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DeepNull models non-linear covariate effects to improve phenotypic prediction and association power. Nat Commun 2022; 13:241. [PMID: 35017556 PMCID: PMC8752755 DOI: 10.1038/s41467-021-27930-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWASs) examine the association between genotype and phenotype while adjusting for a set of covariates. Although the covariates may have non-linear or interactive effects, due to the challenge of specifying the model, GWAS often neglect such terms. Here we introduce DeepNull, a method that identifies and adjusts for non-linear and interactive covariate effects using a deep neural network. In analyses of simulated and real data, we demonstrate that DeepNull maintains tight control of the type I error while increasing statistical power by up to 20% in the presence of non-linear and interactive effects. Moreover, in the absence of such effects, DeepNull incurs no loss of power. When applied to 10 phenotypes from the UK Biobank (n = 370K), DeepNull discovered more hits (+6%) and loci (+7%), on average, than conventional association analyses, many of which are biologically plausible or have previously been reported. Finally, DeepNull improves upon linear modeling for phenotypic prediction (+23% on average). GWAS often assume a linear phenotype-covariate relationship which may not hold in practice. Here the authors present DeepNull, in which they apply deep learning to identify and adjust for complex non-linear relationships, improving phenotypic prediction and GWAS power.
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152
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Yu Z, Xu C, Fang C, Zhang F. Causal effect of iron status on lung function: A Mendelian randomization study. Front Nutr 2022; 9:1025212. [PMID: 36590211 PMCID: PMC9798299 DOI: 10.3389/fnut.2022.1025212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Background The association between systemic iron status and lung function was conflicting in observational studies. We aim to explore the potential causal relationships between iron status and the levels of lung function using the two-sample Mendelian randomization (MR) design. Methods Genetic instruments associated with iron status biomarkers were retrieved from the Genetics of Iron Status (GIS) consortium (N = 48,972). Summary statistics of these genetic instruments with lung function were extracted from a meta-analysis of UK Biobank and SpiroMeta consortium (N = 400,102). The main analyses were performed using the inverse-variance weighted method, and complemented by multiple sensitivity analyses. Results Based on conservative genetic instruments, MR analyses showed that genetically predicted higher iron (beta: 0.036 per 1 SD increase, 95% confidence interval (CI): 0.016 to 0.056, P = 3.51 × 10-4), log10-transformed ferritin (beta: 0.081, 95% CI: 0.047 to 0.116, P = 4.11 × 10-6), and transferrin saturation (beta: 0.027, 95% CI: 0.015 to 0.038, P = 1.09 × 10-5) were associated with increased forced expiratory volume in 1 s (FEV1), whereas higher transferrin was associated with decreased FEV1 (beta: -0.036, 95% CI: -0.064 to -0.008, P = 0.01). A significant positive association between iron status and forced vital capacity (FVC) was also observed. However, there is no causal association between iron status and FEV1-to-FVC ratio (P = 0.10). Similar results were obtained from the liberal instruments analyses and multiple sensitivity analyses. Conclusion Our study provided strong evidence to support that higher iron status is causally associated with higher levels of FEV1 and FVC, but has no impact on airway obstruction, confirming iron status as an important target for lung function management.
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Affiliation(s)
- Zhimin Yu
- Department of General Medicine and Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Cardiology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Chengkai Xu
- Department of General Medicine and Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Chenggang Fang
- Department of General Medicine and Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Fangfang Zhang
- Department of Pediatrics, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- *Correspondence: Fangfang Zhang
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Keefe J, Yao C, Hwang SJ, Courchesne P, Lee GY, Dupuis J, Mizgerd JP, O’Connor G, Washko GR, Cho MH, Silverman EK, Levy D. An Integrative Genomic Strategy Identifies sRAGE as a Causal and Protective Biomarker of Lung Function. Chest 2022; 161:76-84. [PMID: 34237330 PMCID: PMC8783029 DOI: 10.1016/j.chest.2021.06.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND There are few clinically useful circulating biomarkers of lung function and lung disease. We hypothesized that genome-wide association studies (GWAS) of circulating proteins in conjunction with GWAS of pulmonary traits represents a clinically relevant approach to identifying causal proteins and therapeutically useful insights into mechanisms related to lung function and disease. STUDY QUESTION Can an integrative genomic strategy using GWAS of plasma soluble receptor for advanced glycation end-products (sRAGE) levels in conjunction with GWAS of lung function traits identify putatively causal relations of sRAGE to lung function? STUDY DESIGN AND METHODS Plasma sRAGE levels were measured in 6,861 Framingham Heart Study participants and GWAS of sRAGE was conducted to identify protein quantitative trait loci (pQTL), including cis-pQTL variants at the sRAGE protein-coding gene locus (AGER). We integrated sRAGE pQTL variants with variants from GWAS of lung traits. Colocalization of sRAGE pQTL variants with lung trait GWAS variants was conducted, and Mendelian randomization was performed using sRAGE cis-pQTL variants to infer causality of sRAGE for pulmonary traits. Cross-sectional and longitudinal protein-trait association analyses were conducted for sRAGE in relation to lung traits. RESULTS Colocalization identified shared genetic signals for sRAGE with lung traits. Mendelian randomization analyses suggested protective causal relations of sRAGE to several pulmonary traits. Protein-trait association analyses demonstrated higher sRAGE levels to be cross-sectionally and longitudinally associated with preserved lung function. INTERPRETATION sRAGE is produced by type I alveolar cells, and it acts as a decoy receptor to block the inflammatory cascade. Our integrative genomics approach provides evidence for sRAGE as a causal and protective biomarker of lung function, and the pattern of associations is suggestive of a protective role of sRAGE against restrictive lung physiology. We speculate that targeting the AGER/sRAGE axis may be therapeutically beneficial for the treatment and prevention of inflammation-related lung disease.
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Affiliation(s)
- Joshua Keefe
- Framingham Heart Study, Framingham, MA,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Chen Yao
- Framingham Heart Study, Framingham, MA,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Shih-Jen Hwang
- Framingham Heart Study, Framingham, MA,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Paul Courchesne
- Framingham Heart Study, Framingham, MA,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Gha Young Lee
- Framingham Heart Study, Framingham, MA,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Joseph P. Mizgerd
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA
| | - George O’Connor
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA
| | - George R. Washko
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Michael H. Cho
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Edwin K. Silverman
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD,CORRESPONDENCE TO: Daniel Levy, MD
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154
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Niarchou M, Gustavson DE, Sathirapongsasuti JF, Anglada-Tort M, Eising E, Bell E, McArthur E, Straub P, McAuley JD, Capra JA, Ullén F, Creanza N, Mosing MA, Hinds DA, Davis LK, Jacoby N, Gordon RL. Genome-wide association study of musical beat synchronization demonstrates high polygenicity. Nat Hum Behav 2022; 6:1292-1309. [PMID: 35710621 PMCID: PMC9489530 DOI: 10.1038/s41562-022-01359-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/21/2022] [Indexed: 02/02/2023]
Abstract
Moving in synchrony to the beat is a fundamental component of musicality. Here we conducted a genome-wide association study to identify common genetic variants associated with beat synchronization in 606,825 individuals. Beat synchronization exhibited a highly polygenic architecture, with 69 loci reaching genome-wide significance (P < 5 × 10-8) and single-nucleotide-polymorphism-based heritability (on the liability scale) of 13%-16%. Heritability was enriched for genes expressed in brain tissues and for fetal and adult brain-specific gene regulatory elements, underscoring the role of central-nervous-system-expressed genes linked to the genetic basis of the trait. We performed validations of the self-report phenotype (through separate experiments) and of the genome-wide association study (polygenic scores for beat synchronization were associated with patients algorithmically classified as musicians in medical records of a separate biobank). Genetic correlations with breathing function, motor function, processing speed and chronotype suggest shared genetic architecture with beat synchronization and provide avenues for new phenotypic and genetic explorations.
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Affiliation(s)
- Maria Niarchou
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA. .,Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Daniel E. Gustavson
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA
| | | | - Manuel Anglada-Tort
- grid.461782.e0000 0004 1795 8610Computational Auditory Perception Group, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany
| | - Else Eising
- grid.419550.c0000 0004 0501 3839Department of Language and Genetics, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Eamonn Bell
- grid.21729.3f0000000419368729Department of Music, Columbia University, New York, NY USA ,grid.8250.f0000 0000 8700 0572Department of Computer Science, Durham University, Durham, UK
| | - Evonne McArthur
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | - Peter Straub
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA
| | | | - J. Devin McAuley
- grid.17088.360000 0001 2150 1785Department of Psychology, Michigan State University, East Lansing, MI USA
| | - John A. Capra
- grid.266102.10000 0001 2297 6811Bakar Computational Health Sciences Institute, University of California, San Francisco, CA USA ,grid.266102.10000 0001 2297 6811Department of Epidemiology & Biostatistics, University of California, San Francisco, CA USA
| | - Fredrik Ullén
- grid.465198.7Department of Neuroscience, Karolinska Institutet, Solna, Sweden ,grid.461782.e0000 0004 1795 8610Department of Cognitive Neuropsychology, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany
| | - Nicole Creanza
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN USA
| | - Miriam A. Mosing
- grid.465198.7Department of Neuroscience, Karolinska Institutet, Solna, Sweden ,grid.461782.e0000 0004 1795 8610Department of Cognitive Neuropsychology, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany ,grid.1008.90000 0001 2179 088XMelbourne School of Psychological Sciences, University of Melbourne, Melbourne, Victoria Australia
| | - David A. Hinds
- grid.420283.f0000 0004 0626 085823andMe, Inc, Sunnyvale, CA USA
| | - Lea K. Davis
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN USA
| | - Nori Jacoby
- grid.461782.e0000 0004 1795 8610Computational Auditory Perception Group, Max Planck Institute for Empirical Aesthetics, Frankfurt am Main, Germany
| | - Reyna L. Gordon
- grid.412807.80000 0004 1936 9916Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN USA ,grid.412807.80000 0004 1936 9916Department of Otolaryngology—Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Psychology, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN USA
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Dai C, Wang Z, Yang H, Xiao S, Xu J, Deng Z, Wu F, Wen X, Zheng Y, Lu L, Zhao N, Huang P, Zhou Y, Ran P. Association Between Serum Total Bilirubin and COPD: Results from a Cross-Sectional Study and a Bidirectional Mendelian Randomization Analysis. Clin Epidemiol 2022; 14:289-298. [PMID: 35299727 PMCID: PMC8922320 DOI: 10.2147/clep.s353389] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/25/2022] [Indexed: 11/23/2022] Open
Abstract
Background The potential protective role of serum total bilirubin (TB) for chronic obstructive pulmonary disease (COPD) is controversial. We aimed to investigate whether serum TB could prevent airflow limitation (reduce the risk of COPD) and whether these associations were causal or reversely causal. Methods We conducted a multi-center and cross-sectional study including 3069 participants. Logistic regression model (LRM) with restricted cubic spline (RCS) and priori defined quintile categories were used to assess the associations of TB with COPD. Besides, ordinary least squares (OLS) regression model with RCS curves were applied to assess the dose-response relationship between serum TB and airflow limitation (FEV1/FVC). To verify the causal direction between TB and COPD, a bidirectional Mendelian randomization analysis was carried out with GWAS data from European ancestry. Results In the cross-sectional study, the relationship between levels of TB and COPD risk was U shaped (P=0.001), and the low and high concentrations of TB apparently increasing the risk of COPD (OR 1.40, 95% CI 1.07 to 1.82 for less than 9 μmol/L; OR 1.36, 95% CI 1.06 to 1.76 for 9.01-1 0.88 μmol/L; OR 1.50, 95% CI 1.16 to 1.95 for more than 13 μmol/L). There was a significant non-linear relationship between TB and FEV1/FVC (non-linear p=0.004). Furthermore, results of bidirectional Mendelian randomization analysis (OR 1.000; 95% CI 0.983 to 1.017 for MR and OR 0.998; 95% CI 0.976 to 1.020 for reversal MR) did not support the causal effects between serum TB and FEV1/FVC after controlling the effect of potential confounders and revised causality. Conclusion Our study reveals that there was non-linear does-response pattern between serum TB and COPD. However, there was little evidence for the linear causal associations of serum TB with airflow limitation. The relationship of TB with COPD needs further study and careful interpretation.
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Affiliation(s)
- Cuiqiong Dai
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zihui Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Huajing Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Shan Xiao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jianwu Xu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zhishan Deng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Fan Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou Laboratory, Bio-Island, Guangzhou, People’s Republic of China
| | - Xiang Wen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Youlan Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Lifei Lu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Ningning Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Peiyu Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yumin Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou Laboratory, Bio-Island, Guangzhou, People’s Republic of China
| | - Pixin Ran
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou Laboratory, Bio-Island, Guangzhou, People’s Republic of China
- Correspondence: Pixin Ran; Yumin Zhou, Tel +86-20 3710 3616, Fax +86-20 81340482, Email ;
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Genetic Risk and Chronic Obstructive Pulmonary Disease Independently Predict the Risk of Incident Severe COVID-19. Ann Am Thorac Soc 2022; 19:58-65. [PMID: 34242153 PMCID: PMC8787794 DOI: 10.1513/annalsats.202102-171oc] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rationale: Both genetic variants and chronic obstructive pulmonary disease (COPD) contribute to the risk of incident severe coronavirus disease (COVID-19). Whether genetic risk of incident severe COVID-19 is the same regardless of preexisting COPD is unknown. Objectives: In this study, we aimed to investigate the potential interaction between genetic risk and COPD in relation to severe COVID-19. Methods: We constructed a polygenic risk score for severe COVID-19 by using 112 single-nucleotide polymorphisms in 430,582 participants from the UK Biobank study. We examined the associations of genetic risk and COPD with severe COVID-19 by using logistic regression models. Results: Of 430,582 participants, 712 developed severe COVID-19 as of February 22, 2021, of whom 19.8% had preexisting COPD. Compared with participants at low genetic risk, those at intermediate genetic risk (odds ratio [OR], 1.34; 95% confidence interval [CI], 1.09-1.66) and high genetic risk (OR, 1.50; 95% CI, 1.18-1.92) had higher risk of severe COVID-19 (P for trend = 0.001), and the association was independent of COPD (P for interaction = 0.76). COPD was associated with a higher risk of incident severe COVID-19 (OR, 1.37; 95% CI, 1.12-1.67; P = 0.002). Participants at high genetic risk and with COPD had a higher risk of severe COVID-19 (OR, 2.05; 95% CI, 1.35-3.04; P < 0.001) than those at low genetic risk and without COPD. Conclusions: The polygenic risk score, which combines multiple risk alleles, can be effectively used in screening for high-risk populations of severe COVID-19. High genetic risk correlates with a higher risk of severe COVID-19, regardless of preexisting COPD.
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157
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Mei X, Lu R, Cui L, Tian Y, Zhao P, Li J. Poly I:C Exacerbates Airway Inflammation and Remodeling in Cigarette Smoke-Exposed Mice. Lung 2022; 200:677-686. [PMID: 36269393 PMCID: PMC9675662 DOI: 10.1007/s00408-022-00574-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/22/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a chronic respiratory disorder characterized by chronic inflammation and airway remodeling. Cigarette smoke (CS) and respiratory viruses are major causes of COPD development and exacerbation, but the mechanisms of these compounding factors on inflammation and pathological changes in airway structure still need further investigation. PURPOSE This work aimed to investigate the effects and mechanisms of Poly I:C on pathological changes in CS-induced COPD mice, such as airway inflammation and remodeling. METHODS From 1 to 8 weeks, the mice were exposed to CS, Poly I:C, or a combination of both. To compare the pathological changes among different groups over time, the mice were sacrificed at week 4, 8, 16, and 24, then the lungs were harvested to measure pulmonary pathology, inflammatory cytokines, and airway remodeling. RESULTS Our data revealed that the fundamental characteristics of COPD, such as pulmonary pathological damage, the release of inflammatory mediators, and the remodeling of airway walls, were observed at week 8 in CS-exposed mice and these pathological changes persisted to week 16. Compared with the CS group, the pathological changes, including decreased lung function, inflammatory cell infiltration, alveolar destruction, and airway wall thickening, were weaker in the Poly I:C group. These pathological changes were observed at week 8 and persisted to week 16 in Poly I:C-induced mice. Furthermore, Poly I:C exacerbated lung tissue damage in CS-induced COPD mice. The decreased lung function, airway inflammation and remodeling were observed in the combined group at week 4, and these pathological changes persisted to week 24. Our research indicated that Poly I:C enhanced the expression of p-P38, p-JNK and p-NF-κB in CS-exposed mice. CONCLUSION Poly I:C could promote airway inflammation and remodeling in CS-induced COPD mice probably by NF-κB and MAPK signaling.
