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. Overall design: 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).