Switching OFF the Maladaptive Repair Cell State to Halt AKI-to-CKD Progression - PROJECT SUMMARY Switching OFF the Maladaptive Repair cell state to Halt AKI-to-CKD Progression We previously identified that injured proximal tubular epithelial cells (PTECs) reactivate SOX9 to regenerate after AKI. Recently, funded by an R01 grant, we discovered a dynamic SOX9 switch in its lineages that determines healing with or without fibrosis at the single-cell level in mammalian kidneys and interconnects AKI to CKD. Using a multimodal approach, we identified SOX9on-onCDH6+ unresolved regenerated cell states that interconnect AKI to CKD. Similar responses were observed in human transplanted kidneys, where SOX9/CDH6/WNT2B-expressing single cells strongly correlated with fibrosis. An independent commentary on the paper highlighted SOX9 flips the switch between regeneration and fibrosis as a substantial mechanistic advance in the injury/repair/fibrosis field. Using KPMP single-cell datasets, another article confirmed these findings in native kidneys AKI/CKD. In this proposal, we address a critical, unexamined question: Is this maladaptive repair cell state druggable? Integrating SOX9 lineage-specific single-nuclei ATAC-seq and single- cell RNA-seq, we identified two druggable candidates: SMARCC1, a chromatin remodeler, and RUNX1, a transcription factor. RUNX1 is uniquely druggable among transcription factors, and chromatin remodeler therapeutics is a highly promising therapeutic strategy in cancer. Using in vivo, RUNX1 pharmacological inhibition, and in vitro genetic silencing, and human transplant biopsies profiling studies, our preliminary data highlights RUNX1/SMARCC1 in AKI-to-CKD. We propose rigorous and comprehensive mechanistic studies of the RUNX1/SMARCC1 in two clinically relevant models of AKI-to-CKD progression. By coupling tamoxifen- inducible, maladaptive repair cell state-specific Runx1 loss-of-function studies with lineage-specific scRNA- seq, snATAC-seq, and CUT&RUN/CUT&TAG genomic occupancy assays, we aim to uncover how maladaptive repair cells can be directly targeted to halt AKI-to-CKD progression. To mechanistically link the identified axis to human AKI-to-CKD, we propose to leverage deidentified human kidney transplant biopsy specimens, generated from a published NIH-funded clinical trial, for spatial transcriptomic studies. Taken together, using rigorous, unbiased, and feasible approaches and assembling a collaborative team of complementary scientific skill set, our comprehensive studies aim to provide paradigm-shifting findings on how maladaptive repair cells can be directly therapeutically targeted to halt AKI-to-CKD progression.