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Affiliation(s)
- Xiaofeng Mei
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046 Henan Province China ,Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province & Education Ministry of P.R. China, Zhengzhou, 450046 Henan Province China
| | - Ruilong Lu
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046 Henan Province China ,Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province & Education Ministry of P.R. China, Zhengzhou, 450046 Henan Province China
| | - Lili Cui
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046 Henan Province China ,Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province & Education Ministry of P.R. China, Zhengzhou, 450046 Henan Province China
| | - Yange Tian
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046 Henan Province China ,Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province & Education Ministry of P.R. China, Zhengzhou, 450046 Henan Province China ,Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, 450000 China
| | - Peng Zhao
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046 Henan Province China ,Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province & Education Ministry of P.R. China, Zhengzhou, 450046 Henan Province China ,Department of Respiratory Diseases, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000 China ,Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, 450000 China
| | - Jiansheng Li
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046 Henan Province China ,Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province & Education Ministry of P.R. China, Zhengzhou, 450046 Henan Province China ,Department of Respiratory Diseases, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000 China
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158
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Gill D, Burgess S. Distinguishing causation from genetic correlation in a Mendelian randomisation framework. Eur Respir J 2021; 58:58/6/2101346. [PMID: 34887314 PMCID: PMC7614493 DOI: 10.1183/13993003.01346-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/28/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Dipender Gill
- Dept of Epidemiology and Biostatistics, School Public Health, Imperial College London, London, UK .,Clinical Pharmacology and Therapeutics Section, Institute of Medical and Biomedical Education and Institute for Infection and Immunity, St George's, University of London, London, UK.,Clinical Pharmacology Group, Pharmacy and Medicines Directorate, St George's University Hospitals NHS Foundation Trust, London, UK.,Genetics Dept, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Stephen Burgess
- Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,Medical Research Council Biostatistics Unit, University of Cambridge, Cambridge, UK
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Zhang Q, Zhang X, Zhang J, Wang B, Meng X, Tian Q, Zhang J, Jiang M, Zhang Y, Zheng D, Wu L, Wang W, Wang B, Wang Y. Causal Relationship Between Lung Function and Atrial Fibrillation: A Two Sample Univariable and Multivariable, Bidirectional Mendelian Randomization Study. Front Cardiovasc Med 2021; 8:769198. [PMID: 34869686 PMCID: PMC8635999 DOI: 10.3389/fcvm.2021.769198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/21/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Observational studies have identified impaired lung function accessed by forced expiratory volume in one second (FEV1), forced vital capacity (FVC) or the ratio of FEV1 over FVC (FEV1/FVC) as an independent risk factor for atrial fibrillation (AF). However, the result may be affected by confounders or reverse causality. Methods: We performed univariable MR (uvMR), multivariable MR (mvMR) and bidirectional two-sample MR to jointly estimate the causality of lung function with AF. Apart from the inverse variance weighted (IVW) approach as the main MR analysis, three complementary sensitive analyses approaches including MR-Egger regression, weighted median (WM) MR and Pleiotropy Residual Sum and Outlier (MR-PRESSO) in uvMR as well as mvMR-Egger and mvMR-PRESSO in mvMR were applied to control for pleiotropy. Linkage disequilibrium score (LDSC) regression was applied to estimate genetic correlation between lung function and AF. Results: All forward and reverse uvMR analyses consistently suggested absent causal relations between lung function and AF risk [forward IVW: odds ratio (OR)FEV1 = 1.031, 95% CI = 0.909–1.169, P = 0.630; ORFVC = 1.002, 95% CI = 0.834–1.204, P = 0.982; ORFEV1/FVC = 1.076, 95% CI = 0.966–1.199, P = 0.182; reverse IVW: ORFEV1 = 0.986, 95% CI = 0.966–1.007, P = 0.187; ORFVC = 0.985, 95% CI = 0.965–1.006, P = 0.158; ORFEV1/FVC = 0.994, 95% CI = 0.973–1.015, P = 0.545]. The forward MR-Egger showed that each standard deviation (SD) increase in FEV1/FVC was related to a higher AF risk (OR = 1.502, 95% CI = 1.178–1.915, P = 0.006) without heterogeneity (Q_pval = 0.064), but pleiotropy effect exist (intercept = −0.017, P = 0.012). However, this significant effect disappeared after adjustment of FEV1 and FVC (OR = 1.523, 95% CI = 0.445–5.217, P = 0.503) in mvMR. No evidence was found for independent causal effects of FEV1 and FVC on AF in mvMR analysis by using mvIVW method (ORFEV1 = 0.501, 95% CI = 0.056–4.457, P = 0.496; ORFVC = 1.969, 95% CI = 0.288–13.474, P = 0.490). Notably, the association between lung function and AF were replicated using the FinnGen cohort data. Conclusions: Our findings reported no coheritability between lung function and AF, and failed to find substantial causal relation between decreased lung function and risk of AF. However, lung function and AF were both associated with inflammation, which may be potential pathway, warranting further study.
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Affiliation(s)
- Qiaoyun Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Xiaoyu Zhang
- Department of Anesthesiology, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Jie Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Biyan Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Xiaoni Meng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Qiuyue Tian
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Jinxia Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Mengyang Jiang
- Department of Anesthesiology, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yiqiang Zhang
- Department of Anesthesiology, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Deqiang Zheng
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Lijuan Wu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Wei Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China.,Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
| | - Baoguo Wang
- Department of Anesthesiology, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China.,Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
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160
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Kim W, Moll M, Qiao D, Hobbs BD, Shrine N, Sakornsakolpat P, Tobin MD, Dudbridge F, Wain LV, Ladd-Acosta C, Chatterjee N, Silverman EK, Cho MH, Beaty TH. Interaction of Cigarette Smoking and Polygenic Risk Score on Reduced Lung Function. JAMA Netw Open 2021; 4:e2139525. [PMID: 34913977 PMCID: PMC8678715 DOI: 10.1001/jamanetworkopen.2021.39525] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
IMPORTANCE The risk of airflow limitation and chronic obstructive pulmonary disease (COPD) is influenced by combinations of cigarette smoking and genetic susceptibility, yet it remains unclear whether gene-by-smoking interactions are associated with quantitative measures of lung function. OBJECTIVE To assess the interaction of cigarette smoking and polygenic risk score in association with reduced lung function. DESIGN, SETTING, AND PARTICIPANTS This UK Biobank cohort study included UK citizens of European ancestry aged 40 to 69 years with genetic and spirometry data passing quality control metrics. Data was analyzed from July 2020 to March 2021. EXPOSURES PRS of combined forced expiratory volume in 1 second (FEV1) and percent of forced vital capacity exhaled in the first second (FEV1/FVC), self-reported pack-years of smoking, ever- vs never-smoking status, and current- vs former- or never-smoking status. MAIN OUTCOMES AND MEASURES FEV1/FVC was the primary outcome. Models were used to test for interactions with models, including the main effects of PRS, different smoking variables, and their cross-product terms. The association between pack-years of smoking and FEV1/FVC were compared for those in the highest vs lowest decile of estimated genetic risk for low lung function. RESULTS We included 319 730 individuals, of whom 24 915 (8%) had moderate-to-severe COPD cases, and 44.4% were men. Participants had a mean (SD) age 56.5 of (8.02) years. The PRS and pack-years were significantly associated with lower FEV1/FVC (PRS: β, -0.03; 95% CI, -0.031 to -0.03; pack-years: β, -0.0064; 95% CI, -0.0064 to -0.0063) and the interaction term (β, -0.0028; 95% CI, -0.0029 to -0.0026). A stepwise increment in estimated effect sizes for these interaction terms was observed per 10 pack-years of smoking exposure. The interaction of PRS with 11 to 20, 31 to 40, and more than 50 pack-years categories were β (interaction) -0.0038 (95% CI, -0.0046 to -0.0031); -0.013 (95% CI, -0.014 to -0.012); and -0.017 (95% CI, -0.019 to -0.016), respectively. There was evidence of significant interaction between PRS with ever- or never- smoking status (β, interaction; -0.0064; 95% CI, -0.0068 to -0.0060) and current or not-current smoking (β, interaction; -0.0091; 95% CI, -0.0097 to -0.0084). For any given level of pack-years of smoking exposure, FEV1/FVC was significantly lower for individuals in the tenth decile (ie, highest risk) than the first decile (ie, lowest risk) of genetic risk. For every 20 pack-years of smoking, those in the tenth decile compared with the first decile of genetic risk showed nearly a 2-fold reduction in FEV1/FVC. CONCLUSIONS AND RELEVANCE COPD is characterized by diminished lung function, and our analyses suggest there is substantial interaction between genome-wide PRS and smoking exposures. While smoking was associated with decreased lung function across all genetic risk categories, the associations were strongest in individuals with higher estimated genetic risk.
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Affiliation(s)
- Woori Kim
- Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Matthew Moll
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Brian D. Hobbs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Phuwanat Sakornsakolpat
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Nilanjan Chatterjee
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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161
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Akenroye AT, Brunetti T, Romero K, Daya M, Kanchan K, Shankar G, Chavan S, Preethi Boorgula M, Ampleford EA, Fonseca HF, Hawkins GA, Pitangueira Teixeira HM, Campbell M, Rafaels N, Winters A, Bleecker ER, Cruz AA, Barreto ML, Meyers DA, Ortega VE, Figueiredo CA, Barnes KC, Checkley W, Hansel NN, Mathias RA. Genome-wide association study of asthma, total IgE, and lung function in a cohort of Peruvian children. J Allergy Clin Immunol 2021; 148:1493-1504. [PMID: 33713768 PMCID: PMC8429514 DOI: 10.1016/j.jaci.2021.02.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Genetic ancestry plays a role in asthma health disparities. OBJECTIVE Our aim was to evaluate the impact of ancestry on and identify genetic variants associated with asthma, total serum IgE level, and lung function. METHODS A total of 436 Peruvian children (aged 9-19 years) with asthma and 291 without asthma were genotyped by using the Illumina Multi-Ethnic Global Array. Genome-wide proportions of indigenous ancestry populations from continental America (NAT) and European ancestry from the Iberian populations in Spain (IBS) were estimated by using ADMIXTURE. We assessed the relationship between ancestry and the phenotypes and performed a genome-wide association study. RESULTS The mean ancestry proportions were 84.7% NAT (case patients, 84.2%; controls, 85.4%) and 15.3% IBS (15.8%; 14.6%). With adjustment for asthma, NAT was associated with higher total serum IgE levels (P < .001) and IBS was associated with lower total serum IgE levels (P < .001). NAT was associated with higher FEV1 percent predicted values (P < .001), whereas IBS was associated with lower FEV1 values in the controls but not in the case patients. The HLA-DR/DQ region on chromosome 6 (Chr6) was strongly associated with total serum IgE (rs3135348; P = 3.438 × 10-10) and was independent of an association with the haplotype HLA-DQA1∼HLA-DQB1:04.01∼04.02 (P = 1.55 × 10-05). For lung function, we identified a locus (rs4410198; P = 5.536 × 10-11) mapping to Chr19, near a cluster of zinc finger interacting genes that colocalizes to the long noncoding RNA CTD-2537I9.5. This novel locus was replicated in an independent sample of pediatric case patients with asthma with similar admixture from Brazil (P = .005). CONCLUSION This study confirms the role of HLA in atopy, and identifies a novel locus mapping to a long noncoding RNA for lung function that may be specific to children with NAT.
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Affiliation(s)
- Ayobami T Akenroye
- Division of Pediatric Allergy and Immunology, Johns Hopkins University School of Medicine, Baltimore, Md
| | - Tonya Brunetti
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - Karina Romero
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Md; A.B. PRISMA, Lima, Peru
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - Kanika Kanchan
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Md
| | - Gautam Shankar
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Md
| | - Sameer Chavan
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - Meher Preethi Boorgula
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - Elizabeth A Ampleford
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC
| | | | - Gregory A Hawkins
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | | | - Monica Campbell
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - Nicholas Rafaels
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - Alexandra Winters
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Md
| | | | | | - Mauricio L Barreto
- Centro de Integração de Dados e Conhecimento para Saúde, Fiocruz, Salvador, Brazil
| | | | - Victor E Ortega
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC
| | - Camila A Figueiredo
- Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador, Brazil
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, Colo
| | - William Checkley
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Md; Department of International Health, Program in Global Disease Epidemiology and Control, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md
| | - Nadia N Hansel
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Md.
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, Md.
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162
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Hancock DB. Compelling Interaction of Cigarette Smoking and Polygenetic Risk Emerges for Lung Function and COPD. JAMA Netw Open 2021; 4:e2140347. [PMID: 34913983 DOI: 10.1001/jamanetworkopen.2021.40347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, North Carolina
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163
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Zhang K, Hocker JD, Miller M, Hou X, Chiou J, Poirion OB, Qiu Y, Li YE, Gaulton KJ, Wang A, Preissl S, Ren B. A single-cell atlas of chromatin accessibility in the human genome. Cell 2021; 184:5985-6001.e19. [PMID: 34774128 PMCID: PMC8664161 DOI: 10.1016/j.cell.2021.10.024] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/30/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022]
Abstract
Current catalogs of regulatory sequences in the human genome are still incomplete and lack cell type resolution. To profile the activity of gene regulatory elements in diverse cell types and tissues in the human body, we applied single-cell chromatin accessibility assays to 30 adult human tissue types from multiple donors. We integrated these datasets with previous single-cell chromatin accessibility data from 15 fetal tissue types to reveal the status of open chromatin for ∼1.2 million candidate cis-regulatory elements (cCREs) in 222 distinct cell types comprised of >1.3 million nuclei. We used these chromatin accessibility maps to delineate cell-type-specificity of fetal and adult human cCREs and to systematically interpret the noncoding variants associated with complex human traits and diseases. This rich resource provides a foundation for the analysis of gene regulatory programs in human cell types across tissues, life stages, and organ systems.
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Affiliation(s)
- Kai Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - James D Hocker
- Ludwig Institute for Cancer Research, La Jolla, CA, USA; Medical Scientist Training Program, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Michael Miller
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Xiaomeng Hou
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA
| | - Olivier B Poirion
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Yunjiang Qiu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Yang E Li
- Ludwig Institute for Cancer Research, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Kyle J Gaulton
- Department of Pediatrics, Pediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Allen Wang
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, USA; Center for Epigenomics, University of California San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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164
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Ma S, Dalgleish J, Lee J, Wang C, Liu L, Gill R, Buxbaum JD, Chung WK, Aschard H, Silverman EK, Cho MH, He Z, Ionita-Laza I. Powerful gene-based testing by integrating long-range chromatin interactions and knockoff genotypes. Proc Natl Acad Sci U S A 2021; 118:e2105191118. [PMID: 34799441 PMCID: PMC8617518 DOI: 10.1073/pnas.2105191118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2021] [Indexed: 02/03/2023] Open
Abstract
Gene-based tests are valuable techniques for identifying genetic factors in complex traits. Here, we propose a gene-based testing framework that incorporates data on long-range chromatin interactions, several recent technical advances for region-based tests, and leverages the knockoff framework for synthetic genotype generation for improved gene discovery. Through simulations and applications to genome-wide association studies (GWAS) and whole-genome sequencing data for multiple diseases and traits, we show that the proposed test increases the power over state-of-the-art gene-based tests in the literature, identifies genes that replicate in larger studies, and can provide a more narrow focus on the possible causal genes at a locus by reducing the confounding effect of linkage disequilibrium. Furthermore, our results show that incorporating genetic variation in distal regulatory elements tends to improve power over conventional tests. Results for UK Biobank and BioBank Japan traits are also available in a publicly accessible database that allows researchers to query gene-based results in an easy fashion.
