Controlling proximal nephron precursor differentiation to generate proximal-biased kidney organoids with emerging maturity [snRNA-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. SnRNA-sequencing was performed on differentiaton day 21 proximal-biased and differentiation day 27 proximal-biased kidney organoids. Proximal-biased kidney organoids are treated from differentiation days 10 to 12 (48 hours) with 10 µM LY294002. Organoids were flash-frozen in liquid nitrogen before nuclei isolation. SnRNA-sequencing libraries were constructed using 10X Genomics Chromium Next GEM Single Cell Multiome Reagents PN-1000283, following 10X Genomics CG000338 Rev E. Raw fastq files were processed using Cell Ranger (v9.0.0) and aligned to the human reference genome (GRCh38-2024-A). Feature-barcode matricies were read into Seurat 5.2 using the Read10X function.