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Staton AD, Koff JL, Chen Q, Ayer T, Flowers CR. Next-generation prognostic assessment for diffuse large B-cell lymphoma. Future Oncol 2015; 11:2443-57. [PMID: 26289217 DOI: 10.2217/fon.15.144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Current standard of care therapy for diffuse large B-cell lymphoma (DLBCL) cures a majority of patients with additional benefit in salvage therapy and autologous stem cell transplant for patients who relapse. The next generation of prognostic models for DLBCL aims to more accurately stratify patients for novel therapies and risk-adapted treatment strategies. This review discusses the significance of host genetic and tumor genomic alterations seen in DLBCL, clinical and epidemiologic factors, and how each can be integrated into risk stratification algorithms. In the future, treatment prediction and prognostic model development and subsequent validation will require data from a large number of DLBCL patients to establish sufficient statistical power to correctly predict outcome. Novel modeling approaches can augment these efforts.
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Affiliation(s)
- Ashley D Staton
- Department of Hematology & Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Jean L Koff
- Department of Hematology & Medical Oncology, Emory University, Atlanta, GA 30322, USA
| | - Qiushi Chen
- H Milton Stewart School of Industrial & Systems Engineering, Georgia Institute of Technology, Atlanta, GA 30318, USA
| | - Turgay Ayer
- H Milton Stewart School of Industrial & Systems Engineering, Georgia Institute of Technology, Atlanta, GA 30318, USA
| | - Christopher R Flowers
- Department of Hematology & Medical Oncology, Emory University, Atlanta, GA 30322, USA
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An IL-13 promoter polymorphism associated with liver fibrosis in patients with Schistosoma japonicum. PLoS One 2015; 10:e0135360. [PMID: 26258681 PMCID: PMC4530950 DOI: 10.1371/journal.pone.0135360] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/21/2015] [Indexed: 12/20/2022] Open
Abstract
The aim of this study was to determine whether two polymorphisms in the gene encoding IL13 previously associated with Schistosoma hematobium (S. hematobium) and S. mansoni infection are associated with S. japonicum infection. Single nucleotide polymorphisms (SNPs) rs1800925 (IL13/-1112C>T) and rs20541 (IL13R130Q) were genotyped in 947 unrelated individuals (307 chronically infected, 339 late-stage with liver fibrosis, 301 uninfected controls) from a schistosomiasis-endemic area of Hubei province in China. Regression models were used to evaluate allelic and haplotypic associations with chronic and late-stage schistosomiasis adjusted for non-genetic covariates. Expression of IL-13 was measured in S. japonicun-infected liver fibrosis tissue and normal liver tissue from uninfected controls by immunohistochemistry (IHC). The role of rs1800925 in IL-13 transcription was further determined by Luciferase report assay using the recombinant PGL4.17-rs180092 plasmid. We found SNP rs1800925T was associated with late-stage schistosomiasis caused by S. japonicum but not chronic schistosomiasis (OR = 1.39, 95%CI = 1.02-1.91, p = 0.03) and uninfected controls (OR = 1.49, 95%CI = 1.03-2.13, p = 0.03). Moreover, the haplotype rs1800925T-rs20541C increased the risk of disease progression to late-stage schistosomiasis (OR = 1.46, p = 0.035), whereas haplotype rs1800925C-rs20541A showed a protective role against development of late-stage schistosomiasis (F = 0.188, OR = 0.61, p = 0.002). Furthermore, S. japonicum-induced fibrotic liver tissue had higher IL13 expression than normal liver tissue. Plasmid PGL4.17-rs1800925T showed a stronger relative luciferase activity than Plasmid PGL4.17-rs1800925C in 293FT, QSG-7701 and HL-7702 cell lines. In conclusion, the functional IL13 polymorphism, rs1800925T, previously associated with risk of schistosomiasis, also contributes to risk of late-stage schistosomiasis caused by S. japonicum.
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Larkin EK, Hartert TV. Genes associated with RSV lower respiratory tract infection and asthma: the application of genetic epidemiological methods to understand causality. Future Virol 2015; 10:883-897. [PMID: 26478738 DOI: 10.2217/fvl.15.55] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Infants with respiratory syncytial virus (RSV) lower respiratory tract infections (LRIs) are at increased risk for childhood asthma. The objectives of this article are to review the genes associated with both RSV LRI and asthma, review analytic approaches to assessing shared genetic risk and propose a future perspective on how these approaches can help us to understand the role of infant RSV infection as both an important risk factor for asthma and marker of shared genetic etiology between the two conditions. The review of shared genes and thus pathways associated with severity of response to RSV infection and asthma risk can help us to understand mechanisms of disease and ultimately propose new and novel targets for primary prevention of both diseases.
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Affiliation(s)
- Emma K Larkin
- Department of Medicine, Division of Allergy, Pulmonary & Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Tina V Hartert
- Department of Medicine, Division of Allergy, Pulmonary & Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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54
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Inherited genetic variation in childhood acute lymphoblastic leukemia. Blood 2015; 125:3988-95. [PMID: 25999454 DOI: 10.1182/blood-2014-12-580001] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 01/30/2015] [Indexed: 02/06/2023] Open
Abstract
Although somatically acquired genomic alterations have long been recognized as the hallmarks of acute lymphoblastic leukemia (ALL), the last decade has shown that inherited genetic variations (germline) are important determinants of interpatient variability in ALL susceptibility, drug response, and toxicities of ALL therapy. In particular, unbiased genome-wide association studies have identified germline variants strongly associated with the predisposition to ALL in children, providing novel insight into the mechanisms of leukemogenesis and evidence for complex interactions between inherited and acquired genetic variations in ALL. Similar genome-wide approaches have also discovered novel germline genetic risk factors that independently influence ALL prognosis and those that strongly modify host susceptibility to adverse effects of antileukemic agents (eg, vincristine, asparaginase, glucocorticoids). There are examples of germline genomic associations that warrant routine clinical use in the treatment of childhood ALL (eg, TPMT and mercaptopurine dosing), but most have not reached this level of actionability. Future studies are needed to integrate both somatic and germline variants to predict risk of relapse and host toxicities, with the eventual goal of implementing genetics-driven precision-medicine approaches in ALL treatment.
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Implications of population structure and ancestry on asthma genetic studies. Curr Opin Allergy Clin Immunol 2015; 14:381-9. [PMID: 25153337 DOI: 10.1097/aci.0000000000000102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW The frequency and severity of asthma differ between different racial and ethnic groups. An understanding of the genetic basis for these differences could constitute future genetic biomarker panels for predicting asthma risk and progression in individuals from different ethnic groups. RECENT THEMES The recent mixing of different ancestries during the European colonization of the Americas and the African slave trade has resulted in the complex population structures identified in different ethnic groups. These population structures represent varying degrees of genetic diversity which impacts the allele frequency of individual variants and, thus, how the gene variation is utilized in genetic association studies. In this review, we will discuss the basis for the complex population structures of modern human genomes and the impact of genetic diversity on genetic studies in different ethnic groups. We will also highlight the potential for admixture and rare variant-based genetic studies to identify novel genetic loci for asthma susceptibility and severity. SUMMARY The ability to account for the consequences of genetic diversity in different racial and ethnic groups will be critical in developing genetic profiles for personalized or precision medicine approaches tailored to asthmatic patients from different ethnic groups.
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Peprah E, Xu H, Tekola-Ayele F, Royal CD. Genome-wide association studies in Africans and African Americans: expanding the framework of the genomics of human traits and disease. Public Health Genomics 2014; 18:40-51. [PMID: 25427668 DOI: 10.1159/000367962] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 08/29/2014] [Indexed: 01/11/2023] Open
Abstract
Genomic research is one of the tools for elucidating the pathogenesis of diseases of global health relevance and paving the research dimension to clinical and public health translation. Recent advances in genomic research and technologies have increased our understanding of human diseases, genes associated with these disorders, and the relevant mechanisms. Genome-wide association studies (GWAS) have proliferated since the first studies were published several years ago and have become an important tool in helping researchers comprehend human variation and the role genetic variants play in disease. However, the need to expand the diversity of populations in GWAS has become increasingly apparent as new knowledge is gained about genetic variation. Inclusion of diverse populations in genomic studies is critical to a more complete understanding of human variation and elucidation of the underpinnings of complex diseases. In this review, we summarize the available data on GWAS in recent African ancestry populations within the western hemisphere (i.e. African Americans and peoples of the Caribbean) and continental African populations. Furthermore, we highlight ways in which genomic studies in populations of recent African ancestry have led to advances in the areas of malaria, HIV, prostate cancer, and other diseases. Finally, we discuss the advantages of conducting GWAS in recent African ancestry populations in the context of addressing existing and emerging global health conditions.
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Tripathi P, Hong X, Caruso D, Gao P, Wang X. Genetic determinants in the development of sensitization to environmental allergens in early childhood. IMMUNITY INFLAMMATION AND DISEASE 2014; 2:193-204. [PMID: 25505553 PMCID: PMC4257764 DOI: 10.1002/iid3.38] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/01/2014] [Accepted: 10/03/2014] [Indexed: 11/12/2022]
Abstract
Sensitization to environmental allergens remains one of the strongest risk factors for asthma, and there is likely a genetic basis. We sought to identify genetic determinants for the development of allergic sensitization to environmental allergens, particularly cockroach allergen, in early childhood. A total of 631 children with the information about genotypic data on 895 single nucleotide polymorphisms (SNPs) in 179 candidate genes were selected from an existing dataset (Boston Birth Cohort). Genetic analysis was performed for allergic sensitizations among all subjects and sub-population, Black/African, respectively. Eight SNPs in seven genes showed significant association with allergic sensitization with P < 0.05, including two top SNPs, rs7851969 in JAK2 (P = 0.003) and rs11739089 in CNOT6 (P = 0.008). When analyses were specifically performed for cockroach sensitization, 16 SNPs in 13 genes showed P < 0.05, including five genes with SNPs at P < 0.01 (JAK1, JAK3, IL5RA, FCER1A, and ADAM33). Particularly, haplotype analyses demonstrated that multiple-haplotypes in FCER1A were significantly associated with cockroach sensitization with the strongest association for a 2-marker haplotype (rs6665683T-rs12136904T, P = 0.001). Furthermore, SNP rs6665683 was marginally associated with the levels of cockroach allergen specific IgE. When a similar analysis was performed for house dust mite, four SNPs in three genes (JAK2, MAML1, and NOD1) had P < 0.01. Of these, JAK2 appeared to be an only gene showing association across the sensitizations we analyzed. Some of findings were further validated when analysis was limited to black population. Our study identified several loci that may confer the susceptibility to allergic sensitization, and suggested that sensitization to allergens may depend on their unique loci.
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Affiliation(s)
- Priya Tripathi
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine Baltimore, Maryland, 21224
| | - Xiumei Hong
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health Baltimore, Maryland, 21205
| | - Deanna Caruso
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health Baltimore, Maryland, 21205
| | - Peisong Gao
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine Baltimore, Maryland, 21224
| | - Xiaobin Wang
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health Baltimore, Maryland, 21205
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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: 28] [Impact Index Per Article: 2.8] [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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Social disadvantage and asthma control in children. Paediatr Respir Rev 2014; 15:256-62; quiz 262-3. [PMID: 24928775 PMCID: PMC4146695 DOI: 10.1016/j.prrv.2014.04.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 04/29/2014] [Indexed: 12/22/2022]
Abstract
This review discusses various aspects of social disadvantage and their association with poor asthma control, including socioeconomic status, exposure to psychosocial stress and violence, minority affiliation, environmental concerns such as allergens and pollution, and poverty in rural settings. Each of these elements has been linked with worsened asthma outcomes in children. Known and hypothesized mechanisms behind these associations are described in an effort to further understand the complex entity of poorly controlled asthma among socially deprived children. Intervention studies to improve asthma outcomes in these vulnerable populations are also described.
