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Cao Z, Zhao S, Hu S, Wu T, Sun F, Shi LI. Screening COPD-Related Biomarkers and Traditional Chinese Medicine Prediction Based on Bioinformatics and Machine Learning. Int J Chron Obstruct Pulmon Dis 2024; 19:2073-2095. [PMID: 39346628 PMCID: PMC11438478 DOI: 10.2147/copd.s476808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 09/16/2024] [Indexed: 10/01/2024] Open
Abstract
Purpose To employ bioinformatics and machine learning to predict the characteristics of immune cells and genes associated with the inflammatory response and ferroptosis in chronic obstructive pulmonary disease (COPD) patients and to aid in the development of targeted traditional Chinese medicine (TCM). Mendelian randomization analysis elucidates the causal relationships among immune cells, genes, and COPD, offering novel insights for the early diagnosis, prevention, and treatment of COPD. This approach also provides a fresh perspective on the use of traditional Chinese medicine for treating COPD. Methods R software was used to extract COPD-related data from the Gene Expression Omnibus (GEO) database, differentially expressed genes were identified for enrichment analysis, and WGCNA was used to pinpoint genes within relevant modules associated with COPD. This analysis included determining genes linked to the inflammatory response in COPD patients and analyzing their correlation with ferroptosis. Further steps involved filtering core genes, constructing TF-miRNA‒mRNA network diagrams, and employing three types of machine learning to predict the core miRNAs, key immune cells, and characteristic genes of COPD patients. This process also delves into their correlations, single-gene GSEA, and diagnostic model predictions. Reverse inference complemented by molecular docking was used to predict compounds and traditional Chinese medicines for treating COPD; Mendelian randomization was applied to explore the causal relationships among immune cells, genes, and COPD. Results We identified 2443 differential genes associated with COPD through the GEO database, along with 8435 genes relevant to WGCNA and 1226 inflammation-related genes. A total of 141 genes related to the inflammatory response in COPD patients were identified, and 37 core genes related to ferroptosis were selected for further enrichment analysis and analysis. The core miRNAs predicted for COPD include hsa-miR-543, hsa-miR-181c, and hsa-miR-200a, among others. The key immune cells identified were plasma cells, activated memory CD4 T cells, gamma delta T cells, activated NK cells, M2 macrophages, and eosinophils. Characteristic genes included EGF, PLG, PTPN22, and NR4A1. A total of 78 compounds and 437 traditional Chinese medicines were predicted. Mendelian randomization analysis revealed a causal relationship between 36 types of immune cells and COPD, whereas no causal relationship was found between the core genes and COPD. Conclusion A definitive causal relationship exists between immune cells and COPD, while the prediction of core miRNAs, key immune cells, characteristic genes, and targeted traditional Chinese medicines offers novel insights for the early diagnosis, prevention, and treatment of COPD.
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Affiliation(s)
- Zhenghua Cao
- Changchun University of Traditional Chinese Medicine, Changchun, Jilin, People's Republic of China
| | - Shengkun Zhao
- Changchun University of Traditional Chinese Medicine, Changchun, Jilin, People's Republic of China
| | - Shaodan Hu
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, People's Republic of China
| | - Tong Wu
- Geriatric Department, Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Suzhou, Jiangsu, People's Republic of China
| | - Feng Sun
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, People's Republic of China
| | - L I Shi
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, Jilin, People's Republic of China
