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Packer RJ, Shrine N, Hall R, Melbourne CA, Thompson R, Williams AT, Paynton ML, Guyatt AL, Allen RJ, Lee PH, John C, Campbell A, Hayward C, de Vries M, Vonk JM, Davitte J, Hessel E, Michalovich D, Betts JC, Sayers I, Yeo A, Hall IP, Tobin MD, Wain LV. Genome-wide association study of chronic sputum production implicates loci involved in mucus production and infection. Eur Respir J 2023; 61:2201667. [PMID: 37263751 PMCID: PMC10284065 DOI: 10.1183/13993003.01667-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/17/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Chronic sputum production impacts on quality of life and is a feature of many respiratory diseases. Identification of the genetic variants associated with chronic sputum production in a disease agnostic sample could improve understanding of its causes and identify new molecular targets for treatment. METHODS We conducted a genome-wide association study (GWAS) of chronic sputum production in UK Biobank. Signals meeting genome-wide significance (p<5×10-8) were investigated in additional independent studies, were fine-mapped and putative causal genes identified by gene expression analysis. GWASs of respiratory traits were interrogated to identify whether the signals were driven by existing respiratory disease among the cases and variants were further investigated for wider pleiotropic effects using phenome-wide association studies (PheWASs). RESULTS From a GWAS of 9714 cases and 48 471 controls, we identified six novel genome-wide significant signals for chronic sputum production including signals in the human leukocyte antigen (HLA) locus, chromosome 11 mucin locus (containing MUC2, MUC5AC and MUC5B) and FUT2 locus. The four common variant associations were supported by independent studies with a combined sample size of up to 2203 cases and 17 627 controls. The mucin locus signal had previously been reported for association with moderate-to-severe asthma. The HLA signal was fine-mapped to an amino acid change of threonine to arginine (frequency 36.8%) in HLA-DRB1 (HLA-DRB1*03:147). The signal near FUT2 was associated with expression of several genes including FUT2, for which the direction of effect was tissue dependent. Our PheWAS identified a wide range of associations including blood cell traits, liver biomarkers, infections, gastrointestinal and thyroid-associated diseases, and respiratory disease. CONCLUSIONS Novel signals at the FUT2 and mucin loci suggest that mucin fucosylation may be a driver of chronic sputum production even in the absence of diagnosed respiratory disease and provide genetic support for this pathway as a target for therapeutic intervention.
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Affiliation(s)
- Richard J Packer
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Nick Shrine
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Robert Hall
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Carl A Melbourne
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Rebecca Thompson
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Alex T Williams
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Megan L Paynton
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Richard J Allen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Paul H Lee
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Catherine John
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Maaike de Vries
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | | | | | | | | | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | | | - Ian P Hall
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Louise V Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Leicester, UK
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Ren YM, Duan YH, Sun YB, Yang T, Hou WY, Liu C, Tian MQ. mRNA and long non-coding RNA expression profiles of rotator cuff tear patients reveal inflammatory features in long head of biceps tendon. BMC Med Genomics 2022; 15:140. [PMID: 35725478 PMCID: PMC9210618 DOI: 10.1186/s12920-022-01292-y] [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: 11/06/2021] [Accepted: 06/15/2022] [Indexed: 02/06/2024] Open
Abstract
Background This study aimed to identify the differentially expressed mRNAs and lncRNAs in inflammatory long head of biceps tendon (LHBT) of rotator cuff tear (RCT) patients and further explore the function and potential targets of differentially expressed lncRNAs in biceps tendon pathology. Methods Human gene expression microarray was made between 3 inflammatory LHBT samples and 3 normal LHBT samples from RCT patients. GO analysis and KEGG pathway analysis were performed to annotate the function of differentially expressed mRNAs. The real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was admitted to verify their expression. LncRNA-mRNA co-expression network, cis-acting element, trans-acting element and transcription factor (TF) regulation analysis were constructed to predict the potential molecular regulatory mechanisms and targets for LHB tendinitis. Results 103 differentially expressed lncRNAs and mRNAs, of which 75 were up-regulated and 28 were down-regulated, were detected to be differentially expressed in LHBT. The expressions of 4 most differentially expressed lncRNAs (A2MP1, LOC100996671, COL6A4P, lnc-LRCH1-5) were confirmed by qRT-PCR. GO functional analysis indicated that related lncRNAs and mRNAs were involved in the biological processes of regulation of innate immune response, neutrophil chemotaxis, interleukin-1 cell response and others. KEGG pathway analysis indicated that related lncRNAs and mRNAs were involved in MAPK signaling pathway, NF-kappa B signaling pathway, cAMP signaling pathway and others. TF regulation analysis revealed that COL6A4P2, A2MP1 and LOC100996671 target NFKB2. Conclusions LlncRNA-COL6A4P2, A2MP1 and LOC100996671 may regulate the inflammation of LHBT in RCT patients through NFKB2/NF-kappa B signaling pathway, and preliminarily revealed the pathological molecular mechanism of tendinitis of LHBT. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01292-y.
