ArticleTranslational cancer research2020
Identification of tumor microenvironment-related genes in lower-grade gliomas by mining TCGA database.
Article in Translational cancer research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
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- Silencing DTX3L Inhibits the Progression of Cervical Carcinoma by Regulating PI3K/AKT/mTOR Signaling Pathway.International journal of molecular sciences · 2023Article
- Tripartite motif protein 6 promotes hepatocellular carcinoma progression via multiple pathways.Turkish journal of medical sciences · 2023Article
- Factors to be considered in designing frameworks for automated bioinformatics pipelines-a perspective based on application setting.Translational cancer research · 2020Article
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Abstract
backgroundLower-grade gliomas (LGGs) are ubiquitous and fatal branches of brain neoplasm. Finding biomarkers related to diagnosis and treatment is essential for the treatment of LGG. It is possible to reveal the potential links between tumor microenvironment and overall survival (OS) in LGG by mining the mRNA expression profile from the TCGA database. Our primary purpose was to explore key genes that can be applied for diagnosis or treatment in LGG microenvironment.
methodsBased on the ESTIMATE algorithm, the immune and stromal scores were calculated to measure the extent of infiltration of immune cells and stromal cells, respectively. The LGG samples from TCGA database were assigned into high- or low-score groups per the immune and stromal scores and differentially expressed genes (DEGs) were selected by comparing gene expression levels in the two groups. Functional enrichment analysis and protein-protein interaction (PPI) networks were performed to analyze DEGs. Finally, selected DEGs were validated using another independent LGG cohort from CGGA dataset.
resultsThe results indicated that immune/stromal scores correlated with LGG prognosis. Furtherly, survival analysis conducted for each subtype shown that immune/stromal scores were only significantly associated with the prognosis of astrocytoma, IDH-wildtype, and there was no significant statistical difference in the other subtypes. Functional enrichment analysis and protein-protein interaction (PPI) networks further showed that the upregulated DEGs were primarily involved in immune response, plasma membrane, and cytokine binding. Accordingly, a series of genes that have significant impacts on prognosis and are significantly associated with the tumor microenvironment were obtained.
conclusionsBased on the ESTIMATE algorithm, we first explored the relationship between immune/stromal scores and prognosis in different subtypes of LGG and the result shown that the scores were only strongly associated with the prognosis of astrocytoma, IDH-wildtype. Furtherly, a comprehensive bioinformatics analysis of the gene expression profiles of astrocytoma, IDH-wildtype patients was conducted,
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