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Campbell CD, Mohajeri K, Malig M, Hormozdiari F, Nelson B, Du G, Patterson KM, Eng C, Torgerson DG, Hu D, Herman C, Chong JX, Ko A, O'Roak BJ, Krumm N, Vives L, Lee C, Roth LA, Rodriguez-Cintron W, Rodriguez-Santana J, Brigino-Buenaventura E, Davis A, Meade K, LeNoir MA, Thyne S, Jackson DJ, Gern JE, Lemanske RF, Shendure J, Abney M, Burchard EG, Ober C, Eichler EE. Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma. PLoS One 2014; 9:e104396. [PMID: 25116239 PMCID: PMC4130548 DOI: 10.1371/journal.pone.0104396] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/12/2014] [Indexed: 12/30/2022] Open
Abstract
Asthma is a complex genetic disease caused by a combination of genetic and environmental risk factors. We sought to test classes of genetic variants largely missed by genome-wide association studies (GWAS), including copy number variants (CNVs) and low-frequency variants, by performing whole-genome sequencing (WGS) on 16 individuals from asthma-enriched and asthma-depleted families. The samples were obtained from an extended 13-generation Hutterite pedigree with reduced genetic heterogeneity due to a small founding gene pool and reduced environmental heterogeneity as a result of a communal lifestyle. We sequenced each individual to an average depth of 13-fold, generated a comprehensive catalog of genetic variants, and tested the most severe mutations for association with asthma. We identified and validated 1960 CNVs, 19 nonsense or splice-site single nucleotide variants (SNVs), and 18 insertions or deletions that were out of frame. As follow-up, we performed targeted sequencing of 16 genes in 837 cases and 540 controls of Puerto Rican ancestry and found that controls carry a significantly higher burden of mutations in IL27RA (2.0% of controls; 0.23% of cases; nominal p = 0.004; Bonferroni p = 0.21). We also genotyped 593 CNVs in 1199 Hutterite individuals. We identified a nominally significant association (p = 0.03; Odds ratio (OR) = 3.13) between a 6 kbp deletion in an intron of NEDD4L and increased risk of asthma. We genotyped this deletion in an additional 4787 non-Hutterite individuals (nominal p = 0.056; OR = 1.69). NEDD4L is expressed in bronchial epithelial cells, and conditional knockout of this gene in the lung in mice leads to severe inflammation and mucus accumulation. Our study represents one of the early instances of applying WGS to complex disease with a large environmental component and demonstrates how WGS can identify risk variants, including CNVs and low-frequency variants, largely untested in GWAS.
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Affiliation(s)
- Catarina D. Campbell
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kiana Mohajeri
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Maika Malig
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Fereydoun Hormozdiari
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Benjamin Nelson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Gaixin Du
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Kristen M. Patterson
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Dara G. Torgerson
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Catherine Herman
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jessica X. Chong
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Arthur Ko
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Brian J. O'Roak
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Niklas Krumm
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Laura Vives
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Lindsey A. Roth
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | | | | | - Emerita Brigino-Buenaventura
- Department of Allergy & Immunology, Kaiser Permanente-Vallejo Medical Center, Vallejo, California, United States of America
| | - Adam Davis
- Children's Hospital and Research Center Oakland, Oakland, California, United States of America
| | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, California, United States of America
| | | | - Shannon Thyne
- San Francisco General Hospital, San Francisco, California, and the Department of Pediatrics, University of California San Francisco, San Francisco, California, United States of America
| | - Daniel J. Jackson
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Robert F. Lemanske
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Mark Abney
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Esteban G. Burchard
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
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Lima JJ. Do genetic polymorphisms alter patient response to inhaled bronchodilators? Expert Opin Drug Metab Toxicol 2014; 10:1231-40. [PMID: 25102170 DOI: 10.1517/17425255.2014.939956] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Short- and long-acting β agonists (SABA and LABA) are bronchodilators for treating asthma. Bronchodilator response (BDR) is quantified by measuring air expired in the first second during a forced expiratory maneuver, prior to and following inhalation of SABA. BDR has been associated with a significant degree of heterogeneity, in part attributable to genetic variation. Heritability, the proportion of phenotypic variability accounted for by genetic variation is estimated to account for 50% of pulmonary function and 28.5% for BDR. AREAS COVERED A MEDLINE search for English articles published from January 1990 to June 2014 was completed using the terms: bronchodilator, bronchodilator response, short-acting bronchodilator, long-acting bronchodilator, β2 adrenergic receptor gene (ADRB2), asthma and pharmacogenomics. The effects of ADRB2 variants on BDR and the safety of SABA and LABA + inhaled corticosteroids have been studied with equivocal results. Single and candidate gene studies have identified variants in other genes that alter response to bronchodilators. Associations were recently observed between hospital admission rates and two rare ADRB2 polymorphisms: Thr164Ile and a 25 base pair insertion-deletion at nucleotide -376. This was the first report of life-threatening events associated with LABA being linked to rare ADRB2 variants. EXPERT OPINION Pharmacogenomic studies over the last two decades clearly demonstrate that polymorphisms alter patient response to bronchodilators in patients with asthma.
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Affiliation(s)
- John J Lima
- Center for Pharmacogenomics and Translational Research, Nemours Children's Clinic , 807 Children's Way, Jacksonville, FL 32207 , USA , +1 904 697 3683 ; +1 904 687 7988 ;
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Lama M, Chatterjee M, Chaudhuri TK. A study of the association of childhood asthma with HLA alleles in the population of Siliguri, West Bengal, India. ACTA ACUST UNITED AC 2014; 84:316-20. [PMID: 24962747 DOI: 10.1111/tan.12403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 05/02/2014] [Accepted: 05/27/2014] [Indexed: 10/25/2022]
Abstract
Asthma is a heterogeneous disease for which a strong genetic basis is firmly established. It is a complex disorder influenced by gene-environment interaction. Human leukocyte antigen (HLA) genes have been shown to be consistently associated with asthma and its related phenotypes in various populations. The aim of this study was to determine the frequency of the selected HLA classes I and II allelic groups in asthmatic and control groups. HLA typing was performed using polymerase chain reaction-sequence-specific typing (PCR-SSP) method. The allele frequency was estimated by direct counting. Frequency of each HLA allelic group was compared between asthmatic group and control group using χ(2) test. P-value was corrected by multiplying with the number of the allelic groups studied. Odds ratio (OR) and its corresponding 95% confidence interval (CI) for each allelic group were calculated using graphpad instat 3.10. The results of this study showed a significantly higher frequency of HLA-DRB1*03 in asthmatics than in controls (11.43% vs 3.64%, OR = 3.78, 95% CI = 1.61-8.85, P = 0.0025, Pcorr < 0.05). Analysis of HLA alleles in low and high total serum immunoglobulin E (IgE) level in asthmatics revealed no significant association. HLA-DRB1*03 may be implicated in the susceptibility to asthma in the pediatric population.
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Affiliation(s)
- M Lama
- Cellular Immunology Laboratory, Department of Zoology, University of North Bengal, Siliguri, West Bengal, India; Department of Zoology, The University of Burdwan, Golapbag, West Bengal, India
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Yang G, Chen J, Xu F, Bao Z, Yao Y, Zhou J. Association between tumor necrosis factor-α rs1800629 polymorphism and risk of asthma: a meta-analysis. PLoS One 2014; 9:e99962. [PMID: 24936650 PMCID: PMC4061054 DOI: 10.1371/journal.pone.0099962] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/20/2014] [Indexed: 01/08/2023] Open
Abstract
Objective The purpose of this study was to explore the association between the TNF-α rs1800629 (also refers as -308G/A) polymorphism and asthma susceptibility. Methods We searched the Pubmed, Embase, Cochrane Central Register of Controlled Trials (CENTRAL) and Wanfang databases. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to calculate the strength of association. Results A total of 34 studies involving 5477 asthma patients and 5962 controls were included in present study. The results indicated that TNF-α rs1800629 polymorphism was significantly associated with asthma risk in a recessive genetic model (OR = 1.46, 95% CI 1.21–1.76, P<0.0001). Subgroup analyses found that the TNF-α rs1800629 polymorphism was significantly associated with asthma risk in West Asians and South Asians (OR = 2.47, 95% CI = 1.48–4.12, P = 0.0005; OR = 1.83, 95% CI = 1.42–2.36, P<0.00001), but not East Asians and Caucasians. Furthermore, significant association also was observed in allergic asthma (OR = 1.51, 95% CI = 1.24–1.83, P<0.0001), adults and children (OR = 1.43, 95 CI% = 1.07–1.91, P = 0.02; OR = 1.57, 95% CI = 1.19–2.06, P = 0.001). Conclusions This meta-analysis suggested that the rs1800629 polymorphism in TNF-α was a risk factor for asthma.
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Affiliation(s)
- Guangdie Yang
- Department of Respiratory Diseases, The First Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| | - Junjun Chen
- Department of Respiratory Diseases, The First Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| | - Fei Xu
- Department of Respiratory Diseases, The First Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| | - Zhang Bao
- Department of Respiratory Diseases, The First Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| | - Yake Yao
- Department of Respiratory Diseases, The First Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| | - Jianying Zhou
- Department of Respiratory Diseases, The First Affiliated Hospital of College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
- * E-mail:
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Al-Muhsen S, Vazquez-Tello A, Jamhawi A, Al-Jahdali H, Bahammam A, Al Saadi M, Iqbal SM, Alfrayh A, Afzal S, Al-Khamis N, Halwani R. Association of the STAT-6 rs324011 (C2892T) variant but not rs324015 (G2964A), with atopic asthma in a Saudi Arabian population. Hum Immunol 2014; 75:791-5. [PMID: 24912007 DOI: 10.1016/j.humimm.2014.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 05/29/2014] [Accepted: 05/29/2014] [Indexed: 10/25/2022]
Abstract
BACKGROUND The signal transducer and activator of transcription 6 (STAT6) transduces signals in response to IL-4 and IL-13 cytokine stimulations, resulting in many cell-specific responses. Some common STAT6 SNPs were associated with asthma predisposition and/or IgE levels, although discrepancies have also been reported. OBJECTIVE To determine whether STAT6 rs324011 and rs324015 polymorphisms are associated with atopic asthma in Saudi Arabian patients. METHODS A total of 536 Saudi individuals aged 11-70years old (230 atopic asthmatics, 306 healthy subjects) were recruited. DNA was purified from peripheral blood and genotyping for rs324011 and rs324015 polymorphisms was performed by PCR amplification, followed by cycle sequencing of the purified PCR fragments using BigDye chain terminator and capillary electrophoresis. RESULTS By the contrast of alleles tests, no significant differences between asthma and healthy groups were detected for both variants (rs324011: X(2)=0.25, Pearson's P-value=0.617; rs324015: X(2)=0.068, Pearson's P=0.814).When testing for genotypes, rs324011 homozygous T/T genotype was significantly associated with asthma, when the Recessive model is considered (T/T vs. C/C+C/T) (adjusted, OR=2.49, 95% CI=1.18-5.25, Pearson's P=0.014(∗), Yates' P=0.022(∗)). In contrast, rs324015 variant was not significantly associated with asthma. CONCLUSIONS Rs324011 homozygous T/T genotype was significantly associated with asthma risk whereas rs324015 genotypes were not in the Saudi population.