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Moll M, Hecker J, Platig J, Zhang J, Ghosh AJ, Pratte KA, Wang RS, Hill D, Konigsberg IR, Chiles JW, Hersh CP, Castaldi PJ, Glass K, Dy JG, Sin DD, Tal-Singer R, Mouded M, Rennard SI, Anderson GP, Kinney GL, Bowler RP, Curtis JL, McDonald ML, Silverman EK, Hobbs BD, Cho MH. Polygenic and transcriptional risk scores identify chronic obstructive pulmonary disease subtypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.20.24307621. [PMID: 38826461 PMCID: PMC11142287 DOI: 10.1101/2024.05.20.24307621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Rationale Genetic variants and gene expression predict risk of chronic obstructive pulmonary disease (COPD), but their effect on COPD heterogeneity is unclear. Objectives Define high-risk COPD subtypes using both genetics (polygenic risk score, PRS) and blood gene expression (transcriptional risk score, TRS) and assess differences in clinical and molecular characteristics. Methods We defined high-risk groups based on PRS and TRS quantiles by maximizing differences in protein biomarkers in a COPDGene training set and identified these groups in COPDGene and ECLIPSE test sets. We tested multivariable associations of subgroups with clinical outcomes and compared protein-protein interaction networks and drug repurposing analyses between high-risk groups. Measurements and Main Results We examined two high-risk omics-defined groups in non-overlapping test sets (n=1,133 NHW COPDGene, n=299 African American (AA) COPDGene, n=468 ECLIPSE). We defined "High activity" (low PRS/high TRS) and "severe risk" (high PRS/high TRS) subgroups. Participants in both subgroups had lower body-mass index (BMI), lower lung function, and alterations in metabolic, growth, and immune signaling processes compared to a low-risk (low PRS, low TRS) reference subgroup. "High activity" but not "severe risk" participants had greater prospective FEV 1 decline (COPDGene: -51 mL/year; ECLIPSE: - 40 mL/year) and their proteomic profiles were enriched in gene sets perturbed by treatment with 5-lipoxygenase inhibitors and angiotensin-converting enzyme (ACE) inhibitors. Conclusions Concomitant use of polygenic and transcriptional risk scores identified clinical and molecular heterogeneity amongst high-risk individuals. Proteomic and drug repurposing analysis identified subtype-specific enrichment for therapies and suggest prior drug repurposing failures may be explained by patient selection.
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Smilnak GJ, Lee Y, Chattopadhyay A, Wyss AB, White JD, Sikdar S, Jin J, Grant AJ, Motsinger-Reif AA, Li JL, Lee M, Yu B, London SJ. Plasma protein signatures of adult asthma. Allergy 2024; 79:643-655. [PMID: 38263798 PMCID: PMC10994188 DOI: 10.1111/all.16000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/08/2023] [Accepted: 12/04/2023] [Indexed: 01/25/2024]
Abstract
BACKGROUND Adult asthma is complex and incompletely understood. Plasma proteomics is an evolving technique that can both generate biomarkers and provide insights into disease mechanisms. We aimed to identify plasma proteomic signatures of adult asthma. METHODS Protein abundance in plasma was measured in individuals from the Agricultural Lung Health Study (ALHS) (761 asthma, 1095 non-case) and the Atherosclerosis Risk in Communities study (470 asthma, 10,669 non-case) using the SOMAScan 5K array. Associations with asthma were estimated using covariate adjusted logistic regression and meta-analyzed using inverse-variance weighting. Additionally, in ALHS, we examined phenotypes based on both asthma and seroatopy (asthma with atopy (n = 207), asthma without atopy (n = 554), atopy without asthma (n = 147), compared to neither (n = 948)). RESULTS Meta-analysis of 4860 proteins identified 115 significantly (FDR<0.05) associated with asthma. Multiple signaling pathways related to airway inflammation and pulmonary injury were enriched (FDR<0.05) among these proteins. A proteomic score generated using machine learning provided predictive value for asthma (AUC = 0.77, 95% CI = 0.75-0.79 in training set; AUC = 0.72, 95% CI = 0.69-0.75 in validation set). Twenty proteins are targeted by approved or investigational drugs for asthma or other conditions, suggesting potential drug repurposing. The combined asthma-atopy phenotype showed significant associations with 20 proteins, including five not identified in the overall asthma analysis. CONCLUSION This first large-scale proteomics study identified over 100 plasma proteins associated with current asthma in adults. In addition to validating previous associations, we identified many novel proteins that could inform development of diagnostic biomarkers and therapeutic targets in asthma management.
