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      International Journal of COPD (submit here)

      This international, peer-reviewed Open Access journal by Dove Medical Press focuses on pathophysiological processes underlying Chronic Obstructive Pulmonary Disease (COPD) interventions, patient focused education, and self-management protocols. Sign up for email alerts here.

      39,063 Monthly downloads/views I 2.893 Impact Factor I 5.2 CiteScore I 1.16 Source Normalized Impact per Paper (SNIP) I 0.804 Scimago Journal & Country Rank (SJR)

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      Identification and Validation of Autophagy-Related Genes in Chronic Obstructive Pulmonary Disease

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          Abstract

          Purpose

          Autophagy plays essential roles in the development of COPD. We aim to identify and validate the potential autophagy-related genes of COPD through bioinformatics analysis and experiment validation.

          Methods

          The mRNA expression profile dataset GSE38974 was obtained from GEO database. The potential differentially expressed autophagy-related genes of COPD were screened by R software. Then, protein–protein interactions (PPI), correlation analysis, gene-ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied for the differentially expressed autophagy-related genes. Finally, RNA expression of top five differentially expressed autophagy-related genes was validated in blood samples from COPD patients and healthy controls by qRT-PCR.

          Results

          A total of 40 differentially expressed autophagy-related genes (14 up-regulated genes and 26 down-regulated genes) were identified between 23 COPD patients and 9 healthy controls. The PPI results demonstrated that these autophagy-related genes interacted with each other. The GO and KEGG enrichment analysis of differentially expressed autophagy-related genes indicated several enriched terms related to autophagy and mitophagy. The results of qRT-PCR showed that the expression levels of HIF1A, CDKN1A, BAG3, ERBB2 and ATG16L1 in COPD patients and healthy controls were consistent with the bioinformatics analysis results from mRNA microarray.

          Conclusion

          We identified 40 potential autophagy-related genes of COPD through bioinformatics analysis. HIF1A, CDKN1A, BAG3, ERBB2 and ATG16L1 may affect the development of COPD by regulating autophagy. These results may expand our understanding of COPD and might be useful in the treatment of COPD.

          Most cited references31

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          Molecular definitions of autophagy and related processes.

          Lorenzo Galluzzi, Eric H. Baehrecke, Andrea Ballabio … (2017)
          Over the past two decades, the molecular machinery that underlies autophagic responses has been characterized with ever increasing precision in multiple model organisms. Moreover, it has become clear that autophagy and autophagy-related processes have profound implications for human pathophysiology. However, considerable confusion persists about the use of appropriate terms to indicate specific types of autophagy and some components of the autophagy machinery, which may have detrimental effects on the expansion of the field. Driven by the overt recognition of such a potential obstacle, a panel of leading experts in the field attempts here to define several autophagy-related terms based on specific biochemical features. The ultimate objective of this collaborative exchange is to formulate recommendations that facilitate the dissemination of knowledge within and outside the field of autophagy research.
          Article 0 comments Cited 398 times – based on 0 reviews     Review now
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            Chronic obstructive pulmonary disease.

            Klaus F Rabe, Henrik Watz (2017)
            Chronic obstructive pulmonary disease (COPD) kills more than 3 million people worldwide every year. Despite progress in the treatment of symptoms and prevention of acute exacerbations, few advances have been made to ameliorate disease progression or affect mortality. A better understanding of the complex disease mechanisms resulting in COPD is needed. Smoking cessation programmes, increasing physical activity, and early detection and treatment of comorbidities are further key components to reduce the burden of the disease. However, without a global political and economic effort to reduce tobacco use, to regulate environmental exposure, and to find alternatives to the massive use of biomass fuel, COPD will remain a major health-care problem for decades to come.
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              Pathogenesis of chronic obstructive pulmonary disease (COPD) induced by cigarette smoke

