1
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Weathington N, O’Brien ME, Radder J, Whisenant TC, Bleecker ER, Busse WW, Erzurum SC, Gaston B, Hastie AT, Jarjour NN, Meyers DA, Milosevic J, Moore WC, Tedrow JR, Trudeau JB, Wong HP, Wu W, Kaminski N, Wenzel SE, Modena BD. BAL Cell Gene Expression in Severe Asthma Reveals Mechanisms of Severe Disease and Influences of Medications. Am J Respir Crit Care Med 2019; 200:837-856. [PMID: 31161938 PMCID: PMC6812436 DOI: 10.1164/rccm.201811-2221oc] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/03/2019] [Indexed: 01/16/2023] Open
Abstract
Rationale: Gene expression of BAL cells, which samples the cellular milieu within the lower respiratory tract, has not been well studied in severe asthma.Objectives: To identify new biomolecular mechanisms underlying severe asthma by an unbiased, detailed interrogation of global gene expression.Methods: BAL cell expression was profiled in 154 asthma and control subjects. Of these participants, 100 had accompanying airway epithelial cell gene expression. BAL cell expression profiles were related to participant (age, sex, race, and medication) and sample traits (cell proportions), and then severity-related gene expression determined by correlating transcripts and coexpression networks to lung function, emergency department visits or hospitalizations in the last year, medication use, and quality-of-life scores.Measurements and Main Results: Age, sex, race, cell proportions, and medications strongly influenced BAL cell gene expression, but leading severity-related genes could be determined by carefully identifying and accounting for these influences. A BAL cell expression network enriched for cAMP signaling components most differentiated subjects with severe asthma from other subjects. Subsequently, an in vitro cellular model showed this phenomenon was likely caused by a robust upregulation in cAMP-related expression in nonsevere and β-agonist-naive subjects given a β-agonist before cell collection. Interestingly, ELISAs performed on BAL lysates showed protein levels may partly disagree with expression changes.Conclusions: Gene expression in BAL cells is influenced by factors seldomly considered. Notably, β-agonist exposure likely had a strong and immediate impact on cellular gene expression, which may not translate to important disease mechanisms or necessarily match protein levels. Leading severity-related genes were discovered in an unbiased, system-wide analysis, revealing new targets that map to asthma susceptibility loci.
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Affiliation(s)
- Nathaniel Weathington
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Michael E. O’Brien
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Josiah Radder
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Thomas C. Whisenant
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California
| | - Eugene R. Bleecker
- Division of Genetics, Genomics and Precision Medicine, University of Arizona, Tucson, Arizona
| | - William W. Busse
- Division of Allergy, Pulmonary, and Critical Care Medicine, University of Wisconsin, Madison, Wisconsin
| | - Serpil C. Erzurum
- Lerner Research Institute, Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - Benjamin Gaston
- Division of Pediatric Pulmonary, Allergy and Immunology, Case Western Reserve University and Rainbow Babies Children’s Hospital, Cleveland, Ohio
| | - Annette T. Hastie
- Section on Pulmonary, Critical Care, Allergy and Immunologic Diseases, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Nizar N. Jarjour
- Division of Allergy, Pulmonary, and Critical Care Medicine, University of Wisconsin, Madison, Wisconsin
| | - Deborah A. Meyers
- Division of Genetics, Genomics and Precision Medicine, University of Arizona, Tucson, Arizona
| | - Jadranka Milosevic
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Wendy C. Moore
- Section on Pulmonary, Critical Care, Allergy and Immunologic Diseases, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - John R. Tedrow
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - John B. Trudeau
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Hesper P. Wong
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Wei Wu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Sally E. Wenzel
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania; and
| | - Brian D. Modena
- Division of Allergy, National Jewish Hospital, Denver, Colorado
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2
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Bragina EY, Goncharova IA, Garaeva AF, Nemerov EV, Babovskaya AA, Karpov AB, Semenova YV, Zhalsanova IZ, Gomboeva DE, Saik OV, Zolotareva OI, Ivanisenko VA, Dosenko VE, Hofestaedt R, Freidin MB. Molecular Relationships between Bronchial Asthma and Hypertension as Comorbid Diseases. J Integr Bioinform 2018; 15:/j/jib.ahead-of-print/jib-2018-0052/jib-2018-0052.xml. [PMID: 30530896 PMCID: PMC6348747 DOI: 10.1515/jib-2018-0052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/13/2018] [Indexed: 01/14/2023] Open
Abstract
Comorbidity, a co-incidence of several disorders in an individual, is a common phenomenon. Their development is governed by multiple factors, including genetic variation. The current study was set up to look at associations between isolated and comorbid diseases of bronchial asthma and hypertension, on one hand, and single nucleotide polymorphisms associated with regulation of gene expression (eQTL), on the other hand. A total of 96 eQTL SNPs were genotyped in 587 Russian individuals. Bronchial asthma alone was found to be associated with rs1927914 (TLR4), rs1928298 (intergenic variant), and rs1980616 (SERPINA1); hypertension alone was found to be associated with rs11065987 (intergenic variant); rs2284033 (IL2RB), rs11191582 (NT5C2), and rs11669386 (CARD8); comorbidity between asthma and hypertension was found to be associated with rs1010461 (ANG/RNASE4), rs7038716, rs7026297 (LOC105376244), rs7025144 (intergenic variant), and rs2022318 (intergenic variant). The results suggest that genetic background of comorbidity of asthma and hypertension is different from genetic backgrounds of both diseases manifesting isolated.
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Affiliation(s)
- Elena Yu Bragina
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | | | - Anna F Garaeva
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia.,Siberian State Medical University, Tomsk, Russia
| | | | | | - Andrey B Karpov
- Seversk Biophysical Research Centre of the Federal Medico-Biological Agency, Seversk, Russia
| | - Yulia V Semenova
- Seversk Clinical Hospital, Siberian Federal Research and Clinical Centre of the Federal Medico-Biological Agency, Seversk, Russia
| | | | | | - Olga V Saik
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga I Zolotareva
- Bielefeld University, Bioinformatics/Medical Informatics Department, Bielefeld, Germany.,International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes" and Genome Informatics, Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Vladimir A Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Victor E Dosenko
- Bogomoletz Institute of Physiology, National Academy of Science, Kiev, Ukraine
| | - Ralf Hofestaedt
- Bielefeld University, Bioinformatics/Medical Informatics Department, Bielefeld, Germany
| | - Maxim B Freidin
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
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3
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Cornejo-García JA, Perkins JR, Jurado-Escobar R, García-Martín E, Agúndez JA, Viguera E, Pérez-Sánchez N, Blanca-López N. Pharmacogenomics of Prostaglandin and Leukotriene Receptors. Front Pharmacol 2016; 7:316. [PMID: 27708579 PMCID: PMC5030812 DOI: 10.3389/fphar.2016.00316] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 09/02/2016] [Indexed: 01/15/2023] Open
Abstract
Individual genetic background together with environmental effects are thought to be behind many human complex diseases. A number of genetic variants, mainly single nucleotide polymorphisms (SNPs), have been shown to be associated with various pathological and inflammatory conditions, representing potential therapeutic targets. Prostaglandins (PTGs) and leukotrienes (LTs) are eicosanoids derived from arachidonic acid and related polyunsaturated fatty acids that participate in both normal homeostasis and inflammatory conditions. These bioactive lipid mediators are synthesized through two major multistep enzymatic pathways: PTGs by cyclooxygenase and LTs by 5-lipoxygenase. The main physiological effects of PTGs include vasodilation and vascular leakage (PTGE2); mast cell maturation, eosinophil recruitment, and allergic responses (PTGD2); vascular and respiratory smooth muscle contraction (PTGF2), and inhibition of platelet aggregation (PTGI2). LTB4 is mainly involved in neutrophil recruitment, vascular leakage, and epithelial barrier function, whereas cysteinyl LTs (CysLTs) (LTC4, LTD4, and LTE4) induce bronchoconstriction and neutrophil extravasation, and also participate in vascular leakage. PTGs and LTs exert their biological functions by binding to cognate receptors, which belong to the seven transmembrane, G protein-coupled receptor superfamily. SNPs in genes encoding these receptors may influence their functionality and have a role in disease susceptibility and drug treatment response. In this review we summarize SNPs in PTGs and LTs receptors and their relevance in human diseases. We also provide information on gene expression. Finally, we speculate on future directions for this topic.
