PROJECT SUMMARY (CORE B: PROTEOMICS) Rare MAPT mutations have long been known to be a cause of familial frontotemporal dementia (FTD-Tau). A common haplotype (H1) encompassing the MAPT locus is also associated with increased risk for multiple, sporadic Tauopathies, including Frontotemporal Dementia (FTD) and Progressive Supranuclear Palsy (PSP), while the H2 haplotype confers reduced risk. Despite this difference, very little is known regarding the mechanisms behind the differences in risk between the H1 and H2 haplotypes or whether these common haplotypes affect expression of rare MAPT mutations. A comprehensive analysis of the molecular differences mediating this risk will represent a significant and essential resource for the neurological disorder community. The work proposed by this core will be performed at the Thermo Fisher Scientific Proteomics Facility for Disease Target Discovery located at the J. David Gladstone Institutes at the UCSF campus. Both this facility and the Proteomics Core, will be led by Dr. Swaney, an expert in mass-spectrometry based proteomics research with a track record in the development and application of novel proteomics approaches to enable biological discoveries. The objective of the Proteomics Core is to provide cutting-edge and innovative technologies for quantitative proteomic characterization of the molecular mechanisms regulating differential risk between MAPT H1 and H2 haplotypes in a reliable, reproducible, and cost-efficient manner. It will support Projects 1 & 2 by enabling proteomics experiments, and interact with both the Human Tissue Validation Core to validate findings, and with the Data Core to integrate datasets as a resource for the CWOW project members and the research community. Importantly, it will also serve as a resource to the wider scientific community by dissemination of new assays and protocols. Efforts of this core will be focused on applying state-of-the-art discovery proteomics technologies to precisely quantify differences in protein abundance and phosphorylation signaling for a variety of brain cell types harboring different MAPT haplotypes or MAPT mutations on different haplotypic backgrounds. These results will provide a proteome-wide view of specific proteins and pathways that are differentially regulated by MAPT haplotypes. We will also complement this analysis with a hypothesis-driven targeted proteomics approach to quantify a small number of proteins mapping to the H1/H2 inversion region and exhibiting cell type and haplotype specific differences in gene expression and regulation. Lastly, we will validate at the protein level the novel splice variants resulting from the ISO-seq and transcriptomic analyses.