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. 2023 Feb 6:2023:8405945.
doi: 10.1155/2023/8405945. eCollection 2023.

Identification of Differentially Methylated Genes Associated with Clear Cell Renal Cell Carcinoma and Their Prognostic Values

Bin Wan  1 , Yang Yang  1 , Zhuo Zhang  1
Affiliations

Identification of Differentially Methylated Genes Associated with Clear Cell Renal Cell Carcinoma and Their Prognostic Values

Bin Wan et al. J Environ Public Health. .

Retraction in

Abstract

Objective: Renal cell carcinoma (RCC) is a heterogeneous disease comprising histologically defined subtypes among which clear cell RCC (ccRCC) accounts for 70% of all RCC cases. DNA methylation constitutes a main part of the molecular mechanism of cancer evolution and prognosis. In this study, we aim to identify differentially methylated genes related to ccRCC and their prognostic values.

Methods: The GSE168845 dataset was downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs) between ccRCC tissues and paired tumor-free kidney tissues. DEGs were submitted to public databases for functional and pathway enrichment analysis, protein-protein interaction (PPI) analysis, promoter methylation analysis, and survival correlation analysis.

Results: In the setting of |log2FC| ≥ 2 and adjusted p value <0.05 during differential expression analysis of the GSE168845 dataset, 1659 DEGs between ccRCC tissues and paired tumor-free kidney tissues were sorted out. The most enriched pathways were "T cell activation" and "cytokine-cytokine receptor interaction." After PPI analysis, 22 hub genes related to ccRCC stood out, among which CD4, PTPRC, ITGB2, TYROBP, BIRC5, and ITGAM exhibited higher methylation levels, and BUB1B, CENPF, KIF2C, and MELK exhibited lower methylation levels in ccRCC tissues compared with paired tumor-free kidney tissues. Among these differentially methylated genes, TYROBP, BIRC5, BUB1B, CENPF, and MELK were significantly correlated with the survival of ccRCC patients (p < 0.001).

Conclusion: Our study indicates the DNA methylation of TYROBP, BIRC5, BUB1B, CENPF, and MELK may be promising results for the prognosis of ccRCC.

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Conflict of interest statement

The authors declare that they have no conflicts of interest.

Figures

Figure 1
Figure 1
The volcano map (a) and heatmap (b) showing a total of 1659 DEGs (776 upregulated genes and 883 downregulated genes) and representative 50 DEGs between ccRCC tissues and paired tumor-free kidney tissues.
Figure 2
Figure 2
The bubble plots showing the top 10 GO terms at the BP, CC, and MF domains (a) and the top 20 KEGG-defined pathways (b) significantly enriched by DEGs between ccRCC tissues and paired tumor-free kidney tissues.
Figure 3
Figure 3
The PPI network containing 22 genes with degree values not less than 50 which were deemed as hub genes related to ccRCC.
Figure 4
Figure 4
The UALCAN database analysis of methylation levels of hub genes in ccRCC tissue samples (n = 324) compared with normal kidney tissue samples (n = 160) derived from TCGA.
Figure 5
Figure 5
The Kaplan–Meier plotter analysis of the correlations between differentially methylated genes and ccRCC patient survival (n = 530).
See this image and copyright information in PMC

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