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Affiliation(s)
- Saleh Al-Muhsen
- Prince Naif Center for Immunology Research, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Alejandro Vazquez-Tello
- Prince Naif Center for Immunology Research, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Amer Jamhawi
- Prince Naif Center for Immunology Research, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Ahmed Bahammam
- Department of Internal Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Muslim Al Saadi
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Shaikh Mohammed Iqbal
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alfrayh
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Sibtain Afzal
- Prince Naif Center for Immunology Research, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Nouf Al-Khamis
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Rabih Halwani
- Prince Naif Center for Immunology Research, College of Medicine, King Saud University, Riyadh, Saudi Arabia; Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia.
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Mathias RA. Introduction to genetics and genomics in asthma: genetics of asthma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 795:125-55. [PMID: 24162907 DOI: 10.1007/978-1-4614-8603-9_9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
While asthma is a heterogeneous disease, a strong genetic basis has been firmly established. Rather than being a single disease entity, asthma consists of related, overlapping syndromes [Barnes (Proc Am Thor Soc 8:143-148, 2011)] including three general domains: variable airway obstruction, airway hyper-responsiveness, and airway inflammation with a considerable proportion, but not all, of asthma being IgE-mediated further adding to its heterogeneity. This chapter reviews the approaches to the elucidation of genetics of asthma from the early evidence of familial clustering to the current state of knowledge with genome-wide approaches. The conclusion is that research efforts have led to a tremendous repository of genetic determinants of asthma, most of which fall into the above phenotypic domains of the syndrome. We now look to future integrative approaches of genetics, genomics (Chap. 10), and epigenetics (Chap. 11) to better understand the causal mechanism through which, these genetic loci act in manifesting asthma.
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Affiliation(s)
- Rasika Ann Mathias
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, 5501 Hopkins Bayview Circle, 3B.79, Baltimore, MD, 21224, USA,
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Al-Muhsen S, Vazquez-Tello A, Alzaabi A, Al-Hajjaj MS, Al-Jahdali HH, Halwani R. IL-4 receptor alpha single-nucleotide polymorphisms rs1805010 and rs1801275 are associated with increased risk of asthma in a Saudi Arabian population. Ann Thorac Med 2014; 9:81-6. [PMID: 24791170 PMCID: PMC4005166 DOI: 10.4103/1817-1737.128849] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 01/22/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The IL-4 receptor alpha subunit (IL-4Rα), when associated with the common gamma chain receptor, or the IL-13Rα1 subunit, transduces signals to STAT6 in response to IL-4 and IL-13 stimulations. This results in a number of cell-specific responses including Th2 differentiation, lymphocyte proliferation and IgE production. Given the prominent role of IL-4Rα in allergic disorders, several single-nucleotide polymorphisms (SNPs) have been found associated with asthma and other atopic disorders, including rs1805010 (I75V) and rs1801275 (Q576R) SNPs; however, lack of significant association have also been reported for some ethnic groups. The objective of this study was to determine whether IL-4Rα rs1805010 and rs1801275 polymorphisms are associated with asthma in patients from Saudi Arabia. MATERIALS AND METHODS One hundred and ninety severe asthmatic patients (11-70 years old) and 194 healthy subjects of equivalent age range were recruited for blood donation. DNA was purified and genotyping for rs1801275 and rs1805010 polymorphisms in the IL-4Rα gene was performed by PCR amplification, followed by cycle sequencing of the purified PCR fragments using BigDye chain terminator and capillary electrophoresis. RESULTS Pearson's Chi-square tests showed that the minor alleles, G, for both rs1805010 and rs1801275 SNPs, were significantly more frequent in asthmatics than in the healthy group (Yates' P < 0.05); conversely, the major alleles, A, were significantly more frequent in healthy than in asthmatics (P < 0.05). Concerning association analysis, odds for A/G-G/G genotypes were significantly higher to be associated with asthma predisposition (rs1801275: OR = 2.12; 95% CI = 1.39-3.22; P < 0.001*; rs1805010: OR = 1.6; 95% CI = 1.01-2.53; P < 0.05*; dominant model). Analysis of gender-genotype interactions, with genders nested within A/G-G/G, indicated higher odds for females than males of significant association with asthma (rs1801275: OR = 5.19, 95% CI = 2.09-12.94*; rs1805010: OR = 3.73, 95% CI = 2.06-6.74*). Rs1805010 and rs1801275 were in linkage disequilibrium (D' = 0.27; P < 0.0004*), with G-G haplotype being more frequent in asthmatics than in healthy subjects (OR = 2.43, 95% CI = 1.59-3.71*). CONCLUSIONS The risk alleles, G, of IL-4Rα rs1805010 and rs1801275 SNPs and corresponding A/G-G/G genotypes were significantly associated with asthma predisposition in asthmatics from Saudi Arabia.
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Affiliation(s)
- Saleh Al-Muhsen
- Prince Naif Center for Immunology Research, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Department of Paediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Alejandro Vazquez-Tello
- Prince Naif Center for Immunology Research, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Mohamed S. Al-Hajjaj
- Department of Internal Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Rabih Halwani
- Prince Naif Center for Immunology Research, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Department of Paediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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Thompson MD, Cole DEC, Capra V, Siminovitch KA, Rovati GE, Burnham WM, Rana BK. Pharmacogenetics of the G protein-coupled receptors. Methods Mol Biol 2014; 1175:189-242. [PMID: 25150871 DOI: 10.1007/978-1-4939-0956-8_9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pharmacogenetics investigates the influence of genetic variants on physiological phenotypes related to drug response and disease, while pharmacogenomics takes a genome-wide approach to advancing this knowledge. Both play an important role in identifying responders and nonresponders to medication, avoiding adverse drug reactions, and optimizing drug dose for the individual. G protein-coupled receptors (GPCRs) are the primary target of therapeutic drugs and have been the focus of these studies. With the advance of genomic technologies, there has been a substantial increase in the inventory of naturally occurring rare and common GPCR variants. These variants include single-nucleotide polymorphisms and insertion or deletions that have potential to alter GPCR expression of function. In vivo and in vitro studies have determined functional roles for many GPCR variants, but genetic association studies that define the physiological impact of the majority of these common variants are still limited. Despite the breadth of pharmacogenetic data available, GPCR variants have not been included in drug labeling and are only occasionally considered in optimizing clinical use of GPCR-targeted agents. In this chapter, pharmacogenetic and genomic studies on GPCR variants are reviewed with respect to a subset of GPCR systems, including the adrenergic, calcium sensing, cysteinyl leukotriene, cannabinoid CB1 and CB2 receptors, and the de-orphanized receptors such as GPR55. The nature of the disruption to receptor function is discussed with respect to regulation of gene expression, expression on the cell surface (affected by receptor trafficking, dimerization, desensitization/downregulation), or perturbation of receptor function (altered ligand binding, G protein coupling, constitutive activity). The large body of experimental data generated on structure and function relationships and receptor-ligand interactions are being harnessed for the in silico functional prediction of naturally occurring GPCR variants. We provide information on online resources dedicated to GPCRs and present applications of publically available computational tools for pharmacogenetic studies of GPCRs. As the breadth of GPCR pharmacogenomic data becomes clearer, the opportunity for routine assessment of GPCR variants to predict disease risk, drug response, and potential adverse drug effects will become possible.
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Affiliation(s)
- Miles D Thompson
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON, Canada, M5S 1A8,
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Peprah E, Wonkam A. Biomedical research, a tool to address the health issues that affect African populations. Global Health 2013; 9:50. [PMID: 24143865 PMCID: PMC4015770 DOI: 10.1186/1744-8603-9-50] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 08/05/2013] [Indexed: 12/22/2022] Open
Abstract
Traditionally, biomedical research endeavors in low to middle resources countries have focused on communicable diseases. However, data collected over the past 20 years by the World Health Organization (WHO) show a significant increase in the number of people suffering from non-communicable diseases (e.g. heart disease, diabetes, cancer and pulmonary diseases). Within the coming years, WHO predicts significant decreases in communicable diseases while non-communicable diseases are expected to double in low and middle income countries in sub-Saharan Africa. The predicted increase in the non-communicable diseases population could be economically burdensome for the basic healthcare infrastructure of countries that lack resources to address this emerging disease burden. Biomedical research could stimulate development of healthcare and biomedical infrastructure. If this development is sustainable, it provides an opportunity to alleviate the burden of both communicable and non-communicable diseases through diagnosis, prevention and treatment. In this paper, we discuss how research using biomedical technology, especially genomics, has produced data that enhances the understanding and treatment of both communicable and non-communicable diseases in sub-Saharan Africa. We further discuss how scientific development can provide opportunities to pursue research areas responsive to the African populations. We limit our discussion to biomedical research in the areas of genomics due to its substantial impact on the scientific community in recent years however, we also recognize that targeted investments in other scientific disciplines could also foster further development in African countries.
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Affiliation(s)
- Emmanuel Peprah
- Current address: National Institutes of Health, Building 1, RM 256A, Bethesda MD 20892, USA
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road-7925, Observatory, Cape Town, South Africa
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Pino-Yanes M, Corrales A, Cumplido J, Poza P, Sánchez-Machín I, Sánchez-Palacios A, Figueroa J, Acosta-Fernández O, Buset N, García-Robaina JC, Hernández M, Villar J, Carrillo T, Flores C. Assessing the validity of asthma associations for eight candidate genes and age at diagnosis effects. PLoS One 2013; 8:e73157. [PMID: 24039878 PMCID: PMC3767824 DOI: 10.1371/journal.pone.0073157] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 07/18/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Before the advent of genome-wide association studies (GWAS), ADAM33, ADRB2, CD14, MS4A2 (alias FCER1B), IL13, IL4, IL4R, and TNF constituted the most replicated non-HLA candidate genes with asthma and related traits. However, except for the IL13-IL4 region, none of these genes have been found in close proximity of genome-wide significant hits among GWAS for asthma or related traits. Here we aimed to assess the reproducibility of these asthma associations and to test if associations were more evident considering the effect of age at diagnosis. METHODOLOGY/PRINCIPAL FINDINGS We systematically evaluated 286 common single nucleotide polymorphisms (SNPs) of these 8 genes in a sample of 1,865 unrelated Spanish individuals (606 asthmatics and 1,259 controls). We found that variants at MS4A2, IL4R and ADAM33 genes demonstrated varying association effects with the age at diagnosis of asthma, with 10 SNPs showing study-wise significance after the multiple comparison adjustment. In addition, in silico replication with GWAS data supported the association of IL4R. CONCLUSIONS/SIGNIFICANCE Our results support the important role of MS4A2, IL4R and ADAM33 genes in asthma and/or atopy susceptibility. However, additional studies in larger samples sets are needed to firmly implicate these genes in asthma susceptibility, and also to identify the causal variation underlying the associations found.
