scholarly journals Prioritizing chronic obstructive pulmonary disease (COPD) candidate genes in COPD-related networks

Oncotarget ◽  
2017 ◽  
Vol 8 (61) ◽  
pp. 103375-103384 ◽  
Author(s):  
Yihua Zhang ◽  
Wan Li ◽  
Yuyan Feng ◽  
Shanshan Guo ◽  
Xilei Zhao ◽  
...  
Biologia ◽  
2008 ◽  
Vol 63 (1) ◽  
Author(s):  
Eva Slabá ◽  
Pavol Joppa ◽  
Ján Šalagovič ◽  
Ružena Tkáčová

AbstractChronic obstructive pulmonary disease (COPD) is a major cause of morbidity and mortality worldwide. Irreversible airflow limitation, both progressive and associated with an inflammatory response of the lungs to noxious particles or gases, is a hallmark of the disease. Cigarette smoking is the most important environmental risk factor for COPD, nevertheless, only approximately 20–30% of smokers develop symptomatic disease. Epidemiological studies, case-control studies in relatives of patients with COPD, and twin studies suggest that COPD is a genetically complex disease with environmental factors and many involved genes interacting together. Two major strategies have been employed to identify the genes and the polymorphisms that likely contribute to the development of complex diseases: association studies and linkage analyses. Biologically plausible pathogenetic mechanisms are prerequisites to focus the search for genes of known function in association studies. Protease-antiprotease imbalance, generation of oxidative stress, and chronic inflammation are recognized as the principal mechanisms leading to irreversible airflow obstruction and parenchymal destruction in the lung. Therefore, genes which have been implicated in the pathogenesis of COPD are involved in antiproteolysis, antioxidant barrier and metabolism of xenobiotic substances, inflammatory response to cigarette smoke, airway hyperresponsiveness, and pulmonary vascular remodelling. Significant associations with COPD-related phenotypes have been reported for polymorphisms in genes coding for matrix metalloproteinases, microsomal epoxide hydrolase, glutathione-S-transferases, heme oxygenase, tumor necrosis factor, interleukines 1, 8, and 13, vitamin D-binding protein and β-2-adrenergic receptor (ADRB2), whereas adequately powered replication studies failed to confirm most of the previously observed associations. Genome-wide linkage analyses provide us with a novel tool to identify the general locations of COPD susceptibility genes, and should be followed by association analyses of positional candidate genes from COPD pathophysiology, positional candidate genes selected from gene expression studies, or dense single nucleotide polymorphism panels across regions of linkage. Haplotype analyses of genes with multiple polymorphic sites in linkage disequilibrium, such as the ADRB2 gene, provide another promising field that has yet to be explored in patients with COPD. In the present article we review the current knowledge about gene polymorphisms that have been recently linked to the risk of developing COPD and/or may account for variations in the disease course.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Wan Li ◽  
Yihua Zhang ◽  
Yahui Wang ◽  
Zherou Rong ◽  
Chenyu Liu ◽  
...  

Abstract Background Identifying or prioritizing genes for chronic obstructive pulmonary disease (COPD), one type of complex disease, is particularly important for its prevention and treatment. Methods In this paper, a novel method was proposed to Prioritize genes using Expression information in Protein–protein interaction networks with disease risks transferred between genes (abbreviated as PEP). A weighted COPD PPI network was constructed using expression information and then COPD candidate genes were prioritized based on their corresponding disease risk scores in descending order. Results Further analysis demonstrated that the PEP method was robust in prioritizing disease candidate genes, and superior to other existing prioritization methods exploiting either topological or functional information. Top-ranked COPD candidate genes and their significantly enriched functions were verified to be related to COPD. The top 200 candidate genes might be potential disease genes in the diagnosis and treatment of COPD. Conclusions The proposed method could provide new insights to the research of prioritizing candidate genes of COPD or other complex diseases with expression information from sequencing or microarray data.


