Abstract
BackgroundLupus nephritis (LN) is a common complication of systemic lupus erythematosus that presents a high risk of end-stage renal disease. In the present study, we used CIBERSORT and gene set enrichment analysis (GSEA) of gene expression profiles to identify immune cell infiltration characteristics and related core genes in LN.ResultsDatasets from the Gene Expression Omnibus, GSE32591 and GSE113342, were downloaded for further analysis. The GSE32591 dataset, which included 32 LN glomerular biopsy tissues and 14 glomerular tissues from living donors, was analyzed by CIBERSORT. Different immune cell types in LN were analyzed by the Limma software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis based on GSEA were performed by clusterProfiler software. Lists of core genes were derived from Spearman correlation between the most significant GO term and differentially expressed immune cell gene from CIBERSORT. GSE113342 was employed to validate the association between selected core genes and clinical manifestation. Five types of immune cells revealed important associations with LN, and monocytes emerged as having the most prominent differences. GO and KEGG analyses indicated that immune response pathways are significantly enriched in LN. The Spearman correlation indicated that 15 genes, including FCER1G, CLEC7A, MARCO, CLEC7A, PSMB9, and PSMB8, were closely related to clinical features.ConclusionsThis study is the first to identify immune cell infiltration with microarray data of glomeruli in LN by using CIBERSORT analysis and provides novel evidence and clues for further research of the molecular mechanisms of LN.
Highlights
Lupus nephritis (LN) is a common complication of systemic lupus erythematosus that presents a high risk of end-stage renal disease
This study aimed to describe the characteristics of LN glomerular immune infiltration for the first time and to identify some key genes related to immune infiltration that affect clinical manifestation, so as to provide data resources for future research
A total of 46 samples from GSE32591 were used in this study, including 32 LN glomerular biopsy tissues and 14 glomerular tissues from living donors
Summary
Lupus nephritis (LN) is a common complication of systemic lupus erythematosus that presents a high risk of end-stage renal disease. We used CIBERSORT and gene set enrichment analysis (GSEA) of gene expression profiles to identify immune cell infiltration characteristics and related core genes in LN. Systemic lupus erythematosus (SLE), one of the most complicated autoimmune diseases in the world, is caused by various endogenous antigens [1]. Lupus nephritis (LN), a common and serious complication of SLE, is characterized by hematuria, proteinuria, and impaired glomerular filtration rate [2]. Many previous works found that immune cell infiltration is associated with treatment and clinical outcome in different types of cancer [9, 10]. Given the functionally distinct cell types that comprise the immune response, assessing
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