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Affiliation(s)
- José A Cornejo-García
- Research Laboratory, International Business Information Management Association (IBIMA)-Regional University Hospital of Malaga, University of Málaga (UMA)Malaga, Spain; Allergy Unit, International Business Information Management Association (IBIMA)-Regional University Hospital of Malaga, University of Málaga (UMA)Malaga, Spain
| | - James R Perkins
- Research Laboratory, International Business Information Management Association (IBIMA)-Regional University Hospital of Malaga, University of Málaga (UMA) Malaga, Spain
| | - Raquel Jurado-Escobar
- Research Laboratory, International Business Information Management Association (IBIMA)-Regional University Hospital of Malaga, University of Málaga (UMA) Malaga, Spain
| | | | - José A Agúndez
- Department of Pharmacology, University of Extremadura Caceres, Spain
| | - Enrique Viguera
- Genetics Unit, Department of Cell Biology, Genetics and Physiology, Faculty of Sciences, University of Málaga Malaga, Spain
| | - Natalia Pérez-Sánchez
- Allergy Unit, International Business Information Management Association (IBIMA)-Regional University Hospital of Malaga, University of Málaga (UMA) Malaga, Spain
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4
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Costa GNO, Dudbridge F, Fiaccone RL, da Silva TM, Conceição JS, Strina A, Figueiredo CA, Magalhães WCS, Rodrigues MR, Gouveia MH, Kehdy FSG, Horimoto ARVR, Horta B, Burchard EG, Pino-Yanes M, Del Rio Navarro B, Romieu I, Hancock DB, London S, Lima-Costa MF, Pereira AC, Tarazona E, Rodrigues LC, Barreto ML. A genome-wide association study of asthma symptoms in Latin American children. BMC Genet 2015; 16:141. [PMID: 26635092 PMCID: PMC4669662 DOI: 10.1186/s12863-015-0296-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 11/17/2015] [Indexed: 01/14/2023] Open
Abstract
Background Asthma is a chronic disease of the airways and, despite the advances in the knowledge of associated genetic regions in recent years, their mechanisms have yet to be explored. Several genome-wide association studies have been carried out in recent years, but none of these have involved Latin American populations with a high level of miscegenation, as is seen in the Brazilian population. Methods 1246 children were recruited from a longitudinal cohort study in Salvador, Brazil. Asthma symptoms were identified in accordance with an International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire. Following quality control, 1 877 526 autosomal SNPs were tested for association with childhood asthma symptoms by logistic regression using an additive genetic model. We complemented the analysis with an estimate of the phenotypic variance explained by common genetic variants. Replications were investigated in independent Mexican and US Latino samples. Results Two chromosomal regions reached genome-wide significance level for childhood asthma symptoms: the 14q11 region flanking the DAD1 and OXA1L genes (rs1999071, MAF 0.32, OR 1.78, 95 % CI 1.45–2.18, p-value 2.83 × 10−8) and 15q22 region flanking the FOXB1 gene (rs10519031, MAF 0.04, OR 3.0, 95 % CI 2.02–4.49, p-value 6.68 × 10−8 and rs8029377, MAF 0.03, OR 2.49, 95 % CI 1.76–3.53, p-value 2.45 × 10−7). eQTL analysis suggests that rs1999071 regulates the expression of OXA1L gene. However, the original findings were not replicated in the Mexican or US Latino samples. Conclusions We conclude that the 14q11 and 15q22 regions may be associated with asthma symptoms in childhood. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0296-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gustavo N O Costa
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil.
| | - Frank Dudbridge
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
| | | | - Thiago M da Silva
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil.
| | | | - Agostino Strina
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil.
| | - Camila A Figueiredo
- Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil.
| | - Wagner C S Magalhães
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Maira R Rodrigues
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Mateus H Gouveia
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Fernanda S G Kehdy
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | | | - Bernardo Horta
- Programa de Pós Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas, Brazil.
| | | | - Maria Pino-Yanes
- Department of Medicine, University of California, San Francisco, USA.
| | - Blanca Del Rio Navarro
- Department of Health and Human Services, Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
| | | | - Dana B Hancock
- Behavioral and Urban Health Program, Research Triangle Institute (RTI) International, Research Triangle Park, North Carolina, USA.
| | - Stephanie London
- Department of Health and Human Services, Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
| | | | - Alexandre C Pereira
- Instituto de Pesquisas Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil.
| | - Eduardo Tarazona
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Laura C Rodrigues
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Mauricio L Barreto
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, Salvador, Brazil. .,Centro de Pesquisa Gonçalo Muniz, Fundação Osvaldo Cruz, Salvador, Brazil.
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5
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Pino-Yanes M, Gignoux CR, Galanter JM, Levin AM, Campbell CD, Eng C, Huntsman S, Nishimura KK, Gourraud PA, Mohajeri K, O'Roak BJ, Hu D, Mathias RA, Nguyen EA, Roth LA, Padhukasahasram B, Moreno-Estrada A, Sandoval K, Winkler CA, Lurmann F, Davis A, Farber HJ, Meade K, Avila PC, Serebrisky D, Chapela R, Ford JG, Lenoir MA, Thyne SM, Brigino-Buenaventura E, Borrell LN, Rodriguez-Cintron W, Sen S, Kumar R, Rodriguez-Santana JR, Bustamante CD, Martinez FD, Raby BA, Weiss ST, Nicolae DL, Ober C, Meyers DA, Bleecker ER, Mack SJ, Hernandez RD, Eichler EE, Barnes KC, Williams LK, Torgerson DG, Burchard EG. Genome-wide association study and admixture mapping reveal new loci associated with total IgE levels in Latinos. J Allergy Clin Immunol 2014; 135:1502-10. [PMID: 25488688 DOI: 10.1016/j.jaci.2014.10.033] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 09/06/2014] [Accepted: 10/15/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND IgE is a key mediator of allergic inflammation, and its levels are frequently increased in patients with allergic disorders. OBJECTIVE We sought to identify genetic variants associated with IgE levels in Latinos. METHODS We performed a genome-wide association study and admixture mapping of total IgE levels in 3334 Latinos from the Genes-environments & Admixture in Latino Americans (GALA II) study. Replication was evaluated in 454 Latinos, 1564 European Americans, and 3187 African Americans from independent studies. RESULTS We confirmed associations of 6 genes identified by means of previous genome-wide association studies and identified a novel genome-wide significant association of a polymorphism in the zinc finger protein 365 gene (ZNF365) with total IgE levels (rs200076616, P = 2.3 × 10(-8)). We next identified 4 admixture mapping peaks (6p21.32-p22.1, 13p22-31, 14q23.2, and 22q13.1) at which local African, European, and/or Native American ancestry was significantly associated with IgE levels. The most significant peak was 6p21.32-p22.1, where Native American ancestry was associated with lower IgE levels (P = 4.95 × 10(-8)). All but 22q13.1 were replicated in an independent sample of Latinos, and 2 of the peaks were replicated in African Americans (6p21.32-p22.1 and 14q23.2). Fine mapping of 6p21.32-p22.1 identified 6 genome-wide significant single nucleotide polymorphisms in Latinos, 2 of which replicated in European Americans. Another single nucleotide polymorphism was peak-wide significant within 14q23.2 in African Americans (rs1741099, P = 3.7 × 10(-6)) and replicated in non-African American samples (P = .011). CONCLUSION We confirmed genetic associations at 6 genes and identified novel associations within ZNF365, HLA-DQA1, and 14q23.2. Our results highlight the importance of studying diverse multiethnic populations to uncover novel loci associated with total IgE levels.
