Using Human Urinary-Derived Renal Epithelial Cells for Deep Phenotyping of NPHP1 and Determining Response to Novel Therapeutics

Background: Nephronophthisis (NPHP) is an autosomal recessive tubulointerstitial nephropathy / renal ciliopathy disorder and recognised as the leading genetic cause of kidney failure in children and young adults. NPHP1 is the most common genetic cause and encodes nephrocystin-1, a protein that plays crucial roles in the primary cilium. Here we utilise personalised medicine and deep phenotyping, which enable us to explore mechanistic pathways and identify potential therapeutic strategies. Methods: In a family where we detected a homozygous NPHP1 whole-gene deletion in three affected siblings, we compared kidney biopsy tissue and human urine-derived renal epithelial cells (hURECs). Bulk RNA-seq on patient hURECs was used to generate disease signatures of NPHP1 whole-gene deletion. We assessed treatment of patient hURECs with alprostadil, a recently proposed therapy for NPHP as well as an EGFR kinase inhibitor for phenotypic and transcriptomic rescue. Results: Both the kidney biopsy and the hURECs demonstrated renal epithelial cells with an elongated and tortuous primary ciliary phenotype. Bulk RNA-seq on patient hURECs revealed disease signatures of NPHP1 deletion, which included changes in EGFR signaling, as well as extracellular matrix interactions and adherens junctions. Treatment of patient hURECs with alprostadil, a proposed therapy for NPHP, caused an increase in overall ciliation rate, but also an exaggerated primary ciliary length. In contrast, treatment of patient hURECs with an EGFR kinase inhibitor produced a phenotypic rescue of ciliary length and tortuosity. Following hUREC treatments, alprostadil did not fully restore the disease-associated transcriptional profile, whereas treatment with the EGFR kinase inhibitor AG556 caused a more complete rescue of the transcriptomic disease signature, in keeping with the observed phenotypic rescue. Conclusion: We conclude that patient-derived hURECS enable the deep phenotyping of nephronophthisis, replicate human kidney biopsy findings, and can be used to develop disease pathway signatures and screen candidate drug molecules, providing novel insights into disease pathogenesis and therapies. EGFR inhibition is now a potential therapy for renal ciliopathies, which should be tested within in vivo models of NPHP as a prelude to human studies.