              Mari Hikichi, Kenji Mizumura, Shuichiro Maruoka … (2019)
              Chronic obstructive pulmonary disease (COPD) is a common respiratory disease that is characterized by functional and structural alterations primarily caused by long-term inhalation of harmful particles. Cigarette smoke (CS) induces airway inflammation in COPD, which is known to persist even after smoking cessation. This review discusses the basic pathogenesis of COPD, with particular focus on an endogenous protective mechanism against oxidative stress via Nrf2, altered immune response of the airway inflammatory cells, exaggerated cellular senescence of the lung structural cells, and cell death with expanded inflammation. Recently, CS-induced mitochondria autophagy is reported to initiate programmed necrosis (necroptosis). Necroptosis is a new concept of cell death which is driven by a defined molecular pathway along with exaggerated inflammation. This new cell death mechanism is of importance due to its ability to produce more inflammatory substances during the process of epithelial death, contributing to persistent airway inflammation that cannot be explained by apoptosis-derived cell death. Autophagy is an auto-cell component degradation system executed by lysosomes that controls protein and organelle degradation for successful homeostasis. As well as in the process of necroptosis, autophagy is also observed during cellular senescence. Aging of the lungs results in the acquisition of senescence-associated secretory phenotypes (SASP) that are known to secrete inflammatory cytokines, chemokines, growth factors, and matrix metalloproteinases resulting in chronic low-grade inflammation. In future research, we intend to highlight the genetic and epigenetic approaches that can facilitate the understanding of disease susceptibility. The goal of precision medicine is to establish more accurate diagnosis and treatment methods based on the patient-specific pathogenic characteristics. This review provides insights into CS-induced COPD pathogenesis, which contributes to a very complex disease. Investigating the mechanism of developing COPD, along with the availability of the particular inhibitors, will lead to new therapeutic approaches in COPD treatment.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Int J Chron Obstruct Pulmon Dis
                Journal ID (iso-abbrev): Int J Chron Obstruct Pulmon Dis
                Journal ID (publisher-id): copd
                Journal ID (pmc): copd
                Title: International Journal of Chronic Obstructive Pulmonary Disease
                Publisher: Dove
                ISSN (Print): 1176-9106
                ISSN (Electronic): 1178-2005
                Publication date (Electronic): 12 January 2021
                Publication date Collection: 2021
                Volume: 16
                Pages: 67-78
                Affiliations
                [1 ]Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital , Tianjin 300052, People’s Republic of China
                Author notes
                Correspondence: Jing Zhang Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital , 154 Anshan Road, Heping District, Tianjin300052, People’s Republic of ChinaTel +86-22-60361612Fax +86-22-60361720 Email tjzyyzhangjing@163.com
                Article
                Publisher ID: 288428
                DOI: 10.2147/COPD.S288428
                PMC ID: 7811454
                PubMed ID: 33469280
                SO-VID: 965e1f32-9596-4421-b2aa-0e52be273035
                Copyright © © 2021 Sun et al.
                License:

                This work is published and licensed by Dove Medical Press Limited. The full terms of this license are available at https://www.dovepress.com/terms.php and incorporate the Creative Commons Attribution – Non Commercial (unported, v3.0) License ( http://creativecommons.org/licenses/by-nc/3.0/). By accessing the work you hereby accept the Terms. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. For permission for commercial use of this work, please see paragraphs 4.2 and 5 of our Terms ( https://www.dovepress.com/terms.php).

                History
                Date received : 23 October 2020
                Date accepted : 30 December 2020
                Page count
                Figures: 7, Tables: 4, References: 31, Pages: 12
                Categories
                Subject: Original Research

                ScienceOpen disciplines: Respiratory medicine
                Keywords: autophagy,copd,bioinformatics analysis,gene expression omnibus dataset
                Data availability:
                ScienceOpen disciplines: Respiratory medicine
                Keywords: autophagy, copd, bioinformatics analysis, gene expression omnibus dataset

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