Probe-dependent Proximity Profiling (ProPPr) Uncovers Similarities and Differences in Phospho-Tau-Associated Proteomes Between Tauopathies

Abstract

Tauopathies represent a diverse group of neurodegenerative disorders characterized by the abnormal aggregation of the microtubule-associated protein tau. Despite extensive research, the mechanisms underlying the diversity of neuronal and glial tau pathology in different tauopathies are poorly understood. While there is a growing understanding of tauopathy-specific differences in tau isoforms and fibrillar structures, the specific composition of heterogenous tau lesions remains unknown. Here we study the protein composition of tau aggregates in four major tauopathies: Alzheimer's disease (AD), corticobasal degeneration (CBD), Pick's disease (PiD), and progressive supranuclear palsy (PSP). We developed an approach for in situ proximity labeling and isolation of aggregate-associated proteins using glass slides with formalin-fixed paraffin-embedded (FFPE) human postmortem brain tissue, termed Probe-dependent Proximity Profiling (ProPPr). We used ProPPr for the analysis of proteomes associated with AT8-positive cellular lesions from frontal cortices. Isolated proximity proteomes were analyzed by data-independent acquisition mass spectrometry. Co-immunofluorescence staining and quantitative data analysis for selected proteins in human brain tissue was performed to further investigate associations with diverse tau pathologies. Proteomics data analysis identified numerous common and tauopathy-specific proteins associated with phospho-tau aggregates. Extensive validations of candidates through quantitative immunofluorescence imaging of distinct aggregates across disease cases demonstrate successful implementation of ProPPr for unbiased discovery of aggregate-associated proteins in in human brain tissue. Our results reveal the association of retromer complex component vacuolar protein sorting-associated protein 35 (VPS35) and lysosome-associated membrane glycoprotein 2 (LAMP2) with specific types of phospho-tau lesions in tauopathies. Furthermore, we discovered a disease-specific association of certain proteins with distinct pathological lesions, including glycogen synthase kinase alpha (GSK3α), ferritin light chain (FTL), and the neuropeptide precursor VGF. Notably, the identification of FTL-positive microglia in CBD astrocytic plaques indicate their potential role in the pathogenesis of these lesions. Our findings demonstrate the suitability of the ProPPr approach in FFPE brain tissue for unbiased discovery of local proteomes that provide valuable insights into the underlying proteomic landscape of tauopathies, shedding light on the molecular mechanisms underlying tau pathology. This first comprehensive characterization of tau-associated proteomes in a range of distinct tauopathies enhances our understanding of disease heterogeneity and mechanisms, informing strategies for the development of diagnostic biomarkers and targeted therapies.