Clusterin marks maladaptive regenerative responses throughout the kidney following ischemia reperfusion.

The proliferative capacity of the kidney declines after birth due to loss of its reserves of nephrogenic progenitors. Nevertheless, kidney tubules maintain a limited capacity to regenerate following various insults, through transient de-differentiation of the tubular epithelium into a progenitor phenotype. Recent studies describing the transcriptional changes underlying this process have primarily focused on proximal tubules with few studies examining the regenerative potential of other renal segments. To address this knowledge gap, we employed single cell RNA sequencing (scRNAseq) and lineage tracing experiments to dissect the transcriptional changes in cells expressing the secreted factor Clusterin (Clu), a known biomarker and potential regulator of acute kidney injury (AKI) in mice and humans. Our data indicates that de novo induction of Clu mRNA serves initially as a robust marker of injured distal tubules and collecting duct cells following ischemia reperfusion injury (IRI). Fate mapping revealed that while Clu+ nephron progenitors were multipotent, Clu+ collecting duct cells in the adult initially activated a transient proliferative program but ultimately persisted in a de-differentiated state or were lost. By scRNAseq, we also identified delayed and maladaptive responses in injured proximal tubules and the loop of Henle that are marked by Clu. Furthermore, we uncovered a “mixed lineage” gene signature comprised partly of podocyte and glomerular parietal epithelial cell identity markers that is activated in converging epithelial, mesenchymal and macrophages within the medulla. Together these data indicate that Clu marks maladaptive responses in the kidney and highlights the medulla as a particularly vulnerable site to the fibro-inflammatory cascade triggered by ischemic injury.