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Li TT, Bai HY, Zhang JH, Kang XH, Qu YQ. Identification and Validation of Aging Related Genes Signature in Chronic Obstructive Pulmonary Disease. COPD 2024; 21:2379811. [PMID: 39138958 DOI: 10.1080/15412555.2024.2379811] [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] [Received: 03/10/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 08/15/2024]
Abstract
PURPOSE Chronic Obstructive Pulmonary Disease (COPD) is regarded as an accelerated aging disease. Aging-related genes in COPD are still poorly understood. METHOD Data set GSE76925 was obtained from the Gene Expression Omnibus (GEO) database. The "limma" package identified the differentially expressed genes. The weighted gene co-expression network analysis (WGCNA) constructes co-expression modules and detect COPD-related modules. The least absolute shrinkage and selection operator (LASSO) and the support vector machine recursive feature elimination (SVM-RFE) algorithms were chosen to identify the hub genes and the diagnostic ability. Three external datasets were used to identify differences in the expression of hub genes. Real-time reverse transcription polymerase chain reaction (RT-qPCR) was used to verify the expression of hub genes. RESULT We identified 15 differentially expressed genes associated with aging (ARDEGs). The SVM-RFE and LASSO algorithms pinpointed four potential diagnostic biomarkers. Analysis of external datasets confirmed significant differences in PIK3R1 expression. RT-qPCR results indicated decreased expression of hub genes. The ROC curve demonstrated that PIK3R1 exhibited strong diagnostic capability for COPD. CONCLUSION We identified 15 differentially expressed genes associated with aging. Among them, PIK3R1 showed differences in external data sets and RT-qPCR results. Therefore, PIK3R1 may play an essential role in regulating aging involved in COPD.
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Affiliation(s)
- Tian-Tian Li
- Department of Pulmonary and Critical Care Medicine, Shandong Key Laboratory of Infectious Respiratory Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Hong-Yan Bai
- Department of Pulmonary and Critical Care Medicine, Shandong Key Laboratory of Infectious Respiratory Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Jing-Hong Zhang
- Department of Pulmonary and Critical Care Medicine, Shandong Key Laboratory of Infectious Respiratory Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Xiu-He Kang
- Department of Pulmonary and Critical Care Medicine, Shandong Key Laboratory of Infectious Respiratory Diseases, Qilu Hospital of Shandong University, Jinan, China
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Shandong Key Laboratory of Infectious Respiratory Diseases, Qilu Hospital of Shandong University, Jinan, China
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Zhang Y, Liu C. Transcriptomic analysis of mRNAs in human whole blood identified age-specific changes in healthy individuals. Medicine (Baltimore) 2023; 102:e36486. [PMID: 38065846 PMCID: PMC10713173 DOI: 10.1097/md.0000000000036486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Older age is one of the most important shared risk factors for multiple chronic diseases, increasing the medical burden to contemporary societies. Current research focuses on identifying aging biomarkers to predict aging trajectories and developing interventions aimed at preventing and delaying the progression of multimorbidity with aging. Here, a transcriptomic changes analysis of whole blood genes with age was conducted. The age-related whole blood gene-expression profiling datasets were downloaded from the Gene Expression Omnibus (GEO) database. We screened the differentially expressed genes (DEGs) between healthy young and old individuals and performed functional enrichment analysis. Cytoscape with Cytohubba and MCODE was used to perform an interaction network of DEGs and identify hub genes. In addition, ROC curves and correlation analysis were used to evaluate the accuracy of hub genes. In total, we identified 29 DEGs between young and old samples that were enriched mainly in immunoglobulin binding and complex, humoral immune response, and immune response-activating signaling pathways. In combination with the PPI network and topological analysis, 4 hub genes (IGLL5, Jchain, POU2AF1, and Bach2) were identified. Pearson analysis showed that the expression changes of these hub genes were highly correlated with age. Among them, 3 hub genes (IGLL5, POU2AF1, and Bach2) were identified with good accuracy (AUC score > 0.7), indicating that these genes were the best indicators of age. Together, our results provided potential biomarkers IGLL5, POU2AF1, and Bach2 to identify individuals at high early risk of age-related disease to be targeted for early interventions and contribute to understanding the molecular mechanisms in the progression of aging.
