Identification and Validation of Prognostic Biomarkers Specifically Expressed in Macrophage in IgA Nephropathy Patients Based on Integrated Bioinformatics Analyses

Yuqing Ding; Hua Li; Lichen Xu; Yukun Wang; Huiying Yang

doi:10.3389/fmolb.2022.884588

Identification and Validation of Prognostic Biomarkers Specifically Expressed in Macrophage in IgA Nephropathy Patients Based on Integrated Bioinformatics Analyses

Front Mol Biosci. 2022 May 5:9:884588. doi: 10.3389/fmolb.2022.884588. eCollection 2022.

Authors

Yuqing Ding¹, Hua Li¹, Lichen Xu¹, Yukun Wang², Huiying Yang¹

Affiliations

¹ Department of Nephrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
² Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.

Abstract

Background: Immunoglobulin A nephropathy (IgAN) is the most common type of primary glomerulonephritis worldwide and a frequent cause of end-stage renal disease. The inflammation cascade due to the infiltration and activation of immune cells in glomeruli plays an essential role in the progression of IgAN. In this study, we aimed to identify hub genes involved in immune infiltration and explore potential prognostic biomarkers and therapeutic targets in IgAN. Methods: We combined the single-cell and bulk transcriptome profiles of IgAN patients and controls with clinical data. Through single-cell analysis and weighted gene co-expression network analysis (WGCNA), Gene Ontology (GO) enrichment analysis, and differentially expressed gene (DEG) analysis in the bulk profile, we identified cell-type-specific potential hub genes in IgAN. Real hub genes were extracted via validation analysis and clinical significance analysis of the correlation between the expression levels of genes and the estimated glomerular filtration rate (eGFR) in the external dataset. Gene set enrichment analysis was performed to predict the probable roles of the real hub genes in IgAN. Results: A total of eleven cell clusters were classified via single-cell analysis, among which macrophages showed a variable proportion between the IgAN and normal control samples. We recognized six functional co-expression gene modules through WGCNA, among which the black module was deemed an IgAN-related and immune-involving module via GO enrichment analysis. DEG analysis identified 45 potential hub genes from genes enriched in GO terms. A total of twenty-three potential hub genes were specifically expressed in macrophages. Furthermore, we validated the differential expression of the 23 potential hub genes in the external dataset and identified nine genes with prognostic significance as real hub genes, viz., CSF1R, CYBB, FPR3, GPR65, HCLS1, IL10RA, PLA2G7, TYROBP, and VSIG4. The real hub gens are thought to contribute to immune cell regulation, immunoreaction, and regulation of oxidative stress, cell proliferation, and material metabolism. Conclusion: In this study, we demonstrated that macrophages infiltrated the glomeruli and contributed to the inflammatory response in IgAN. Based on integrated bioinformatics analyses of single-cell and bulk transcriptome data, we highlighted nine genes as novel prognostic biomarkers, which may enable the development of innovative prognostic and therapeutic strategies for IgAN.

Keywords: IgA nephropathy; bulk transcriptome; integrated bioinformatics analyses; prognostic biomarkers; single-cell RNA sequencing.