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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: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [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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2
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Gautam Y, Johansson E, Mersha TB. Multi-Omics Profiling Approach to Asthma: An Evolving Paradigm. J Pers Med 2022; 12:jpm12010066. [PMID: 35055381 PMCID: PMC8778153 DOI: 10.3390/jpm12010066] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/23/2021] [Accepted: 12/28/2021] [Indexed: 02/04/2023] Open
Abstract
Asthma is a complex multifactorial and heterogeneous respiratory disease. Although genetics is a strong risk factor of asthma, external and internal exposures and their interactions with genetic factors also play important roles in the pathophysiology of asthma. Over the past decades, the application of high-throughput omics approaches has emerged and been applied to the field of asthma research for screening biomarkers such as genes, transcript, proteins, and metabolites in an unbiased fashion. Leveraging large-scale studies representative of diverse population-based omics data and integrating with clinical data has led to better profiling of asthma risk. Yet, to date, no omic-driven endotypes have been translated into clinical practice and management of asthma. In this article, we provide an overview of the current status of omics studies of asthma, namely, genomics, transcriptomics, epigenomics, proteomics, exposomics, and metabolomics. The current development of the multi-omics integrations of asthma is also briefly discussed. Biomarker discovery following multi-omics profiling could be challenging but useful for better disease phenotyping and endotyping that can translate into advances in asthma management and clinical care, ultimately leading to successful precision medicine approaches.
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3
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Lenga Ma Bonda W, Iochmann S, Magnen M, Courty Y, Reverdiau P. Kallikrein-related peptidases in lung diseases. Biol Chem 2019; 399:959-971. [PMID: 29604204 DOI: 10.1515/hsz-2018-0114] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/26/2018] [Indexed: 02/06/2023]
Abstract
Human tissue kallikreins (KLKs) are 15 members of the serine protease family and are present in various healthy human tissues including airway tissues. Multiple studies have revealed their crucial role in the pathophysiology of a number of chronic, infectious and tumour lung diseases. KLK1, 3 and 14 are involved in asthma pathogenesis, and KLK1 could be also associated with the exacerbation of this inflammatory disease caused by rhinovirus. KLK5 was demonstrated as an influenza virus activating protease in humans, and KLK1 and 12 could also be involved in the activation and spread of these viruses. KLKs are associated with lung cancer, with up- or downregulation of expression depending on the KLK, cancer subtype, stage of tumour and also the microenvironment. Functional studies showed that KLK12 is a potent pro-angiogenic factor. Moreover, KLK6 promotes malignant-cell proliferation and KLK13 invasiveness. In contrast, KLK8 and KLK10 reduce proliferation and invasion of malignant cells. Considering the involvement of KLKs in various physiological and pathological processes, KLKs appear to be potential biomarkers and therapeutic targets for lung diseases.
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Affiliation(s)
- Woodys Lenga Ma Bonda
- Centre d'Etude des Pathologies Respiratoires, INSERM UMR 1100, Faculté de Médecine, 10 Boulevard Tonnellé, F-37032 Tours, France.,Université de Tours, F-37032 Tours, France
| | - Sophie Iochmann
- Centre d'Etude des Pathologies Respiratoires, INSERM UMR 1100, Faculté de Médecine, 10 Boulevard Tonnellé, F-37032 Tours, France.,Université de Tours, F-37032 Tours, France.,IUT de Tours, Université de Tours, F-37082 Tours, France
| | - Mélia Magnen
- Centre d'Etude des Pathologies Respiratoires, INSERM UMR 1100, Faculté de Médecine, 10 Boulevard Tonnellé, F-37032 Tours, France.,Université de Tours, F-37032 Tours, France
| | - Yves Courty
- Centre d'Etude des Pathologies Respiratoires, INSERM UMR 1100, Faculté de Médecine, 10 Boulevard Tonnellé, F-37032 Tours, France.,Université de Tours, F-37032 Tours, France
| | - Pascale Reverdiau
- Centre d'Etude des Pathologies Respiratoires, INSERM UMR 1100, Faculté de Médecine, 10 Boulevard Tonnellé, F-37032 Tours, France.,Université de Tours, F-37032 Tours, France.,IUT de Tours, Université de Tours, F-37082 Tours, France
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4
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Gignoux CR, Torgerson DG, Pino-Yanes M, Uricchio LH, Galanter J, Roth LA, Eng C, Hu D, Nguyen EA, Huntsman S, Mathias RA, Kumar R, Rodriguez-Santana J, Thakur N, Oh SS, McGarry M, Moreno-Estrada A, Sandoval K, Winkler CA, Seibold MA, Padhukasahasram B, Conti DV, Farber HJ, Avila P, Brigino-Buenaventura E, Lenoir M, Meade K, Serebrisky D, Borrell LN, Rodriguez-Cintron W, Thyne S, Joubert BR, Romieu I, Levin AM, Sienra-Monge JJ, Del Rio-Navarro BE, Gan W, Raby BA, Weiss ST, Bleecker E, Meyers DA, Martinez FJ, Gauderman WJ, Gilliland F, London SJ, Bustamante CD, Nicolae DL, Ober C, Sen S, Barnes K, Williams LK, Hernandez RD, Burchard EG. An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos. J Allergy Clin Immunol 2019; 143:957-969. [PMID: 30201514 PMCID: PMC6927816 DOI: 10.1016/j.jaci.2016.08.057] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 08/20/2016] [Accepted: 08/29/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Asthma is a common but complex disease with racial/ethnic differences in prevalence, morbidity, and response to therapies. OBJECTIVE We sought to perform an analysis of genetic ancestry to identify new loci that contribute to asthma susceptibility. METHODS We leveraged the mixed ancestry of 3902 Latinos and performed an admixture mapping meta-analysis for asthma susceptibility. We replicated associations in an independent study of 3774 Latinos, performed targeted sequencing for fine mapping, and tested for disease correlations with gene expression in the whole blood of more than 500 subjects from 3 racial/ethnic groups. RESULTS We identified a genome-wide significant admixture mapping peak at 18q21 in Latinos (P = 6.8 × 10-6), where Native American ancestry was associated with increased risk of asthma (odds ratio [OR], 1.20; 95% CI, 1.07-1.34; P = .002) and European ancestry was associated with protection (OR, 0.86; 95% CI, 0.77-0.96; P = .008). Our findings were replicated in an independent childhood asthma study in Latinos (P = 5.3 × 10-3, combined P = 2.6 × 10-7). Fine mapping of 18q21 in 1978 Latinos identified a significant association with multiple variants 5' of SMAD family member 2 (SMAD2) in Mexicans, whereas a single rare variant in the same window was the top association in Puerto Ricans. Low versus high SMAD2 blood expression was correlated with case status (13.4% lower expression; OR, 3.93; 95% CI, 2.12-7.28; P < .001). In addition, lower expression of SMAD2 was associated with more frequent exacerbations among Puerto Ricans with asthma. CONCLUSION Ancestry at 18q21 was significantly associated with asthma in Latinos and implicated multiple ancestry-informative noncoding variants upstream of SMAD2 with asthma susceptibility. Furthermore, decreased SMAD2 expression in blood was strongly associated with increased asthma risk and increased exacerbations.
