Adegunsoye A, Liu S, Li J, Elicker BM, Henry TS, Golden JA, Jones KD, Dressen A, Yaspan BL, Arron JR, Noth I, Hoffmann TJ, Wolters PJ. Rare Protein-Altering Telomere-related Gene Variants in Patients with Chronic Hypersensitivity Pneumonitis. Am J Respir Crit Care Med 2019; 200:1154-1163. [PMID: 31268371 PMCID: PMC6888660 DOI: 10.1164/rccm.201902-0360oc] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 07/02/2019] [Indexed: 12/30/2022] Open
Abstract
Rationale: Rare genetic variants in telomere-related genes have been identified in familial, idiopathic, and rheumatoid arthritis-associated pulmonary fibrosis. Short peripheral blood leukocyte (PBL) telomere length predicts poor outcomes in chronic hypersensitivity pneumonitis (CHP).Objectives: Determine the prevalence and clinical relevance of rare protein-altering variants in telomere-related genes in patients with CHP.Methods: Next-generation sequences from two CHP cohorts were analyzed to identify variants in TERT (telomerase reverse transcriptase), TERC (telomerase RNA component), DKC1 (dyskerin pseudouridine synthase 1), RTEL1 (regulator of telomere elongation helicase 1), PARN (poly[A]-specific RNase), and TINF2 (TERF1-interacting nuclear factor 2). To qualify, variants were required to have a minor allele frequency less than 0.005 and be predicted to be damaging to protein function. Variant status (binary variable) was used in statistical association tests, including Cox proportional hazard models for transplant-free survival. PBL telomere length was measured using quantitative PCR.Measurements and Main Results: Qualifying variants were identified in 16 of 144 patients (11.1%; 95% confidence interval [CI], 6.5-17.4) in the discovery cohort and 17 of 209 patients (8.1%; 95% CI, 4.8-12.7) in the replication cohort. Age- and ancestry-adjusted PBL telomere length was significantly shorter in the presence of a variant in both cohorts (discovery: -561 bp; 95% CI, -933 to -190; P = 0.003; replication: -612 bp; 95% CI, -870 to -354; P = 5.30 × 10-6). Variant status was significantly associated with transplant-free survival in both cohorts (discovery: age-, sex-, and ancestry-adjusted hazard ratio, 3.73; 95% CI, 1.92-7.28; P = 0.0001; replication: hazard ratio, 2.72; 95% CI, 1.26-5.88; P = 0.011).Conclusions: A substantial proportion of patients diagnosed with CHP have rare, protein-altering variants in telomere-related genes, which are associated with short peripheral blood telomere length and significantly reduced transplant-free survival.
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Affiliation(s)
| | - Dara G. Torgerson
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Justin M. Oldham
- Department of Medicine, University of California Davis, Davis, California
| | | | - Shuo Liu
- Department of Respiratory Medicine, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, People’s Republic of China
| | - Jie Li
- University of California Davis Bioinformatics Core, Davis, California
| | | | | | | | | | - Amy Dressen
- Genentech, South San Francisco, California; and
| | | | | | - Imre Noth
- Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Thomas J. Hoffmann
- Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California San Francisco, San Francisco, California
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21
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Pollack S, Igo RP, Jensen RA, Christiansen M, Li X, Cheng CY, Ng MCY, Smith AV, Rossin EJ, Segrè AV, Davoudi S, Tan GS, Chen YDI, Kuo JZ, Dimitrov LM, Stanwyck LK, Meng W, Hosseini SM, Imamura M, Nousome D, Kim J, Hai Y, Jia Y, Ahn J, Leong A, Shah K, Park KH, Guo X, Ipp E, Taylor KD, Adler SG, Sedor JR, Freedman BI, Lee IT, Sheu WHH, Kubo M, Takahashi A, Hadjadj S, Marre M, Tregouet DA, Mckean-Cowdin R, Varma R, McCarthy MI, Groop L, Ahlqvist E, Lyssenko V, Agardh E, Morris A, Doney ASF, Colhoun HM, Toppila I, Sandholm N, Groop PH, Maeda S, Hanis CL, Penman A, Chen CJ, Hancock H, Mitchell P, Craig JE, Chew EY, Paterson AD, Grassi MA, Palmer C, Bowden DW, Yaspan BL, Siscovick D, Cotch MF, Wang JJ, Burdon KP, Wong TY, Klein BEK, Klein R, Rotter JI, Iyengar SK, Price AL, Sobrin L. Multiethnic Genome-Wide Association Study of Diabetic Retinopathy Using Liability Threshold Modeling of Duration of Diabetes and Glycemic Control. Diabetes 2019; 68:441-456. [PMID: 30487263 PMCID: PMC6341299 DOI: 10.2337/db18-0567] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/12/2018] [Indexed: 12/18/2022]
Abstract
To identify genetic variants associated with diabetic retinopathy (DR), we performed a large multiethnic genome-wide association study. Discovery included eight European cohorts (n = 3,246) and seven African American cohorts (n = 2,611). We meta-analyzed across cohorts using inverse-variance weighting, with and without liability threshold modeling of glycemic control and duration of diabetes. Variants with a P value <1 × 10-5 were investigated in replication cohorts that included 18,545 European, 16,453 Asian, and 2,710 Hispanic subjects. After correction for multiple testing, the C allele of rs142293996 in an intron of nuclear VCP-like (NVL) was associated with DR in European discovery cohorts (P = 2.1 × 10-9), but did not reach genome-wide significance after meta-analysis with replication cohorts. We applied the Disease Association Protein-Protein Link Evaluator (DAPPLE) to our discovery results to test for evidence of risk being spread across underlying molecular pathways. One protein-protein interaction network built from genes in regions associated with proliferative DR was found to have significant connectivity (P = 0.0009) and corroborated with gene set enrichment analyses. These findings suggest that genetic variation in NVL, as well as variation within a protein-protein interaction network that includes genes implicated in inflammation, may influence risk for DR.
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Affiliation(s)
- Samuela Pollack
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Robert P Igo
- Department of Population and Quantitative Health Sciences, Case Western University, Cleveland, OH
| | - Richard A Jensen
- Cardiovascular Health Research Unit, Department of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA
| | - Mark Christiansen
- Cardiovascular Health Research Unit, Department of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA
| | - Xiaohui Li
- Institute for Translational Genomics and Population Sciences, LA BioMed and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Ching-Yu Cheng
- Duke-NUS Medical School, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | - Albert V Smith
- Department of Medicine, University of Iceland, Reykjavík, Iceland
| | - Elizabeth J Rossin
- Massachusetts Eye and Ear Department of Ophthalmology, Harvard Medical School, Boston, MA
| | - Ayellet V Segrè
- Massachusetts Eye and Ear Department of Ophthalmology, Harvard Medical School, Boston, MA
| | - Samaneh Davoudi
- Massachusetts Eye and Ear Department of Ophthalmology, Harvard Medical School, Boston, MA
| | - Gavin S Tan
- Duke-NUS Medical School, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, LA BioMed and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Jane Z Kuo
- Institute for Translational Genomics and Population Sciences, LA BioMed and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
- Medical Affairs, Ophthalmology, Sun Pharmaceutical Industries, Inc., Princeton, NJ
| | - Latchezar M Dimitrov
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | - Lynn K Stanwyck
- Massachusetts Eye and Ear Department of Ophthalmology, Harvard Medical School, Boston, MA
| | - Weihua Meng
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee School of Medicine, Scotland, U.K
| | - S Mohsen Hosseini
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Minako Imamura
- Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara, Japan
| | - Darryl Nousome
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jihye Kim
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Yang Hai
- Institute for Translational Genomics and Population Sciences, LA BioMed and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Yucheng Jia
- Institute for Translational Genomics and Population Sciences, LA BioMed and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Jeeyun Ahn
- Department of Ophthalmology, SMG-SNU Boramae Medical Center, Seoul National University College of Medicine, Seoul, Korea
| | - Aaron Leong
- Endocrine Unit and Diabetes Unit, Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Kaanan Shah
- Section of Genetic Medicine, University of Chicago, Chicago, IL
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, LA BioMed and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Eli Ipp
- Section of Diabetes and Metabolism, Harbor-UCLA Medical Center, University of California, Los Angeles, Los Angeles, CA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, LA BioMed and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Sharon G Adler
- Department of Nephrology and Hypertension, Los Angeles Biomedical Research Institute at Harbor-University of California, Torrance, CA
| | - John R Sedor
- Department of Medicine, Case Western Reserve University, Cleveland, OH
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH
- Division of Nephrology, MetroHealth System, Cleveland, OH
| | - Barry I Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC
| | - I-Te Lee
- Division of Endocrinology and Metabolism, Department of 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
| | - Wayne H-H Sheu
- Division of Endocrinology and Metabolism, Department of 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
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Samy Hadjadj
- CHU de Poitiers, Centre d'Investigation Clinique, Poitiers, France
- Université de Poitiers, UFR Médecine Pharmacie, Centre d'Investigation Clinique 1402, Poitiers, France
- INSERM, Centre d'Investigation Clinique 1402, Poitiers, France
- L'Institut du Thorax, INSERM, CNRS, CHU Nantes, Nantes, France
| | - Michel Marre
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Department of Diabetology, Endocrinology and Nutrition, Assistance Publique-Hôpitaux de Paris, Bichat Hospital, DHU FIRE, Paris, France
- INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
| | - David-Alexandre Tregouet
- Team Genomics & Pathophysiology of Cardiovascular Diseases, UPMC, Sorbonne Universités, INSERM, UMR_S 1166, Paris, France
- Institute of Cardiometabolism and Nutrition, Paris, France
| | - Roberta Mckean-Cowdin
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA
| | - Rohit Varma
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Department of Ophthalmology, USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, U.K
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, U.K
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, U.K
| | - Leif Groop
- Department of Clinical Sciences, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Emma Ahlqvist
- Department of Clinical Sciences, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Valeriya Lyssenko
- Department of Clinical Sciences, Faculty of Medicine, Lund University, Malmö, Sweden
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway
| | - Elisabet Agardh
- Department of Clinical Sciences, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Andrew Morris
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, U.K
| | - Alex S F Doney
- Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, U.K
| | - Helen M Colhoun
- Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, U.K
| | - Iiro Toppila
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Abdominal Center, Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Shiro Maeda
- Laboratory for Endocrinology, Metabolism and Kidney Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara, Japan
| | - Craig L Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Alan Penman
- Department of Preventive Medicine, John D. Bower School of Population Health, University of Mississippi Medical Center, Jackson, MS
| | - Ching J Chen
- Department of Ophthalmology, University of Mississippi Medical Center, Jackson, MS
| | - Heather Hancock
- Department of Ophthalmology, University of Mississippi Medical Center, Jackson, MS
| | - Paul Mitchell
- Centre for Vision Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia
| | - Emily Y Chew
- Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Andrew D Paterson
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics & Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Epidemiology and Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Michael A Grassi
- Grassi Retina, Naperville, IL
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL
| | - Colin Palmer
- Pat MacPherson Centre for Pharmacogenetics and Pharmacogenomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, U.K
| | - Donald W Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | | | - David Siscovick
- Institute for Urban Health, New York Academy of Medicine, New York, NY
| | - Mary Frances Cotch
- Division of Epidemiology and Clinical Applications, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Jie Jin Wang
- Duke-NUS Medical School, Singapore
- Centre for Vision Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Tien Y Wong
- Duke-NUS Medical School, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Barbara E K Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, WI
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, LA BioMed and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Sudha K Iyengar
- Department of Population and Quantitative Health Sciences, Case Western University, Cleveland, OH
| | - Alkes L Price
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Lucia Sobrin
- Massachusetts Eye and Ear Department of Ophthalmology, Harvard Medical School, Boston, MA
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22
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White MJ, Yaspan BL, Veatch OJ, Goddard P, Risse-Adams OS, Contreras MG. Strategies for Pathway Analysis Using GWAS and WGS Data. ACTA ACUST UNITED AC 2018; 100:e79. [PMID: 30387919 DOI: 10.1002/cphg.79] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single-allele study designs, commonly used in genome-wide association studies (GWAS) as well as the more recently developed whole genome sequencing (WGS) studies, are a standard approach for investigating the relationship of common variation within the human genome to a given phenotype of interest. However, single-allele association results published for many GWAS studies represent only the tip of the iceberg for the information that can be extracted from these datasets. The primary analysis strategy for GWAS entails association analysis in which only the single nucleotide polymorphisms (SNPs) with the strongest p-values are declared statistically significant due to issues arising from multiple testing and type I errors. Factors such as locus heterogeneity, epistasis, and multiple genes conferring small effects contribute to the complexity of the genetic models underlying phenotype expression. Thus, many biologically meaningful associations having lower effect sizes at individual genes are overlooked, making it difficult to separate true associations from a sea of false-positive associations. Organizing these individual SNPs into biologically meaningful groups to look at the overall effects of minor perturbations to genes and pathways is desirable. This pathway-based approach provides researchers with insight into the functional foundations of the phenotype being studied and allows testing of various genetic scenarios. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Marquitta J White
- Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, California
