SEC22B modulates ClC-5/TMEM9 trafficking and serves as a urinary marker for Dent’s Disease

Abstract

The Cl − /H + antiporter ClC-5 is a key regulator of renal proximal tubule function, primarily by controlling endosomal acidification. Loss-of-function mutations in ClC-5 cause Dent’s Disease type 1 (DD1), a rare renal tubulopathy that progresses to kidney failure with significant phenotypic heterogeneity. The molecular mechanisms linking specific ClC-5 variants to this clinical variability, however, remain incompletely understood. We investigated three ClC-5 pathogenic variants (I524K, E527D and V523∆) using renal proximal tubule epithelial cells (RPTEC/TERT1). An interactome analysis was performed to identify novel ClC-5 protein partners. The functional role of the identified interactor, SEC22B, was evaluated in RPTEC cells depleted of this protein, focusing on its impact on ClC-5 trafficking, endolysosomal pH, and epithelial differentiation. Finally, SEC22B levels were quantified in urinary extracellular vesicles (uEVs) from a DD1 patients’ cohort. ClC-5 mutants exhibited distinct intracellular retention patterns, all of which resulted in altered endolysosomal pH and disrupted secretory pathway organization. We identified the R-SNARE SEC22B as a novel partner that specifically interacts with wild-type ClC-5, but not DD1 mutants. SEC22B deletion impaired ClC-5 trafficking, leading to its retention at the Golgi and endosomes. This loss of SEC22B recapitulated key DD1 cellular hallmarks, including defective endocytosis, epithelial dedifferentiation, and altered secretory pathway. Intriguingly, SEC22B depletion paradoxically enhanced endosomal acidification. We resolve this mechanism by showing that SEC22B also regulates the trafficking of TMEM9, a known ClC-5 inhibitor that associates with both wild-type and mutant ClC-5 forms. Thus, our findings strongly suggest that SEC22B is essential for the proper sorting of the ClC-5/TMEM9 complex. Clinically, we observed elevated SEC22B levels in urinary extracellular vesicles from DD1 patients. Our findings establish SEC22B as a critical modifier of DD1 pathophysiology and a promising non-invasive biomarker for monitoring the disease.