Single cell sequencing and kidney organoids generated from pluripotent stem cells

Methods to differentiate human pluripotent stem cells into kidney organoids were first introduced about 5 years ago, and since that time, the field has grown substantially. Protocols are producing increasingly complex threedimensional structures, have been used tomodelhuman kidney disease, andhave beenadapted forhigh-throughput screening.Over this same time frame, technologies formassively parallel, single-cellRNAsequencing (scRNA-seq) have matured. Now, both of these powerful approaches are being combined to better understand how kidney organoids can be applied to the understanding of kidney development and disease. There are several reasons why this is a synergistic combination. Kidneyorganoids are complicatedandcontainmanydifferent cell typesof variable maturity. scRNA-seq is an unbiased technology that can comprehensively categorize cell types, making it ideally suited to catalog all cell types present in organoids. These same characteristics also make scRNA-seq a powerful approach for quantitative comparisons between protocols, batches, and pluripotent cell lines as it becomes clear that reproducibility and quality can vary across all three variables. Lineage trajectories can be reconstructed using scRNA-seq data, enabling the rational adjustment of differentiation strategies to promote maturation of desired kidney cell types or inhibit differentiation of undesired off-target cell types. Here, we review the ways that scRNA-seq has been successfully applied in the organoid field and predict future applications for this powerful technique.Wealso reviewother developing single-cell technologies and discuss howtheymay be combined, using “multiomic” approaches, to improve our understanding of kidney organoid differentiation and usefulness in modeling development, disease, and toxicity testing.