LC MS/MS of kidney organoids during differentiation from day 21 to 29

Kidney organoids are a valuable and innovative model to understand genetic diseases, kidney development and transcriptomic dynamics. However, their proteome has not been analyzed so far. Here, we analyzed the organoid proteome trajectory during differentiation. Genes involved in podocytopathies and cystic kidney diseases were abundantly expressed on protein level, distinguishing organoids from almost every available cell culture model. On their pathway to terminal differentiation, organoids developed increased deposition of extracellular matrix. Single cell transcriptomic analysis suggests that most changes locate to podocytes and early podocyte progenitors. This matrix deposition is different from commonly used animal models of glomerular disease. We grew organoids from two independent batches according to the Freedman protocol, and performed proteomic profiling (Freedman, Brooks et al. 2015, Czerniecki, Cruz et al. 2018). The IPSCs were differentiated for a three-week period until first spheroids from. From day 21 of the culture they were used in our experiments up until day 29, where off-target differentiation of organoids becomes an issue.