Axial Nephron Fate Switching Demonstrates a Plastic System Tunable on Demand

The human nephron is a highly patterned tubular structure. Approximately 1 million nephrons form in each kidney during embryonic and fetal development and develop specialized cells that regulate bodily fluid homeostasis, blood pressure, and urine secretion throughout life. This raises the question of how these cells originally develop. Here we interrogate early human nephron patterning using an iPSC-based kidney organoid system that generates hundreds of developmentally synchronized nephron structures. We show that human nephron patterning is controlled by integrated WNT/BMP/FGF signaling. Imposing a WNThigh/BMPlow state established a distal identity that matures into thick ascending loop of Henle cell identities by activating FGF. Simultaneous suppression of FGF signaling reverts cells to a proximal cell-state, thereby indicating the dependence on FGF signaling for distal cell formation in the human nephron. Our system highlights plasticity in nephron identities and mechanisms controlling normal patterning. Single-cell RNA-sequencing data from control and distal-enriched (treated with 10 uM Ly29 for 48 hours between differentiation days 10-12, and 1uM CHIR and 1.5 uM LDN between differentiation days 11-12) kidney organoids. Single-cell data are from differentiation day 14 and include both DMSO control and treated organoids. Raw data were aligned to hg38, annotation Ensembl 105, using splitpipe (Parse Biosciences), and these processed scRNA-seq data used in Figure S4 (all cells, nephrogenic and insterstitial) are provided as an .rds file.