Forbes, Thomas A., Howden, Sara E., Lawlor, Kynan, Phipson, Belinda, Maksimovic, Jovana, Hale, Lorna, Wilson, Sean, Quinlan, Catherine, Ho, Gladys, Holman, Katherine, Bennetts, Bruce, Crawford, Joanna, Trnka, Peter, Oshlack, Alicia, Patel, Chirag, Mallett, Andrew, Simons, Cas, and Little, Melissa H. (2018) Patient-iPSC-derived kidney organoids show functional validation of a ciliopathic renal phenotype and reveal underlying pathogenetic mechanisms. American Journal of Human Genetics, 102 (5). pp. 816-831.

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Abstract

Despite the increasing diagnostic rate of genomic sequencing, the genetic basis of more than 50% of heritable kidney disease remainsunresolved. Kidney organoids differentiated from induced pluripotent stem cells (iPSCs) of individuals affected by inherited renal diseaserepresent a potential, but unvalidated, platform for the functional validation of novel gene variants and investigation of underlyingpathogenetic mechanisms. In this study, trio whole-exome sequencing of a prospectively identified nephronophthisis (NPHP) probandand her parents identified compound-heterozygous variants inIFT140, a gene previously associated with NPHP-related ciliopathies.IFT140plays a key role in retrograde intraflagellar transport, but the precise downstream cellular mechanisms responsible for diseasepresentation remain unknown. A one-step reprogramming and gene-editing protocol was used to derive both uncorrected probandiPSCs and isogenic gene-corrected iPSCs, which were differentiated to kidney organoids. Proband organoid tubules demonstrated short-ened, club-shaped primary cilia, whereas gene correction rescued this phenotype. Differential expression analysis of epithelial cellsisolated from organoids suggested downregulation of genes associated with apicobasal polarity, cell-cell junctions, and dynein motorassembly in proband epithelial cells. Matrigel cyst cultures confirmed a polarization defect in proband versus gene-corrected renalepithelium. As such, this study represents a "proof of concept" for using proband-derived iPSCs to model renal disease and illustratesdysfunctional cellular pathways beyond the primary cilium in the setting ofIFT140mutations, which are established for other NPHPgenotypes

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