Screening TCGA Database for Prognostic Genes in Lower Grade Glioma Microenvironment

Jie Ni 1, Siwen Liu 2, Feng Qi 3, Xiao Li 4, Shaorong Yu 1, Jifeng Feng 1, Yuxiao Zheng 4

Affiliations

PMID: 32309356
PMCID: PMC7154476
DOI: 10.21037/atm.2020.01.73

Abstract

Background: To identify prognostic hub genes which associated with tumor microenvironment (TME) in lower grade glioma (LGG) of central nervous system.

Methods: We downloaded LGG patients gene transcriptome profiles of the central nervous system in The Cancer Genome Atlas (TCGA) database. Clinical characteristics and survival data through the Genomic Data Commons (GDC) tool were extracted. We used limma package for normalization processing. Scores of immune, stromal and ESTIMATE were calculated using ESTIMATE algorithm. Then, box plots were applied to explore the association between immune scores, stromal scores, ESTIMATE scores and histological type, tumor grade. Kaplan-Meier (K-M) analysis was utilized to explore the prognostic value of scores. Furthermore, heatmaps and volcano plots were applied for visualizing expression of differential expressed-gene screening and cluster analysis. Venn plots were constructed to screen the intersected differentially expressed genes (DEGs). In addition, enrichment of functions and signaling pathways and Gene Set Enrichment Analysis (GESA) of the DEGs were performed. Then we used protein-protein interaction (PPI) network and Cytoscape software to identify hub genes. We evaluated the prognostic value of hub genes and risk score (RS) calculated based on multivariate cox regression analysis. Finally, relationships of hub genes with the TME of LGG patients were evaluated based on tumor immune estimation resource (TIMER) database.

Results: Gene expression profiles and clinical data of 514 LGG samples were extracted and the results revealed that higher scores were significantly related with histological types and higher tumor grade (P<0.0001, respectively). Besides, higher scores were associated with worse survival outcomes in immune scores (P=0.0167), stromal scores (P=0.0035) and ESTIMATE scores (P=0.0190). Then, 785 up-regulated intersected genes and 357 down-regulated intersected genes were revealed. Functional enrichment analysis revealed that intersected genes were associated with immune response, inflammatory response, plasma membrane and receptor activity. After PPI network construction and cytoHubba analysis, 25 tumor immune-related hub genes were identified and enriched pathways were identified by GSEA. Besides, receiver operating characteristic (ROC) curves showed significantly predictive accuracy [area under curve (AUC) =0.771] of RS. Furthermore, significant prognostic values of hub genes were observed, and the relationships between hub genes and LGG TME were demonstrated.

Conclusions: We identified 25 TME-related genes which significantly associated with overall survival in patients with central nervous system LGG from TCGA database.

Keywords: Immune/stromal scores; biomarkers; immune infiltrates; lower grade glioma (LGG); tumor microenvironment (TME).