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Molecular Biomarkers of Pulmonary Diseases
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Molecular Biomarkers of Pulmonary Diseases

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (26 February 2021) | Viewed by 20467

Special Issue Editor

Dr. Jelena Knezevic

E-Mail Website
Guest Editor
Institute Ruder Boskovic, 10000 Zagreb, Croatia
Interests: genetic diversity of innate immunity; molecular and genetic background of different disorders; functional characterization of genetic variants; naturally occurring variants of PRRs; chronic inflammation; COPD; lung cancer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Pulmonary diseases affect lungs and other parts of the respiratory system and are a leading cause of death worldwide. Pulmonary diseases include asthma, chronic obstructive pulmonary disease (COPD), pulmonary fibrosis, pneumonia, and lung cancer. They may be caused by infection of the respiratory system or by exposure to harmful substances, like smoking tobacco or other forms of air pollution. Persistent exposure to inhaled air pollutants, or frequent infections, in a certain number of individuals will lead to the development of the chronic inflammation of the airways, which is recognized as a major contributor to development of the most lethal pulmonary disease: lung cancer. It is well known that innate immune response is essential for maintaining lung health and tissue homeostasis, but unbalanced inflammation of the lungs is associated with diseased conditions. There is still a lack of knowledge how the genetic, epigenetic, and proteomic variability of specific molecules that orchestrate inflammation in the lungs contributes to the development of diseased conditions. Because of a global increase in pulmonary disease prevalence and the absence of specific therapeutic targets, the identification of specific molecular biomarkers and their involvement in diseased conditions will improve disease treatment at a personalized level.

In this Special Issue, we invite authors to discuss the epidemiology and genetic, epigenetic, and proteomic background of common pulmonary diseases, especially those related to the chronic inflammation and development of pulmonary malignancies, namely, pneumonia, chronic obstructive pulmonary disease, and idiopathic pulmonary fibrosis. We welcome reviews, mini-reviews, new methods, and original research articles.

Topics of interest include the following:

(a) The role of genetic, epigenetic, and proteomic specificities in pulmonary disease development and progression and its potential clinical implications for diagnosis, prognosis, and the prediction of therapeutic efficacies and outcomes;

(b) The discovery of new molecular biomarkers to monitor the treatment response and early detection of disease and the identification of mechanisms of response to therapy;

(c) Clinical trials related to different pulmonary diseases.

Dr. Jelena Knezevic
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. Genes 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

  • Pulmonary diseases
  • Genetic biomarkers
  • Epigenetics biomarkers
  • Proteomic biomarkers
  • Diagnosis, prognosis, and prediction
  • Therapy response
  • Early detection of disease
  • Clinical trials for pulmonary diseases

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Published Papers (5 papers)

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Research

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15 pages, 3312 KiB  
Article
Pilot Study to Detect Genes Involved in DNA Damage and Cancer in Humans: Potential Biomarkers of Exposure to E-Cigarette Aerosols
by Samera H. Hamad, Marielle C. Brinkman, Yi-Hsuan Tsai, Namya Mellouk, Kandice Cross, Ilona Jaspers, Pamela I. Clark and Courtney A. Granville
Genes 2021, 12(3), 448; https://doi.org/10.3390/genes12030448 - 22 Mar 2021
Cited by 12 | Viewed by 5279
Abstract
There is a paucity of data on how gene expression enables identification of individuals who are at risk of exposure to carcinogens from e-cigarette (e-cig) vaping; and how human vaping behaviors modify these exposures. This pilot study aimed to identify genes regulated from [...] Read more.
There is a paucity of data on how gene expression enables identification of individuals who are at risk of exposure to carcinogens from e-cigarette (e-cig) vaping; and how human vaping behaviors modify these exposures. This pilot study aimed to identify genes regulated from acute exposure to e-cig using RT-qPCR. Three subjects (2M and 1F) made three visits to the lab (nTOT = 9 visits); buccal and blood samples were collected before and immediately after scripted vaping 20 puffs (nTOT = 18 samples); vaping topography data were collected in each session. Subjects used their own e-cig containing 50:50 propylene glycol (PG):vegetable glycerine (VG) +3–6 mg/mL nicotine. The tumor suppressor TP53 was significantly upregulated in buccal samples. TP53 expression was puff volume and flow rate dependent in both tissues. In blood, the significant downregulation of N-methylpurine DNA glycosylase (MPG), a base excision repair gene, was consistent across all subjects. In addition to DNA repair pathway, cell cycle and cancer pathways were the most enriched pathways in buccal and blood samples, respectively. This pilot study demonstrates that vaping 20 puffs significantly alters expression of TP53 in human tissues; vaping behavior is an important modifier of this response. A larger study is needed to confirm these relationships. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Pulmonary Diseases)
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Graphical abstract

