Yan Shuo, Xu Jichong, Liu Bingyan, Ma Lin, Tan Huaqiao, Fang Chun
Department of Interventional Radiology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China.
Department of Interventional Radiology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
Transl Cancer Res. 2021 Apr;10(4):1804-1812. doi: 10.21037/tcr-20-2529.
Esophageal cancer (EC) is one of the most common gastrointestinal cancers and the incidence is on the increase in recent years. The aim of the present study was to assess novel long non-coding RNA (lncRNA) biomarkers for the prognosis of EC through the analysis of gene expression microarrays.
Three datasets (GSE53622, GSE53624, and GSE53625) were downloaded from the Gene Expression Omnibus (GEO) database and EC patients' clinical information were from The Cancer Genome Atlas (TCGA) databases. Differentially expressed genes (DEGs) were screened by comparing tumor tissues with normal tissues using limma R package. The Gene Expression Profiling Interactive Analysis 2 (GEPIA2) database was used to obtain the novel lncRNAs and their co-expression genes in EC and these were visualized with the Cytoscape software. The Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology Based Annotation System (KOBAS) database was used to analyze the functions enrichment of selected DEGs. Cell Counting Kit-8 (CCK8) and Transwell assays were used to further confirm the function of target lncRNAs.
We identified 24 differentially expressed (DE) lncRNAs and 659 DE mRNAs from the intersection of GEO and TCGA databases. And we found that only LINC01614 was concerned with a candidate prognostic signature in EC. "Extracellular matrix (ECM)-receptor interaction" and "PI3K-Akt signaling pathway" were observed, and we constructed a lncRNA-mRNA co-expression network for EC that includes LINC01614 and 64 mRNAs. The results of CCK8 and Transwell assays showed that suppression of LINC01614 inhibited EC cell proliferation and migration.
Our study might provide LINC01614 as a novel lncRNA biomarker for diagnosis and prognosis in EC.
食管癌（EC）是最常见的胃肠道癌症之一，近年来其发病率呈上升趋势。本研究的目的是通过基因表达微阵列分析评估用于预测食管癌预后的新型长链非编码RNA（lncRNA）生物标志物。
从基因表达综合数据库（GEO）下载了三个数据集（GSE53622、GSE53624和GSE53625），食管癌患者的临床信息来自癌症基因组图谱（TCGA）数据库。使用limma R包通过比较肿瘤组织与正常组织筛选差异表达基因（DEG）。利用基因表达谱交互式分析2（GEPIA2）数据库获取食管癌中的新型lncRNA及其共表达基因，并用Cytoscape软件进行可视化。使用基于京都基因与基因组百科全书（KEGG）直系同源注释系统（KOBAS）数据库分析所选DEG的功能富集情况。采用细胞计数试剂盒-8（CCK8）和Transwell实验进一步确认靶lncRNA的功能。
我们从GEO和TCGA数据库的交集中鉴定出24个差异表达的lncRNA和659个差异表达的mRNA。并且我们发现只有LINC01614与食管癌的候选预后特征相关。观察到“细胞外基质（ECM）-受体相互作用”和“PI3K-Akt信号通路”，并构建了一个包含LINC01614和64个mRNA的食管癌lncRNA-mRNA共表达网络。CCK8和Transwell实验结果表明，抑制LINC01614可抑制食管癌细胞的增殖和迁移。
我们的研究可能提供LINC01614作为食管癌诊断和预后的新型lncRNA生物标志物。
