China Medical University, Shenyang North New Area, Shenyang, Liaoning, China.
School of Nursing, China Medical University, Shenyang, Liaoning, China.
Cancer Biomark. 2021;31(2):165-176. doi: 10.3233/CBM-203078.
More and more studies have shown that long non-coding RNA (LncRNA) as a competing endogenous RNA (ceRNA) plays an important role in lung cancer. Therefore, we analyzed the RNA expression profiles of 82 lung cancer patients which were all from Gene Expression Omnibus (GEO).
Firstly, we used BLASTN (evalue = 1e-10) to annotate the gene sets, performed in-group correction and batched normalization of the three data sets with R. Secondly, we used the limma and sva packages to compare tumor tissues with normal tissues. Then through WGCNA, we obtained the 4 gene modules most related to the trait.
We intersected the genes of above 4 modules with the differential expression genes: 28 LncRNAs (up: 5, down: 23) and 265 mRNAs (up:11, down: 254). Based on these genes, we picked up 6 LncRNAs (CCDC39, FAM182A, SRGAP3-AS2, ADAMTS9-AS2, AC020907.2, SFTA1P), then set and visualized the LncRNA-miRNA-mRNA ceRNA network with 12 miRNAs related to 12 mRNAs. Finally, we performed downstream analysis of 265 mRNAs by Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Protein-Protein Interaction (PPI) network.
After analyzing, we think this study provides a new direction for basic and clinical research related to LAD, and is expected to provide new targets for early diagnosis, prognostic evaluation and clinical treatment of lung cancer.
越来越多的研究表明，长链非编码 RNA（LncRNA）作为竞争性内源性 RNA（ceRNA）在肺癌中发挥着重要作用。因此，我们分析了 82 名肺癌患者的 RNA 表达谱，这些患者均来自基因表达综合数据库（GEO）。
首先，我们使用 BLASTN（evalue = 1e-10）注释基因集，使用 R 对三个数据集进行组内校正和分批归一化。其次，我们使用 limma 和 sva 包比较肿瘤组织与正常组织。然后通过 WGCNA，我们获得了与性状最相关的 4 个基因模块。
我们将上述 4 个模块的基因与差异表达基因进行了交集：28 个 LncRNAs（上调：5 个，下调：23 个）和 265 个 mRNAs（上调：11 个，下调：254 个）。基于这些基因，我们选择了 6 个 LncRNAs（CCDC39、FAM182A、SRGAP3-AS2、ADAMTS9-AS2、AC020907.2、SFTA1P），然后设置并可视化了与 12 个 mRNAs 相关的 12 个 miRNA 的 LncRNA-miRNA-mRNA ceRNA 网络。最后，我们对 265 个 mRNAs 进行了基因本体论（GO）富集分析、京都基因与基因组百科全书（KEGG）通路富集分析和蛋白质-蛋白质相互作用（PPI）网络的下游分析。
通过分析，我们认为本研究为 LAD 相关的基础和临床研究提供了新的方向，并有望为肺癌的早期诊断、预后评估和临床治疗提供新的靶点。