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Affiliation(s)
- Maria Pino-Yanes
- Department of Medicine, University of California, San Francisco, Calif; CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| | - Christopher R Gignoux
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif; Department of Genetics, Stanford University, Palo Alto, Calif
| | - Joshua M Galanter
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Mich
| | | | - Celeste Eng
- Department of Medicine, University of California, San Francisco, Calif
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, Calif
| | | | | | - Kiana Mohajeri
- Department of Genome Sciences, University of Washington, Seattle, Wash
| | - Brian J O'Roak
- Department of Genome Sciences, University of Washington, Seattle, Wash; Molecular & Medical Genetics Department, Oregon Health and Science University, Portland, Ore
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, Calif
| | - Rasika A Mathias
- Division of Allergy & Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Md
| | | | - Lindsey A Roth
- Department of Medicine, University of California, San Francisco, Calif
| | - Badri Padhukasahasram
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, Mich
| | | | - Karla Sandoval
- Department of Genetics, Stanford University, Palo Alto, Calif
| | - Cheryl A Winkler
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Leidos Biomedical, Frederick National Laboratory for Cancer Research, Frederick, Md
| | | | - Adam Davis
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, Tex
| | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, Calif
| | - Pedro C Avila
- Department of Medicine, Northwestern University, Chicago, Ill
| | | | - Rocio Chapela
- Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, Mexico
| | - Jean G Ford
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md
| | | | - Shannon M Thyne
- Department of Pediatrics, University of California San Francisco, San Francisco General Hospital, San Francisco, Calif
| | | | - Luisa N Borrell
- Department of Health Sciences, Graduate Program in Public Health, City University of New York, Bronx, NY
| | | | - Saunak Sen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, Calif
| | - Rajesh Kumar
- Children's Memorial Hospital and the Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | | | | | - Fernando D Martinez
- Arizona Respiratory Center, University of Arizona, Tucson, Ariz; BIO5 Institute, University of Arizona, Tucson, Ariz
| | - Benjamin A Raby
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Dan L Nicolae
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Deborah A Meyers
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
| | - Eugene R Bleecker
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
| | - Steven J Mack
- Children's Hospital Oakland Research Institute, Oakland, Calif
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, Wash; Howard Hughes Medical Institute, Seattle, Wash
| | - Kathleen C Barnes
- Division of Allergy & Clinical Immunology, 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
| | - Dara G Torgerson
- Department of Medicine, University of California, San Francisco, Calif
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
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6
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Jamrozik EF, Warrington N, McClenaghan J, Hui J, Musk AW, James A, Beilby JP, Hansen J, DE Klerk NH, Palmer LJ. Functional haplotypes in the PTGDR gene fail to associate with asthma in two Australian populations. Respirology 2011; 16:359-66. [PMID: 21199159 DOI: 10.1111/j.1440-1843.2010.01917.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND OBJECTIVE Haplotypes in the promoter region of the prostanoid DP receptor (PTGDR) gene have been shown to functionally influence gene transcription and to be associated with asthma in two previous case-control studies in Caucasians. This study tested the association of PTGDR haplotypes with asthma phenotypes in two large Caucasian-Australian populations. These results were incorporated in a meta-analysis with previously published data to determine the overall role for these haplotypes in the risk of asthma. METHODS Three PTGDR promoter-region single nucleotide polymorphisms (SNP) were genotyped in 368 individuals from the Western Australian Twin Child Health study and 2988 individuals from the Busselton Health Study. Logistic regression and transition disequilibrium tests were used to assess whether SNP genotypes and three SNP haplotypes were associated with doctor-diagnosed asthma or intermediate quantitative traits. Longitudinal data from the Busselton Health Study were used to examine whether PTGDR influences changes in lung function over time. Meta-analysis incorporated the findings of this study with those of two previous studies in Caucasian populations. RESULTS Cross-sectional associations between PTGDR haplotypes and asthma phenotypes were non-significant (P > 0.05) in both populations. Longitudinal analyses of PTGDR and lung function were also non-significant. Meta-analysis, however, suggested that haplotype TCT was significantly associated with decreased risk of asthma (OR = 0.76; P = 0.02) while haplotype CCC was not significantly associated with asthma (OR = 1.30; P = 0.07). CONCLUSIONS These results suggest that despite the non-significant findings in the present study populations, PTGDR promoter haplotypes may account for a small but significant proportion of the risk of asthma in Caucasian populations.
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Affiliation(s)
- Euzebiusz F Jamrozik
- Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, West Perth, Western Australia, Australia.
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7
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Abstract
The discovery of immunoglobulin E (IgE) was a breakthrough in the field of Allergy and Immunology. Our understanding of mechanisms of allergic reactions and the role of IgE in these disorders has paralleled to the discovery of treatment modalities for patients with allergy. Apart from allergic diseases, IgE is involved in pathogenesis of other disorders. Much controversy exists about the control of total IgE (tIgE) levels and allergen-specific IgE (sIgE) profiles in allergic individuals. This review aims at giving a comprehensive overview of IgE molecule and discussing the issues related to its importance in clinical setting.
