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Kidney Week

Abstract: PO0253

Spatial Transcriptomic Signatures in Murine AKI Models

Session Information

  • AKI Mechanisms - 3
    October 22, 2020 | Location: On-Demand
    Abstract Time: 10:00 AM - 12:00 PM

Category: Acute Kidney Injury

  • 103 AKI: Mechanisms

Authors

  • Melo ferreira, Ricardo, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • El-Achkar, Tarek M., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Collins, Kimberly S., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Cheng, Yinghua, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Winfree, Seth, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Dagher, Pierre C., Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Eadon, Michael T., Indiana University School of Medicine, Indianapolis, Indiana, United States
Background

The localization of whole transcriptome differential expression in different forms of acute kidney injury (AKI) is incompletely understood. We investigated the distribution of expression across the entire kidney, mapping expression patterns to renal histology in the ischemia-reperfusion injury (IRI) and cecal ligation and puncture (CLP) murine models of AKI.

Methods

Sham, IRI, and CLP kidneys were excised and sections were affixed to Visium 10x genomics slides. Sections underwent H+E staining, followed by permeabilization, RNA isolation, and sequencing. The IRI and CLP samples were clustered using Seurat and differential expression was assessed in clusters co-defined by histology and marker gene expression in both models. We then assessed pathway enrichment of differentially expressed genes (DEGs) using ClusterProfiler and ReactomePA.

Results

We examined the distribution of total expression (sum of all gene counts) across the entire kidney between IRI and CLP. In CLP, uniform upregulation was seen in the medullary S3 cluster. In contrast, total expression differences were patchy in the IRI model with regions of increased and reduced expression seen in both the cortex and medulla. Using spatial transcriptomics clustering, we compared the affected clusters, including the cortical collecting duct, S3 outer stripe proximal tubule, and thick ascending loop of Henle. The IRI model was enriched in wound healing and apoptosis related pathways, while the CLP model was enriched in oxidative phosphorylation and energy metabolism. Strong neutrophil signatures were identified in IRI and macrophage signatures in CLP.

Conclusion

Using spatial transcriptomics, we uncovered regional differences in total RNA expression between the IRI and CLP models. The identified regions housed specific cell types with differences in enriched pathways. The enriched apoptotic pathways in IRI may be consistent with a lower relative expression compared to sepsis. The neutrophil and macrophage spatial distribution indicate how those models respond to injury. The localization of transcriptomic alterations in AKI is not uniform across both models.

Funding

  • NIDDK Support