Single-Nucleus RNA Sequencing Identifies Transcriptional Differences in Sepsis- and Ischemia-Induced AKI in Mice

Background: Acute kidney injury (AKI) is frequently observed in hospitalized patients and associated with increased mortality. Two of the most common causes of AKI are sepsis and conditions with kidney ischemia. However, whether and how these two AKI causes differ at the molecular level is incompletely understood. Here, we aimed to identify gene sets that are specific for sepsis or kidney ischemia associated AKI using well-defined mouse models. Methods: Septic AKI was induced by cecal ligation and puncture (CLP) in adult male C57BL/6 mice (n=6) with sham operated mice as controls (n=3). Kidneys were harvested at 4 and 20 hours after CLP (n=3 each and subjected to single nucleus RNA sequencing (snRNA-seq). Unbiased clustering and marker gene expression analysis enabled the identification of major renal cell types. To account for molecular differences with ischemia-reperfusion injury (IRI)-induced AKI, we integrated our data with two published IRI datasets. To derive sepsis- and IRI-specific gene sets, we systematically searched for genes that are exclusively up- or downregulated in sepsis when compared to IRI in each major cell type and vice versa. Results: Our analysis resulted in lists of sepsis- and IRI-specific gene sets for each cell type. Sepsis-specific genes (specifically up- or downregulated in CLP kidneys but not in IRI) showed cell type-specific gene expression patterns with little overlap between the cell types. Sepsis-specific genes were mostly present in collecting duct principal cells, endothelial and interstitial cells at 20 hours post-CLP. These genes were enriched in pathways associated with cytoskeletal remodeling (collecting duct principal cells), endothelial activation (endothelial cells) and extracellular matrix production (interstitial cells). In contrast, genes specifically upregulated in IRI were mostly restricted to the proximal tubules. These genes were strongly enriched in pathways associated with cell cycling and DNA damage repair. Conclusion: Our analyses provide a comprehensive set of cell type-specific marker genes specific for sepsis- and IRI-induced AKI. We highlight strong transcriptional differences between sepsis- and IRI-induced AKI, which involve different cell types.