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Affiliation(s)
- Gordon J. Smilnak
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Yura Lee
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Abhijnan Chattopadhyay
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Annah B. Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Julie D. White
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
- GenOmics and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Sinjini Sikdar
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
- Department of Mathematics and Statistics, Old Dominion University, Norfolk, VA, USA
| | | | - Andrew J. Grant
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Alison A. Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Jian-Liang Li
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Mikyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
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Liu G, Hu J, Yang J, Song J. Predicting early-onset COPD risk in adults aged 20-50 using electronic health records and machine learning. PeerJ 2024; 12:e16950. [PMID: 38410800 PMCID: PMC10896079 DOI: 10.7717/peerj.16950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a major public health concern, affecting estimated 164 million people worldwide. Early detection and intervention strategies are essential to reduce the burden of COPD, but current screening approaches are limited in their ability to accurately predict risk. Machine learning (ML) models offer promise for improved accuracy of COPD risk prediction by combining genetic and electronic medical record data. In this study, we developed and evaluated eight ML models for primary screening of COPD utilizing routine screening data, polygenic risk scores (PRS), additional clinical data, or a combination of all three. To assess our models, we conducted a retrospective analysis of approximately 329,396 patients in the UK Biobank database. Incorporating personal information and blood biochemical test results significantly improved the model's accuracy for predicting COPD risk, achieving a best performance of 0.8505 AUC, a specificity of 0.8539 and a sensitivity of 0.7584. These results indicate that ML models can be effectively utilized for accurate prediction of COPD risk in individuals aged 20 to 50 years, providing a valuable tool for early detection and intervention.
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Affiliation(s)
- Guanglei Liu
- School of Information Science and Engineering, Yunnan University, Kunming, Yunnan, China
| | - Jiani Hu
- Ailurus Biotechnology Ltd., Shenzhen, Guangdong, China
| | - Jianzhe Yang
- Ailurus Biotechnology Ltd., Shenzhen, Guangdong, China
| | - Jie Song
- Ailurus Biotechnology Ltd., Shenzhen, Guangdong, China
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Moll M, Silverman EK. Precision Approaches to Chronic Obstructive Pulmonary Disease Management. Annu Rev Med 2024; 75:247-262. [PMID: 37827193 DOI: 10.1146/annurev-med-060622-101239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of morbidity and mortality worldwide. COPD heterogeneity has hampered progress in developing pharmacotherapies that affect disease progression. This issue can be addressed by precision medicine approaches, which focus on understanding an individual's disease risk, and tailoring management based on pathobiology, environmental exposures, and psychosocial issues. There is an urgent need to identify COPD patients at high risk for poor outcomes and to understand at a mechanistic level why certain individuals are at high risk. Genetics, omics, and network analytic techniques have started to dissect COPD heterogeneity and identify patients with specific pathobiology. Drug repurposing approaches based on biomarkers of specific inflammatory processes (i.e., type 2 inflammation) are promising. As larger data sets, additional omics, and new analytical approaches become available, there will be enormous opportunities to identify high-risk individuals and treat COPD patients based on their specific pathophysiological derangements. These approaches show great promise for risk stratification, early intervention, drug repurposing, and developing novel therapeutic approaches for COPD.
