Structural alterations in PPP1R13L, SAE1, ATP5A1 and PCK2 disrupt NF-κB signalling and mitochondrial metabolism in primary dermal fibroblasts in systemic sclerosis

Objective Systemic sclerosis (SSc) is a proteopathy with limited diagnostic and therapeutic options. This study aimed to uncover structural protein alterations in dermal fibroblasts from diffuse cutaneous (dc)SSc patients using a novel method: limited proteolysis–mass spectrometry (LiP-MS). Methods Untreated primary dermal dcSSc fibroblasts and healthy control (HCs) fibroblasts were analyzed by LiP-MS to detect proteome-wide conformational changes. Fibroblasts were further stimulated with inflammatory cytokines: TNFα, IL-1β, TGF-β and IL-17A, highly relevant in SSc. NF-κB activity was assessed via luciferase reporter assays, while immunoblotting measured total and phosphorylated p65. ATP levels were quantified with luminescent assays, and caspase-3/7 activity was used to assess apoptosis. Results LiP-MS identified 53 263 peptides corresponding to 5,310 proteins, of which 41 showed significant conformational differences in SSc fibroblasts compared with HCs. Four proteins mapped to NF-κB signalling, while eight were linked to metabolism. Notably, structural changes were detected near functional domains of PPP1R13L and SAE1 (NF-κB regulators) and in ATP5A1 and PCK2 (mitochondrial metabolism). Functional analyses showed that TGF-β stimulation modulated NF-κB activity and the phospho-p65/total-p65 ratio, while IL-17A stimulation induced more pronounced ATP alterations in SSc fibroblasts compared with HCs. Conclusion Novel method LiP-MS successfully revealed protein conformational changes in SSc fibroblasts, particularly in domains central to NF-κB signalling and metabolic regulation. LiP-MS represents a powerful proteome-wide strategy for mapping protein structural perturbations and identifying candidate proteins and pathways for future mechanistic investigation, thereby offering a unique opportunity to connect protein conformational changes with cellular dysfunction and to potentially guide precision therapeutic approaches in SSc.