| | | | - Olivia J Veatch
- Center for Sleep and Circadian Neurobiology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Pagé Goddard
- Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, California
| | - Oona S Risse-Adams
- Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, California
| | - Maria G Contreras
- Department of Medicine, Lung Biology Center, University of California San Francisco, San Francisco, California.,MARC, San Francisco State University, San Francisco, California
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23
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Yaspan BL, Williams DF, Holz FG, Regillo CD, Li Z, Dressen A, van Lookeren Campagne M, Le KN, Graham RR, Beres T, Bhangale TR, Honigberg LA, Smith A, Henry EC, Ho C, Strauss EC. Targeting factor D of the alternative complement pathway reduces geographic atrophy progression secondary to age-related macular degeneration. Sci Transl Med 2017. [PMID: 28637922 DOI: 10.1126/scitranslmed.aaf1443] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Frank G Holz
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | | | - Zhengrong Li
- Genentech Inc., South San Francisco, CA 94080, USA
| | - Amy Dressen
- Genentech Inc., South San Francisco, CA 94080, USA
| | | | - Kha N Le
- Genentech Inc., South San Francisco, CA 94080, USA
| | | | | | | | | | - Ashley Smith
- Genentech Inc., South San Francisco, CA 94080, USA
| | - Erin C Henry
- Genentech Inc., South San Francisco, CA 94080, USA
| | - Carole Ho
- Genentech Inc., South San Francisco, CA 94080, USA
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24
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Yang C, Hojer CD, Zhou M, Wu X, Wuster A, Lee WP, Yaspan BL, Chan AC. Regulation of T-cell receptor downmodulation by DENND1B in TH2 cells and allergic disease. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.192.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The DENN-domain is an evolutionary conserved protein module found in all eukaryotes and serves as an exchange factor for Rab-GTPases to regulate diverse cellular functions. Variants in DENND1B are associated with development of childhood asthma and other immune disorders. To understand how DENND1B may contribute to diseases, Dennd1b−/− mice were generated and exhibit hyper-allergic responses following antigen challenge. Dennd1b−/− TH2, but not other TH cells, exhibit delayed receptor-induced TCR downmodulation, enhanced TCR signaling, and increased production of effector cytokines. As DENND1B interacts with AP-2 and Rab35, TH2 cells deficient in AP-2 or Rab35 also exhibit enhanced TCR-mediated effector functions. Moreover, human TH2 cells carrying asthma-associated DENND1B variants express less DENND1B and phenocopy Dennd1b−/− TH2 cells. These results provide a molecular basis for how DENND1B, a previously unrecognized regulator of TCR downmodulation in TH2 cells, contributes to asthma pathogenesis and how DENN-domain containing proteins may contribute to other human disorders.
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25
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Butkiewicz M, Cooke Bailey JN, Frase A, Dudek S, Yaspan BL, Ritchie MD, Pendergrass SA, Haines JL. Pathway analysis by randomization incorporating structure-PARIS: an update. ACTA ACUST UNITED AC 2016; 32:2361-3. [PMID: 27153576 DOI: 10.1093/bioinformatics/btw130] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/03/2016] [Indexed: 01/11/2023]
Abstract
MOTIVATION We present an update to the pathway enrichment analysis tool 'Pathway Analysis by Randomization Incorporating Structure (PARIS)' that determines aggregated association signals generated from genome-wide association study results. Pathway-based analyses highlight biological pathways associated with phenotypes. PARIS uses a unique permutation strategy to evaluate the genomic structure of interrogated pathways, through permutation testing of genomic features, thus eliminating many of the over-testing concerns arising with other pathway analysis approaches. RESULTS We have updated PARIS to incorporate expanded pathway definitions through the incorporation of new expert knowledge from multiple database sources, through customized user provided pathways, and other improvements in user flexibility and functionality. AVAILABILITY AND IMPLEMENTATION PARIS is freely available to all users at https://ritchielab.psu.edu/software/paris-download CONTACT jnc43@case.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mariusz Butkiewicz
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Jessica N Cooke Bailey
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Alex Frase
- Biomedical and Translational Informatics Program, Geisinger Health System, Danville, PA, USA
| | - Scott Dudek
- Biomedical and Translational Informatics Program, Geisinger Health System, Danville, PA, USA
| | - Brian L Yaspan
- Department of Human Genetics, Genentech, Inc, South San Francisco, CA, USA
| | - Marylyn D Ritchie
- Biomedical and Translational Informatics Program, Geisinger Health System, Danville, PA, USA
| | - Sarah A Pendergrass
- Biomedical and Translational Informatics Program, Geisinger Health System, Danville, PA, USA
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
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26
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Bailey JNC, Loomis SJ, Kang JH, Allingham RR, Gharahkhani P, Khor CC, Burdon KP, Aschard H, Chasman DI, Igo RP, Hysi PG, Glastonbury CA, Ashley-Koch A, Brilliant M, Brown AA, Budenz DL, Buil A, Cheng CY, Choi H, Christen WG, Curhan G, De Vivo I, Fingert JH, Foster PJ, Fuchs C, Gaasterland D, Gaasterland T, Hewitt AW, Hu F, Hunter DJ, Khawaja AP, Lee RK, Li Z, Lichter PR, Mackey DA, McGuffin P, Mitchell P, Moroi SE, Perera SA, Pepper KW, Qi Q, Realini T, Richards JE, Ridker PM, Rimm E, Ritch R, Ritchie M, Schuman JS, Scott WK, Singh K, Sit AJ, Song YE, Tamimi RM, Topouzis F, Viswanathan AC, Verma SS, Vollrath D, Wang JJ, Weisschuh N, Wissinger B, Wollstein G, Wong TY, Yaspan BL, Zack DJ, Zhang K, Study ENE, Weinreb RN, Pericak-Vance MA, Small K, Hammond CJ, Aung T, Liu Y, Vithana EN, MacGregor S, Craig JE, Kraft P, Howell G, Hauser MA, Pasquale LR, Haines JL, Wiggs JL. Genome-wide association analysis identifies TXNRD2, ATXN2 and FOXC1 as susceptibility loci for primary open-angle glaucoma. Nat Genet 2016; 48:189-94. [PMID: 26752265 PMCID: PMC4731307 DOI: 10.1038/ng.3482] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 12/09/2015] [Indexed: 12/13/2022]
Abstract
Primary open angle glaucoma (POAG) is a leading cause of blindness world-wide. To identify new susceptibility loci, we meta-analyzed GWAS results from 8 independent studies from the United States (3,853 cases and 33,480 controls) and investigated the most significant SNPs in two Australian studies (1,252 cases and 2,592 controls), 3 European studies (875 cases and 4,107 controls) and a Singaporean Chinese study (1,037 cases and 2,543 controls). A meta-analysis of top SNPs identified three novel loci: rs35934224[T] within TXNRD2 (odds ratio (OR) = 0.78, P = 4.05×10−11 encoding a mitochondrial protein required for redox homeostasis; rs7137828[T] within ATXN2 (OR = 1.17, P = 8.73×10−10), and rs2745572[A] upstream of FOXC1 (OR = 1.17, P = 1.76×10−10). Using RT-PCR and immunohistochemistry, we show TXNRD2 and ATXN2 expression in retinal ganglion cells and the optic nerve head. These results identify new pathways underlying POAG susceptibility and suggest novel targets for preventative therapies.
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Affiliation(s)
- Jessica N Cooke Bailey
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Stephanie J Loomis
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, USA
| | - Puya Gharahkhani
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Chiea Chuen Khor
- Division of Human Genetics, Genome Institute of Singapore, Singapore.,Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kathryn P Burdon
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia.,Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Hugues Aschard
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Robert P Igo
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Craig A Glastonbury
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Allison Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Murray Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA
| | - Andrew A Brown
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Ching-Yu Cheng
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Eye Academic Clinical Program, Duke-National University of Singapore Graduate Medical School, Singapore
| | - Hyon Choi
- Section of Rheumatology and Clinical Epidemiology Unit, Boston University School of Medicine, Boston, Massachusetts, USA
| | - William G Christen
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Gary Curhan
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Immaculata De Vivo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - John H Fingert
- Department of Ophthalmology, University of Iowa, College of Medicine, Iowa City, Iowa, USA.,Department of Anatomy and Cell Biology, University of Iowa, College of Medicine, Iowa City, Iowa, USA
| | - Paul J Foster
- National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital, London, UK.,Department of Ophthalmology, University College London, London, UK
| | - Charles Fuchs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego, California, USA
| | - Alex W Hewitt
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Victoria, Australia.,Department of Ophthalmology, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Frank Hu
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.,Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - David J Hunter
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.,Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Anthony P Khawaja
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Richard K Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Zheng Li
- Division of Human Genetics, Genome Institute of Singapore, Singapore
| | - Paul R Lichter
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - David A Mackey
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia.,Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Peter McGuffin
- Medical Research Council Social Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, King's College London, London, UK
| | - Paul Mitchell
- Centre for Vision Research, Westmead Millennium Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Sayoko E Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Shamira A Perera
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Duke-National University of Singapore Graduate Medical School, Singapore
| | | | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Tony Realini
- Department of Ophthalmology, West Virginia University Eye Institute, Morgantown, West Virginia, USA
| | - Julia E Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, USA.,Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric Rimm
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.,Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Robert Ritch
- Einhorn Clinical Research Center, Department of Ophthalmology, New York Eye and Ear Infirmary of Mount Sinai, New York, New York, USA
| | - Marylyn Ritchie
- Center for Systems Genomics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Joel S Schuman
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - William K Scott
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Arthur J Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
| | - Yeunjoo E Song
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Rulla M Tamimi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Fotis Topouzis
- Department of Ophthalmology, School of Medicine, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Ananth C Viswanathan
- National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital, London, UK
| | - Shefali Setia Verma
- Center for Systems Genomics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Douglas Vollrath
- Department of Genetics, Stanford University School of Medicine, Palo Alto, California, USA
| | - Jie Jin Wang
- Centre for Vision Research, Westmead Millennium Institute, University of Sydney, Westmead, New South Wales, Australia
| | - Nicole Weisschuh
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Gadi Wollstein
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tien Y Wong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | | | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, Maryland, USA
| | - Kang Zhang
- Hamilton Glaucoma Center, Shiley Eye Institute, University of California, San Diego, San Diego, California, USA
| | - Epic-Norfolk Eye Study
- Department of Cellular Biology and Anatomy, Georgia Regents University, Augusta, Georgia, USA
| | | | - Robert N Weinreb
- Hamilton Glaucoma Center, Shiley Eye Institute, University of California, San Diego, San Diego, California, USA
| | - Margaret A Pericak-Vance
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Kerrin Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Christopher J Hammond
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Tin Aung
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Eye Academic Clinical Program, Duke-National University of Singapore Graduate Medical School, Singapore
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Georgia Regents University, Augusta, Georgia, USA.,James and Jean Culver Vision Discovery Institute, Georgia Regents University, Augusta, Georgia, USA
| | - Eranga N Vithana
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore.,Eye Academic Clinical Program, Duke-National University of Singapore Graduate Medical School, Singapore
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Adelaide, South Australia, Australia
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.,Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, Massachusetts, USA
| | | | - Michael A Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, USA.,Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Louis R Pasquale
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
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27
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Yang CW, Hojer CD, Zhou M, Wu X, Wuster A, Lee WP, Yaspan BL, Chan AC. Regulation of T Cell Receptor Signaling by DENND1B in TH2 Cells and Allergic Disease. Cell 2016; 164:141-155. [PMID: 26774822 DOI: 10.1016/j.cell.2015.11.052] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/11/2015] [Accepted: 11/16/2015] [Indexed: 10/22/2022]
Abstract
The DENN domain is an evolutionary conserved protein module found in all eukaryotes and serves as an exchange factor for Rab-GTPases to regulate diverse cellular functions. Variants in DENND1B are associated with development of childhood asthma and other immune disorders. To understand how DENND1B may contribute to human disease, Dennd1b(-/-) mice were generated and exhibit hyper-allergic responses following antigen challenge. Dennd1b(-/-) TH2, but not other TH cells, exhibit delayed receptor-induced T cell receptor (TCR) downmodulation, enhanced TCR signaling, and increased production of effector cytokines. As DENND1B interacts with AP-2 and Rab35, TH2 cells deficient in AP-2 or Rab35 also exhibit enhanced TCR-mediated effector functions. Moreover, human TH2 cells carrying asthma-associated DENND1B variants express less DENND1B and phenocopy Dennd1b(-/-) TH2 cells. These results provide a molecular basis for how DENND1B, a previously unrecognized regulator of TCR downmodulation in TH2 cells, contributes to asthma pathogenesis and how DENN-domain-containing proteins may contribute to other human disorders.
