GSE171417
Single-nuclear transcriptomics reveals a diversity of proximal tubule cell states in a dynamic response to acute kidney injury.
We performed a mild-to-moderate ischemia reperfusion injury (IRI) to model injury responses reflective of kidney injury in a variety of clinical settings. Single-nuclear RNA-sequencing (snRNA-seq) of genetically labeled injured PTCs at 7-days (“early”) and 28-days (“late”) time points post-IRI identified specific gene and pathway activity in the injury-repair transition. In particular, we identified Vcam1+/Ccl2+ proximal tubule cells at a late injury stage distinguished by marked activation of NF-kB-, TNF- and AP-1-signaling pathways. This population of PTCs showed features of a senescence-associated secretory phenotype but did not exhibit G2/M cell cycle arrest. These pro-inflammatory, pro-fibrotic proximal tubule cells are likely triggers for chronic disease progression. Overall design: Krt20 was previously identified as a marker of injured proximal tubule cells (Liu et al., JCI Insight, 2017). We generated a Krt20T2A-CE; INTACTnuGFP/+ mouse line to enable the isolation and tracing of Krt20+ cells in acute kidney injury. A reporter mouse expressing GFP linked to the histone protein H2B in all nephron cells was used as control (Legouis et al., Nature Metabolism, 2020). In total nine samples were processed for snRNA-seq: two Krt20T2A-CE; INTACTnuGFP/+ samples collected on day 7 after IRI, three Krt20T2A-CE; INTACTnuGFP/+ samples collected on day 28 after IRI and four control samples (three sham surgery mice and one non-surgery mouse).