Comparative analysis of kidney organoids by single cell transcriptomics

Kidney organoids differentiated from human pluripotent stem cells hold great promise for understanding organogenesis, disease mechanisms and ultimately as a source of replacement tissue but how closely current protocols model adult kidney is undefined. Here we compared two different directed differentiation protocols by analyzing single cell gene expression in 83,130 cells isolated from 65 organoids. Both protocols generate kidney organoids that contain a diverse range of kidney cells at differing ratios but 10-20% of these cells are non-renal. Evaluation of the differentiation state of organoid kidney cell types against fetal and adult kidney single cell transcriptomes revealed the immaturity of all organoid-derived cell types. Reconstruction of lineage relationships by pseudotemporal ordering identified ligands, receptors and transcription factor networks associated with fate decisions. Brain-derived neurotrophic factor (BDNF) and its receptor neurotrophic tyrosine kinase, receptor, type 2 (NTRK2) was expressed exclusively in off-target neurons, and inhibition of this pathway reduced neurons by 90% without altering kidney differentiation. Our analysis reveals the power of single cell analysis both to characterize and to optimize organoid differentiation protocols.