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Affiliation(s)
- Shiyang Ma
- Department of Biostatistics, Columbia University, New York, NY 10032
| | - James Dalgleish
- Department of Biostatistics, Columbia University, New York, NY 10032
| | - Justin Lee
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA 94305
| | - Chen Wang
- Department of Biostatistics, Columbia University, New York, NY 10032
| | - Linxi Liu
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA 15260
| | - Richard Gill
- Department of Human Genetics, Genentech, South San Francisco, CA 94080
- Department of Epidemiology, Columbia University, New York, NY 10032
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY 10032
- Department of Medicine, Columbia University, New York, NY 10032
| | - Hugues Aschard
- Department of Computational Biology, Institut Pasteur, 75015 Paris, France
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Zihuai He
- Quantitative Sciences Unit, Department of Medicine, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
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165
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Wang T, Wang W, Li W, Duan H, Xu C, Tian X, Zhang D. Genome-wide DNA methylation analysis of pulmonary function in middle and old-aged Chinese monozygotic twins. Respir Res 2021; 22:300. [PMID: 34809630 PMCID: PMC8609861 DOI: 10.1186/s12931-021-01896-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/12/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Previous studies have determined the epigenetic association between DNA methylation and pulmonary function among various ethnics, whereas this association is largely unknown in Chinese adults. Thus, we aimed to explore epigenetic relationships between genome-wide DNA methylation levels and pulmonary function among middle-aged Chinese monozygotic twins. METHODS The monozygotic twin sample was drawn from the Qingdao Twin Registry. Pulmonary function was measured by three parameters including forced expiratory volume the first second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio. Linear mixed effect model was used to regress the methylation level of CpG sites on pulmonary function. After that, we applied Genomic Regions Enrichment of Annotations Tool (GREAT) to predict the genomic regions enrichment, and used comb-p python library to detect differentially methylated regions (DMRs). Gene expression analysis was conducted to validate the results of differentially methylated analyses. RESULTS We identified 112 CpG sites with the level of P < 1 × 10-4 which were annotated to 40 genes. We identified 12 common enriched pathways of three pulmonary function parameters. We detected 39 DMRs located at 23 genes, of which PRDM1 was related to decreased pulmonary function, and MPL, LTB4R2, and EPHB3 were related to increased pulmonary function. The gene expression analyses validated DIP2C, ASB2, SLC6A5, and GAS6 related to decreased pulmonary function. CONCLUSION Our DNA methylation sequencing analysis on identical twins provides new references for the epigenetic regulation on pulmonary function. Several CpG sites, genes, biological pathways and DMRs are considered as possible crucial to pulmonary function.
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Affiliation(s)
- Tong Wang
- Department of Epidemiology and Health Statistics, the College of Public Health of Qingdao University, NO. 308 Ning Xia Street, Qingdao, 266071, Shandong Province, People's Republic of China
| | - Weijing Wang
- Department of Epidemiology and Health Statistics, the College of Public Health of Qingdao University, NO. 308 Ning Xia Street, Qingdao, 266071, Shandong Province, People's Republic of China
| | - Weilong Li
- Population Research Unit, Faculty of Social Sciences, University of Helsinki, Helsinki, Finland
| | - Haiping Duan
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong Province, People's Republic of China.,Qingdao Institute of Preventive Medicine, Qingdao, Shandong Province, People's Republic of China
| | - Chunsheng Xu
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong Province, People's Republic of China.,Qingdao Institute of Preventive Medicine, Qingdao, Shandong Province, People's Republic of China
| | - Xiaocao Tian
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong Province, People's Republic of China.,Qingdao Institute of Preventive Medicine, Qingdao, Shandong Province, People's Republic of China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, the College of Public Health of Qingdao University, NO. 308 Ning Xia Street, Qingdao, 266071, Shandong Province, People's Republic of China.
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166
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Yamada M, Motoike IN, Kojima K, Fuse N, Hozawa A, Kuriyama S, Katsuoka F, Tadaka S, Shirota M, Sakurai M, Nakamura T, Hamanaka Y, Suzuki K, Sugawara J, Ogishima S, Uruno A, Kodama EN, Fujino N, Numakura T, Ichikawa T, Mitsune A, Ohe T, Kinoshita K, Ichinose M, Sugiura H, Yamamoto M. Genetic loci for lung function in Japanese adults with adjustment for exhaled nitric oxide levels as airway inflammation indicator. Commun Biol 2021; 4:1288. [PMID: 34782693 PMCID: PMC8593164 DOI: 10.1038/s42003-021-02813-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 10/27/2021] [Indexed: 11/08/2022] Open
Abstract
Lung function reflects the ability of the respiratory system and is utilized for the assessment of respiratory diseases. Because type 2 airway inflammation influences lung function, genome wide association studies (GWAS) for lung function would be improved by adjustment with an indicator of the inflammation. Here, we performed a GWAS for lung function with adjustment for exhaled nitric oxide (FeNO) levels in two independent Japanese populations. Our GWAS with genotype imputations revealed that the RNF5/AGER locus including AGER rs2070600 SNP, which introduces a G82S substitution of AGER, was the most significantly associated with FEV1/FVC. Three other rare missense variants of AGER were further identified. We also found genetic loci with three candidate genes (NOS2, SPSB2 and RIPOR2) associated with FeNO levels. Analyses with the BioBank-Japan GWAS resource revealed genetic links of FeNO and asthma-related traits, and existence of common genetic background for allergic diseases and their biomarkers. Our study identified the genetic locus most strongly associated with airway obstruction in the Japanese population and three genetic loci associated with FeNO, an indicator of type 2 airway inflammation in adults.
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Affiliation(s)
- Mitsuhiro Yamada
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shu Tadaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Miyuki Sakurai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomohiro Nakamura
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yohei Hamanaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kichiya Suzuki
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Eiichi N Kodama
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoya Fujino
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tadahisa Numakura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomohiro Ichikawa
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ayumi Mitsune
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Ohe
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | | | - Hisatoshi Sugiura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
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167
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Pietzner M, Wheeler E, Carrasco-Zanini J, Cortes A, Koprulu M, Wörheide MA, Oerton E, Cook J, Stewart ID, Kerrison ND, Luan J, Raffler J, Arnold M, Arlt W, O’Rahilly S, Kastenmüller G, Gamazon ER, Hingorani AD, Scott RA, Wareham NJ, Langenberg C. Mapping the proteo-genomic convergence of human diseases. Science 2021; 374:eabj1541. [PMID: 34648354 PMCID: PMC9904207 DOI: 10.1126/science.abj1541] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Characterization of the genetic regulation of proteins is essential for understanding disease etiology and developing therapies. We identified 10,674 genetic associations for 3892 plasma proteins to create a cis-anchored gene-protein-disease map of 1859 connections that highlights strong cross-disease biological convergence. This proteo-genomic map provides a framework to connect etiologically related diseases, to provide biological context for new or emerging disorders, and to integrate different biological domains to establish mechanisms for known gene-disease links. Our results identify proteo-genomic connections within and between diseases and establish the value of cis-protein variants for annotation of likely causal disease genes at loci identified in genome-wide association studies, thereby addressing a major barrier to experimental validation and clinical translation of genetic discoveries.
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Affiliation(s)
- Maik Pietzner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK,Computational Medicine, Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Eleanor Wheeler
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Julia Carrasco-Zanini
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | | | - Mine Koprulu
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Maria A. Wörheide
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Erin Oerton
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - James Cook
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Isobel D. Stewart
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Nicola D. Kerrison
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Jian’an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Johannes Raffler
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany,Institut für Digitale Medizin, Universitätsklinikum Augsburg, 86156 Augsburg, Germany
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany,Department of Psychiatry and Behavioural Sciences, Duke University, Durham, NC 27710, USA
| | - Wiebke Arlt
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Stephen O’Rahilly
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany,German Centre for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Eric R. Gamazon
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37203, USA,Clare Hall, University of Cambridge, Cambridge CB3 9AL, United Kingdom
| | - Aroon D. Hingorani
- UCL British Heart Foundation Research Accelerator, Institute of Cardiovascular Science, University College London, WC1E 6BT, UK.,Health Data Research UK, Gibbs Building, 215 Euston Road, London NW1 2BE, UK,Institute of Health Informatics, University College London, 222 Euston Road, London NW1 2DA, UK
| | | | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK,Health Data Research UK, Gibbs Building, 215 Euston Road, London NW1 2BE, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK,Computational Medicine, Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, 10117 Berlin, Germany,Health Data Research UK, Gibbs Building, 215 Euston Road, London NW1 2BE, UK,Correspondence to Dr. Claudia Langenberg ()
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168
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Kinchen JM, Mohney RP, Pappan KL. Long-Chain Acylcholines Link Butyrylcholinesterase to Regulation of Non-neuronal Cholinergic Signaling. J Proteome Res 2021; 21:599-611. [PMID: 34758617 DOI: 10.1021/acs.jproteome.1c00538] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Acylcholines are comprised of an acyl chain esterified to a choline moiety; acetylcholine is the best-characterized member of this class, functioning as a neurotransmitter in the central and peripheral nervous systems as well as an inhibitor of cytokine production by macrophages and other innate immune cells. Acylcholines are metabolized by a class of cholinesterases, including acetylcholinesterase (a specific regulator of acetylcholine levels) and butyrylcholinesterase (BChE, an enigmatic enzyme whose function has not been resolved by genetic knockout models). BChE provides reserve capacity to hydrolyze acetylcholine, but its importance is arguable given acetylcholinesterase is the most catalytically efficient enzyme characterized to date. While known to be substrates of BChE in vitro, endogenous production of long-chain acylcholines is a recent discovery enabled by untargeted metabolomics. Compared to acetylcholine, long-chain acylcholines show greater stability in circulation with homeostatic levels-dictated by synthesis and clearance-suggested to impact cholinergic receptor sensitivity of acetylcholine with varying levels of antagonism. Acylcholines then provide a link between BChE and non-neuronal acetylcholine signaling, filling a gap in understanding around how imbalances between acylcholines and BChE could modulate inflammatory disease, such as the "cytokine storm" identified in severe COVID-19. Areas for further research, development, and clinical testing are outlined.
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Affiliation(s)
- Jason M Kinchen
- Owlstone Medical Inc., 600 Park Office Drive, Suite 140, Research Triangle Park, North Carolina 27709, United States
| | - Robert P Mohney
- Owlstone Medical Inc., 600 Park Office Drive, Suite 140, Research Triangle Park, North Carolina 27709, United States
| | - Kirk L Pappan
- Owlstone Medical Inc., 600 Park Office Drive, Suite 140, Research Triangle Park, North Carolina 27709, United States
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169
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Hanscombe KB, Persyn E, Traylor M, Glanville KP, Hamer M, Coleman JRI, Lewis CM. The genetic case for cardiorespiratory fitness as a clinical vital sign and the routine prescription of physical activity in healthcare. Genome Med 2021; 13:180. [PMID: 34753499 PMCID: PMC8579601 DOI: 10.1186/s13073-021-00994-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Cardiorespiratory fitness (CRF) and physical activity (PA) are well-established predictors of morbidity and all-cause mortality. However, CRF is not routinely measured and PA not routinely prescribed as part of standard healthcare. The American Heart Association (AHA) recently presented a scientific case for the inclusion of CRF as a clinical vital sign based on epidemiological and clinical observation. Here, we leverage genetic data in the UK Biobank (UKB) to strengthen the case for CRF as a vital sign and make a case for the prescription of PA. METHODS We derived two CRF measures from the heart rate data collected during a submaximal cycle ramp test: CRF-vo2max, an estimate of the participants' maximum volume of oxygen uptake, per kilogram of body weight, per minute; and CRF-slope, an estimate of the rate of increase of heart rate during exercise. Average PA over a 7-day period was derived from a wrist-worn activity tracker. After quality control, 70,783 participants had data on the two derived CRF measures, and 89,683 had PA data. We performed genome-wide association study (GWAS) analyses by sex, and post-GWAS techniques to understand genetic architecture of the traits and prioritise functional genes for follow-up. RESULTS We found strong evidence that genetic variants associated with CRF and PA influenced genetic expression in a relatively small set of genes in the heart, artery, lung, skeletal muscle and adipose tissue. These functionally relevant genes were enriched among genes known to be associated with coronary artery disease (CAD), type 2 diabetes (T2D) and Alzheimer's disease (three of the top 10 causes of death in high-income countries) as well as Parkinson's disease, pulmonary fibrosis, and blood pressure, heart rate, and respiratory phenotypes. Genetic variation associated with lower CRF and PA was also correlated with several disease risk factors (including greater body mass index, body fat and multiple obesity phenotypes); a typical T2D profile (including higher insulin resistance, higher fasting glucose, impaired beta-cell function, hyperglycaemia, hypertriglyceridemia); increased risk for CAD and T2D; and a shorter lifespan. CONCLUSIONS Genetics supports three decades of evidence for the inclusion of CRF as a clinical vital sign. Given the genetic, clinical and epidemiological evidence linking CRF and PA to increased morbidity and mortality, regular measurement of CRF as a marker of health and routine prescription of PA could be a prudent strategy to support public health.
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Affiliation(s)
- Ken B Hanscombe
- Department of Medical & Molecular Genetics, King's College London, London, UK. .,Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK.
| | - Elodie Persyn
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | | | - Kylie P Glanville
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Mark Hamer
- Institute of Sport Exercise & Health, Division of Surgery and Interventional Science, University College London, London, UK
| | - Jonathan R I Coleman
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Cathryn M Lewis
- Department of Medical & Molecular Genetics, King's College London, London, UK.,Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
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170
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Routhier J, Pons S, Freidja ML, Dalstein V, Cutrona J, Jonquet A, Lalun N, Mérol JC, Lathrop M, Stitzel JA, Kervoaze G, Pichavant M, Gosset P, Tournier JM, Birembaut P, Dormoy V, Maskos U. An innate contribution of human nicotinic receptor polymorphisms to COPD-like lesions. Nat Commun 2021; 12:6384. [PMID: 34737286 PMCID: PMC8568944 DOI: 10.1038/s41467-021-26637-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/14/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic Obstructive Pulmonary Disease is a generally smoking-linked major cause of morbidity and mortality. Genome-wide Association Studies identified a locus including a non-synonymous single nucleotide polymorphism in CHRNA5, rs16969968, encoding the nicotinic acetylcholine receptor α5 subunit, predisposing to both smoking and Chronic Obstructive Pulmonary Disease. Here we report that nasal polyps from rs16969968 non-smoking carriers exhibit airway epithelium remodeling and inflammation. These hallmarks of Chronic Obstructive Pulmonary Disease occur spontaneously in mice expressing human rs16969968. They are significantly amplified after exposure to porcine pancreatic elastase, an emphysema model, and to oxidative stress with a polymorphism-dependent alteration of lung function. Targeted rs16969968 expression in epithelial cells leads to airway remodeling in vivo, increased proliferation and production of pro-inflammatory cytokines through decreased calcium entry and increased adenylyl-cyclase activity. We show that rs16969968 directly contributes to Chronic Obstructive Pulmonary Disease-like lesions, sensitizing the lung to the action of oxidative stress and injury, and represents a therapeutic target. Human polymorphisms in nicotinic acetylcholine receptor genes have been linked to both smoking and lung diseases like Chronic Obstructive Pulmonary Disease (COPD) or lung cancer. Here the authors identify a direct role for a human coding polymorphism in COPD-like lesions independent of smoke or nicotine exposure.
