Yang Changhong, Chen Jialei, Yu Zhe, Luo Jing, Li Xuemei, Zhou Baoyong, Jiang Ning
Department of Bioinformatics, Chongqing Medical University, Chongqing, China.
Department of Otolaryngology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
Front Oncol. 2021 Feb 25;11:621806. doi: 10.3389/fonc.2021.621806. eCollection 2021.
Gallbladder carcinoma (GBC), which has high invasion and metastasis risks, remains the most common biliary tract malignancy. Surgical resection for GBC is the only effective treatment, but most patients miss the opportunity for curative surgery because of a lack of timely diagnosis. The aim of this study was to identify and verify early candidate diagnostic and prognostic RNA methylation related genes for GBC integrated transcriptome bioinformatics analysis. Lists of GBC-related genes and methylation-related genes were collected from public databases to screen differentially expressed genes (DEGs) by using the limma package and the RobustRankAggreg (RRA) package. The core genes were collected with batch effects corrected by the RRA algorithm through protein interaction network analysis, signaling pathway enrichment analysis and gene ranking. Four modules obtained from four public microarray datasets were found to be related to GBC, and , , , , , , , , , , , , , , , , and were revealed to be potential hub genes involved in methylation-related pathways and bile metabolism-related pathways. Among these, , , , , and were predicted to be methylated genes in GBC, but had no modification sites for RNA methylation. Furthermore, survival analysis of TCGA (the Cancer Genome Atlas) database showed that six genes among the hub genes, , , , , , and , were highly expressed and significantly correlated with worse prognosis. Gene correlation analysis revealed that the was positively correlated with the , , and , while was positively correlated with the , , and . In addition, the results of immunohistochemistry (IHC) showed that the expressions of FGA, F2, CFH, PIPOX, ITIH4, GNMT, MAT1A, MTHFD1, HPX, CFHR3, NAT2, and ENPP1 were higher in GBC tissues than that in control tissues. In conclusion, two genes, and , were identified as RNA methylation-related genes also involved in bile metabolism in GBC, which may be novel biomarkers to early diagnose and evaluate prognosis for GBC.
胆囊癌（GBC）具有较高的侵袭和转移风险，仍然是最常见的胆道恶性肿瘤。GBC的手术切除是唯一有效的治疗方法，但由于缺乏及时诊断，大多数患者错失了根治性手术的机会。本研究的目的是通过整合转录组生物信息学分析来鉴定和验证GBC早期候选诊断和预后相关的RNA甲基化基因。从公共数据库收集GBC相关基因和甲基化相关基因列表，使用limma软件包和RobustRankAggreg（RRA）软件包筛选差异表达基因（DEG）。通过蛋白质相互作用网络分析、信号通路富集分析和基因排名，利用RRA算法校正批次效应后收集核心基因。从四个公共微阵列数据集中获得的四个模块被发现与GBC相关，并且，，，，，，，，，，，，，，，，和被揭示为参与甲基化相关途径和胆汁代谢相关途径的潜在枢纽基因。其中，，，，，和被预测为GBC中的甲基化基因，但没有RNA甲基化修饰位点。此外，对TCGA（癌症基因组图谱）数据库的生存分析表明，枢纽基因中的六个基因，，，，，和高表达，并且与较差的预后显著相关。基因相关性分析表明与，，和呈正相关，而与，，和呈正相关。此外，免疫组织化学（IHC）结果表明，FGA、F2、CFH、PIPOX、ITIH4、GNMT、MAT1A、MTHFD1、HPX、CFHR3、NAT2和ENPP1在GBC组织中的表达高于对照组织。总之，两个基因和被鉴定为与GBC中胆汁代谢相关的RNA甲基化相关基因，可能是GBC早期诊断和评估预后的新型生物标志物。