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Affiliation(s)
- María Pino-Yanes
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain ; Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
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Kantor DB, Palmer CD, Young TR, Meng Y, Gajdos ZK, Lyon H, Price AL, Pollack S, London SJ, Loehr LR, Smith LJ, Kumar R, Jacobs DR, Petrini MF, O’Connor GT, White WB, Papanicolaou G, Burkart KM, Heckbert SR, Barr RG, Hirschhorn JN. Replication and fine mapping of asthma-associated loci in individuals of African ancestry. Hum Genet 2013; 132:1039-47. [PMID: 23666277 PMCID: PMC3975655 DOI: 10.1007/s00439-013-1310-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 04/19/2013] [Indexed: 12/14/2022]
Abstract
Asthma originates from genetic and environmental factors with about half the risk of disease attributable to heritable causes. Genome-wide association studies, mostly in populations of European ancestry, have identified numerous asthma-associated single nucleotide polymorphisms (SNPs). Studies in populations with diverse ancestries allow both for identification of robust associations that replicate across ethnic groups and for improved resolution of associated loci due to different patterns of linkage disequilibrium between ethnic groups. Here we report on an analysis of 745 African-American subjects with asthma and 3,238 African-American control subjects from the Candidate Gene Association Resource (CARe) Consortium, including analysis of SNPs imputed using 1,000 Genomes reference panels and adjustment for local ancestry. We show strong evidence that variation near RAD50/IL13, implicated in studies of European ancestry individuals, replicates in individuals largely of African ancestry. Fine mapping in African ancestry populations also refined the variants of interest for this association. We also provide strong or nominal evidence of replication at loci near ORMDL3/GSDMB, IL1RL1/IL18R1, and 10p14, all previously associated with asthma in European or Japanese populations, but not at the PYHIN1 locus previously reported in studies of African-American samples. These results improve the understanding of asthma genetics and further demonstrate the utility of genetic studies in populations other than those of largely European ancestry.
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Affiliation(s)
- David B. Kantor
- Division of Critical Care Medicine, Department of Anesthesiology, Perioperative and Pain Medicine, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Cameron D. Palmer
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Taylor R. Young
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Yan Meng
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Zofia K. Gajdos
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Helen Lyon
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Alkes L. Price
- Departments of Epidemiology and Biostatistics, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Samuela Pollack
- Departments of Epidemiology and Biostatistics, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Stephanie J. London
- Division of Intramural Research, DHHS, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, Research Triangle Park, NC 27709, USA
| | - Laura R. Loehr
- Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Lewis J. Smith
- Northwestern University, Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, 240 E. Huron Ave, Chicago, IL 60611, USA
| | - Rajesh Kumar
- Ann & Robert H. Lurie Children’s Hospital of Chicago, 225 E Chicago Avenue, Chicago, IL 60611, USA
| | - David R. Jacobs
- Division of Epidemiology and Community Health, University of Minnesota, 1300 S. 2nd Street Suite 300, Minneapolis, MN 55454, USA
| | - Marcy F. Petrini
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Mississippi Medical Center, 2500 North State St, Jackson, MS 39216-4505, USA
| | - George T. O’Connor
- Department of Medicine, Pulmonary Center, Boston University School of Medicine, Room R 304, 72. E. Concord St, Boston, MA 02118, USA
| | - Wendy B. White
- Tougaloo College and Jackson Heart Study, 500 West County Line Road, Tougaloo, MS 39174, USA
| | - George Papanicolaou
- Division of Prevention and Population Sciences, National Heart, Lung and Blood Institute, National Institutes of Health, Two Rockledge Center, Suite 10018 6701 Rockledge Drive, MSC 7936, Bethesda, MD 20892-7936, USA
| | - Kristin M. Burkart
- Division of Pulmonary, Allergy and Critical Care, College of Physicians and Surgeons, Columbia University, 622 West 168th Street, PH 8 East, Room 101, New York, NY 10032, USA
| | - Susan R. Heckbert
- University of Washington, Department of Epidemiology, School of Public Health, Cardiovascular Health Research Unit, 1730 Minor Avenue, Suite 1360, Seattle, WA 98101-1466, USA
| | - R. Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Department of Epidemiology, Mailman School of Public Health, Columbia University, PH 9 East, Room 105, New York, NY 10032, USA
| | - Joel N. Hirschhorn
- Program in Medical and Population Genetics, Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
- Division of Endocrinology, Boston Children’s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
- Departments of Genetics and Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
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Lang JE, Blake KV. Role of biomarkers in understanding and treating children with asthma: towards personalized care. PHARMACOGENOMICS & PERSONALIZED MEDICINE 2013; 6:73-84. [PMID: 24019751 PMCID: PMC3760446 DOI: 10.2147/pgpm.s30626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Asthma is one of the most common chronic diseases affecting children. Despite publicized expert panels on asthma management and the availability of high-potency inhaled corticosteroids, asthma continues to pose an enormous burden on quality of life for children. Research into the genetic and molecular origins of asthma are starting to show how distinct disease entities exist within the syndrome of "asthma". Biomarkers can be used to diagnose underlying molecular mechanisms that can predict the natural course of disease or likely response to drug treatment. The progress of personalized medicine in the care of children with asthma is still in its infancy. We are not yet able to apply stratified asthma treatments based on molecular phenotypes, although that time may be fast approaching. This review discusses some of the recent advances in asthma genetics and the use of current biomarkers that can help guide improved treatment. For example, the fraction of expired nitric oxide and serum Immunoglobulin E (IgE) (including allergen-specific IgE), when evaluated in the context of recurrent asthma symptoms, are general predictors of allergic airway inflammation. Biomarker assays for secondhand tobacco smoke exposure and cysteinyl leukotrienes are both promising areas of study that can help personalize management, not just for pharmacologic management, but also education and prevention efforts.
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Affiliation(s)
- Jason E Lang
- Division of Pulmonary and Sleep Medicine, Nemours Children's Hospital, Orlando, FL, USA
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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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Kumar Y, Bhatia A. Immunopathogenesis of allergic disorders: current concepts. Expert Rev Clin Immunol 2013; 9:211-26. [PMID: 23445196 DOI: 10.1586/eci.12.104] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allergic disorders are a group of immune-mediated disorders that are associated with considerable morbidity and ill health. There has been significant rise in the prevalence of allergy in the last few years. This has heightened interest in uncovering the novel mechanisms involved in etiopathogenesis of allergic disorders. Understanding the pathways underlying allergy will help in developing effective modalities for its prevention and treatment. This review focuses primarily on common IgE-mediated allergic conditions and recent developments in their immunopathogenesis, especially those involving respiratory mucosa.
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Affiliation(s)
- Yashwant Kumar
- Department of Immunopathology, Post Graduate Institute of Medical Education & Research, Chandigarh 160012, India.
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Matullo G, Di Gaetano C, Guarrera S. Next generation sequencing and rare genetic variants: from human population studies to medical genetics. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2013; 54:518-532. [PMID: 23922201 DOI: 10.1002/em.21799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 05/31/2013] [Accepted: 06/09/2013] [Indexed: 06/02/2023]
Abstract
The allelic frequency spectrum emerging from several Next Generation Sequencing (NGS) projects is revealing important details about evolutionary and demographic forces that shaped the human genome. Herein, we discuss some of the achievements of the use of low-frequency and rare variants from NGS studies. The majority of variants that affect protein-coding regions are recent and rare. Often, the novel rare variants are enriched for deleterious alleles and are population-specific, making them suitable for the study of disease susceptibility. To investigate this kind of variation and its effects in association studies, very large sample sizes will be necessary to achieve sufficient statistical power. Moreover, as these variants are typically population-specific, the replication of disease associations across populations could be very difficult due to population stratification. Therefore, the design of experiments focusing on the identification of rare variants and their effects should be carefully planned. Although several successes have already been achieved through NGS for genetic epidemiology, pharmacogenetic and clinical purposes, with improvements of the sequencing technology and decreased costs, further advances are expected in the near future.
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Affiliation(s)
- Giuseppe Matullo
- Dipartimento di Scienze Mediche, Università di Torino, Torino, Italy.
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Lasky-Su J, Himes BE, Raby BA, Klanderman BJ, Sylvia JS, Lange C, Melen E, Martinez FD, Israel E, Gauderman J, Gilliland F, Sleiman P, Hakonarson H, Celedón JC, Soto-Quiros M, Avila L, Lima JJ, Irvin CG, Peters SP, Boushey H, Chinchilli VM, Mauger D, Tantisira K, Weiss ST. HLA-DQ strikes again: genome-wide association study further confirms HLA-DQ in the diagnosis of asthma among adults. Clin Exp Allergy 2013. [PMID: 23181788 DOI: 10.1111/cea.12000] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Asthma is a common chronic respiratory disease in children and adults. An important genetic component to asthma susceptibility has long been recognized, most recently through the identification of several genes (e.g., ORMDL3, PDE4D, HLA-DQ, and TLE4) via genome-wide association studies. OBJECTIVE To identify genetic variants associated with asthma affection status using genome-wide association data. METHODS We describe results from a genome-wide association study on asthma performed in 3855 subjects using a panel of 455 089 single nucleotide polymorphisms (SNPs). RESULT The genome-wide association study resulted in the prioritization of 33 variants for immediate follow-up in a multi-staged replication effort. Of these, a common polymorphism (rs9272346) localizing to within 1 Kb of HLA-DQA1 (chromosome 6p21.3) was associated with asthma in adults (P-value = 2.2E-08) with consistent evidence in the more heterogeneous group of adults and children (P-value = 1.0E-04). Moreover, some genes identified in prior asthma GWAS were nominally associated with asthma in our populations. CONCLUSION Overall, our findings further replicate the HLA-DQ region in the pathogenesis of asthma. HLA-DQA1 is the fourth member of the HLA family found to be associated with asthma, in addition to the previously identified HLA-DRA, HLA-DQB1 and HLA-DQA2.
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Affiliation(s)
- J Lasky-Su
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
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March ME, Sleiman PM, Hakonarson H. Genetic polymorphisms and associated susceptibility to asthma. Int J Gen Med 2013; 6:253-65. [PMID: 23637549 PMCID: PMC3636804 DOI: 10.2147/ijgm.s28156] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
As complex common diseases, asthma and allergic diseases are caused by the interaction of multiple genetic variants with a variety of environmental factors. Candidate-gene studies have examined the involvement of a very large list of genes in asthma and allergy, demonstrating a role for more than 100 loci. These studies have elucidated several themes in the biology and pathogenesis of these diseases. A small number of genes have been associated with asthma or allergy through traditional linkage analyses. The publication of the first asthma-focused genome-wide association (GWA) study in 2007 has been followed by nearly 30 reports of GWA studies targeting asthma, allergy, or associated phenotypes and quantitative traits. GWA studies have confirmed several candidate genes and have identified new, unsuspected, and occasionally uncharacterized genes as asthma susceptibility loci. Issues of results replication persist, complicating interpretation and making conclusions difficult to draw, and much of the heritability of these diseases remains undiscovered. In the coming years studies of complex diseases like asthma and allergy will probably involve the use of high-throughput next-generation sequencing, which will bring a tremendous influx of new information as well as new problems in dealing with vast datasets.