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Affiliation(s)
- Julie Routhier
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France
| | - Stéphanie Pons
- Institut Pasteur, Université de Paris, Integrative Neurobiology of Cholinergic Systems, CNRS UMR 3571, Paris, France
| | - Mohamed Lamine Freidja
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France.,Department of Biochemistry and Microbiology, Faculty of Sciences, University of M'sila, M'sila, Algeria
| | - Véronique Dalstein
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France.,Department of Biopathology, CHU of Reims, Reims, France
| | - Jérôme Cutrona
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France
| | - Antoine Jonquet
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France
| | - Nathalie Lalun
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France
| | - Jean-Claude Mérol
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France.,Department of Otorhinolaryngology, CHU of Reims, Reims, France
| | - Mark Lathrop
- McGill University Genome Center, Montréal, QC, Canada
| | - Jerry A Stitzel
- Institute for Behavioral Genetics, University of Colorado, Boulder, CO, USA
| | - Gwenola Kervoaze
- University of Lille, CNRS UMR9017, Inserm U1019, CHU Lille, Institut Pasteur de Lille, CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Muriel Pichavant
- University of Lille, CNRS UMR9017, Inserm U1019, CHU Lille, Institut Pasteur de Lille, CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Philippe Gosset
- University of Lille, CNRS UMR9017, Inserm U1019, CHU Lille, Institut Pasteur de Lille, CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Jean-Marie Tournier
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France
| | - Philippe Birembaut
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France.,Department of Biopathology, CHU of Reims, Reims, France
| | - Valérian Dormoy
- Université de Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, Reims, France.
| | - Uwe Maskos
- Institut Pasteur, Université de Paris, Integrative Neurobiology of Cholinergic Systems, CNRS UMR 3571, Paris, France.
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171
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Espín R, Baiges A, Blommaert E, Herranz C, Roman A, Saez B, Ancochea J, Valenzuela C, Ussetti P, Laporta R, Rodríguez-Portal JA, van Moorsel CHM, van der Vis JJ, Quanjel MJR, Villar-Piqué A, Diaz-Lucena D, Llorens F, Casanova Á, Molina-Molina M, Plass M, Mateo F, Moss J, Pujana MA. Heterogeneity and Cancer-Related Features in Lymphangioleiomyomatosis Cells and Tissue. Mol Cancer Res 2021; 19:1840-1853. [PMID: 34312290 PMCID: PMC8568632 DOI: 10.1158/1541-7786.mcr-21-0220] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/23/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022]
Abstract
Lymphangioleiomyomatosis (LAM) is a rare, low-grade metastasizing disease characterized by cystic lung destruction. LAM can exhibit extensive heterogeneity at the molecular, cellular, and tissue levels. However, the molecular similarities and differences among LAM cells and tissue, and their connection to cancer features are not fully understood. By integrating complementary gene and protein LAM signatures, and single-cell and bulk tissue transcriptome profiles, we show sources of disease heterogeneity, and how they correspond to cancer molecular portraits. Subsets of LAM diseased cells differ with respect to gene expression profiles related to hormones, metabolism, proliferation, and stemness. Phenotypic diseased cell differences are identified by evaluating lumican (LUM) proteoglycan and YB1 transcription factor expression in LAM lung lesions. The RUNX1 and IRF1 transcription factors are predicted to regulate LAM cell signatures, and both regulators are expressed in LAM lung lesions, with differences between spindle-like and epithelioid LAM cells. The cancer single-cell transcriptome profiles most similar to those of LAM cells include a breast cancer mesenchymal cell model and lines derived from pleural mesotheliomas. Heterogeneity is also found in LAM lung tissue, where it is mainly determined by immune system factors. Variable expression of the multifunctional innate immunity protein LCN2 is linked to disease heterogeneity. This protein is found to be more abundant in blood plasma from LAM patients than from healthy women. IMPLICATIONS: This study identifies LAM molecular and cellular features, master regulators, cancer similarities, and potential causes of disease heterogeneity.
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Affiliation(s)
- Roderic Espín
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Alexandra Baiges
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Eline Blommaert
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Carmen Herranz
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Antonio Roman
- Lung Transplant Unit, Pneumology Service, Lymphangioleiomyomatosis Clinic, Vall d'Hebron University Hospital, Barcelona, Catalonia, Spain
| | - Berta Saez
- Lung Transplant Unit, Pneumology Service, Lymphangioleiomyomatosis Clinic, Vall d'Hebron University Hospital, Barcelona, Catalonia, Spain
| | - Julio Ancochea
- Pneumology Service, University Hospital La Princesa, La Princesa Research Institute (IIS-IP), Madrid, Spain
| | - Claudia Valenzuela
- Pneumology Service, University Hospital La Princesa, La Princesa Research Institute (IIS-IP), Madrid, Spain
| | - Piedad Ussetti
- Pneumology Service, University Hospital Clínica Puerta del Hierro, Majadahonda, Madrid, Spain
| | - Rosalía Laporta
- Pneumology Service, University Hospital Clínica Puerta del Hierro, Majadahonda, Madrid, Spain
| | - José A Rodríguez-Portal
- Medical-Surgical Unit of Respiratory Diseases, University Hospital Virgen del Rocío, Institute of Biomedicine of Seville (IBiS), Seville, Spain
- Biomedical Research Network Centre in Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Coline H M van Moorsel
- Interstitial Lung Disease (ILD) Center of Excellence, St. Antonius Hospital, Nieuwegein, the Netherlands
| | - Joanne J van der Vis
- Interstitial Lung Disease (ILD) Center of Excellence, St. Antonius Hospital, Nieuwegein, the Netherlands
| | - Marian J R Quanjel
- Interstitial Lung Disease (ILD) Center of Excellence, St. Antonius Hospital, Nieuwegein, the Netherlands
| | - Anna Villar-Piqué
- Neuroscience Program, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Biomedical Research Network Centre in Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Daniela Diaz-Lucena
- Neuroscience Program, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Biomedical Research Network Centre in Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Franc Llorens
- Neuroscience Program, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Biomedical Research Network Centre in Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Neurology, Clinical Dementia Center and National Reference Center for CJD Surveillance, University Medical School, Göttingen, Germany
| | - Álvaro Casanova
- Pneumology Service, University Hospital of Henares, University Francisco de Vitoria, Coslada, Madrid, Spain
| | - María Molina-Molina
- Biomedical Research Network Centre in Respiratory Diseases (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Interstitial Lung Disease Unit, Department of Respiratory Medicine, University Hospital of Bellvitge, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Mireya Plass
- Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
- Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
- Biomedical Research Network Centre on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Francesca Mateo
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Joel Moss
- Pulmonary Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Miquel Angel Pujana
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain.
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Farré X, Espín R, Baiges A, Blommaert E, Kim W, Giannikou K, Herranz C, Román A, Sáez B, Casanova Á, Ancochea J, Valenzuela C, Ussetti P, Laporta R, Rodríguez-Portal JA, van Moorsel CH, van der Vis JJ, Quanjel MJ, Tena-Garitaonaindia M, Sánchez de Medina F, Mateo F, Molina-Molina M, Won S, Kwiatkowski DJ, de Cid R, Pujana MA. Evidence for shared genetic risk factors between lymphangioleiomyomatosis and pulmonary function. ERJ Open Res 2021; 8:00375-2021. [PMID: 35083324 PMCID: PMC8784893 DOI: 10.1183/23120541.00375-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/17/2021] [Indexed: 11/05/2022] Open
Abstract
IntroductionLymphangioleiomyomatosis (LAM) is a rare low-grade metastasising disease characterised by cystic lung destruction. The genetic basis of LAM remains incompletely determined, and the disease cell-of-origin is uncertain. We analysed the possibility of a shared genetic basis between LAM and cancer, and LAM and pulmonary function.MethodsThe results of genome-wide association studies of LAM, 17 cancer types and spirometry measures (forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), FEV1/FVC ratio and peak expiratory flow (PEF)) were analysed for genetic correlations, shared genetic variants and causality. Genomic and transcriptomic data were examined, and immunodetection assays were performed to evaluate pleiotropic genes.ResultsThere were no significant overall genetic correlations between LAM and cancer, but LAM correlated negatively with FVC and PEF, and a trend in the same direction was observed for FEV1. 22 shared genetic variants were uncovered between LAM and pulmonary function, while seven shared variants were identified between LAM and cancer. The LAM-pulmonary function shared genetics identified four pleiotropic genes previously recognised in LAM single-cell transcriptomes: ADAM12, BNC2, NR2F2 and SP5. We had previously associated NR2F2 variants with LAM, and we identified its functional partner NR3C1 as another pleotropic factor. NR3C1 expression was confirmed in LAM lung lesions. Another candidate pleiotropic factor, CNTN2, was found more abundant in plasma of LAM patients than that of healthy women.ConclusionsThis study suggests the existence of a common genetic aetiology between LAM and pulmonary function.
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173
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Tobin MD, Izquierdo AG. Improving ethnic diversity in respiratory genomics research. Eur Respir J 2021; 58:58/4/2101615. [PMID: 34649971 DOI: 10.1183/13993003.01615-2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Martin D Tobin
- Dept of Health Sciences, University of Leicester, Leicester, UK .,Leicester NIHR Biomedical Research Centre, Leicester, UK
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174
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Zhu Z, Li J, Si J, Ma B, Shi H, Lv J, Cao W, Guo Y, Millwood IY, Walters RG, Lin K, Yang L, Chen Y, Du H, Yu B, Hasegawa K, Camargo CA, Moffatt MF, Cookson WOC, Chen J, Chen Z, Li L, Yu C, Liang L. A large-scale genome-wide association analysis of lung function in the Chinese population identifies novel loci and highlights shared genetic aetiology with obesity. Eur Respir J 2021; 58:2100199. [PMID: 33766948 PMCID: PMC8513692 DOI: 10.1183/13993003.00199-2021] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/02/2021] [Indexed: 01/25/2023]
Abstract
BACKGROUND Lung function is a heritable complex phenotype with obesity being one of its important risk factors. However, knowledge of their shared genetic basis is limited. Most genome-wide association studies (GWASs) for lung function have been based on European populations, limiting the generalisability across populations. Large-scale lung function GWASs in other populations are lacking. METHODS We included 100 285 subjects from the China Kadoorie Biobank (CKB). To identify novel loci for lung function, single-trait GWAS analyses were performed on forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC in the CKB. We then performed genome-wide cross-trait analysis between lung function and obesity traits (body mass index (BMI), BMI-adjusted waist-to-hip ratio and BMI-adjusted waist circumference) to investigate the shared genetic effects in the CKB. Finally, polygenic risk scores (PRSs) of lung function were developed in the CKB and their interaction with BMI's association on lung function were examined. We also conducted cross-trait analysis in parallel with the CKB using up to 457 756 subjects from the UK Biobank (UKB) for replication and investigation of ancestry-specific effects. RESULTS We identified nine genome-wide significant novel loci for FEV1, six for FVC and three for FEV1/FVC in the CKB. FEV1 and FVC showed significant negative genetic correlation with obesity traits in both the CKB and UKB. Genetic loci shared between lung function and obesity traits highlighted important biological pathways, including cell proliferation, embryo, skeletal and tissue development, and regulation of gene expression. Mendelian randomisation analysis suggested significant negative causal effects of BMI on FEV1 and on FVC in both the CKB and UKB. Lung function PRSs significantly modified the effect of change in BMI on change in lung function during an average follow-up of 8 years. CONCLUSION This large-scale GWAS of lung function identified novel loci and shared genetic aetiology between lung function and obesity. Change in BMI might affect change in lung function differently according to a subject's polygenic background. These findings may open new avenues for the development of molecular-targeted therapies for obesity and lung function improvement.
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Affiliation(s)
- Zhaozhong Zhu
- Program in Genetic Epidemiology and Statistical Genetics, Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- These four authors contributed equally to this article
| | - Jiachen Li
- Dept of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
- These four authors contributed equally to this article
| | - Jiahui Si
- Program in Genetic Epidemiology and Statistical Genetics, Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Dept of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
- These four authors contributed equally to this article
| | - Baoshan Ma
- College of Information Science and Technology, Dalian Maritime University, Dalian, China
- These four authors contributed equally to this article
| | - Huwenbo Shi
- Program in Genetic Epidemiology and Statistical Genetics, Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jun Lv
- Dept of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
- Key Laboratory of Molecular Cardiovascular Sciences (Peking University), Ministry of Education, Beijing, China
- Peking University Institute of Environmental Medicine, Beijing, China
| | - Weihua Cao
- Dept of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Yu Guo
- Chinese Academy of Medical Sciences, Beijing, China
| | - Iona Y Millwood
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Robin G Walters
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Kuang Lin
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Ling Yang
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Yiping Chen
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Huaidong Du
- Medical Research Council Population Health Research Unit at the University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Bo Yu
- NCDs Prevention and Control Dept, Nangang CDC, Harbin, China
| | - Kohei Hasegawa
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Carlos A Camargo
- Program in Genetic Epidemiology and Statistical Genetics, Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Dept of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Miriam F Moffatt
- Section of Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - William O C Cookson
- Section of Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Junshi Chen
- China National Center for Food Safety Risk Assessment, Beijing, China
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit (CTSU), Nuffield Dept of Population Health, University of Oxford, Oxford, UK
| | - Liming Li
- Dept of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Canqing Yu
- Dept of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
- These two authors contributed equally to this article as lead authors and supervised the work
| | - Liming Liang
- Program in Genetic Epidemiology and Statistical Genetics, Dept of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Dept of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- These two authors contributed equally to this article as lead authors and supervised the work
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175
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Higbee DH, Granell R, Sanderson E, Davey Smith G, Dodd JW. Lung function and cardiovascular disease: a two-sample Mendelian randomisation study. Eur Respir J 2021; 58:13993003.03196-2020. [PMID: 33574079 DOI: 10.1183/13993003.03196-2020] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/21/2021] [Indexed: 01/04/2023]
Abstract
BACKGROUND Observational studies suggest an association between reduced lung function and risk of coronary artery disease and ischaemic stroke, independent of shared cardiovascular risk factors such as cigarette smoking. We use the latest genetic epidemiological methods to determine whether impaired lung function is causally associated with an increased risk of cardiovascular disease. METHODS AND FINDINGS Mendelian randomisation uses genetic variants as instrumental variables to investigate causation. Preliminary analysis used two-sample Mendelian randomisation with lung function single nucleotide polymorphisms. To avoid collider bias, the main analysis used single nucleotide polymorphisms for lung function identified from UKBiobank in a multivariable Mendelian randomisation model conditioning for height, body mass index and smoking.Multivariable Mendelian randomisation shows strong evidence that reduced forced vital capacity (FVC) causes increased risk of coronary artery disease (OR 1.32, 95% CI 1.19-1.46 per standard deviation). Reduced forced expiratory volume in 1 s (FEV1) is unlikely to cause increased risk of coronary artery disease, as evidence of its effect becomes weak after conditioning for height (OR 1.08, 95% CI 0.89-1.30). There is weak evidence that reduced lung function increases risk of ischaemic stroke. CONCLUSION There is strong evidence that reduced FVC is independently and causally associated with coronary artery disease. Although the mechanism remains unclear, FVC could be taken into consideration when assessing cardiovascular risk and considered a potential target for reducing cardiovascular events. FEV1 and airflow obstruction do not appear to cause increased cardiovascular events; confounding and collider bias may explain previous findings of a causal association.