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Affiliation(s)
- Christopher R Gignoux
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, Calif; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif.
| | - Dara G Torgerson
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Maria Pino-Yanes
- Department of Medicine, University of California, San Francisco, San Francisco, Calif; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Lawrence H Uricchio
- Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif
| | - Joshua Galanter
- Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif; Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Lindsey A Roth
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Elizabeth A Nguyen
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | | | - Rajesh Kumar
- Ann and Robert H. Lurie Children's Hospital of Chicago, Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | | | - Neeta Thakur
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Meghan McGarry
- Department of Pediatrics, University of California, San Francisco, San Francisco, Calif
| | | | - Karla Sandoval
- Department of Genetics, Stanford University, Palo Alto, Calif
| | - Cheryl A Winkler
- Molecular Genetics Epidemiology Section, Frederick National Laboratory for Cancer Research, Frederick, Md
| | - Max A Seibold
- Integrated Center for Genes, Environment, and Health, Department of Pediatrics, Division of Pulmonary and Critical Care Medicine, National Jewish Health, Denver, Colo
| | - Badri Padhukasahasram
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich
| | - David V Conti
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, Tex
| | - Pedro Avila
- Division of Allergy-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | | | | | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | | | - Luisa N Borrell
- Department of Health Sciences, Graduate Program in Public Health, Lehman College, City University of New York, Bronx, NY
| | | | - Shannon Thyne
- Department of Medicine, University of California, San Francisco, San Francisco, Calif
| | - Bonnie R Joubert
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Isabelle Romieu
- Nutritional Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Albert M Levin
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich
| | - Juan-Jose Sienra-Monge
- Departmento de Alergia e Inmunologia, Clinica Hospital Infantil de Mexico Federico Gomez, Mexico City, Mexico
| | | | - Weiniu Gan
- Division of Lung Diseases, National Heart, Lung, and Blood Institute, Bethesda, Md
| | - Benjamin A Raby
- Department of Medicine, Harvard Medical School, Boston, Mass
| | - Scott T Weiss
- Department of Medicine, Harvard Medical School, Boston, Mass
| | - Eugene Bleecker
- Center for Genomics & Personalized Medicine Research, Wake Forest University, Winston-Salem, NC
| | - Deborah A Meyers
- Center for Genomics & Personalized Medicine Research, Wake Forest University, Winston-Salem, NC
| | | | - W James Gauderman
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - Frank Gilliland
- Department of Preventative Medicine, University of Southern California, Los Angeles, Calif
| | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | | | - Dan L Nicolae
- Physical Sciences Division, Department of Statistics, University of Chicago, Chicago, Ill
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, Tenn
| | - Kathleen Barnes
- Department of Medicine, Johns Hopkins University, Baltimore, Md
| | - L Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich; Department of Internal Medicine, Henry Ford Health System, Detroit, Mich
| | - Ryan D Hernandez
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, Calif; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif
| | - Esteban G Burchard
- Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, San Francisco, Calif; Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, Calif; Department of Medicine, University of California, San Francisco, San Francisco, Calif
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5
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Phenome-wide association studies across large population cohorts support drug target validation. Nat Commun 2018; 9:4285. [PMID: 30327483 PMCID: PMC6191429 DOI: 10.1038/s41467-018-06540-3] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 09/05/2018] [Indexed: 12/12/2022] Open
Abstract
Phenome-wide association studies (PheWAS) have been proposed as a possible aid in drug development through elucidating mechanisms of action, identifying alternative indications, or predicting adverse drug events (ADEs). Here, we select 25 single nucleotide polymorphisms (SNPs) linked through genome-wide association studies (GWAS) to 19 candidate drug targets for common disease indications. We interrogate these SNPs by PheWAS in four large cohorts with extensive health information (23andMe, UK Biobank, FINRISK, CHOP) for association with 1683 binary endpoints in up to 697,815 individuals and conduct meta-analyses for 145 mapped disease endpoints. Our analyses replicate 75% of known GWAS associations (P < 0.05) and identify nine study-wide significant novel associations (of 71 with FDR < 0.1). We describe associations that may predict ADEs, e.g., acne, high cholesterol, gout, and gallstones with rs738409 (p.I148M) in PNPLA3 and asthma with rs1990760 (p.T946A) in IFIH1. Our results demonstrate PheWAS as a powerful addition to the toolkit for drug discovery. Testing the association between genetic variants and a range of phenotypes can assist drug development. Here, in a phenome-wide association study in up to 697,815 individuals, Diogo et al. identify genotype–phenotype associations predicting efficacy, alternative indications or adverse drug effects.
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6
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Farzan N, Vijverberg SJ, Kabesch M, Sterk PJ, Maitland-van der Zee AH. The use of pharmacogenomics, epigenomics, and transcriptomics to improve childhood asthma management: Where do we stand? Pediatr Pulmonol 2018; 53:836-845. [PMID: 29493882 DOI: 10.1002/ppul.23976] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/01/2018] [Indexed: 01/11/2023]
Abstract
Asthma is a complex multifactorial disease and it is the most common chronic disease in children. There is a high variability in response to asthma treatment, even in patients with good adherence to maintenance treatment, and a correct inhalation technique. Distinct underlying disease mechanisms in childhood asthma might be the reason of this heterogeneity. A deeper knowledge of the underlying molecular mechanisms of asthma has led to the recent development of advanced and mechanism-based treatments such as biologicals. However, biologicals are recommended only for patients with specific asthma phenotypes who remain uncontrolled despite high dosages of conventional asthma treatment. One of the main unmet needs in their application is lack of clinically available biomarkers to individualize pediatric asthma management and guide treatment. Pharmacogenomics, epigenomics, and transcriptomics are three omics fields that are rapidly advancing and can provide tools to identify novel asthma mechanisms and biomarkers to guide treatment. Pharmacogenomics focuses on variants in the DNA, epigenomics studies heritable changes that do not involve changes in the DNA sequence but lead to alteration of gene expression, and transcriptomics investigates gene expression by studying the complete set of mRNA transcripts in a cell or a population of cells. Advances in high-throughput technologies and statistical tools together with well-phenotyped patient inclusion and collaborations between different centers will expand our knowledge of underlying molecular mechanisms involved in disease onset and progress. Furthermore, it could help to select and stratify appropriate therapeutic strategies for subgroups of patients and hopefully bring precision medicine to daily practice.
