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Sayers I, John C, Chen J, Hall IP. Genetics of chronic respiratory disease. Nat Rev Genet 2024; 25:534-547. [PMID: 38448562 DOI: 10.1038/s41576-024-00695-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/08/2024]
Abstract
Chronic respiratory diseases, such as chronic obstructive pulmonary disease (COPD), asthma and interstitial lung diseases are frequently occurring disorders with a polygenic basis that account for a large global burden of morbidity and mortality. Recent large-scale genetic epidemiology studies have identified associations between genetic variation and individual respiratory diseases and linked specific genetic variants to quantitative traits related to lung function. These associations have improved our understanding of the genetic basis and mechanisms underlying common lung diseases. Moreover, examining the overlap between genetic associations of different respiratory conditions, along with evidence for gene-environment interactions, has yielded additional biological insights into affected molecular pathways. This genetic information could inform the assessment of respiratory disease risk and contribute to stratified treatment approaches.
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Affiliation(s)
- Ian Sayers
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, University Park, Nottingham, UK
- Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, UK
| | - Catherine John
- University of Leicester, Leicester, UK
- University Hospitals of Leicester, Leicester, UK
| | - Jing Chen
- University of Leicester, Leicester, UK
| | - Ian P Hall
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, University Park, Nottingham, UK.
- Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, UK.
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2
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Wang AL, Lahousse L, Dahlin A, Edris A, McGeachie M, Lutz SM, Sordillo JE, Brusselle G, Lasky-Su J, Weiss ST, Iribarren C, Lu MX, Tantisira KG, Wu AC. Novel genetic variants associated with inhaled corticosteroid treatment response in older adults with asthma. Thorax 2023; 78:432-441. [PMID: 35501119 PMCID: PMC9810110 DOI: 10.1136/thoraxjnl-2021-217674] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 04/01/2022] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Older adults have the greatest burden of asthma and poorest outcomes. The pharmacogenetics of inhaled corticosteroid (ICS) treatment response is not well studied in older adults. METHODS A genome-wide association study of ICS response was performed in asthmatics of European ancestry in Genetic Epidemiology Research on Adult Health and Aging (GERA) by fitting Cox proportional hazards regression models, followed by validation in the Mass General Brigham (MGB) Biobank and Rotterdam Study. ICS response was measured using two definitions in asthmatics on ICS treatment: (1) absence of oral corticosteroid (OCS) bursts using prescription records and (2) absence of asthma-related exacerbations using diagnosis codes. A fixed-effect meta-analysis was performed for each outcome. The validated single-nucleotide polymorphisms (SNPs) were functionally annotated to standard databases. RESULTS In 5710 subjects in GERA, 676 subjects in MGB Biobank, and 465 subjects in the Rotterdam Study, four novel SNPs on chromosome six near PTCHD4 validated across all cohorts and met genome-wide significance on meta-analysis for the OCS burst outcome. In 4541 subjects in GERA and 505 subjects in MGB Biobank, 152 SNPs with p<5 × 10-5 were validated across these two cohorts for the asthma-related exacerbation outcome. The validated SNPs included methylation and expression quantitative trait loci for CPED1, CRADD and DST for the OCS burst outcome and GM2A, SNW1, CACNA1C, DPH1, and RPS10 for the asthma-related exacerbation outcome. CONCLUSIONS Multiple novel SNPs associated with ICS response were identified in older adult asthmatics. Several SNPs annotated to genes previously associated with asthma and other airway or allergic diseases, including PTCHD4.
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Affiliation(s)
- Alberta L Wang
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ahmed Edris
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Sharon M Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Joanne E Sordillo
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Guy Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Carlos Iribarren
- Kaiser Permanente Division of Research, Kaiser Permanente, Oakland, California, USA
| | - Meng X Lu
- Kaiser Permanente Division of Research, Kaiser Permanente, Oakland, California, USA
| | - Kelan G Tantisira
- Division of Pediatric Respiratory Medicine, Rady's Children's Hospital-San Diego, University of California San Diego School of Medicine, San Diego, California, USA
| | - Ann C Wu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
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3
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Hanif T, Ivaska LE, Ahmad F, Tan G, Mikola E, Puhakka T, Palomares O, Akdis CA, Toppila-Salmi S, Jartti T. Tonsillar transcriptional profiles in atopic and non-atopic subjects. Allergy 2023; 78:522-536. [PMID: 35899482 PMCID: PMC10087516 DOI: 10.1111/all.15458] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/29/2022] [Accepted: 07/09/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Emerging research suggests that local lymphatic tissue such as tonsils have important role in regulating the immune responses. However, allergen sensitization-induced alterations in transcriptome of tonsils are not known. OBJECTIVES To examine the key differences in tonsillar gene expression between atopic and non-atopic subjects and further by type of sensitization. METHODS RNA-sequencing was performed on 52 tonsillar samples from atopic and non-atopic tonsillectomy patients. Sensitization to common food- and aero-allergen was defined by allergen specific IgE. Following groups were studied: (1) aero- and food-allergen sensitized (AS+FS) versus non-sensitized (NS), (2) aeroallergen-sensitized (AS) versus food-allergen sensitized (FS), (3) AS versus NS, (4) FS versus NS. Bioinformatics analysis was done using DESeq2(v3.10.2), WGCNA and GATK pipeline in R software (v3.3.1). Protein-protein interaction network was made from String database. RESULTS We studied 13 aeroallergen-sensitized, 6 food-allergen sensitized, 4 both food-and aero-allergen-sensitized and 29 non-sensitized tonsillectomy patients. Overall, 697 unique differentially expressed genes (DEGs) were detected in all sensitized subgroups including chemokines (CXCL2, CXCL8, CXCL10, CXCL11), IL-20RA, MUC1 and MUC20. When comparing different groups, the gene expression profiles overlapped except the AS versus FS group comparison, suggesting significantly different gene expression between the two sensitization subgroups. Furthermore, aeroallergen-sensitized subjects had more prominent immune responses compared with non-sensitized and food-allergen sensitized subjects including gene expression for IL-17 pathway and Toll-like receptor signalling pathway. CONCLUSION Allergic sensitization is associated with extensive tonsillar transcriptomic alterations and changes in immune related genes and pathways. Distinct differences were found between aero-allergen and food-allergen sensitization.
