Lung cancer is the second most common cancer in the world. The aim of this study is to identify biomarkers for lung cancer that can aid in its diagnosis and treatment. The gene expression profiles from GEO database were analyzed by GEO2R to identify Differentially Expressed Genes (DEGs) and further analyzed using Cytoscape. The data was divided into two categories: non-treatment and treatment groups. A total of 407 DEGs (254 upregulated and 153 downregulated) and 259 DEGs (124 upregulated and 135 downregulated) were isolated for non-treatment and treatment studies respectively. The significant Gene Ontologies and pathways enriched with DEGS were identified using Cytoscape apps, BiNGO and ReactomeFIPlugIn, respectively. Hub genes based on network parameters - Degree, Closeness and Betweenness - were isolated using CytoHubba. In conclusion, DEGs identified in this study may play an important role in early diagnosis or as biomarkers of lung cancer.
This content will become publicly available on July 1, 2023
Transcriptomic Evidence That Switching from Tobacco to Electronic Cigarettes Does Not Reverse Damage to the Respiratory Epithelium
The health benefits of switching from tobacco to electronic cigarettes (ECs) are neither confirmed nor well characterized. To address this problem, we used RNA-seq analysis to compare the nasal epithelium transcriptome from the following groups (n = 3 for each group): (1) former smokers who completely switched to second generation ECs for at least 6 months, (2) current tobacco cigarette smokers (CS), and (3) non-smokers (NS). Group three included one former cigarette smoker. The nasal epithelial biopsies from the EC users vs. NS had a higher number of differentially expressed genes (DEGs) than biopsies from the CS vs. NS and CS vs. EC sets (1817 DEGs total for the EC vs. NS, 407 DEGs for the CS vs. NS, and 116 DEGs for the CS vs. EC comparison). In the EC vs. NS comparison, enriched gene ontology terms for the downregulated DEGs included cilium assembly and organization, whereas gene ontologies for upregulated DEGs included immune response, keratinization, and NADPH oxidase. Similarly, ontologies for cilium movement were enriched in the downregulated DEGs for the CS vs. NS group. Reactome pathway analysis gave similar results and also identified keratinization and cornified envelope in the upregulated DEGs in the EC vs. NS comparison. more »
- Award ID(s):
- 1661152
- Publication Date:
- NSF-PAR ID:
- 10351566
- Journal Name:
- Toxics
- Volume:
- 10
- Issue:
- 7
- Page Range or eLocation-ID:
- 370
- ISSN:
- 2305-6304
- Sponsoring Org:
- National Science Foundation
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