Single-cell RNA sequencing reveals the transcriptomic landscape of kidneys in patients with ischemic acute kidney injury

Background:Ischemic acute kidney injury(AKI)is a common syndrome associated with considerable mortality and healthcare costs.Up to now,the underlying pathogenesis of ischemic AKI remains incompletely understood,and specific strategies for early diagnosis and treatment of ischemic AKI are still lacking.Here,this study aimed to define the transcriptomic landscape of AKI patients through single-cell RNA sequencing(scRNA-seq)analysis in kidneys.Methods:In this study,scRNA-seq technology was applied to kidneys from two ischemic AKI patients,and three human public scRNA-seq datasets were collected as controls.Differentially expressed genes(DEGs)and cell clusters of kidneys were determined.Gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis,as well as the ligand-receptor interaction between cells,were performed.We also validated several DEGs expression in kidneys from human ischemic AKI and ischemia/reperfusion(I/R)injury induced AKI mice through immunohistochemistry staining.Results:15 distinct cell clusters were determined in kidney from subjects of ischemic AKI and control.The injured proximal tubules(PT)displayed a proapoptotic and proinflammatory phenotype.PT cells of ischemic AKI had up-regulation of novel pro-apoptotic genes including USP47,RASSF4,EBAG9,IER3,SASH1,SEPTIN7,and NUB1,which have not been reported in ischemic AKI previously.Several hub genes were validated in kidneys from human AKI and renal I/R injury mice,respectively.Furthermore,PT highly expressed DEGs enriched in endoplasmic reticulum stress,autophagy,and retinoic acid-inducible gene I(RIG-I)signaling.DEGs overexpressed in other tubular cells were primarily enriched in nucleotide-binding and oligomerization domain(NOD)-like receptor signaling,estrogen signaling,interleukin(IL)-12 signaling,and IL-17 signaling.Overexpressed genes in kidney-resident immune cells including macrophages,natural killer T(NKT)cells,monocytes,and dendritic cells were associated with leukocyte activation,chemotaxis,cell adhesion,and complement activation.In addition,the ligand-receptor interactions analysis revealed prominent communications between macrophages and monocytes with other cells in the process of ischemic AKI.Conclusion:Together,this study reveals distinct cell-specific transcriptomic atlas of kidney in ischemic AKI patients,altered signaling pathways,and potential cell-cell crosstalk in the development of AKI.These data reveal new insights into the pathogenesis and potential therapeutic strategies in ischemic AKI.

Single-cell analysis of angiotensin-converting enzyme II expression in human kidneys and bladders reveals a potential route of 2019 novel coronavirus infection

Background::Since 2019,a novel coronavirus named 2019 novel coronavirus(2019-nCoV)has emerged worldwide.Apart from fever and respiratory complications,acute kidney injury has been observed in a few patients with coronavirus disease 2019.Furthermore,according to recent findings,the virus has been detected in urine.Angiotensin-converting enzyme II(ACE2)has been proposed to serve as the receptor for the entry of 2019-nCoV,which is the same as that for the severe acute respiratory syndrome.This study aimed to investigate the possible cause of kidney damage and the potential route of 2019-nCoV infection in the urinary system.Methods::We used both published kidney and bladder cell atlas data and new independent kidney single-cell RNA sequencing data generated in-house to evaluate ACE2 gene expression in all cell types in healthy kidneys and bladders.The Pearson correlation coefficients between ACE2 and all other genes were first generated.Then,genes with r values larger than 0.1 and P values smaller than 0.01 were deemed significant co-expression genes with ACE2.Results::Our results showed the enriched expression of ACE2 in all subtypes of proximal tubule(PT)cells of the kidney.ACE2 expression was found in 5.12%,5.80%,and 14.38%of the proximal convoluted tubule cells,PT cells,and proximal straight tubule cells,respectively,in three published kidney cell atlas datasets.In addition,ACE2 expression was also confirmed in 12.05%,6.80%,and 10.20%of cells of the proximal convoluted tubule,PT,and proximal straight tubule,respectively,in our own two healthy kidney samples.For the analysis of public data from three bladder samples,ACE2 expression was low but detectable in bladder epithelial cells.Only 0.25%and 1.28%of intermediate cells and umbrella cells,respectively,had ACE2 expression.Conclusion::This study has provided bioinformatics evidence of the potential route of 2019-nCoV infection in the urinary system.