Proteome Analysis of Isolated Podocytes Reveals Stress Responses in Glomerular Sclerosis

Significance Statement Analyses of entire glomeruli using a proteomic, transcriptomic, or other “omic” approach may obscure the molecular footprints of early and decisive processes in podocytes responding to injury. To pinpoint mechanisms underlying glomerulosclerosis, the authors performed ultrasensitive proteomics of purified podocyte fractions at early injury stages in mouse models of glomerular disease induced by doxorubicin or LPS. These analyses revealed an early stress response that involves upregulation of metabolic, proteostatic, and mechanoresponsive mechanisms. They also identified conserved upregulated proteins involved in the podocyte stress response, including the mechanosensor Filamin-B, and found a high correlation between proteinuria and Filamin-B levels. The work demonstrates that proteome integration at the single glomerulus and the individual organism levels can link “omics” datasets to physiological function at high resolution. Background Understanding podocyte-specific responses to injury at a systems level is difficult because injury leads to podocyte loss or an increase of extracellular matrix, altering glomerular cellular composition. Finding a window into early podocyte injury might help identify molecular pathways involved in the podocyte stress response. Methods We developed an approach to apply proteome analysis to very small samples of purified podocyte fractions. To examine podocytes in early disease states in FSGS mouse models, we used podocyte fractions isolated from individual mice after chemical induction of glomerular disease (with Doxorubicin or LPS). We also applied single-glomerular proteome analysis to tissue from patients with FSGS. Results Transcriptome and proteome analysis of glomeruli from patients with FSGS revealed an underrepresentation of podocyte-specific genes and proteins in late-stage disease. Proteome analysis of purified podocyte fractions from FSGS mouse models showed an early stress response that includes perturbations of metabolic, mechanical, and proteostasis proteins. Additional analysis revealed a high correlation between the amount of proteinuria and expression levels of the mechanosensor protein Filamin-B. Increased expression of Filamin-B in podocytes in biopsy samples from patients with FSGS, in single glomeruli from proteinuric rats, and in podocytes undergoing mechanical stress suggests that this protein has a role in detrimental stress responses. In Drosophila , nephrocytes with reduced filamin homolog Cher displayed altered filtration capacity, but exhibited no change in slit diaphragm structure. Conclusions We identified conserved mechanisms of the podocyte stress response through ultrasensitive proteome analysis of human glomerular FSGS tissue and purified native mouse podocytes during early disease stages. This approach enables systematic comparisons of large-scale proteomics data and phenotype-to-protein correlation.