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Affiliation(s)
- M Amarasekera
- Department of Physiology, Faculty of Medicine, University of Kelaniya, Ragama 11010, Sri Lanka
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8
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Sjakste T, Trapina I, Rumba-Rozenfelde I, Lunin R, Sugoka O, Sjakste N. Identification of a novel candidate locus for juvenile idiopathic arthritis at 14q13.2 in the Latvian population by association analysis with microsatellite markers. DNA Cell Biol 2010; 29:543-51. [PMID: 20136554 DOI: 10.1089/dna.2009.0970] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
To identify novel juvenile idiopathic arthritis (JIA) susceptibility loci, a 270 kb genomic region encompassing FAM177A1, KIAA0391, and PSMA6 genes was genotyped in 97 oligoarthritis (JIoA) and 50 polyarthritis (JIpA) patients and 230 individuals without autoimmune disorders by five microsatellites (MS) previously described as HSMS markers of the 14q13.2 region. Direct sequencing revealed two variable components of the (CAA)(n)(A)(m) motif in HSMS602 marker (FAM177A1 gene). Repeat (AC)(5)AT(AC)(n) of the HSMS701 (KIAA0391 gene) was variable in the Latvian population only in its downstream part. Allele (AC)(5)AT(AC)(15) of HSMS701 was found to be strongly associated with JIA (p = 4.91 x 10(-5), odds ratio [OR] = 18.87) and modestly associated with JIpA (p = 1.64 x 10(-3), OR = 15.69). Alleles (AC)(5)AT(AC)(18) of HSMS701 and (TG)(10) of HSMS702 appear to be JIA and JIoA risk factors (p = 1.09 x 10(-3), OR = 2.64 and p = 2.00 x 10(-3), OR = 7.67, respectively), but allele 168 bp of HSMS602 (p = 9.02 x 10(-4), OR = 0.35) appears to be protective. Two heterozygote genotypes (TG)(20/23) of the HSMS006 and (AC)(22/23) of the HSMS801 showed association with JIA (p < 2 x 10(-3)), but homozygote (TG)(19/19) was found to be protective (p = 5.41 x 10(-4), OR = 0.12). Our results define an additional susceptibility locus for JIA at the 14q13.2 genomic region encompassing KIAA0391 and PSMA6 genes.
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Affiliation(s)
- Tatjana Sjakste
- Genomics and Bioinformatics, Institute of Biology, University of Latvia , Salaspils, Latvia
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9
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Saini Y, Greenwood KK, Merrill C, Kim KY, Patial S, Parameswaran N, Harkema JR, LaPres JJ. Acute cobalt-induced lung injury and the role of hypoxia-inducible factor 1alpha in modulating inflammation. Toxicol Sci 2010; 116:673-81. [PMID: 20511350 PMCID: PMC2905409 DOI: 10.1093/toxsci/kfq155] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 05/14/2010] [Indexed: 12/31/2022] Open
Abstract
Air pollution is a critical factor in the development and exacerbation of pulmonary diseases. Ozone, automobile exhaust, cigarette smoke, and metallic dust are among the potentially harmful pollution components that are linked to disease progression. Transition metals, such as cobalt, have been identified at significant levels in air pollution. Cobalt exerts numerous biological effects, including mimicking hypoxia. Similar to hypoxia, cobalt exposure results in the stabilization of hypoxia-inducible factors (HIFs), a family of proteins that regulate the cellular response to oxygen deficit. HIFs also play an important role in innate immunity and inflammatory processes. To characterize the role of HIF1alpha, the most ubiquitously expressed HIF, in the early events during cobalt-induced lung inflammation, an inducible lung-specific HIF1alpha deletion model was employed. Control mice showed classical signs of metal-induced injury following cobalt exposure, including neutrophilic infiltration and induction of Th1 cytokines. In contrast, HIF1alpha-deficient mice exhibited pronounced eosinophil counts in bronchoalveolar lavage fluid and lung tissue complemented with Th2 cytokine induction. The timing of these results suggests that the loss of epithelial-derived HIF1alpha alters the lung's innate immune response and biases the tissue toward a Th2-mediated inflammation.
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Affiliation(s)
- Yogesh Saini
- Department of Biochemistry and Molecular Biology
- Genetics Program
- Center for Integrative Toxicology
| | - Krista K. Greenwood
- Department of Biochemistry and Molecular Biology
- Center for Integrative Toxicology
| | | | - Kyung Y. Kim
- Department of Biochemistry and Molecular Biology
| | | | | | - Jack R. Harkema
- Center for Integrative Toxicology
- Department of Pathobiology and Diagnostic Investigation
| | - John J. LaPres
- Department of Biochemistry and Molecular Biology
- Genetics Program
- Center for Integrative Toxicology
- Cell and Molecular Biology Program
- National Food Safety and Toxicology Center, Michigan State University, East Lansing, Michigan 48824-1319
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10
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Dittrich AM, Meyer HA, Krokowski M, Quarcoo D, Ahrens B, Kube SM, Witzenrath M, Esworthy RS, Chu FF, Hamelmann E. Glutathione peroxidase-2 protects from allergen-induced airway inflammation in mice. Eur Respir J 2009; 35:1148-54. [PMID: 19897562 DOI: 10.1183/09031936.00026108] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The aim of the present study was to identify and validate the biological significance of new genes/proteins involved in the development of allergic airway disease in a murine asthma model. Gene microarrays were used to identify genes with at least a two-fold increase in gene expression in lungs of two separate mouse strains with high and low allergic susceptibility. Validation of mRNA data was obtained by western blotting and immunohistochemistry, followed by functional analysis of one of the identified genes in mice with targeted disruption of specific gene expression. Expression of two antioxidant enzymes, glutathione peroxidase-2 (GPX2) and glutathione S-transferase omega (GSTO) 1-1 was increased in both mouse strains after induction of allergic airway disease and localised in lung epithelial cells. Mice with targeted disruption of the Gpx-2 gene showed significantly enhanced airway inflammation compared to sensitised and challenged wild-type mice. Our data indicate that genes encoding the antioxidants GPX2 and GSTO 1-1 are common inflammatory genes expressed upon induction of allergic airway inflammation, and independently of allergic susceptibility. Furthermore, we provide evidence to illustrate the importance of a single antioxidant enzyme, GPX2, in protection from allergen-induced disease.
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Affiliation(s)
- A M Dittrich
- Dept of Paediatric Pneumology and Immunology, Charité Humboldt University, Germany
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11
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Sanz C, Isidoro-García M, Dávila I, de Pedro MP, Méndez SDA, Padrón J, Ruiz-SanFrancisco A, Lorente F. A new PTGDR promoter polymorphism in a population of children with asthma. Pediatr Allergy Immunol 2009; 20:151-6. [PMID: 18811623 DOI: 10.1111/j.1399-3038.2008.00772.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Recently, functional genetic variants of the PTGDR gene have been associated with asthma. The objective of this work was to study polymorphisms of the promoter region of PTGDR and their haplotype and diplotype combinations in a Spanish population of children with asthma. In this study, 200 Caucasian individuals were included. Asthma was specialist-physician diagnosed according to the ATS criteria. The polymorphisms were analyzed by direct sequencing. In the study, the new polymorphism (-613C > T) in the promoter region of PTGDR was analyzed. The CT genotype was more common in controls (17%) than in patients with asthma (1%) (p-value = 0.0003; OR, 0.057; 95% CI, 0.007-0.441). The CCCT CCCC diplotype (promoter positions -613, -549, -441, and -197) was more frequent in the group of patients with asthma [Fisher's p-value = 0.012; OR, 10.24; 95% CI (1.25-83.68)]; this diplotype is unambiguous. To our knowledge, this is the first study of -613C > T PTGDR polymorphism in patients. This analysis provides more complete information on influence of diplotype combinations of PTGDR polymorphisms in asthma.
