Bioinformatics analysis of the hub genes and immune microenvironment in BK virus-associated nephropathy after renal transplantation

doi:10.3877/cma.j.issn.1674-3903.2022.04.002

Abstract

Abstract:

Objective

To analyze hub genes in BK virus-associated nephropathy (BKVAN) after renal transplantation and its relationship with infiltrating immune cells by bioinformatics methods.

Methods

GSE75693 and GSE72925 (BKVAN-related datasets) and GSE47199 (a BK viremia-related dataset) were downloaded from GEO database. Then GSE75693 and GSE72925 were combined to screen for differential expression genes (DEGs), followed by gene ontology biological process (BPGO), Kyoto encyclopedia of genes and genomes (KEGG) pathway and protein-protein interaction (PPI) network analysis to further screen hub genes. Immune infiltration analysis was performed using CIBERSORT, and then correlations between differential immune cells and hub genes were calculated. Finally, common hub genes in both BK viremia and BKVAN were screened in the GSE47199 dataset, and the biological process of common hub genes in BKVAN and BK viremia were identified using gene set enrichment analysis (GSEA). All statistical analysis and visualizations were based on R language (4.0.2). P<0.05 was considered statistically significant.

Results

A total of 175 up-regulated and 70 down-regulated DEGs were screened from the combined dataset. Nine hub genes were obtained from the PPI network by five methods of intersection, and the hub genes were mainly enriched in the processes related to immune cell activation and function; in the KEGG analysis, the hub genes were mainly enriched in viral proteins, cytokine and cytokine receptor interactions, cytokine-cytokine receptor interactions and chemokine signaling pathways. Immune infiltration analysis showed that PTPRC, CCL5, TYROBP, CXCL10, CD2 and CXCL9 were associated with infiltrating immune cells in BKVAN. CD2 was the common hub gene for both BKVAN and BK viremia.

Conclusions

In this study, the hub genes of BKVAN were screened by bioinformatics, among which PTPRC, CCL5, TYROBP, CXCL10, CD2 and CXCL9 were associated with immune cells infiltration in BKVAN, and CD2 was the common hub gene of BKVAN and BK viremia.

Key words: Renal transplantation, BK virus-associated nephropathy, BK viremia, Bioinformatics

Boqing Dong, Meng Dou, Jing Zhang, Xinshun Feng, Jin Zheng, Xiao Li, Xiaoming Ding, Wujun Xue, Yang Li. Bioinformatics analysis of the hub genes and immune microenvironment in BK virus-associated nephropathy after renal transplantation[J]. Chinese Journal of Transplantation(Electronic Edition), 2022, 16(04): 201-209.

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References 34

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