Colon adenocarcinoma (COAD) is one of the most common gastrointestinal cancers globally. Molecular aberrations of tumor suppressors and/or oncogenes are the main contributors to tumorigenesis. However, the exact underlying mechanisms of COAD pathogenesis are clearly not known yet. In this regard, there is an urgent need to indicate promising potential diagnostic and prognostic biomarkers in COAD patients. In the current study, level 3 RNA-Seq and miR-Seq data and corresponding clinical data of colon adenocarcinoma (COAD) were retrieved from the TCGA database. The “limma” package in R software was utilized to indicate the differentially expressed genes. For in silico functional analysis, GO and KEGG signaling pathways were conducted. PPI network was constructed based on the STRING online database by Cytoscape 3.7.2. A ceRNA network was also constructed by “GDCRNATools” package in R software. Kaplan-Meier survival analysis (log-rank test) and ROC curve analysis were used to indicate the diagnostic and prognostic values of the biomarkers. The differential expression data demonstrated that 2995 mRNAs, 205 lncRNAs, and 345 miRNAs were differentially expressed in COAD. The GO and KEGG pathway analysis indicated that the differentially expressed mRNAs were primarily enriched in canonical processes in cancer. The PPI network showed that the CDKN2A, CCND1, MYC, E2F, CDK4, BRCA2, CDC25B, and CDKN1A proteins were the critical hubs. In addition, the Kaplan-Meier analysis revealed that 215 mRNAs, 14 lncRNAs, and 39 miRNAs were associated with overall survival time in the patients. Also, the ceRNA network data demonstrated that three lncRNAs including MIR17HG, H19, SNHG1, KCNQ1OT1, MALAT1, GAS5, SNHG20, OR2A1-AS1, and MAGI2-AS3 genes were involved in the development of COAD. Our data suggested several promising lncRNAs in the diagnosis and prognosis of patients with COAD.

中文翻译：

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长期非编码RNA（lncRNA）在结肠腺癌发生中的作用的整合分析。

结肠腺癌（COAD）是全球最常见的胃肠道癌症之一。肿瘤抑制因子和/或癌基因的分子畸变是肿瘤发生的主要因素。但是，COAD发病机理的确切潜在机制尚不清楚。在这方面，迫切需要在COAD患者中指出有希望的潜在诊断和预后生物标志物。在当前的研究中，从TCGA数据库中检索了3级RNA-Seq和miR-Seq数据以及相应的结肠腺癌（COAD）临床数据。R软件中的“ limma”软件包用于指示差异表达的基因。对于计算机功能分析，进行了GO和KEGG信号通路。PPI网络是由Cytoscape 3.7.2在STRING在线数据库的基础上构建的。还通过R软件中的“ GDCRNATools”软件包构建了一个ceRNA网络。Kaplan-Meier生存分析（对数秩检验）和ROC曲线分析用于指示生物标志物的诊断和预后价值。差异表达数据表明在COAD中差异表达了2995个mRNA，205个lncRNA和345个miRNA。GO和KEGG途径分析表明，差异表达的mRNA在癌症的典型过程中主要富集。PPI网络显示CDKN2A，CCND1，MYC，E2F，CDK4，BRCA2，CDC25B和CDKN1A蛋白是关键枢纽。另外，Kaplan-Meier分析显示215个mRNA，14个lncRNA和39个miRNA与患者的总生存时间有关。此外，ceRNA网络数据还显示了三个lncRNA，包括MIR17HG，H19，SNHG1，KCNQ1OT1，MALAT1，GAS5，SNHG20，OR2A1-AS1和MAGI2-AS3基因参与了COAD的发展。我们的数据表明在COAD患者的诊断和预后中有几种有前景的lncRNA。