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Affiliation(s)
- Tanzeela Hanif
- Department of Pediatrics and Adolescent Medicine, University of Turku, Turku, Finland.,Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Lotta E Ivaska
- Department of Otorhinolaryngology - Head and Neck Surgery, Turku University Hospital and University of Turku, Turku, Finland
| | - Freed Ahmad
- Department of Biology University of Turku, Turku, Finland
| | - Ge Tan
- Functional Genomics Center Zurich, ETH Zürich/University of Zürich, Zurich, Switzerland.,Swiss Institute of Allergy and Asthma Research, University of Zürich, Davos, Switzerland.,Christine Kuhne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Emilia Mikola
- Department of Otorhinolaryngology, Satakunta Central Hospital, Pori, Finland
| | - Tuomo Puhakka
- Department of Otorhinolaryngology - Head and Neck Surgery, Turku University Hospital and University of Turku, Turku, Finland
| | - Oscar Palomares
- Swiss Institute of Allergy and Asthma Research, University of Zürich, Davos, Switzerland.,Christine Kuhne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.,Department of Biochemistry and Molecular Biology, School of Chemistry, Complutense University of Madrid, Madrid, Spain
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research, University of Zürich, Davos, Switzerland.,Christine Kuhne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Sanna Toppila-Salmi
- Haartman Institute, University of Helsinki & Skin and Allergy Hospital, Helsinki University Hospital, Helsinki, Finland
| | - Tuomas Jartti
- Department of Pediatrics and Adolescent Medicine, University of Turku, Turku, Finland.,PEDEGO Research Unit, Medical Research Center, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
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4
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Boulund U, Bastos DM, Ferwerda B, van den Born BJ, Pinto-Sietsma SJ, Galenkamp H, Levin E, Groen AK, Zwinderman AH, Nieuwdorp M. Gut microbiome associations with host genotype vary across ethnicities and potentially influence cardiometabolic traits. Cell Host Microbe 2022; 30:1464-1480.e6. [PMID: 36099924 DOI: 10.1016/j.chom.2022.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/16/2022] [Accepted: 08/17/2022] [Indexed: 12/13/2022]
Abstract
Previous studies in mainly European populations have reported that the gut microbiome composition is associated with the human genome. However, the genotype-microbiome interaction in different ethnicities is largely unknown. We performed a large fecal microbiome genome-wide association study of a single multiethnic cohort, the Healthy Life in an Urban Setting (HELIUS) cohort (N = 4,117). Mendelian randomization was performed using the multiethnic Pan-UK Biobank (N = 460,000) to dissect potential causality. We identified ethnicity-specific associations between host genomes and gut microbiota. Certain microbes were associated with genotype in multiple ethnicities. Several of the microbe-associated loci were found to be related to immune functions, interact with glutamate and the mucus layer, or be expressed in the gut or brain. Additionally, we found that gut microbes potentially influence cardiometabolic health factors such as BMI, cholesterol, and blood pressure. This provides insight into the relationship of ethnicity and gut microbiota and into the possible causal effects of gut microbes on cardiometabolic traits.
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Affiliation(s)
- Ulrika Boulund
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Diogo M Bastos
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Bart Ferwerda
- Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Bert-Jan van den Born
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands; Department of Public and Occupational Health, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Sara-Joan Pinto-Sietsma
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands; Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Henrike Galenkamp
- Department of Public and Occupational Health, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Evgeni Levin
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands; HorAIzon BV, 2645 LT Delfgauw, the Netherlands
| | - Albert K Groen
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands.