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Affiliation(s)
- Matthew Moll
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Pulmonary, Critical Care, Sleep and Allergy, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Bertels X, Ross JC, Faner R, Cho MH, Ikram MA, Brusselle GG, Lahousse L. Clinical relevance of lung function trajectory clusters in middle-aged and older adults. ERJ Open Res 2024; 10:00793-2023. [PMID: 38333649 PMCID: PMC10851953 DOI: 10.1183/23120541.00793-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 02/10/2024] Open
Abstract
Background The determinants and health outcomes of lung function trajectories in adults among the general population are poorly understood. We aimed to identify and characterise clusters of lung function trajectories in adults aged ≥45 years. Methods Gaussian finite-mixture modelling was applied to baseline and annualised change of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC ratio z-scores in participants of the Rotterdam Study, a prospective population-based cohort study, with repeated spirometry (n=3884; mean±sd age 64.7±8.9 years). Longitudinal outcomes were all-cause mortality, respiratory outcomes (symptoms, COPD (FEV1/FVC <0.7 in absence of asthma), preserved ratio impaired spirometry (PRISm; FEV1/FVC ≥0.7 and FEV1 or FVC <80%)), smoking cessation and weight changes. Independent risk factors, including genetics, were identified by multiple logistic regression. Results We identified eight trajectory clusters, with the reference group having persistently normal spirometry (prevalence 42.8%). Three clusters showed higher mortality, adjusted for confounders: 1) the persistently low FEV1 cluster (prevalence 6.8%, hazard ratio (HR) 1.71, 95% CI 1.37-2.13); 2) rapid FEV1 decliners (prevalence 4.6%, HR 1.48, 95% CI 1.10-1.99); and 3) FVC decliners (prevalence 3.7%, HR 1.49, 95% CI 1.09-2.03). In contrast, FVC improvers (prevalence 6.7%, HR 0.61, 95% CI 0.41-0.90) and persistently high FEV1 (prevalence 29.2%, HR 0.82, 95% CI 0.69-0.98) were protective trajectory clusters. Clusters were characterised by differences in genetic predisposition (polygenic scores of FEV1 and FEV1/FVC), demographics, cigarette smoking, respiratory symptoms (chronic cough, wheezing and dyspnoea), cardiovascular factors (body mass index, hypertension and heart failure) and serum C-reactive protein levels. Frailty, weight changes and the development of respiratory symptoms, COPD and PRISm were significantly associated with trajectory clusters. Conclusions This study reveals clinically relevant lung function trajectory clusters in older adults of the general population.
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Affiliation(s)
- Xander Bertels
- Department of Bioanalysis, Ghent University, Ghent, Belgium
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - James C. Ross
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rosa Faner
- Institut d'Investigacions Biomédiques August Pi i Sunyer, Hospital Clinic de Barcelona, Barcelona, Spain
- Department of Biomedical Sciences, University of Barcelona, Barcelona, Spain
- Centro Investigaciones Biomédicas en Red, Instituto de Salud Carlos III, Madrid, Spain
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Guy G. Brusselle
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Lies Lahousse
- Department of Bioanalysis, Ghent University, Ghent, Belgium
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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He Y, Qian DC, Diao JA, Cho MH, Silverman EK, Gusev A, Manrai AK, Martin AR, Patel CJ. Prediction and stratification of longitudinal risk for chronic obstructive pulmonary disease across smoking behaviors. Nat Commun 2023; 14:8297. [PMID: 38097585 PMCID: PMC10721891 DOI: 10.1038/s41467-023-44047-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023] Open
Abstract
Smoking is the leading risk factor for chronic obstructive pulmonary disease (COPD) worldwide, yet many people who never smoke develop COPD. We perform a longitudinal analysis of COPD in the UK Biobank to derive and validate the Socioeconomic and Environmental Risk Score which captures additive and cumulative environmental, behavioral, and socioeconomic exposure risks beyond tobacco smoking. The Socioeconomic and Environmental Risk Score is more predictive of COPD than smoking status and pack-years. Individuals in the highest decile of the risk score have a greater risk for incident COPD compared to the remaining population. Never smokers in the highest decile of exposure risk are more likely to develop COPD than previous and current smokers in the lowest decile. In general, the prediction accuracy of the Social and Environmental Risk Score is lower in non-European populations. While smoking status is often considered in screening COPD, our finding highlights the importance of other non-smoking environmental and socioeconomic variables.