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Affiliation(s)
- Michael E March
- Center for Applied Genomics, Abramson Research Center of the Joseph Stokes Jr Research Institute, The Children's Hospital of Philadelphia
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77
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Yang M, Fu X, Zhang Y, Zhang J, He J, Tian C, Huang J, Fan H. The +252A/G polymorphism in the lymphotoxin-α gene increases the risk of asthma: a meta-analysis. Respirology 2013; 17:1229-36. [PMID: 22882567 DOI: 10.1111/j.1440-1843.2012.02243.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND AND OBJECTIVE A number of studies have shown that the +252A/G polymorphism (rs909253) in the lymphotoxin-α (LT-α) gene is implicated in susceptibility to asthma. However, the findings have been inconclusive. The aim of this study was to investigate the association between the +252A/G polymorphism in the LT-α gene and the risk of asthma by performing a meta-analysis. METHODS The Pubmed and Embase databases were searched for all studies relating to this polymorphism and the risk of asthma. Statistical analyses were performed using the Revman4.2 and STATA 10.0 software. RESULTS Thirteen case-control studies that included a total of 2220 cases and 6428 controls were included in the meta-analysis. There was no significant association between this polymorphism and the risk of asthma in the all-combined analysis (odds ratio (OR) 1.14, 95% confidence interval (CI): 0.89-1.45 for GG+GA vs AA). In a subgroup analysis by ethnicity, no significant association with asthma risk was identified in Asians (OR 1.31, 95% CI: 0.97-1.77) or Europeans (OR 1.08, 95% CI: 0.77-1.53). In a subgroup analysis by age, a significantly increased risk was identified among adults (OR 1.25, 95% CI: 1.03-1.50) but not children (OR 1.04, 95% CI: 0.28-3.89). In a subgroup analysis by atopic status, a significantly elevated risk was identified among atopic (OR 1.55, 95% CI: 1.28-1.87) but not non-atopic individuals (OR 0.94, 95% CI: 0.53-1.68). CONCLUSIONS This meta-analysis suggested that the +252A/G polymorphism in the LT-α gene is a risk factor for asthma in adults and atopic populations.
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Affiliation(s)
- Min Yang
- Department of Respiratory Medicine, West China Hospital of Sichuan University, Chengdu, China
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Vergara C, Murray T, Rafaels N, Lewis R, Campbell M, Foster C, Gao L, Faruque M, Oliveira RR, Carvalho E, Araujo MI, Cruz AA, Watson H, Mercado D, Knight-Madden J, Ruczinski I, Dunston G, Ford J, Caraballo L, Beaty TH, Mathias RA, Barnes KC. African ancestry is a risk factor for asthma and high total IgE levels in African admixed populations. Genet Epidemiol 2013; 37:393-401. [PMID: 23554133 DOI: 10.1002/gepi.21702] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 11/21/2012] [Accepted: 11/22/2012] [Indexed: 12/16/2022]
Abstract
Characterization of genetic admixture of populations in the Americas and the Caribbean is of interest for anthropological, epidemiological, and historical reasons. Asthma has a higher prevalence and is more severe in populations with a high African component. Association of African ancestry with asthma has been demonstrated. We estimated admixture proportions of samples from six trihybrid populations of African descent and determined the relationship between African ancestry and asthma and total serum IgE levels (tIgE). We genotyped 237 ancestry informative markers in asthmatics and nonasthmatic controls from Barbados (190/277), Jamaica (177/529), Brazil (40/220), Colombia (508/625), African Americans from New York (207/171), and African Americans from Baltimore/Washington, D.C. (625/757). We estimated individual ancestries and evaluated genetic stratification using Structure and principal component analysis. Association of African ancestry and asthma and tIgE was evaluated by regression analysis. Mean ± SD African ancestry ranged from 0.76 ± 0.10 among Barbadians to 0.33 ± 0.13 in Colombians. The European component varied from 0.14 ± 0.05 among Jamaicans and Barbadians to 0.26 ± 0.08 among Colombians. African ancestry was associated with risk for asthma in Colombians (odds ratio (OR) = 4.5, P = 0.001) Brazilians (OR = 136.5, P = 0.003), and African Americans of New York (OR: 4.7; P = 0.040). African ancestry was also associated with higher tIgE levels among Colombians (β = 1.3, P = 0.04), Barbadians (β = 3.8, P = 0.03), and Brazilians (β = 1.6, P = 0.03). Our findings indicate that African ancestry can account for, at least in part, the association between asthma and its associated trait, tIgE levels.
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Affiliation(s)
- Candelaria Vergara
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University (JHU), Baltimore, MD, USA
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79
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Ried JS, Baurecht H, Stückler F, Krumsiek J, Gieger C, Heinrich J, Kabesch M, Prehn C, Peters A, Rodriguez E, Schulz H, Strauch K, Suhre K, Wang-Sattler R, Wichmann HE, Theis FJ, Illig T, Adamski J, Weidinger S. Integrative genetic and metabolite profiling analysis suggests altered phosphatidylcholine metabolism in asthma. Allergy 2013; 68:629-36. [PMID: 23452035 DOI: 10.1111/all.12110] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2012] [Indexed: 11/30/2022]
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified many risk loci for asthma, but effect sizes are small, and in most cases, the biological mechanisms are unclear. Targeted metabolite quantification that provides information about a whole range of pathways of intermediary metabolism can help to identify biomarkers and investigate disease mechanisms. Combining genetic and metabolic information can aid in characterizing genetic association signals with high resolution. This work aimed to investigate the interrelation of current asthma, candidate asthma risk alleles and a panel of metabolites. METHODS We investigated 151 metabolites, quantified by targeted mass spectrometry, in fasting serum of asthmatic and nonasthmatic individuals from the population-based KORA F4 study (N = 2925). In addition, we analysed effects of single-nucleotide polymorphisms (SNPs) at 24 asthma risk loci on these metabolites. RESULTS Increased levels of various phosphatidylcholines and decreased levels of various lyso-phosphatidylcholines were associated with asthma. Likewise, asthma risk alleles from the PDED3 and MED24 genes at the asthma susceptibility locus 17q21 were associated with increased concentrations of various phosphatidylcholines with consistent effect directions. CONCLUSIONS Our study demonstrated the potential of metabolomics to infer asthma-related biomarkers by the identification of potentially deregulated phospholipids that associate with asthma and asthma risk alleles.
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Affiliation(s)
- J. S. Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health; Neuherberg; Germany
| | - H. Baurecht
- Department of Dermatology, Allergology, and Venerology; University Hospital Schleswig-Holstein, Campus Kiel; Kiel; Germany
| | - F. Stückler
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health; Neuherberg; Germany
| | - J. Krumsiek
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München - German Research Center for Environmental Health; Neuherberg; Germany
| | - C. Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health; Neuherberg; Germany
| | - J. Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health; Neuherberg; Germany
| | - M. Kabesch
- University Children's Hospital Regensburg (KUNO); Department of Pediatric Pneumology and Allergy; Regensburg
| | - C. Prehn
- Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health; Neuherberg; Germany
| | | | - E. Rodriguez
- Department of Dermatology, Allergology, and Venerology; University Hospital Schleswig-Holstein, Campus Kiel; Kiel; Germany
| | - H. Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health; Neuherberg; Germany
| | | | | | - R. Wang-Sattler
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health; Neuherberg; Germany
| | | | | | | | | | - S. Weidinger
- Department of Dermatology, Allergology, and Venerology; University Hospital Schleswig-Holstein, Campus Kiel; Kiel; Germany
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80
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Wegienka G, Havstad S, Joseph CLM, Zoratti E, Ownby D, Woodcroft K, Johnson CC. Racial disparities in allergic outcomes in African Americans emerge as early as age 2 years. Clin Exp Allergy 2013; 42:909-17. [PMID: 22909162 DOI: 10.1111/j.1365-2222.2011.03946.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Racial disparities in allergic disease outcomes have been reported with African Americans suffering disproportionately compared to White individuals. OBJECTIVE To examine whether or not racial disparities are present as early as age 2 years in a racially diverse birth cohort in the Detroit metropolitan area. METHODS All children who were participants in a birth cohort study in the Detroit metropolitan area were invited for a standardized physician exam with skin prick testing and parental interview at age 2 years. Physicians made inquiries regarding wheezing and allergy symptoms and inspected for and graded any atopic dermatitis (AD). Skin testing was performed for Alternaria, cat, cockroach, dog, Dermatophagoides farinae (Der F), Short Ragweed, Timothy grass, egg, milk and peanut. Specific IgE was measured for these same allergens and total IgE was determined. RESULTS African American children (n = 466) were more likely than White children (n = 223) to have experienced any of the outcomes examined: at least 1 positive skin prick test from the panel of 10 allergens (21.7% vs. 11.0%, P = 0.001); at least one specific IgE ≥ 0.35 IU/mL (out of a panel of 10 allergens) (54.0% vs. 42.9%, P = 0.02); had AD (27.0% vs. 13.5%, Chi-square P < 0.001); and to ever have wheezed (44.9% vs. 36.0%, P = 0.03). African American children also tended to have higher total IgE (geometric means 23.4 IU/mL (95%CI 20.8, 27.6) vs. 16.7 IU/mL (95%CI 13.6, 20.6 IU/mL), Wilcoxon Rank Sum P = 0.004). With the exception of wheezing, the associations did not vary after adjusting for common social economic status variables (e.g. household income), environmental variables (endotoxin; dog, cat and cockroach allergen in house dust) or variables that differed between the racial groups (e.g. breastfeeding). After adjustment, the wheeze difference was ameliorated. CONCLUSIONS With disparities emerging as early as age 2 years, investigations into sources of the disparities should include the prenatal period and early life.
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Affiliation(s)
- G Wegienka
- Department of Public Health Sciences, Henry Ford Hospital, Detroit, MI, USA.
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81
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Leong AB, Ramsey CD, Celedón JC. The challenge of asthma in minority populations. Clin Rev Allergy Immunol 2013; 43:156-83. [PMID: 21538075 DOI: 10.1007/s12016-011-8263-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The burden and disparity of asthma in race/ethnic minorities present a significant challenge. In this review, we will evaluate data on asthma epidemiology in minorities, examine potential reasons for asthma disparities, and discuss strategies of intervention and culturally sensitive care.
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Affiliation(s)
- Albin B Leong
- Pediatric Pulmonology and Allergy, Roseville Kaiser Medical Center, 1600 Eureka Road, Roseville, CA 95661, USA.
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82
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Yang IV, Schwartz DA. Epigenetic mechanisms and the development of asthma. J Allergy Clin Immunol 2012; 130:1243-55. [PMID: 23026498 PMCID: PMC3518374 DOI: 10.1016/j.jaci.2012.07.052] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/26/2012] [Accepted: 07/27/2012] [Indexed: 12/19/2022]
Abstract
Asthma is heritable, influenced by the environment, and modified by in utero exposures and aging; all of these features are also common to epigenetic regulation. Furthermore, the transcription factors that are involved in the development of mature T cells that are critical to the T(H)2 immune phenotype in asthmatic patients are regulated by epigenetic mechanisms. Epigenetic marks (DNA methylation, modifications of histone tails, and noncoding RNAs) work in concert with other components of the cellular regulatory machinery to control the spatial and temporal levels of expressed genes. Technology to measure epigenetic marks on a genomic scale and comprehensive approaches to data analysis have recently emerged and continue to improve. Alterations in epigenetic marks have been associated with exposures relevant to asthma, particularly air pollution and tobacco smoke, as well as asthma phenotypes, in a few population-based studies. On the other hand, animal studies have begun to decipher the role of epigenetic regulation of gene expression associated with the development of allergic airway disease. Epigenetic mechanisms represent a promising line of inquiry that might, in part, explain the inheritance and immunobiology of asthma.
