Functional proteomic analysis of altered protein signaling modules in Alzheimer's disease

Neuritic plaques comprised of amyloid beta (Abeta) are one of the primary neuropathological hallmarks of Alzheimer's disease (AD). However, Abeta plaque deposition is preceded by aberrations of the endosomal/lysosomal system, including abnormally enlarged endosomal compartments, accumulation of protease-resistant proteins, and atypical activation of the lysosomal system. The functional mechanisms accounting for these abnormalities have not yet been delineated. Towards our goal of identifying the proteins whose dysfunction contributes to the development of endosomal/lysosomal pathology in AD, we have found that: (1) proteins implicated in regulating late endosomal trafficking are among the targets of oxidation (carbonylation) in the brain of a presenilin 1/amyloid precursor protein (PS1/APP) transgenic mouse model of AD; (2) reduced neuronal expression of synaptic membrane protein HNK-1/NCAM is associated with Abeta pathology in models of Abeta deposition in cell culture and an amyloid precursor protein (APP) transgenic mouse, and is a potential consequence of impaired endosomal sorting of proteins that are trafficked to synaptic terminals under non-pathological conditions; and (3) perturbation of the function of vacuolar protein sorting protein 4b (Vps4b) in regulating multivesicular body (MVB) biogenesis and endosomal trafficking results in its abnormal association with proteins involved in cell death and protein turnover.; Our functional proteomic approach relies upon the specific isolation of sub-proteomes, or protein interaction modules, that are assembled in a sub-cellular location- and stimulus-specific manner to carry out distinct cellular tasks. The physical association of the components of these protein interaction modules results in the causation of a particular phenotype that may or may not have a role in disease pathogenesis depending upon the post-translational modification, sub-cellular localization, and relative abundances of the protein interaction module constituents. We have applied sensitive mass spectrometry techniques and robust computational biology methods to the qualitative and quantitative anaylsis of protein interaction modules that are potentially involved in the causation of the endosomal/lysosomal abnormalities associated with neurodegeneration in AD using various cell culture and transgenic mouse models of AD pathogenesis.