Proteomics and Post-translational Modification

Abstract Lysosomes are highly specialized and dynamic cellular organelles that help maintain protein homeostasis. Lysosomes also act as a signaling center of the cell. Many of these signals are transduced to the nucleus and ultimately modulate transcription of genes and the expression of protein products. This includes genes and proteins that are essential to lysosome function and biogenesis. Dysregulation of lysosomal genes and the dysfunction of the lysosome system are associated with aging and age-associated diseases, including Alzheimer’s disease. The Proteomics and Quantitative Post-translational Modification core (proteomics core) (Core B) will support all three research projects in this PPG proposal to elucidate changes in the proteome and the mechanisms by which protein expression is altered during aging and Alzheimer’s disease. We will use methods as described in our preliminary data to measure changes in (1) the lysosomal proteome, including isoforms and post-translational modifications, (2) post translational modifications in lysosome-associated signaling events upstream of transcription, and (3) histone post-translational modifications in lysosomal gene regulatory mechanisms. The proteomics core will leverage our expertise and current capacity in the proteomic analysis of subcellular organelles, targeted proteomic characterization and quantitation of protein modification state (proteoforms), as well as extensive expertise in signal transduction and histone modifications. The focus of Core B is to provide reproducible quantitation and detailed characterization of the lysosome and crucial proteins that are essential to the regulation of lysosomal biology in aging and tauopathy. This level of molecular detail is important because protein attributes, such as isoforms, proteolysis, and post-translational modifications, often function in concert or in specific hierarchies to execute their core function. Together, these studies will provide unparalleled detailed characterization that reveal molecular mechanisms of lysosome function, regulation, and biogenesis in aging biology, and Alzheimer’s disease pathophysiology. Core B will also actively collaborate with other Cores and Projects to create a first-in- class Aging- and Tauopathy-associated Lysosomal atlas (ATLas) of the lysosomal proteome and metabolome for mouse cortex and hippocampus to be shared with the general research community.