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Affiliation(s)
- Ivana V Yang
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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83
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Hancock DB, Levy JL, Gaddis NC, Bierut LJ, Saccone NL, Page GP, Johnson EO. Assessment of genotype imputation performance using 1000 Genomes in African American studies. PLoS One 2012; 7:e50610. [PMID: 23226329 PMCID: PMC3511547 DOI: 10.1371/journal.pone.0050610] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/26/2012] [Indexed: 11/19/2022] Open
Abstract
Genotype imputation, used in genome-wide association studies to expand coverage of single nucleotide polymorphisms (SNPs), has performed poorly in African Americans compared to less admixed populations. Overall, imputation has typically relied on HapMap reference haplotype panels from Africans (YRI), European Americans (CEU), and Asians (CHB/JPT). The 1000 Genomes project offers a wider range of reference populations, such as African Americans (ASW), but their imputation performance has had limited evaluation. Using 595 African Americans genotyped on Illumina's HumanHap550v3 BeadChip, we compared imputation results from four software programs (IMPUTE2, BEAGLE, MaCH, and MaCH-Admix) and three reference panels consisting of different combinations of 1000 Genomes populations (February 2012 release): (1) 3 specifically selected populations (YRI, CEU, and ASW); (2) 8 populations of diverse African (AFR) or European (AFR) descent; and (3) all 14 available populations (ALL). Based on chromosome 22, we calculated three performance metrics: (1) concordance (percentage of masked genotyped SNPs with imputed and true genotype agreement); (2) imputation quality score (IQS; concordance adjusted for chance agreement, which is particularly informative for low minor allele frequency [MAF] SNPs); and (3) average r2hat (estimated correlation between the imputed and true genotypes, for all imputed SNPs). Across the reference panels, IMPUTE2 and MaCH had the highest concordance (91%-93%), but IMPUTE2 had the highest IQS (81%-83%) and average r2hat (0.68 using YRI+ASW+CEU, 0.62 using AFR+EUR, and 0.55 using ALL). Imputation quality for most programs was reduced by the addition of more distantly related reference populations, due entirely to the introduction of low frequency SNPs (MAF≤2%) that are monomorphic in the more closely related panels. While imputation was optimized by using IMPUTE2 with reference to the ALL panel (average r2hat = 0.86 for SNPs with MAF>2%), use of the ALL panel for African American studies requires careful interpretation of the population specificity and imputation quality of low frequency SNPs.
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Affiliation(s)
- Dana B Hancock
- Behavioral Health Epidemiology Program, Research Triangle Institute International, Research Triangle Park, North Carolina, United States of America.
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84
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Hao K, Bossé Y, Nickle DC, Paré PD, Postma DS, Laviolette M, Sandford A, Hackett TL, Daley D, Hogg JC, Elliott WM, Couture C, Lamontagne M, Brandsma CA, van den Berge M, Koppelman G, Reicin AS, Nicholson DW, Malkov V, Derry JM, Suver C, Tsou JA, Kulkarni A, Zhang C, Vessey R, Opiteck GJ, Curtis SP, Timens W, Sin DD. Lung eQTLs to help reveal the molecular underpinnings of asthma. PLoS Genet 2012; 8:e1003029. [PMID: 23209423 PMCID: PMC3510026 DOI: 10.1371/journal.pgen.1003029] [Citation(s) in RCA: 222] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 08/14/2012] [Indexed: 12/26/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified loci reproducibly associated with pulmonary diseases; however, the molecular mechanism underlying these associations are largely unknown. The objectives of this study were to discover genetic variants affecting gene expression in human lung tissue, to refine susceptibility loci for asthma identified in GWAS studies, and to use the genetics of gene expression and network analyses to find key molecular drivers of asthma. We performed a genome-wide search for expression quantitative trait loci (eQTL) in 1,111 human lung samples. The lung eQTL dataset was then used to inform asthma genetic studies reported in the literature. The top ranked lung eQTLs were integrated with the GWAS on asthma reported by the GABRIEL consortium to generate a Bayesian gene expression network for discovery of novel molecular pathways underpinning asthma. We detected 17,178 cis- and 593 trans- lung eQTLs, which can be used to explore the functional consequences of loci associated with lung diseases and traits. Some strong eQTLs are also asthma susceptibility loci. For example, rs3859192 on chr17q21 is robustly associated with the mRNA levels of GSDMA (P = 3.55×10−151). The genetic-gene expression network identified the SOCS3 pathway as one of the key drivers of asthma. The eQTLs and gene networks identified in this study are powerful tools for elucidating the causal mechanisms underlying pulmonary disease. This data resource offers much-needed support to pinpoint the causal genes and characterize the molecular function of gene variants associated with lung diseases. Recent genome-wide association studies (GWAS) have identified genetic variants associated with lung diseases. The challenge now is to find the causal genes in GWAS–nominated chromosomal regions and to characterize the molecular function of disease-associated genetic variants. In this paper, we describe an international effort to systematically capture the genetic architecture of gene expression regulation in human lung. By studying lung specimens from 1,111 individuals of European ancestry, we found a large number of genetic variants affecting gene expression in the lung, or lung expression quantitative trait loci (eQTL). These lung eQTLs will serve as an important resource to aid in the understanding of the molecular underpinnings of lung biology and its disruption in disease. To demonstrate the utility of this lung eQTL dataset, we integrated our data with previous genetic studies on asthma. Through integrative techniques, we identified causal variants and genes in GWAS–nominated loci and found key molecular drivers for asthma. We feel that sharing our lung eQTLs dataset with the scientific community will leverage the impact of previous large-scale GWAS on lung diseases and function by providing much needed functional information to understand the molecular changes introduced by the susceptibility genetic variants.
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Affiliation(s)
- Ke Hao
- Merck Research Laboratories, Boston, Massachusetts, United States of America
- Merck, Rahway, New Jersey, United States of America
- Genetics, Rosetta Inpharmatics, Merck, Seattle, Washington, United States of America
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec City, Canada
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Canada
| | - David C. Nickle
- Merck Research Laboratories, Boston, Massachusetts, United States of America
- Merck, Rahway, New Jersey, United States of America
- Genetics, Rosetta Inpharmatics, Merck, Seattle, Washington, United States of America
- * E-mail:
| | - Peter D. Paré
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Dirkje S. Postma
- Department of Pulmonology, University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Michel Laviolette
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Canada
| | - Andrew Sandford
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - Tillie L. Hackett
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
| | - Denise Daley
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, Canada
| | - James C. Hogg
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - W. Mark Elliott
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
| | - Christian Couture
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Canada
| | - Maxime Lamontagne
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Canada
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Department of Pulmonology, University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Gerard Koppelman
- Department of Pediatric Pulmonology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | | | | | - Christine Suver
- Sage Bionetworks, Seattle, Washington, United States of America
| | | | | | | | | | | | | | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Don D. Sin
- The University of British Columbia James Hogg Research Laboratory, St Paul's Hospital, Vancouver, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, Canada
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85
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Levin AM, Mathias RA, Huang L, Roth LA, Daley D, Myers RA, Himes BE, Romieu I, Yang M, Eng C, Park JE, Zoratti K, Gignoux CR, Torgerson DG, Galanter JM, Huntsman S, Nguyen EA, Becker AB, Chan-Yeung M, Kozyrskyj AL, Kwok PY, Gilliland FD, Gauderman WJ, Bleecker ER, Raby BA, Meyers DA, London SJ, Martinez FD, Weiss ST, Burchard EG, Nicolae DL, Ober C, Barnes KC, Williams LK. A meta-analysis of genome-wide association studies for serum total IgE in diverse study populations. J Allergy Clin Immunol 2012; 131:1176-84. [PMID: 23146381 DOI: 10.1016/j.jaci.2012.10.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/28/2012] [Accepted: 10/02/2012] [Indexed: 01/27/2023]
Abstract
BACKGROUND IgE is both a marker and mediator of allergic inflammation. Despite reported differences in serum total IgE levels by race-ethnicity, African American and Latino subjects have not been well represented in genetic studies of total IgE. OBJECTIVE We sought to identify the genetic predictors of serum total IgE levels. METHODS We used genome-wide association data from 4292 subjects (2469 African Americans, 1564 European Americans, and 259 Latinos) in the EVE Asthma Genetics Consortium. Tests for association were performed within each cohort by race-ethnic group (ie, African American, Latino, and European American) and asthma status. The resulting P values were meta-analyzed, accounting for sample size and direction of effect. Top single nucleotide polymorphism associations from the meta-analysis were reassessed in 6 additional cohorts comprising 5767 subjects. RESULTS We identified 10 unique regions in which the combined association statistic was associated with total serum IgE levels (P<5.0×10(-6)) and the minor allele frequency was 5% or greater in 2 or more population groups. Variant rs9469220, corresponding to HLA-DQB1, was the single nucleotide polymorphism most significantly associated with serum total IgE levels when assessed in both the replication cohorts and the discovery and replication sets combined (P=.007 and 2.45×10(-7), respectively). In addition, findings from earlier genome-wide association studies were also validated in the current meta-analysis. CONCLUSION This meta-analysis independently identified a variant near HLA-DQB1 as a predictor of total serum IgE levels in multiple race-ethnic groups. This study also extends and confirms the findings of earlier genome-wide association analyses in African American and Latino subjects.
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Affiliation(s)
- Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
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86
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Myers RA, Himes BE, Gignoux CR, Yang JJ, Gauderman WJ, Rebordosa C, Xie J, Torgerson DG, Levin AM, Baurley J, Graves PE, Mathias RA, Romieu I, Roth LA, Conti D, Avila L, Eng C, Vora H, LeNoir MA, Soto-Quiros M, Liu J, Celedón JC, Galanter JM, Farber HJ, Kumar R, Avila PC, Meade K, Serebrisky D, Thyne S, Rodriguez-Cintron W, Rodriguez-Santana JR, Borrell LN, Lemanske RF, Bleecker ER, Meyers DA, London SJ, Barnes KC, Raby BA, Martinez FD, Gilliland FD, Williams LK, Burchard EG, Weiss ST, Nicolae DL, Ober C. Further replication studies of the EVE Consortium meta-analysis identifies 2 asthma risk loci in European Americans. J Allergy Clin Immunol 2012; 130:1294-301. [PMID: 23040885 DOI: 10.1016/j.jaci.2012.07.054] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 07/27/2012] [Accepted: 07/31/2012] [Indexed: 11/26/2022]
Abstract
BACKGROUND Genome-wide association studies of asthma have implicated many genetic risk factors, with well-replicated associations at approximately 10 loci that account for only a small proportion of the genetic risk. OBJECTIVES We aimed to identify additional asthma risk loci by performing an extensive replication study of the results from the EVE Consortium meta-analysis. METHODS We selected 3186 single nucleotide polymorphisms for replication based on the P values from the EVE Consortium meta-analysis. These single nucleotide polymorphisms were genotyped in ethnically diverse replication samples from 9 different studies, totaling 7202 cases, 6426 controls, and 507 case-parent trios. Association analyses were conducted within each participating study, and the resulting test statistics were combined in a meta-analysis. RESULTS Two novel associations were replicated in European Americans: rs1061477 in the KLK3 gene on chromosome 19 (combined odds ratio = 1.18; 95% CI, 1.10-1.25) and rs9570077 (combined odds ratio =1.20; 95% CI, 1.12-1.29) on chromosome 13q21. We could not replicate any additional associations in the African Americans or Latinos. CONCLUSIONS This extended replication study identified 2 additional asthma risk loci in populations of European descent. The absence of additional loci for African Americans and Latinos highlights the difficulty in replicating associations in admixed populations.