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Affiliation(s)
- Yixuan He
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - David C Qian
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - James A Diao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Edwin K Silverman
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Alexander Gusev
- Department of Medicine, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Arjun K Manrai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Alicia R Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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Moll M, Sordillo JE, Ghosh AJ, Hayden LP, McDermott G, McGeachie MJ, Dahlin A, Tiwari A, Manmadkar MG, Abston ED, Pavuluri C, Saferali A, Begum S, Ziniti JP, Gulsvik A, Bakke PS, Aschard H, Iribarren C, Hersh CP, Sparks JA, Hobbs BD, Lasky-Su JA, Silverman EK, Weiss ST, Wu AC, Cho MH. Polygenic risk scores identify heterogeneity in asthma and chronic obstructive pulmonary disease. J Allergy Clin Immunol 2023; 152:1423-1432. [PMID: 37595761 PMCID: PMC10841234 DOI: 10.1016/j.jaci.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/27/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Asthma and chronic obstructive pulmonary disease (COPD) have distinct and overlapping genetic and clinical features. OBJECTIVE We sought to test the hypothesis that polygenic risk scores (PRSs) for asthma (PRSAsthma) and spirometry (FEV1 and FEV1/forced vital capacity; PRSspiro) would demonstrate differential associations with asthma, COPD, and asthma-COPD overlap (ACO). METHODS We developed and tested 2 asthma PRSs and applied the higher performing PRSAsthma and a previously published PRSspiro to research (Genetic Epidemiology of COPD study and Childhood Asthma Management Program, with spirometry) and electronic health record-based (Mass General Brigham Biobank and Genetic Epidemiology Research on Adult Health and Aging [GERA]) studies. We assessed the association of PRSs with COPD and asthma using modified random-effects and binary-effects meta-analyses, and ACO and asthma exacerbations in specific cohorts. Models were adjusted for confounders and genetic ancestry. RESULTS In meta-analyses of 102,477 participants, the PRSAsthma (odds ratio [OR] per SD, 1.16 [95% CI, 1.14-1.19]) and PRSspiro (OR per SD, 1.19 [95% CI, 1.17-1.22]) both predicted asthma, whereas the PRSspiro predicted COPD (OR per SD, 1.25 [95% CI, 1.21-1.30]). However, results differed by cohort. The PRSspiro was not associated with COPD in GERA and Mass General Brigham Biobank. In the Genetic Epidemiology of COPD study, the PRSAsthma (OR per SD: Whites, 1.3; African Americans, 1.2) and PRSspiro (OR per SD: Whites, 2.2; African Americans, 1.6) were both associated with ACO. In GERA, the PRSAsthma was associated with asthma exacerbations (OR, 1.18) in Whites; the PRSspiro was associated with asthma exacerbations in White, LatinX, and East Asian participants. CONCLUSIONS PRSs for asthma and spirometry are both associated with ACO and asthma exacerbations. Genetic prediction performance differs in research versus electronic health record-based cohorts.
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Affiliation(s)
- Matthew Moll
- Department of Medicine, Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, Mass; Harvard Medical School, Brigham and Women's Hospital, Boston, Mass
| | - Joanne E Sordillo
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care, Boston, Mass
| | - Auyon J Ghosh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, SUNY Upstate Medical Center, Syracuse, NY
| | - Lystra P Hayden
- Department of Pediatrics, Division of Pulmonary Medicine, Boston Children's Hospital, Harvard Medical School, Massachusetts General Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Gregory McDermott
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, Mass
| | - Michael J McGeachie
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Amber Dahlin
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Anshul Tiwari
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Monica G Manmadkar
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Eric D Abston
- Department of Thoracic Surgery, Massachusetts General Hospital, Boston, Mass
| | - Chandan Pavuluri
- Department of Medicine, Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, Mass; Harvard Medical School, Brigham and Women's Hospital, Boston, Mass
| | - Aabida Saferali
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Sofina Begum
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - John P Ziniti
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Hugues Aschard
- Department of Computational Biology, Institut Pasteur, Universit de Paris, Paris, France
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Craig P Hersh
- Department of Medicine, Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, Mass; Harvard Medical School, Brigham and Women's Hospital, Boston, Mass
| | - Jeffrey A Sparks
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, Mass
| | - Brian D Hobbs
- Department of Medicine, Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, Mass; Harvard Medical School, Brigham and Women's Hospital, Boston, Mass
| | - Jessica A Lasky-Su
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Edwin K Silverman
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Scott T Weiss
- Harvard Medical School, Brigham and Women's Hospital, Boston, Mass; Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Mass
| | - Ann Chen Wu
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care, Boston, Mass
| | - Michael H Cho
- Department of Medicine, Channing Division of Network Medicine, Division of Pulmonary and Critical Care Medicine, Harvard Medical School, Boston, Mass; Harvard Medical School, Brigham and Women's Hospital, Boston, Mass.
