Human fetal kidney organoids model early human nephrogenesis and notch-driven cell fate

Pluripotent stem cell–derived kidney organoids (PSC-KOs) have been put forward as a preferred culture system in which to study human kidney development and disease. In contrast, the development of human fetal kidney tissue–derived organoids (hFKOs) that could serve as a benchmark for PSC-KOs has not advanced very far. Herein, utilizing a chemically defined serum-free medium, we established a long-term culture protocol for hFKOs that self-organize into polarized renal epithelium and faithfully recapitulate nephrogenic and ureteric bud cell lineages. Bulk transcriptomics, single-cell RNA sequencing, and pseudotime analysis along with immunostaining revealed diverse populations among hFKOs, with a preserved differentiation axis mostly at higher levels and to a greater extent than for PSC-KOs. Accordingly, compared to PSC-KOs, hFKOs were significantly enriched for the NOTCH signaling pathway genes, allowing single-cell analysis of changes following NOTCH inhibition. We observed a preferential increase of mature distal tubules at the expense of early proximal tubules and defined a new adaptive prominin 1–expressing (PROM1+, or CD133+) cell state that escapes NOTCH inhibition to generate proximal and distal tubules. Overall, the concomitant understanding of developmental processes using hFKOs is a key development for the fields of kidney stem cell biology and regenerative medicine. Characterization of human fetal kidney organoids (hFKOs) at P0 and P2 via bulk RNA sequencing, along with adult kidney organoids (AKOs) and iPSC-derived kidney organoids (iPSC-KOs) for comparison. P0 (3 weeks cluture) of week 18 human fetal kidney, with 3 replicates. P2 (8 weeks of culture) of week 18 human fetal kidney, with 3 replicates. Adult kidney organoids from a single donor of an elective nephrectomy, 3 replicates from each passage. iPSC-derived kidney organoids day 16 of Freedman et al. differentiation protocol, two patient cell lines, 8GA7 and 123A9, 2 replicates from each donor. In addtion, 3 replicates from the source tissue material of each organoid type were sequenced (Adult kidney tissue and human fetal kidney tissue).