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Affiliation(s)
- Rachel A Myers
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
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87
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Roth HM, Wadsworth SJ, Kahn M, Knight DA. The airway epithelium in asthma: developmental issues that scar the airways for life? Pulm Pharmacol Ther 2012; 25:420-6. [PMID: 23022283 DOI: 10.1016/j.pupt.2012.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 08/19/2012] [Accepted: 09/11/2012] [Indexed: 11/30/2022]
Abstract
While allergies are very common, affecting ∼40% of the population in most Western countries, only a proportion of allergic people develop asthma. This highlights the importance of tissue and cell specific mechanisms that contribute to the disease. As the interface between the inhaled environment and the internal environment of the lung, the epithelium normally possesses numerous mechanisms to maintain an effective protective barrier. However, the inability of the airway epithelium of asthmatics to effectively defend the lung against normally innocuous inhaled agents strongly suggests that asthma must involve defects in the epithelial barrier rather than being primarily an allergic disease. Evidence is accumulating that in asthma, the epithelium does not go through normal stages of development and differentiation and as a consequence, remain somewhat "immature". This in turn leads to a chronic cycle of dysregulated damage and repair which ultimately impacts on the airways function by increasing inflammation, but also by initiating processes that ultimately lead to changes to the structure and function of the airway.
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Affiliation(s)
- Hollis M Roth
- UBC James Hogg Research Centre, Institute for Heart + Lung Health, Canada
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88
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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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89
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Slager RE, Hawkins GA, Li X, Postma DS, Meyers DA, Bleecker ER. Genetics of asthma susceptibility and severity. Clin Chest Med 2012; 33:431-43. [PMID: 22929093 DOI: 10.1016/j.ccm.2012.05.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This article summarizes major findings in genome-wide studies of asthma susceptibility and severity. Two large meta-analyses identified four chromosomal regions which were consistently associated with development of asthma. Genes that are associated with asthma subphenotypes such as lung function, biomarker levels, and asthma therapeutic responses can provide insight into mechanisms of asthma severity and disease progression. Future genetic studies will incorporate sequencing in comprehensively phenotyped asthmatics to lead to the development of personalized therapy.
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Affiliation(s)
- Rebecca E Slager
- Center for Genomics and Personalized Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA
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90
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Torgerson DG, Gignoux CR, Galanter JM, Drake KA, Roth LA, Eng C, Huntsman S, Torres R, Avila PC, Chapela R, Ford JG, Rodríguez-Santana JR, Rodríguez-Cintrón W, Hernandez RD, Burchard EG. Case-control admixture mapping in Latino populations enriches for known asthma-associated genes. J Allergy Clin Immunol 2012; 130:76-82.e12. [PMID: 22502797 PMCID: PMC3593143 DOI: 10.1016/j.jaci.2012.02.040] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Revised: 12/20/2011] [Accepted: 02/02/2012] [Indexed: 12/22/2022]
Abstract
BACKGROUND Polymorphisms in more than 100 genes have been associated with asthma susceptibility, yet much of the heritability remains to be explained. Asthma disproportionately affects different racial and ethnic groups in the United States, suggesting that admixture mapping is a useful strategy to identify novel asthma-associated loci. OBJECTIVE We sought to identify novel asthma-associated loci in Latino populations using case-control admixture mapping. METHODS We performed genome-wide admixture mapping by comparing levels of local Native American, European, and African ancestry between children with asthma and nonasthmatic control subjects in Puerto Rican and Mexican populations. Within candidate peaks, we performed allelic tests of association, controlling for differences in local ancestry. RESULTS Between the 2 populations, we identified a total of 62 admixture mapping peaks at a P value of less than 10(-3) that were significantly enriched for previously identified asthma-associated genes (P= .0051). One of the peaks was statistically significant based on 100 permutations in the Mexican sample (6q15); however, it was not significant in Puerto Rican subjects. Another peak was identified at nominal significance in both populations (8q12); however, the association was observed with different ancestries. CONCLUSION Case-control admixture mapping is a promising strategy for identifying novel asthma-associated loci in Latino populations and implicates genetic variation at 6q15 and 8q12 regions with asthma susceptibility. This approach might be useful for identifying regions that contribute to both shared and population-specific differences in asthma susceptibility.
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Affiliation(s)
- Dara G Torgerson
- Department of Medicine, University of California San Francisco, San Francisco, CA 94158, USA.
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91
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Li X, Ampleford EJ, Howard TD, Moore WC, Torgerson DG, Li H, Busse WW, Castro M, Erzurum SC, Israel E, Nicolae DL, Ober C, Wenzel SE, Hawkins GA, Bleecker ER, Meyers DA. Genome-wide association studies of asthma indicate opposite immunopathogenesis direction from autoimmune diseases. J Allergy Clin Immunol 2012; 130:861-8.e7. [PMID: 22694930 DOI: 10.1016/j.jaci.2012.04.041] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 03/09/2012] [Accepted: 04/09/2012] [Indexed: 12/16/2022]
Abstract
BACKGROUND Genome-wide association studies (GWASs) of asthma have consistently implicated the ORM1-like 3 and gasdermin B (ORMDL3-GSDMB), IL33, IL-1 receptor-like 1 and IL-18 receptor 1 (IL1RL1-IL18R1), RAD50-IL13, thymic stromal lymphopoietin and WD repeat domain 36 region (TSLP-WDR36), and HLA-DR/DQ regions. OBJECTIVE A GWAS of asthma was performed in a non-Hispanic white population. METHODS A GWAS was performed in 813 Severe Asthma Research Program/Collaborative Studies on the Genetics of Asthma/Chicago Asthma Genetics Study cases and 1564 control subjects. The GWAS results were compared with those of the published GWASs of autoimmune diseases. RESULTS Multiple single nucleotide polymorphisms in the TNFAIP3 interacting protein 1 (TNIP1) gene, which interacts with TNFAIP3 and inhibits the TNF-α-induced nuclear factor κB inflammation pathway, were associated with asthma: rs1422673 (P = 3.44 × 10(-7)) and rs10036748 (P = 1.41 × 10(-6), r(2) = 0.67). rs1422673 was also associated with asthma in the published GABRIEL (P = .018) and EVE (P = 1.31 × 10(-5)) studies. The minor allele T of rs20541 in IL13 is the risk allele for asthma but the protective allele for psoriasis. The minor allele T of rs2395185 in HLA-DRA is the risk allele for asthma but the protective allele for ulcerative colitis. The minor allele A of rs2872507 in GSDMB is the protective allele for asthma but the risk allele for rheumatoid arthritis, Crohn disease, and ulcerative colitis. The T allele of rs10036748 in the TNIP1 gene is the minor protective allele for asthma but the minor or major risk allele for systemic lupus erythematosus and systemic sclerosis in non-Hispanic white or Chinese subjects, respectively. CONCLUSIONS Our study suggests that single nucleotide polymorphisms associated with both asthma and autoimmune diseases might have opposite effects on immunopathogenesis.
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Affiliation(s)
- Xingnan Li
- Center for Genomics and Personalized Medicine Research, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.
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92
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Torgerson DG, Capurso D, Ampleford EJ, Li X, Moore WC, Gignoux CR, Hu D, Eng C, Mathias RA, Busse WW, Castro M, Erzurum SC, Fitzpatrick AM, Gaston B, Israel E, Jarjour NN, Teague WG, Wenzel SE, Rodríguez-Santana JR, Rodríguez-Cintrón W, Avila PC, Ford JG, Barnes KC, Burchard EG, Howard TD, Bleecker ER, Meyers DA, Cox NJ, Ober C, Nicolae DL. Genome-wide ancestry association testing identifies a common European variant on 6q14.1 as a risk factor for asthma in African American subjects. J Allergy Clin Immunol 2012; 130:622-629.e9. [PMID: 22607992 DOI: 10.1016/j.jaci.2012.03.045] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 02/22/2012] [Accepted: 03/06/2012] [Indexed: 12/14/2022]
Abstract
BACKGROUND Genetic variants that contribute to asthma susceptibility might be present at varying frequencies in different populations, which is an important consideration and advantage for performing genetic association studies in admixed populations. OBJECTIVE We sought to identify asthma-associated loci in African American subjects. METHODS We compared local African and European ancestry estimated from dense single nucleotide polymorphism genotype data in African American adults with asthma and nonasthmatic control subjects. Allelic tests of association were performed within the candidate regions identified, correcting for local European admixture. RESULTS We identified a significant ancestry association peak on chromosome 6q. Allelic tests for association within this region identified a single nucleotide polymorphism (rs1361549) on 6q14.1 that was associated with asthma exclusively in African American subjects with local European admixture (odds ratio, 2.2). The risk allele is common in Europe (42% in the HapMap population of Utah residents with Northern and Western European ancestry from the Centre d'Etude du Polymorphisme Humain collection) but absent in West Africa (0% in the HapMap population of Yorubans in Ibadan, Nigeria), suggesting the allele is present in African American subjects because of recent European admixture. We replicated our findings in Puerto Rican subjects and similarly found that the signal of association is largely specific to subjects who are heterozygous for African and non-African ancestry at 6q14.1. However, we found no evidence for association in European American or Puerto Rican subjects in the absence of local African ancestry, suggesting that the association with asthma at rs1361549 is due to an environmental or genetic interaction. CONCLUSION We identified a novel asthma-associated locus that is relevant to admixed populations with African ancestry and highlight the importance of considering local ancestry in genetic association studies of admixed populations.
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Affiliation(s)
- Dara G Torgerson
- Department of Human Genetics, University of Chicago, Chicago, Il 60637, USA
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93
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Blumenthal MN. Genetic, epigenetic, and environmental factors in asthma and allergy. Ann Allergy Asthma Immunol 2012; 108:69-73. [PMID: 22289722 DOI: 10.1016/j.anai.2011.12.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/18/2011] [Accepted: 12/04/2011] [Indexed: 12/20/2022]
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94
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Gao PS, Leung DYM, Rafaels NM, Boguniewicz M, Hand T, Gao L, Hata TR, Schneider LC, Hanifin JM, Beaty TH, Beck LA, Weinberg A, Barnes KC. Genetic variants in interferon regulatory factor 2 (IRF2) are associated with atopic dermatitis and eczema herpeticum. J Invest Dermatol 2012; 132:650-7. [PMID: 22113474 PMCID: PMC3278591 DOI: 10.1038/jid.2011.374] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Interferon regulatory factor 2 (IRF2) is a member of a family of transcriptional factors involved in the modulation of IFN-induced immune responses to viral infection. To test whether genetic variants in IRF2 predict risk of atopic dermatitis (AD) and ADEH (atopic dermatitis complicated by eczema herpeticum), we genotyped 78 IRF2 tagging single-nucleotide polymorphisms (SNPs) in both European-American (n = 435) and African-American (n = 339) populations. Significant associations were observed between AD and two SNPs (rs793814, P = 0.007, odds ratio (OR) = 0.52; rs3756094, P = 0.037, OR = 0.66) among European Americans and one SNP (rs3775572, P = 0.016, OR = 0.46) among African Americans. Significant associations were also observed between ADEH and five SNPs (P = 0.049-0.022) among European Americans. The association with ADEH was further strengthened by haplotype analyses, wherein a five-SNP (CAGGA) haplotype showed the strongest association with ADEH (P = 0.0008). Eight IRF2 SNPs were significantly associated with IFN-γ production after herpes simplex virus (HSV) stimulation (P = 0.048-0.0008), including an AD-associated SNP (rs13139310, P = 0.008). Our findings suggest that distinct markers in IRF2 may be associated with AD and ADEH, which may depend upon ethnic ancestry, and genetic variants in IRF2 may contribute to an abnormal immune response to HSV.
