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

Abstract

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.

Circulating long non‐coding RNA GAS5 and SOX2OT as potential biomarkers for diagnosis and prognosis of non‐small cell lung cancer

“…Previous researchers showed similar results concerning the association with the histology type. Scholars recommended that the expression levels of SOX2OT might be a key biomarker to discriminate ADCs from SCCs of the lung . We found an association between TNM stage and SOX2OT expression levels, which was confirmed by ROC analysis, that SOX2OT is a prognostic marker with 80% sensitivity and 76% specificity to discriminate between early and late stages of NSCLC.…”

Cost-Effectiveness Analysis of Nivolumab Plus Ipilimumab vs. Chemotherapy as First-Line Therapy in Advanced Non-Small Cell Lung Cancer

“…Around the globe, lung cancer is the leading cause of cancer incidence and mortality, with 2.1 million new lung cancer cases and 1.8 million deaths worldwide (1)(2)(3)(4). Up to 61% of patients with NSCLC had advanced disease at the time of diagnosis, with a 5-years survival rate of 18% (5,6).…”

Prognostic value of long non-coding RNA SNHG20 in cancer

“…[ 2 ] Comparing to our understanding about microRNAs (miRNA) as a commonly studied ncRNAs, the function of the subset long non-coding RNAs (lncRNAs) is relatively unknown. [ 3 – 7 ] Small nucleolar RNA host gene 20 (SNHG20) has attracted more attention in the past few years due to its potential role in tumorigenesis. Locating on chromosome 17q25.2 with the length of 2183 base-pairs, SNHG20 was firstly identified in hepatocellular carcinoma (HCC) and subsequent studies suggested that SNHG20 played important roles including colorectal cancer, cervical cancer, and breast cancer.…”