Construction of a Competing Endogenous RNA Network and Identification of Potential Regulatory Axes in Gastric Cancer Chemoresistance

Purpose: Emerging evidence highlights the multifunctional role of noncoding RNAs (ncRNAs) in gastric cancer (GC) chemoresistance. However, the comprehensive expression profile and competing endogenous RNAs (ceRNAs) regulatory network of GC chemoresistance remain unanswered. Methods: The whole-transcriptome sequencing (RNA sequencing) was performed to comprehensively analyze the differentially expressed (DE) lncRNAs, miRNAs and mRNAs in cisplatin-resistant cells MGC-803/DDP and GC cells MGC-803. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to investigate the biological functions implicated with the DEncRNAs. Then, the cisplatin-resistant-related ceRNA network and potential regulatory axes were constructed by bioinformatic analysis. Results: We successfully generated cisplatin-resistant GC cell line MGC-803/DDP. Differential expression analysis showed that a total of 1,936 DElncRNAs, 2,194 DEmRNAs and 174 DEmiRNAs were identified. Functional enrichment analysis indicated that those DEncRNAs were mainly involved in neuroactive ligand-receptor interaction, drug metabolism and Hippo signaling pathway. Subsequently, the cisplatin-resistant-related ceRNA network was constructed with the widely accepted vital chemo-resistant-related genes and signaling pathways. In addition, two constructed regulatory axes (include FAM66C/miR-129-5p/7 mRNAs and SFTA1P/miR-206/FN1 or NRP1) were successfully validated by the Genomic Data Commons (GDC) GC data. Conclusion: The novel ceRNA network and the potential regulatory axes may provide the most comprehensive view of GC chemoresistance to date. Our findings uncovered potential biomarkers for prognostic prediction and novel therapeutic targets for reversing cisplatin resistance in GC. Overall design: Transcriptomic profilling of MGC-803 and cisplatin-resistant GC cell line MGC-803/DDP

研究背景（Purpose）：越来越多的研究证据表明，非编码RNA（noncoding RNAs, ncRNAs）在胃癌（gastric cancer, GC）的化疗耐药中发挥多维度调控作用。然而，目前胃癌化疗耐药相关的全面表达谱以及内源竞争RNA（competing endogenous RNAs, ceRNAs）调控网络仍未得到系统阐明。
研究方法：本研究通过全转录组测序（whole-transcriptome sequencing，即RNA测序），全面分析了顺铂耐药细胞株MGC-803/DDP与亲本胃癌细胞株MGC-803中的差异表达（differentially expressed, DE）长链非编码RNA（lncRNAs）、微小RNA（miRNAs）以及信使RNA（mRNAs）的表达情况。通过基因本体论（Gene Ontology, GO）与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路富集分析，探究了差异表达非编码RNA所涉及的生物学功能。随后，借助生物信息学分析构建了顺铂耐药相关的ceRNA调控网络及潜在调控轴。
研究结果：本研究成功构建了胃癌顺铂耐药细胞株MGC-803/DDP。差异表达分析结果显示，本研究共鉴定得到1936个差异表达长链非编码RNA（DElncRNAs）、2194个差异表达信使RNA（DEmRNAs）以及174个差异表达微小RNA（DEmiRNAs）。功能富集分析结果表明，这些差异表达非编码RNA主要参与神经活性配体-受体相互作用、药物代谢以及Hippo信号通路（Hippo signaling pathway）。随后，本研究基于公认的关键化疗耐药相关基因及信号通路，构建了顺铂耐药相关的ceRNA调控网络。此外，本研究借助基因组数据共享库（Genomic Data Commons, GDC）中的胃癌数据集，成功验证了两条构建的调控轴：FAM66C/miR-129-5p/7种信使RNA以及SFTA1P/miR-206/FN1或NRP1。
研究结论：本研究构建的新型ceRNA调控网络及潜在调控轴，可为目前已知的胃癌化疗耐药机制提供最为全面的解析视角。本研究结果揭示了可用于胃癌预后预测的潜在生物标志物，以及可用于逆转胃癌顺铂耐药的新型治疗靶点。
整体实验设计：胃癌细胞株MGC-803及其顺铂耐药株MGC-803/DDP的转录组分析。