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Affiliation(s)
- Pei-Song Gao
- Department of Medicine, Johns Hopkins Asthma and Allergy Center, Johns Hopkins University, Baltimore, Maryland 21224, USA
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95
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Torgerson D, Capurso D, Mathias R, Graves P, Hernandez R, Beaty T, Bleecker E, Raby B, Meyers D, Barnes K, Weiss S, Martinez F, Nicolae D, Ober C. Resequencing candidate genes implicates rare variants in asthma susceptibility. Am J Hum Genet 2012; 90:273-81. [PMID: 22325360 PMCID: PMC3276672 DOI: 10.1016/j.ajhg.2012.01.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 12/20/2011] [Accepted: 01/13/2012] [Indexed: 01/12/2023] Open
Abstract
Common variation in over 100 genes has been implicated in the risk of developing asthma, but the contribution of rare variants to asthma susceptibility remains largely unexplored. We selected nine genes that showed the strongest signatures of weak purifying selection from among 53 candidate asthma-associated genes, and we sequenced the coding exons and flanking noncoding regions in 450 asthmatic cases and 515 nonasthmatic controls. We observed an overall excess of p values <0.05 (p = 0.02), and rare variants in four genes (AGT, DPP10, IKBKAP, and IL12RB1) contributed to asthma susceptibility among African Americans. Rare variants in IL12RB1 were also associated with asthma susceptibility among European Americans, despite the fact that the majority of rare variants in IL12RB1 were specific to either one of the populations. The combined evidence of association with rare noncoding variants in IL12RB1 remained significant (p = 3.7 × 10(-4)) after correcting for multiple testing. Overall, the contribution of rare variants to asthma susceptibility was predominantly due to noncoding variants in sequences flanking the exons, although nonsynonymous rare variants in DPP10 and in IL12RB1 were associated with asthma in African Americans and European Americans, respectively. This study provides evidence that rare variants contribute to asthma susceptibility. Additional studies are required for testing whether prioritizing genes for resequencing on the basis of signatures of purifying selection is an efficient means of identifying novel rare variants that contribute to complex disease.
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Affiliation(s)
- Dara G. Torgerson
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Daniel Capurso
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Penelope E. Graves
- Arizona Respiratory Center and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Ryan D. Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Terri H. Beaty
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Eugene R. Bleecker
- Center for Genomics, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA
| | - Benjamin A. Raby
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Deborah A. Meyers
- Center for Genomics, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA
| | - Kathleen C. Barnes
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Scott T. Weiss
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Fernando D. Martinez
- Arizona Respiratory Center and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Dan L. Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Department of Statistics, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
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96
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Adcock IM, Barnes PJ. Con: Genome-wide association studies have not been useful in understanding asthma. Am J Respir Crit Care Med 2012; 184:633-6. [PMID: 21920926 DOI: 10.1164/rccm.201103-0446ed] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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97
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Weiss ST, Silverman EK. Pro: Genome-wide association studies (GWAS) in asthma. Am J Respir Crit Care Med 2012; 184:631-3. [PMID: 21920925 DOI: 10.1164/rccm.201103-0485ed] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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98
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African ancestry is associated with asthma risk in African Americans. PLoS One 2012; 7:e26807. [PMID: 22235241 PMCID: PMC3250386 DOI: 10.1371/journal.pone.0026807] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 10/04/2011] [Indexed: 11/19/2022] Open
Abstract
Background Asthma is a common complex condition with clear racial and ethnic differences in both prevalence and severity. Asthma consultation rates, mortality, and severe symptoms are greatly increased in African descent populations of developed countries. African ancestry has been associated with asthma, total serum IgE and lower pulmonary function in African-admixed populations. To replicate previous findings, here we aimed to examine whether African ancestry was associated with asthma susceptibility in African Americans. In addition, we examined for the first time whether African ancestry was associated with asthma exacerbations. Methodology/Principal Findings After filtering for self-reported ancestry and genotype data quality, samples from 1,117 self-reported African-American individuals from New York and Baltimore (394 cases, 481 controls), and Chicago (321 cases followed for asthma exacerbations) were analyzed. Genetic ancestry was estimated based on ancestry informative markers (AIMs) selected for being highly divergent among European and West African populations (95 AIMs for New York and Baltimore, and 66 independent AIMs for Chicago). Among case-control samples, the mean African ancestry was significantly higher in asthmatics than in non-asthmatics (82.0±14.0% vs. 77.8±18.1%, mean difference 4.2% [95% confidence interval (CI):2.0–6.4], p<0.0001). This association remained significant after adjusting for potential confounders (odds ratio: 4.55, 95% CI: 1.69–12.29, p = 0.003). African ancestry failed to show an association with asthma exacerbations (p = 0.965) using a model based on longitudinal data of the number of exacerbations followed over 1.5 years. Conclusions/Significance These data replicate previous findings indicating that African ancestry constitutes a risk factor for asthma and suggest that elevated asthma rates in African Americans can be partially attributed to African genetic ancestry.
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99
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Borysova ME, Mitchell O, Sultan DH, Williams AR. Racial and Ethnic Health Disparities in Incarcerated Populations. JOURNAL OF HEALTH DISPARITIES RESEARCH AND PRACTICE 2012; 5:92-100. [PMID: 23338674 PMCID: PMC3546523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Alarming disparities in population health and wellness in the United States have led to multidisciplinary research efforts to create health equity. Identifying disparities, elucidating the etiological bases of disparities, and implementing solutions to eliminate disparities are part of the U.S. national health agenda. Racial and ethnic disparities have been identified throughout the cancer control continuum, in cardiovascular disease, diabetes and a multitude of other conditions. The causes of disparities are complex, condition specific, and conjectured to result from combinations of biological and socio-behavioral factors. Racial and ethnic health disparities within the vast incarcerated communities have been excluded from most studies, yet are of significant ethical and fiscal concern to inmates, governing bodies, and non-incarcerated communities into which inmates return. Importantly, research on racial and ethnic disparities in this unique population may shed light on the relative etiologies of health disparities and solutions for creating health equity throughout the general population in the United States.
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100
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Ma SF, Xie L, Pino-Yanes M, Sammani S, Wade MS, Letsiou E, Siegler J, Wang T, Infusino G, Kittles RA, Flores C, Zhou T, Prabhakar BS, Moreno-Vinasco L, Villar J, Jacobson JR, Dudek SM, Garcia JGN. Type 2 deiodinase and host responses of sepsis and acute lung injury. Am J Respir Cell Mol Biol 2011; 45:1203-11. [PMID: 21685153 PMCID: PMC3262665 DOI: 10.1165/rcmb.2011-0179oc] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 06/10/2011] [Indexed: 12/21/2022] Open
Abstract
The role of thyroid hormone metabolism in clinical outcomes of the critically ill remains unclear. Using preclinical models of acute lung injury (ALI), we assessed the gene and protein expression of type 2 deiodinase (DIO2), a key driver for synthesis of biologically active triiodothyronine, and addressed potential association of DIO2 genetic variants with ALI in a multiethnic cohort. DIO2 gene and protein expression levels in murine lung were validated by microarrays and immunoblotting. Lung injury was assessed by levels of bronchoalveolar lavage protein and leukocytes. Single-nucleotide polymorphisms were genotyped and ALI susceptibility association assessed. Significant increases in both DIO2 gene and D2 protein expression were observed in lung tissues from murine ALI models (LPS- and ventilator-induced lung injury), with expression directly increasing with the extent of lung injury. Mice with reduced levels of DIO2 expression (by silencing RNA) demonstrated reduced thyroxine levels in plasma and increased lung injury (increased bronchoalveolar lavage protein and leukocytes), suggesting a protective role for DIO2 in ALI. The G (Ala) allele of the Thr92Ala coding single-nucleotide polymorphism (rs225014) was protective in severe sepsis and severe sepsis-associated ALI after adjustments for age, sex, and genetic ancestry in a logistic regression model in European Americans. Our studies indicate that DIO2 is a novel ALI candidate gene, the nonsynonymous Thr92Ala coding variant of which confers ALI protection. Increased DIO2 expression may dampen the ALI inflammatory response, thereby strengthening the premise that thyroid hormone metabolism is intimately linked to the integrated response to inflammatory injury in critically ill patients.
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Affiliation(s)
- Shwu-Fan Ma
- Section of Pulmonary and Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Lishi Xie
- Institute for Personalized Respiratory Medicine, Section of Pulmonary, Critical Care Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois
| | - Maria Pino-Yanes
- Centro de Investigacion Biomedica en Red Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Tenerife, Spain
| | - Saad Sammani
- Institute for Personalized Respiratory Medicine, Section of Pulmonary, Critical Care Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois
| | - Michael S. Wade
- Institute for Personalized Respiratory Medicine, Section of Pulmonary, Critical Care Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois
| | - Eleftheria Letsiou
- Institute for Personalized Respiratory Medicine, Section of Pulmonary, Critical Care Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois
| | - Jessica Siegler
- Institute for Personalized Respiratory Medicine, Section of Pulmonary, Critical Care Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois
| | - Ting Wang
- Institute for Personalized Respiratory Medicine, Section of Pulmonary, Critical Care Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois
| | - Giovanni Infusino
- Institute for Personalized Respiratory Medicine, Section of Pulmonary, Critical Care Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois
| | - Rick A. Kittles
- Section of Hematology and Oncology, Department of Medicine, and
| | - Carlos Flores
- Centro de Investigacion Biomedica en Red Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Tenerife, Spain
| | - Tong Zhou
- Institute for Personalized Respiratory Medicine, Section of Pulmonary, Critical Care Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois
| | - Bellur S. Prabhakar
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois
| | - Liliana Moreno-Vinasco
- Institute for Personalized Respiratory Medicine, Section of Pulmonary, Critical Care Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois
| | - Jesus Villar
- Centro de Investigacion Biomedica en Red Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Research Unit, Hospital Universitario Dr. Negrin, Las Palmas de Gran Canaria, Spain; and
- Keenan Research Center at the Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Canada
| | - Jeffrey R. Jacobson
- Institute for Personalized Respiratory Medicine, Section of Pulmonary, Critical Care Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois
| | - Steven M. Dudek
- Institute for Personalized Respiratory Medicine, Section of Pulmonary, Critical Care Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois
| | - Joe G. N. Garcia
- Institute for Personalized Respiratory Medicine, Section of Pulmonary, Critical Care Sleep and Allergy, University of Illinois at Chicago, Chicago, Illinois
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