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Affiliation(s)
- Daniel H Higbee
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK.,Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, UK
| | - Raquel Granell
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
| | - Eleanor Sanderson
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
| | - James W Dodd
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK ).,Academic Respiratory Unit, University of Bristol, Southmead Hospital, Bristol, UK
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176
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Hosking L, Yeo A, Hoffman J, Chiano M, Fraser D, Ghosh S, Lipson DA, Martin N, Condreay LD, Cox C, St Jean P. Genetics plays a limited role in predicting chronic obstructive pulmonary disease treatment response and exacerbation. Respir Med 2021; 187:106573. [PMID: 34428673 DOI: 10.1016/j.rmed.2021.106573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 07/27/2021] [Accepted: 08/08/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Combination treatments, targeting multiple disease processes, benefit subjects with acute exacerbation of chronic obstructive pulmonary disease (AECOPD). However, predicting treatment response and exacerbation risk remain challenging. OBJECTIVE To identify genetic associations with AECOPD risk and response to combination therapy (fluticasone furoate, umeclidinium bromide and vilanterol). METHODS The genetic basis of AECOPD disease was investigated in 19,841 subjects from 23 clinical studies and 2 disease cohorts to identify exacerbation disease targets. AECOPD pharmacogenetic effects were examined in 8439 moderate to severe COPD patients with exacerbation rate, lung function and quality of life endpoints; results were followed up in an additional 2201 subjects. RESULTS We did not identify significant associations in the AECOPD disease analysis. In the AECOPD pharmacogenetics analysis, rs56195836 (MAPK8) was significantly associated with moderate to severe exacerbation rate in subjects on fluticasone furoate with baseline blood eosinophils ≥150 cells/μl (P = 1.8 × 10-8). Post-hoc, one variant was associated with on-treatment moderate to severe exacerbation rate stratifying by exacerbation history. AZU1 rs1962343 was significantly associated in subjects with frequent moderate exacerbation history when treated with fluticasone furoate/vilanterol (P = 1.1 × 10-8). Neither of these signals was supported in independent follow-up. CONCLUSION Common genetic variants do not play major roles in AECOPD disease nor predict response to triple therapy or its components in moderate to very severe COPD.
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Affiliation(s)
| | | | | | | | | | | | - David A Lipson
- GSK, Collegeville, PA, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Neil Martin
- GSK, Brentford, Middlesex, UK; University of Leicester, Leicester, Leicestershire, UK.
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177
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Bhakta NR, Kaminsky DA, Bime C, Thakur N, Hall GL, McCormack MC, Stanojevic S. Addressing Race in Pulmonary Function Testing by Aligning Intent and Evidence With Practice and Perception. Chest 2021; 161:288-297. [PMID: 34437887 PMCID: PMC8783030 DOI: 10.1016/j.chest.2021.08.053] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/29/2021] [Accepted: 08/17/2021] [Indexed: 10/27/2022] Open
Abstract
The practice of using race or ethnicity in medicine to explain differences between individuals is being called into question because it may contribute to biased medical care and research that perpetuates health disparities and structural racism. A commonly cited example is the use of race or ethnicity in the interpretation of pulmonary function test (PFT) results, yet the perspectives of practicing pulmonologists and physiologists are missing from this discussion. This discussion has global relevance for increasingly multicultural communities in which the range of values that represent normal lung function is uncertain. We review the underlying sources of differences in lung function, including those that may be captured by race or ethnicity, and demonstrate how the current practice of PFT measurement and interpretation is imperfect in its ability to describe accurately the relationship between function and health outcomes. We summarize the arguments against using race-specific equations as well as address concerns about removing race from the interpretation of PFT results. Further, we outline knowledge gaps and critical questions that need to be answered to change the current approach of including race or ethnicity in PFT results interpretation thoughtfully. Finally, we propose changes in interpretation strategies and future research to reduce health disparities.
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Affiliation(s)
- Nirav R Bhakta
- University of California, San Francisco, San Francisco, CA.
| | | | - Christian Bime
- College of Medicine, The University of Arizona Health Science, Tucson, AZ
| | - Neeta Thakur
- University of California, San Francisco, San Francisco, CA; Zuckerberg San Francisco General Hospital, San Francisco, CA
| | - Graham L Hall
- Children's Lung Health, Wal-yan Respiratory Research Centre, Telethon Kids Institute and School of Allied Health, Curtin University, Perth, WA, Australia
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178
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Chen Q, Heijink IH, de Vries M. Connecting GWAS Susceptibility Genes in COPD: Do We Need to Consider TGF-β2? Am J Respir Cell Mol Biol 2021; 65:468-470. [PMID: 34411507 PMCID: PMC8641857 DOI: 10.1165/rcmb.2021-0265ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
- Qing Chen
- Department of Pathology and Medical Biology.,Groningen Research Institute for Asthma and COPD University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Irene H Heijink
- Groningen Research Institute for Asthma and COPD University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Pathology and Medical Biology Department of Pulmonology
| | - Maaike de Vries
- Groningen Research Institute for Asthma and COPD University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Department of Epidemiology
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179
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Stein CM, Benchek P, Bartlett J, Igo RP, Sobota RS, Chervenak K, Mayanja-Kizza H, von Reyn CF, Lahey T, Bush WS, Boom WH, Scott WK, Marsit C, Sirugo G, Williams SM. Methylome-wide Analysis Reveals Epigenetic Marks Associated With Resistance to Tuberculosis in Human Immunodeficiency Virus-Infected Individuals From East Africa. J Infect Dis 2021; 224:695-704. [PMID: 33400784 DOI: 10.1093/infdis/jiaa785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/04/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is the most deadly infectious disease globally and is highly prevalent in the developing world. For individuals infected with both Mycobacterium tuberculosis (Mtb) and human immunodeficiency virus (HIV), the risk of active TB is 10% or more annually. Previously, we identified in a genome-wide association study (GWAS) a region on chromosome 5 associated with resistance to TB, which included epigenetic marks that could influence gene regulation. We hypothesized that HIV-infected individuals exposed to Mtb who remain disease free carry epigenetic changes that strongly protect them from active TB. METHODS We conducted a methylome-wide study in HIV-infected, TB-exposed cohorts from Uganda and Tanzania and integrated data from our GWAS. RESULTS We identified 3 regions of interest that included markers that were differentially methylated between TB cases and controls with latent TB infection: chromosome 1 (RNF220, P = 4 × 10-5), chromosome 2 (between COPS8 and COL6A3, P = 2.7 × 10-5), and chromosome 5 (CEP72, P = 1.3 × 10-5). These methylation results co-localized with associated single-nucleotide polymorphisms (SNPs), methylation QTLs, and methylation × SNP interaction effects. These markers were in regions with regulatory markers for cells involved in TB immunity and/or lung. CONCLUSIONS Epigenetic regulation is a potential biologic factor underlying resistance to TB in immunocompromised individuals that can act in conjunction with genetic variants.
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Affiliation(s)
- Catherine M Stein
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA.,Division of Infectious Disease and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Penelope Benchek
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jacquelaine Bartlett
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robert P Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Rafal S Sobota
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Keith Chervenak
- Division of Infectious Disease and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Harriet Mayanja-Kizza
- Department of Medicine and Mulago Hospital, School of Medicine, Makerere University, Kampala, Uganda
| | - C Fordham von Reyn
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Timothy Lahey
- Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - W Henry Boom
- Division of Infectious Disease and HIV Medicine, Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - William K Scott
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Carmen Marsit
- Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Giorgio Sirugo
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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180
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Higbee DH, Granell R, Hemani G, Smith GD, Dodd JW. Lung function, COPD and cognitive function: a multivariable and two sample Mendelian randomization study. BMC Pulm Med 2021; 21:246. [PMID: 34294062 PMCID: PMC8296721 DOI: 10.1186/s12890-021-01611-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Observational studies show an association between reduced lung function and impaired cognition. Cognitive dysfunction influences important health outcomes and is a precursor to dementia, but treatments options are currently very limited. Attention has therefore focused on identifying modifiable risk factors to prevent cognitive decline and preserve cognition. Our objective was to determine if lung function or risk of COPD causes reduced cognitive function using Mendelian randomization (MR). METHODS Single nucleotide polymorphisms from genome wide association studies of lung function and COPD were used as exposures. We examined their effect on general cognitive function in a sample of 132,452 individuals. We then performed multivariable MR (MVMR), examining the effect of lung function before and after conditioning for covariates. RESULTS We found only weak evidence that reduced lung function (Beta - 0.002 (SE 0.02), p-value 0.86) or increased liability to COPD (- 0.008 (0.008), p-value 0.35) causes lower cognitive function. MVMR found both reduced FEV1 and FVC do cause lower cognitive function, but that after conditioning for height (- 0.03 (0.03), p-value 0.29 and - 0.01 (0.03) p-value 0.62, for FEV1 and FVC respectively) and educational attainment (- 0.03 (0.03) p-value 0.33 and - 0.01 (0.02), p-value 0.35) the evidence became weak. CONCLUSION We did not find evidence that reduced lung function or COPD causes reduced cognitive function. Previous observational studies are probably affected by residual confounding. Research efforts should focus on shared risk factors for reduced lung function and cognition, rather than lung function alone as a modifiable risk factor.
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Affiliation(s)
- Daniel H Higbee
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Oakfield Grove, Bristol, BS8 2BN, UK
- Academic Respiratory Unit, Southmead Hospital, University of Bristol, Bristol, BS10 5NB, UK
| | - Raquel Granell
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Oakfield Grove, Bristol, BS8 2BN, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Oakfield Grove, Bristol, BS8 2BN, UK
| | - James W Dodd
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Oakfield Grove, Bristol, BS8 2BN, UK.
- Academic Respiratory Unit, Southmead Hospital, University of Bristol, Bristol, BS10 5NB, UK.
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181
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Higbee D, Granell R, Walton E, Korologou-Linden R, Davey Smith G, Dodd J. Examining the possible causal relationship between lung function, COPD and Alzheimer's disease: a Mendelian randomisation study. BMJ Open Respir Res 2021; 8:8/1/e000759. [PMID: 34233891 PMCID: PMC8264898 DOI: 10.1136/bmjresp-2020-000759] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/21/2021] [Accepted: 04/16/2021] [Indexed: 11/06/2022] Open
Abstract
Rationale Large retrospective case-control studies have reported an association between chronic obstructive pulmonary disease (COPD), reduced lung function and an increased risk of Alzheimer’s disease. However, it remains unclear if these diseases are causally linked, or due to shared risk factors. Conventional observational epidemiology suffers from unmeasured confounding and reverse causation. Additional analyses addressing causality are required. Objectives To examine a causal relationship between COPD, lung function and Alzheimer’s disease. Methods Using two-sample Mendelian randomisation, we used single nucleotide polymorphisms (SNPs) identified in a genome wide association study (GWAS) for lung function as instrumental variables (exposure). Additionally, we used SNPs discovered in a GWAS for COPD in those with moderate to very severe obstruction. The effect of these SNPs on Alzheimer’s disease (outcome) was taken from a GWAS based on a sample of 24 807 patients and 55 058 controls. Results We found minimal evidence for an effect of either lung function (OR: 1.02 per SD; 95% CI 0.91 to 1.13; p value 0.68) or liability for COPD on Alzheimer’s disease (OR: 0.97 per SD; 95% CI 0.92 to 1.03; p value 0.40). Conclusion Neither reduced lung function nor liability COPD are likely to be causally associated with an increased risk of Alzheimer’s, any observed association is likely due to unmeasured confounding. Scientific attention and health prevention policy may be better focused on overlapping risk factors, rather than attempts to reduce risk of Alzheimer’s disease by targeting impaired lung function or COPD directly.
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Affiliation(s)
- Daniel Higbee
- Academic Respiratory Unit, Southmead Hospital, Bristol, UK.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Raquel Granell
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Esther Walton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Department of Psychology, University of Bath, Bath, Somerset, UK
| | | | | | - James Dodd
- Academic Respiratory Unit, Southmead Hospital, Bristol, UK .,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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182
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LINC01414/LINC00824 genetic polymorphisms in association with the susceptibility of chronic obstructive pulmonary disease. BMC Pulm Med 2021; 21:213. [PMID: 34233676 PMCID: PMC8261955 DOI: 10.1186/s12890-021-01579-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/24/2021] [Indexed: 11/18/2022] Open
Abstract
Objective Chronic obstructive pulmonary disease (COPD) is a complicated multi-factor, multi-gene disease. Here, we aimed to assess the association of genetic polymorphisms in LINC01414/ LINC00824 and interactions with COPD susceptibility. Methods Three single nucleotide polymorphisms (SNPs) in LINC01414/LINC00824 was genotyped by Agena MassARRAY platform among 315 COPD patients and 314 controls. Logistic analysis adjusted by age and gender were applied to estimate the genetic contribution of selected SNPs to COPD susceptibility. Results LINC01414 rs699467 (OR = 0.73, 95% CI 0.56–0.94, p = 0.015) and LINC00824 rs7815944 (OR = 0.56, 95% CI 0.31–0.99, p = 0.046) might be protective factors for COPD occurrence, while LINC01414 rs298207 (OR = 2.88, 95% CI 1.31–6.31, p = 0.008) risk-allele was related to the increased risk of COPD in the whole population. Rs7815944 was associated with the reduced risk of COPD in the subjects aged > 70 years (OR = 0.29, p = 0.005). Rs6994670 (OR = 0.57, p = 0.007) contribute to a reduced COPD risk, while rs298207 (OR = 7.94, p = 0.009) was related to a higher susceptibility to COPD at age ≤ 70 years. Rs298207 (OR = 2.54, p = 0.043) and rs7815944 (OR = 0.43, p = 0.028) variants was associated COPD risk among males. Rs7815944 (OR = 0.16, p = 0.031) was related to the reduced susceptibility of COPD in former smokers. Moreover, the association between rs298207 genotype and COPD patients with dyspnea was found (OR = 0.50, p = 0.016), and rs7815944 was related to COPD patients with wheezing (OR = 0.22, p = 0.008). Conclusion Our finding provided further insights into LINC01414/LINC00824 polymorphisms at risk of COPD occurrence and accumulated evidence for the genetic susceptibility of COPD. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01579-3.
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Harbaum L, Hennigs JK, Simon M, Oqueka T, Watz H, Klose H. Genetic evidence for a causative effect of airflow obstruction on left ventricular filling: a Mendelian randomisation study. Respir Res 2021; 22:199. [PMID: 34233669 PMCID: PMC8261939 DOI: 10.1186/s12931-021-01795-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/30/2021] [Indexed: 11/10/2022] Open
Abstract
Background Observational studies on the general population have suggested that airflow obstruction associates with left ventricular (LV) filling. To limit the influence of environmental risk factors/exposures, we used a Mendelian randomisation (MR) approach based on common genetic variations and tested whether a causative relation between airflow obstruction and LV filling can be detected. Methods We used summary statistics from large genome-wide association studies (GWAS) on the ratio of forced expiratory volume in 1 s to forced vital capacity (FEV1/FVC) measured by spirometry and the LV end-diastolic volume (LVEDV) as assessed by cardiac magnetic resonance imaging. The primary MR was based on an inverse variance weighted regression. Various complementary MR methods and subsets of the instrument variables were used to assess the plausibility of the findings. Results We obtained consistent evidence in our primary MR analysis and subsequent sensitivity analyses that reducing airflow obstruction leads to increased inflow to the LV (odds ratio [OR] from inverse variance weighted regression 1.05, 95% confidence interval [CI] 1.01–1.09, P = 0.0172). Sensitivity analyses indicated a certain extent of negative horizontal pleiotropy and the estimate from biased-corrected MR-Egger was adjusted upward (OR 1.2, 95% CI 1.09–1.31, P < 0.001). Prioritisation of single genetic variants revealed rs995758, rs2070600 and rs7733410 as major contributors to the MR result. Conclusion Our findings indicate a causal relationship between airflow obstruction and LV filling in the general population providing genetic context to observational associations. The results suggest that targeting (even subclinical) airflow obstruction can lead to direct cardiac improvements, demonstrated by an increase in LVEDV. Functional annotation of single genetic variants contributing most to the causal effect estimate could help to prioritise biological underpinnings. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-021-01795-9.