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Affiliation(s)
- Catalina Sanz
- Department of Allergy, University of Salamanca, Salamanca, Spain
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12
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Sharma M, Batra J, Mabalirajan U, Sharma S, Nagarkatti R, Aich J, Sharma SK, Niphadkar PV, Ghosh B. A genetic variation in inositol polyphosphate 4 phosphatase a enhances susceptibility to asthma. Am J Respir Crit Care Med 2008; 177:712-9. [PMID: 18187694 DOI: 10.1164/rccm.200705-781oc] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Microarray data from mouse studies have identified a number of genes to be differentially expressed in allergen-sensitized mice lungs. OBJECTIVES Taking leads from these datasets, we attempted to identify novel genes associated with atopic asthma in humans. METHODS We performed family-based genetic association analysis on selected markers within or in proximity of 21 human homologs of genes short-listed from ovalbumin-sensitized mouse studies in the Gene Expression Omnibus database of the National Center for Biotechnology Information. Family-based and case-control studies were undertaken for fine mapping and functional variation analysis of INPP4A (inositol polyphosphate 4 phosphatase type I). Western blot analysis was performed to analyze INPP4A protein stability from human platelets. MEASUREMENTS AND MAIN RESULTS Our genetic association studies of 21 human genes in 171 trios led to the identification of a biallelic repeat (rs3217304) in INPP4A, associated with atopic asthma (P = 0.009). Further studies using additional three single nucleotide polymorphisms (SNPs), +92031A/T, +92344C/T, and +131237C/T, and two microsatellite markers, D2S2311 and D2S2187, revealed significant genetic associations with loci +92031A/T (P = 0.0012) and +92344C/T (P = 0.004). A nonsynonymous SNP, +110832A/G (Thr/Ala), present within a sequence enriched with proline, glutamic acid, serine, and threonine (PEST), in proximity of these two loci, showed a significant association with atopic asthma (P = 0.0006). The association results were also replicated in an independent cohort of 288 patients and 293 control subjects (P = 0.004). PEST score and Western blot analyses indicated a functional role of this SNP in regulating INPP4A protein stability. CONCLUSIONS In our study, INPP4A was identified as a novel asthma candidate gene, whereby the +110832A/G (Thr/Ala) variant affected its stability and was significantly associated with asthma.
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Affiliation(s)
- Mamta Sharma
- Molecular Immunogenetics Laboratory, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India
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13
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Pillai SG, Tang Y, van den Oord E, Klotsman M, Barnes K, Carlsen K, Gerritsen J, Lenney W, Silverman M, Sly P, Sundy J, Tsanakas J, von Berg A, Whyte M, Ortega HG, Anderson WH, Helms PJ. Factor analysis in the Genetics of Asthma International Network family study identifies five major quantitative asthma phenotypes. Clin Exp Allergy 2008; 38:421-9. [PMID: 18177490 DOI: 10.1111/j.1365-2222.2007.02918.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Asthma is a clinically heterogeneous disease caused by a complex interaction between genetic susceptibility and diverse environmental factors. In common with other complex diseases the lack of a standardized scheme to evaluate the phenotypic variability poses challenges in identifying the contribution of genes and environments to disease expression. OBJECTIVE To determine the minimum number of sets of features required to characterize subjects with asthma which will be useful in identifying important genetic and environmental contributors. Methods Probands aged 7-35 years with physician diagnosed asthma and symptomatic siblings were identified in 1022 nuclear families from 11 centres in six countries forming the Genetics of Asthma International Network. Factor analysis was used to identify distinct phenotypes from questionnaire, clinical, and laboratory data, including baseline pulmonary function, allergen skin prick test (SPT). RESULTS Five distinct factors were identified:(1) baseline pulmonary function measures [forced expiratory volume in 1 s (FEV(1)) and forced vital capacity (FVC)], (2) specific allergen sensitization by SPT, (3) self-reported allergies, (4) symptoms characteristic of rhinitis and (5) symptoms characteristic of asthma. Replication in symptomatic siblings was consistent with shared genetic and/or environmental effects, and was robust across age groups, gender, and centres. Cronbach's alpha ranged from 0.719 to 0.983 suggesting acceptable internal scale consistencies. Derived scales were correlated with serum IgE, methacholine PC(20), age and asthma severity (interrupted sleep). IgE correlated with all three atopy-related factors, the strongest with the SPT factor whereas severity only correlated with baseline lung function, and with symptoms characteristic of rhinitis and of asthma. CONCLUSION In children and adolescents with established asthma, five distinct sets of correlated patient characteristics appear to represent important aspects of the disease. Factor scores as quantitative traits may be better phenotypes in epidemiological and genetic analyses than those categories derived from the presence or absence of combinations of +ve SPTs and/or elevated IgE.
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Affiliation(s)
- S G Pillai
- Medical Genetics, GlaxoSmithKline, Research Triangle Park, NC, USA
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Li J, Liu Q, Wang P, Li H, Wei C, Guo C, Gong Y. Lack of association between three promoter polymorphisms of PTGDR gene and asthma in a Chinese Han population. Int J Immunogenet 2007; 34:353-7. [PMID: 17845306 DOI: 10.1111/j.1744-313x.2007.00699.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The PTGDR gene has been suggested to be an asthma susceptibility gene in previous genome-wide linkage studies as well as in functional studies in a mouse model of asthma. Recently, promoter polymorphisms of the PTGDR gene have been reported to be associated with asthma in American and European populations. In order to determine the association of PTGDR promoter polymorphisms and asthma susceptibility in a Chinese Han population, three promoter single nucleotide polymorphisms (SNP) -549T/C, -441C/T, and -197T/C were genotyped in 336 patients with asthma and 264 healthy controls. Asthma was diagnosed according to the American Thoracic Society (ATS) criteria. SNPs -549T/C and -441C/T were genotyped by Tetra-primer Amplification Refractory Mutation System PCR method and -197T/C by polymerase chain reaction-restriction fragment length polymorphism method. Unlike the results observed in American and European populations, none of the three SNPs nor any haplotypes in the PTGDR promoter region were found to be associated with asthma susceptibility in this Chinese Han population (all P-value > 0.05). The frequencies for both high-transcriptional-efficiency haplotype (CCC) and low-transcriptional-efficiency haplotype (TCT) were lower than 1% in patients and controls, significantly different from those observed in American and European populations. These results suggest that the three PTGDR gene promoter polymorphisms studied are not important risk factors for asthma susceptibility in the Chinese Han population.
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Affiliation(s)
- J Li
- Key Laboratory of Experimental Teratology, Ministry of Education, China
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15
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Zhu G, Vestbo J, Lenney W, Silverman M, Whyte M, Helms P, Anderson WH, Pillai SG. Association of PTGDR gene polymorphisms with asthma in two Caucasian populations. Genes Immun 2007; 8:398-403. [PMID: 17538632 DOI: 10.1038/sj.gene.6364399] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The prostanoid DP receptor (PTGDR) is shown to be involved in the asthma patho-physiology and the results from the published genetic association studies are inconsistent. Four single nucleotide polymorphisms (SNPs) in PTGDR were genotyped in 342 and 294 families from UK and Denmark respectively. Asthma and asthma-related phenotypes were analyzed using family-based association analyses. In the UK families, a promoter polymorphism (-731A/G) showed significant associations with asthma (P=0.0022), atopic asthma (P=0.0044), bronchial hyperreactivity or BHR (P=0.00120) and strict asthma (P=0.0008). The P-values for asthma, BHR and strict asthma were significant even after the most stringent correction for the number of markers and the number of phenotypes analyzed (<0.0031). An intronic polymorphism (+6651C/T) also showed significant associations with asthma (P=0.0302), atopic asthma (P=0.0131), BHR (P=0.0249) and strict asthma (P=0.0261). In the Danish families, an intronic polymorphism (+6541C/T) showed significant associations with asthma (P=0.0071), atopic asthma (P=0.0348), BHR (P=0.0033) and strict asthma (P=0.0381). The results of haplotype analyses supported the ones of the single SNP analyses. Thus, we demonstrated significant evidence of association between polymorphisms in PTGDR with asthma phenotypes in the two Caucasian populations.
