Single-nuclear transcriptomics reveals diversity of proximal tubule cell states in a dynamic response to acute kidney injury

LMS Gerhardt, J Liu, K Koppitch… - Proceedings of the …, 2021 - National Acad Sciences
LMS Gerhardt, J Liu, K Koppitch, PE Cippą, AP McMahon
Proceedings of the National Academy of Sciences, 2021National Acad Sciences
Acute kidney injury (AKI), commonly caused by ischemia, sepsis, or nephrotoxic insult, is
associated with increased mortality and a heightened risk of chronic kidney disease (CKD).
AKI results in the dysfunction or death of proximal tubule cells (PTCs), triggering a poorly
understood autologous cellular repair program. Defective repair associates with a long-term
transition to CKD. We performed a mild-to-moderate ischemia–reperfusion injury (IRI) to
model injury responses reflective of kidney injury in a variety of clinical settings, including …
Acute kidney injury (AKI), commonly caused by ischemia, sepsis, or nephrotoxic insult, is associated with increased mortality and a heightened risk of chronic kidney disease (CKD). AKI results in the dysfunction or death of proximal tubule cells (PTCs), triggering a poorly understood autologous cellular repair program. Defective repair associates with a long-term transition to CKD. We performed a mild-to-moderate ischemia–reperfusion injury (IRI) to model injury responses reflective of kidney injury in a variety of clinical settings, including kidney transplant surgery. Single-nucleus RNA sequencing of genetically labeled injured PTCs at 7-d (“early”) and 28-d (“late”) time points post-IRI identified specific gene and pathway activity in the injury–repair transition. In particular, we identified Vcam1+/Ccl2+ PTCs at a late injury stage distinguished by marked activation of NF-κB–, 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, distinct from other reports of maladaptive PTCs following kidney injury. Fate-mapping experiments identified spatially and temporally distinct origins for these cells. At the cortico-medullary boundary (CMB), where injury initiates, the majority of Vcam1+/Ccl2+ PTCs arose from early replicating PTCs. In contrast, in cortical regions, only a subset of Vcam1+/Ccl2+ PTCs could be traced to early repairing cells, suggesting late-arising sites of secondary PTC injury. Together, these data indicate even moderate IRI is associated with a lasting injury, which spreads from the CMB to cortical regions. Remaining failed-repair PTCs are likely triggers for chronic disease progression.
National Acad Sciences