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Recent Advances in Genetics and Genomics of Pulmonary Diseases

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A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Genetics".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 9106

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Special Issue Editor

Dr. Matija Rijavec

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Guest Editor

Laboratory for Clinical Immunology and Molecular Genetics, University Clinic of Respiratory and Allergic Diseases, 4204 Golnik, Slovenia
Interests: human genetics; human genomics; transcriptomics; next-generation sequencing; allergology; in vitro allergology testing

Special Issue Information

Dear Colleagues,

This Special Issue will focus on recent advances in the genetics and genomics of pulmonary diseases. Some pulmonary diseases, such as cystic fibrosis, are monogenic and hence inherited in classical Mendelian fashion, while for others, such as asthma and chronic obstructive pulmonary disease, genetic factors contribute to disease development and susceptibility. Genetic factors can also increase the risk of respiratory infections. Over the last decade, the increased use of high-throughput technologies, including genomics and transcriptomics, have expanded our knowledge of underlying mechanisms. Characterization of the pathophysiology and identifying novel genetic variants underlying the development and progression of pulmonary diseases will lead to the development of new therapeutic strategies toward improving the clinical management of affected patients.

This Special Issue, “Recent Advances in Genetics and Genomics of Pulmonary Diseases”, will address novel insights into the genetics and pharmacogenetics of a plethora of pulmonary diseases, including but not limited to asthma, α1-antitrypsin deficiency, bronchiectasis, chronic obstructive pulmonary disease, cystic fibrosis, emphysema, lung cancer, primary ciliary dyskinesia, pulmonary fibrosis, sarcoidosis, recurrent respiratory infections, and tuberculosis. Moreover, the contribution of the microbiome to the development and progress of pulmonary diseases are also topics of interest in this field.

We welcome original research and review papers that will improve our understanding of the underlying molecular mechanisms and genetic basis of pulmonary diseases.

Dr. Matija Rijavec
Guest Editor

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. Biomolecules 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 2700 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

pulmonary disease
genomics
pharmacogenomic
transcriptomics

Published Papers (3 papers)

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Research

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15 pages, 2486 KiB

Open AccessArticle

Differential Gene Expression Induced by Different TLR Agonists in A549 Lung Epithelial Cells Is Modulated by CRISPR Activation of TLR10

by Špela Knez, Mojca Narat and Jernej Ogorevc

Biomolecules 2023, 13(1), 19; https://doi.org/10.3390/biom13010019 - 22 Dec 2022

Cited by 2 | Viewed by 2078

Abstract

Toll-like receptor 10 (TLR10) is the only member of the TLR family whose function and ligand have not been clearly described. Literature reports on its function are contradictory and suggest a possible immunomodulatory role that depends on the cell type, the pathogen, and the level of TLR10 expression. To investigate the regulatory role of TLR10 in A549 lung epithelial cells, we overexpressed TLR10 using CRISPRa technology and examined the differential expression of various genes involved in TLR signaling activated by different TLR ligands, namely dsRNA, LPS, and Pam3Cys. The expression of proinflammatory cytokines, such as IL1β, IFNβ, TNFα, IL8, CXCL10, and CCL20, decreased in the challenged cells overexpressing TLR10, whereas the expression of the anti-inflammatory cytokine IL10 and the antimicrobial peptide hβD-2 increased. For several of the regulated inflammatory markers, we were able to show the change in gene expression was translated to the protein level. It appears that TLR10 can function as an anti-inflammatory in A549 cells, depending on its expression level and that the mode of action may be virulence factor-specific. The potential suppression of inflammation by regulating expression of TLR10 in lung epithelial cells may allow the development of new approaches to balance an inflammatory response and prevent extensive tissue damage in respiratory diseases. Full article

(This article belongs to the Special Issue Recent Advances in Genetics and Genomics of Pulmonary Diseases)

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13 pages, 3984 KiB

Open AccessArticle

Exome and Sputum Microbiota as Predictive Markers of Frequent Exacerbations in Chronic Obstructive Pulmonary Disease

by Linfan Su, Yixian Qiao, Jinmei Luo, Rong Huang and Yi Xiao

Biomolecules 2022, 12(10), 1481; https://doi.org/10.3390/biom12101481 - 14 Oct 2022