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Backman H, Blomberg A, Lundquist A, Strandkvist V, Sawalha S, Nilsson U, Eriksson-Ström J, Hedman L, Stridsman C, Rönmark E, Lindberg A. Lung Function Trajectories and Associated Mortality among Adults with and without Airway Obstruction. Am J Respir Crit Care Med 2023; 208:1063-1074. [PMID: 37460250 PMCID: PMC10867942 DOI: 10.1164/rccm.202211-2166oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/17/2023] [Indexed: 08/18/2023] Open
Abstract
Rationale: Spirometry is essential for diagnosis and assessment of prognosis in patients with chronic obstructive pulmonary disease (COPD). Objectives: To identify FEV1 trajectories and their determinants on the basis of annual spirometry measurements among individuals with and without airway obstruction (AO) and to assess mortality in relation to trajectories. Methods: From 2002 through 2004, individuals with AO (FEV1/VC < 0.70, n = 993) and age- and sex-matched nonobstructive (NO) referents were recruited from population-based cohorts. Annual spirometry until 2014 was used in joint-survival latent-class mixed models to identify lung function trajectories. Mortality data were collected during 15 years of follow-up. Measurements and Main Results: Three trajectories were identified among the subjects with AO and two among the NO referents. Trajectory membership was driven by baseline FEV1% predicted (FEV1%pred) in both groups and also by pack-years in subjects with AO and current smoking in NO referents. Longitudinal FEV1%pred depended on baseline FEV1%pred, pack-years, and obesity. The trajectories were distributed as follows: among individuals with AO, 79.6% in AO trajectory 1 (FEV1 high with normal decline), 12.8% in AO trajectory 2 (FEV1 high with rapid decline), and 7.7% in AO trajectory 3 (FEV1 low with normal decline) (mean, 27, 72, and 26 ml/yr, respectively) and, among NO referents, 96.7% in NO trajectory 1 (FEV1 high with normal decline) and 3.3% in NO trajectory 2 (FEV1 high with rapid decline) (mean, 34 and 173 ml/yr, respectively). Hazard for death was increased for AO trajectories 2 (hazard ratio [HR], 1.56) and 3 (HR, 3.45) versus AO trajectory 1 and for NO trajectory 2 (HR, 2.99) versus NO trajectory 1. Conclusions: Three different FEV1 trajectories were identified among subjects with AO and two among NO referents, with different outcomes in terms of FEV1 decline and mortality. The FEV1 trajectories among subjects with AO and the relationship between low FVC and trajectory outcome are of particular clinical interest.
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Affiliation(s)
| | | | - Anders Lundquist
- Department of Statistics, Umeå School of Business, Economics and Statistics (USBE), Umeå University, Umeå, Sweden; and
| | - Viktor Strandkvist
- Department of Health and Technology, Luleå University of Technology, Luleå, Sweden
| | - Sami Sawalha
- Department of Public Health and Clinical Medicine, and
| | - Ulf Nilsson
- Department of Public Health and Clinical Medicine, and
| | | | | | | | | | - Anne Lindberg
- Department of Public Health and Clinical Medicine, and
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He Y, Qian DC, Diao JA, Cho MH, Silverman EK, Gusev A, Manrai AK, Martin AR, Patel CJ. Prediction and stratification of longitudinal risk for chronic obstructive pulmonary disease across smoking behaviors. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.04.23288086. [PMID: 37066248 PMCID: PMC10104210 DOI: 10.1101/2023.04.04.23288086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Smoking is the leading risk factor for chronic obstructive pulmonary disease (COPD) worldwide, yet many people who never smoke develop COPD. We hypothesize that considering other socioeconomic and environmental factors can better predict and stratify the risk of COPD in both non-smokers and smokers. We performed longitudinal analysis of COPD in the UK Biobank to develop the Socioeconomic and Environmental Risk Score (SERS) which captures additive and cumulative environmental, behavioral, and socioeconomic exposure risks beyond tobacco smoking. We tested the ability of SERS to predict and stratify the risk of COPD in current, previous, and never smokers of European and non-European ancestries in comparison to a composite genome-wide polygenic risk score (PGS). We tested associations using Cox regression models and assessed the predictive performance of models using Harrell's C index. SERS (C index = 0.770, 95% CI 0.756 to 0.784) was more predictive of COPD than smoking status (C index = 0.738, 95% CI 0.724 to 0.752), pack-years (C index = 0.742, 95% CI 0.727 to 0.756). Compared to the remaining population, individuals in the highest decile of the SERS had hazard ratios (HR) = 7.24 (95% CI 6.51 to 8.05, P < 0.0001) for incident COPD. Never smokers in the highest decile of exposure risk were more likely to develop COPD than previous and current smokers in the lowest decile with HR=4.95 (95% CI 1.56 to 15.69, P=6.65×10-3) and 2.92 (95%CI 1.51 to 5.61, P=1.38×10-3), respectively. In general, the prediction accuracy of SERS was lower in the non-European populations compared to the European evaluation set. In addition to genetic factors, socioeconomic and environmental factors beyond smoking can predict and stratify COPD risk for both non- and smoking individuals. Smoking status is often considered in screening; other non-smoking environmental and non-genetic variables should be evaluated prospectively for their clinical utility.