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Affiliation(s)
- Chiao-Wen Yang
- Department of Immunology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Caroline D Hojer
- Department of Immunology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Meijuan Zhou
- Department of Translational Immunology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Xiumin Wu
- Department of Translational Immunology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Arthur Wuster
- Department of Human Genetics, Genentech, One DNA Way, South San Francisco, CA 94080, USA; Department of Bioinformatics and Computational Biology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Brian L Yaspan
- Department of Human Genetics, Genentech, One DNA Way, South San Francisco, CA 94080, USA
| | - Andrew C Chan
- Research, Genentech, One DNA Way, South San Francisco, CA 94080, USA.
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28
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van Lookeren Campagne M, Strauss EC, Yaspan BL. Age-related macular degeneration: Complement in action. Immunobiology 2015; 221:733-9. [PMID: 26742632 DOI: 10.1016/j.imbio.2015.11.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 07/03/2015] [Accepted: 11/19/2015] [Indexed: 02/06/2023]
Abstract
The complement system plays a key role in host-defense against common pathogens but must be tightly controlled to avoid inflammation and tissue damage. Polymorphisms in genes encoding two important negative regulators of the alternative complement pathway, complement factor H (CFH) and complement factor I (CFI), are associated with the risk for Age-Related Macular Degeneration (AMD), a leading cause of vision impairment in the ageing population. In this review, we will discuss the genetic basis of AMD and the potential impact of complement de-regulation on disease pathogenesis. Finally, we will highlight recent therapeutic approaches aimed at controlling complement activation in patients with AMD.
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Affiliation(s)
| | - Erich C Strauss
- Clinical Science, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Brian L Yaspan
- Human Genetics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
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Arron JR, Townsend MJ, Keir ME, Yaspan BL, Chan AC. Stratified medicine in inflammatory disorders: From theory to practice. Clin Immunol 2015; 161:11-22. [PMID: 25934386 DOI: 10.1016/j.clim.2015.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 04/17/2015] [Indexed: 02/08/2023]
Abstract
Chronic inflammatory disorders are complex and characterized by significant heterogeneity in molecular, pathological, and clinical features. This heterogeneity poses challenges for the development of targeted molecular interventions for these disorders, as not all patients with a given clinical diagnosis have disease driven by a single dominant molecular pathway, hence not all patients will benefit equally from a given intervention. Biomarkers related to molecular manifestations of disease are increasingly being applied to enable stratified approaches to drug development. Biomarkers may be used to identify which patients are most likely to benefit from an intervention (predictive), identify patients at increased risk of disease progression (prognostic), and monitor biological responsiveness to an intervention (pharmacodynamic). Here we consider how biomarker-guided stratification of patients may increase benefit from targeted therapies for asthma, rheumatoid arthritis and inflammatory bowel diseases.
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Affiliation(s)
- Joseph R Arron
- Department of Immunology Diagnostic Discovery, Genentech, Inc., One DNA Way, South San Francisco, CA 94080, USA.
| | - Michael J Townsend
- Department of Immunology Diagnostic Discovery, Genentech, Inc., One DNA Way, South San Francisco, CA 94080, USA
| | - Mary E Keir
- Department of Immunology Diagnostic Discovery, Genentech, Inc., One DNA Way, South San Francisco, CA 94080, USA
| | - Brian L Yaspan
- Department of Human Genetics, Genentech, Inc., One DNA Way, South San Francisco, CA 94080, USA
| | - Andrew C Chan
- Department of Immunology, Genentech, Inc., One DNA Way, South San Francisco, CA 94080, USA.
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Liu Y, Garrett ME, Yaspan BL, Bailey JC, Loomis SJ, Brilliant M, Budenz DL, Christen WG, Fingert JH, Gaasterland D, Gaasterland T, Kang JH, Lee RK, Lichter P, Moroi SE, Realini A, Richards JE, Schuman JS, Scott WK, Singh K, Sit AJ, Vollrath D, Weinreb R, Wollstein G, Zack DJ, Zhang K, Pericak-Vance MA, Haines JL, Pasquale LR, Wiggs JL, Allingham RR, Ashley-Koch AE, Hauser MA. DNA copy number variants of known glaucoma genes in relation to primary open-angle glaucoma. Invest Ophthalmol Vis Sci 2014; 55:8251-8. [PMID: 25414181 DOI: 10.1167/iovs.14-15712] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
PURPOSE We examined the role of DNA copy number variants (CNVs) of known glaucoma genes in relation to primary open angle glaucoma (POAG). METHODS Our study included DNA samples from two studies (NEIGHBOR and GLAUGEN). All the samples were genotyped with the Illumina Human660W_Quad_v1 BeadChip. After removing non-blood-derived and amplified DNA samples, we applied quality control steps based on the mean Log R Ratio and the mean B allele frequency. Subsequently, data from 3057 DNA samples (1599 cases and 1458 controls) were analyzed with PennCNV software. We defined CNVs as those ≥5 kilobases (kb) in size and interrogated by ≥5 consecutive probes. We further limited our investigation to CNVs in known POAG-related genes, including CDKN2B-AS1, TMCO1, SIX1/SIX6, CAV1/CAV2, the LRP12-ZFPM2 region, GAS7, ATOH7, FNDC3B, CYP1B1, MYOC, OPTN, WDR36, SRBD1, TBK1, and GALC. RESULTS Genomic duplications of CDKN2B-AS1 and TMCO1 were each found in a single case. Two cases carried duplications in the GAS7 region. Genomic deletions of SIX6 and ATOH7 were each identified in one case. One case carried a TBK1 deletion and another case carried a TBK1 duplication. No controls had duplications or deletions in these six genes. A single control had a duplication in the MYOC region. Deletions of GALC were observed in five cases and two controls. CONCLUSIONS The CNV analysis of a large set of cases and controls revealed the presence of rare CNVs in known POAG susceptibility genes. Our data suggest that these rare CNVs may contribute to POAG pathogenesis and merit functional evaluation.
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Affiliation(s)
- Yutao Liu
- Department of Cellular Biology and Anatomy, Georgia Regents University, Augusta, Georgia, United States Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Melanie E Garrett
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Brian L Yaspan
- Genentech, Inc., San Francisco, California, United States
| | - Jessica Cooke Bailey
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Stephanie J Loomis
- Department of Ophthalmology, Massachusetts Eye & Ear, Boston, Massachusetts, United States
| | - Murray Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, United States
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina, United States
| | - William G Christen
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - John H Fingert
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States
| | | | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego, California, United States
| | - Jae H Kang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Richard K Lee
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Paul Lichter
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Sayoko E Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Anthony Realini
- Department of Ophthalmology, West Virginia University Eye Institute, Morgantown, West Virginia, United States
| | - Julia E Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, United States
| | - Joel S Schuman
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - William K Scott
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University, Palo Alto, California, United States
| | - Arthur J Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States
| | - Douglas Vollrath
- Department of Ophthalmology, Stanford University, Palo Alto, California, United States
| | - Robert Weinreb
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, California, United States
| | - Gadi Wollstein
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, Maryland, United States
| | - Kang Zhang
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, California, United States
| | - Margaret A Pericak-Vance
- Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States
| | - Louis R Pasquale
- Department of Ophthalmology, Massachusetts Eye & Ear, Boston, Massachusetts, United States Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Janey L Wiggs
- Department of Ophthalmology, Massachusetts Eye & Ear, Boston, Massachusetts, United States
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Allison E Ashley-Koch
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Michael A Hauser
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
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Bailey JNC, Yaspan BL, Pasquale LR, Hauser MA, Kang JH, Loomis SJ, Brilliant M, Budenz DL, Christen WG, Fingert J, Gaasterland D, Gaasterland T, Kraft P, Lee RK, Lichter PR, Liu Y, McCarty CA, Moroi SE, Richards JE, Realini T, Schuman JS, Scott WK, Singh K, Sit AJ, Vollrath D, Wollstein G, Zack DJ, Zhang K, Pericak-Vance MA, Allingham RR, Weinreb RN, Haines JL, Wiggs JL. Hypothesis-independent pathway analysis implicates GABA and acetyl-CoA metabolism in primary open-angle glaucoma and normal-pressure glaucoma. Hum Genet 2014; 133:1319-30. [PMID: 25037249 DOI: 10.1007/s00439-014-1468-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 07/08/2014] [Indexed: 12/15/2022]
Abstract
Primary open-angle glaucoma (POAG) is a leading cause of blindness worldwide. Using genome-wide association single-nucleotide polymorphism data from the Glaucoma Genes and Environment study and National Eye Institute Glaucoma Human Genetics Collaboration comprising 3,108 cases and 3,430 controls, we assessed biologic pathways as annotated in the KEGG database for association with risk of POAG. After correction for genic overlap among pathways, we found 4 pathways, butanoate metabolism (hsa00650), hematopoietic cell lineage (hsa04640), lysine degradation (hsa00310) and basal transcription factors (hsa03022) related to POAG with permuted p < 0.001. In addition, the human leukocyte antigen (HLA) gene family was significantly associated with POAG (p < 0.001). In the POAG subset with normal-pressure glaucoma (NPG), the butanoate metabolism pathway was also significantly associated (p < 0.001) as well as the MAPK and Hedgehog signaling pathways (hsa04010 and hsa04340), glycosaminoglycan biosynthesis-heparan sulfate pathway (hsa00534) and the phenylalanine, tyrosine and tryptophan biosynthesis pathway (hsa0400). The butanoate metabolism pathway overall, and specifically the aspects of the pathway that contribute to GABA and acetyl-CoA metabolism, was the only pathway significantly associated with both POAG and NPG. Collectively these results implicate GABA and acetyl-CoA metabolism in glaucoma pathogenesis, and suggest new potential therapeutic targets.