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Affiliation(s)
- Lars Harbaum
- Abteilung für Pneumologie, Centrum für Pulmonal Arterielle Hypertonie Hamburg (CPAHH), Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.
| | - Jan K Hennigs
- Abteilung für Pneumologie, Centrum für Pulmonal Arterielle Hypertonie Hamburg (CPAHH), Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Marcel Simon
- Abteilung für Pneumologie, Centrum für Pulmonal Arterielle Hypertonie Hamburg (CPAHH), Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Tim Oqueka
- Abteilung für Pneumologie, Centrum für Pulmonal Arterielle Hypertonie Hamburg (CPAHH), Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Henrik Watz
- Pneumologische Forschungsinstitut an der LungenClinic Grosshansdorf, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Hans Klose
- Abteilung für Pneumologie, Centrum für Pulmonal Arterielle Hypertonie Hamburg (CPAHH), Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
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Moll M, Jackson VE, Yu B, Grove ML, London SJ, Gharib SA, Bartz TM, Sitlani CM, Dupuis J, O'Connor GT, Xu H, Cassano PA, Patchen BK, Kim WJ, Park J, Kim KH, Han B, Barr RG, Manichaikul A, Nguyen JN, Rich SS, Lahousse L, Terzikhan N, Brusselle G, Sakornsakolpat P, Liu J, Benway CJ, Hall IP, Tobin MD, Wain LV, Silverman EK, Cho MH, Hobbs BD. A systematic analysis of protein-altering exonic variants in chronic obstructive pulmonary disease. Am J Physiol Lung Cell Mol Physiol 2021; 321:L130-L143. [PMID: 33909500 PMCID: PMC8321852 DOI: 10.1152/ajplung.00009.2021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/15/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified regions associated with chronic obstructive pulmonary disease (COPD). GWASs of other diseases have shown an approximately 10-fold overrepresentation of nonsynonymous variants, despite limited exonic coverage on genotyping arrays. We hypothesized that a large-scale analysis of coding variants could discover novel genetic associations with COPD, including rare variants with large effect sizes. We performed a meta-analysis of exome arrays from 218,399 controls and 33,851 moderate-to-severe COPD cases. All exome-wide significant associations were present in regions previously identified by GWAS. We did not identify any novel rare coding variants with large effect sizes. Within GWAS regions on chromosomes 5q, 6p, and 15q, four coding variants were conditionally significant (P < 0.00015) when adjusting for lead GWAS single-nucleotide polymorphisms A common gasdermin B (GSDMB) splice variant (rs11078928) previously associated with a decreased risk for asthma was nominally associated with a decreased risk for COPD [minor allele frequency (MAF) = 0.46, P = 1.8e-4]. Two stop variants in coiled-coil α-helical rod protein 1 (CCHCR1), a gene involved in regulating cell proliferation, were associated with COPD (both P < 0.0001). The SERPINA1 Z allele was associated with a random-effects odds ratio of 1.43 for COPD (95% confidence interval = 1.17-1.74), though with marked heterogeneity across studies. Overall, COPD-associated exonic variants were identified in genes involved in DNA methylation, cell-matrix interactions, cell proliferation, and cell death. In conclusion, we performed the largest exome array meta-analysis of COPD to date and identified potential functional coding variants. Future studies are needed to identify rarer variants and further define the role of coding variants in COPD pathogenesis.
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Affiliation(s)
- Matthew Moll
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Bing Yu
- School of Public Health, University of Texas Health Science Center, Houston, Texas
| | - Megan L Grove
- School of Public Health, University of Texas Health Science Center, Houston, Texas
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services Research, Research Triangle Park, Durham, North Carolina
| | - Sina A Gharib
- Center for Lung Biology, Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, Seattle, Washington
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, Washington
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - George T O'Connor
- Division of Pulmonary, Allergy, Sleep, and Critical Care Medicine, Department of Medicine, Pulmonary Center, Boston University School of Medicine, Boston Medical Center, Boston, Massachusetts
| | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
- Division of Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, New York, New York
| | | | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University, Chuncheon, South Korea
| | - Jinkyeong Park
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Internal Medicine, Dongguk University Ilsan Hospital, Goyang-Si, Gyeonggi-do, South Korea
| | - Kun Hee Kim
- Department of Convergence Medicine and Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Buhm Han
- Department of Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, New York
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jennifer N Nguyen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Lies Lahousse
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Bioanalysis, Ghent University, Ghent, Belgium
| | - Natalie Terzikhan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Guy Brusselle
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Phuwanat Sakornsakolpat
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jiangyuan Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Christopher J Benway
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ian P Hall
- NIHR Nottingham Biomedical Research Centre, Queen's Medical Centre, Nottingham, United Kingdom
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Brian D Hobbs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
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185
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Benway CJ, Liu J, Guo F, Du F, Randell SH, Cho MH, Silverman EK, Zhou X. Chromatin Landscapes of Human Lung Cells Predict Potentially Functional Chronic Obstructive Pulmonary Disease Genome-Wide Association Study Variants. Am J Respir Cell Mol Biol 2021; 65:92-102. [PMID: 33788674 DOI: 10.1165/rcmb.2020-0475oc] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Genome-wide association studies (GWASs) have identified dozens of loci associated with risk of chronic obstructive pulmonary disease (COPD). However, identifying the causal variants and their functional role in the appropriate cell type remains a major challenge. We aimed to identify putative causal variants in 82 GWAS loci associated with COPD susceptibility and predict the regulatory impact of these variants in lung-cell types. We used an integrated approach featuring statistical fine mapping, open chromatin profiling, and machine learning to identify functional variants. We generated chromatin accessibility data using the Assay for Transposase-Accessible Chromatin with High-Throughput Sequencing (ATAC-seq) for human primary lung-cell types implicated in COPD pathobiology. We then evaluated the enrichment of COPD risk variants in lung-specific open chromatin regions and generated cell type-specific regulatory predictions for >6,500 variants corresponding to 82 COPD GWAS loci. Integration of the fine-mapped variants with lung open chromatin regions helped prioritize 22 variants in putative regulatory elements with potential functional effects. Comparison with functional predictions from 222 Encyclopedia of DNA Elements (ENCODE) cell samples revealed cell type-specific regulatory effects of COPD variants in the lung epithelium, endothelium, and immune cells. We identified potential causal variants for COPD risk by integrating fine mapping in GWAS loci with cell-specific regulatory profiling, highlighting the importance of leveraging the chromatin status in relevant cell types to predict the molecular effects of risk variants in lung disease.
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Affiliation(s)
| | | | - Feng Guo
- Channing Division of Network Medicine and
| | - Fei Du
- Channing Division of Network Medicine and
| | - Scott H Randell
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael H Cho
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; and
| | - Edwin K Silverman
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; and
| | - Xiaobo Zhou
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; and
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186
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Baumeister SE, Baurecht H, Nolde M, Alayash Z, Gläser S, Johansson M, Amos CI, Johnson EC, Hung RJ. Cannabis Use, Pulmonary Function, and Lung Cancer Susceptibility: A Mendelian Randomization Study. J Thorac Oncol 2021; 16:1127-1135. [PMID: 33852959 DOI: 10.1016/j.jtho.2021.03.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Because of widespread use, understanding the pulmonary effects of cannabis use is important; but its role independent from tobacco smoking is yet to be elucidated. We used Mendelian randomization (MR) to assess the effect of genetic liability to lifetime cannabis use and cannabis use disorder on pulmonary function and lung cancer. METHODS We used four single nucleotide polymorphisms associated with lifetime cannabis use (p value <5 × 10-8) from a genome-wide association study (GWAS) of 184,765 individuals of European descent from the International Cannabis Consortium, 23andme, and U.K. Biobank as instrumental variables. Seven single nucleotide polymorphisms (p value <5 × 10-8) were selected as instruments for cannabis use disorder from a GWAS meta-analysis of 17,068 European ancestry cases and 357,219 controls of European descent from Psychiatric Genomics Consortium Substance Use Disorders working group, Lundbeck Foundation Initiative for Integrative PsychiatricResearch, and deCode. To assess lung function, GWAS included 79,055 study participants of the SpiroMeta Consortium, and for lung cancer GWAS from the International Lung Cancer Consortium contained 29,266 cases and 56,450 controls. RESULTS MR revealed that genetic liability to lifetime cannabis use was associated with increased risk of squamous cell carcinoma (OR = 1.22, 95%, confidence interval = 1.07-1.39, p value = 0.003, q value = 0.025). Pleiotropy-robust methods and positive and negative control analyses did not indicate bias in the primary analysis. CONCLUSIONS The findings of this MR analysis suggest evidence for a potential causal association between genetic liability for cannabis use and the risk of squamous cell carcinoma. Triangulating MR and observational studies and addressing orthogonal sources of bias are necessary to confirm this finding.
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Affiliation(s)
- Sebastian-Edgar Baumeister
- Department of Epidemiology, Ludwig-Maximilian University of Munich, University Center for Health Sciences at the Klinikum (UNIKA-T) Augsburg, Augsburg, Germany; Independent Research Group Clinical Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany; Institute of Health Services Research in Dentistry, University of Münster, Münster, Germany.
| | - Hansjörg Baurecht
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Germany
| | - Michael Nolde
- Department of Epidemiology, Ludwig-Maximilian University of Munich, University Center for Health Sciences at the Klinikum (UNIKA-T) Augsburg, Augsburg, Germany; Independent Research Group Clinical Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Zoheir Alayash
- Department of Epidemiology, Ludwig-Maximilian University of Munich, University Center for Health Sciences at the Klinikum (UNIKA-T) Augsburg, Augsburg, Germany
| | - Sven Gläser
- Department of Internal Medicine B Cardiology, Intensive Care, Pulmonary Medicine, and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany; Vivantes Klinikum Neukölln und Spandau, Klinik für Innere Medizin-Pneumologie und Infektiologie, Berlin, Germany
| | - Mattias Johansson
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Emma C Johnson
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
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187
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Hall RJ, O'Loughlin J, Billington CK, Thakker D, Hall IP, Sayers I. Functional genomics of GPR126 in airway smooth muscle and bronchial epithelial cells. FASEB J 2021; 35:e21300. [PMID: 34165809 DOI: 10.1096/fj.202002073r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/01/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022]
Abstract
GPR126 is an adhesion G protein-coupled receptor which lies on chromosome 6q24. Genetic variants in this region are reproducibly associated with lung function and COPD in genome wide association studies (GWAS). The aims of this study were to define the role of GPR126 in the human lung and in pulmonary disease and identify possible casual variants. Online tools (GTEx and LDlink) identified SNPs which may have effects on GPR126 function/ expression, including missense variant Ser123Gly and an intronic variant that shows eQTL effects on GPR126 expression. GPR126 signaling via cAMP-mediated pathways was identified in human structural airway cells when activated with the tethered agonist, stachel. RNA-seq was used to identify downstream genes/ pathways affected by stachel-mediated GPR126 activation in human airway smooth muscle cells. We identified ~350 differentially expressed genes at 4 and 24 hours post stimulation with ~20% overlap. We identified that genes regulated by GPR126 activation include IL33, CTGF, and SERPINE1, which already have known roles in lung biology. Pathways altered by GPR126 included those involved in cell cycle progression and cell proliferation. Here, we suggest a role for GPR126 in airway remodeling.
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Affiliation(s)
- Robert J Hall
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Jonathan O'Loughlin
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Charlotte K Billington
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Dhruma Thakker
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Ian P Hall
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Ian Sayers
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, Biodiscovery Institute, University of Nottingham, Nottingham, UK
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188
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Zhang PD, Zhang XR, Zhang A, Li ZH, Liu D, Zhang YJ, Mao C. Associations of genetic risk and smoking with incident chronic obstructive pulmonary disease. Eur Respir J 2021; 59:13993003.01320-2021. [PMID: 34172472 DOI: 10.1183/13993003.01320-2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/14/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Genetic and smoking contribute to chronic obstructive pulmonary disease (COPD), but whether a combined polygenic risk score (PRS) is associated with incident COPD and whether it has a synergistic effect on the smoking remains unclear. We aimed to investigate the association of PRS with COPD and explore whether smoking behaviors could modify such association. METHODS Multivariable Cox proportional models were used to estimate hazard ratios (HRs) and 95% confidence intervals (95% CIs) for the association of the PRS and smoking with COPD. RESULTS The study included 439 255 participants (mean age 56.5; 53.9% female), with a median follow-up of 9.0 years. The PRSlasso containing 2.5 million variants showed better discrimination and a stronger association for incident COPD than the PRS279 containing 279 genome-wide significance variants. Compared with the low genetic risk, the HRs of the medium and high genetic risk were 1.39 (95% CI, 1.31-1.48) and 2.40 (95% CI, 2.24-2.56), respectively. The HR of high genetic risk and current smoking was 11.62 (95% CI, 10.31-13.10) times of low genetic risk and never smoking. There were significant interactions between the PRSlasso and smoking status for incident COPD (p for interaction<0.001). From low genetic risk to high genetic risk, the HRs of current smoking increased from 4.32 (95% CI, 3.69-5.06) to 6.89 (95% CI, 6.21-7.64), and the population-attributable risks of smoking increased from 42.7% to 61.1%. CONCLUSION PRS constructed from millions of variants below genome-wide significance showed significant associations with incident COPD. Participants with a high genetic risk may be more susceptible to developing COPD when exposed to smoking.
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Affiliation(s)
- Pei-Dong Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,The Laboratory for Precision Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Pei-Dong Zhang and Xi-Ru Zhang contributed to the work equally
| | - Xi-Ru Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.,Pei-Dong Zhang and Xi-Ru Zhang contributed to the work equally
| | - Ao Zhang
- State Key Laboratory of Molecular Neuroscience and Center of Systems Biology and Human Health, Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhi-Hao Li
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Dan Liu
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Yu-Jie Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Chen Mao
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China .,Department of Laboratory Medicine, Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Chr15q25 Genetic Variant rs16969968 Alters Cell Differentiation in Respiratory Epithelia. Int J Mol Sci 2021; 22:ijms22136657. [PMID: 34206324 PMCID: PMC8268843 DOI: 10.3390/ijms22136657] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/11/2021] [Accepted: 06/17/2021] [Indexed: 12/26/2022] Open
Abstract
The gene cluster region, CHRNA3/CHRNA5/CHRNB4, encoding for nicotinic acetylcholine receptor (nAChR) subunits, contains several genetic variants linked to nicotine addiction and brain disorders. The CHRNA5 single-nucleotide polymorphism (SNP) rs16969968 is strongly associated with nicotine dependence and lung diseases. Using immunostaining studies on tissue sections and air-liquid interface airway epithelial cell cultures, in situ hybridisation, transcriptomic and cytokines detection, we analysed rs16969968 contribution to respiratory airway epithelial remodelling and modulation of inflammation. We provide cellular and molecular analyses which support the genetic association of this polymorphism with impaired ciliogenesis and the altered production of inflammatory mediators. This suggests its role in lung disease development.
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190
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Au Yeung SL, Borges MC, Lawlor DA, Schooling CM. Impact of lung function on cardiovascular diseases and cardiovascular risk factors: a two sample bidirectional Mendelian randomisation study. Thorax 2021; 77:164-171. [PMID: 34155093 DOI: 10.1136/thoraxjnl-2020-215600] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Observational studies suggested lung function is inversely associated with cardiovascular disease (CVD) although these studies could be confounded. We conducted a two sample Mendelian randomisation study using summary statistics from genome-wide association studies (GWAS) to clarify the role of lung function in CVD and its risk factors, and conversely the role of CVD in lung function. METHODS We obtained genetic instruments for forced expiratory volume in 1 s (FEV1: 260) and forced vital capacity (FVC: 320) from publicly available UK Biobank summary statistics (n=421 986) and applied to GWAS summary statistics for coronary artery disease (CAD) (n=184 305), stroke (n=446 696), atrial fibrillation (n=1 030 836) and heart failure (n=977 320) and cardiovascular risk factors. Inverse variance weighting was used to assess the impact of lung function on these outcomes, with various sensitivity analyses. Bidirectional Mendelian randomisation was used to assess reverse causation. RESULTS FEV1 and FVC were inversely associated with CAD (OR per SD increase, 0.72 (95% CI 0.63 to 0.82) and 0.70 (95%CI 0.62 to 0.78)), overall stroke (0.87 (95%CI 0.77 to 0.97), 0.90 (95% CI 0.82 to 1.00)) and some stroke subtypes. FEV1 and FVC were inversely associated with type 2 diabetes and systolic blood pressure. Sensitivity analyses produced similar findings although the association with CAD was attenuated after adjusting for height (eg, OR for 1SD FEV10.95 (0.75 to 1.19), but not for stroke or type 2 diabetes. There was no strong evidence for reverse causation. CONCLUSION Higher lung function likely protect against CAD and stroke.
