Alternative Splicing Dysregulation by Pin1 Mediates Tuberous Sclerosis Kidney Disease

Background: Tuberous sclerosis complex (TSC) is a genetic disorder characterized by the formation of cystic kidney disease, often progressing to chronic kidney disease. While mTORC1 hyperactivation is the hallmark of TSC, the molecular mechanisms linking mTORC1 dysregulation to kidney cystogenesis remain incompletely understood. Pin1, the only mammalian peptidyl-prolyl isomerase that specifically recognizes phosphorylated Ser/Thr-Pro motifs, is a logical candidate mediator as mTORC1 activation increases such phosphorylation events. This study investigates the role of Pin1 in TSC-associated kidney cystogenesis. Methods: We utilized a kidney-specific Tsc1 knockout (KO) mouse model, human proximal tubule cell line (HK2), and human TSC kidney sections. We examined Pin1 activity, protein interactions, and impact on alternative splicing using biochemical assays, immunohistochemistry, RNA sequencing, and mass spectrometry. Results: Tsc1 KO kidneys exhibited elevated mTORC1 activity and increased Ser/Thr-Pro phosphorylation. While total Pin1 protein levels remained unchanged, Pin1 activity increased significantly due to reduced inhibitory phosphorylation at Ser16 and Ser71. GST-pull down and co-immunoprecipitation experiments revealed enhanced interaction between Pin1 and spliceosome components SRRM2 and SRSF2 in Tsc1 kidneys, promoting their nuclear translocation. RNA sequencing identified 2,263 differential alternative splicing events in Tsc1 KO kidneys, including intron retention in PKD1 transcript leading to increased polycystin-1 expression. Importantly, pharmacological inhibition of Pin1 with sulfopin reversed these splicing alterations, restored PKD1 splicing patterns and expression and significantly reduced cyst burden without affecting mTOR hyperactivation. Human TSC kidney sections confirmed elevated SRRM2, SRSF2, and PKD1 expression. Conclusion: Pin1 plays a critical role in TSC-related cystogenesis by modulating alternative splicing through mTOR-dependent but rapamycin-insensitive mechanisms. This newly identified pathway presents Pin1 as a promising therapeutic target for TSC and potentially other cystic kidney diseases.