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van Lookeren Campagne M, LeCouter J, Yaspan BL, Ye W. Mechanisms of age-related macular degeneration and therapeutic opportunities. J Pathol 2013; 232:151-64. [DOI: 10.1002/path.4266] [Citation(s) in RCA: 222] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 12/27/2022]
Affiliation(s)
| | - Jennifer LeCouter
- Molecular Biology Department; Genentech; South San Francisco CA 94080 USA
| | - Brian L Yaspan
- ITGR Human Genetics Department; Genentech; South San Francisco CA 94080 USA
| | - Weilan Ye
- Molecular Biology Department; Genentech; South San Francisco CA 94080 USA
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Loomis SJ, Kang JH, Weinreb RN, Yaspan BL, Cooke Bailey JN, Gaasterland D, Gaasterland T, Lee RK, Lichter PR, Budenz DL, Liu Y, Realini T, Friedman DS, McCarty CA, Moroi SE, Olson L, Schuman JS, Singh K, Vollrath D, Wollstein G, Zack DJ, Brilliant M, Sit AJ, Christen WG, Fingert J, Kraft P, Zhang K, Allingham RR, Pericak-Vance MA, Richards JE, Hauser MA, Haines JL, Pasquale LR, Wiggs JL. Association of CAV1/CAV2 genomic variants with primary open-angle glaucoma overall and by gender and pattern of visual field loss. Ophthalmology 2013; 121:508-16. [PMID: 24572674 DOI: 10.1016/j.ophtha.2013.09.012] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 09/04/2013] [Accepted: 09/08/2013] [Indexed: 10/26/2022] Open
Abstract
PURPOSE The CAV1/CAV2 (caveolin 1 and caveolin 2) genomic region previously was associated with primary open-angle glaucoma (POAG), although replication among independent studies has been variable. The aim of this study was to assess the association between CAV1/CAV2 single nucleotide polymorphisms (SNPs) and POAG in a large case-control dataset and to explore associations by gender and pattern of visual field (VF) loss further. DESIGN Case-control study. PARTICIPANTS We analyzed 2 large POAG data sets: the Glaucoma Genes and Environment (GLAUGEN) study (976 cases, 1140 controls) and the National Eye Institute Glaucoma Human Genetics Collaboration (NEIGHBOR) consortium (2132 cases, 2290 controls). METHODS We studied the association between 70 SNPs located within the CAV1/CAV2 genomic region in the GLAUGEN and NEIGHBOR studies, both genotyped on the Illumina Human 660WQuadv1C BeadChip array and imputed with the Markov Chain Haplotyping algorithm using the HapMap 3 reference panel. We used logistic regression models of POAG in the overall population and separated by gender, as well as by POAG subtypes defined by type of VF defect (peripheral or paracentral). Results from GLAUGEN and NEIGHBOR were meta-analyzed, and a Bonferroni-corrected significance level of 7.7 × 10(-4) was used to account for multiple comparisons. MAIN OUTCOME MEASURES Overall POAG, overall POAG by gender, and POAG subtypes defined by pattern of early VF loss. RESULTS We found significant associations between 10 CAV1/CAV2 SNPs and POAG (top SNP, rs4236601; pooled P = 2.61 × 10(-7)). Of these, 9 were significant only in women (top SNP, rs4236601; pooled P = 1.59 × 10(-5)). Five of the 10 CAV1/CAV2 SNPs were associated with POAG with early paracentral VF (top SNP, rs17588172; pooled P = 1.07 × 10(-4)), and none of the 10 were associated with POAG with peripheral VF loss only or POAG among men. CONCLUSIONS CAV1/CAV2 SNPs were associated significantly with POAG overall, particularly among women. Furthermore, we found an association between CAV1/CAV2 SNPs and POAG with paracentral VF defects. These data support a role for caveolin 1, caveolin 2, or both in POAG and suggest that the caveolins particularly may affect POAG pathogenesis in women and in patients with early paracentral VF defects.
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Affiliation(s)
- Stephanie J Loomis
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
| | - Jae H Kang
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Robert N Weinreb
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, La Jolla, California
| | | | - Jessica N Cooke Bailey
- Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, La Jolla, California
| | - Richard K Lee
- Bascom Palmer Eye Institute and Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Paul R Lichter
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Donald L Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, North Carolina
| | - Yutao Liu
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina; Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Tony Realini
- Department of Ophthalmology, West Virginia University Eye Institute, Morgantown, West Virginia
| | - David S Friedman
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, Maryland
| | | | - Sayoko E Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Lana Olson
- Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Joel S Schuman
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University, Palo Alto, California
| | - Douglas Vollrath
- Department of Genetics, Stanford University, Palo Alto, California
| | - Gadi Wollstein
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Donald J Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, Maryland
| | - Murray Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin
| | - Arthur J Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
| | - William G Christen
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - John Fingert
- Departments of Ophthalmology and Anatomy/Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Peter Kraft
- Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Harvard University, Boston, Massachusetts
| | - Kang Zhang
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, La Jolla, California
| | - R Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina
| | - Margaret A Pericak-Vance
- Bascom Palmer Eye Institute and Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Julia E Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Michael A Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina; Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Jonathan L Haines
- Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Louis R Pasquale
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts.
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Ozel AB, Moroi SE, Reed DM, Nika M, Schmidt CM, Akbari S, Scott K, Rozsa F, Pawar H, Musch DC, Lichter PR, Gaasterland D, Branham K, Gilbert J, Garnai SJ, Chen W, Othman M, Heckenlively J, Swaroop A, Abecasis G, Friedman DS, Zack D, Ashley-Koch A, Ulmer M, Kang JH, Liu Y, Yaspan BL, Haines J, Allingham RR, Hauser MA, Pasquale L, Wiggs J, Richards JE, Li JZ. Genome-wide association study and meta-analysis of intraocular pressure. Hum Genet 2013; 133:41-57. [PMID: 24002674 DOI: 10.1007/s00439-013-1349-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
Elevated intraocular pressure (IOP) is a major risk factor for glaucoma and is influenced by genetic and environmental factors. Recent genome-wide association studies (GWAS) reported associations with IOP at TMCO1 and GAS7, and with primary open-angle glaucoma (POAG) at CDKN2B-AS1, CAV1/CAV2, and SIX1/SIX6. To identify novel genetic variants and replicate the published findings, we performed GWAS and meta-analysis of IOP in >6,000 subjects of European ancestry collected in three datasets: the NEI Glaucoma Human genetics collaBORation, GLAUcoma Genes and ENvironment study, and a subset of the Age-related Macular Degeneration-Michigan, Mayo, AREDS and Pennsylvania study. While no signal achieved genome-wide significance in individual datasets, a meta-analysis identified significant associations with IOP at TMCO1 (rs7518099-G, p = 8.0 × 10(-8)). Focused analyses of five loci previously reported for IOP and/or POAG, i.e., TMCO1, CDKN2B-AS1, GAS7, CAV1/CAV2, and SIX1/SIX6, revealed associations with IOP that were largely consistent across our three datasets, and replicated the previously reported associations in both effect size and direction. These results confirm the involvement of common variants in multiple genomic regions in regulating IOP and/or glaucoma risk.
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Affiliation(s)
- A Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
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Campbell NG, Zhu CB, Lindler KM, Yaspan BL, Kistner-Griffin E. Rare coding variants of the adenosine A3 receptor are increased in autism: on the trail of the serotonin transporter regulome. Mol Autism 2013; 4:28. [PMID: 23953133 PMCID: PMC3882891 DOI: 10.1186/2040-2392-4-28] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 07/30/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Rare genetic variation is an important class of autism spectrum disorder (ASD) risk factors and can implicate biological networks for investigation. Altered serotonin (5-HT) signaling has been implicated in ASD, and we and others have discovered multiple, rare, ASD-associated variants in the 5-HT transporter (SERT) gene leading to elevated 5-HT re-uptake and perturbed regulation. We hypothesized that loci encoding SERT regulators harbor variants that impact SERT function and/or regulation and therefore could contribute to ASD risk. The adenosine A3 receptor (A3AR) regulates SERT via protein kinase G (PKG) and other signaling pathways leading to enhanced SERT surface expression and catalytic activity. METHODS To test our hypothesis, we asked whether rare variants in the A3AR gene (ADORA3) were increased in ASD cases vs. controls. Discovery sequencing in a case-control sample and subsequent analysis of comparison exome sequence data were conducted. We evaluated the functional impact of two variants from the discovery sample on A3AR signaling and SERT activity. RESULTS Sequencing discovery showed an increase of rare coding variants in cases vs. controls (P=0.013). While comparison exome sequence data did not show a significant enrichment (P=0.071), combined analysis strengthened evidence for association (P=0.0025). Two variants discovered in ASD cases (Leu90Val and Val171Ile) lie in or near the ligand-binding pocket, and Leu90Val was enriched individually in cases (P=0.040). In vitro analysis of cells expressing Val90-A3AR revealed elevated basal cGMP levels compared with the wildtype receptor. Additionally, a specific A3AR agonist increased cGMP levels across the full time course studied in Val90-A3AR cells, compared to wildtype receptor. In Val90-A3AR/SERT co-transfections, agonist stimulation elevated SERT activity over the wildtype receptor with delayed 5-HT uptake activity recovery. In contrast, Ile171-A3AR was unable to support agonist stimulation of SERT. Although both Val90 and Ile171 were present in greater numbers in these ASD cases, segregation analysis in families showed incomplete penetrance, consistent with other rare ASD risk alleles. CONCLUSIONS Our results validate the hypothesis that the SERT regulatory network harbors rare, functional variants that impact SERT activity and regulation in ASD, and encourages further investigation of this network for other variation that may impact ASD risk.
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Affiliation(s)
- Nicholas G Campbell
- Department of Molecular Physiology & Biophysics and Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232-8548, USA
| | - Chong-Bin Zhu
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232-8548, USA
| | - Kathryn M Lindler
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232-8548, USA
| | - Brian L Yaspan
- Department of Molecular Physiology & Biophysics and Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN 37232-8548, USA
| | - Emily Kistner-Griffin
- Biostatistics and Epidemiology, Medical University of South Carolina, Charleston, SC 29425, USA
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Pasquale LR, Loomis SJ, Weinreb RN, Kang JH, Yaspan BL, Bailey JC, Gaasterland D, Gaasterland T, Lee RK, Scott WK, Lichter PR, Budenz DL, Liu Y, Realini T, Friedman DS, McCarty CA, Moroi SE, Olson L, Schuman JS, Singh K, Vollrath D, Wollstein G, Zack DJ, Brilliant M, Sit AJ, Christen WG, Fingert J, Kraft P, Zhang K, Allingham RR, Pericak-Vance MA, Richards JE, Hauser MA, Haines JL, Wiggs JL. Estrogen pathway polymorphisms in relation to primary open angle glaucoma: an analysis accounting for gender from the United States. Mol Vis 2013; 19:1471-81. [PMID: 23869166 PMCID: PMC3712669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/05/2013] [Indexed: 11/15/2022] Open
Abstract
PURPOSE Circulating estrogen levels are relevant in glaucoma phenotypic traits. We assessed the association between an estrogen metabolism single nucleotide polymorphism (SNP) panel in relation to primary open angle glaucoma (POAG), accounting for gender. METHODS We included 3,108 POAG cases and 3,430 controls of both genders from the Glaucoma Genes and Environment (GLAUGEN) study and the National Eye Institute Glaucoma Human Genetics Collaboration (NEIGHBOR) consortium genotyped on the Illumina 660W-Quad platform. We assessed the relation between the SNP panels representative of estrogen metabolism and POAG using pathway- and gene-based approaches with the Pathway Analysis by Randomization Incorporating Structure (PARIS) software. PARIS executes a permutation algorithm to assess statistical significance relative to the pathways and genes of comparable genetic architecture. These analyses were performed using the meta-analyzed results from the GLAUGEN and NEIGHBOR data sets. We evaluated POAG overall as well as two subtypes of POAG defined as intraocular pressure (IOP) ≥22 mmHg (high-pressure glaucoma [HPG]) or IOP <22 mmHg (normal pressure glaucoma [NPG]) at diagnosis. We conducted these analyses for each gender separately and then jointly in men and women. RESULTS Among women, the estrogen SNP pathway was associated with POAG overall (permuted p=0.006) and HPG (permuted p<0.001) but not NPG (permuted p=0.09). Interestingly, there was no relation between the estrogen SNP pathway and POAG when men were considered alone (permuted p>0.99). Among women, gene-based analyses revealed that the catechol-O-methyltransferase gene showed strong associations with HTG (permuted gene p≤0.001) and NPG (permuted gene p=0.01). CONCLUSIONS The estrogen SNP pathway was associated with POAG among women.
