Wang Xiwen, Su Rui, Guo Qiqiang, Liu Jia, Ruan Banlai, Wang Guiling
Department of The First Thoracic Surgery, Shengjing Hospital, China Medical University, Shenyang, Liaoning, China.
Institute of Translational Medicine, China Medical University, Shenyang, Liaoning, China.
PeerJ. 2019 Nov 7;7:e8024. doi: 10.7717/peerj.8024. eCollection 2019.
Non-small cell lung cancer (NSCLC) is a major subtype of lung cancer with high malignancy and bad prognosis, consisted of lung adenocarcinomas (LUAD) and lung squamous cell carcinomas (LUSC) chiefly. Multiple studies have indicated that competing endogenous RNA (ceRNA) network centered long noncoding RNAs (lncRNAs) can regulate gene expression and the progression of various cancers. However, the research about lncRNAs-mediated ceRNA network in LUAD is still lacking.
In this study, we analyzed the RNA-seq database from The Cancer Genome Atlas (TCGA) and obtained dysregulated lncRNAs in NSCLC, then further identified survival associated lncRNAs through Kaplan-Meier analysis. Quantitative real time PCR (qRT-PCR) was performed to confirm their expression in LUAD tissues and cell lines. The ceRNA networks were constructed based on DIANA-TarBase and TargetScan databases and visualized with OmicShare tools. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to investigate the potential function of ceRNA networks.
In total, 1,437 and 1,699 lncRNAs were found to be up-regulated in LUAD and LUSC respectively with 895 lncRNAs overlapping (|log2FC| > 3, adjusted value <0.01). Among which, 222 lncRNAs and 46 lncRNAs were associated with the overall survival (OS) of LUAD and LUSC, and 18 out of 222 up-regulated lncRNAs were found to have inverse correlation with LUAD patients' OS (|log2FC| > 3, adjusted value < 0.02). We selected 3 lncRNAs (CASC8, LINC01842 and VPS9D1-AS1) out of these 18 lncRNAs and confirmed their overexpression in lung cancer tissues and cells. CeRNA networks were further constructed centered CASC8, LINC01842 and VPS9D1-AS1 with 3 miRNAs and 100 mRNAs included respectively.
Through comprehensively analyses of TCGA, our study identified specific lncRNAs as candidate diagnostic and prognostic biomarkers for LUAD. The novel ceRNA network we created provided more insights into the regulatory mechanisms underlying LUAD.
非小细胞肺癌（NSCLC）是肺癌的主要亚型，恶性程度高，预后差，主要由肺腺癌（LUAD）和肺鳞状细胞癌（LUSC）组成。多项研究表明，以长链非编码RNA（lncRNA）为中心的竞争性内源RNA（ceRNA）网络可调节基因表达及多种癌症的进展。然而，关于lncRNA介导的ceRNA网络在LUAD中的研究仍较为缺乏。
在本研究中，我们分析了来自癌症基因组图谱（TCGA）的RNA测序数据库，获得了NSCLC中失调的lncRNA，然后通过Kaplan-Meier分析进一步鉴定了与生存相关的lncRNA。采用定量实时PCR（qRT-PCR）来确认它们在LUAD组织和细胞系中的表达。基于DIANA-TarBase和TargetScan数据库构建ceRNA网络，并用OmicShare工具进行可视化。进行基因本体（GO）和京都基因与基因组百科全书（KEGG）通路分析以研究ceRNA网络的潜在功能。
总共发现分别有1437个lncRNA和1699个lncRNA在LUAD和LUSC中上调，其中895个lncRNA重叠（|log2FC|>3，校正P值<0.01）。其中，222个lncRNA和46个lncRNA与LUAD和LUSC的总生存期（OS）相关，在222个上调的lncRNA中，发现有18个与LUAD患者的OS呈负相关（|log2FC|>3，校正P值<0.02）。我们从这18个lncRNA中选择了3个lncRNA（CASC8、LINC01842和VPS9D1-AS1），并证实它们在肺癌组织和细胞中过表达。进一步构建了以CASC8、LINC01842和VPS9D1-AS1为中心的ceRNA网络，分别包含3个miRNA和100个mRNA。
通过对TCGA的综合分析，我们的研究鉴定了特定的lncRNA作为LUAD的候选诊断和预后生物标志物。我们创建的新型ceRNA网络为LUAD潜在的调控机制提供了更多见解。
