Sox9 switch links regeneration to fibrosis at the single-cell level in mammalian kidneys [RNA-Seq 1]

The steps governing healing with or without fibrosis within the same microenvironment are unclear. After acute kidney injury (AKI), the injured proximal tubular epithelial cells activate Sox9 for self-restoration. Using head-to-head comparison of injury- induced Sox9-lineages via spatiotemporal mapping, single-cell sequencing, and single-nuclei chromatin accessibility profiling, we identified a dynamic SOX9 switch. Lineages that regenerated epithelia silenced SOX9 and healed without fibrosis (SOX9on-off). In contrast, lineages that maintained Sox9 activity in attempt to regenerate, demarcated by SOX9-induced Cadherin 6 (SOX9on-on CDH6pos ) cell state, generated single-cell Wnt activity to provoke a fibroproliferative response in adjacent fibroblasts, driving AKI to chronic kidney disease. Transplanted human kidneys displayed similar SOX9/CDH6/WNT2B responses post-injury. Thus, we uncovered a mechanism linking fibrosis to sustained efforts to regenerate the injured tissue. Overall design: RNAseq datasets from FACS-sorted (enriched) control cells that activate Axin2, a reporter of canonical Wnt pathway, "the Wnt responsive cells"; and the myofibroblast population early after kidney ischemia reperfusion injury (IRI) induced AKI. To this end, tamoxifen was administered at d2, and d4 to Axin2CreERT2/+:R26RtdT/+:Acta2-GFP animals, and at d6 dual positive (tdT positive and GFP positive) and tdT negative, GFP positive cells were enriched via FACS. 3 biological replicates.