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Affiliation(s)
- Shiu Lun Au Yeung
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Adminstrative Region, China
| | - Maria Carolina Borges
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust and University of Bristol, Bristol, UK
| | - C Mary Schooling
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Adminstrative Region, China.,School of Public Health and Health Policy, City University of New York, New York, New York, USA
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191
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Ekström M, Johannessen A, Abramson MJ, Benediktsdottir B, Franklin K, Gislason T, Gómez Real F, Holm M, Janson C, Jogi R, Lowe A, Malinovschi A, Martínez-Moratalla J, Oudin A, Sánchez-Ramos JL, Schlünssen V, Svanes C. Breathlessness across generations: results from the RHINESSA generation study. Thorax 2021; 77:172-177. [PMID: 34127557 PMCID: PMC8762033 DOI: 10.1136/thoraxjnl-2021-217271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/15/2021] [Indexed: 11/04/2022]
Abstract
Background Breathlessness is a major cause of suffering and disability globally. The symptom relates to multiple factors including asthma and lung function, which are influenced by hereditary factors. No study has evaluated potential inheritance of breathlessness itself across generations. Methods We analysed the association between breathlessness in parents and their offspring in the Respiratory Health in Northern Europe, Spain and Australia generation study. Data on parents and offspring aged ≥18 years across 10 study centres in seven countries included demographics, self-reported breathlessness, asthma, depression, smoking, physical activity level, measured Body Mass Index and spirometry. Data were analysed using multivariable logistic regression accounting for clustering within centres and between siblings. Results A total of 1720 parents (mean age at assessment 36 years, 55% mothers) and 2476 offspring (mean 30 years, 55% daughters) were included. Breathlessness was reported by 809 (32.7%) parents and 363 (14.7%) offspring. Factors independently associated with breathlessness in parents and offspring included obesity, current smoking, asthma, depression, lower lung function and female sex. After adjusting for potential confounders, parents with breathlessness were more likely to have offspring with breathlessness, adjusted OR 1.8 (95% CI 1.1 to 2.9). The association was not modified by sex of the parent or offspring. Conclusion Parents with breathlessness were more likely to have children who developed breathlessness, after adjusting for asthma, lung function, obesity, smoking, depression and female sex in both generations. The hereditary components of breathlessness need to be further explored.
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Affiliation(s)
- Magnus Ekström
- Department of Respiratory Medicine and Allergology, Lund University, Lund, Sweden
| | - Ane Johannessen
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Michael J Abramson
- School of Public Health & Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Bryndis Benediktsdottir
- Department of Sleep, Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Karl Franklin
- Department of Surgery and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Thorarinn Gislason
- Department of Sleep, Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Francisco Gómez Real
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Mathias Holm
- Occupational and Environmental Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Christer Janson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Rain Jogi
- The Lung Clinic, Tartu University Hospital, Tartu, Estonia
| | - Adrian Lowe
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Jesús Martínez-Moratalla
- Servicio de Pneumologıa del Complejo Hospitalario Universitario de Albacete (CHUA), Servicio de Salud de Castilla-La Mancha (SESCAM), Albacete, Spain
| | - Anna Oudin
- Department of Public Health and Clinical Medicine, Sustainable Health, Umeå University, Umeå, Sweden
| | | | - Vivi Schlünssen
- Department of Public Health, Environment, Work and Health, Danish Ramazzini Center, Aarhus University, Aarhus, Denmark.,Department of Public Health, Department of Public Health, Environment, Work and Health, Danish Ramazzini Center, Copenhagen, Denmark
| | - Cecilie Svanes
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway
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192
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Serban KA, Pratte KA, Bowler RP. Protein Biomarkers for COPD Outcomes. Chest 2021; 159:2244-2253. [PMID: 33434499 PMCID: PMC8213963 DOI: 10.1016/j.chest.2021.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/14/2020] [Accepted: 01/01/2021] [Indexed: 12/15/2022] Open
Abstract
COPD is a clinically heterogeneous syndrome characterized by injury to airways, airspaces, and lung vasculature and usually caused by tobacco smoke and/or air pollution exposure. COPD is also independently associated with nonpulmonary comorbidities (eg, cardiovascular disease) and malignancies (eg, GI, bladder), suggesting a role for systemic injury. Since not all those with exposure develop COPD, there has been a search for plasma and lung biomarkers that confer increased cross-sectional and longitudinal risk. This search typically focuses on clinically relevant COPD outcomes such as FEV1, FEV1 decline, CT measurements of emphysema, or exacerbation frequency. The rapid advances in omics technology and the molecular phenotyping of COPD cohorts now permit large-scale evaluation of genetic, transcriptomic, proteomic, and metabolic biomarkers. This review focuses on protein biomarkers associated with clinically relevant COPD outcomes. The prototypic COPD protein biomarker is alpha-1 antitrypsin; however, this biomarker only accounts for 1% to 5% of COPD. This article reviews and summarizes the evidence for other validated biomarkers for each COPD outcome, and discusses their advantages, weaknesses, and required regulatory steps to move the biomarker from the bench into clinic. Although we highlight the emergence of many novel biomarkers (eg, fibrinogen, soluble receptor for advanced glycation, surfactant protein D, club cell secretory protein), there is increasing evidence that individual biomarkers only explain a fraction of the increased COPD risk and that multiple biomarker panels are needed to completely explain clinical variation and risk in individuals and populations.
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Affiliation(s)
- Karina A Serban
- National Jewish Health, Denver; University of Colorado, Anschutz Medical Campus, Aurora, CO.
| | | | - Russell P Bowler
- National Jewish Health, Denver; University of Colorado, Anschutz Medical Campus, Aurora, CO
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193
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Baumeister SE, Nolde M, Holtfreter B, Baurecht H, Gläser S, Kocher T, Ehmke B. Periodontitis and pulmonary function: a Mendelian randomization study. Clin Oral Investig 2021; 25:5109-5112. [PMID: 34046741 PMCID: PMC8342344 DOI: 10.1007/s00784-021-04000-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/19/2021] [Indexed: 11/30/2022]
Abstract
Objectives Observational research suggests that periodontitis affects pulmonary function; however, observational studies are subject to confounding and reverse causation, making causal inference and the direction of these associations difficult. We used Mendelian randomization (MR) to assess the potential causal association between genetic liability to periodontitis and pulmonary function. Materials and methods We used six single-nucleotide polymorphisms (SNPs) associated with periodontitis (P < 5 × 10−6) from a genome-wide association study (GWAS) of 17,353 European descent periodontitis cases and 28,210 controls from the GeneLifestyle Interactions in Dental Endpoints consortium and the UK Biobank, and related these to SNPs from a lung function GWAS including 79,055 study participants of the SpiroMeta Consortium. Results MR analysis suggested no effect of periodontitis on the ratio of forced expiratory volume in one second to lower forced vital capacity (standard deviation increment in outcome per doubling of the odds of the exposure (95% confidence interval) = − 0.004 (− 0.028; 0.020)). Replication analysis using genetic instruments from two different GWAS and sensitivity analyses to address potential pleiotropy led to no substantial changes in estimates. Conclusions Collectively, these findings do not support a relationship between genetic liability for periodontitis and pulmonary function. Clinical relevance Periodontitis does not seem to be a risk factor for worsening of pulmonary function.
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Affiliation(s)
- Sebastian-Edgar Baumeister
- Institute of Health Services Research in Dentistry, University of Münster, Albert-Schweitzer-Campus 1 48149, Münster, Germany.
| | - Michael Nolde
- Institute of Health Services Research in Dentistry, University of Münster, Albert-Schweitzer-Campus 1 48149, Münster, Germany
- Chair of Epidemiology, University of Augsburg, Augsburg, Germany
| | - Birte Holtfreter
- Unit of Periodontology, Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, University Medicine Greifswald, Greifswald, Germany
| | - Hansjörg Baurecht
- Department of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Sven Gläser
- Department of Internal Medicine B Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
- Vivantes Klinikum Neukölln Und Spandau, Klinik Für Innere Medizin - Pneumologie Und Infektiologie, Berlin, Germany
| | - Thomas Kocher
- Unit of Periodontology, Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, University Medicine Greifswald, Greifswald, Germany
| | - Benjamin Ehmke
- Clinic for Periodontology and Conservative Dentistry, University of Münster, Münster, Germany
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194
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Fawcett KA, Obeidat M, Melbourne C, Shrine N, Guyatt AL, John C, Luan J, Richmond A, Moksnes MR, Granell R, Weiss S, Imboden M, May-Wilson S, Hysi P, Boutin TS, Portas L, Flexeder C, Harris SE, Wang CA, Lyytikäinen LP, Palviainen T, Foong RE, Keidel D, Minelli C, Langenberg C, Bossé Y, Van den Berge M, Sin DD, Hao K, Campbell A, Porteous D, Padmanabhan S, Smith BH, Evans DM, Ring S, Langhammer A, Hveem K, Willer C, Ewert R, Stubbe B, Pirastu N, Klaric L, Joshi PK, Patasova K, Massimo M, Polasek O, Starr JM, Karrasch S, Strauch K, Meitinger T, Rudan I, Rantanen T, Pietiläinen K, Kähönen M, Raitakari OT, Hall GL, Sly PD, Pennell CE, Kaprio J, Lehtimäki T, Vitart V, Deary IJ, Jarvis D, Wilson JF, Spector T, Probst-Hensch N, Wareham NJ, Völzke H, Henderson J, Strachan DP, Brumpton BM, Hayward C, Hall IP, Tobin MD, Wain LV. Variants associated with HHIP expression have sex-differential effects on lung function. Wellcome Open Res 2021; 5:111. [PMID: 33728380 PMCID: PMC7938335 DOI: 10.12688/wellcomeopenres.15846.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2021] [Indexed: 02/02/2023] Open
Abstract
Background: Lung function is highly heritable and differs between the sexes throughout life. However, little is known about sex-differential genetic effects on lung function. We aimed to conduct the first genome-wide genotype-by-sex interaction study on lung function to identify genetic effects that differ between males and females. Methods: We tested for interactions between 7,745,864 variants and sex on spirometry-based measures of lung function in UK Biobank (N=303,612), and sought replication in 75,696 independent individuals from the SpiroMeta consortium. Results: Five independent single-nucleotide polymorphisms (SNPs) showed genome-wide significant (P<5x10 -8) interactions with sex on lung function, and 21 showed suggestive interactions (P<1x10 -6). The strongest signal, from rs7697189 (chr4:145436894) on forced expiratory volume in 1 second (FEV 1) (P=3.15x10 -15), was replicated (P=0.016) in SpiroMeta. The C allele increased FEV 1 more in males (untransformed FEV 1 β=0.028 [SE 0.0022] litres) than females (β=0.009 [SE 0.0014] litres), and this effect was not accounted for by differential effects on height, smoking or pubertal age. rs7697189 resides upstream of the hedgehog-interacting protein ( HHIP) gene and was previously associated with lung function and HHIP lung expression. We found HHIP expression was significantly different between the sexes (P=6.90x10 -6), but we could not detect sex differential effects of rs7697189 on expression. Conclusions: We identified a novel genotype-by-sex interaction at a putative enhancer region upstream of the HHIP gene. Establishing the mechanism by which HHIP SNPs have different effects on lung function in males and females will be important for our understanding of lung health and diseases in both sexes.
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Affiliation(s)
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - Carl Melbourne
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
| | - Anna L. Guyatt
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
| | - Catherine John
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Anne Richmond
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Marta R. Moksnes
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Raquel Granell
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
| | - Stefan Weiss
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastian May-Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
| | - Pirro Hysi
- The Department of Twin Research & Genetic Epidemiology, King’s College London, St Thomas’ Campus, Lambeth Palace Road, London, UK
| | - Thibaud S. Boutin
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Laura Portas
- Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College London, London, UK
| | - Claudia Flexeder
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Carol A. Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Callaghan, Australia
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, 33520, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, 33521, Finland
| | - Teemu Palviainen
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, FI-00014, Finland
| | - Rachel E. Foong
- Telethon Kids Institute, Perth, Australia
- School of Physiotherapy and Exercise Science, Faculty of Health Sciences, Curtin University, Perth, Australia
| | - Dirk Keidel
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Cosetta Minelli
- Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College London, London, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - Maarten Van den Berge
- University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Don D. Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - David Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Sandosh Padmanabhan
- British Heart Foundation Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Blair H. Smith
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - David M. Evans
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD 4072, Australia
| | - Sue Ring
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Arnulf Langhammer
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Cristen Willer
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, USA
| | - Ralf Ewert
- Department of Internal Medicine B, Cardiology, Pneumology, Infectious Diseases, Intensive Care Medicine, University Medicine Greifswald, Greifswald, 17475, Germany
| | - Beate Stubbe
- Department of Internal Medicine B, Cardiology, Pneumology, Infectious Diseases, Intensive Care Medicine, University Medicine Greifswald, Greifswald, 17475, Germany
| | - Nicola Pirastu
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
| | - Lucija Klaric
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Peter K. Joshi
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
| | - Karina Patasova
- The Department of Twin Research & Genetic Epidemiology, King’s College London, St Thomas’ Campus, Lambeth Palace Road, London, UK
| | - Mangino Massimo
- The Department of Twin Research & Genetic Epidemiology, King’s College London, St Thomas’ Campus, Lambeth Palace Road, London, UK
| | - Ozren Polasek
- University of Split School of Medicine, Split, Croatia
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Stefan Karrasch
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, 80336, Germany
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, 81377, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, 81377, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Institute of Human Genetics, Klinikum rechts der Isar der TU Muenchen, Muenchen, 81675, Germany
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
| | - Taina Rantanen
- Faculty of Sport and Health Sciences, Gerontology Research Center, University of Jyväskylä, Jyväskylä, Finland
| | - Kirsi Pietiläinen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, FI-00014, Finland
- Obesity Centre, Abdominal Centre, Helsinki University Hospital and University of Helsinki, Helsinki, FI-00029, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Olli T. Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Graham L. Hall
- Telethon Kids Institute, Perth, Australia
- School of Physiotherapy and Exercise Science, Faculty of Health Sciences, Curtin University, Perth, Australia
| | - Peter D. Sly
- Children's Health and Environment Program, The University of Queensland, Brisbane, Australia
| | - Craig E. Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Callaghan, Australia
| | - Jaakko Kaprio
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, FI-00014, Finland
- Department of Public Health, University of Helsinki, Helsinki, FI-00014, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, 33520, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Veronique Vitart
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Debbie Jarvis
- Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College London, London, UK
- MRC-PHE Centre for the Environment and Health, London, UK
| | - James F. Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, UK
| | - Tim Spector
- The Department of Twin Research & Genetic Epidemiology, King’s College London, St Thomas’ Campus, Lambeth Palace Road, London, UK
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Henry Völzke
- Intitute for Community Medicine, University Medicine Greifswald, Greifswald, 17487, Germany
| | - John Henderson
- Population Health Sciences Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - David P. Strachan
- Population Health Research Institute, St George's, University of London, London, SW17 0RE, UK
| | - Ben M. Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Clinic of Thoracic and Occupational Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Ian P. Hall
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, LE3 9QP, UK
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195
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Tejwani V, Fawzy A, Putcha N, Castaldi P, Cho MH, Pratte KA, Bhatt SP, Lynch DA, Humphries SM, Kinney GL, D'Alessio FR, Hansel NN. Emphysema Progression and Lung Function Decline Among Angiotensin Converting Enzyme Inhibitors and Angiotensin-Receptor Blockade Users in the COPDGene Cohort. Chest 2021; 160:1245-1254. [PMID: 34029566 DOI: 10.1016/j.chest.2021.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 10/21/2022] Open
Abstract
BACKGROUND Attenuation of transforming growth factor β by blocking angiotensin II has been shown to reduce emphysema in a murine model. General population studies have demonstrated that the use of angiotensin converting enzyme inhibitors (ACEis) and angiotensin-receptor blockers (ARBs) is associated with reduction of emphysema progression in former smokers and that the use of ACEis is associated with reduction of FEV1 progression in current smokers. RESEARCH QUESTION Is use of ACEi and ARB associated with less progression of emphysema and FEV1 decline among individuals with COPD or baseline emphysema? METHODS Former and current smokers from the Genetic Epidemiology of COPD Study who attended baseline and 5-year follow-up visits, did not change smoking status, and underwent chest CT imaging were included. Adjusted linear mixed models were used to evaluate progression of adjusted lung density (ALD), percent emphysema (%total lung volume <-950 Hounsfield units [HU]), 15th percentile of the attenuation histogram (attenuation [in HU] below which 15% of voxels are situated plus 1,000 HU), and lung function decline over 5 years between ACEi and ARB users and nonusers in those with spirometry-confirmed COPD, as well as all participants and those with baseline emphysema. Effect modification by smoking status also was investigated. RESULTS Over 5 years of follow-up, compared with nonusers, ACEi and ARB users with COPD showed slower ALD progression (adjusted mean difference [aMD], 1.6; 95% CI, 0.34-2.9). Slowed lung function decline was not observed based on phase 1 medication (aMD of FEV1 % predicted, 0.83; 95% CI, -0.62 to 2.3), but was when analysis was limited to consistent ACEi and ARB users (aMD of FEV1 % predicted, 1.9; 95% CI, 0.14-3.6). No effect modification by smoking status was found for radiographic outcomes, and the lung function effect was more pronounced in former smokers. Results were similar among participants with baseline emphysema. INTERPRETATION Among participants with spirometry-confirmed COPD or baseline emphysema, ACEi and ARB use was associated with slower progression of emphysema and lung function decline. TRIAL REGISTRY ClinicalTrials.gov; No.: NCT00608764; URL: www.clinicaltrials.gov.
