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26 August 2020 : Database Analysis  

Bioinformatic Profiling of Prognosis-Related Genes in Malignant Glioma Microenvironment

Yong Li1ABCDE, Gang Deng1ABCDE, Yangzhi Qi1BCD, Huikai Zhang1BCD, Lun Gao1BCD, Hongxiang Jiang1BCD, Zhang Ye1BCD, Baohui Liu1ABCDE, Qianxue Chen1ABCDE*

DOI: 10.12659/MSM.924054

Med Sci Monit 2020; 26:e924054

Abstract

BACKGROUND: Gliomas are the most common primary tumors of the brain and spinal cord. The tumor microenvironment (TME) is the cellular environment in which tumors exist. This study aimed to identify the role of the TME and the effects of genes involved in the TME of malignant glioma.

MATERIAL AND METHODS: The ESTIMATE algorithms in the R package were used to calculate the immune and stromal scores of samples in the TCGA and GSE4290 datasets. The associations of stromal and immune scores with clinicopathological characteristics and overall survival of malignant glioma patients were assessed by analysis of variance and Kaplan-Meier analysis. Differentially expressed genes (DEGs) were obtained through the median immune and stromal score using the R package “limma”. Functional enrichment analysis and the PPI network MCODE were used to analyze DEGs.

RESULTS: Increased immune and stromal scores were closely related with advanced glioma grade and poor prognosis (all P<0.01). In total, 558 DEGs were found and most were related to tumor prognosis. Functional enrichment analysis showed that DEGs were associated with cell-matrix regulation and immune response. Four hub modules related to tumor angiogenesis, collagen formation, and immune response were found and analyzed. Previously overlooked microenvironment-related genes such as LAMB1, FN1, ACTN1, TRIM, SERPINH1, CYBA, LAIR1, and LILRB2 showed prognostic values in malignant glioma patients.

CONCLUSIONS: The glioma stromal/immune scores are closely related to glioma grade, histology, and survival time. Some glioma microenvironment-related genes including LAMB1, FN1, ACTN1, TRIM6, SERPINH1, CYBA, LAIR1, and LILRB2 show prognostic values in malignant gliomas and serve as potential biomarkers.

Keywords: Glioma, Stromal Cells, tumor microenvironment, Algorithms, Biomarkers, Tumor, Computational Biology, Datasets as Topic, Gene Expression Profiling, Prognosis

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Medical Science Monitor eISSN: 1643-3750
Medical Science Monitor eISSN: 1643-3750