Identification of driver genes in lupus nephritis based on comprehensive bioinformatics and machine learning

Abstract

BackgroundLupus nephritis (LN) is a common and severe glomerulonephritis that often occurs as an organ manifestation of systemic lupus erythematosus (SLE). However, the complex pathological mechanisms associated with LN have hindered the progress of targeted therapies.MethodsWe analyzed glomerular tissues from 133 patients with LN and 51 normal controls using data obtained from the GEO database. Differentially expressed genes (DEGs) were identified and subjected to enrichment analysis. Weighted gene co-expression network analysis (WGCNA) was utilized to identify key gene modules. The least absolute shrinkage and selection operator (LASSO) and random forest were used to identify hub genes. We also analyzed immune cell infiltration using CIBERSORT. Additionally, we investigated the relationships between hub genes and clinicopathological features, as well as examined the distribution and expression of hub genes in the kidney.ResultsA total of 270 DEGs were identified in LN. Using weighted gene co-expression network analysis (WGCNA), we clustered these DEGs into 14 modules. Among them, the turquoise module displayed a significant correlation with LN (cor=0.88, p<0.0001). Machine learning techniques identified four hub genes, namely CD53 (AUC=0.995), TGFBI (AUC=0.997), MS4A6A (AUC=0.994), and HERC6 (AUC=0.999), which are involved in inflammation response and immune activation. CIBERSORT analysis suggested that these hub genes may contribute to immune cell infiltration. Furthermore, these hub genes exhibited strong correlations with the classification, renal function, and proteinuria of LN. Interestingly, the highest hub gene expression score was observed in macrophages.ConclusionCD53, TGFBI, MS4A6A, and HERC6 have emerged as promising candidate driver genes for LN. These hub genes hold the potential to offer valuable insights into the molecular diagnosis and treatment of LN.

Lupus Nephritis Biomarkers: A Critical Review

“…These genes have been shown to correlate with both the occurrence and severity of LN; this has been confirmed across various cohorts [139][140][141][142][143]. Wang et al used weighted gene co-expression network analysis to identify four hub genes, namely CD53 (AUC = 0.995), TGFBI (AUC = 0.997), MS4A6A (AUC = 0.994), and HERC6 (AUC = 0.999), which are involved in the development of the inflammatory response and immune activation in LN (p < 0.0001) [144]. Yavuz et al discovered that MERTK, a novel genetic region, contributes to the risk of developing LN and ESRD in patients with SLE, a finding that has been replicated across various ethnicities [145].…”