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Affiliation(s)
- Yixuan He
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - David C. Qian
- Department of Radiation Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - James A. Diao
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02215
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Edwin K. Silverman
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Alexander Gusev
- Department of Medicine, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Arjun K. Manrai
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02215
| | - Alicia R. Martin
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Chirag J. Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02215
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11
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Han H, Hao L. Revealing lncRNA Biomarkers Related to Chronic Obstructive Pulmonary Disease Based on Bioinformatics. Int J Chron Obstruct Pulmon Dis 2022; 17:2487-2515. [PMID: 36217332 PMCID: PMC9547624 DOI: 10.2147/copd.s354634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 09/09/2022] [Indexed: 11/23/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a common chronic disease of the respiratory tract, with high prevalence, high disability, and poor prognosis. However, the molecular mechanism of COPD needs to be further revealed. Methods We obtained the gene expression profile and miRNA expression profile of COPD patients from Gene Expression Omnibus (GEO) database, and the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmis) in COPD were identified. Subsequently, the COPD-related ceRNA network was constructed based on the interaction between lncRNA, miRNA, and mRNA using the lncACTdb database. Finally, the Cytoscape software was used to analyze the network topology and COPD-related lncRNAs. Results Firstly, the 519 DEGs and 17 DEmis were identified from COPD GEO datasets. GO enrichment showed that leukocyte chemotaxis, cell chemotaxis, and myeloid leukocyte migration were upregulated, and muscle and membrane repolarization-related biological progress were downregulated in COPD. KEGG pathway enrichment shows that the p53 pathway was upregulated in COPD. Hallmark enrichment showed that chronic neutrophil inflammation was a sign of the pathogenesis of COPD. Next, a ceRNA network including 93 DEGs, 2 DEmi, 463 lncRNAs, and 1157 DEG-lncRNA, DEmi-lncRNA, and DEmi-DEG interactions were obtained. The hub-lncRNA (the network is ranked in the top 10) as the core marker of COPD, including SNHG12, SLFNL1-AS1, KCNQ1OT1, XIST, EAF1-AS1, FOXD2-AS1, NORAD, PINK1-AS and RP11-69E11.4. And the cytoHubba analysis identified ATM, SMAD7 and HIF1A as hub genes of ceRNA network. Conclusion This study provides a landscape of ceRNA network of COPD, which help to reveal the underlying pathophysiological mechanisms of COPD and shed light on novel therapeutic strategies for COPD.
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Affiliation(s)
- Hui Han
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, People’s Republic of China
| | - Lu Hao
- Department of Respiratory and Critical Care Medicine, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, People’s Republic of China,Correspondence: Lu Hao, Area B, Department of Respiratory Medicine, Affiliated Hospital of Inner Mongolia Medical University, No. 1 Tongdao North Street, Huimin District, Hohhot, 010010, Inner Mongolia Autonomous Region, People’s Republic of China, Email
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