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A nine-gene signature as prognostic biomarker in gastric cancer by bioinformatics analysis

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Abstract

Purpose

The prognosis of advanced gastric cancer (GC) remains poor. It is urgent and necessary to find suitable prognostic markers. miR-619-5p is highly expressed in GC. However, the value of miR-619-5p and its target genes as prognostic biomarkers of GC is unclear.

Methods

RT-PCR was performed to verify the expression of miR-619-5p in GC cell lines and their exosomes. Western blotting and transmission electron microscope were used to identify exosomes. The target genes of miR-619-5p were predicted by RNA22 and TargetScan. The differentially expressed genes (DEGs) and prognosis-related genes (PRGs) were obtained using The Cancer Genome Atlas (TCGA) database. The DAVID database was used to analyse pathway enrichment and functional annotation of common target genes. The STRING database and Cytoscape software were used to screen key genes and visualize their functional modules. The survival analysis was conducted using TCGA and Kaplan–Meier Plotter (KMP) databases. Finally, a prognostic model was constructed on the foundation of the key genes to assess the reliability of the screening process.

Results

The expression of miR-619-5p in GC cells and their exosomes was proved to be significantly higher than that in normal cell lines. There are 129 common target genes involved in 3 pathways and 28 functional annotations. Finally, nine key target genes of GC (BRCA1, RAD51, KIF11, ERCC6L, BRIP1, TIMELESS, CDC25A, CLSPN and NCAPG2) were identified, and a prognostic model was successfully constructed with a good predictive ability.

Conclusions

The model of 9-gene signature could effectively predict the prognosis of GC, and have great potential to be novel prognostic factors and therapeutic targets for patients with GC.

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Data availability

All data and results of this study are available from the corresponding author upon reasonable request.

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Acknowledgements

We thank all members in the Key Laboratory of Digestive System Tumours of Gansu Province.

Funding

This research was supported by Major Science and Technology Special Project of Gansu Province (20ZD7FA003), the Department of Science and Technology of Gansu Province (21JR1RA122), the Fundamental Research Funds for the central Universities (lzujbky-2021-ct18, lzujbky-2022-sp08), the Science Foundation of Gansu Province (20JR10RA732) and the Medical Research Improvement Project of Lanzhou University (lzuyxcx-2022-154).

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Author notes

  1. Guan Wang and ZhiJian Ren have contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Digestive System Tumours of Gansu Province, The Second Clinical Medical College of Lanzhou University, Second Hospital of Lanzhou University, 82 Cuiying Gate, Lanzhou, 730030, Gansu, China

    Guan Wang, Zhijian Ren, Yang Zhao & Yumin Li

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  1. Guan Wang
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Correspondence to Yumin Li.

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Wang, G., Ren, Z., Zhao, Y. et al. A nine-gene signature as prognostic biomarker in gastric cancer by bioinformatics analysis. Clin Transl Oncol 25, 3296–3306 (2023). https://doi.org/10.1007/s12094-023-03180-y

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