Distinct cerebrospinal fluid proteomic signatures define clinicopathological subtypes of sporadic Creutzfeldt-Jakob disease and predict patient survival.

Sporadic Creutzfeldt-Jakob disease (sCJD) is a highly heterogeneous neurodegenerative disorder encompassing six major histopathological and molecular subtypes, showing diverse clinical features and prognosis. Currently, no accurate biomarkers are available for the antemortem differentiation and prognostication of sCJD subtypes. We retrospectively analyzed the cerebrospinal fluid (CSF) proteome from 126 sCJD patients belonging to the prevalent MM(V)1, VV2, and MV2K subtypes and 42 non-neurodegenerative controls (CTRL) using proximity extension assay technology, quantifying 797 unique proteins in each sample. Differential expression analysis, machine learning models, and Cox regression analyses were employed to uncover subtype-specific protein signatures and identify diagnostic and prognostic biomarkers. A workflow combining Weighted Gene Co-expression Network Analysis (WGCNA) and Hierarchical HotNet was used for the unsupervised discovery of novel dysregulated biological pathways. A subset of proteins, including HDGF, FOSB, PAG1, APEX1, CCDC80, WASF1, and GPC5, emerged as robust biomarkers for subtype classification (model receiver operating characteristics-area under the curve 0.93). WASF1, CCDC80, and GPC5 were among the most informative biomarkers distinguishing MM(V)1 from V2 strain-related subtypes (VV2 and MV2K). Survival analysis identified ten proteins, most notably CCDC80 (HR 1.49, 95% CI 1.17–1.91, p = 0.001), as independent prognostic biomarkers in prion disease. WGCNA identified six modules of co-regulated proteins underlying distinct biological processes. Some, such as response to toxic substances, nervous system development, and chemotaxis, were altered across all subtypes compared to the CTRL group (all p < 0.01), while others showed subtype-specific dysregulation. Specifically, the intracellular signal transduction module was selectively altered in V2 strain-related subtypes, while the epithelium morphogenesis one was dysregulated in MM(V)1 (all p < 0.001). In conclusion, this study reveals distinct and shared CSF proteomic signatures across sCJD subtypes, identifying novel diagnostic and prognostic biomarkers and dysregulated molecular pathways. These findings enhance our understanding of prion disease heterogeneity and suggest new pathogenic mechanisms.