Increased mTOR signaling secondary to a human ILK missense variant inhibits nephrogenesis with decreased metabolism

Nephrogenesis is critical to mammalian kidney function throughout life. Decreased nephron formation, an embryonic process dependent on ureteric-mesenchymal tissue interactions, is a fundamental feature of Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) and an antecedent to adult-onset cardiovascular and renal disease. Yet, mechanisms controlling the number of nephrons formed during embryogenesis are largely undefined. Here, we elucidated deleterious effects of increased mTOR signaling on murine nephrogenesis. A rare human genetic missense variant ( ILK T173I ) in Integrin-Linked Kinase ( ILK ) was identified in a human CAKUT cohort. Replacement of the mouse ILK WT allele with Ilk T173I caused increased kidney mTOR signaling, low nephron number, and decreased ureteric branching, the latter of which was rescued by rapamycin. Transcriptomic analysis of sorted embryonic kidney cells suggested that elevated mTOR signaling is limited to non-ureteric mesenchyme, a finding that was substantiated by immunostaining in situ. Maturation of nephrogenic cells in Ilk T173I -knock-in kidneys was decreased as demonstrated by nephrogenic-specific markers, morphologic analysis, and proliferation of nephrogenic progenitors. Metabolic profiling of non-ureteric cells demonstrated decreased oxidative ATP production. Together, our data revealed a deleterious role of excessive mTOR signaling downstream of ILK T173I by inhibiting maturation, cell proliferation and metabolism in the nephrogenic cell lineage. CONCLUSION ILK p.T173I increases mTOR signaling in developing kidneys, which plays a deleterious role primarily in development of the nephrogenic lineage, eventually resulting in renal hypoplasia that can be rescued by rapamycin treatment. Hu et al., 2025 • A human variant of Integrin-Linked Kinase upregulates mTOR signaling in developing kidneys. • Elevated mTOR signaling inhibits kidney development, which can be rescued by rapamycin. • Elevated mTOR signaling inhibits cell proliferation and maturation in the nephrogenic lineage. • Kidneys with elevated mTOR signaling demonstrate decreased oxidative metabolism.