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Affiliation(s)
- Yi-Ming Ren
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Nankai University Affiliated People's Hospital, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, People's Republic of China
| | - Yuan-Hui Duan
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Nankai University Affiliated People's Hospital, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, People's Republic of China
| | - Yun-Bo Sun
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Nankai University Affiliated People's Hospital, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, People's Republic of China
| | - Tao Yang
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Nankai University Affiliated People's Hospital, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, People's Republic of China
| | - Wei-Yu Hou
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Nankai University Affiliated People's Hospital, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, People's Republic of China
| | - Chang Liu
- Schoole of Medicine, Nankai University, Tianjin, People's Republic of China
| | - Meng-Qiang Tian
- Department of Joint and Sport Medicine, Tianjin Union Medical Center, Nankai University Affiliated People's Hospital, Jieyuan Road 190, Hongqiao District, Tianjin, 300121, People's Republic of China.
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Lee S, Lasky-Su JA, Lange C, Kim W, Kumar PL, McDonald MLN, Vaz Fragoso CA, Laurie C, Raby BA, Celedón JC, Cho MH, Won S, Weiss ST, Hecker J. A novel locus for exertional dyspnoea in childhood asthma. Eur Respir J 2021; 57:2001224. [PMID: 32855217 PMCID: PMC8185954 DOI: 10.1183/13993003.01224-2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/31/2020] [Indexed: 12/18/2022]
Abstract
Most children diagnosed with asthma have respiratory symptoms such as cough, dyspnoea and wheezing, which are also important markers of overall respiratory function. A decade of genome-wide association studies (GWAS) have investigated genetic susceptibility to asthma itself, but few have focused on important respiratory symptoms that characterise childhood asthma.Using whole-genome sequencing (WGS) data for 894 asthmatic trios from a Costa Rican cohort, we performed family-based association tests (FBATs) to assess the association between genetic variants and multiple asthma-relevant respiratory phenotypes: cough, phlegm, wheezing, exertional dyspnoea and exertional chest tightness. We tested whether genome-wide significant associations were replicated in two additional studies: 1) 286 asthmatic trios from the Childhood Asthma Management Program (CAMP), and 2) 2691 African American current or former smokers from the COPDGene study.In the 894 Costa Rican trios, we identified a genome-wide significant association (p=2.16×10-9) between exertional dyspnoea and the single nucleotide polymorphism (SNP) rs10165869, located on chromosome 2q37.3, that was replicated in the CAMP cohort (p=0.023) with the same direction of association (combined p=3.28×10-10). This association was not found in the African American participants from COPDGene. We also found suggestive evidence for an association between SNP rs10165869 and the atypical chemokine receptor 3 (ACKR3).Our finding encourages the secondary association analysis of a wider range of phenotypes that characterise respiratory symptoms in other airway diseases/studies.
