Microarray data re-annotation reveals specific lncRNAs and their potential functions in non-small cell lung cancer subtypes

Non-small-cell lung cancer (NSCLC) is a leading cause of cancer mortality worldwide. The most common subtypes of NSCLC are adenocarcinoma (AC) and squamous cell carcinoma (SCC). However, the pathophysiological mechanisms contributing to AC and SCC are still largely unknown, especially the roles of long non-coding RNAs (lncRNAs). The present study identified differentially expressed lncRNAs between lung AC and SCC by re-annotation of NSCLC microarray data analysis profiling. The potential functions of lncRNAs were predicted by using coding-non-coding gene co-expressing network. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to investigate lncRNA expression levels in AC cell lines (A549 and L78), SCC cell lines (H226 and H520) and normal cells (NL-20). Western blotting analysis was used to investigate the protein expression levels in these cell lines. A total of 65 lncRNAs were differentially expressed between AC and SCC including 28 lncRNAs that were downregulated in SCC subtypes compared with those in AC ones, and 37 upregulated lncRNAs in SCC subtypes compared with AC subtypes. Three lncRNAs, sex determining region Y-box 2 overlapping transcript (SOX2-OT), NCBP2 antisense RNA 2 (NCBP2-AS2) and ubiquitin like with PHD and ring finger domains 1 (UHRF1), were predicted to be associated with lung cancer; RT-qPCR confirmed that SOX2-OT and NCBP2-AS2 were associated with lung cancer. Finally, western blot assays demonstrated that there was no difference in β-catenin and glycogen synthase kinase 3β (GSK-3β) expression in cancer cells compared with NL-20, but increased phosphorylated (p-)β-catenin and p-GSK-3β was detected in lung cancer cell lines compared with NL-20, particularly in A549 cells. Although these results require further experimental verification, the analysis of lncRNA signatures between AC and SCC has provided insights into the regulatory mechanism of NSCLC development.