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Chang D, Hunkapiller J, Bhangale T, Reeder J, Mukhyala K, Tom J, Cowgill A, Vogel J, Forrest WF, Khan Z, Stockwell A, McCarthy MI, Staton TL, Olsson J, Holweg CTJ, Cheung DS, Chen H, Brauer MJ, Graham RR, Behrens T, Wilson MS, Arron JR, Choy DF, Yaspan BL. A whole genome sequencing study of moderate to severe asthma identifies a lung function locus associated with asthma risk. Sci Rep 2022; 12:5574. [PMID: 35368043 PMCID: PMC8976834 DOI: 10.1038/s41598-022-09447-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/23/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractGenome-wide association studies (GWAS) have identified many common variant loci associated with asthma susceptibility, but few studies investigate the genetics underlying moderate-to-severe asthma risk. Here, we present a whole-genome sequencing study comparing 3181 moderate-to-severe asthma patients to 3590 non-asthma controls. We demonstrate that asthma risk is genetically correlated with lung function measures and that this component of asthma risk is orthogonal to the eosinophil genetics that also contribute to disease susceptibility. We find that polygenic scores for reduced lung function are associated with younger asthma age of onset. Genome-wide, seven previously reported common asthma variant loci and one previously reported lung function locus, near THSD4, reach significance. We replicate association of the lung function locus in a recently published GWAS of moderate-to-severe asthma patients. We additionally replicate the association of a previously reported rare (minor allele frequency < 1%) coding variant in IL33 and show significant enrichment of rare variant burden in genes from common variant allergic disease loci. Our findings highlight the contribution of lung function genetics to moderate-to-severe asthma risk, and provide initial rare variant support for associations with moderate-to-severe asthma risk at several candidate genes from common variant loci.
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6
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Wu M, Zheng X, Huang J, Hu X. Association of IL33, IL1RL1, IL1RAP Polymorphisms and Asthma in Chinese Han Children. Front Cell Dev Biol 2022; 9:759542. [PMID: 34977013 PMCID: PMC8714920 DOI: 10.3389/fcell.2021.759542] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/22/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Genome-wide association studies have identified interleukin 33 (IL33), interleukin 1 receptor-like 1 (IL1RL1), interleukin 1 receptor accessory protein (IL1RAP) as asthma susceptibility loci in Europeans. IL33, IL1RL1, and IL1RAP constitute a ligand-receptor complex. Objective: We analyzed associations of asthma susceptibility, eosinophilic airway inflammation, and response to inhaled corticosteroid (ICS) with single nucleotide polymorphisms (SNPs) of 3 genes encoding IL33, IL1RL1, and its coreceptor IL1RAP in Chinese Han nationality children. Methods: A total of 153 non-asthmatic children and 265 asthmatic children who visited the Xiangya Hospital between September 2015 and August 2019 were recruited for this study. Pulmonary function tests, peripheral blood eosinophil counts (PBEC), and fractional exhaled nitric oxide (FeNO) tests were performed before treatment, and 3 months after treatment. Each participant’s DNA was extracted from the peripheral blood, and a Mass ARRAY system was used to genotype the SNPs. Results: The T allele of rs4742170 in IL33 was associated with a risk of higher FeNO at baseline, and no improvement in FeNO and airway hyperresponsiveness was found after ICS treatment. The A allele of rs10208293 and C allele of rs13424006 in IL1RL1 both were associated with lower susceptibility to asthma and lower FeNO. The TT genotype of rs1420101 and AA genotype of rs4142132 in IL1RL1 were associated with a greater probability of improvement in PBEC after ICS treatment. Conclusion: IL33-IL1RL1-IL1RAP complex polymorphisms are associated with childhood asthma susceptibility, eosinophilic airway inflammation, and ICS response in Chinese Han children in Hunan. We speculate that IL33-IL1RL1-IL1RAP complex polymorphisms affect the development of asthma, airway inflammation, and subsequent ICS response in childhood.
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Affiliation(s)
- Maolan Wu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Xiangrong Zheng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Juan Huang
- Department of Pediatrics, The First Hospital of Changsha, Changsha, China
| | - Xiaolei Hu
- National Institution of Drug Clinical Trial, Xiangya Hospital, Central South University, Changsha, China
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7
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Multiomics Analysis Identifies BIRC3 as a Novel Glucocorticoid Response-Associated Gene. J Allergy Clin Immunol 2021; 149:1981-1991. [PMID: 34971648 DOI: 10.1016/j.jaci.2021.11.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 11/08/2021] [Accepted: 11/16/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Inhaled corticosteroid (ICS) response among patients with asthma is influenced by genetics, but biologically actionable insights based on associations have not been found. Various glucocorticoid response omics datasets are available to interrogate their biological effects. OBJECTIVE We sought to identify functionally relevant ICS response genetic associations by integrating complementary multiomics datasets. METHODS Variants with p-values<10-4 from a previous ICS response genome-wide association study were re-ranked based on integrative scores determined from: i) glucocorticoid receptor (GR)- and ii) RNA polymerase II (RNAP II)-binding regions inferred from ChIP-Seq data for three airway cell types, iii) glucocorticoid response element (GRE) motifs, iv) differentially expressed genes in response to glucocorticoid exposure according to 20 transcriptomic datasets, and v) expression quantitative trait loci (eQTLs) from GTEx. Candidate variants were tested for association with ICS response and asthma in six independent studies. RESULTS Four variants had significant (q-value<0.05) multiomics integrative scores. These variants were in a locus consisting of 52 variants in high LD (r2≥0.8) near GR-binding sites by the gene BIRC3. Variants were also BIRC3 eQTLs in lung, and two were within/near putative GRE motifs. BIRC3 had increased RNAP II occupancy and gene expression with glucocorticoid exposure in two ChIP-Seq and 13 transcriptomic datasets. Some BIRC3 variants in the 52-variant locus were associated (p-value<0.05) with ICS response in three independent studies and others with asthma in one study. CONCLUSION BIRC3 should be prioritized for further functional studies of ICS response. CLINICAL IMPLICATION Genetic variation near BIRC3 may influence ICS response in people with asthma.
