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Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer

Chronic obstructive pulmonary disease (COPD) is a multifactorial progressive airflow obstruction in the lungs, accounting for high morbidity and mortality across the world. This study aims to identify potential COPD blood-based biomarkers by analyzing the dysregulated gene expression patterns in blo...

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Autores principales: Banaganapalli, Babajan, Mallah, Bayan, Alghamdi, Kawthar Saad, Albaqami, Walaa F., Alshaer, Dalal Sameer, Alrayes, Nuha, Elango, Ramu, Shaik, Noor A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9531836/
https://www.ncbi.nlm.nih.gov/pubmed/36194576
http://dx.doi.org/10.1371/journal.pone.0274629
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author Banaganapalli, Babajan
Mallah, Bayan
Alghamdi, Kawthar Saad
Albaqami, Walaa F.
Alshaer, Dalal Sameer
Alrayes, Nuha
Elango, Ramu
Shaik, Noor A.
author_facet Banaganapalli, Babajan
Mallah, Bayan
Alghamdi, Kawthar Saad
Albaqami, Walaa F.
Alshaer, Dalal Sameer
Alrayes, Nuha
Elango, Ramu
Shaik, Noor A.
author_sort Banaganapalli, Babajan
collection PubMed
description Chronic obstructive pulmonary disease (COPD) is a multifactorial progressive airflow obstruction in the lungs, accounting for high morbidity and mortality across the world. This study aims to identify potential COPD blood-based biomarkers by analyzing the dysregulated gene expression patterns in blood and lung tissues with the help of robust computational approaches. The microarray gene expression datasets from blood (136 COPD and 6 controls) and lung tissues (16 COPD and 19 controls) were analyzed to detect shared differentially expressed genes (DEGs). Then these DEGs were used to construct COPD protein network-clusters and functionally enrich them against gene ontology annotation terms. The hub genes in the COPD network clusters were then queried in GWAS catalog and in several cancer expression databases to explore their pathogenic roles in lung cancers. The comparison of blood and lung tissue datasets revealed 63 shared DEGs. Of these DEGs, 12 COPD hub gene-network clusters (SREK1, TMEM67, IRAK2, MECOM, ASB4, C1QTNF2, CDC42BPA, DPF3, DET1, CCDC74B, KHK, and DDX3Y) connected to dysregulations of protein degradation, inflammatory cytokine production, airway remodeling, and immune cell activity were prioritized with the help of protein interactome and functional enrichment analysis. Interestingly, IRAK2 and MECOM hub genes from these COPD network clusters are known for their involvement in different pulmonary diseases. Additional COPD hub genes like SREK1, TMEM67, CDC42BPA, DPF3, and ASB4 were identified as prognostic markers in lung cancer, which is reported in 1% of COPD patients. This study identified 12 gene network- clusters as potential blood based genetic biomarkers for COPD diagnosis and prognosis.
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spelling pubmed-95318362022-10-05 Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer Banaganapalli, Babajan Mallah, Bayan Alghamdi, Kawthar Saad Albaqami, Walaa F. Alshaer, Dalal Sameer Alrayes, Nuha Elango, Ramu Shaik, Noor A. PLoS One Research Article Chronic obstructive pulmonary disease (COPD) is a multifactorial progressive airflow obstruction in the lungs, accounting for high morbidity and mortality across the world. This study aims to identify potential COPD blood-based biomarkers by analyzing the dysregulated gene expression patterns in blood and lung tissues with the help of robust computational approaches. The microarray gene expression datasets from blood (136 COPD and 6 controls) and lung tissues (16 COPD and 19 controls) were analyzed to detect shared differentially expressed genes (DEGs). Then these DEGs were used to construct COPD protein network-clusters and functionally enrich them against gene ontology annotation terms. The hub genes in the COPD network clusters were then queried in GWAS catalog and in several cancer expression databases to explore their pathogenic roles in lung cancers. The comparison of blood and lung tissue datasets revealed 63 shared DEGs. Of these DEGs, 12 COPD hub gene-network clusters (SREK1, TMEM67, IRAK2, MECOM, ASB4, C1QTNF2, CDC42BPA, DPF3, DET1, CCDC74B, KHK, and DDX3Y) connected to dysregulations of protein degradation, inflammatory cytokine production, airway remodeling, and immune cell activity were prioritized with the help of protein interactome and functional enrichment analysis. Interestingly, IRAK2 and MECOM hub genes from these COPD network clusters are known for their involvement in different pulmonary diseases. Additional COPD hub genes like SREK1, TMEM67, CDC42BPA, DPF3, and ASB4 were identified as prognostic markers in lung cancer, which is reported in 1% of COPD patients. This study identified 12 gene network- clusters as potential blood based genetic biomarkers for COPD diagnosis and prognosis. Public Library of Science 2022-10-04 /pmc/articles/PMC9531836/ /pubmed/36194576 http://dx.doi.org/10.1371/journal.pone.0274629 Text en © 2022 Banaganapalli et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Banaganapalli, Babajan
Mallah, Bayan
Alghamdi, Kawthar Saad
Albaqami, Walaa F.
Alshaer, Dalal Sameer
Alrayes, Nuha
Elango, Ramu
Shaik, Noor A.
Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer
title Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer
title_full Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer
title_fullStr Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer
title_full_unstemmed Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer
title_short Integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for COPD and lung cancer
title_sort integrative weighted molecular network construction from transcriptomics and genome wide association data to identify shared genetic biomarkers for copd and lung cancer
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9531836/
https://www.ncbi.nlm.nih.gov/pubmed/36194576
http://dx.doi.org/10.1371/journal.pone.0274629
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