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Affiliation(s)
- G Zhu
- Medical Genetics, Glaxo SmithKline, Research Triangle Park, NC 27709, USA
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16
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Sanz C, Isidoro-García M, Dávila I, Moreno E, Laffond E, Avila C, Lorente F. Promoter genetic variants of prostanoid DP receptor (PTGDR) gene in patients with asthma. Allergy 2006; 61:543-8. [PMID: 16629782 DOI: 10.1111/j.1398-9995.2006.01025.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND PTGDR gene has been identified as an asthma-susceptibility gene. Recently, functional genetic variants have been associated with asthma. The objective of this work was to study -549T>C, -441C>T and -197T>C PTGDR promoter polymorphisms in a Spanish population. METHODS In this study, 197 Caucasian individuals were included. Asthma was specialist-physician diagnosed according to the American Thoracic Society (ATS) criteria and classified following the Global Initiative for Asthma (GINA) guidelines. Skin prick tests were performed in all patients. The polymorphisms were analyzed by direct sequencing. RESULTS -197T>C polymorphism was significantly associated with asthma [Fisher's P-value = 0.007, Monte Carlo P-value (10(4) simulations) = 0.004]. Multivariate analysis adjusted for age and sex confirmed this association with an increased risk of asthma (OR, 3.06; 95% CI, 1.28-7.32; P-value = 0.012). CCT CCC diplotype was associated with asthma (P-value < 0.0001; OR, 1.15; 95% CI, 1.07-1.23), specifically with allergic asthma (P-value < 0.0001). CCT CCC diplotype is unambiguous. All individuals carrying this diplotype had asthma. CONCLUSION We identified a specific promoter variant of PTGDR that could be associated with asthma. This diplotype is a combination of the two highest transcriptional efficiency haplotypes, recently described. Our in vivo results would support for the first time what was demonstrated in vitro about high-transcriptional efficiency PTGDR haplotypes in asthma.
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Affiliation(s)
- C Sanz
- Department of Allergy, University Hospital of Salamanca, Salamanca, Spain
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17
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Mansur AH, Bishop DT, Holgate ST, Markham AF, Morrison JFJ. Linkage/association study of a locus modulating total serum IgE on chromosome 14q13-24 in families with asthma. Thorax 2004; 59:876-82. [PMID: 15454654 PMCID: PMC1746835 DOI: 10.1136/thx.2003.014092] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND A study was undertaken to validate a locus modulating total serum IgE levels on 14q13-24. METHODS A linkage and association study was performed between total serum IgE and a panel of seven microsatellites which map to the 14q13-24 region in 69 families with asthma recruited from Leeds, UK. RESULTS Non-parametric, multipoint, sib pair analysis showed no evidence of genetic linkage between the quantitative trait "log IgE" and any of the tested markers. However, a significant association was observed between locus D14S63 (14q23) and total serum IgE (p = 0.017). Allelic analysis showed an association between low total IgE and allele 157 of D14S63 (p = 0.01, OR = 0.63, 95% CI 0.44 to 0.90). Modelling of allele 157 genotypes as a continuous covariate indicated evidence of a significant inverse linear trend across the three genotypes where 157 homozygotes had the lowest mean log IgE (p = 0.045). Association of D14S63 with log IgE was confirmed in the analysis of a combined dataset of 53 families from Southampton, UK and the 69 families from Leeds (total 122 families). An association was observed at the locus level (p = 0.022) and the allelic level where allele 165 showed an association with high total IgE (p = 0.001, OR = 3.79, 95% CI 1.54 to 9.7) and allele 157 showed an association with low total IgE (p = 0.041, OR = 0.77, 95% CI 0.6 to 0.99). The transmission disequilibrium test was positive for allele 165 (p<0.05) and negative for allele 157 (p>0.05). CONCLUSIONS Despite the lack of linkage, the findings of this study support the previous observation of a gene(s) at 14q23 that modulates total serum IgE.
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Affiliation(s)
- A H Mansur
- Respiratory Department, Birmingham Heartlands Hospital, Bordesley Green East, Birmingham B9 5SS, UK.
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18
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Oguma T, Palmer LJ, Birben E, Sonna LA, Asano K, Lilly CM. Role of prostanoid DP receptor variants in susceptibility to asthma. N Engl J Med 2004; 351:1752-63. [PMID: 15496624 DOI: 10.1056/nejmoa031785] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Previous genetic studies have associated the region of the human genome (14q22.1) containing the gene for the prostanoid DP receptor (PTGDR) with asthma. A study of a mouse model suggests that the receptor is required for the expression of the asthma phenotype. Our associations of asthma with functional genetic variants of PTGDR link these observations. METHODS We identified and evaluated combinations of genetic variants that influence PTGDR transcription for disease association in case-control studies of 518 white patients with asthma and 175 white controls and 80 black patients with asthma and 45 black controls. RESULTS We identified four novel and two previously reported single-nucleotide polymorphisms (SNPs) in PTGDR and its vicinity. These define four common three-SNP haplotypes, which vary in their ability to support transcription of PTGDR and have distinct DNA-binding-protein affinity profiles. Individual PTGDR SNPs were significantly associated with asthma in both populations. Specific PTGDR haplotypes were significantly associated with a diagnosis of asthma in a large case-control study of whites (P=0.002); we confirmed these findings in a second population of blacks (P=0.01). Multivariate analysis of the haplotype combinations (diplotypes) demonstrated that both whites (odds ratio, 0.55; 95 percent confidence interval, 0.38 to 0.80; P=0.002) and blacks (odds ratio, 0.32; 95 percent confidence interval, 0.12 to 0.89; P=0.03) who had at least one copy of the haplotype with a low transcriptional efficiency had a lower risk of asthma than subjects with no copies of the haplotype. CONCLUSIONS Our functional and genetic findings identify PTGDR as an asthma-susceptibility gene.
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Affiliation(s)
- Tsuyoshi Oguma
- Combined Program in Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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Jackola DR, Blumenthal MN, Rosenberg A. Evidence for two independent distributions of serum immunoglobulin E in atopic families: cognate and non-cognate IgE. Hum Immunol 2004; 65:20-30. [PMID: 14700592 DOI: 10.1016/j.humimm.2003.10.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Genetic studies of IgE-mediated atopic disease have produced conflicting results, due largely to variable phenotype definitions. Total IgE concentrations and 14 allergen skin prick tests (SPT) were determined in 1099 members of families with history of atopy. Log10 [Total IgE] values were normally distributed in both atopic (SPT [+]) and non-atopic (SPT [-]) groups. The mean Log10 [Total IgE] value was higher in the atopic group, although the standard deviations of the distributions were the same. The mean Log10 [Total IgE] value of the non-atopic distribution was subtracted from the individual Log10 [Total IgE] values of the atopic group giving an allergen-specific fraction. There was a strong positive correlation between the specific IgE fraction and the number (#) SPT [+] results, defined as Cognate IgE. Among the atopics, subtracting the Cognate IgE value from total IgE yielded Non-Cognate IgE. The Cognate and Non-Cognate IgE distributions were statistically uncorrelated. Evidence is presented for two serum IgE fractions that are statistically and physiologically independent of one another in atopic families; a Cognate IgE fraction associated with atopic sensitization and a Non-Cognate IgE fraction unrelated to atopic disease. Elevated serum IgE is a consequence, not a predisposing cause, of allergen sensitization.