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8
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Mobini Kesheh M, Shavandi S, Hosseini P, Kakavand-Ghalehnoei R, Keyvani H. Bioinformatic HLA Studies in the Context of SARS-CoV-2 Pandemic and Review on Association of HLA Alleles with Preexisting Medical Conditions. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6693909. [PMID: 34136572 PMCID: PMC8162251 DOI: 10.1155/2021/6693909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/10/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022]
Abstract
After the announcement of a new coronavirus in China in December 2019, which was then called SARS-CoV-2, this virus changed to a global concern and it was then declared as a pandemic by WHO. Human leukocyte antigen (HLA) alleles, which are one of the most polymorphic genes, play a pivotal role in both resistance and vulnerability of the body against viruses and other infections as well as chronic diseases. The association between HLA alleles and preexisting medical conditions such as cardiovascular diseases and diabetes mellitus is reported in various studies. In this review, we focused on the bioinformatic HLA studies to summarize the HLA alleles which responded to SARS-CoV-2 peptides and have been used to design vaccines. We also reviewed HLA alleles that are associated with comorbidities and might be related to the high mortality rate among COVID-19 patients. Since both genes and patients' medical conditions play a key role in both severity of the disease and the mortality rate in COVID-19 patients, a better understanding of the connection between HLA alleles and SARS-CoV-2 can provide a wider perspective on the behavior of the virus. Such understanding can help scientists, especially in terms of protecting healthcare workers and designing effective vaccines.
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Affiliation(s)
- Mina Mobini Kesheh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Shavandi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Parastoo Hosseini
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Hossein Keyvani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Ntontsi P, Photiades A, Zervas E, Xanthou G, Samitas K. Genetics and Epigenetics in Asthma. Int J Mol Sci 2021; 22:ijms22052412. [PMID: 33673725 PMCID: PMC7957649 DOI: 10.3390/ijms22052412] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 12/11/2022] Open
Abstract
Asthma is one of the most common respiratory disease that affects both children and adults worldwide, with diverse phenotypes and underlying pathogenetic mechanisms poorly understood. As technology in genome sequencing progressed, scientific efforts were made to explain and predict asthma’s complexity and heterogeneity, and genome-wide association studies (GWAS) quickly became the preferred study method. Several gene markers and loci associated with asthma susceptibility, atopic and childhood-onset asthma were identified during the last few decades. Markers near the ORMDL3/GSDMB genes were associated with childhood-onset asthma, interleukin (IL)33 and IL1RL1 SNPs were associated with atopic asthma, and the Thymic Stromal Lymphopoietin (TSLP) gene was identified as protective against the risk to TH2-asthma. The latest efforts and advances in identifying and decoding asthma susceptibility are focused on epigenetics, heritable characteristics that affect gene expression without altering DNA sequence, with DNA methylation being the most described mechanism. Other less studied epigenetic mechanisms include histone modifications and alterations of miR expression. Recent findings suggest that the DNA methylation pattern is tissue and cell-specific. Several studies attempt to describe DNA methylation of different types of cells and tissues of asthmatic patients that regulate airway remodeling, phagocytosis, and other lung functions in asthma. In this review, we attempt to briefly present the latest advancements in the field of genetics and mainly epigenetics concerning asthma susceptibility.
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Affiliation(s)
- Polyxeni Ntontsi
- 7th Respiratory Medicine Department and Asthma Center, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece; (P.N.); (A.P.); (E.Z.)
| | - Andreas Photiades
- 7th Respiratory Medicine Department and Asthma Center, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece; (P.N.); (A.P.); (E.Z.)
| | - Eleftherios Zervas
- 7th Respiratory Medicine Department and Asthma Center, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece; (P.N.); (A.P.); (E.Z.)
| | - Georgina Xanthou
- Cellular Immunology Laboratory, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
| | - Konstantinos Samitas
- 7th Respiratory Medicine Department and Asthma Center, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece; (P.N.); (A.P.); (E.Z.)
