Bioinformatic Profiling of Prognosis-Related Genes in Malignant Glioma Microenvironment

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/METHODS...

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Autores principales: Li, Yong, Deng, Gang, Qi, Yangzhi, Zhang, Huikai, Gao, Lun, Jiang, Hongxiang, Ye, Zhang, Liu, Baohui, Chen, Qianxue
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Scientific Literature, Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7780890/
https://www.ncbi.nlm.nih.gov/pubmed/32843610
http://dx.doi.org/10.12659/MSM.924054
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author Li, Yong
Deng, Gang
Qi, Yangzhi
Zhang, Huikai
Gao, Lun
Jiang, Hongxiang
Ye, Zhang
Liu, Baohui
Chen, Qianxue
author_facet Li, Yong
Deng, Gang
Qi, Yangzhi
Zhang, Huikai
Gao, Lun
Jiang, Hongxiang
Ye, Zhang
Liu, Baohui
Chen, Qianxue
author_sort Li, Yong
collection PubMed
description 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/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.
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spelling pubmed-77808902021-01-07 Bioinformatic Profiling of Prognosis-Related Genes in Malignant Glioma Microenvironment Li, Yong Deng, Gang Qi, Yangzhi Zhang, Huikai Gao, Lun Jiang, Hongxiang Ye, Zhang Liu, Baohui Chen, Qianxue Med Sci Monit Database Analysis 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/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. International Scientific Literature, Inc. 2020-08-26 /pmc/articles/PMC7780890/ /pubmed/32843610 http://dx.doi.org/10.12659/MSM.924054 Text en © Med Sci Monit, 2020 This work is licensed under Creative Common Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0 (https://creativecommons.org/licenses/by-nc-nd/4.0/) )
spellingShingle Database Analysis
Li, Yong
Deng, Gang
Qi, Yangzhi
Zhang, Huikai
Gao, Lun
Jiang, Hongxiang
Ye, Zhang
Liu, Baohui
Chen, Qianxue
Bioinformatic Profiling of Prognosis-Related Genes in Malignant Glioma Microenvironment
title Bioinformatic Profiling of Prognosis-Related Genes in Malignant Glioma Microenvironment
title_full Bioinformatic Profiling of Prognosis-Related Genes in Malignant Glioma Microenvironment
title_fullStr Bioinformatic Profiling of Prognosis-Related Genes in Malignant Glioma Microenvironment
title_full_unstemmed Bioinformatic Profiling of Prognosis-Related Genes in Malignant Glioma Microenvironment
title_short Bioinformatic Profiling of Prognosis-Related Genes in Malignant Glioma Microenvironment
title_sort bioinformatic profiling of prognosis-related genes in malignant glioma microenvironment
topic Database Analysis
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7780890/
https://www.ncbi.nlm.nih.gov/pubmed/32843610
http://dx.doi.org/10.12659/MSM.924054
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