Cited by 2 | Viewed by 1605

Abstract

Frequent acute exacerbations are the leading cause of high rates of hospitalization and mortality in chronic obstructive pulmonary disease (COPD). Despite the enormous worldwide medical burden, reliable molecular markers for effective early diagnosis and prognosis of acute exacerbations are still lacking. Both the host genetics and airway microbiome are known to play potential roles in the pathogenesis of frequent exacerbations. Here, we performed whole exome sequencing (WES) and 16S rRNA gene sequencing to explore the interaction between these two factors and their implications in the pathogenesis of frequent exacerbations. We collected peripheral blood (n = 82), sputum samples (n = 59) and clinical data from 50 frequent-exacerbation phenotype (FE) COPD patients and 32 infrequent-exacerbation phenotype (IE) as controls. Based on filtering the deleterious sites, candidate mutated genes shared only in FE patients and did not occur in the IE group were identified. Microbiota analysis revealed significant differences in bacterial diversity and composition between FE and IE groups. We report the underlying pathogenic gene including, AATF, HTT, CEP350, ADAMTS9, TLL2 genes, etc., and explore their possible genotypic-phenotypic correlations with microbiota dysbiosis. Importantly, we observed that AATF gene mutations were significantly negatively correlated with microbial richness and diversity. Our study indicated several deleterious mutations in candidate genes that might be associated with microbial dysbiosis and the increased risk of frequent acute exacerbations in COPD patients. These results provide novel evidence that exomes and related microbiomes may potentially serve as biomarkers for predicting frequent acute exacerbations in COPD patients. Full article

(This article belongs to the Special Issue Recent Advances in Genetics and Genomics of Pulmonary Diseases)

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Review

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21 pages, 885 KiB

Open AccessReview

Molecular Pathogenesis of Fibrosis, Thrombosis and Surfactant Dysfunction in the Lungs of Severe COVID-19 Patients

by Adrian Krygier, Dagmara Szmajda-Krygier, Rafał Świechowski, Jacek Pietrzak, Agnieszka Wosiak, Damian Wodziński and Ewa Balcerczak

Biomolecules 2022, 12(12), 1845; https://doi.org/10.3390/biom12121845 - 10 Dec 2022

Cited by 7 | Viewed by 4654

Abstract

The global scope and scale of the SARS-CoV-2 pandemic led to huge amounts of important data from clinical observations and experimental analyses being collected, in particular, regarding the long-term impact of COVID-19 on lung tissue. Visible changes in lung tissue mainly relate to the destruction of the alveolar architecture, dense cellularity, and pulmonary fibrosis with myofibroblast proliferation and collagen deposition. These changes are the result of infection, mainly with virus variants from the first pandemic waves (Alpha to Delta). In addition, proper regulation of immune responses to pathogenic viral stimuli is critical for the control of and recovery from tissue/organ damage, including in the lungs. We can distinguish three main processes in the lungs during SARS-CoV-2 infection: damage or deficiency of the pulmonary surfactant, coagulation processes, and fibrosis. Understanding the molecular basis of these processes is extremely important in the context of elucidating all pathologies occurring after virus entry. In the present review, data on the abovementioned three biochemical processes that lead to pathological changes are gathered together and discussed. Systematization of the knowledge is necessary to explore the three key pathways in lung tissue after SARS-CoV-2 virus infection as a result of a prolonged and intense inflammatory process in the context of pulmonary fibrosis, hemostatic disorders, and disturbances in the structure and/or metabolism of the surfactant. Despite the fact that the new Omicron variant does not affect the lungs as much as the previous variants, we cannot ignore the fact that other new mutations and emerging variants will not cause serious damage to the lung tissue. In the future, this review will be helpful to stratify the risk of serious complications in patients, to improve COVID-19 treatment outcomes, and to select those who may develop complications before clinical manifestation. Full article

(This article belongs to the Special Issue Recent Advances in Genetics and Genomics of Pulmonary Diseases)

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