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Biomedicines
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Advances in Genetic Research of Chronic Obstructive Pulmonary Disease(COPD)
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Advances in Genetic Research of Chronic Obstructive Pulmonary Disease(COPD)

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular Genetics and Genetic Diseases".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 9021

Special Issue Editors

Prof. Dr. Don D. Sin

E-Mail Website
Guest Editor
Department of Medicine (Respirology), University of British Columbia & Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC V6Z1Y6, Canada
Interests: COPD; genetics; epigenetics; biomarkers; lung health; knowledge translation
Dr. Ana I. Hernandez Cordero

E-Mail Website
Guest Editor
Centre for Heart Lung Innovation, University of British Columbia, St. Paul's Hospital, Vancouver, BC V6Z1Y6, Canada
Interests: COPD; genetics; epigenetics; biomarkers

Special Issue Information

Dear Colleagues,

We are in the golden age of genomic medicine, which promises novel therapeutic and biomarker discoveries for complex disorders such as chronic obstructive pulmonary disease (COPD). Over the past two decades, research has shown that 30% to 50% of the risk in COPD and its phenotypes is related to individuals’ underlying genetic architecture. However, only SERPINA1 has been unequivocally shown to be a causal genetic risk factor for COPD. With the advent of genome-wide association studies (GWASs) and more recently high-throughput exome and whole-genome sequencing, new risk alleles are being elucidated at an unprecedented rate. Researchers around the world are working feverishly to understand the functional and translational importance of newly discovered genetic variants using novel genomic and epigenetic approaches.

We thus invite investigators to submit their best papers to advance personalized medicine in COPD through genetic, genomic and epigenetic research. We welcome both original research and review manuscripts. Topics of interest in this Special Issue of Biomedicines include but are not limited to the biological characterization of genes in COPD; gene dysfunction; the identification of COPD biomarkers or phenotypes through genetics, methylation, spatial profiling or multi-omics; the role of COPD genetic research in personalized medicine; the identification of novel expression or methylation quantitative trait loci (QTLs) and the detailed characterization of cellular subpopulations of cells in lungs using single-cell RNA sequencing or other technologies.

We also invite authors to send us queries to resolve any ambiguities in the instructions or to determine the potential fit of the proposed article to this series. We expect that these papers will significantly move the field forward, with the ultimate goal of improving the lives of the millions of patients who suffer from COPD worldwide. Despite advances in its management over the past three decades, COPD remains one of the top five causes of mortality and hospitalization worldwide. We believe that advances in genetic research will usher in a new era of personalized medicine for our COPD patients.

Prof. Dr. Don D. Sin
Dr. Ana I. Hernandez Cordero
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomedicines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • COPD
  • genes
  • biomarkers
  • omics
  • knowledge translation

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Published Papers (4 papers)