- Cellular Immunology Laboratory, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
- Correspondence: ; Tel.: +30-210-778-1720
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Combustion-derived particles from biomass sources differently promote epithelial-to-mesenchymal transition on A549 cells. Arch Toxicol 2021; 95:1379-1390. [PMID: 33481051 PMCID: PMC8032642 DOI: 10.1007/s00204-021-02983-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 01/06/2021] [Indexed: 01/26/2023]
Abstract
Combustion-derived particles (CDPs), due to the presence in their composition of several toxic and carcinogenic chemical compounds, such as polycyclic aromatic hydrocarbons (PAHs) and metals, are linked to several respiratory diseases, including lung cancer. Epithelial-to-mesenchymal transition (EMT) is a crucial step in lung cancer progression, involving several morphological and phenotypical changes. The study aims to investigate how exposure to CDPs from different biomass sources might be involved in cancer development, focusing mainly on the effects linked to EMT and invasion on human A549 lung cells. Biomass combustion-derived particles (BCDPs) were collected from a stove fuelled with pellet, charcoal or wood, respectively. A time course and dose response evaluation on cell viability and pro-inflammatory response was performed to select the optimal conditions for EMT-related studies. A significant release of IL-8 was found after 72 h of exposure to 2.5 μg/cm2 BCDPs. The EMT activation was then examined by evaluating the expression of some typical markers, such as E-cadherin and N-cadherin, and the possible enhanced migration and invasiveness. Sub-acute exposure revealed that BCDPs differentially modulated cell viability, migration and invasion, as well as the expression of proteins linked to EMT. Results showed a reduction in the epithelial marker E-cadherin and a parallel increase in the mesenchymal markers N-cadherin, mainly after exposure to charcoal and wood. Migration and invasion were also increased. In conclusion, our results suggest that BCDPs with a higher content of organic compounds (e.g. PAHs) in their chemical composition might play a crucial role in inducing pro-carcinogenic effects on epithelial cells.
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11
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Asthma genomics and pharmacogenomics. Curr Opin Immunol 2020; 66:136-142. [PMID: 33171417 DOI: 10.1016/j.coi.2020.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/04/2020] [Indexed: 12/16/2022]
Abstract
In this review, we summarize recent published work interrogating the relationship between genetic variation or gene expression regulation across the genome and asthma or asthma treatment outcomes. This includes 11 genome-wide association studies of asthma phenotypes that collectively identified 64 novel loci; transcriptome-wide asthma association studies which identified genes involved in virus recognition, bacterial infection, lung tissue remodeling, eosinophilic and neutrophilic inflammation and genes in the chromosome 17q12 asthma susceptibility locus; and three epigenome-wide studies of asthma that had robust sample sizes and replicated findings. We also highlight pharmacogenomic studies of corticosteroids, bronchodilator response to albuterol and zileuton, although finding from these studies may still be preliminary due to their relatively small sample sizes and limited availability of replication cohorts.
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12
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Dong Z, Ma Y, Zhou H, Shi L, Ye G, Yang L, Liu P, Zhou L. Integrated genomics analysis highlights important SNPs and genes implicated in moderate-to-severe asthma based on GWAS and eQTL datasets. BMC Pulm Med 2020; 20:270. [PMID: 33066754 PMCID: PMC7568423 DOI: 10.1186/s12890-020-01303-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/27/2020] [Indexed: 02/06/2023] Open
Abstract
Background Severe asthma is a chronic disease contributing to disproportionate disease morbidity and mortality. From the year of 2007, many genome-wide association studies (GWAS) have documented a large number of asthma-associated genetic variants and related genes. Nevertheless, the molecular mechanism of these identified variants involved in asthma or severe asthma risk remains largely unknown. Methods In the current study, we systematically integrated 3 independent expression quantitative trait loci (eQTL) data (N = 1977) and a large-scale GWAS summary data of moderate-to-severe asthma (N = 30,810) by using the Sherlock Bayesian analysis to identify whether expression-related variants contribute risk to severe asthma. Furthermore, we performed various bioinformatics analyses, including pathway enrichment analysis, PPI network enrichment analysis, in silico permutation analysis, DEG analysis and co-expression analysis, to prioritize important genes associated with severe asthma. Results In the discovery stage, we identified 1129 significant genes associated with moderate-to-severe asthma by using the Sherlock Bayesian analysis. Two hundred twenty-eight genes were prominently replicated by using MAGMA gene-based analysis. These 228 replicated genes were enriched in 17 biological pathways including antigen processing and presentation (Corrected P = 4.30 × 10− 6), type I diabetes mellitus (Corrected P = 7.09 × 10− 5), and asthma (Corrected P = 1.72 × 10− 3). With the use of a series of bioinformatics analyses, we highlighted 11 important genes such as GNGT2, TLR6, and TTC19 as authentic risk genes associated with moderate-to-severe/severe asthma. With respect to GNGT2, there were 3 eSNPs of rs17637472 (PeQTL = 2.98 × 10− 8 and PGWAS = 3.40 × 10− 8), rs11265180 (PeQTL = 6.0 × 10− 6 and PGWAS = 1.99 × 10− 3), and rs1867087 (PeQTL = 1.0 × 10− 4 and PGWAS = 1.84 × 10− 5) identified. In addition, GNGT2 is significantly expressed in severe asthma compared with mild-moderate asthma (P = 0.045), and Gngt2 shows significantly distinct expression patterns between vehicle and various glucocorticoids (Anova P = 1.55 × 10− 6). Conclusions Our current study provides multiple lines of evidence to support that these 11 identified genes as important candidates implicated in the pathogenesis of severe asthma.
