基于GEO数据库探索miRNA靶基因通过泛素化参与食管鳞状细胞癌

doi:10.3969/j.issn.1674-8115.2022.04.008

摘要/Abstract

摘要：

目的·筛选食管鳞状细胞癌疾病过程中新的潜在致病基因。方法·通过GEO数据库获取miRNA芯片GSE122497和GSE164174的数据，利用GEO2R分别筛选出食管鳞状细胞癌患者和健康人的差异miRNA，Venn diagram webtool 工具取交集；采用Target Scan工具及DIANATOOLS工具预测差异miRNA的靶基因，取2款工具的预测靶基因交集进行基因功能分析；利用STRING工具分析靶基因的蛋白质相互作用并选取Hub基因。结果·①芯片中共计108个差异miRNA。②取Target Scan工具和DIANATOOLS工具的交集后，共有1 354个差异靶基因。③基因本体（Gene Ontology，GO）分析结果表明，差异靶基因的基因功能显著富集于DNA模板转录调控、RNA聚合酶Ⅱ启动子的转录调控等生物过程，RNA聚合酶Ⅱ核心启动子近端序列特异性DNA结合、蛋白结合、金属离子结合等分子功能；主要存在于细胞核、核质、细胞质等细胞成分。按照富集的基因数目降序排列，京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）分析结果表明上述基因显著富集于肿瘤通路、丝裂原活化蛋白激酶信号通路、干细胞多能性调控信号通路等。④蛋白质相互作用网络共有1 326个节点，2 300条边，平均节点连接度为3.47。筛选出的Hub基因：SMAD特异性E3泛素蛋白连接酶2（SMAD specific E3 ubiquitin protein ligase 2，SMURF2）、β-转导重复蛋白E3泛素蛋白连接酶（β-transducin repeat containing E3 ubiquitin protein ligase，BTRC）、SMAD特异性E3泛素蛋白连接酶1（SMAD specific E3 ubiquitin protein ligase 1，SMURF 1）、泛素结合酶E2 D1（ubiquitin conjugating enzyme E2 D1，UBE2D1）、E3泛素连接酶枯灵素2（cullin 2，CUL2），以往研究表明上述基因与泛素化有关。结论·经GEO数据库筛选出的SMURF2、BTRC、SMURF1、UBE2D1、CUL2基因可能通过靶向调控蛋白的泛素化参与食管鳞状细胞癌的疾病过程。

关键词: 食管鳞状细胞癌, GEO数据库, 泛素化, 生物信息学

Abstract:

objective·To screen new potential pathogenic genes in the course of esophageal squamous cell carcinoma.

Methods·The data of miRNA chips GSE122497 and GSE164174 were obtained by GEO database. The differential mirnas of esophageal cancer patients and healthy people were screened by GEO2R, and the intersection was obtained by Venn Diagram Webtool. Target Scan tool and DIANATOOLS tool were used to predict the target genes of differential miRNA, and the intersection of predicted target genes of the two tools was used for gene function analysis. The protein interactions of target genes were analyzed by using STRING tool and Hub genes were selected.

Results·① A total of 108 differential miRNAs were detected in the chip. ② After taking the intersection of Target Scan tool and DIANATOOLS tool, there were 1 354 different target genes. ③Gene Ontology (GO) analysis showed that gene functions of differential target genes were significantly enriched in biological processes such as DNA template transcriptional regulation and RNA polymerase Ⅱ promoter transcriptional regulation, as well as RNA polymerase Ⅱ core promoter proximal sequence specific DNA binding, protein binding, metal ion binding and other molecular functions. It mainly existed in nucleus, cytoplasm, cytoplasm and other cellular components. In descending order of the number of enriched genes, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the above genes were significantly enriched in tumor pathway, MAPK signaling pathway, stem cell pluripotency regulation signaling pathway, etc. ④ There were 1 326 nodes and 2 300 edges in the protein interaction network, and the average node connectivity was 3.47. The selected Hub genes were SMAD specific E3 ubiquitin protein ligase 2 (SMURF2), β-transducin repeat containing E3 ubiquitin protein ligase (BTRC), SMAD specific E3 ubiquitin protein ligase 1 (SMURF 1), ubiquitin conjugating enzyme E2 D1 (UBE2D1), and cullin 2 (CUL2). Previous studies have shown that the above genes are related to ubiquitination.

Conclusion·SMURF2, BTRC, SMURF1, UBE2D1 and CUL2 genes screened from GEO database may be involved in the disease process of esophageal squamous cell carcinoma through the ubiquitin of targeted regulatory proteins.

Key words: esophageal squamous cell carcinoma, GEO database, ubiquitin, bioinformatics

中图分类号:

R735.1

靳步, 袁颖, 陈婉玉, 徐浒东, 黄晓蕾, 何佳璐, 于红. 基于GEO数据库探索miRNA靶基因通过泛素化参与食管鳞状细胞癌[J]. 上海交通大学学报（医学版）, 2022, 42(4): 464-471.

JIN Bu, YUAN Ying, CHEN Wanyu, XU Hudong, HUANG Xiaolei, HE Jialu, YU Hong. Involvement of miRNA target genes in esophageal squamous cell carcinoma through ubiquitination based on GEO database[J]. Journal of Shanghai Jiao Tong University (Medical Science), 2022, 42(4): 464-471.

图/表 4

图1 韦恩图显示2个GEO数据集的DEMsNote：A. Upregulated miRNA. B. Downregulated miRNA.

Fig1 Venn diagram showing DEMs of two GEO datasets

图2 韦恩图显示同时被TargetScan及microT-CDS预测到的靶基因

Fig2 Target genes predicted by both TargetScan and microT-CDS

图3 靶基因功能富集分析Note：A. GO analysis of target genes; B. KEGG analysis of target genes; C. miEAA.

Fig 3 Functional enrichmeWnt analysis of target genes

图4 靶基因PPI网络分析Note：A. PPI network. B. Hub genes. C. Comparison of target genes in ESCC and normal tissues; D. GeneMANIA Cytoscape.

Fig.4 PPI network constructed with the target genes

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