Identification of biomarkers in common chronic lung diseases by co-expression networks and drug-target interactions analysis

Abstract

Background: asthma, chronic obstructive pulmonary disease (COPD), and idiopathic pulmonary fibrosis (IPF) are three serious pulmonary diseases that contain common and unique characteristics. Therefore, the identification of biomarkers that differentiate these diseases is of importance for preventing misdiagnosis. In this regard, the present study aimed to identify the disorders at the early stages, based on lung transcriptomics data and drug-target interactions. Methods: To this end, the differentially expressed genes were found in each disease. Then, WGCNA was utilized to find specific and consensus gene modules among the three diseases. Finally, the disease-disease similarity was analyzed, followed by determining candidate drug-target interactions. Results: The results confirmed that the asthma lung transcriptome was more similar to COPD than IPF. In addition, the biomarkers were found in each disease and thus were proposed for further clinical validations. These genes included RBM42, STX5, and TRIM41 in asthma, CYP27A1, GM2A, LGALS9, SPI1, and NLRC4 in COPD, ATF3, PPP1R15A, ZFP36, SOCS3, NAMPT, and GADD45B in IPF, LRRC48 and CETN2 in asthma-COPD, COL15A1, GIMAP6, and JAM2 in asthma-IPF and LMO7, TSPAN13, LAMA3, and ANXA3 in COPD-IPF. Finally, analyzing drug-target networks suggested anti-inflammatory candidate drugs for treating the above mentioned diseases. Conclusion: In general, the results revealed the unique and common biomarkers among three chronic lung diseases. Eventually, some drugs were suggested for treatment purposes.

Age-Dependent Assessment of Genes Involved in Cellular Senescence, Telomere, and Mitochondrial Pathways in Human Lung Tissue of Smokers, COPD, and IPF: Associations With SARS-CoV-2 COVID-19 ACE2-TMPRSS2-Furin-DPP4 Axis

“…Some of the common gene targets like GADD45B needs further attention and characterization especially in the chronic lung diseases like COPD and IPF. Recent biomarker identification study indicated GADD45B in their list of genes that can be targeted in chronic diseases like asthma, IPF, and COPD (Maghsoudloo et al, 2020).…”

“…Aging influences many chronic lung diseases, such as COPD, idiopathic pulmonary fibrosis (IPF), and asthma. Also chronic lung diseases like asthma and IPF share some of the common yet distinct features compared to COPD (Maghsoudloo et al, 2020). Environmental stress factors like smoking remains a common influencing factor for the disease progression in all these three cases.…”

Sex‐specific associations of asthma acquisition with changes in DNA methylation during adolescence

“…Accompanied by the opposite direction of changes in DNAm between males and females at most of the identified CpGs in both cohorts, this suggests that DNAm may represent a mechanism underlying the well-established gender reversal in asthma prevalence across adolescence. 15,16 In addition, assessment of the biological relevance for 9 of the cases compared to controls, 52 and gene CCDC146 is also identified as one of the differentially expressed genes in relation to asthma, 53 although it is unclear whether such differentiation is different be- At most of the CpGs identified in IOWBC, consistent direction of interaction effects was found in ALSPAC. However, statistical significance was not observed at those CpG sites except for cg20891917.…”

Age-dependent assessment of genes involved in cellular senescence, telomere and mitochondrial pathways in human lung tissue of smokers, COPD and IPF: Associations with SARS-CoV-2 COVID-19 ACE2-TMPRSS2-Furin-DPP4 axis

“…Some of the common gene targets like GADD45B needs further attention and characterization especially in the chronic lung diseases like COPD and IPF. Recent biomarker identification study indicated GADD45B i n their list of genes that can be targeted in chronic diseases like asthma, IPF and COPD 6 .…”