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Affiliation(s)
- Sanghun Lee
- Dept of Medical Consilience, Division of Medicine, Graduate
School, Dankook University, Yongin, South Korea
- Dept of Biostatistics, Harvard T.H. Chan School of Public
Health, Boston, MA, USA
| | - Jessica Ann Lasky-Su
- Channing Division of Network Medicine, Brigham and
Women’s Hospital, Boston, MA, USA
| | - Christoph Lange
- Dept of Biostatistics, Harvard T.H. Chan School of Public
Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and
Women’s Hospital, Boston, MA, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and
Women’s Hospital, Boston, MA, USA
| | - Preeti Lakshman Kumar
- Division of Pulmonary, Allergy and Critical Care Medicine,
University of Alabama at Birmingham, Birmingham, AL, USA
| | - Merry-Lynn N. McDonald
- Division of Pulmonary, Allergy and Critical Care Medicine,
University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Cecelia Laurie
- Dept of Biostatistics, University of Washington, Seattle,
WA, USA
| | - Benjamin A. Raby
- Channing Division of Network Medicine, Brigham and
Women’s Hospital, Boston, MA, USA
| | - Juan C. Celedón
- Division of Pediatric Pulmonary Medicine, UPMC
Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA,
USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and
Women’s Hospital, Boston, MA, USA
| | - Sungho Won
- Dept of Public Health Science, Seoul National University,
Seoul, South Korea
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and
Women’s Hospital, Boston, MA, USA
| | - Julian Hecker
- Channing Division of Network Medicine, Brigham and
Women’s Hospital, Boston, MA, USA
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Zeng X, Vonk JM, van der Plaat DA, Faiz A, Paré PD, Joubert P, Nickle D, Brandsma CA, Kromhout H, Vermeulen R, Xu X, Huo X, de Jong K, Boezen HM. Genome-wide interaction study of gene-by-occupational exposures on respiratory symptoms. ENVIRONMENT INTERNATIONAL 2019; 122:263-269. [PMID: 30449631 DOI: 10.1016/j.envint.2018.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/05/2018] [Accepted: 11/08/2018] [Indexed: 02/05/2023]
Abstract
Respiratory symptoms are important indicators of respiratory diseases. Both genetic and environmental factors contribute to respiratory symptoms development but less is known about gene-environment interactions. We aimed to assess interactions between single nucleotide polymorphisms (SNPs) and occupational exposures on respiratory symptoms cough, dyspnea and phlegm. As identification cohort LifeLines I (n = 7976 subjects) was used. Job-specific exposure was estimated using the ALOHA + job exposure matrix. SNP-by-occupational exposure interactions on respiratory symptoms were tested using logistic regression adjusted for gender, age, and current smoking. SNP-by-exposure interactions with a p-value <10-4 were tested for replication in two independent cohorts: LifeLines II (n = 5260) and the Vlagtwedde-Vlaardingen cohort (n = 1529). The interaction estimates of the replication cohorts were meta-analyzed using PLINK. Replication was achieved when the meta-analysis p-value was <0.05 and the interaction effect had the same direction as in the identification cohort. Additionally, we assessed whether replicated SNPs associated with gene expression by analyzing if they were cis-acting expression quantitative trait loci (eQTL) in lung tissue. In the replication meta-analysis, sixteen out of 477 identified SNP-by-occupational exposure interactions had a p-value <0.05 and 9 of these interactions had the same direction as in the identification cohort. Several identified loci were plausible candidates for respiratory symptoms, such as TMPRSS9, SERPINH1, TOX3, and ARHGAP18. Three replicated SNPs were cis-eQTLs for FCER1A, CHN1, and TIMM13 in lung tissue. Taken together, this genome-wide SNP-by-occupational exposure interaction study in relation to cough, dyspnea, and phlegm identified several suggestive susceptibility genes. Further research should determine if these genes are true susceptibility loci for respiratory symptoms in relation to occupational exposures.
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Affiliation(s)
- Xiang Zeng
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; Shantou University Medical College, Laboratory of Environmental Medicine and Developmental Toxicology, Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, China; Xinxiang Medical University, School of Public Health, Department of Epidemiology and Health Statistics, Xinxiang, China
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Diana A van der Plaat
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Alen Faiz
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Peter D Paré
- University of British Columbia, Department of Medicine, Center for Heart Lung Innovation and Institute for Heart and Lung Health, St. Paul's Hospital, Vancouver, BC, Canada
| | - Philippe Joubert
- Institut universitaire de cardiologie et de pneumologie de Québec, Laval University, Québec, QC, Canada
| | | | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
| | - Hans Kromhout
- University of Utrecht, Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht, the Netherlands
| | - Roel Vermeulen
- University of Utrecht, Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht, the Netherlands
| | - Xijin Xu
- Shantou University Medical College, Laboratory of Environmental Medicine and Developmental Toxicology, Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou, China
| | - Xia Huo
- Jinan University, School of Environment, Guangdong Key Laboratory of Environmental Pollution and Health, Guangzhou Key Laboratory of Environmental Exposure and Health, Guangzhou, China
| | - Kim de Jong
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands.
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