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13 pages, 1518 KiB  
Article
Systemic and Airway Epigenetic Disruptions Are Associated with Health Status in COPD
by Ana I. Hernandez Cordero, Xuan Li, Chen Xi Yang, Julia Yang, Julia L. MacIsaac, Kristy Dever, Michael S. Kobor, Stephen Milne, Stephan F. van Eeden, Tawimas Shaipanich, Stephen Lam, Janice M. Leung and Don D. Sin
Biomedicines 2023, 11(1), 134; https://doi.org/10.3390/biomedicines11010134 - 5 Jan 2023
Cited by 3 | Viewed by 1910
Abstract
Epigenetic modifications are common in chronic obstructive pulmonary disease (COPD); however, their clinical relevance is largely unknown. We hypothesized that epigenetic disruptions are associated with symptoms and health status in COPD. We profiled the blood (n = 57) and airways (n [...] Read more.
Epigenetic modifications are common in chronic obstructive pulmonary disease (COPD); however, their clinical relevance is largely unknown. We hypothesized that epigenetic disruptions are associated with symptoms and health status in COPD. We profiled the blood (n = 57) and airways (n = 62) of COPD patients for DNA methylation (n = 55 paired). The patients’ health status was assessed using the St. George’s Respiratory Questionnaire (SGRQ). We conducted differential methylation analyses and identified pathways characterized by epigenetic disruptions associated with SGRQ scores and its individual domains. 29,211 and 5044 differentially methylated positions (DMPs) were associated with total SGRQ scores in blood and airway samples, respectively. The activity, impact, and symptom domains were associated with 9161, 25,689 and 17,293 DMPs in blood, respectively; and 4674, 3730 and 5063 DMPs in airways, respectively. There was a substantial overlap of DMPs between airway and blood. DMPs were enriched for pathways related to common co-morbidities of COPD (e.g., ageing, cancer and neurological) in both tissues. Health status in COPD is associated with airway and systemic epigenetic changes especially in pathways related to co-morbidities of COPD. There are more blood DMPs than in the airways suggesting that blood epigenome is a promising source to discover biomarkers for clinical outcomes in COPD. Full article
(This article belongs to the Special Issue Advances in Genetic Research of Chronic Obstructive Pulmonary Disease(COPD))
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23 pages, 3402 KiB  
Article
TLR5 Variants Are Associated with the Risk for COPD and NSCLC Development, Better Overall Survival of the NSCLC Patients and Increased Chemosensitivity in the H1299 Cell Line
by Jurica Baranašić, Maja Šutić, Calogerina Catalano, Gordana Drpa, Stefanie Huhn, Dragomira Majhen, Davor Nestić, Matea Kurtović, Lada Rumora, Martina Bosnar, Andrea Vukić Dugac, Irena Sokolović, Sanja Popovic-Grle, Nada Oršolić, Sanda Škrinjarić-Cincar, Marko Jakopović, Miroslav Samaržija, Alexander N. R. Weber, Asta Försti and Jelena Knežević
Biomedicines 2022, 10(9), 2240; https://doi.org/10.3390/biomedicines10092240 - 9 Sep 2022
Cited by 1 | Viewed by 2372
Abstract
Chronic obstructive pulmonary disease (COPD) is considered as the strongest independent risk factor for lung cancer (LC) development, suggesting an overlapping genetic background in both diseases. A common feature of both diseases is aberrant immunity in respiratory epithelia that is mainly regulated by [...] Read more.
Chronic obstructive pulmonary disease (COPD) is considered as the strongest independent risk factor for lung cancer (LC) development, suggesting an overlapping genetic background in both diseases. A common feature of both diseases is aberrant immunity in respiratory epithelia that is mainly regulated by Toll-like receptors (TLRs), key regulators of innate immunity. The function of the flagellin-sensing TLR5 in airway epithelia and pathophysiology of COPD and LC has remained elusive. We performed case–control genetic association and functional studies on the importance of TLR5 in COPD and LC development, comparing Caucasian COPD/LC patients (n = 974) and healthy donors (n = 1283). Association analysis of three single nucleotide polymorphisms (SNPs) (rs725084, rs2072493_N592S, and rs5744174_F616L) indicated the minor allele of rs2072493_N592S to be associated with increased risk for COPD (OR = 4.41, p < 0.0001) and NSCLC (OR = 5.17, p < 0.0001) development and non-small cell LC risk in the presence of COPD (OR = 1.75, p = 0.0031). The presence of minor alleles (rs5744174 and rs725084) in a co-dominant model was associated with overall survival in squamous cell LC patients. Functional analysis indicated that overexpression of the rs2072493_N592S allele affected the activation of NF-κB and AP-1, which could be attributed to impaired phosphorylation of p38 and ERK. Overexpression of TLR5N592S was associated with increased chemosensitivity in the H1299 cell line. Finally, genome-wide transcriptomic analysis on WI-38 and H1299 cells overexpressing TLR5WT or TLR5N592S, respectively, indicated the existence of different transcription profiles affecting several cellular pathways potentially associated with a dysregulated immune response. Our results suggest that TLR5 could be recognized as a potential biomarker for COPD and LC development with functional relevance. Full article
