Identification of the hub genes and transcription factor-miRNA axes involved in Helicobacter pylori-associated gastric cancer

Peng Zhao; Xianxiong Ma; Jiancheng Cheng; Hengyu Chen; Lei Li

doi:10.3892/ol.2022.13209

Identification of the hub genes and transcription factor-miRNA axes involved in Helicobacter pylori-associated gastric cancer

Oncol Lett. 2022 Mar;23(3):89. doi: 10.3892/ol.2022.13209. Epub 2022 Jan 21.

Authors

Peng Zhao¹, Xianxiong Ma², Jiancheng Cheng³, Hengyu Chen^{4

5}, Lei Li⁶

Affiliations

¹ Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.
² Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.
³ Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.
⁴ Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan 570100, P.R. China.
⁵ Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.
⁶ Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China.

Abstract

It has been previously reported that transcription factor-microRNA (TF-miRNA) axes play a significant role in the carcinogenesis of several types of malignant tumor. However, there is a lack of research into the differences in the mechanism of Helicobacter pylori (HP)-positive [HP(+)] and HP-negative [HP(-)] gastric cancer. The aim of the present study was to identify the hub genes and TF-miRNA axes, and to determine the potential mechanisms involved in HP-associated gastric cancer. HP-associated mRNA and miRNA data, as well as the corresponding clinical information, was downloaded from The Cancer Genome Atlas database. Differentially expressed genes (DEGs) and DE miRNAs (DEMs) were then identified from the HP(+) and HP(-) cancer mRNA and miRNA datasets, respectively. Subsequently, gene set enrichment analysis and the protein-protein interaction (PPI) networks were investigated using the ClusterProfiler packages. Lastly, TF-miRNA-DEG networks were constructed using the miRWalk online tool. A total of 1,050 DEGs and 13 DEMs were identified from the normalized mRNA and miRNA expression datasets, respectively. In addition, 180 Gene Ontology terms and 30 Kyoto Encyclopedia of Genes and Genomes pathways were found to be enriched, while 6 hub genes were identified from the PPI analysis. Furthermore, 7 TF-miRNA interactions and 181 TF-miRNA-DEG axes were constructed using an integrated bioinformatics approach, while 2 TF-miRNA interactions (ZEB1-miRNA-144-3p and PAX2-miRNA-592) were confirmed using reverse transcription-quantitative PCR in samples from enrolled patients. Moreover, the ZEB1-miRNA-144-3p axis was further validated based on dual luciferase reporter assay results. In summary, an integrated bioinformatics approach was used to screen the significant molecular and regulatory axes, which may provide a novel direction to investigate the pathogenesis of gastric cancer associated with HP.

Keywords: Helicobacter pylori; The Cancer Genome Atlas; bioinformatics; gastric cancer; microRNA; transcription factor.

Grants and funding

This study was supported by the National Natural Science Foundation of China (grant no. 81702397). This project supported by Hainan Province Clinical Medical Center.