15 pages, 6927 KiB  
Article
Potential Impacts of Interleukin-17A Promoter Polymorphisms on the EGFR Mutation Status and Progression of Non-Small Cell Lung Cancer in Taiwan
by Kai-Ling Lee, Tsung-Ching Lai, Yao-Chen Wang, Pei-Chun Shih, Yi-Chieh Yang, Thomas Chang-Yao Tsao, Tu-Chen Liu, Yu-Ching Wen, Lun-Ching Chang, Shun-Fa Yang and Ming-Hsien Chien
Genes 2021, 12(3), 427; https://doi.org/10.3390/genes12030427 - 17 Mar 2021
Cited by 5 | Viewed by 2453
Abstract
Non-small cell lung cancer (NSCLC) is a typical inflammation-associated cancer, and lung adenocarcinoma (LUAD) is the most common histopathological subtype. Epidermal growth factor receptor (EGFR) mutations are the most common driver mutations of LUAD, and they have been identified as important therapeutic targets [...] Read more.
Non-small cell lung cancer (NSCLC) is a typical inflammation-associated cancer, and lung adenocarcinoma (LUAD) is the most common histopathological subtype. Epidermal growth factor receptor (EGFR) mutations are the most common driver mutations of LUAD, and they have been identified as important therapeutic targets by EGFR tyrosine kinase inhibitors. Interleukin (IL)-17A secreted by T-helper 17 lymphocytes is a proinflammatory cytokine that plays an important role in cancer pathogenesis. The present study was designed to investigate the possible associations among IL-17A genetic polymorphisms, EGFR mutation status, and the clinicopathologic development of LUAD in a Taiwanese population. Our study population consisted of 277 LUAD patients harboring the wild-type (WT) EGFR or a mutant (MT) EGFR. Four single-nucleotide polymorphisms (SNPs) of IL-17A in the peripheral blood, including rs8193036(C > T), rs8193037(G > A), rs2275913(G > A), and rs3748067(C > T) loci, were genotyped using a TaqMan allelic discrimination assay. Our results showed that none of these IL-17A SNPs were correlated with the risk of developing mutant EGFR. However, patients with a smoking habit who carried the GA genotype of IL-17A rs8193037 had a significantly lower susceptibility to EGFR mutations (adjusted odds ratio (AOR): 0.225; 95% confidence interval (CI): 0.056~0.900, p = 0.035). Moreover, compared to individuals carrying the CC genotype of rs8193036 at IL-17A, T-allele carriers (CT + TT) were at higher risk of developing more-advanced stages (stage III or IV; p = 0.020). In the WT EGFR subgroup analysis, IL-17A rs8193036 T-allele carriers had higher risks of developing an advanced tumor stage (p = 0.016) and lymphatic invasion (p = 0.049). Further analyses of clinical datasets revealed correlations of IL-17 receptor A (IL-17RA) and IL-17RC expressions with a poor prognosis of LUAD patients with a smoking history or with higher levels of tumor-infiltrating lymphocytes. In conclusion, our results suggested that two functional promoter polymorphisms of IL-17A, i.e., rs8193036 and rs8193037, were associated with the EGFR mutation status and progression in LUAD patients, indicating that these two genetic variants might act as possible markers for predicting patients’ clinical prognoses. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Pulmonary Diseases)
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17 pages, 3515 KiB  
Article
Identification and Validation of Potential miRNAs, as Biomarkers for Sepsis and Associated Lung Injury: A Network-Based Approach
by Shaniya Ahmad, Mohd Murshad Ahmed, P. M. Z. Hasan, Archana Sharma, Anwar L. Bilgrami, Kailash Manda, Romana Ishrat and Mansoor Ali Syed
Genes 2020, 11(11), 1327; https://doi.org/10.3390/genes11111327 - 10 Nov 2020
Cited by 23 | Viewed by 3525
Abstract
Sepsis is a dysregulated immune response disease affecting millions worldwide. Delayed diagnosis, poor prognosis, and disease heterogeneity make its treatment ineffective. miRNAs are imposingly involved in personalized medicine such as therapeutics, due to their high sensitivity and accuracy. Our study aimed to reveal [...] Read more.
Sepsis is a dysregulated immune response disease affecting millions worldwide. Delayed diagnosis, poor prognosis, and disease heterogeneity make its treatment ineffective. miRNAs are imposingly involved in personalized medicine such as therapeutics, due to their high sensitivity and accuracy. Our study aimed to reveal the biomarkers that may be involved in the dysregulated immune response in sepsis and lung injury using a computational approach and in vivo validation studies. A sepsis miRNA Gene Expression Omnibus (GEO) dataset based on the former analysis of blood samples was used to identify differentially expressed miRNAs (DEMs) and associated hub genes. Sepsis-associated genes from the Comparative Toxicogenomics Database (CTD) that overlapped with identified DEM targets were utilized for network construction. In total, 317 genes were found to be regulated by 10 DEMs (three upregulated, namely miR-4634, miR-4638-5p, and miR-4769-5p, and seven downregulated, namely miR-4299, miR-451a, miR181a-2-3p, miR-16-5p, miR-5704, miR-144-3p, and miR-1290). Overall hub genes (HIP1, GJC1, MDM4, IL6R, and ERC1) and for miR-16-5p (SYNRG, TNRC6B, and LAMTOR3) were identified based on centrality measures (degree, betweenness, and closeness). In vivo validation of miRNAs in lung tissue showed significantly downregulated expression of miR-16-5p corroborating with our computational findings, whereas expression of miR-181a-2-3p and miR-451a were found to be upregulated in contrast to the computational approach. In conclusion, the differential expression pattern of miRNAs and hub genes reported in this study may help to unravel many unexplored regulatory pathways, leading to the identification of critical molecular targets for increased prognosis, diagnosis, and drug efficacy in sepsis and associated organ injuries. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Pulmonary Diseases)
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Review

