TMT proteomics reveals distinct cerebrospinal fluid signatures across genetic frontotemporal dementia subtypes

Background: Frontotemporal dementia (FTD) encompasses a group of complex disorders characterized by progressive neurodegeneration in the brain"s frontal and temporal lobes. The multifaceted clinical and neuropathological nature of FTD has so far hampered diagnostic and therapeutic advances. Notably, the two major brain pathologies encountered in FTD are protein aggregates composed of either TAR DNA-binding protein 43 (TDP-43) or tau. To date, the scientific community lacks established biomarkers to distinguish between pathologies antemortem as well as markers to predict or track disease progression.

Aim: This study set out to explore proteomic differences in the cerebrospinal fluid (CSF) of genetic FTD cases, exhibiting a clear relationship between genetic mutation and underlying pathology, to discern FTD pathology-specific proteomic signatures. We further aimed to identify proteins associated with disease onset and progression.

Methods: We analysed 238 CSF samples from C9orf72 (TDP-43 pathology; n=71), GRN (TDP-43 pathology; n=55), and MAPT (tau pathology; n=36) presymptomatic and symptomatic mutation carriers, as well as 76 controls using TMTpro 18-plex proteomics. TMT multiplex samples were fractionated into 24 concatenated fractions by reversed-phase chromatography at basic pH and analysed by LC-MS on an Orbitrap hybrid mass spectrometer (Lumos Tribrid, Thermo Scientific). Protein correlation network analysis (WGCNA) was performed to detect subtype-specific proteomic and pathophysiological alterations.

Results: Leveraging WGCNA, we identified several biological processes affected across all symptomatic mutation carriers and pathologies (Figure 1): Proteins associated with neurodegeneration ("Core markers", e.g. YWHAG), actin binding (e.g. MSN), and cellular stress response were increased in symptomatic mutation carriers compared to presymptomatic individuals and controls. These protein clusters strongly correlated with clinical measures of disease severity (FTLD-CDR-SOB, p<0.001) and expected year of symptom onset (EYO, p<0.001), suggesting their potential utility as prognostic biomarkers. Besides common proteomic alterations, we observed that subpopulations of proteins were uniquely associated with each genetic mutation: GPI and HK1, for instance, showed a stepwise increase in abundance from presymptomatic to symptomatic C9orf72 mutation carriers, hinting at early changes in glucose metabolism within this genetic group. Notably, we also found a cluster of proteins with the potential to distinguish between tau and TDP-43 pathology: lysosomal proteins (e.g. DNASE2 and PLBD2) were lower in abundance in symptomatic MAPT mutation carriers (p<0.05) compared with controls, while their levels remained unchanged in GRN and C9orf72 mutation carriers.

Conclusion: We discovered shared and distinct proteomic signatures of genetic FTD subtypes that may have prognostic value and distinguish between FTD-pathologies.