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Affiliation(s)
- Louis R. Pasquale
- Department of Ophthalmology, Mass Eye & Ear Infirmary, Harvard Medical School, Boston, MA,Channing Division of Network Medicine, Harvard Medical School, Boston, MA
| | - Stephanie J. Loomis
- Department of Ophthalmology, Mass Eye & Ear Infirmary, Harvard Medical School, Boston, MA
| | - Robert N. Weinreb
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, SD, CA
| | - Jae H. Kang
- Channing Division of Network Medicine, Harvard Medical School, Boston, MA
| | | | - Jessica Cooke Bailey
- Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville TN
| | | | - Terry Gaasterland
- Scripps Genome Center, University of California at San Diego, San Diego, CA
| | - Richard K. Lee
- Bascom Palmer Eye Institute and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL
| | - William K. Scott
- Bascom Palmer Eye Institute and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL
| | - Paul R. Lichter
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI
| | - Donald L. Budenz
- Department of Ophthalmology, University of North Carolina, Chapel Hill, NC
| | - Yutao Liu
- Department of Ophthalmology, Duke University Medical Center, Durham, NC,Medicine, Duke University Medical Center, Durham, NC
| | - Tony Realini
- Department of Ophthalmology, West Virginia University Eye Institute, Morgantown, WV
| | - David S. Friedman
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, MD
| | | | - Sayoko E. Moroi
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI
| | - Lana Olson
- Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville TN
| | - Joel S. Schuman
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, PA
| | - Kuldev Singh
- Department of Ophthalmology, Stanford University, Palo Alto, CA
| | | | - Gadi Wollstein
- Department of Ophthalmology, UPMC Eye Center, University of Pittsburgh, Pittsburgh, PA
| | - Donald J. Zack
- Wilmer Eye Institute, Johns Hopkins University Hospital, Baltimore, MD
| | - Murray Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI
| | - Arthur J. Sit
- Department of Ophthalmology, Mayo Clinic, Rochester, MN
| | | | - John Fingert
- Departments of Ophthalmology and Anatomy/Cell Biology, University of Iowa, College of Medicine, Iowa City, IO
| | - Peter Kraft
- Department of Biostatistics, Harvard School of Public Health, Boston, MA
| | - Kang Zhang
- Department of Ophthalmology and Hamilton Glaucoma Center, University of California, San Diego, SD, CA
| | - R. Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, NC
| | - Margaret A. Pericak-Vance
- Bascom Palmer Eye Institute and Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL
| | - Julia E. Richards
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI
| | - Michael A. Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, NC,Medicine, Duke University Medical Center, Durham, NC
| | - Jonathan L. Haines
- Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville TN
| | - Janey L. Wiggs
- Department of Ophthalmology, Mass Eye & Ear Infirmary, Harvard Medical School, Boston, MA
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Fritsche LG, Chen W, Schu M, Yaspan BL, Yu Y, Thorleifsson G, Zack DJ, Arakawa S, Cipriani V, Ripke S, Igo RP, Buitendijk GHS, Sim X, Weeks DE, Guymer RH, Merriam JE, Francis PJ, Hannum G, Agarwal A, Armbrecht AM, Audo I, Aung T, Barile GR, Benchaboune M, Bird AC, Bishop PN, Branham KE, Brooks M, Brucker AJ, Cade WH, Cain MS, Campochiaro PA, Chan CC, Cheng CY, Chew EY, Chin KA, Chowers I, Clayton DG, Cojocaru R, Conley YP, Cornes BK, Daly MJ, Dhillon B, Edwards AO, Evangelou E, Fagerness J, Ferreyra HA, Friedman JS, Geirsdottir A, George RJ, Gieger C, Gupta N, Hagstrom SA, Harding SP, Haritoglou C, Heckenlively JR, Holz FG, Hughes G, Ioannidis JPA, Ishibashi T, Joseph P, Jun G, Kamatani Y, Katsanis N, N Keilhauer C, Khan JC, Kim IK, Kiyohara Y, Klein BEK, Klein R, Kovach JL, Kozak I, Lee CJ, Lee KE, Lichtner P, Lotery AJ, Meitinger T, Mitchell P, Mohand-Saïd S, Moore AT, Morgan DJ, Morrison MA, Myers CE, Naj AC, Nakamura Y, Okada Y, Orlin A, Ortube MC, Othman MI, Pappas C, Park KH, Pauer GJT, Peachey NS, Poch O, Priya RR, Reynolds R, Richardson AJ, Ripp R, Rudolph G, Ryu E, Sahel JA, Schaumberg DA, Scholl HPN, Schwartz SG, Scott WK, Shahid H, Sigurdsson H, Silvestri G, Sivakumaran TA, Smith RT, Sobrin L, Souied EH, Stambolian DE, Stefansson H, Sturgill-Short GM, Takahashi A, Tosakulwong N, Truitt BJ, Tsironi EE, Uitterlinden AG, van Duijn CM, Vijaya L, Vingerling JR, Vithana EN, Webster AR, Wichmann HE, Winkler TW, Wong TY, Wright AF, Zelenika D, Zhang M, Zhao L, Zhang K, Klein ML, Hageman GS, Lathrop GM, Stefansson K, Allikmets R, Baird PN, Gorin MB, Wang JJ, Klaver CCW, Seddon JM, Pericak-Vance MA, Iyengar SK, Yates JRW, Swaroop A, Weber BHF, Kubo M, Deangelis MM, Léveillard T, Thorsteinsdottir U, Haines JL, Farrer LA, Heid IM, Abecasis GR. Seven new loci associated with age-related macular degeneration. Nat Genet 2013; 45:433-9, 439e1-2. [PMID: 23455636 PMCID: PMC3739472 DOI: 10.1038/ng.2578] [Citation(s) in RCA: 573] [Impact Index Per Article: 52.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 02/07/2012] [Indexed: 12/11/2022]
Abstract
Age-related macular degeneration (AMD) is a common cause of blindness in older individuals. To accelerate the understanding of AMD biology and help design new therapies, we executed a collaborative genome-wide association study, including >17,100 advanced AMD cases and >60,000 controls of European and Asian ancestry. We identified 19 loci associated at P < 5 × 10(-8). These loci show enrichment for genes involved in the regulation of complement activity, lipid metabolism, extracellular matrix remodeling and angiogenesis. Our results include seven loci with associations reaching P < 5 × 10(-8) for the first time, near the genes COL8A1-FILIP1L, IER3-DDR1, SLC16A8, TGFBR1, RAD51B, ADAMTS9 and B3GALTL. A genetic risk score combining SNP genotypes from all loci showed similar ability to distinguish cases and controls in all samples examined. Our findings provide new directions for biological, genetic and therapeutic studies of AMD.
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Affiliation(s)
- Lars G Fritsche
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
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Pasquale LR, Loomis SJ, Kang JH, Yaspan BL, Abdrabou W, Budenz DL, Chen TC, Delbono E, Friedman DS, Gaasterland D, Gaasterland T, Grosskreutz CL, Lee RK, Lichter PR, Liu Y, McCarty CA, Moroi SE, Olson LM, Realini T, Rhee DJ, Schuman JS, Singh K, Vollrath D, Wollstein G, Zack DJ, Allingham RR, Pericak-Vance MA, Weinreb RN, Zhang K, Hauser MA, Richards JE, Haines JL, Wiggs JL. CDKN2B-AS1 genotype-glaucoma feature correlations in primary open-angle glaucoma patients from the United States. Am J Ophthalmol 2013; 155:342-353.e5. [PMID: 23111177 DOI: 10.1016/j.ajo.2012.07.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/24/2012] [Accepted: 07/24/2012] [Indexed: 11/16/2022]
Abstract
PURPOSE To assess the association between single nucleotide polymorphisms (SNPs) of the gene region containing cyclin-dependent kinase inhibitor 2B antisense noncoding RNA (CDKN2B-AS1) and glaucoma features among primary open-angle glaucoma (POAG) patients. DESIGN Retrospective observational case series. METHODS We studied associations between 10 CDKN2B-AS1 SNPs and glaucoma features among 976 POAG cases from the Glaucoma Genes and Environment (GLAUGEN) study and 1971 cases from the National Eye Institute Glaucoma Human Genetics Collaboration (NEIGHBOR) consortium. For each patient, we chose the feature from the eye with the higher value. We created cohort-specific multivariable models for glaucoma features and then meta-analyzed the results. RESULTS For 9 of the 10 protective CDKN2B-AS1 SNPs with minor alleles associated with reduced disease risk (eg, the G allele at rs2157719), POAG patients carrying these minor alleles had smaller cup-to-disc ratio (0.05 units smaller per G allele at diagnosis; 95% CI: -0.08, -0.03; P = 6.23E-05) despite having higher intraocular pressure (IOP) (0.70 mm Hg higher per G allele at DNA collection; 95% CI: 0.40, 1.00; P = 5.45E-06). For the 1 adverse rs3217992 SNP with minor allele A associated with increased disease risk, POAG patients with A alleles had larger cup-to-disc ratio (0.05 units larger per A allele at diagnosis; 95% CI: 0.02, 0.07; P = 4.74E-04) despite having lower IOP (-0.57 mm Hg per A allele at DNA collection; 95% CI: -0.84, -0.29; P = 6.55E-05). CONCLUSION Alleles of CDKN2B-AS1 SNPs, which influence risk of developing POAG, also modulate optic nerve degeneration among POAG patients, underscoring the role of CDKN2B-AS1 in POAG.
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Affiliation(s)
- Louis R Pasquale
- Department of Ophthalmology, Massachusetts Eye & Ear Infirmary, Harvard Medical School, Boston, Massachusetts 02114, USA.