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Affiliation(s)
- Yan Zhang
- Department of Ophthalmology, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chonghui Liu
- College of Life Science, Northeast Forestry University, Harbin, China
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Kim SH, Lee H, Kim Y, Rhee CK, Min KH, Hwang YI, Kim DK, Park YB, Yoo KH, Moon JY. Recent Prevalence of and Factors Associated With Chronic Obstructive Pulmonary Disease in a Rapidly Aging Society: Korea National Health and Nutrition Examination Survey 2015-2019. J Korean Med Sci 2023; 38:e108. [PMID: 37038644 PMCID: PMC10086381 DOI: 10.3346/jkms.2023.38.e108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/03/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND The prevalence of chronic obstructive pulmonary disease (COPD) increases with age, and aging is an important risk factor for COPD development. In the era of global aging, demographic information about the prevalence of and factors associated with COPD are important to establish COPD care plans. However, limited information is available in rapidly aging societies, including Korea. METHODS We conducted a cross-sectional observational study using Korea National Health and Nutrition Examination Survey data from 2015-2019. We included 15,613 participants and analyzed trends of and factors associated with COPD. RESULTS During the study period, the overall prevalence of COPD was 12.9%. Over five years, the yearly prevalence of COPD was fairly constant, ranging from 11.5% to 13.6%. Among individuals aged ≥ 70 years, nearly one-third met COPD diagnostic criteria. In the multivariable analysis, age 70 years or older was the most strong factor associated with COPD (adjusted odds ratio [aOR], 17.86; 95% confidence interval [CI], 14.16-22.52; compared with age 40-49), followed by asthma (aOR, 3.39; 95% CI, 2.44-4.71), male sex (aOR, 2.64; 95% CI, 2.18-3.19), and current smokers (aOR, 2.60; 95% CI, 2.08-3.25). Additionally, ex-smokers, low income, decreased forced expiratory volume in 1 second %pred, and a history of pulmonary tuberculosis were associated with COPD. On the other hand, body mass index (BMI) ≥ 25 kg/m² (aOR, 0.62; 95% CI, 0.54-0.71; compared with BMI 18.5-24.9 kg/m²) had an inverse association with COPD. CONCLUSION Recent trends in the prevalence of COPD in South Korea are relatively stable. Approximately one-third of participants aged 70 years and older had COPD. Aging was the most important factor associated with COPD.
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Affiliation(s)
- Sang Hyuk Kim
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Dongguk University Gyeongju Hospital, Dongguk University College of Medicine, Gyeongju, Korea
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - Hyun Lee
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea
| | - Youlim Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - Chin Kook Rhee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyung Hoon Min
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Yong Il Hwang
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Sacred Heart Hospital, Anyang, Korea
| | - Deog Kyeom Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, Korea
| | - Yong Bum Park
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangdong Sacred Heart Hospital, Seoul, Korea
| | - Kwang Ha Yoo
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Konkuk University School of Medicine, Seoul, Korea
| | - Ji-Yong Moon
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Korea.
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Wang Y, Su X, Yin Y, Wang Q. Identification and Analysis of Necroptosis-Related Genes in COPD by Bioinformatics and Experimental Verification. Biomolecules 2023; 13:biom13030482. [PMID: 36979417 PMCID: PMC10046193 DOI: 10.3390/biom13030482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/16/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a heterogeneous and complex progressive inflammatory disease. Necroptosis is a newly identified type of programmed cell death. However, the role of necroptosis in COPD is unclear. This study aimed to identify necroptosis-related genes in COPD and explore the roles of necroptosis and immune infiltration through bioinformatics. The analysis identified 49 differentially expressed necroptosis-related genes that were primarily engaged in inflammatory immune response pathways. The infiltration of CD8+ T cells and M2 macrophages in COPD lung tissue was relatively reduced, whereas that of M0 macrophages was increased. We identified 10 necroptosis-related hub genes significantly associated with infiltrated immune cells. Furthermore, 7 hub genes, CASP8, IL1B, RIPK1, MLKL, XIAP, TNFRSF1A, and CFLAR, were validated using an external dataset and experimental mice. CFLAR was considered to have the best COPD-diagnosing capability. TF and miRNA interactions with common hub genes were identified. Several related potentially therapeutic molecules for COPD were also identified. The present findings suggest that necroptosis occurs in COPD pathogenesis and is correlated with immune cell infiltration, which indicates that necroptosis may participate in the development of COPD by interacting with the immune response.
