Unraveling the Molecular and Cellular Complexities of the Kidney in Health and Disease

Abstract

Chronic kidney disease (CKD) affects over 500 million people worldwide, and despite this significant disease burden, therapeutic innovation in nephrology has lagged. This trend is partly attributed both to an incomplete understanding of the molecular mechanisms of kidney dysfunction and a lack of appropriate in vitro and in vivo models, a reflection of the multifactorial nature CKD and the complex cellular complexity of the kidney. Genetically defined rare diseases can provide insight into disease pathogenesis. We thus, sought to understand the mechanism underlying a rare Coenzyme Q (CoQ)-deficiency-associated podocytopathy. Podocytes are a terminally differentiated, post-mitotic cell type, essential for kidney filter function. An in vitro podocyte model of CoQ deficiency revealed a susceptibility to ROS-mediated injury and a perturbation in polyunsaturated fatty acid metabolism. Single nucleus sequencing from the kidneys of CoQ-deficient mice validated podocyte-specific transcriptomic changes consistent with in vitro findings and revealed a novel, disease-specific parietal epithelial cell population. Our analysis further revealed the BRAF-targeting GDC-0879 as a putative therapeutic strategy. Kidney organoids derived from human induced pluripotent stem cells (iPSCs) are an emerging technology with the potential to both recapitulate the cellular diversity of the kidney and to further our understanding of disease. However, this progress is dependent on understanding the reproducibility and quality of organoids derived from multiple patients-donors. Thus, we generated a 412,358 single cell census of 47 organoid and iPSC samples derived from four cell lines across four time points of differentiation. All cell lines contained representative segments of the developing nephron, but varied in their proportions of cell types and in the presence of off-target populations. Comparison to single cell fetal kidney data revealed that the organoids were most similar to first trimester fetal kidney. While long-term in vitro culture did not affect organoid composition, in vivo transplantation of organoids resulted in reduced off-target populations.