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39
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Lu Y, Vitart V, Burdon KP, Khor CC, Bykhovskaya Y, Mirshahi A, Hewitt AW, Koehn D, Hysi PG, Ramdas WD, Zeller T, Vithana EN, Cornes BK, Tay WT, Tai ES, Cheng CY, Liu J, Foo JN, Saw SM, Thorleifsson G, Stefansson K, Dimasi DP, Mills RA, Mountain J, Ang W, Hoehn R, Verhoeven VJM, Grus F, Wolfs R, Castagne R, Lackner KJ, Springelkamp H, Yang J, Jonasson F, Leung DYL, Chen LJ, Tham CCY, Rudan I, Vatavuk Z, Hayward C, Gibson J, Cree AJ, MacLeod A, Ennis S, Polasek O, Campbell H, Wilson JF, Viswanathan AC, Fleck B, Li X, Siscovick D, Taylor KD, Rotter JI, Yazar S, Ulmer M, Li J, Yaspan BL, Ozel AB, Richards JE, Moroi SE, Haines JL, Kang JH, Pasquale LR, Allingham RR, Ashley-Koch A, Mitchell P, Wang JJ, Wright AF, Pennell C, Spector TD, Young TL, Klaver CCW, Martin NG, Montgomery GW, Anderson MG, Aung T, Willoughby CE, Wiggs JL, Pang CP, Thorsteinsdottir U, Lotery AJ, Hammond CJ, van Duijn CM, Hauser MA, Rabinowitz YS, Pfeiffer N, Mackey DA, Craig JE, Macgregor S, Wong TY. Genome-wide association analyses identify multiple loci associated with central corneal thickness and keratoconus. Nat Genet 2013; 45:155-63. [PMID: 23291589 DOI: 10.1038/ng.2506] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 11/29/2012] [Indexed: 12/13/2022]
Abstract
Central corneal thickness (CCT) is associated with eye conditions including keratoconus and glaucoma. We performed a meta-analysis on >20,000 individuals in European and Asian populations that identified 16 new loci associated with CCT at genome-wide significance (P < 5 × 10(-8)). We further showed that 2 CCT-associated loci, FOXO1 and FNDC3B, conferred relatively large risks for keratoconus in 2 cohorts with 874 cases and 6,085 controls (rs2721051 near FOXO1 had odds ratio (OR) = 1.62, 95% confidence interval (CI) = 1.4-1.88, P = 2.7 × 10(-10), and rs4894535 in FNDC3B had OR = 1.47, 95% CI = 1.29-1.68, P = 4.9 × 10(-9)). FNDC3B was also associated with primary open-angle glaucoma (P = 5.6 × 10(-4); tested in 3 cohorts with 2,979 cases and 7,399 controls). Further analyses implicate the collagen and extracellular matrix pathways in the regulation of CCT.
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Affiliation(s)
- Yi Lu
- Queensland Institute of Medical Research, Statistical Genetics, Herston, Brisbane, Queensland, Australia
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40
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Ulmer M, Li J, Yaspan BL, Ozel AB, Richards JE, Moroi SE, Hawthorne F, Budenz DL, Friedman DS, Gaasterland D, Haines J, Kang JH, Lee R, Lichter P, Liu Y, Pasquale LR, Pericak-Vance M, Realini A, Schuman JS, Singh K, Vollrath D, Weinreb R, Wollstein G, Zack DJ, Zhang K, Young T, Allingham RR, Wiggs JL, Ashley-Koch A, Hauser MA. Genome-wide analysis of central corneal thickness in primary open-angle glaucoma cases in the NEIGHBOR and GLAUGEN consortia. Invest Ophthalmol Vis Sci 2012; 53:4468-74. [PMID: 22661486 DOI: 10.1167/iovs.12-9784] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To investigate the effects of central corneal thickness (CCT)-associated variants on primary open-angle glaucoma (POAG) risk using single nucleotide polymorphisms (SNP) data from the Glaucoma Genes and Environment (GLAUGEN) and National Eye Institute (NEI) Glaucoma Human Genetics Collaboration (NEIGHBOR) consortia. METHODS A replication analysis of previously reported CCT SNPs was performed in a CCT dataset (n = 1117) and these SNPs were then tested for association with POAG using a larger POAG dataset (n = 6470). Then a CCT genome-wide association study (GWAS) was performed. Top SNPs from this analysis were selected and tested for association with POAG. cDNA libraries from fetal and adult brain and ocular tissue samples were generated and used for candidate gene expression analysis. RESULTS Association with one of 20 previously published CCT SNPs was replicated: rs12447690, near the ZNF469 gene (P = 0.001; β = -5.08 μm/allele). None of these SNPs were significantly associated with POAG. In the CCT GWAS, no SNPs reached genome-wide significance. After testing 50 candidate SNPs for association with POAG, one SNP was identified, rs7481514 within the neurotrimin (NTM) gene, that was significantly associated with POAG in a low-tension subset (P = 0.00099; Odds Ratio [OR] = 1.28). Additionally, SNPs in the CNTNAP4 gene showed suggestive association with POAG (top SNP = rs1428758; P = 0.018; OR = 0.84). NTM and CNTNAP4 were shown to be expressed in ocular tissues. CONCLUSIONS The results suggest previously reported CCT loci are not significantly associated with POAG susceptibility. By performing a quantitative analysis of CCT and a subsequent analysis of POAG, SNPs in two cell adhesion molecules, NTM and CNTNAP4, were identified and may increase POAG susceptibility in a subset of cases.
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Affiliation(s)
- Megan Ulmer
- Duke University Center for Human Genetics, Durham, North Carolina 27710, USA
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41
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Wiggs JL, Yaspan BL, Hauser MA, Kang JH, Allingham RR, Olson LM, Abdrabou W, Fan BJ, Wang DY, Brodeur W, Budenz DL, Caprioli J, Crenshaw A, Crooks K, Delbono E, Doheny KF, Friedman DS, Gaasterland D, Gaasterland T, Laurie C, Lee RK, Lichter PR, Loomis S, Liu Y, Medeiros FA, McCarty C, Mirel D, Moroi SE, Musch DC, Realini A, Rozsa FW, Schuman JS, Scott K, Singh K, Stein JD, Trager EH, Vanveldhuisen P, Vollrath D, Wollstein G, Yoneyama S, Zhang K, Weinreb RN, Ernst J, Kellis M, Masuda T, Zack D, Richards JE, Pericak-Vance M, Pasquale LR, Haines JL. Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. PLoS Genet 2012; 8:e1002654. [PMID: 22570617 PMCID: PMC3343074 DOI: 10.1371/journal.pgen.1002654] [Citation(s) in RCA: 226] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/01/2012] [Indexed: 01/07/2023] Open
Abstract
Optic nerve degeneration caused by glaucoma is a leading cause of blindness worldwide. Patients affected by the normal-pressure form of glaucoma are more likely to harbor risk alleles for glaucoma-related optic nerve disease. We have performed a meta-analysis of two independent genome-wide association studies for primary open angle glaucoma (POAG) followed by a normal-pressure glaucoma (NPG, defined by intraocular pressure (IOP) less than 22 mmHg) subgroup analysis. The single-nucleotide polymorphisms that showed the most significant associations were tested for association with a second form of glaucoma, exfoliation-syndrome glaucoma. The overall meta-analysis of the GLAUGEN and NEIGHBOR dataset results (3,146 cases and 3,487 controls) identified significant associations between two loci and POAG: the CDKN2BAS region on 9p21 (rs2157719 [G], OR = 0.69 [95%CI 0.63-0.75], p = 1.86×10⁻¹⁸), and the SIX1/SIX6 region on chromosome 14q23 (rs10483727 [A], OR = 1.32 [95%CI 1.21-1.43], p = 3.87×10⁻¹¹). In sub-group analysis two loci were significantly associated with NPG: 9p21 containing the CDKN2BAS gene (rs2157719 [G], OR = 0.58 [95% CI 0.50-0.67], p = 1.17×10⁻¹²) and a probable regulatory region on 8q22 (rs284489 [G], OR = 0.62 [95% CI 0.53-0.72], p = 8.88×10⁻¹⁰). Both NPG loci were also nominally associated with a second type of glaucoma, exfoliation syndrome glaucoma (rs2157719 [G], OR = 0.59 [95% CI 0.41-0.87], p = 0.004 and rs284489 [G], OR = 0.76 [95% CI 0.54-1.06], p = 0.021), suggesting that these loci might contribute more generally to optic nerve degeneration in glaucoma. Because both loci influence transforming growth factor beta (TGF-beta) signaling, we performed a genomic pathway analysis that showed an association between the TGF-beta pathway and NPG (permuted p = 0.009). These results suggest that neuro-protective therapies targeting TGF-beta signaling could be effective for multiple forms of glaucoma.
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Affiliation(s)
- Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America.
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42
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Casey JP, Magalhaes T, Conroy JM, Regan R, Shah N, Anney R, Shields DC, Abrahams BS, Almeida J, Bacchelli E, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bolton PF, Bourgeron T, Brennan S, Cali P, Correia C, Corsello C, Coutanche M, Dawson G, de Jonge M, Delorme R, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Foley S, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Green J, Guter SJ, Hakonarson H, Holt R, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Lamb JA, Leboyer M, Le Couteur A, Leventhal BL, Lord C, Lund SC, Maestrini E, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Miller J, Minopoli F, Mirza GK, Munson J, Nelson SF, Nygren G, Oliveira G, Pagnamenta AT, Papanikolaou K, Parr JR, Parrini B, Pickles A, Pinto D, Piven J, Posey DJ, Poustka A, Poustka F, Ragoussis J, Roge B, Rutter ML, Sequeira AF, Soorya L, Sousa I, Sykes N, Stoppioni V, Tancredi R, Tauber M, Thompson AP, Thomson S, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Vorstman JAS, Wallace S, Wang K, Wassink TH, White K, Wing K, Wittemeyer K, Yaspan BL, Zwaigenbaum L, Betancur C, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Geschwind DH, Haines JL, Hallmayer J, Monaco AP, Nurnberger JI, Pericak-Vance MA, Schellenberg GD, Scherer SW, Sutcliffe JS, Szatmari P, Vieland VJ, Wijsman EM, Green A, Gill M, Gallagher L, Vicente A, Ennis S. A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder. Hum Genet 2012; 131:565-79. [PMID: 21996756 PMCID: PMC3303079 DOI: 10.1007/s00439-011-1094-6] [Citation(s) in RCA: 147] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 09/15/2011] [Indexed: 01/18/2023]
Abstract
Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data.
