Ultrastructural comparison of human kidney organoids and human fetal kidneys reveals features of hyperglycemic culture

Induced pluripotent stem cell (iPSC)-derived kidney organoids have the potential for a large variety of applications. However, they do not persist long in culture, for which reasons are still unclear. Furthermore, their morphological maturation, an essential feature for kidney function, has not been sufficiently assessed. Kidney organoids are transcriptionally much alike end-of-first-trimester fetal kidneys and present many of the same cell types. From large transmission electron microscopy tilescans of specific regions of interest, we compared the ultrastructures of iPSC-derived kidney organoids at various timepoints to human fetal kidneys of the first trimester. Unlike healthy fetal kidneys, large glycogen deposits developed over time in all organoid cell types, but particularly in podocytes and in chondrocytes, one of the off-target populations that contaminate the culture. Deeper investigation showed that glycogen synthase kinase 3b (GSK3{beta}) levels and activation were diminished over time, correlated with the accumulation of glycogen. Activated YAP was strongly expressed and large lipid droplets accumulated over time in proximal tubules. Accordingly, EGFR signaling increased significantly over time. Mitochondria in glomeruli and tubules contained few or no cristae, indicating mitochondrial damage. Together these features are known for hyperglycemic cultures and diabetic nephropathy. Measuring the glucose concentration in the kidney organoid culture medium showed a concentration of 2.94 g/mL, which is considered an elevated, pre-diabetic-like concentration in vitro. In summary, our ultrastructural assessment of iPSC-derived kidney organoids using an age-matched fetal human reference allowed the evaluation of cellular morphology, and we identified intracellular features that can inform the cellular state, which is particularly important while physiological testing of organoids is limited. Translational StatementKidney organoids hold promise as a future treatment for patients with end-stage kidney disease. The engineering of kidney organoids with correct and healthy morphology in vitro is therefore essential, to guarantee functionality after transplantation. The present study provided deeper insights into the structural organization and ultrastructure of cells in kidney organoids compared to age-matched human fetal kidneys. Accordingly, we found several features in the regular kidney organoid culture, which are known to occur in hyperglycemic cultures and diabetic nephropathy, indicating that the current medium composition may be inducing pathological cellular phenotypes. This study therefore creates a better understanding of current limitations in the kidney organoid culture, increases knowledge of their function and cellular organization, and sets the foundation for further research to create advanced organoids.