Ift46 deficiency causes renal cyst via enhanced Limk2 through lack of autophagy flux

Intraflagellar transport protein 46 (IFT46) is a core protein of the IFT B complex linked to signal transduction systems with primary cilia. Although the function of Ift46 has been extensively fully investigated, the study of Ift46 other than ciliogenesis has not. Recent studies have shown that Ift46 could control autophagy progression in addition to the mechanism of cilia formation. To investigate the biological function of Ift46, we performed and analyzed total RNA sequencing using Ift46 knockdown mouse inner medullary collecting duct cells. Gene ontology analysis revealed that Ift46 is associated with partial epithelial–mesenchymal transition (EMT). In vitro experiments demonstrated that Ift46 regulated partial EMT, LIM domain kinase 2 (Limk2) and autophagy flux. The direct interaction between Limk2 and p62/sequestosome 1 was verified through co-immunoprecipitation, and various drugs affecting autophagy were found to impact Limk2 stability. The role of Ift46, autophagy, and Limk2 in the renal cyst formation and the progression of EMT was highlighted using an in vitro three-dimensional culture system. Furthermore, the Ift46-autophagy-Limk2 axis was validated in a collecting duct-specific Ift46-deficient mouse and in human autosomal dominant polycystic kidney disease. Ift46 regulated autophagy in mouse collecting duct cells, and Ift46 deficiency surprisingly led to an increase in Limk2 translation. Moreover, the translational changes in Limk2 were influenced by the regulation of autophagy. In Ift46-deficient mice, which exhibit a polycystic kidney disease phenotype, the upregulated Limk2 promoted mesenchymal characteristics despite minimal epithelial changes. Furthermore, the induction of autophagy suppressed Limk2, leading to the proposal of the ‘Ift46-autophagy-Limk2’ axis. Our study provides a novel finding that Ift46-regulated autophagy controls partial EMT through Limk2 regulation, suggesting a Limk2-dependent mechanism of cystogenesis in PKD.