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Affiliation(s)
- Jillian P. Casey
- School of Medicine and Medical Science University College, Dublin 4, Ireland
| | - Tiago Magalhaes
- Instituto Nacional de Saude Dr Ricardo Jorge, Av Padre Cruz 1649-016, Lisbon, Portugal
- BioFIG, Center for Biodiversity, Functional and Integrative Genomics, Campus da FCUL, C2.2.12, Campo Grande, 1749-016 Lisbon, Portugal
- Instituto Gulbenkian de Cîencia, Rua Quinta Grande, 2780-156 Oeiras, Portugal
| | - Judith M. Conroy
- School of Medicine and Medical Science University College, Dublin 4, Ireland
| | - Regina Regan
- School of Medicine and Medical Science University College, Dublin 4, Ireland
| | - Naisha Shah
- School of Medicine and Medical Science University College, Dublin 4, Ireland
| | - Richard Anney
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Denis C. Shields
- School of Medicine and Medical Science University College, Dublin 4, Ireland
| | - Brett S. Abrahams
- Department of Neurology, Center for Autism Research and Treatment, Program in Neurogenetics, Semel Institute, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Joana Almeida
- Hospital Pediátrico de Coimbra, 3000–076 Coimbra, Portugal
| | - Elena Bacchelli
- Department of Biology, University of Bologna, 40126 Bologna, Italy
| | - Anthony J. Bailey
- Department of Psychiatry, University of British Columbia, Vancouver, V6T 2A1 Canada
| | | | - Agatino Battaglia
- Stella Maris Institute for Child and Adolescent Neuropsychiatry, 56128 Calambrone, Pisa, Italy
| | - Tom Berney
- Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
- Institute of Health and Society, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
| | - Nadia Bolshakova
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Patrick F. Bolton
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, London, SE5 8AF UK
| | - Thomas Bourgeron
- Department of Human Genetics and Cognitive Functions, Institut Pasteur, University Paris Diderot-Paris 7, CNRS URA 2182, Fondation FondaMental, 75015 Paris, France
| | - Sean Brennan
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Phil Cali
- Department of Psychiatry, Institute for Juvenile Research, University of Illinois at Chicago, Chicago, IL 60612 USA
| | - Catarina Correia
- Instituto Nacional de Saude Dr Ricardo Jorge, Av Padre Cruz 1649-016, Lisbon, Portugal
- BioFIG, Center for Biodiversity, Functional and Integrative Genomics, Campus da FCUL, C2.2.12, Campo Grande, 1749-016 Lisbon, Portugal
- Instituto Gulbenkian de Cîencia, Rua Quinta Grande, 2780-156 Oeiras, Portugal
| | - Christina Corsello
- Autism and Communicative Disorders Centre, University of Michigan, Ann Arbor, MI 48109-2054 USA
| | - Marc Coutanche
- Department of Psychiatry, University of Oxford, Warneford Hospital, Headington, Oxford, OX3 7JX UK
| | - Geraldine Dawson
- Autism Speaks, New York, 10016 USA
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599-3366 USA
| | - Maretha de Jonge
- Department of Child and Adolescent Psychiatry, University Medical Center, 3508 Utrecht, GA The Netherlands
| | - Richard Delorme
- INSERM U 955, Fondation FondaMental, APHP, Hôpital Robert Debré, Child and Adolescent Psychiatry, 75019 Paris, France
| | - Eftichia Duketis
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany
| | | | - Annette Estes
- Department of Speech and Hearing Sciences, University of Washington, Seattle, WA 98195 USA
| | - Penny Farrar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Bridget A. Fernandez
- Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St John’s Newfoundland, A1B 3V6 Canada
| | - Susan E. Folstein
- Department of Psychiatry, University of Miami School of Medicine, Miami, FL 33136 USA
| | - Suzanne Foley
- Department of Psychiatry, University of Oxford, Warneford Hospital, Headington, Oxford, OX3 7JX UK
| | - Eric Fombonne
- Division of Psychiatry, McGill University, Montreal, QC H3A 1A1 Canada
| | - Christine M. Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany
| | - John Gilbert
- The John P. Hussman Institute for Human Genomics, University of Miami School of Medicine, Miami, FL 33136 USA
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, Sahlgrenska Academy, University of Gothenburg, S41345 Gothenburg, Sweden
| | - Joseph T. Glessner
- The Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Jonathan Green
- Academic Department of Child Psychiatry, Booth Hall of Children’s Hospital, Blackley, Manchester, M9 7AA UK
| | - Stephen J. Guter
- Department of Psychiatry, Institute for Juvenile Research, University of Illinois at Chicago, Chicago, IL 60612 USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 USA
| | - Richard Holt
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Gillian Hughes
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Vanessa Hus
- Autism and Communicative Disorders Centre, University of Michigan, Ann Arbor, MI 48109-2054 USA
| | - Roberta Igliozzi
- Stella Maris Institute for Child and Adolescent Neuropsychiatry, 56128 Calambrone, Pisa, Italy
| | - Cecilia Kim
- The Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Sabine M. Klauck
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Alexander Kolevzon
- Department of Psychiatry, The Seaver Autism Center for Research and Treatment, Mount Sinai School of Medicine, New York, 10029 USA
| | - Janine A. Lamb
- Centre for Integrated Genomic Medical Research, University of Manchester, Manchester, M13 9PT UK
| | - Marion Leboyer
- INSERM U995, Department of Psychiatry, Groupe Hospitalier Henri Mondor-Albert Chenevier, AP-HP, University Paris 12, Fondation FondaMental, 94000 Créteil, France
| | - Ann Le Couteur
- Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
- Institute of Health and Society, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
| | - Bennett L. Leventhal
- Nathan Kline Institute for Psychiatric Research (NKI), 140 Old Orangeburg Road, Orangeburg, NY 10962 USA
- Department of Child and Adolescent Psychiatry, New York University, NYU Child Study Center, 550 First Avenue, New York, NY 10016 USA
| | - Catherine Lord
- Autism and Communicative Disorders Centre, University of Michigan, Ann Arbor, MI 48109-2054 USA
| | - Sabata C. Lund
- Department of Molecular Physiology and Biophysics, Vanderbilt Kennedy Center, Centers for Human Genetics Research and Molecular Neuroscience, Vanderbilt University, Nashville, TN 37232 USA
| | - Elena Maestrini
- Department of Biology, University of Bologna, 40126 Bologna, Italy
| | - Carine Mantoulan
- Octogone/CERPP (Centre d’Eudes et de Recherches en Psychopathologie), University de Toulouse Le Mirail, 31058 Toulouse Cedex, France
| | - Christian R. Marshall
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, ON M5G 1L7 Canada
| | - Helen McConachie
- Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
- Institute of Health and Society, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
| | | | - Jane McGrath
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - William M. McMahon
- Psychiatry Department, University of Utah Medical School, Salt Lake City, UT 84108 USA
| | - Alison Merikangas
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Judith Miller
- Psychiatry Department, University of Utah Medical School, Salt Lake City, UT 84108 USA
| | | | - Ghazala K. Mirza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Jeff Munson
- Department of Psychiatry and Behavioural Sciences, University of Washington, Seattle, WA 98195 USA
| | - Stanley F. Nelson
- Department of Human Genetics, University of California, Los Angeles School of Medicine, Los Angeles, CA 90095 USA
| | - Gudrun Nygren
- Gillberg Neuropsychiatry Centre, Sahlgrenska Academy, University of Gothenburg, S41345 Gothenburg, Sweden
| | | | | | - Katerina Papanikolaou
- University Department of Child Psychiatry, Athens University, Medical School, Agia Sophia Children’s Hospital, 115 27 Athens, Greece
| | - Jeremy R. Parr
- Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
- Institute of Health and Society, Newcastle University, Newcastle Upon Tyne, NE1 7RU UK
| | - Barbara Parrini
- Stella Maris Institute for Child and Adolescent Neuropsychiatry, 56128 Calambrone, Pisa, Italy
| | - Andrew Pickles
- Department of Medicine, School of Epidemiology and Health Science, University of Manchester, Manchester, M13 9PT UK
| | - Dalila Pinto
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, ON M5G 1L7 Canada
| | - Joseph Piven
- Carolina Institute for Developmental Disabilities, CB3366, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3366 USA
| | - David J. Posey
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Annemarie Poustka
- Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Fritz Poustka
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany
| | - Jiannis Ragoussis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Bernadette Roge
- Octogone/CERPP (Centre d’Eudes et de Recherches en Psychopathologie), University de Toulouse Le Mirail, 31058 Toulouse Cedex, France
| | - Michael L. Rutter
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, London, SE5 8AF UK
| | - Ana F. Sequeira
- Instituto Nacional de Saude Dr Ricardo Jorge, Av Padre Cruz 1649-016, Lisbon, Portugal
- BioFIG, Center for Biodiversity, Functional and Integrative Genomics, Campus da FCUL, C2.2.12, Campo Grande, 1749-016 Lisbon, Portugal
- Instituto Gulbenkian de Cîencia, Rua Quinta Grande, 2780-156 Oeiras, Portugal
| | - Latha Soorya
- Department of Psychiatry, The Seaver Autism Center for Research and Treatment, Mount Sinai School of Medicine, New York, 10029 USA
| | - Inês Sousa
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Nuala Sykes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Vera Stoppioni
- Neuropsichiatria Infantile, Ospedale Santa Croce, 61032 Fano, Italy
| | - Raffaella Tancredi
- Stella Maris Institute for Child and Adolescent Neuropsychiatry, 56128 Calambrone, Pisa, Italy
| | - Maïté Tauber
- Octogone/CERPP (Centre d’Eudes et de Recherches en Psychopathologie), University de Toulouse Le Mirail, 31058 Toulouse Cedex, France
| | - Ann P. Thompson
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON L8N 3Z5 Canada
| | - Susanne Thomson
- Department of Molecular Physiology and Biophysics, Vanderbilt Kennedy Center, Centers for Human Genetics Research and Molecular Neuroscience, Vanderbilt University, Nashville, TN 37232 USA
| | - John Tsiantis
- University Department of Child Psychiatry, Athens University, Medical School, Agia Sophia Children’s Hospital, 115 27 Athens, Greece
| | - Herman Van Engeland
- Department of Child and Adolescent Psychiatry, University Medical Center, 3508 Utrecht, GA The Netherlands
| | - John B. Vincent
- Department of Psychiatry, Centre for Addiction and Mental Health, Clarke Institute, University of Toronto, Toronto, ON M5G 1X8 Canada
| | - Fred Volkmar
- Child Study Centre, Yale University, New Haven, CT 06520 USA
| | - Jacob A. S. Vorstman
- Department of Child and Adolescent Psychiatry, University Medical Center, 3508 Utrecht, GA The Netherlands
| | - Simon Wallace
- Department of Psychiatry, University of Oxford, Warneford Hospital, Headington, Oxford, OX3 7JX UK
| | - Kai Wang
- The Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Thomas H. Wassink
- Department of Psychiatry, Carver College of Medicine, Iowa City, IA 52242 USA
| | - Kathy White
- Department of Psychiatry, University of Oxford, Warneford Hospital, Headington, Oxford, OX3 7JX UK
| | - Kirsty Wing
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Kerstin Wittemeyer
- Autism Centre for Education and Research, School of Education, University of Birmingham, Birmingham, B15 2TT UK
| | - Brian L. Yaspan
- Department of Molecular Physiology and Biophysics, Vanderbilt Kennedy Center, Centers for Human Genetics Research and Molecular Neuroscience, Vanderbilt University, Nashville, TN 37232 USA
| | - Lonnie Zwaigenbaum
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 2J3 Canada
| | - Catalina Betancur
- INSERM U952 and CNRS UMR 7224, UPMC Univ Paris 06, Paris, 75005 France
| | - Joseph D. Buxbaum
- Department of Psychiatry, The Seaver Autism Center for Research and Treatment, Mount Sinai School of Medicine, New York, 10029 USA
- Departments of Genetics and Genomic Sciences and Neuroscience, Mount Sinai School of Medicine, New York, 10029 USA
- Department of Neuroscience, Mount Sinai School of Medicine, New York, 10029 USA
| | - Rita M. Cantor
- Department of Human Genetics, University of California, Los Angeles School of Medicine, Los Angeles, CA 90095 USA
| | - Edwin H. Cook
- Department of Psychiatry, Institute for Juvenile Research, University of Illinois at Chicago, Chicago, IL 60612 USA
| | - Hilary Coon
- Psychiatry Department, University of Utah Medical School, Salt Lake City, UT 84108 USA
| | - Michael L. Cuccaro
- The John P. Hussman Institute for Human Genomics, University of Miami School of Medicine, Miami, FL 33136 USA
| | - Daniel H. Geschwind
- Department of Neurology, Center for Autism Research and Treatment, Program in Neurogenetics, Semel Institute, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Jonathan L. Haines
- Department of Molecular Physiology and Biophysics, Vanderbilt Kennedy Center, Centers for Human Genetics Research and Molecular Neuroscience, Vanderbilt University, Nashville, TN 37232 USA
| | - Joachim Hallmayer
- Department of Psychiatry, Division of Child and Adolescent Psychiatry and Child Development, Stanford University School of Medicine, Stanford, CA 94304 USA
| | - Anthony P. Monaco
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - John I. Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami School of Medicine, Miami, FL 33136 USA
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Pennsylvania, 19104 USA
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, ON M5G 1L7 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1 Canada
| | - James S. Sutcliffe
- Department of Molecular Physiology and Biophysics, Vanderbilt Kennedy Center, Centers for Human Genetics Research and Molecular Neuroscience, Vanderbilt University, Nashville, TN 37232 USA
| | - Peter Szatmari
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON L8N 3Z5 Canada
| | - Veronica J. Vieland
- Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital and The Ohio State University, Columbus, OH 43205 USA
| | - Ellen M. Wijsman
- Department of Biostatistics, University of Washington, Seattle, WA 98195 USA
- Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Andrew Green
- School of Medicine and Medical Science University College, Dublin 4, Ireland
| | - Michael Gill
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Louise Gallagher
- Autism Genetics Group, Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
| | - Astrid Vicente
- Instituto Nacional de Saude Dr Ricardo Jorge, Av Padre Cruz 1649-016, Lisbon, Portugal
- BioFIG, Center for Biodiversity, Functional and Integrative Genomics, Campus da FCUL, C2.2.12, Campo Grande, 1749-016 Lisbon, Portugal
- Instituto Gulbenkian de Cîencia, Rua Quinta Grande, 2780-156 Oeiras, Portugal
| | - Sean Ennis
- School of Medicine and Medical Science University College, Dublin 4, Ireland
- Health Sciences Centre, University College Dublin, Dublin, Ireland
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Abstract
Genome-wide association studies (GWAS) are a standard approach for investigating the relationship of common variation within the human genome to a given phenotype of interest. However, single-allele association results published for many GWAS studies represent only the tip of the iceberg for the information that can be extracted from these datasets. The primary analysis strategy for GWAS entails association analysis in which only the single nucleotide polymorphisms (SNPs) with the strongest p values are declared statistically significant due to issues arising from multiple testing and type I error concerns. Factors such as locus heterogeneity, epistasis, and multiple genes conferring small effects contribute to the complexity of the genetic models underlying phenotype expression. Thus, many biologically meaningful associations having lower effect sizes at individual genes are overlooked, as they are difficult to separate from a sea of false-positive associations. Organizing these individual SNPs into biologically meaningful groups to look at overall effects of minor perturbations to genes and pathways is desirable. This pathway-based approach provides researchers with insight into the functional foundations of the phenotype being studied and allows testing of various genetic scenarios.