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12 pages, 920 KiB  
Review
Angiotensin-Converting Enzyme 2 (ACE2) as a Potential Diagnostic and Prognostic Biomarker for Chronic Inflammatory Lung Diseases
by Dejan Marčetić, Miroslav Samaržija, Andrea Vukić Dugac and Jelena Knežević
Genes 2021, 12(7), 1054; https://doi.org/10.3390/genes12071054 - 9 Jul 2021
Cited by 6 | Viewed by 4243
Abstract
Chronic inflammatory lung diseases are characterized by uncontrolled immune response in the airways as their main pathophysiological manifestation. The lack of specific diagnostic and therapeutic biomarkers for many pulmonary diseases represents a major challenge for pulmonologists. The majority of the currently approved therapeutic [...] Read more.
Chronic inflammatory lung diseases are characterized by uncontrolled immune response in the airways as their main pathophysiological manifestation. The lack of specific diagnostic and therapeutic biomarkers for many pulmonary diseases represents a major challenge for pulmonologists. The majority of the currently approved therapeutic approaches are focused on achieving disease remission, although there is no guarantee of complete recovery. It is known that angiotensin-converting enzyme 2 (ACE2), an important counter-regulatory component of the renin–angiotensin–aldosterone system (RAAS), is expressed in the airways. It has been shown that ACE2 plays a role in systemic regulation of the cardiovascular and renal systems, lungs and liver by acting on blood pressure, electrolyte balance control mechanisms and inflammation. Its protective role in the lungs has also been presented, but the exact pathophysiological mechanism of action is still elusive. The aim of this study is to review and discuss recent findings about ACE2, including its potential role in the pathophysiology of chronic inflammatory lung diseases:, i.e., chronic obstructive pulmonary disease, asthma, and pulmonary hypertension. Additionally, in the light of the coronavirus 2019 disease (COVID-19), we will discuss the role of ACE2 in the pathophysiology of this disease, mainly represented by different grades of pulmonary problems. We believe that these insights will open up new perspectives for the future use of ACE2 as a potential biomarker for early diagnosis and monitoring of chronic inflammatory lung diseases. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Pulmonary Diseases)
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15 pages, 248 KiB  
Review
Biomarkers in Different Asthma Phenotypes
by Sanja Popović-Grle, Anamarija Štajduhar, Marina Lampalo and Dina Rnjak
Genes 2021, 12(6), 801; https://doi.org/10.3390/genes12060801 - 25 May 2021
Cited by 25 | Viewed by 4151
Abstract
Asthma is the most common respiratory disease. It has multiple phenotypes thatcan be partially differentiated by measuring the disease’s specific characteristics—biomarkers. The pathogenetic mechanisms are complex, and it is still a challenge to choose suitable biomarkers to adequately stratify patients, which became especially [...] Read more.
Asthma is the most common respiratory disease. It has multiple phenotypes thatcan be partially differentiated by measuring the disease’s specific characteristics—biomarkers. The pathogenetic mechanisms are complex, and it is still a challenge to choose suitable biomarkers to adequately stratify patients, which became especially important with the introduction of biologicals in asthma treatment. Usage of biomarkers and an understanding of the underlying pathobiological mechanisms lead to the definition of endotypes. Asthma can be broadly divided into two endotypes, T2-high and T2-low. The right combination of various biomarkers in different phenotypes is under investigation, hoping to help researchers and clinicians in better disease evaluation since theindividual approach and personalized medicine are imperative. Multiple biomarkers are superior to a single biomarker. Full article
(This article belongs to the Special Issue Molecular Biomarkers of Pulmonary Diseases)
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