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Affiliation(s)
- Zhouzhou Dong
- Critical Care Unit, Ningbo Medical Center Lihuili Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang, 315100, P.R. China
| | - Yunlong Ma
- Institute of Biomedical Big Data, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.,School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Hua Zhou
- Department of Respiratory Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China
| | - Linhui Shi
- Critical Care Unit, Ningbo Medical Center Lihuili Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang, 315100, P.R. China
| | - Gongjie Ye
- Critical Care Unit, Ningbo Medical Center Lihuili Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang, 315100, P.R. China
| | - Lei Yang
- Critical Care Unit, Ningbo Medical Center Lihuili Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang, 315100, P.R. China
| | - Panpan Liu
- Critical Care Unit, Ningbo Medical Center Lihuili Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang, 315100, P.R. China
| | - Li Zhou
- Department of Immunology and Rheumatology, Ningbo Medical Center Lihuili Hospital, Taipei Medical University Ningbo Medical Center, Ningbo, Zhejiang, 315100, P.R. China.
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13
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Ma X, Wang P, Xu G, Yu F, Ma Y. Integrative genomics analysis of various omics data and networks identify risk genes and variants vulnerable to childhood-onset asthma. BMC Med Genomics 2020; 13:123. [PMID: 32867763 PMCID: PMC7457797 DOI: 10.1186/s12920-020-00768-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/17/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Childhood-onset asthma is highly affected by genetic components. In recent years, many genome-wide association studies (GWAS) have reported a large group of genetic variants and susceptible genes associated with asthma-related phenotypes including childhood-onset asthma. However, the regulatory mechanisms of these genetic variants for childhood-onset asthma susceptibility remain largely unknown. METHODS In the current investigation, we conducted a two-stage designed Sherlock-based integrative genomics analysis to explore the cis- and/or trans-regulatory effects of genome-wide SNPs on gene expression as well as childhood-onset asthma risk through incorporating a large-scale GWAS data (N = 314,633) and two independent expression quantitative trait loci (eQTL) datasets (N = 1890). Furthermore, we applied various bioinformatics analyses, including MAGMA gene-based analysis, pathway enrichment analysis, drug/disease-based enrichment analysis, computer-based permutation analysis, PPI network analysis, gene co-expression analysis and differential gene expression analysis, to prioritize susceptible genes associated with childhood-onset asthma. RESULTS Based on comprehensive genomics analyses, we found 31 genes with multiple eSNPs to be convincing candidates for childhood-onset asthma risk; such as, PSMB9 (cis-rs4148882 and cis-rs2071534) and TAP2 (cis-rs9267798, cis-rs4148882, cis-rs241456, and trans-10,447,456). These 31 genes were functionally interacted with each other in our PPI network analysis. Our pathway enrichment analysis showed that numerous KEGG pathways including antigen processing and presentation, type I diabetes mellitus, and asthma were significantly enriched to involve in childhood-onset asthma risk. The co-expression patterns among 31 genes were remarkably altered according to asthma status, and 25 of 31 genes (25/31 = 80.65%) showed significantly or suggestively differential expression between asthma group and control group. CONCLUSIONS We provide strong evidence to highlight 31 candidate genes for childhood-onset asthma risk, and offer a new insight into the genetic pathogenesis of childhood-onset asthma.