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Affiliation(s)
- Brian L Yaspan
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Wiggs JL, Kang JH, Yaspan BL, Mirel DB, Laurie C, Crenshaw A, Brodeur W, Gogarten S, Olson LM, Abdrabou W, DelBono E, Loomis S, Haines JL, Pasquale LR. Common variants near CAV1 and CAV2 are associated with primary open-angle glaucoma in Caucasians from the USA. Hum Mol Genet 2011; 20:4707-13. [PMID: 21873608 DOI: 10.1093/hmg/ddr382] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Primary open-angle glaucoma (POAG) is a genetically complex common disease characterized by progressive optic nerve degeneration that results in irreversible blindness. Recently, a genome-wide association study (GWAS) for POAG in an Icelandic population identified significant associations with single nucleotide polymorphisms (SNPs) between the CAV1 and CAV2 genes on chromosome 7q31. In this study, we confirm that the identified SNPs are associated with POAG in our Caucasian US population and that specific haplotypes located in the CAV1/CAV2 intergenic region are associated with the disease. We also present data suggesting that associations with several CAV1/CAV2 SNPs are significant mostly in women.
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Affiliation(s)
- Janey L Wiggs
- Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA.
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Yaspan BL, Bush WS, Torstenson ES, Ma D, Pericak-Vance MA, Ritchie MD, Sutcliffe JS, Haines JL. Genetic analysis of biological pathway data through genomic randomization. Hum Genet 2011; 129:563-71. [PMID: 21279722 PMCID: PMC3107984 DOI: 10.1007/s00439-011-0956-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 01/19/2011] [Indexed: 10/18/2022]
Abstract
Genome Wide Association Studies (GWAS) are a standard approach for large-scale common variation characterization and for identification of single loci predisposing to disease. However, due to issues of moderate sample sizes and particularly multiple testing correction, many variants of smaller effect size are not detected within a single allele analysis framework. Thus, small main effects and potential epistatic effects are not consistently observed in GWAS using standard analytical approaches that consider only single SNP alleles. Here, we propose unique methodology that aggregates variants of interest (for example, genes in a biological pathway) using GWAS results. Multiple testing and type I error concerns are minimized using empirical genomic randomization to estimate significance. Randomization corrects for common pathway-based analysis biases, such as SNP coverage and density, linkage disequilibrium, gene size and pathway size. Pathway Analysis by Randomization Incorporating Structure (PARIS) applies this randomization and in doing so directly accounts for linkage disequilibrium effects. PARIS is independent of association analysis method and is thus applicable to GWAS datasets of all study designs. Using the KEGG database as an example, we apply PARIS to the publicly available Autism Genetic Resource Exchange GWAS dataset, revealing pathways with a significant enrichment of positive association results.
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Affiliation(s)
- Brian L. Yaspan
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - William S. Bush
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Eric S. Torstenson
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Deqiong Ma
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33101, USA Running title: GWA-based pathway analysis by genome randomization
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL 33101, USA Running title: GWA-based pathway analysis by genome randomization
| | - Marylyn D. Ritchie
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James S. Sutcliffe
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jonathan L. Haines
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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Anney R, Klei L, Pinto D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Sykes N, Pagnamenta AT, Almeida J, Bacchelli E, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Carson AR, Casallo G, Casey J, Chu SH, Cochrane L, Corsello C, Crawford EL, Crossett A, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Melhem NM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Piven J, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Wing K, Wittemeyer K, Wood S, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Betancur C, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Gallagher L, Geschwind DH, Gill M, Haines JL, Miller J, Monaco AP, Nurnberger JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Scherer SW, Sutcliffe JS, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Devlin B, Ennis S, Hallmayer J. A genome-wide scan for common alleles affecting risk for autism. Hum Mol Genet 2010; 19:4072-82. [PMID: 20663923 PMCID: PMC2947401 DOI: 10.1093/hmg/ddq307] [Citation(s) in RCA: 432] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10−8. When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10−8 threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
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Affiliation(s)
- Richard Anney
- Department of Psychiatry, School of Medicine, Trinity College, Dublin 8, Ireland
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Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BHY, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, McConachie H, McDougle CJ, McGrath J, McMahon WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C. Functional impact of global rare copy number variation in autism spectrum disorders. Nature 2010; 466:368-72. [PMID: 20531469 DOI: 10.1038/nature09146] [Citation(s) in RCA: 1442] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 05/07/2010] [Indexed: 12/18/2022]
Abstract
The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable ( approximately 90%), the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4 x 10(-4)). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
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Affiliation(s)
- Dalila Pinto
- The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
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Breyer JP, McReynolds KM, Yaspan BL, Bradley KM, Dupont WD, Smith JR. Genetic variants and prostate cancer risk: candidate replication and exploration of viral restriction genes. Cancer Epidemiol Biomarkers Prev 2009; 18:2137-44. [PMID: 19567509 DOI: 10.1158/1055-9965.epi-08-1223] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The genetic variants underlying the strong heritable component of prostate cancer remain largely unknown. Genome-wide association studies of prostate cancer have yielded several variants that have significantly replicated across studies, predominantly in cases unselected for family history of prostate cancer. Additional candidate gene variants have also been proposed, many evaluated within familial prostate cancer study populations. Such variants hold great potential value for risk stratification, particularly for early-onset or aggressive prostate cancer, given the comorbidities associated with current therapies. Here, we investigate a Caucasian study population of 523 independent familial prostate cancer cases and 523 age-matched controls without a personal or family history of prostate cancer. We replicate identified associations at genome-wide association study loci 8q24, 11q13, and 2p15 (P = 2.9 x 10(-4) to P = 4.7 x 10(-5)), showing study population power. We also find evidence to support reported associations at candidate genes RNASEL, EZH2, and NKX3-1 (P = 0.031 to P = 0.0085). We further explore a set of candidate genes related to RNASEL and to its role in retroviral restriction, identifying nominal associations at XPR1 and RBM9. The effects at 8q24 seem more pronounced for those diagnosed at an early age, whereas at 2p15 and RNASEL the effects were more pronounced at a later age. However, these trends did not reach statistical significance. The effects at 2p15 were statistically significantly more pronounced for those diagnosed with aggressive disease.
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Affiliation(s)
- Joan P Breyer
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232-0275, USA
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Breyer JP, Sanders ME, Airey DC, Cai Q, Yaspan BL, Schuyler PA, Dai Q, Boulos F, Olivares MG, Bradley KM, Gao YT, Page DL, Dupont WD, Zheng W, Smith JR. Heritable variation of ERBB2 and breast cancer risk. Cancer Epidemiol Biomarkers Prev 2009; 18:1252-8. [PMID: 19336545 PMCID: PMC2730036 DOI: 10.1158/1055-9965.epi-08-1202] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Amplification of the epithelial growth factor receptor gene ERBB2 (HER2, NEU) in breast cancer is associated with a poor clinical prognosis. In mammary gland development, this receptor plays a role in ductal and lobuloalveolar differentiation. We conducted a systematic investigation of the role of genetic variation of the ERBB2 gene in breast cancer risk in a study of 842 histologically confirmed invasive breast cancer cases and 1,108 controls from the Shanghai Breast Cancer Study. We observed that the ERBB2 gene resides within a locus of high linkage disequilibrium, composed of three major ancestral haplotypes in the study population. These haplotypes are marked by simple tandem repeat and single nucleotide polymorphisms, including the missense variants I655V and P1170A. We observed a risk-modifying effect of a highly polymorphic simple tandem repeat within an evolutionarily conserved region, 4.4 kb upstream from the ERBB2 transcription start site. Under a dominant genetic model, the age-adjusted odds ratio was 1.74 (95% confidence interval, 1.27-2.37). Its association with breast cancer, and with breast cancer stratified by histology, by histologic grade, and by stage, remained significant after correction for multiple comparisons. In contrast, we observed no association of ERBB2 single nucleotide polymorphism haplotypes with breast cancer predisposition.
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Affiliation(s)
- Joan P Breyer
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232-0275, USA.
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Gudmundsson J, Sulem P, Rafnar T, Bergthorsson JT, Manolescu A, Gudbjartsson D, Agnarsson BA, Sigurdsson A, Benediktsdottir KR, Blondal T, Jakobsdottir M, Stacey SN, Kostic J, Kristinsson KT, Birgisdottir B, Ghosh S, Magnusdottir DN, Thorlacius S, Thorleifsson G, Zheng SL, Sun J, Chang BL, Elmore JB, Breyer JP, McReynolds KM, Bradley KM, Yaspan BL, Wiklund F, Stattin P, Lindström S, Adami HO, McDonnell SK, Schaid DJ, Cunningham JM, Wang L, Cerhan JR, St Sauver JL, Isaacs SD, Wiley KE, Partin AW, Walsh PC, Polo S, Ruiz-Echarri M, Navarrete S, Fuertes F, Saez B, Godino J, Weijerman PC, Swinkels DW, Aben KK, Witjes JA, Suarez BK, Helfand BT, Frigge ML, Kristjansson K, Ober C, Jonsson E, Einarsson GV, Xu J, Gronberg H, Smith JR, Thibodeau SN, Isaacs WB, Catalona WJ, Mayordomo JI, Kiemeney LA, Barkardottir RB, Gulcher JR, Thorsteinsdottir U, Kong A, Stefansson K. Common sequence variants on 2p15 and Xp11.22 confer susceptibility to prostate cancer. Nat Genet 2008; 40:281-3. [PMID: 18264098 DOI: 10.1038/ng.89] [Citation(s) in RCA: 299] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Accepted: 12/27/2007] [Indexed: 01/11/2023]
Abstract
We conducted a genome-wide SNP association study on prostate cancer on over 23,000 Icelanders, followed by a replication study including over 15,500 individuals from Europe and the United States. Two newly identified variants were shown to be associated with prostate cancer: rs5945572 on Xp11.22 and rs721048 on 2p15 (odds ratios (OR) = 1.23 and 1.15; P = 3.9 x 10(-13) and 7.7 x 10(-9), respectively). The 2p15 variant shows a significantly stronger association with more aggressive, rather than less aggressive, forms of the disease.
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