Abstract Background and Aims The molecular features of idiopathic podocytopathies remain unexplored, preventing the development of effective therapies to control the mechanisms of disease initiation and progression. This includes idiopathic focal segmental glomerulosclerosis (FSGS), one of the most common forms of immune glomerulopathies (IG) and the cause of renal failure and replacement therapy. In FSGS, podocytes undergo pronounced cytoskeletal alterations. Along with a decrease in Wilms tumor protein (WT1) and α-SMA expression, there is evidence for increased expression of intermediate filament proteins (vimentin, desmin, nestin) and Wnt/β-catenin signaling upregulation in IG. Decrease in WT1 is associated with upregulation in Wnt/β-catenin and p53 to promote podocyte dysfunction and albuminuria. Upregulation desmin increases the mechanical stability of cells, allowing podocytes to undergo morphological changes on the tensile glomerular capillary wall. This pilot study was aimed to evaluate the significance of WT1, β-catenin, and desmin glomerular expression in early primary FSGS. Method We reviewed the histopathological and clinical data of patients with biopsy proven FSGS (N = 14, experimental group), IgA nephropathy (N = 12, positive control), without AKI, infectious diseases, heart failure, respiratory insufficiency and cancer pathology. Renal surgery specimens from patients without IG (N = 12) were studied as negative control. Glomerulosclerosis was assessed as percentage of all glomeruli. Mesangial lesions were measured semi-quantitatively in scores (0-3). Glomerular WT1, β-catenin, and desmin expression was assessed by IHC-P with quantitative morphometry of IHC-staining area (open software QuPath, Orbit Image Analysis). Molecule's co-expression was analyzed by IF-p and confocal microscopy (Zeiss LSM 710; study conducted in the Center for Collective Use “Confocal microscopy” by Pavlov Institute of Physiology Russian Academy of Sciences). Results We examined young and middle-aged patients with CKD stages 1-3 and moderate morphological changes in the glomeruli. Gender, age, eGFR and the percentage of glomeruli with segmental sclerosis were not significantly different between IG groups (all p for interaction >0.05). Patients with FSGS have lower levels of serum albumin (p < 0.001) and higher levels of proteinuria (p < 0.001) as compared to IgAN. Glomeruli from IgAN patients showed more mesangial cell proliferation (p = 0.001), expansion of the mesangial matrix (p = 0.05) and global glomerular sclerosis (p = 0.003) as compared to FSGS. An immunomorphological study showed lower WT1 expression in both IG groups compared to the negative control. In the IgAN, lower WT1 expression was associated with higher BC area (Fig. 1A, D). BC expression did not differ between FSGS and negative control (Fig. 1B,D). In the combined IG group, BC directly correlated with global (r = 0.63, p = 0.001) and segmental (r = 0.63, p = 0.001) glomerular sclerosis. In FSGS, a trend towards to increase in the area of desmin IHC-staining was detected, however, no significant differences between groups were found (Fig. 1C,D). BC and desmin were co-localized with the podocyte marker WT1 (Fig. 2). BC and desmin were also expressed in WT1-negative glomerular cells (Fig. 2). Differential molecular expression patterns in glomeruli have been identified. In IgAN, co-expressing WT1 and BC (orange) was dominate in glomerular cells (Fig. 2A); the proportion of IHC expression of WT1 and BC in glomerular cells was directly correlated (r = 0.63, p = 0.031). In FSGS, WT1+ cells predominantly co-expressed desmin (magenta) but not BC; some glomerular cells were only desmin-positive (Fig. 2B). BC was expressed to a lesser extent compared to IgAN, and in some cells it was co-expressed with desmin (Fig. 2B). Conclusion In FSGS, an increase in desmin expression could be an early feature of pathogenesis before significant decrease in the number of WT1+ podocytes and changes in β-catenin expression. Activation of desmin likely characterizes damage and decrease in the number of functioning podocytes.