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Affiliation(s)
- Niloufar Farzan
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne J Vijverberg
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Peter J Sterk
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
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7
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Barreto-Luis A, Corrales A, Acosta-Herrera M, Gonzalez-Colino C, Cumplido J, Martinez-Tadeo J, Carracedo A, Villar J, Carrillo T, Pino-Yanes M, Flores C. A pathway-based association study reveals variants from Wnt signalling genes contributing to asthma susceptibility. Clin Exp Allergy 2017; 47:618-626. [PMID: 28079285 DOI: 10.1111/cea.12883] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 10/07/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
BACKGROUND Genetic susceptibility to asthma is currently linked to a handful of genes which have a limited ability to predict the overall disease risk, suggesting the existence of many other genes involved in disease development. Accumulated evidence from association studies in genes related by biological pathways could reveal novel asthma genes. OBJECTIVE To reveal novel asthma susceptibility genes by means of a pathway-based association study. METHODS Based on summary data from a previous a genomewide association study (GWAS) of asthma, we first identified significant biological pathways using a gene-set enrichment analysis. We then mapped all tested single nucleotide polymorphisms (SNPs) on the genes contributing to significant pathways and prioritized those with a disproportionate number of nominal significant associations for further studies. For those prioritized genes, association studies were performed for selected SNPs in independent case-control samples (n = 1765) using logistic regression models, and results were meta-analysed with those from the GWAS. RESULTS Two biological processes were significantly enriched: the cytokine-cytokine receptor interaction (P = 0.002) and the Wnt signalling (P = 0.012). From the 417 genes interacting in these two pathways, 10 showed an excess of nominal associations, including a known asthma susceptibility locus (encoding SMAD family member 3) and other novel candidate genes. From the latter, association studies of 14 selected SNPs evidenced replication in a locus near the frizzled class receptor 6 (FZD6) gene (P = 9.90 × 10-4 ), which had a consistent direction of effects with the GWAS findings (meta-analysed odds ratio = 1.49; P = 5.87 × 10-6 ) and was in high linkage disequilibrium with expression quantitative trait loci in lung tissues. CONCLUSIONS AND CLINICAL RELEVANCE This study revealed the importance of two biological pathways in asthma pathogenesis and identified a novel susceptibility locus near Wnt signalling genes.
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Affiliation(s)
- A Barreto-Luis
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - A Corrales
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - M Acosta-Herrera
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - C Gonzalez-Colino
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - J Cumplido
- Allergy Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - J Martinez-Tadeo
- Allergy Unit, Hospital Universitario N.S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - A Carracedo
- Grupo de Medicina Xenómica, CIBERER-Universidade de Santiago de Compostela-Fundación Galega de Medicina Xenómica (SERGAS), Santiago de Compostela, Spain
| | - J Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Research Unit, Hospital Universitario Dr. Negrin, Las Palmas de Gran Canaria, Spain
| | - T Carrillo
- Allergy Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria, Spain
| | - M Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - C Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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8
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Faruque MU, Chen G, Doumatey AP, Zhou J, Huang H, Shriner D, Adeyemo AA, Rotimi CN, Dunston GM. Transferability of genome-wide associated loci for asthma in African Americans. J Asthma 2017; 54:1-8. [PMID: 27177148 PMCID: PMC5300042 DOI: 10.1080/02770903.2016.1188941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/05/2016] [Accepted: 05/08/2016] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Transferability of significantly associated loci or GWAS "hits" adds credibility to genotype-disease associations and provides evidence for generalizability across different ancestral populations. We sought evidence of association of known asthma-associated single nucleotide polymorphisms (SNPs) in an African American population. METHODS Subjects comprised 661 participants (261 asthma cases and 400 controls) from the Howard University Family Study. Forty-eight SNPs previously reported to be associated with asthma by GWAS were selected for testing. We adopted a combined strategy by first adopting an "exact" approach where we looked-up only the reported index SNP. For those index SNPs missing form our dataset, we used a "local" approach that examined all the regional SNPs in LD with the index SNP. RESULTS Out of the 48 SNPs, our cohort had genotype data available for 27, which were examined for exact replication. Of these, two SNPs were found positively associated with asthma. These included: rs10508372 (OR = 1.567 [95%CI, 1.133-2.167], P = 0.0066) and rs2378383 (OR = 2.147 [95%CI, 1.149-4.013], P = 0.0166), located on chromosomal bands 10p14 and 9q21.31, respectively. Local replication of the remaining 21 loci showed association at two chromosomal loci (9p24.1-rs2381413 and 6p21.32-rs3132947; Bonferroni-corrected P values: 0.0033 and 0.0197, respectively). Of note, multiple SNPs in LD with rs2381413 located upstream of IL33 were significantly associated with asthma. CONCLUSIONS This study has successfully transferred four reported asthma-associated loci in an independent African American population. Identification of several asthma-associated SNPs in the upstream of the IL33, a gene previously implicated in allergic inflammation of asthmatic airway, supports the generalizability of this finding.
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Affiliation(s)
- Mezbah U. Faruque
- National Human Genome Center, Howard University College of Medicine, Washington, DC, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ayo P. Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jie Zhou
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hanxia Huang
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adebowale A. Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Georgia M. Dunston
- National Human Genome Center, Howard University College of Medicine, Washington, DC, USA
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Involvement of Kallikrein-Related Peptidases in Normal and Pathologic Processes. DISEASE MARKERS 2015; 2015:946572. [PMID: 26783378 PMCID: PMC4689925 DOI: 10.1155/2015/946572] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/16/2015] [Accepted: 10/29/2015] [Indexed: 12/31/2022]
Abstract
Human kallikrein-related peptidases (KLKs) are a subgroup of serine proteases that participate in proteolytic pathways and control protein levels in normal physiology as well as in several pathological conditions. Their complex network of stimulatory and inhibitory interactions may induce inflammatory and immune responses and contribute to the neoplastic phenotype through the regulation of several cellular processes, such as proliferation, survival, migration, and invasion. This family of proteases, which includes one of the most useful cancer biomarkers, kallikrein-related peptidase 3 or PSA, also has a protective effect against cancer promoting apoptosis or counteracting angiogenesis and cell proliferation. Therefore, they represent attractive therapeutic targets and may have important applications in clinical oncology. Despite being intensively studied, many gaps in our knowledge on several molecular aspects of KLK functions still exist. This review aims to summarize recent data on their involvement in different processes related to health and disease, in particular those directly or indirectly linked to the neoplastic process.
