Investigating protein supersaturation as a driver of aging

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PROJECT SUMMARY Protein aggregation is a hallmark of aging and age-associated disease, however a causal relationship has not been demonstrated. Elucidating whether there is a predestined, irreversible driving force in cell aging would enable the development of novel therapies to decelerate aging. Therefore, my long-term goal is to understand this relationship at a fundamental level. My central hypothesis is that probabilistic, irreversible conformational transitions in physiologically supersaturated proteins not only initiate the process of cellular aging, but drive it!. The accumulation of amyloids following such transitions will compromise kinetic proteostasis, or kinetic barriers for supersaturated proteins to remain soluble, and this ultimately compromises thermodynamic proteostasis -- or the processes that maintain the concentrations and stabilities of soluble proteins. I will utilize the following Specific Aims and synergistic approaches, distributed amphifluoric FRET (DAmFRET), Epigenetic Clocks, and RNA-Seq, to distinguish the kinetic from thermodynamic determinants of protein solubility as a function of cell age. In Aim 1, I will compare thermodynamic and kinetic proteostasis as a function of biological age. To do so, I will first obtain primary human fibroblasts (PHFs) from differentially aged donors, and validate their epigenetic age using DNA methylation signatures (DNAm) referenced against previously developed DNAm age prediction algorithms, as well as RNA-Seq. I will then perform DAmFRET experiments in each of the PHFs using a panel of inducible constructs that reliably aggregate in a nucleation- and/or concentration-limited manner. These data will reveal the degree to which kinetic proteostasis and/or thermodynamic proteostasis are impacted by biological age. In Aim 2, I will test if conformational nuclei accelerate the aging of PHFs. I will generate generic light-activated optoSeeds from our reporter library in Aim 1 to elicit a conformational transition, or cross-seeding event, in PHFs of young age. I will then use multiple mass spectrometry approaches to evaluate whether the nucleation event precipitated endogenous proteins, and determine their identities. I will then determine if the treatment accelerates the progression of cell age via DNAmAge and RNA-Seq. In Aim 3, I will test if perturbing kinetic proteostasis in the nucleus enhances the rate of aging as compared to the cytosol. Using our optoSeeds, I will elicit a conformational transition in the nuclear and cytoplasmic compartments. I will again use DNAm age prediction and RNA-Seq to determine whether age is accelerated via conformational transitioning in the nucleus versus the cytosol. Completion of these aims will provide fundamental insights into the thermodynamic reasons for why we age. In addition, completion of the proposed studies will provide me with a strong foundation to continue my research as an independent investigator.