Patient-iPSC-derived kidney organoids show functional validation of a ciliopathic renal phenotype and reveal underlying pathogenetic mechanisms

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;Little, Melissa H.

Andrew Mallett

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

Journal

American Journal of Human Genetics

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102

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1537-6605

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Cell Press

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DOI

10.1016/j.ajhg.2018.03.014