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10
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Johnson EO, Hancock DB, Gaddis NC, Levy JL, Page G, Novak SP, Glasheen C, Saccone NL, Rice JP, Moreau MP, Doheny KF, Romm JM, Brooks AI, Aouizerat BE, Bierut LJ, Kral AH. Novel genetic locus implicated for HIV-1 acquisition with putative regulatory links to HIV replication and infectivity: a genome-wide association study. PLoS One 2015; 10:e0118149. [PMID: 25786224 PMCID: PMC4364715 DOI: 10.1371/journal.pone.0118149] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 01/05/2015] [Indexed: 11/18/2022] Open
Abstract
Fifty percent of variability in HIV-1 susceptibility is attributable to host genetics. Thus identifying genetic associations is essential to understanding pathogenesis of HIV-1 and important for targeting drug development. To date, however, CCR5 remains the only gene conclusively associated with HIV acquisition. To identify novel host genetic determinants of HIV-1 acquisition, we conducted a genome-wide association study among a high-risk sample of 3,136 injection drug users (IDUs) from the Urban Health Study (UHS). In addition to being IDUs, HIV-controls were frequency-matched to cases on environmental exposures to enhance detection of genetic effects. We tested independent replication in the Women's Interagency HIV Study (N=2,533). We also examined publicly available gene expression data to link SNPs associated with HIV acquisition to known mechanisms affecting HIV replication/infectivity. Analysis of the UHS nominated eight genetic regions for replication testing. SNP rs4878712 in FRMPD1 met multiple testing correction for independent replication (P=1.38x10(-4)), although the UHS-WIHS meta-analysis p-value did not reach genome-wide significance (P=4.47x10(-7) vs. P<5.0x10(-8)) Gene expression analyses provided promising biological support for the protective G allele at rs4878712 lowering risk of HIV: (1) the G allele was associated with reduced expression of FBXO10 (r=-0.49, P=6.9x10(-5)); (2) FBXO10 is a component of the Skp1-Cul1-F-box protein E3 ubiquitin ligase complex that targets Bcl-2 protein for degradation; (3) lower FBXO10 expression was associated with higher BCL2 expression (r=-0.49, P=8x10(-5)); (4) higher basal levels of Bcl-2 are known to reduce HIV replication and infectivity in human and animal in vitro studies. These results suggest new potential biological pathways by which host genetics affect susceptibility to HIV upon exposure for follow-up in subsequent studies.
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Affiliation(s)
- Eric O. Johnson
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Dana B. Hancock
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Nathan C. Gaddis
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Joshua L. Levy
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Grier Page
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Scott P. Novak
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Cristie Glasheen
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
| | - Nancy L. Saccone
- Washington University School of Medicine, St. Louis, MO, United States of America
| | - John P. Rice
- Washington University School of Medicine, St. Louis, MO, United States of America
| | - Michael P. Moreau
- Rutgers University Cell and DNA Repository (RUCDR), Piscataway, NJ, United States of America
| | - Kimberly F. Doheny
- Center for Inherited Disease Research (CIDR), Johns Hopkins University, Baltimore, MD, United States of America
| | - Jane M. Romm
- Center for Inherited Disease Research (CIDR), Johns Hopkins University, Baltimore, MD, United States of America
| | - Andrew I. Brooks
- Rutgers University Cell and DNA Repository (RUCDR), Piscataway, NJ, United States of America
| | - Bradley E. Aouizerat
- School of Nursing, University of California San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, United States of America
| | - Laura J. Bierut
- Washington University School of Medicine, St. Louis, MO, United States of America
| | - Alex H. Kral
- RTI International, Research Triangle Park, NC, Atlanta, GA, San Francisco, CA, United States of America
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11
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Igartua C, Myers RA, Mathias RA, Pino-Yanes M, Eng C, Graves PE, Levin AM, Del-Rio-Navarro BE, Jackson DJ, Livne OE, Rafaels N, Edlund CK, Yang JJ, Huntsman S, Salam MT, Romieu I, Mourad R, Gern JE, Lemanske RF, Wyss A, Hoppin JA, Barnes KC, Burchard EG, Gauderman WJ, Martinez FD, Raby BA, Weiss ST, Williams LK, London SJ, Gilliland FD, Nicolae DL, Ober C. Ethnic-specific associations of rare and low-frequency DNA sequence variants with asthma. Nat Commun 2015; 6:5965. [PMID: 25591454 PMCID: PMC4309441 DOI: 10.1038/ncomms6965] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 11/25/2014] [Indexed: 12/11/2022] Open
Abstract
Common variants at many loci have been robustly associated with asthma but explain little of the overall genetic risk. Here we investigate the role of rare (<1%) and low-frequency (1-5%) variants using the Illumina HumanExome BeadChip array in 4,794 asthma cases, 4,707 non-asthmatic controls and 590 case-parent trios representing European Americans, African Americans/African Caribbeans and Latinos. Our study reveals one low-frequency missense mutation in the GRASP gene that is associated with asthma in the Latino sample (P=4.31 × 10(-6); OR=1.25; MAF=1.21%) and two genes harbouring functional variants that are associated with asthma in a gene-based analysis: GSDMB at the 17q12-21 asthma locus in the Latino and combined samples (P=7.81 × 10(-8) and 4.09 × 10(-8), respectively) and MTHFR in the African ancestry sample (P=1.72 × 10(-6)). Our results suggest that associations with rare and low-frequency variants are ethnic specific and not likely to explain a significant proportion of the 'missing heritability' of asthma.
