Revealing the Spatial Structure of IgA Immune Complexes in IgAN Through Volume Electron Microscopy

Background: The defining ultrastructural feature of IgA nephropathy (IgAN) observed under electron microscopy is the presence of electron-dense deposits (EDD) located in the mesangial region. Although it is commonly believed that immune complexes containing galactose-deficient IgA1 (Gd-IgA1) accumulate in the extracellular space surrounding mesangial cells, our earlier studies suggest that Gd-IgA1 may also be internalized by these cells. However, the exact spatial distribution and quantitative features of Gd-IgA1-containing EDDs within the mesangium have not been fully characterized.This study seeks to determine the three-dimensional organization and quantify the deposition patterns of IgA immune complexes within the mesangial area of IgAN patients, and to investigate their potential correlation with disease progression. Methods: We employed volume electron microscopy using focused ion beam-scanning electron microscopy (FIB-SEM) to analyze renal biopsy samples from individuals diagnosed with IgAN and paratumor control tissues. High-resolution serial images were captured and reconstructed into 3D models using a custom-built artificial intelligence algorithm, allowing for detailed visualization and analysis of the mesangial architecture. Results: Our data reveal that Gd-IgA1 forms tubule-like structures closely associated with the surface of mesangial cells, showing a distinct spatial relationship between EDDs, cell nuclei, and adjacent vascular endothelial cells. We successfully generated 3D reconstructions of lysosomes within mesangial cells in situ and found that lysosomes in IgAN samples were both larger and more electron-dense compared to those in controls. Immunoelectron microscopy further confirmed the presence of IgA1-containing EDDs both outside the cells and inside the lysosomes of mesangial cells. Conclusion: Based on these findings, we propose two mechanisms of IgA immune complex deposition in the mesangium: (1) the classical extracellular accumulation pathway, and (2) an intracellular route involving endocytosis followed by lysosomal localization. These results offer novel insights into the pathogenesis of IgAN and suggest that future quantitative assessments could serve as biomarkers for evaluating disease severity and monitoring its progression. Funding: Government Support – Non-U.S.