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. 2019 Oct 30:2019:8901649.
doi: 10.1155/2019/8901649. eCollection 2019.

Data Mining of Prognostic Microenvironment-Related Genes in Clear Cell Renal Cell Carcinoma: A Study with TCGA Database

Bin Chen  1 , Wei Chen  1 , Jing Jin  1 , Xueping Wang  1 , Yifang Cao  1 , Yi He  1
Affiliations

Data Mining of Prognostic Microenvironment-Related Genes in Clear Cell Renal Cell Carcinoma: A Study with TCGA Database

Bin Chen et al. Dis Markers. .

Abstract

Clear cell renal cell carcinoma (ccRCC) is one of the most prevalent kidney malignancies. The tumor microenvironment (TME) is highly related to the oncogenesis, progress, and prognosis of ccRCC. The aim of this study was to infer the level of infiltrating stromal and immune cells and assess the prognostic value of them. The gene expression profile was obtained from TCGA and used for calculating the stromal and immune scores. Based on a cut-off value, patients were divided into low- and high-stromal/immune score groups. Survival analysis was performed to evaluate the prognostic value of stromal and immune scores. Moreover, differentially expressed genes (DEGs) that are highly related to TME were determined and applied for functional enrichment analysis and protein-protein interaction (PPI) network. The Kaplan-Meier plot demonstrated that patients with high-immune scores and stromal scores had poorer clinical outcome. In addition, a total of 89 DEGs were identified and mainly involved in 5 pathways. The top 5 degree genes were extracted from the PPI network; among them, IL10 and XCR1 were highly associated with prognosis of ccRCC. The results of the present study demonstrated that ESTIMATE algorithm-based stromal and immune scores may be a credible indicator of cancer prognosis and IL10 along with XCR1 may be a potential key regulator for the TME of ccRCC.

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Conflict of interest statement

The authors declare that there is no conflict of interests.

Figures

Figure 1
Figure 1
Distribution of stromal and immune scores. (a) Different Fuhrman grades and (b) TNM staging (c) with or without lymph node metastasis. N0, N1, N2, and N3 represent 0, 1, 2, and 3 lymph node metastases. (d) Distant metastasis.
Figure 2
Figure 2
Prognostic values for overall survival: (a) immune scores and (b) stromal scores.
Figure 3
Figure 3
Analysis of DEGs. (a) 42 upregulated overlapping DEGs and (b) 47 downregulated overlapping DEGs. (c) Protein-protein interaction (PPI) network with confidence >0.7. Red and green nodes represent upregulated and downregulated genes, respectively. (d) The enriched pathways with P < 0.05. (e) The enriched GO terms with P < 0.05 and gene count >5.
Figure 4
Figure 4
The distribution of immunomodulators (a) between normal samples and ccRCC samples, (b) low- and high-immune scores, and (c) low- and high-stromal scores. (d) Kaplan-Meier curves for overall survival of CTLA-4 and (e) LAG-3.
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