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Affiliation(s)
- Xiuqing Ma
- Department of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100853 China
| | - Peilan Wang
- Outpatient Department, Chinese PLA General Hospital, Beijing, 100853 China
| | - Guobing Xu
- Department of Cardiovascular Medicine, Zhongxiang People’s Hospital, Zhongxiang, 431900 Hubei Province China
| | - Fang Yu
- Department of Pediatrics, Chinese PLA General Hospital, Beijing, 100853 China
| | - Yunlong Ma
- Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027 P. R. China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, China
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14
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Expression quantitative trait locus fine mapping of the 17q12-21 asthma locus in African American children: a genetic association and gene expression study. THE LANCET RESPIRATORY MEDICINE 2020; 8:482-492. [PMID: 32380068 DOI: 10.1016/s2213-2600(20)30011-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND African ancestry is associated with a higher prevalence and greater severity of asthma than European ancestries, yet genetic studies of the most common locus associated with childhood-onset asthma, 17q12-21, in African Americans have been inconclusive. The aim of this study was to leverage both the phenotyping of the Children's Respiratory and Environmental Workgroup (CREW) birth cohort consortium, and the reduced linkage disequilibrium in African Americans, to fine map the 17q12-21 locus. METHODS We first did a genetic association study and meta-analysis using 17q12-21 tag single-nucleotide polymorphisms (SNPs) for childhood-onset asthma in 1613 European American and 870 African American children from the CREW consortium. Nine tag SNPs were selected based on linkage disequilibrium patterns at 17q12-21 and their association with asthma, considering the effect allele under an additive model (0, 1, or 2 effect alleles). Results were meta-analysed with publicly available summary data from the EVE consortium (on 4303 European American and 3034 African American individuals) for seven of the nine SNPs of interest. Subsequently, we tested for expression quantitative trait loci (eQTLs) among the SNPs associated with childhood-onset asthma and the expression of 17q12-21 genes in resting peripheral blood mononuclear cells (PBMCs) from 85 African American CREW children and in upper airway epithelial cells from 246 African American CREW children; and in lower airway epithelial cells from 44 European American and 72 African American adults from a case-control study of asthma genetic risk in Chicago (IL, USA). FINDINGS 17q12-21 SNPs were broadly associated with asthma in European Americans. Only two SNPs (rs2305480 in gasdermin-B [GSDMB] and rs8076131 in ORMDL sphingolipid biosynthesis regulator 3 [ORMDL3]) were associated with asthma in African Americans, at a Bonferroni-corrected threshold of p<0·0055 (for rs2305480_G, odds ratio [OR] 1·36 [95% CI 1·12-1·65], p=0·0014; and for rs8076131_A, OR 1·37 [1·13-1·67], p=0·0010). In upper airway epithelial cells from African American children, genotype at rs2305480 was the most significant eQTL for GSDMB (eQTL effect size [β] 1·35 [95% CI 1·25-1·46], p<0·0001), and to a lesser extent showed an eQTL effect for post-GPI attachment to proteins phospholipase 3 (β 1·15 [1·08-1·22], p<0·0001). No SNPs were eQTLs for ORMDL3. By contrast, in PBMCs, the five core SNPs were associated only with expression of GSDMB and ORMDL3. Genotype at rs12936231 (in zona pellucida binding protein 2) showed the strongest associations across both genes (for GSDMB, eQTLβ 1·24 [1·15-1·32], p<0·0001; and for ORMDL3 (β 1·19 [1·12-1·24], p<0·0001). The eQTL effects of rs2305480 on GSDMB expression were replicated in lower airway cells from African American adults (β 1·29 [1·15-1·44], p<0·0001). INTERPRETATION Our study suggests that SNPs regulating GSDMB expression in airway epithelial cells have a major role in childhood-onset asthma, whereas SNPs regulating the expression levels of 17q12-21 genes in resting blood cells are not central to asthma risk. Our genetic and gene expression data in African Americans and European Americans indicated GSDMB to be the leading candidate gene at this important asthma locus. FUNDING National Institutes of Health, Office of the Director.
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15
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Fernandez-Rhodes L, Young KL, Lilly AG, Raffield LM, Highland HM, Wojcik GL, Agler C, M Love SA, Okello S, Petty LE, Graff M, Below JE, Divaris K, North KE. Importance of Genetic Studies of Cardiometabolic Disease in Diverse Populations. Circ Res 2020; 126:1816-1840. [PMID: 32496918 PMCID: PMC7285892 DOI: 10.1161/circresaha.120.315893] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies have revolutionized our understanding of the genetic underpinnings of cardiometabolic disease. Yet, the inadequate representation of individuals of diverse ancestral backgrounds in these studies may undercut their ultimate potential for both public health and precision medicine. The goal of this review is to describe the imperativeness of studying the populations who are most affected by cardiometabolic disease, to the aim of better understanding the genetic underpinnings of the disease. We support this premise by describing the current variation in the global burden of cardiometabolic disease and emphasize the importance of building a globally and ancestrally representative genetics evidence base for the identification of population-specific variants, fine-mapping, and polygenic risk score estimation. We discuss the important ethical, legal, and social implications of increasing ancestral diversity in genetic studies of cardiometabolic disease and the challenges that arise from the (1) lack of diversity in current reference populations and available analytic samples and the (2) unequal generation of health-associated genomic data and their prediction accuracies. Despite these challenges, we conclude that additional, unprecedented opportunities lie ahead for public health genomics and the realization of precision medicine, provided that the gap in diversity can be systematically addressed. Achieving this goal will require concerted efforts by social, academic, professional and regulatory stakeholders and communities, and these efforts must be based on principles of equity and social justice.