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Affiliation(s)
- Catherine Igartua
- Department of Human Genetics, University of Chicago, 920 East 58th Street, CLSC 425, Chicago, Illinois 60637, USA
| | - Rachel A. Myers
- Department of Human Genetics, University of Chicago, 920 East 58th Street, CLSC 425, Chicago, Illinois 60637, USA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | - Maria Pino-Yanes
- Department of Medicine, University of California San Francisco, San Francisco, California 94143, USA
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, California 94143, USA
| | - Penelope E. Graves
- Arizona Respiratory Center and BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
| | - Albert M. Levin
- Department of Public Health Science, Henry Ford Health System, Detroit, Michigan 48202, USA
| | | | - Daniel J. Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, USA
| | - Oren E. Livne
- Department of Human Genetics, University of Chicago, 920 East 58th Street, CLSC 425, Chicago, Illinois 60637, USA
| | - Nicholas Rafaels
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | - Christopher K. Edlund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - James J. Yang
- School of Nursing, University of Michigan, Ann Arbor, Michigan 48202, USA
| | - Scott Huntsman
- Department of Medicine, University of California San Francisco, San Francisco, California 94143, USA
| | - Muhammad T. Salam
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Isabelle Romieu
- International Agency for Research on Cancer, Lyon 69372, France
| | - Raphael Mourad
- Department of Human Genetics, University of Chicago, 920 East 58th Street, CLSC 425, Chicago, Illinois 60637, USA
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, USA
- Department of Internal Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, USA
| | - Robert F. Lemanske
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53726, USA
| | - Annah Wyss
- Division of Intramural Research, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Jane A. Hoppin
- Division of Intramural Research, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27607, USA
| | - Kathleen C. Barnes
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21224, USA
| | - Esteban G. Burchard
- Department of Medicine, University of California San Francisco, San Francisco, California 94143, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94143, USA
| | - W. James Gauderman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Fernando D. Martinez
- Arizona Respiratory Center and BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
| | - Benjamin A. Raby
- Channing Division of Network Medicine, Harvard Medical School, Boston, Massachusetts 2115, USA
- Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, Massachusetts 2115, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Harvard Medical School, Boston, Massachusetts 2115, USA
| | - L. Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Michigan 48202, USA
- Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan 48202, USA
| | - Stephanie J. London
- Division of Intramural Research, Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Frank D. Gilliland
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Dan L. Nicolae
- Department of Human Genetics, University of Chicago, 920 East 58th Street, CLSC 425, Chicago, Illinois 60637, USA
- Departments of Medicine and Statistics, University of Chicago, Chicago, Illinois 60637, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, 920 East 58th Street, CLSC 425, Chicago, Illinois 60637, USA
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12
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Myers RA, Scott NM, Gauderman WJ, Qiu W, Mathias RA, Romieu I, Levin AM, Pino-Yanes M, Graves PE, Villarreal AB, Beaty TH, Carey VJ, Croteau-Chonka DC, del Rio Navarro B, Edlund C, Hernandez-Cadena L, Navarro-Olivos E, Padhukasahasram B, Salam MT, Torgerson DG, Van den Berg DJ, Vora H, Bleecker ER, Meyers DA, Williams LK, Martinez FD, Burchard EG, Barnes KC, Gilliland FD, Weiss ST, London SJ, Raby BA, Ober C, Nicolae DL. Genome-wide interaction studies reveal sex-specific asthma risk alleles. Hum Mol Genet 2014; 23:5251-9. [PMID: 24824216 PMCID: PMC4159149 DOI: 10.1093/hmg/ddu222] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 04/09/2014] [Accepted: 05/06/2014] [Indexed: 11/14/2022] Open
Abstract
Asthma is a complex disease with sex-specific differences in prevalence. Candidate gene studies have suggested that genotype-by-sex interaction effects on asthma risk exist, but this has not yet been explored at a genome-wide level. We aimed to identify sex-specific asthma risk alleles by performing a genome-wide scan for genotype-by-sex interactions in the ethnically diverse participants in the EVE Asthma Genetics Consortium. We performed male- and female-specific genome-wide association studies in 2653 male asthma cases, 2566 female asthma cases and 3830 non-asthma controls from European American, African American, African Caribbean and Latino populations. Association tests were conducted in each study sample, and the results were combined in ancestry-specific and cross-ancestry meta-analyses. Six sex-specific asthma risk loci had P-values < 1 × 10(-6), of which two were male specific and four were female specific; all were ancestry specific. The most significant sex-specific association in European Americans was at the interferon regulatory factor 1 (IRF1) locus on 5q31.1. We also identify a Latino female-specific association in RAP1GAP2. Both of these loci included single-nucleotide polymorphisms that are known expression quantitative trait loci and have been associated with asthma in independent studies. The IRF1 locus is a strong candidate region for male-specific asthma susceptibility due to the association and validation we demonstrate here, the known role of IRF1 in asthma-relevant immune pathways and prior reports of sex-specific differences in interferon responses.
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Affiliation(s)
| | | | - W James Gauderman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rasika A Mathias
- Department of Medicine and Epidemiology, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | | | - Maria Pino-Yanes
- Department of Medicine and Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Penelope E Graves
- BIO5 Institute, Arizona Respiratory Care Center, University of Arizona, Tucson, AZ 85721, USA
| | | | - Terri H Beaty
- Department of Medicine and Epidemiology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Vincent J Carey
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Damien C Croteau-Chonka
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Christopher Edlund
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | | | | | | | - Muhammad T Salam
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Dara G Torgerson
- Department of Medicine and Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - David J Van den Berg
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Hita Vora
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Eugene R Bleecker
- Center for Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Deborah A Meyers
- Center for Genomics and Personalized Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - L Keoki Williams
- Center for Health Policy and Health Services Research Department of Internal Medicine, Henry Ford Health System, Detroit, MI 48202, USA
| | - Fernando D Martinez
- BIO5 Institute, Arizona Respiratory Care Center, University of Arizona, Tucson, AZ 85721, USA
| | - Esteban G Burchard
- Department of Medicine and Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Kathleen C Barnes
- Department of Medicine and Epidemiology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Frank D Gilliland
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Benjamin A Raby
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Dan L Nicolae
- Department of Human Genetics Department of Statistics and Medicine, University of Chicago, Chicago, IL 60637, USA
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13
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Kelada SNP, Carpenter DE, Aylor DL, Chines P, Rutledge H, Chesler EJ, Churchill GA, Pardo-Manuel de Villena F, Schwartz DA, Collins FS. Integrative genetic analysis of allergic inflammation in the murine lung. Am J Respir Cell Mol Biol 2014; 51:436-45. [PMID: 24693920 PMCID: PMC4189492 DOI: 10.1165/rcmb.2013-0501oc] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Accepted: 04/03/2014] [Indexed: 01/08/2023] Open
Abstract
Airway allergen exposure induces inflammation among individuals with atopy that is characterized by altered airway gene expression, elevated levels of T helper type 2 cytokines, mucus hypersecretion, and airflow obstruction. To identify the genetic determinants of the airway allergen response, we employed a systems genetics approach. We applied a house dust mite mouse model of allergic airway disease to 151 incipient lines of the Collaborative Cross, a new mouse genetic reference population, and measured serum IgE, airway eosinophilia, and gene expression in the lung. Allergen-induced serum IgE and airway eosinophilia were not correlated. We detected quantitative trait loci (QTL) for airway eosinophilia on chromosome (Chr) 11 (71.802-87.098 megabases [Mb]) and allergen-induced IgE on Chr 4 (13.950-31.660 Mb). More than 4,500 genes expressed in the lung had gene expression QTL (eQTL), the majority of which were located near the gene itself. However, we also detected approximately 1,700 trans-eQTL, and many of these trans-eQTL clustered into two regions on Chr 2. We show that one of these loci (at 147.6 Mb) is associated with the expression of more than 100 genes, and, using bioinformatics resources, fine-map this locus to a 53 kb-long interval. We also use the gene expression and eQTL data to identify a candidate gene, Tlcd2, for the eosinophil QTL. Our results demonstrate that hallmark allergic airway disease phenotypes are associated with distinct genetic loci on Chrs 4 and 11, and that gene expression in the allergically inflamed lung is controlled by both cis and trans regulatory factors.
