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Kidney Week

Abstract: PO0335

Cell Interaction Dynamics in Human AKI Revealed by Single-Cell Transcriptomics

Session Information

Category: Acute Kidney Injury

  • 103 AKI: Mechanisms


  • Muto, Yoshiharu, Washington University in St Louis School of Medicine, St Louis, Missouri, United States
  • Kirita, Yuhei, Washington University in St Louis School of Medicine, St Louis, Missouri, United States
  • Humphreys, Benjamin D., Washington University in St Louis School of Medicine, St Louis, Missouri, United States

Single cell transcriptomic maps of human AKI have not been reported, in part due to the difficulty of obtaining tissue. Acute kidney injury (AKI) is characterized by dynamic changes in cellular interactions among epithelia, stroma and inflammatory cells across the acute injury, repair and failed repair spectrums. Single cell transcriptomic technology is ideally suited to unravel the spectrum of cell states and interactions during injury and repair.


We performed snRNA-seq on 4 human AKI samples (2M and 2F, mean age = 60y, mean sCr = 4.6 mg/dl) and 5 control samples (3M and 2F, mean age = 55.8y, mean sCr = 1.07 mg/dl). Nuclear preparations were processed using 10x Genomics 3’ v3 Chromium kits and sequenced by NovaSeq. Reads were counted with CellRanger and analyzed with Seurat.


After quality control and doublet removal, 62,649 nuclei (18 clusters) were identified in the dataset. GLI1high fibroblasts were enriched in AKI, suggesting hedgehog signaling pathway activation. Among ligands, DHH expression was specifically up-regulated in the ADAMTS6high endothelial subset in AKI, suggesting that AKI-induced endothelial stress may activate fibroblast reprogramming for myofibroblast proliferation. Comprehensive ligand-receptor analysis suggests secreted proteins including TRAIL from injured epithelium signaling to endothelium, driving DHH expression and subsequent myofibroblast proliferation. We define the transcriptomic signature of failed-repair PT in human AKI and show that this is similar to that of primary cultured RPTEC, validating primary RPTEC as a model of failed repair. Indeed, TNFa treatment of RPTEC drove expression of the full complement of failed repair PT marker genes, suggesting a critical role for NFKB activation in human PT injury and repair.


This is the first single cell transcriptomic atlas of human AKI. It reveals a novel PT-endothelium-myofibroblast signaling loop coupling PT injury to endothelial injury and ultimately interstitial fibrosis. This TRAIL and DHH dependent intercellular signaling cascade suggests a molecular mechanism for the AKI to CKD transition.


  • NIDDK Support