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Affiliation(s)
- Lindsay Fernandez-Rhodes
- Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, University Park, PA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Adam G Lilly
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Cary Agler
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Shelly-Ann M Love
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Samson Okello
- Department of Internal Medicine, Mbarara University of Science and Technology, Uganda
- University of Virginia, Charlottesville, VA
- Harvard TH Chan School of Public Health, Boston, MA
| | - Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Vanderbilt, TN
- Department of Genetic Medicine, Vanderbilt University, Vanderbilt, TN
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Vanderbilt, TN
- Department of Genetic Medicine, Vanderbilt University, Vanderbilt, TN
| | - Kimon Divaris
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Center for Genome Sciences, Chapel Hill, NC
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16
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Abstract
PURPOSE OF REVIEW In asthma, there is an increasing focus on personalizing treatment by targeting treatable traits. Ethnicity has effects on many biological and behavioural traits, and so is an important consideration when personalizing asthma care. This review has particular relevance in light of current patterns of international migration, which are leading to unprecedented levels of ethnic heterogeneity in many geographic regions. RECENT FINDINGS This review examines the effect of ethnicity on three key domains - biological traits, behavioural traits and health system behaviour. Ethnicity influences asthma biology by affecting biomarker reference ranges, response to drug therapy and asthma phenotypes. Ethnicity impacts behavioural traits through its effects on psychosocial well being, adherence and asthma self-management. Ethnic minorities are often disadvantaged with regards to healthcare access and healthcare interactions. SUMMARY Concerted action is needed to address current issues around behavioural traits and healthcare behaviour, which are influenced by ethnicity. More research is required to understand the impact of ethnicity on asthma biology, especially the interplay between genetic and environmental influences on asthma, and the differential response to asthma therapies.
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17
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Abstract
PURPOSE OF REVIEW Precision medicine could help to improve diagnosis and treatment of asthma; however, in the tropics there are special conditions to be considered for applying this strategy. In this review, we analyze recent advances of precision allergology in tropical regions, highlighting its limitations and needs in high-admixed populations living under environments with high exposure to house dust mites and helminth infections. RECENT FINDINGS Advances have been made regarding the genetic characterization of the great diversity of populations living in the tropics. Genes involved in shared biological pathways between immune responses to nematodes and the allergic responses suggested new mechanisms of predisposition. Genome wide association studies of asthma are progressively focusing on some highly replicated genes such as those in chromosome 17q31-13, which have been also replicated in African ancestry populations. Some diagnostic difficulties, because of the endemicity of helminth infections, are now more evident in the context of phenotype definition. SUMMARY The clinical impact of the advances in precision medicine for asthma in the tropics is still limited and mainly related to component resolved diagnosis. More basic and clinical research is needed to identify genetic, epigenetic, or other biologic markers that allow and accurate definition of phenotypes and endotypes of this heterogeneous disease. This will substantially improve the selection of personalized treatments.
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18
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McGuirl MR, Smith SP, Sandstede B, Ramachandran S. Detecting Shared Genetic Architecture Among Multiple Phenotypes by Hierarchical Clustering of Gene-Level Association Statistics. Genetics 2020; 215:511-529. [PMID: 32245788 PMCID: PMC7268989 DOI: 10.1534/genetics.120.303096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/31/2020] [Indexed: 12/31/2022] Open
Abstract
Emerging large-scale biobanks pairing genotype data with phenotype data present new opportunities to prioritize shared genetic associations across multiple phenotypes for molecular validation. Past research, by our group and others, has shown gene-level tests of association produce biologically interpretable characterization of the genetic architecture of a given phenotype. Here, we present a new method, Ward clustering to identify Internal Node branch length outliers using Gene Scores (WINGS), for identifying shared genetic architecture among multiple phenotypes. The objective of WINGS is to identify groups of phenotypes, or "clusters," sharing a core set of genes enriched for mutations in cases. We validate WINGS using extensive simulation studies and then combine gene-level association tests with WINGS to identify shared genetic architecture among 81 case-control and seven quantitative phenotypes in 349,468 European-ancestry individuals from the UK Biobank. We identify eight prioritized phenotype clusters and recover multiple published gene-level associations within prioritized clusters.
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Affiliation(s)
- Melissa R McGuirl
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912
| | - Samuel Pattillo Smith
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
| | - Björn Sandstede
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912
- Data Science Initiative, Brown University, Providence, Rhode Island 02912
| | - Sohini Ramachandran
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912
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Schoettler N, Rodríguez E, Weidinger S, Ober C. Advances in asthma and allergic disease genetics: Is bigger always better? J Allergy Clin Immunol 2019; 144:1495-1506. [PMID: 31677964 DOI: 10.1016/j.jaci.2019.10.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022]
Abstract
This review focuses on genome-wide association studies (GWASs) of asthma and allergic diseases published between January 1, 2018, and June 30, 2019. During this time period, there were 38 GWASs reported in 19 articles, including the largest performed to date for many of these conditions. Overall, we learned that childhood-onset asthma is associated with the most independent loci compared with other defined groups of asthma and allergic disease cases; adult-onset asthma and moderate-to-severe asthma are associated with fewer genes, which are largely a subset of those associated with childhood-onset asthma. There is significant genetic overlap between asthma and allergic diseases, particularly with respect to childhood-onset asthma, which involves genes that reflect the importance of barrier function biology, and to HLA region genes, which are the most frequently associated genes overall in both groups of diseases. Although the largest GWASs in African American and Latino/Hispanic populations were reported during this period, they are still significantly underpowered compared with studies reported in populations of European ancestry, highlighting the need for larger studies, particularly in patients with childhood-onset asthma and allergic diseases, in these important populations that carry the greatest burden of disease.
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Affiliation(s)
- Nathan Schoettler
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, Ill; Department of Human Genetics, University of Chicago, Chicago, Ill.
| | - Elke Rodríguez
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
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