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Affiliation(s)
- Samir N. P. Kelada
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
- Department of Genetics
- Marsico Lung Institute, and
| | - Danielle E. Carpenter
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David L. Aylor
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina
| | - Peter Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | | | | | | | | | | | - Francis S. Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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14
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Heijink IH, Nawijn MC, Hackett TL. Airway epithelial barrier function regulates the pathogenesis of allergic asthma. Clin Exp Allergy 2014; 44:620-30. [DOI: 10.1111/cea.12296] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- I. H. Heijink
- Department of Pathology and Medical Biology; Experimental Pulmonology and Inflammation Research; University Medical Center Groningen; University of Groningen; Groningen the Netherlands
- Department of Pulmonology; University Medical Center Groningen; University of Groningen; Groningen the Netherlands
- GRIAC Research Institute; University Medical Center Groningen; University of Groningen; Groningen the Netherlands
| | - M. C. Nawijn
- Department of Pathology and Medical Biology; Experimental Pulmonology and Inflammation Research; University Medical Center Groningen; University of Groningen; Groningen the Netherlands
- GRIAC Research Institute; University Medical Center Groningen; University of Groningen; Groningen the Netherlands
| | - T.-L. Hackett
- Centre for Heart Lung Innovation; St Paul's Hospital; University of British Columbia; Vancouver BC Canada
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15
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Poole A, Urbanek C, Eng C, Schageman J, Jacobson S, O'Connor BP, Galanter JM, Gignoux CR, Roth LA, Kumar R, Lutz S, Liu AH, Fingerlin TE, Setterquist RA, Burchard EG, Rodriguez-Santana J, Seibold MA. Dissecting childhood asthma with nasal transcriptomics distinguishes subphenotypes of disease. J Allergy Clin Immunol 2014; 133:670-8.e12. [PMID: 24495433 PMCID: PMC4043390 DOI: 10.1016/j.jaci.2013.11.025] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/07/2013] [Accepted: 11/20/2013] [Indexed: 10/25/2022]
Abstract
BACKGROUND Bronchial airway expression profiling has identified inflammatory subphenotypes of asthma, but the invasiveness of this technique has limited its application to childhood asthma. OBJECTIVES We sought to determine whether the nasal transcriptome can proxy expression changes in the lung airway transcriptome in asthmatic patients. We also sought to determine whether the nasal transcriptome can distinguish subphenotypes of asthma. METHODS Whole-transcriptome RNA sequencing was performed on nasal airway brushings from 10 control subjects and 10 asthmatic subjects, which were compared with established bronchial and small-airway transcriptomes. Targeted RNA sequencing nasal expression analysis was used to profile 105 genes in 50 asthmatic subjects and 50 control subjects for differential expression and clustering analyses. RESULTS We found 90.2% overlap in expressed genes and strong correlation in gene expression (ρ = .87) between the nasal and bronchial transcriptomes. Previously observed asthmatic bronchial differential expression was strongly correlated with asthmatic nasal differential expression (ρ = 0.77, P = 5.6 × 10(-9)). Clustering analysis identified TH2-high and TH2-low subjects differentiated by expression of 70 genes, including IL13, IL5, periostin (POSTN), calcium-activated chloride channel regulator 1 (CLCA1), and serpin peptidase inhibitor, clade B (SERPINB2). TH2-high subjects were more likely to have atopy (odds ratio, 10.3; P = 3.5 × 10(-6)), atopic asthma (odds ratio, 32.6; P = 6.9 × 10(-7)), high blood eosinophil counts (odds ratio, 9.1; P = 2.6 × 10(-6)), and rhinitis (odds ratio, 8.3; P = 4.1 × 10(-6)) compared with TH2-low subjects. Nasal IL13 expression levels were 3.9-fold higher in asthmatic participants who experienced an asthma exacerbation in the past year (P = .01). Several differentially expressed nasal genes were specific to asthma and independent of atopic status. CONCLUSION Nasal airway gene expression profiles largely recapitulate expression profiles in the lung airways. Nasal expression profiling can be used to identify subjects with IL13-driven asthma and a TH2-skewed systemic immune response.
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Affiliation(s)
- Alex Poole
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colo
| | - Cydney Urbanek
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colo
| | - Celeste Eng
- Department of Medicine, University of California-San Francisco, San Francisco, Calif
| | | | - Sean Jacobson
- Departments of Epidemiology and Biostatistics, Colorado School of Public Health, Aurora, Colo
| | - Brian P O'Connor
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colo; Integrated Department of Immunology, National Jewish Health and the University of Colorado-Denver, Denver, Colo
| | - Joshua M Galanter
- Department of Medicine, University of California-San Francisco, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, Calif
| | - Christopher R Gignoux
- Department of Medicine, University of California-San Francisco, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, Calif
| | - Lindsey A Roth
- Department of Medicine, University of California-San Francisco, San Francisco, Calif
| | - Rajesh Kumar
- Ann and Robert H. Lurie Children's Hospital of Chicago and the Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | - Sharon Lutz
- Departments of Epidemiology and Biostatistics, Colorado School of Public Health, Aurora, Colo
| | - Andrew H Liu
- Department of Pediatrics, National Jewish Health, Denver, Colo
| | - Tasha E Fingerlin
- Departments of Epidemiology and Biostatistics, Colorado School of Public Health, Aurora, Colo
| | | | - Esteban G Burchard
- Department of Medicine, University of California-San Francisco, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California-San Francisco, San Francisco, Calif
| | | | - Max A Seibold
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, Colo; Department of Pediatrics, National Jewish Health, Denver, Colo; Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado-Denver, Denver, Colo.
