Table6_LncRNA–miRNA–mRNA Networks of Gastrointestinal Cancers Representing Common and Specific LncRNAs and mRNAs.XLSX

Gastrointestinal (GI) cancers are responsible for approximately half of cancer-related deaths, highlighting the need for the identification of distinct and common features in their clinicopathological characteristics. Long ncRNA (lncRNAs), which are involved in competitive endogenous RNA (ceRNA) networks with critical roles in biological processes, constitute a substantial number of non-coding RNAs. Therefore, our study aimed to investigate the similarities and differences in the ceRNA networks of The Cancer Genome Atlas (TCGA)-GI cancers. We performed a comprehensive bioinformatics analysis of ceRNA networks for TCGA-GI cancers in terms of the deferential mRNA, lncRNA, and miRNA expression levels, ceRNA networks, overall survival analysis, correlation analysis, pathological cancer stages, and gene set enrichment analysis. Our study revealed several common and distinct mRNAs and lncRNAs with prognostic values in these networks. It was specifically noteworthy that MAGI2-AS3 lncRNA was found to be shared in almost all GI cancers. Moreover, the most common shared mRNAs between GI cancers were MEIS1, PPP1R3C, ADAMTSL3, RIPOR2, and MYLK. For each cancer ceRNA network, we found that the expression level of a number of lncRNAs and mRNAs was specific. Furthermore, our study provided compelling evidence that several genes, most notably KDELC1, can act as novel proto-oncogenes in cancers. This, in turn, can highlight their role as new prognostic and therapeutic targets. Moreover, we found cell cycle and extracellular matrix structural constituent as the top shared KEGG and molecular function, respectively, among GI cancers. Our study revealed several known lncRNAs and known and unknown mRNAs in GI cancers with diagnostic and prognostic values.

胃肠道（GI）癌症约占癌症相关死亡病例的一半，凸显了明确其临床病理特征中独特与共有特征的迫切需求。长链非编码RNA（long ncRNA, lncRNAs）作为一类数量庞大的非编码RNA，可参与内源竞争RNA（ceRNA）网络并在生物学过程中发挥关键作用。因此，本研究旨在探究癌症基因组图谱（TCGA）收录的GI癌症的ceRNA网络异同。我们针对TCGA-GI癌症的ceRNA网络开展了全面的生物信息学分析，分析维度涵盖差异表达mRNA、lncRNA与miRNA水平、ceRNA网络构建、总生存分析、相关性分析、癌症病理分期以及基因集富集分析。本研究在上述网络中鉴定出多个具有预后价值的共有与特异性mRNA及lncRNA。尤为值得关注的是，MAGI2-AS3 lncRNA几乎在所有GI癌症中均存在表达。此外，GI癌症间最常见的共有mRNA为MEIS1、PPP1R3C、ADAMTSL3、RIPOR2及MYLK。针对每种癌症的ceRNA网络，我们发现多个lncRNA与mRNA的表达水平具有癌种特异性。此外，本研究提供了有力证据，表明包括KDELC1在内的多个基因可作为癌症中的新型原癌基因，这一发现可进一步凸显它们作为新型预后与治疗靶点的潜力。我们还发现细胞周期与细胞外基质结构组分分别为GI癌症中最主要的共享KEGG通路与分子功能条目。本研究还鉴定出多个在GI癌症中具有诊断与预后价值的已知lncRNA，以及已知与未知的mRNA。