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Affiliation(s)
- Duaine R Jackola
- Asthma and Allergy Program, University of Minnesota Medical School, Minneapolis, MN 55455, USA.
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20
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Halapi E, Hakonarson H. Recent development in genomic and proteomic research for asthma. Curr Opin Pulm Med 2004; 10:22-30. [PMID: 14749602 DOI: 10.1097/00063198-200401000-00005] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Asthma is a complex genetic disorder with a heterogeneous phenotype attributed to the interactions among many genes and the environment. This review highlights recent developments in asthma genomic and proteomic research. RECENT FINDINGS Numerous loci and candidate genes have been reported to show linkage and association of asthma and the asthma-associated phenotypes, atopy, elevated immunoglobulin E (IgE) levels, and bronchial hyperresponsiveness to alleles of microsatellite markers and single nucleotide polymorphisms within specific cytokine/chemokine, and IgE regulating genes. Although many studies reporting these observations are compelling, only a few genes conferring significant risk have been mapped. Although significant progress has been made in the field of asthma genetics in the past decade, the clinical implications of the genetic variations within the numerous candidate asthma genes, which have been found to associate with the expression of the asthmatic phenotype, remain largely undetermined. However, in the past year the scientific community has benefited from postgenomic discoveries, with the recent cloning of two asthma genes, ADAM 33 and PHF11, and this has generated new information that is benefiting others. SUMMARY The asthma genetics field has advanced considerably in recent years, with new information being generated that has led to improved understanding of the pathobiology underlying this complex disorder. This has also generated interest in the study of gene-gene interaction and how linkage disequilibrium blocks and haplotypes can be used as functional units to pinpoint mutations and capture relative risk of mutated genes in complex disorders.
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Affiliation(s)
- Eva Halapi
- Division of Respiratory and Pharmacogenomic Research, deCODE genetics, Inc., Reykjavik, Iceland
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21
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Hakonarson H, Halapi E. Genetic analyses in asthma: current concepts and future directions. AMERICAN JOURNAL OF PHARMACOGENOMICS : GENOMICS-RELATED RESEARCH IN DRUG DEVELOPMENT AND CLINICAL PRACTICE 2003; 2:155-66. [PMID: 12383022 DOI: 10.2165/00129785-200202030-00001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Asthma is a complex genetic disorder with a heterogeneous phenotype, largely attributed to the interactions among many genes and between these genes and the environment. Numerous loci and candidate genes have been reported to show linkage and association of asthma and the asthma-associated phenotypes, atopy, elevated immunoglobulin E (IgE) levels, and bronchial hyper-responsiveness to alleles of microsatellite markers and single nucleotide polymorphisms (SNPs) within specific cytokine/chemokine, and IgE regulating genes. While many studies reporting these observations are compelling, only one asthma gene conferring high risk has been mapped. In this review, we present studies that support linkage and/or associations to the various genetic loci and genes in asthma. The first genome-wide scan for linkage to quantitative traits underlying asthma identified linkage on chromosome 4q, 6, 7, 11q, 13q and 16. A genome scan in American families from three racial groups revealed linkage to chromosome 2q, 5q, 6p, 12q, 13q and 14q. A two-stage scan in Hutterite families from the US found linkage on chromosome 5q, 12q, 19q and 21q. A screen in German families identified linkage to asthma on chromosome 2q, 6p, 9 and 12q and a two-stage genome scan in French families found replicated linkage on chromosomes 1p, 12q and 17q. A study of asthma in Finland showed linkage to high IgE on 7q14. Apart from a European linkage study of 199 families with atopic dermatitis, which demonstrated significant linkage to chromosome 3q21, three other studies have reported linkage results of genome-wide significance, including a linkage study in 175 Icelandic asthma families (14q24), a study in 533 Chinese families with bronchial hyper-responsiveness (chromosome 2) and a study in 47 Japanese families with mite-sensitive atopic asthma (5q31), suggesting that these regions may harbor genes contributing to the development of asthma and allergies. While significant progress has been made in the field of asthma genetics in the past decade, the clinical implications of the genes and genetic variations within the numerous candidate asthma genes that have been found to associate with the expression of the asthmatic phenotype, remain undetermined.
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Affiliation(s)
- Hakon Hakonarson
- Division of Respiratory and Pharmacogenomics Research, deCODE Genetics, Inc., Reykjavik, Iceland
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22
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Hakonarson H, Bjornsdottir US, Halapi E, Palsson S, Adalsteinsdottir E, Gislason D, Finnbogason G, Gislason T, Kristjansson K, Arnason T, Birkisson I, Frigge ML, Kong A, Gulcher JR, Stefansson K. A major susceptibility gene for asthma maps to chromosome 14q24. Am J Hum Genet 2002; 71:483-91. [PMID: 12119603 PMCID: PMC379187 DOI: 10.1086/342205] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2002] [Accepted: 06/03/2002] [Indexed: 11/03/2022] Open
Abstract
Asthma is a complex genetic disorder with a heterogeneous phenotype, largely attributed to the interactions among many genes and between these genes and the environment. Numerous loci and candidate genes have been reported to show linkage and association to asthma and atopy. Although some studies reporting these observations are compelling, no gene has been mapped that confers a sufficiently high risk of asthma to meet the stringent criteria for genomewide significance. Using 175 extended Icelandic families that included 596 patients with asthma, we performed a genomewide scan with 976 microsatellite markers. The families were identified by cross-matching a list of patients with asthma from the Department of Allergy/Pulmonary Medicine of the National University Hospital of Iceland with a genealogy database of the entire Icelandic nation. We detected linkage of asthma to chromosome 14q24, with an allele-sharing LOD score of 2.66. After we increased the marker density within the locus to an average of one microsatellite every 0.2 cM, the LOD score rose to 4.00. We designate this locus "asthma locus one" (AS1). Taken together, these results provide evidence of a novel susceptibility gene for asthma on chromosome 14q24.
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Affiliation(s)
- Hakon Hakonarson
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Unnur S. Bjornsdottir
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Eva Halapi
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Snaebjorn Palsson
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Elva Adalsteinsdottir
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - David Gislason
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Gudmundur Finnbogason
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Thorarinn Gislason
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Kristleifur Kristjansson
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Thor Arnason
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Illugi Birkisson
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Michael L. Frigge
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Augustine Kong
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Jeffrey R. Gulcher
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
| | - Kari Stefansson
- deCODE Genetics, Inc., and Department of Allergy/Pulmonary Medicine, National University Hospital, Reykjavik, Iceland
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23
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Bousquet J, Van Cauwenberge P, Khaltaev N. Allergic rhinitis and its impact on asthma. J Allergy Clin Immunol 2001; 108:S147-334. [PMID: 11707753 DOI: 10.1067/mai.2001.118891] [Citation(s) in RCA: 2090] [Impact Index Per Article: 90.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- J Bousquet
- Department of Allergy and Respiratory Diseases, University Hospital and INSERM, Montpellier, France
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24
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Abstract
Asthma is a complex genetic disorder with variable phenotype, largely attributed to the interactions of the environment and multiple genes, each potentially having small effects. Numerous asthma and atopy loci have been reported in studies demonstrating associations and/or linkage of the asthma-associated phenotypes, atopy, elevated IgE levels, and bronchial hyperresponsiveness to alleles of microsatellite markers and single nucleotide polymorphisms within specific cytokine/chemokine and IgE regulating genes. Although the studies reporting these observations are compelling, most of them lack statistical power. This review compiles the evidence that supports linkage and associations to the various genetic loci and candidate genes. Whereas significant progress has been made in the field of asthma genetics in the past decade, the roles of the genes and genetic variations within the numerous candidate asthma genes that have been found to associate with the expression of the asthmatic phenotype remain to be determined.
