System analysis based on the migration- and invasion-related gene sets identifies the infiltration-related genes of glioma

Shuang Shi; Jiacheng Zhong; Wen Peng; Haoyang Yin; Dong Zhong; Hongjuan Cui; Xiaochuan Sun

doi:10.3389/fonc.2023.1075716

System analysis based on the migration- and invasion-related gene sets identifies the infiltration-related genes of glioma

Front Oncol. 2023 Apr 6:13:1075716. doi: 10.3389/fonc.2023.1075716. eCollection 2023.

Authors

Shuang Shi¹, Jiacheng Zhong¹, Wen Peng^{2

3}, Haoyang Yin¹, Dong Zhong¹, Hongjuan Cui^{2

3}, Xiaochuan Sun¹

Affiliations

¹ Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.
² State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.
³ Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.

Abstract

The current database has no information on the infiltration of glioma samples. Here, we assessed the glioma samples' infiltration in The Cancer Gene Atlas (TCGA) through the single-sample Gene Set Enrichment Analysis (ssGSEA) with migration and invasion gene sets. The Weighted Gene Co-expression Network Analysis (WGCNA) and the differentially expressed genes (DEGs) were used to identify the genes most associated with infiltration. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the major biological processes and pathways. Protein-protein interaction (PPI) network analysis and the least absolute shrinkage and selection operator (LASSO) were used to screen the key genes. Furthermore, the nomograms and receiver operating characteristic (ROC) curve were used to evaluate the prognostic and predictive accuracy of this clinical model in patients in TCGA and the Chinese Glioma Genome Atlas (CGGA). The results showed that turquoise was selected as the hub module, and with the intersection of DEGs, we screened 104 common genes. Through LASSO regression, TIMP1, EMP3, IGFBP2, and the other nine genes were screened mostly in correlation with infiltration and prognosis. EMP3 was selected to be verified in vitro. These findings could help researchers better understand the infiltration of gliomas and provide novel therapeutic targets for the treatment of gliomas.

Keywords: LASSO; WGCNA; glioma; infiltration; ssGSEA.

Grants and funding

This research was supported by the Natural Science Foundation of Chongqing (cstc2022ycjh-bgzxm0145) and the pilot program of Southwest University (SWU-XDZD22006).