Inference of Common Pathways Underlying Neurodegeneration & Other Age-Progressive Diseases

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Specific proteins within aggregates are diagnostic for most neurodegenerative diseases, including Alzheimer’s, Parkinson’s, and Huntington’s diseases. Protein aggregation, however, is a basic feature of aging in numerous organisms, and may underlie a variety of age-progressive diseases. By defining the aggregate proteomes from several mouse and human tissues, we have identified a very large fraction of aggregate components that are common across diverse organs, and increase with age in all sites. We have tested several dozen “shared” components for functional roles in aggregation by RNAi knockdown in C. elegans, and found that the majority contribute to the aggregation process – suggesting that there is a quasi-pathway for aggregate accrual. To better understand this somewhat orderly adhesion process, we developed improved reagents, protocols and analytic tools for click-chemistry crosslinking of aggregate neighbors. We thus constructed aggregate connectomes, which revealed that a small number of hub connectors mediate coalescence of large aggregates, which would otherwise be isolated, into mega-aggregates that may resist digestion by the normal clearance mechanisms. The strategy proposed here is to compare mice, as they age, for aggregate quantity and composition in cerebrum, heart, and serum. The mice will differ in genotype (wild-type, or their BRI-Aβ42 transgenic littermates, otherwise isogenic with the wild-type mice, but forming brain amyloid with age due to overexpression of a “seed peptide” Aβ1–42), and also with respect to dietary and drug interventions. We propose 3 Specific Aims, as follows: Aim 1. Define aggregate and total proteomes of heart, brain, and serum from wild-type mice as they age (4 – 24 months), ± dietary and drug interventions. Here we will define common aggregate components that accrue with aging, shared by two tissues and partially reflected by aggregates found in serum. We expect many of these proteins or their post-translational modifications to respond to restricted diet (RD) and western diet (WD), and be ameliorated by NSAID-related drugs that were previously shown to reduce aggregation or AD incidence. Aim 2. Define aggregate and total proteomes of heart, brain, and serum from BRI-Aβ42 transgenic mice as they age (4 – 24 months), ± dietary and drug interventions. Goals and procedures parallel those for Aim 1, with the addition of memory and glucose-tolerance tests. We expect accelerated brain aggregation in BRI-Aβ42 mice. Aim 3. Analysis and pursuit of candidate biomarkers of aging and/or disease. We will make pairwise comparisons of controls on normal diet with each intervention group, to identify candidate proteins and PTMs that differ between ages, groups or genotypes by >2-fold, with FDR<0.01. We will seek features that, individually or jointly, can be used to predict age, amyloidosis, memory loss, glucose intolerance, or aggregate burden in heart or cerebrum. Serum aggregates have particular utility since they can be assessed noninvasively. Age-differential features observed in both tissues, if ameliorated by RD, aspirin and PNR502, but exacerbated by WD and BRI- Aβ42 (in brain), will be pursued by cross-linking interactome analysis and functional testing by shRNA knockdown.