2021 ◽  
Vol 3 (1) ◽  
pp. 127-133
Author(s):  
Anjali Trivedi ◽  
Debabrata Ghosh ◽  
Geetanjali Bade ◽  
Randeep Guleria ◽  
Meghashree Sampath ◽  
...  

Chronic Obstructive Pulmonary Disease (COPD) is a complex disease with varying susceptibility. COPD development may be associated with copy number variation (CNV) in susceptible genomic regions. CNV also contributes to COPD heritability as these can cause changes in DNA fragment. CNVs in COPD smokers and COPD ex-smokers have not been examined so far. Thus, genome-wide array based comparative genomic hybridization (aCGH) was performed in COPD (n = 15) and control subjects (n = 13) to identify the vulnerable candidate genes for genetic susceptibility and CNVs in smoker (n = 6) and ex-smoker (n = 9) COPD and compare it with control subjects to identify the candidate genes potentially involved in the pathogenesis of COPD. Copy number gains and losses were detected in several chromosomal regions. Chromosomal regions found to be consistently associated with both subgroups of COPD, as well as, of control group were: 2p11.2, 4q13.2, 8p23.1, 8p11.22, 12p13.31 and 14q32.33. Chromosomal regions associated with COPD were 11p15.5, 15q11.1-q11.2 and Xq28, which had several genes, (viz., CHECK2P2, HERC2P3, GOLGA6L6 and GOLGA8CP) which were associated with COPD smokers, while several other genes (viz., LICAM, LCA10, AVPR2, GDI1, HOTS and H19) were found to be associated with COPD ex-smokers. These loci and genes may be explored further for their potential use as predictive markers and better understanding of pathophysiology of COPD.


2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Hans Matsson ◽  
Cilla Söderhäll ◽  
Elisabet Einarsdottir ◽  
Maxime Lamontagne ◽  
Sanna Gudmundsson ◽  
...  

2020 ◽  
Vol 29 (2) ◽  
pp. 864-872
Author(s):  
Fernanda Borowsky da Rosa ◽  
Adriane Schmidt Pasqualoto ◽  
Catriona M. Steele ◽  
Renata Mancopes

Introduction The oral cavity and pharynx have a rich sensory system composed of specialized receptors. The integrity of oropharyngeal sensation is thought to be fundamental for safe and efficient swallowing. Chronic obstructive pulmonary disease (COPD) patients are at risk for oropharyngeal sensory impairment due to frequent use of inhaled medications and comorbidities including gastroesophageal reflux disease. Objective This study aimed to describe and compare oral and oropharyngeal sensory function measured using noninstrumental clinical methods in adults with COPD and healthy controls. Method Participants included 27 adults (18 men, nine women) with a diagnosis of COPD and a mean age of 66.56 years ( SD = 8.68). The control group comprised 11 healthy adults (five men, six women) with a mean age of 60.09 years ( SD = 11.57). Spirometry measures confirmed reduced functional expiratory volumes (% predicted) in the COPD patients compared to the control participants. All participants completed a case history interview and underwent clinical evaluation of oral and oropharyngeal sensation by a speech-language pathologist. The sensory evaluation explored the detection of tactile and temperature stimuli delivered by cotton swab to six locations in the oral cavity and two in the oropharynx as well as identification of the taste of stimuli administered in 5-ml boluses to the mouth. Analyses explored the frequencies of accurate responses regarding stimulus location, temperature and taste between groups, and between age groups (“≤ 65 years” and “> 65 years”) within the COPD cohort. Results We found significantly higher frequencies of reported use of inhaled medications ( p < .001) and xerostomia ( p = .003) in the COPD cohort. Oral cavity thermal sensation ( p = .009) was reduced in the COPD participants, and a significant age-related decline in gustatory sensation was found in the COPD group ( p = .018). Conclusion This study found that most of the measures of oral and oropharyngeal sensation remained intact in the COPD group. Oral thermal sensation was impaired in individuals with COPD, and reduced gustatory sensation was observed in the older COPD participants. Possible links between these results and the use of inhaled medication by individuals with COPD are discussed.


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