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25
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Malerba G, Patuzzo C, Trabetti E, Lauciello MC, Galavotti R, Pescollderungg L, Whalen MB, Zanoni G, Martinati LC, Boner AL, Pignatti PF. Chromosome 14 linkage analysis and mutation study of 2 serpin genes in allergic asthmatic families. J Allergy Clin Immunol 2001; 107:654-8. [PMID: 11295654 DOI: 10.1067/mai.2001.113865] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND Genome and chromosome screens reported DNA markers on chromosome 14 linked to allergic asthma or intermediate phenotypes in several populations. OBJECTIVE We sought to perform a linkage study on chromosome 14 and a further association study on candidate genes mapped in the region found to be linked to allergic asthma or intermediate phenotypes. METHODS The study consisted of a sample of 189 families (847 genotyped individuals) from a restricted geographic area in northeastern Italy. The subjects were characterized for the following phenotypes: allergic asthma, total serum IgE levels, skin prick test responses, and bronchial hyperresponsiveness (BHR) to methacholine. Genotyping was done with 14 DNA markers and 4 polymorphisms in the genes encoding alpha(1)-anti-trypsin and alpha(1)-antichymotrypsin (ACT). RESULTS Multipoint analysis indicated a potential linkage of BHR with marker D14S617 (nonparametric linkage z score = 2.32, P =.01). Transmission disequilibrium of Thr -15Ala in the gene encoding ACT was observed with all the phenotypes investigated: allergic asthma, BHR, total IgE levels, or skin prick test responses (P =.041,.02,.0053, or.026, respectively). CONCLUSION Chromosome 14 screening and transmission disequilibrium testing on the gene encoding ACT suggest that it or a closely located gene may be involved in susceptibility to allergic asthma in the Italian population.
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Affiliation(s)
- G Malerba
- Department of Mother and Child, Biology and Genetics, University of Verona, Strada la Grazie 8, 37134 Verona, Italy
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26
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Abstract
Genetic research in allergic disease has focused primarily on asthma and its associated phenotypes (eg, total IgE), with very little attention given to the presence or absence of concomitant allergic diseases, especially allergic rhinitis and atopic dermatitis. Because asthma, allergic rhinitis, and atopic dermatitis share common systemic characteristics, it is reasonable to propose that a number of susceptibility genes could contribute to the allergic process regardless of the specific clinical phenotype. Consequently, the many genetic linkages previously reported for asthma may not be specific for asthma per se but rather may reflect an overall predisposition for allergic disease. Finally, epidemiologic data suggest that asthma and allergic rhinitis represent a continuum of disease, whereby those individuals with less severe disease will express rhinitis without asthma and those individuals with more severe disease express more than 1 phenotype. Alternatively, it is plausible that, in addition to the "allergic disease genes," there are "phenotype-specific genes" or possibly certain combinations of susceptibility genes (eg, gene-gene interactions) that contribute to the expression of asthma, allergic rhinitis, or atopic dermatitis.
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Affiliation(s)
- K C Barnes
- Johns Hopkins Asthma & Allergy Center, Baltimore, MD, USA
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27
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Affiliation(s)
- K C Barnes
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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28
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Abstract
Markers in 19 chromosomal regions have shown some evidence of linkage to asthma, atopy, or related phenotypes in multiple independent genome-wide searches. Linkages to five of these regions (5q, 6p, 11q, 12q, and 13q) have also been reported in non-genome-wide screens. In addition, at least two independent studies have reported linkages to markers on 16p. Numerous candidate genes in these regions have shown varying levels of association to asthma or atopic phenotypes, potentially implicating them as disease susceptibility loci. These include the IL4, CD14, and B2ADR genes on 5q, the HLA-DRB1 and TNF genes on 6p, the FCERB1 and CC16 genes on 11q, and the IL4RA gene on 16p. It still remains to be determined whether polymorphisms in these genes account for the reported linkages in these regions. Studies are underway in laboratories around the world to identify the disease-causing variations in these genes that account for the linkages just discussed. Identifying specific genetic polymorphisms that influence asthma and atopic phenotypes will shed light on the molecular pathways involved in these complex disorders and provide a better understanding of the pathophysiology of asthma and atopy.
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MESH Headings
- Asthma/genetics
- Chromosome Mapping
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 12
- Chromosomes, Human, Pair 16
- Chromosomes, Human, Pair 5
- Chromosomes, Human, Pair 6
- Cloning, Molecular
- Humans
- Polymorphism, Genetic
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Affiliation(s)
- C Ober
- Department of Human Genetics, University of Chicago, Illinois, USA.
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29
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Collins A, Ennis S, Tapper W, Morton N. Mapping oligogenes for atopy and asthma by meta-analysis. Genet Mol Biol 2000. [DOI: 10.1590/s1415-47572000000100001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Meta-analysis is presented for published studies on linkage or allelic association that have in common only reported significance levels. Reporting is biassed, and nonsignificance is seldom quantified. Therefore meta-analysis cannot identify oligogenes within a candidate region nor establish their significance, but it defines candidate regions well. Applied to a database on atopy and asthma, candidate regions are identified on chromosomes 6, 5, 16, 11, 12, 13, 14, 7, 20, and 10, in rank order from strongest to weakest evidence. On the other hand, there is little support for chromosomes 9, 8, 18, 1, and 15 in the same rank order. The evidence from 156 publications is reviewed for each region. With reasonable type I and II errors several thousand affected sib pairs would be required to detect a locus accounting for 1/10 of the genetic effect on asthma. Identification of regions by a genome scan for linkage and allelic association requires international collaborative studies to reach the necessary sample size, using lod-based methods that specify a weakly parametric alternative hypothesis and can be combined over studies that differ in ascertainment, phenotypes, and markers. This has become the central problem in complex inheritance.
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30
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Abstract
In this review, two issues are highlighted: 1) the difficulties that can form major hurdles in trying to understand a disease or a fundamental biologic process at the genetic and molecular level and 2) the potential opportunities that genetic models such as the Drosophila or c-elegans can provide in answering clinically or biologically relevant questions. This review also lists in some detail the areas in which these models have been helpful and successes have been scored. For such models to be used, however, requires the "dissection" of a biologic or a disease process into a tractable phenotype that can be assayed in a genetic model and have relevant and interpretable conclusions. The hope is that questions pertaining to sleep, arousal, respiratory neurobiology, and their disorders can be formulated in such a way to be addressed in models that can lend themselves to very exciting discoveries.
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Affiliation(s)
- G G Haddad
- Department of Pediatrics (Respiratory Medicine), Yale University School of Medicine, New Haven, CT, USA.
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