Journal of Shanghai Jiao Tong University (Medical Science) >

2022 , Vol. 42 >Issue 4: 464 - 471

DOI: https://doi.org/10.3969/j.issn.1674-8115.2022.04.008

Basic research

Involvement of miRNA target genes in esophageal squamous cell carcinoma through ubiquitination based on GEO database

  • Bu JIN ,
  • Ying YUAN ,
  • Wanyu CHEN ,
  • Hudong XU ,
  • Xiaolei HUANG ,
  • Jialu HE ,
  • Hong YU
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  • Department of Pathology, Jiading Branch of Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201803, China
YU Hong, E-mail: 1154879190@qq.com.

Received date: 2021-09-03

  Accepted date: 2022-04-06

  Online published: 2022-04-28

Supported by

The Funding of Science and Technology Commission Shanghai Municipality(19511121400)

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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

Cite this article

Bu JIN , Ying YUAN , Wanyu CHEN , Hudong XU , Xiaolei HUANG , Jialu HE , Hong YU . 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 . DOI: 10.3969/j.issn.1674-8115.2022.04.008

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