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16
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Wain LV, Odenthal-Hesse L, Abujaber R, Sayers I, Beardsmore C, Gaillard EA, Chappell S, Dogaru CM, McKeever T, Guetta-Baranes T, Kalsheker N, Kuehni CE, Hall IP, Tobin MD, Hollox EJ. Copy number variation of the beta-defensin genes in europeans: no supporting evidence for association with lung function, chronic obstructive pulmonary disease or asthma. PLoS One 2014; 9:e84192. [PMID: 24404154 PMCID: PMC3880289 DOI: 10.1371/journal.pone.0084192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/13/2013] [Indexed: 12/23/2022] Open
Abstract
Lung function measures are heritable, predict mortality and are relevant in diagnosis of chronic obstructive pulmonary disease (COPD). COPD and asthma are diseases of the airways with major public health impacts and each have a heritable component. Genome-wide association studies of SNPs have revealed novel genetic associations with both diseases but only account for a small proportion of the heritability. Complex copy number variation may account for some of the missing heritability. A well-characterised genomic region of complex copy number variation contains beta-defensin genes (DEFB103, DEFB104 and DEFB4), which have a role in the innate immune response. Previous studies have implicated these and related genes as being associated with asthma or COPD. We hypothesised that copy number variation of these genes may play a role in lung function in the general population and in COPD and asthma risk. We undertook copy number typing of this locus in 1149 adult and 689 children using a paralogue ratio test and investigated association with COPD, asthma and lung function. Replication of findings was assessed in a larger independent sample of COPD cases and smoking controls. We found evidence for an association of beta-defensin copy number with COPD in the adult cohort (OR = 1.4, 95%CI:1.02-1.92, P = 0.039) but this finding, and findings from a previous study, were not replicated in a larger follow-up sample(OR = 0.89, 95%CI:0.72-1.07, P = 0.217). No robust evidence of association with asthma in children was observed. We found no evidence for association between beta-defensin copy number and lung function in the general populations. Our findings suggest that previous reports of association of beta-defensin copy number with COPD should be viewed with caution. Suboptimal measurement of copy number can lead to spurious associations. Further beta-defensin copy number measurement in larger sample sizes of COPD cases and children with asthma are needed.
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Affiliation(s)
- Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | | | - Razan Abujaber
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Ian Sayers
- Division of Respiratory Medicine, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Caroline Beardsmore
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
- Institute for Lung Health, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Erol A. Gaillard
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
- Institute for Lung Health, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Sally Chappell
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Cristian M. Dogaru
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Tricia McKeever
- School of Community Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - Noor Kalsheker
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Claudia E. Kuehni
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Ian P. Hall
- Division of Respiratory Medicine, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Department of Genetics, University of Leicester, Leicester, United Kingdom
- Institute for Lung Health, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Edward J. Hollox
- Department of Genetics, University of Leicester, Leicester, United Kingdom
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17
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Leung TF, Ko FWS, Sy HY, Tsui SKW, Wong GWK. Differences in asthma genetics between Chinese and other populations. J Allergy Clin Immunol 2013; 133:42-8. [PMID: 24188974 DOI: 10.1016/j.jaci.2013.09.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 01/14/2023]
Abstract
Asthma is caused by complex gene-gene and gene-environment interactions. Most asthma genes are not replicable across populations, which is possibly because of differences in the epidemiology of these genes. Our case-control association and next-generation sequencing studies revealed substantial discrepancies in the frequencies of single nucleotide polymorphisms (SNPs) and haplotype blocks for asthma genes between Chinese and other populations. The minor allele frequencies for nearly half of our studied SNPs differed by 0.2 or greater between southern Chinese subjects in Hong Kong and European white populations, African populations, or both. Because genome-wide association studies for asthma have not been performed in Chinese subjects, we cannot tell whether the genomic findings of recent consortium-based genome-wide association studies are applicable to our population. In addition, our group performed Roche 454 pyrosequencing on a 100-kb area spanning each of 10 asthma loci in 24 healthy Hong Kong children. For the 17q21 locus, there was substantial variation in the haplotype structures that were constructed from 224 common SNPs among Hong Kong subjects and 6 ethnic groups under the 1000 Genomes Project. Sixteen mostly small haplotype blocks were formed in Hong Kong, whereas 6 haplotype blocks were identified in Han Chinese in Beijing and central European subjects and 11 and 19 blocks were identified in Puerto Rican and Yoruba African subjects. In conclusion, differences in allele frequencies of asthma genes and haplotype structures of asthma loci are found between Chinese subjects and other ethnic groups. These sequence variations must be considered during the selection of tagging SNPs for replicating genetic associations between populations.
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Affiliation(s)
- Ting F Leung
- Department of Pediatrics, Chinese University of Hong Kong, Hong Kong, China
| | - Fanny W S Ko
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hong Kong, China
| | - Hing Y Sy
- Department of Pediatrics, Chinese University of Hong Kong, Hong Kong, China
| | - Stephen K W Tsui
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Gary W K Wong
- Department of Pediatrics, Chinese University of Hong Kong, Hong Kong, China.
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18
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Abstract
PURPOSE OF REVIEW Most asthma starts early in life. Defining phenotypes of asthma at this age is difficult as many preschool children have asthma-like respiratory symptoms. This review discusses progress in defining early wheezing phenotypes and describes genetic factors associated with the age of onset of asthma. RECENT FINDINGS Latent class analyses confirmed transient and persistent wheezing phenotypes, and identified a novel intermediate-onset wheezing phenotype that was strongly associated with atopy and asthma at age 8 years. However, no single cross-sectional or longitudinal definition of respiratory symptoms in childhood strongly predicts asthma later in life. Genome-wide association (GWA) studies have identified a locus on chromosome 17q12-21 (encoding ORMDL3 and GSDMB) as a risk factor for predominantly childhood-onset asthma, but not for atopy, and overall not for adult-onset asthma. Other loci found by GWA studies appear to increase asthma risk both in children and adults. Atopy genes do not explain early-onset asthma. SUMMARY Although most asthma starts early in life, no valid test is able to identify asthma at that age period. GWA studies have provided more insight into the unique and common genetic origins of adult-onset and childhood-onset asthma. The 17q12-21 locus is predominantly associated with childhood-onset asthma.
