Identification of stage-specific biomarkers in lung adenocarcinoma based on RNA-seq data.

Abstract

Tumorigenesis is a multistep process that attributes to the sequential accumulation of abnormal expression in key oncogenes or tumor suppressors. We aimed to identify stage-specific biomarkers to distinguish lung adenocarcinoma (LAC) stages in cancer progression. RNA-sequencing data of LAC and matched adjacent non-cancer tissues were downloaded from the Cancer Genome Atlas, including 29 pairs of samples from LAC at stage I, 14 from LAC at stage II, 13 from LAC at stage III, and 1 from LAC at stage IV. Differentially expressed genes (DEGs) were analyzed for each case at different stages of LAC. DEGs were further annotated based on transcription factor data information, tumor-associated gene database, and protein-protein interaction database. Functional annotation was performed for genes in PPI network by DAVID online tool. Our analysis identified 11 high-frequency DEGs in the stage I, 29 in the stage II, and 90 in the stage III of LAC. Among them, eight genes were significantly correlated with LAC stages and identified as biomarkers in LAC progression. ANGPTL5, C7orf16, EDN3, LOC150622, HOXA11AS, IL1F5, and USH1G significantly distinguished stage III from stages I and II. GJB6 was significantly enriched in the gap junction trafficking pathway, while C7orf16 and EDN3 were enriched in Wnt signaling pathway, cell cycle, and G protein-coupled receptor (GPCR) signaling. Up-regulated GJB6 especially in LAC stage II and down-regulated C7orf16 and EDN3 specifically in stage III were identified as biomarkers for distinguishing cancer stage in tumor progression through dysregulating gap junction, Wnt signaling, and GPCR signaling pathways.