(This article belongs to the Special Issue Advances in Genetic Research of Chronic Obstructive Pulmonary Disease(COPD))
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10 pages, 1944 KiB  
Communication
Whole-Exome Sequencing of Bronchial Epithelial Cells Reveals a Genetic Print of Airway Remodelling in COPD
by Adeline Germain, Jeanne-Marie Perotin, Gonzague Delepine, Myriam Polette, Gaëtan Deslée and Valérian Dormoy
Biomedicines 2022, 10(7), 1714; https://doi.org/10.3390/biomedicines10071714 - 15 Jul 2022
Cited by 2 | Viewed by 1792
Abstract
The remodelling of the airways is a hallmark of chronic obstructive pulmonary disease, but it is highly heterogeneous and erratically distributed in the airways. To assess the genetic print of remodelling in chronic obstructive pulmonary disease (COPD), we performed a comparative whole-exome sequencing [...] Read more.
The remodelling of the airways is a hallmark of chronic obstructive pulmonary disease, but it is highly heterogeneous and erratically distributed in the airways. To assess the genetic print of remodelling in chronic obstructive pulmonary disease (COPD), we performed a comparative whole-exome sequencing analysis on microdissected bronchial epithelia. Lung resections from four non-COPD and three COPD subjects (ex-smokers and current smokers) were formalin-fixed paraffin-embedded (FFPE). Non-remodelled and remodelled bronchial epithelia were isolated by laser microdissection. Genomic DNA was captured and sequenced. The comparative quantitative analysis identified a list of 109 genes as having variants in remodelled epithelia and 160 genes as having copy number alterations in remodelled epithelia, mainly in COPD patients. The functional analysis highlighted cilia-associated processes. Therefore, bronchial-remodelled epithelia appeared genetically more altered than non-remodelled epithelia. Characterizing the unique molecular print of airway remodelling in respiratory diseases may help uncover additional factors contributing to epithelial dysfunctions, ultimately providing additional targetable proteins to correct epithelial remodelling and improve lung function. Full article
(This article belongs to the Special Issue Advances in Genetic Research of Chronic Obstructive Pulmonary Disease(COPD))
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7 pages, 1033 KiB  
Brief Report
The Blood DNA Methylation Clock GrimAge Is a Robust Surrogate for Airway Epithelia Aging
by Ana I. Hernandez Cordero, Chen Xi Yang, Xuan Li, Julia Yang, Tawimas Shaipanich, Julie L. MacIsaac, David T. S. Lin, Michael S. Kobor, Steve Horvath, Shu Fan Paul Man, Don D. Sin and Janice M. Leung
Biomedicines 2022, 10(12), 3094; https://doi.org/10.3390/biomedicines10123094 - 1 Dec 2022
Cited by 7 | Viewed by 2390
Abstract
One key feature of Chronic Obstructive Pulmonary Disease (COPD) is that its prevalence increases exponentially with age. DNA methylation clocks have become powerful biomarkers to detect accelerated aging in a variety of diseases and can help prognose outcomes in severe COPD. This study [...] Read more.
One key feature of Chronic Obstructive Pulmonary Disease (COPD) is that its prevalence increases exponentially with age. DNA methylation clocks have become powerful biomarkers to detect accelerated aging in a variety of diseases and can help prognose outcomes in severe COPD. This study investigated which DNA methylation clock could best reflect airway epigenetic age when used in more accessible blood samples. Our analyses showed that out of six DNA methylation clocks investigated, DNAmGrimAge demonstrated the strongest correlation and the smallest difference between the airway epithelium and blood. Our findings suggests that blood DNAmGrimAge accurately reflects airway epigenetic age of individuals and that its elevation is highly associated with COPD. Full article
(This article belongs to the Special Issue Advances in Genetic Research of Chronic Obstructive Pulmonary Disease(COPD))
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