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19
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Apter AJ. Advances in adult asthma diagnosis and treatment in 2012: potential therapeutics and gene-environment interactions. J Allergy Clin Immunol 2013; 131:47-54. [PMID: 23265695 DOI: 10.1016/j.jaci.2012.11.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 11/12/2012] [Indexed: 01/10/2023]
Abstract
In the Journal of Allergy and Clinical Immunology in 2012, research reports related to asthma in adults clustered around mechanisms of disease, with a special focus on their potential for informing new therapies. There was also consideration of the effect of the environment on health from pollution, climate change, and epigenetic influences, underlining the importance of understanding gene-environment interactions in the pathogenesis of asthma and response to treatment.
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Affiliation(s)
- Andrea J Apter
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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20
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Giavina-Bianchi P, Agondi RC, Kalil J. Asthma studies should be phenotype specific. J Allergy Clin Immunol 2013; 131:1261-2. [PMID: 23453136 DOI: 10.1016/j.jaci.2013.01.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 01/31/2013] [Indexed: 10/27/2022]
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21
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Himes BE, Sheppard K, Berndt A, Leme AS, Myers RA, Gignoux CR, Levin AM, Gauderman WJ, Yang JJ, Mathias RA, Romieu I, Torgerson DG, Roth LA, Huntsman S, Eng C, Klanderman B, Ziniti J, Senter-Sylvia J, Szefler SJ, Lemanske RF, Zeiger RS, Strunk RC, Martinez FD, Boushey H, Chinchilli VM, Israel E, Mauger D, Koppelman GH, Postma DS, Nieuwenhuis MAE, Vonk JM, Lima JJ, Irvin CG, Peters SP, Kubo M, Tamari M, Nakamura Y, Litonjua AA, Tantisira KG, Raby BA, Bleecker ER, Meyers DA, London SJ, Barnes KC, Gilliland FD, Williams LK, Burchard EG, Nicolae DL, Ober C, DeMeo DL, Silverman EK, Paigen B, Churchill G, Shapiro SD, Weiss ST. Integration of mouse and human genome-wide association data identifies KCNIP4 as an asthma gene. PLoS One 2013; 8:e56179. [PMID: 23457522 PMCID: PMC3572953 DOI: 10.1371/journal.pone.0056179] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/07/2013] [Indexed: 12/29/2022] Open
Abstract
Asthma is a common chronic respiratory disease characterized by airway hyperresponsiveness (AHR). The genetics of asthma have been widely studied in mouse and human, and homologous genomic regions have been associated with mouse AHR and human asthma-related phenotypes. Our goal was to identify asthma-related genes by integrating AHR associations in mouse with human genome-wide association study (GWAS) data. We used Efficient Mixed Model Association (EMMA) analysis to conduct a GWAS of baseline AHR measures from males and females of 31 mouse strains. Genes near or containing SNPs with EMMA p-values <0.001 were selected for further study in human GWAS. The results of the previously reported EVE consortium asthma GWAS meta-analysis consisting of 12,958 diverse North American subjects from 9 study centers were used to select a subset of homologous genes with evidence of association with asthma in humans. Following validation attempts in three human asthma GWAS (i.e., Sepracor/LOCCS/LODO/Illumina, GABRIEL, DAG) and two human AHR GWAS (i.e., SHARP, DAG), the Kv channel interacting protein 4 (KCNIP4) gene was identified as nominally associated with both asthma and AHR at a gene- and SNP-level. In EVE, the smallest KCNIP4 association was at rs6833065 (P-value 2.9e-04), while the strongest associations for Sepracor/LOCCS/LODO/Illumina, GABRIEL, DAG were 1.5e-03, 1.0e-03, 3.1e-03 at rs7664617, rs4697177, rs4696975, respectively. At a SNP level, the strongest association across all asthma GWAS was at rs4697177 (P-value 1.1e-04). The smallest P-values for association with AHR were 2.3e-03 at rs11947661 in SHARP and 2.1e-03 at rs402802 in DAG. Functional studies are required to validate the potential involvement of KCNIP4 in modulating asthma susceptibility and/or AHR. Our results suggest that a useful approach to identify genes associated with human asthma is to leverage mouse AHR association data.
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Affiliation(s)
- Blanca E Himes
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
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22
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Abstract
Last year's "Advances in pediatric asthma: moving forward" concluded the following: "Now is also the time to utilize information recorded in electronic medical records to develop innovative disease management plans that will track asthma over time and enable timely decisions on interventions in order to maintain control that can lead to disease remission and prevention." This year's summary will focus on recent advances in pediatric asthma on modifying disease activity, preventing asthma exacerbations, managing severe asthma, and risk factors for predicting and managing early asthma, as indicated in Journal of Allergy and Clinical Immunology publications in 2012. Recent reports continue to shed light on methods to improve asthma management through steps to assess disease activity, tools to standardize outcome measures in asthma, genetic markers that predict risk for asthma and appropriate treatment, and interventions that alter the early presentation of asthma to prevent progression. We are well on our way to creating a pathway around wellness in asthma care and also to use new tools to predict the risk for asthma and take steps to not only prevent asthma exacerbations but also to prevent the early manifestations of the disease and thus prevent its evolution to severe asthma.
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Affiliation(s)
- Stanley J Szefler
- Division of Pediatric Clinical Pharmacology, Department of Pediatrics, National Jewish Health, Denver, CO 80206, USA.
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23
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Nguyen EA, Burchard EG. Asthma Research for All of the United States. PEDIATRIC ALLERGY IMMUNOLOGY AND PULMONOLOGY 2012; 25:128-131. [PMID: 22970422 DOI: 10.1089/ped.2012.0173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/12/2012] [Indexed: 01/08/2023]
Abstract
Asthma disproportionally affects different ethnic/racial groups, with Puerto Ricans and African Americans suffering the highest asthma prevalence and morbidity, Mexicans the lowest, and non-Hispanic whites in between. Genome-wide association studies of asthma have found both shared and race/ethnic-specific genetic risks factors for asthma. However, the majority of genetic asthma research is performed in populations of European descent, which limits the benefits of genetic research to European populations. It is important to biomedical and clinical research to include more diverse and underrepresented populations. The rich genetic diversity of all populations can be leveraged to scientific advantage. For example, admixture mapping provides a more powerful approach than traditional genome-wide allelic association studies in discovering genetic associations for complex diseases. By being more inclusive we can achieve a better understanding of the genetics of asthma, address health disparities, and ensure that scientific advances will benefit populations worldwide.
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