Immune Cell Metabolism In Kidneys Of Patients With Lupus Nephritis Revealed By Single-Cell RNA Sequencing

Objectives:To explore the metabolic changes of renal immune cells in patients with lupus nephritis(LN)and its correlation with cell function and interferon stimulation signal at the level of single-cell transcriptome.Methods:We obtained the published single-cell sequencing and clinical data of renal immune cells in patients with LN and reproduce the clustering.The gene sets of cell metabolism,cell function,and interferon response were obtained from the molecular signatures database(MSigDB)and the literature.The difference of metabolic gene set scores between cell subsets and their correlation with cell function gene set scores and the interferon-stimulated gene(ISG)score were calculated.For the metabolism pathways related to the ISG score in multiple cell subsets,the correlation and partial correlation between the unique molecular identifier(UMI)count of genes in the metabolic pathway and the ISG score were analyzed.Results:A total of 2737 immune cells from 26 patients with LN and 8 healthy controls were divided into four B cell subsets,six myeloid cell subsets,eight T cell subsets,and two NK cell subsets.The patients'tissue-resident macrophages significantly upregulated amino sugar and nucleotide sugar pathway,and down-regulated 7 metabolism pathways,including the nitrogen metabolism pathway and the arginine and proline metabolism pathway.In the rest subsets of macrophages which expanded in the LN patients,the metabolism pathways positively related to phagocytosis score included some of those upregulated in the polarization of M2 macrophages,while the pathways positively related to the inflammatory score included some of those upregulated for M1 macrophage polarization.In plasmacytoid dendritic cells,there were 17 pathways positively related to the production of type I interferon,such as the glycolysis and gluconeogenesis pathway and the fatty acid metabolism pathway.In CD4+T cells,effector memory T cells from LN patients significantly upregulated two amino acid metabolism pathways and the nicotinate and nicotinamide metabolism pathway while down-regulated two lipid metabolism pathways and two glucose metabolism pathways.In activated B cells,6 pathways positively correlated with the age-associated B cell(ABC)score,including the oxidative phosphorylation pathway,while the nicotinate and nicotinamide metabolism pathway negatively correlated with the ABC score.Compared with immature B cells,activated B cells significantly up-regulated 13 pathways,including the glycolysis and gluconeogenesis pathway,the fatty acid metabolism pathway,and the oxidative phosphorylation pathway.In plasma cells,the pathways positively correlated with the long-lived plasma cell score was the glycine,serine,and threonine metabolism pathway.In multiple cell subsets of LN patients,there were four pathways positively correlated with the ISG score,including the nicotinate and nicotinamide metabolism pathway,in which the transformed UMI count value of NT5C3A,NAMPT,and CD38 was significantly correlated with the ISG score,respectively.The only pathway negatively correlated with the ISG score in multiple clusters was the oxidative phosphorylation pathway.Several mitochondrial genes in this pathway were negatively correlated with the ISG score in macrophages and T cells,respectively.Conclusion:Compared with healthy controls,renal immune cells in patients with LN have metabolic changes at the transcriptional level,and there is a correlation between immune cell metabolism and cell function.Under the condition of interferon stimulation in vivo,oxidative phosphorylation deficiency and changes in nicotinate and nicotinamide levels may occur in multiple immune cell populations.