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Affiliation(s)
- Yingxi Wang
- Institute of Respiratory Disease, Department of Pulmonary and Critical Care Medicine, The First Hospital of China Medical University, Shenyang 110001, China
| | - Xin Su
- Department of Plastic Surgery, The First Hospital of China Medical University, Shenyang 110001, China
| | - Yan Yin
- Institute of Respiratory Disease, Department of Pulmonary and Critical Care Medicine, The First Hospital of China Medical University, Shenyang 110001, China
- Correspondence: (Y.Y.); (Q.W.)
| | - Qiuyue Wang
- Institute of Respiratory Disease, Department of Pulmonary and Critical Care Medicine, The First Hospital of China Medical University, Shenyang 110001, China
- Correspondence: (Y.Y.); (Q.W.)
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Yang Y, Cao Y, Han X, Ma X, Li R, Wang R, Xiao L, Xie L. Revealing EXPH5 as a potential diagnostic gene biomarker of the late stage of COPD based on machine learning analysis. Comput Biol Med 2023; 154:106621. [PMID: 36746116 DOI: 10.1016/j.compbiomed.2023.106621] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/19/2023] [Accepted: 01/28/2023] [Indexed: 02/01/2023]
Abstract
Chronic obstructive pulmonary disease is a kind of chronic lung disease characterized by persistent air flow obstruction, which was the third leading cause of death in China. The incidence of COPD is steadily and increasing and has been a globally sever disease. Accordingly, it is urgently needed to explore how to diagnose and treat COPD timely. This study aims to find key genes to diagnose COPD as soon as possible to avoid COPD processing and analyze immune cell infiltration between COPD early stage and late stage. Two GEO datasets were merged as the merge data for analyses. 157 DEGs were used for GSEA analysis to find the pathway between COPD early stage and late stage. Above all, gene EXPH5 stood out from the screen as the most likely candidate diagnosis biomarker of COPD indicating the late-stage by least LASSO and SVM-RFE. ROC curves of EXPH5 were applied to represent the discriminatory ability through the area under the curve which is the gold standard to evaluate the accuracy of diagnosis and survival rate. The CIBERSORT algorithm was used to assess the distribution of tissue-infiltrating immune cells between two COPD stages. The diagnosis biomarker, gene EXPH5 had a positive correlation with NK cells resting; mast cell resting, eosinophils, and negative correlation with T cell gamma delta, macrophages M1, which underscore the role of gene and immune cell infiltration. To make results more reliable, we further analyzed the gene EXPH5 expression in single-cell transcriptome data and showed again that EXPH5 genes significantly downregulated in the late stage of COPD especially in the main lung cell types AT1 and AT2. In a word, our study identified genes EXPH5 as a marker gene, which adds to the knowledge for clinical diagnosis and pharmaceutical design of COPD.
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Affiliation(s)
- Yuwei Yang
- College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100091, China; Beijing Key Laboratory of OTIR, Beijing, 100091, China.
| | - Yan Cao
- College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100091, China; Beijing Key Laboratory of OTIR, Beijing, 100091, China.
| | - Xiaobo Han
- College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100091, China; Beijing Key Laboratory of OTIR, Beijing, 100091, China.
| | - Xihui Ma
- College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100091, China; Beijing Key Laboratory of OTIR, Beijing, 100091, China.
| | - Rui Li
- College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100091, China; Hebei North Universit, Zhangjiakou, 075000, China.
| | - Rentao Wang
- College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100091, China; Beijing Key Laboratory of OTIR, Beijing, 100091, China.
| | - Li Xiao
- College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100091, China; Beijing Key Laboratory of OTIR, Beijing, 100091, China.
| | - Lixin Xie
- College of Pulmonary & Critical Care Medicine, Chinese PLA General Hospital, Beijing, 100091, China; Beijing Key Laboratory of OTIR, Beijing, 100091, China.
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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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