Single-cell and high-resolution spatial profiling of podocytopathies reveals core mechanisms of podocyte injury

Podocytes (PODs) play a critical role in maintaining glomerular filtration function, and their injury is a key driver of progressive podocytopathies (PCPs). Despite their clinical importance, the molecular and spatial mechanisms underlying POD injury remain poorly understood. We generated a single-nucleus RNA sequencing (snRNA-seq) and high-resolution spatial transcriptomic (ST) dataset from kidney tissues of patients with five major PCP subtypes. Our analysis revealed distinct molecular signatures among PCP subtypes, injury-related cytoskeletal alterations, and POD-centered microenvironmental features associated with clinical outcomes. Through integrative analysis, we found PDE4DIP as a previously unrecognized regulator of the POD cytoskeleton. Functional experiments through in vitro and in vivo gene editing demonstrated that PDE4DIP maintains cytoskeletal integrity by scaffolding with AKAP9 and activating RAS-ERK and AKT signaling. Its expression correlated with renal function and prognosis. This study provides the comprehensive snRNA-seq and high-resolution ST atlas of PCPs, offering a valuable resource for understanding POD injury and identifying potential therapeutic targets.