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Affiliation(s)
- Vickram Tejwani
- Division of Pulmonary and Critical Care, Johns Hopkins University, Baltimore, MD.
| | - Ashraf Fawzy
- Division of Pulmonary and Critical Care, Johns Hopkins University, Baltimore, MD
| | - Nirupama Putcha
- Division of Pulmonary and Critical Care, Johns Hopkins University, Baltimore, MD
| | | | - Michael H Cho
- Division of Pulmonary and Critical Care Medicine, Boston, MA; Harvard Medical School, Boston, MA
| | | | - Surya P Bhatt
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - David A Lynch
- Department of Radiology, National Jewish Health, Denver, CO
| | | | - Gregory L Kinney
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO
| | - Franco R D'Alessio
- Division of Pulmonary and Critical Care, Johns Hopkins University, Baltimore, MD
| | - Nadia N Hansel
- Division of Pulmonary and Critical Care, Johns Hopkins University, Baltimore, MD
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196
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Prisco L, Moll M, Wang J, Hobbs BD, Huang W, Martin LW, Kronzer VL, Huang S, Silverman EK, Doyle TJ, Cho MH, Sparks JA. Relationship between rheumatoid arthritis and pulmonary function measures on spirometry in the UK Biobank. Arthritis Rheumatol 2021; 73:1994-2002. [PMID: 33982900 DOI: 10.1002/art.41791] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/27/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE We investigated the independent relationship of rheumatoid arthritis (RA) with type and severity of pulmonary patterns on spirometry compared to general population controls. METHODS This cross-sectional study investigated the association of RA and pulmonary function measures on spirometry among subjects who had spirometry performed for research purposes in the UK Biobank. RA cases were identified by self-report and current DMARD/glucocorticoid use. General population controls denied RA. Outcomes included continuous % predicted forced expiratory volume in 1 second (FEV1 ) and forced vital capacity (FVC), type of spirometric pattern (restrictive or obstructive), and severity. We used multivariable regression to estimate the effects of RA cases versus controls, adjusting for age, sex, body mass index (BMI), and smoking status/pack-years. RESULTS Among 350,776 analyzed subjects with spirometry performed (mean age 56.3 years, 55.8% female, and 45.5% ever smokers), we identified 2,008 cases of treated RA. In multivariable analyses, RA was associated with lower % predicted FEV1 (β -2.93, 95%CI -3.63,-2.24), % predicted FVC (β -2.08, 95%CI -2.72,-1.45), and FEV1 /FVC (β -0.008, 95%CI -0.010,-0.005) than controls. RA was associated with restrictive (OR 1.36, 95%CI 1.21,1.52) and obstructive (OR 1.21, 95%CI 1.07,1.37) patterns independent of confounders. RA had the strongest associations for severe restrictive and obstructive patterns. CONCLUSION RA was associated with increased odds of restrictive and obstructive patterns, and this relationship was not explained by confounders including smoking. In addition to restrictive lung disease, clinicians should also be aware that airflow obstruction may be a pulmonary manifestation of RA.
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Affiliation(s)
- Lauren Prisco
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew Moll
- Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jiaqi Wang
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Brian D Hobbs
- Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Weixing Huang
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Lily W Martin
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Sicong Huang
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Tracy J Doyle
- Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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197
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Sikdar S, Wyss AB, Lee MK, Hoang TT, Richards M, Beane Freeman LE, Parks C, Thorne PS, Hankinson JL, Umbach DM, Motsinger-Reif A, London SJ. Interaction between Genetic Risk Scores for reduced pulmonary function and smoking, asthma and endotoxin. Thorax 2021; 76:1219-1226. [PMID: 33963087 PMCID: PMC8572320 DOI: 10.1136/thoraxjnl-2020-215624] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 02/17/2021] [Accepted: 03/22/2021] [Indexed: 01/04/2023]
Abstract
Rationale Genome-wide association studies (GWASs) have identified numerous loci associated with lower pulmonary function. Pulmonary function is strongly related to smoking and has also been associated with asthma and dust endotoxin. At the individual SNP level, genome-wide analyses of pulmonary function have not identified appreciable evidence for gene by environment interactions. Genetic Risk Scores (GRSs) may enhance power to identify gene–environment interactions, but studies are few. Methods We analysed 2844 individuals of European ancestry with 1000 Genomes imputed GWAS data from a case–control study of adult asthma nested within a US agricultural cohort. Pulmonary function traits were FEV1, FVC and FEV1/FVC. Using data from a recent large meta-analysis of GWAS, we constructed a weighted GRS for each trait by combining the top (p value<5×10−9) genetic variants, after clumping based on distance (±250 kb) and linkage disequilibrium (r2=0.5). We used linear regression, adjusting for relevant covariates, to estimate associations of each trait with its GRS and to assess interactions. Results Each trait was highly significantly associated with its GRS (all three p values<8.9×10−8). The inverse association of the GRS with FEV1/FVC was stronger for current smokers (pinteraction=0.017) or former smokers (pinteraction=0.064) when compared with never smokers and among asthmatics compared with non-asthmatics (pinteraction=0.053). No significant interactions were observed between any GRS and house dust endotoxin. Conclusions Evaluation of interactions using GRSs supports a greater impact of increased genetic susceptibility on reduced pulmonary function in the presence of smoking or asthma.
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Affiliation(s)
- Sinjini Sikdar
- Department of Mathematics and Statistics, Old Dominion University, Norfolk, Virginia, USA.,Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Thanh T Hoang
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | | | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Christine Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Peter S Thorne
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa, USA
| | | | - David M Umbach
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
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198
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Park S, Lee S, Kim Y, Cho S, Kim K, Kim YC, Han SS, Lee H, Lee JP, Joo KW, Lim CS, Kim YS, Kim DK. Kidney function and obstructive lung disease: a bidirectional Mendelian randomisation study. Eur Respir J 2021; 58:13993003.00848-2021. [PMID: 33958431 DOI: 10.1183/13993003.00848-2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/26/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Additional study is warranted to investigate the causal effects between kidney function and obstructive lung disease. METHODS This study was a bidirectional two-sample Mendelian randomisation (MR) analysis. The CKDGen genome-wide association study (GWAS) meta-analysis for estimated glomerular filtration rate (eGFR) including individuals of European ancestry (N=567 460) provided the genetic instrument for kidney function and outcome summary statistics. A GWAS for FEV1/FVC including individuals of European ancestry from the UK Biobank (N=321 047) provided the genetic instrument for FEV1/FVC and outcome data. A polygenic score (PGS) analysis was performed to test the causal estimates from kidney function to binary obstructive lung disease outcomes, including chronic obstructive pulmonary disease (COPD), asthma, and FEV1/FVC<70%, and to perform non-linear MR with individual-level UK Biobank data. RESULTS The causal estimates by summary-level MR indicated that genetically predicted increased kidney function was significantly associated with increased FEV1/FVC Z scores [10% increase in eGFR, beta 0.055 (0.024, 0.086)]. The PGS for increased eGFR showed a significant association with a reduced risk of FEV1/FVC<70% [OR 0.93 (0.87, 0.99)], COPD [OR 0.93 (0.87, 0.99)] and late-onset (≥50 years old) asthma [OR 0.93 (0.88, 0.99)]. The non-linear MR demonstrated that the causal effect from eGFR to FEV1/FVC was apparent in eGFR ranges lower than 60 mL/min/1.73 m2. On the other hand, genetically predicted FEV1/FVC showed nonsignificant causal estimates of eGFR change [beta 0.568% (-0.458, 1.605%)]. CONCLUSION This study supports kidney function impairment would be a causative factor for obstructive lung disease.
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Affiliation(s)
- Sehoon Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.,Department of Internal Medicine, Armed Forces Capital Hospital, Gyeonggi-do, Korea
| | - Soojin Lee
- Division of Nephrology, Department of Internal Medicine, Uijeongbu Eulji University Medical Center, Gyeonggi-do, Korea
| | - Yaerim Kim
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Semin Cho
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Kwangsoo Kim
- Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital, Seoul, Korea
| | - Yong Chul Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Seung Seok Han
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.,Kidney Research Institute, Seoul National University, Seoul, Korea
| | - Hajeong Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.,Kidney Research Institute, Seoul National University, Seoul, Korea
| | - Jung Pyo Lee
- Kidney Research Institute, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Kwon Wook Joo
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.,Kidney Research Institute, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Chun Soo Lim
- Kidney Research Institute, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Yon Su Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.,Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.,Kidney Research Institute, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Dong Ki Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea .,Kidney Research Institute, Seoul National University, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
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199
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Hernandez-Pacheco N, Vijverberg SJ, Herrera-Luis E, Li J, Sio YY, Granell R, Corrales A, Maroteau C, Lethem R, Perez-Garcia J, Farzan N, Repnik K, Gorenjak M, Soares P, Karimi L, Schieck M, Pérez-Méndez L, Berce V, Tavendale R, Eng C, Sardon O, Kull I, Mukhopadhyay S, Pirmohamed M, Verhamme KMC, Burchard EG, Kabesch M, Hawcutt DB, Melén E, Potočnik U, Chew FT, Tantisira KG, Turner S, Palmer CN, Flores C, Pino-Yanes M, Maitland-van der Zee AH. Genome-wide association study of asthma exacerbations despite inhaled corticosteroid use. Eur Respir J 2021; 57:2003388. [PMID: 33303529 PMCID: PMC8122045 DOI: 10.1183/13993003.03388-2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
RATIONALE Substantial variability in response to asthma treatment with inhaled corticosteroids (ICS) has been described among individuals and populations, suggesting the contribution of genetic factors. Nonetheless, only a few genes have been identified to date. We aimed to identify genetic variants associated with asthma exacerbations despite ICS use in European children and young adults and to validate the findings in non-Europeans. Moreover, we explored whether a gene-set enrichment analysis could suggest potential novel asthma therapies. METHODS A genome-wide association study (GWAS) of asthma exacerbations was tested in 2681 children of European descent treated with ICS from eight studies. Suggestive association signals were followed up for replication in 538 European asthma patients. Further evaluation was performed in 1773 non-Europeans. Variants revealed by published GWAS were assessed for replication. Additionally, gene-set enrichment analysis focused on drugs was performed. RESULTS 10 independent variants were associated with asthma exacerbations despite ICS treatment in the discovery phase (p≤5×10-6). Of those, one variant at the CACNA2D3-WNT5A locus was nominally replicated in Europeans (rs67026078; p=0.010), but this was not validated in non-European populations. Five other genes associated with ICS response in previous studies were replicated. Additionally, an enrichment of associations in genes regulated by trichostatin A treatment was found. CONCLUSIONS The intergenic region of CACNA2D3 and WNT5A was revealed as a novel locus for asthma exacerbations despite ICS treatment in European populations. Genes associated were related to trichostatin A, suggesting that this drug could regulate the molecular mechanisms involved in treatment response.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Genomics and Health Group, Dept of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Susanne J Vijverberg
- Dept of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Dept of Paediatric Respiratory Medicine and Allergy, Emma's Children Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Esther Herrera-Luis
- Genomics and Health Group, Dept of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Jiang Li
- The Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yang Yie Sio
- Dept of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Raquel Granell
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Almudena Corrales
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Cyrielle Maroteau
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Ryan Lethem
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Javier Perez-Garcia
- Genomics and Health Group, Dept of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Niloufar Farzan
- Dept of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Breathomix B.V., El Reeuwijk, The Netherlands
| | - Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Mario Gorenjak
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Patricia Soares
- Academic Dept of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
- Escola Nacional de Saúde Pública, Lisboa, Portugal
| | - Leila Karimi
- Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maximilian Schieck
- Dept of Paediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
- Dept of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Lina Pérez-Méndez
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Dept of Clinic Epidemiology and Biostatistics, Research Unit, Hospital Universitario N.S. de Candelaria, Gerencia de Atención Primaria, Santa Cruz de Tenerife, Spain
| | - Vojko Berce
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Dept of Paediatrics, University Medical Centre Maribor, Maribor, Slovenia
| | - Roger Tavendale
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Celeste Eng
- Dept of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Olaia Sardon
- Division of Paediatric Respiratory Medicine, Hospital Universitario Donostia, San Sebastián, Spain
- Dept of Paediatrics, University of the Basque Country (UPV/EHU), San Sebastián, Spain
| | - Inger Kull
- Dept of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet and Sachs' Children's Hospital, Stockholm, Sweden
| | - Somnath Mukhopadhyay
- Academic Dept of Paediatrics, Brighton and Sussex Medical School, Royal Alexandra Children's Hospital, Brighton, UK
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Munir Pirmohamed
- Dept of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Katia M C Verhamme
- Dept of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Esteban G Burchard
- Dept of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Dept of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Michael Kabesch
- Dept of Paediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Daniel B Hawcutt
- Dept of Women's and Children's Health, University of Liverpool, Liverpool, UK
- Alder Hey Children's Hospital, Liverpool, UK
| | - Erik Melén
- Dept of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet and Sachs' Children's Hospital, Stockholm, Sweden
- Institute of Environmental Medicine, Karolinska Institutet, Solna, Sweden
| | - Uroš Potočnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- Laboratory for Biochemistry, Molecular Biology and Genomics, Faculty for Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - Fook Tim Chew
- Dept of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Dept of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Steve Turner
- Child Health, University of Aberdeen, Aberdeen, UK
| | - Colin N Palmer
- Population Pharmacogenetics Group, Biomedical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Genomics and Health Group, Dept of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- These authors contributed equally to this work
| | - Anke H Maitland-van der Zee
- Dept of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Division of Pharmacoepidemiology and Clinical Pharmacology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
- Dept of Paediatric Respiratory Medicine and Allergy, Emma's Children Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- These authors contributed equally to this work
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200
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Deary IJ, Sternberg RJ. Ian Deary and Robert Sternberg answer five self-inflicted questions about human intelligence. INTELLIGENCE 2021. [DOI: 10.1016/j.intell.2021.101539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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