Controlling nephron precursor differentiation to generate proximal-biased kidney organoids with emerging maturity [bulk RNA-seq]

The kidney maintains fluid homeostasis by reabsorbing essential compounds and excreting waste. Proximal tubule cells, crucial for reabsorbing sugars, ions, and amino acids, are highly susceptible to injury, often leading to pathologies necessitating dialysis or transplants. Human pluripotent stem cell-derived kidney organoids offer a platform to model renal development, function, and disease, but proximal nephron differentiation and maturation in these structures is incomplete. Here, we drive proximal tubule development in pluripotent stem cell-derived kidney organoids by mimicking in vivo proximal differentiation. Transient PI3K inhibition during early nephrogenesis activates Notch signaling, shifting nephron axial differentiation towards epithelial and proximal precursor states that mature to proximal convoluted tubule cells broadly expressing physiology-imparting solute carriers including organic cation and organic anion family members. The “proximal-biased” organoids thus acquire function, and on exposure to nephrotoxic injury, display tubular collapse and DNA damage, and upregulate injury response markers HAVCR1/KIM1 and SOX9 while downregulating proximal transcription factor HNF4A. Here, we show that proximally biased human-derived kidney organoids provide a robust model to study nephron development, injury responses, and a platform for therapeutic discovery. Overall design: Bulk RNA-sequencing data from control and proximal-biased (treated with 10 uM Ly29 for 48 hours from differentiation days 10 to 12) kidney organoids. Data are from differentiation days 10 (untreated), 12, 14, and 18. Days 12, 14, and 18 include both control and proximal-biased cells. There are n = 3 single organoid replicates for days 10, 12 control, and 12 Ly29-treated, and n = 2 replicates for each control and proximal-biased condition for days 14 and 18. Processed (raw feature counts table) data were aligned to hg38, Ensembl 105 annotation using STAR.