Yeast as a gateway to conquering protein misfolding diseases.

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ABSTRACT Certain proteins misfold to form self-seeding prion-like aggregates associated with disease. We focus on one such protein, TDP-43, the major protein associated with neuronal aggregates in several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia and LATE. A prevalent TDP- 43 proteinopathy, LATE causes dementia often misdiagnosed as Alzheimer’s disease (AD). TDP-43 is also found along with other proteins in AD and Parkinson’s neuronal inclusions. TDP-43 and other human misfold- ing disease proteins form aggregates and inhibit growth in yeast. This allows yeast to be used to find therapeu- tic targets. Remarkably, yeast genes that modify the toxicity of human misfolding disease proteins, including TDP-43, identified both previously unknown and established human disease risk factors, demonstrating the relevancy of the yeast model to human disease. We have used our expertise with yeast self-seeding prion pro- teins to study human misfolding disease proteins with the yeast model. Now, we expect to learn how TDP-43 causes toxicity in yeast and, with the help of collaborators, in what ways our findings relate to TDP-43 toxicity in higher cells and organisms. A central task is to identify the range of condensates, oligomers and aggregates formed by TDP-43, and their toxicities. Determining which TDP-43 species is most toxic will advance under- standing of toxicity mechanisms. As it is largely unknown what cellular functions are targeted by toxic TDP-43 species or the affiliated mechanisms, this work explores cellular targets of toxicity focusing on TDP-43 gain of function toxicity. New models of therapeutic approaches will be developed by investigating if overexpression of TDP-43 binding proteins can inhibit the formation of toxic TDP-43 species, if titration of essential or important cellular proteins by TDP-43 toxic species contributes to toxicity, and if mutations in TDP-43 can protect wild- type TDP-43 expressed in the same cell from forming toxic aggregates. Another gap to be addressed is why TDP-43 is associated with different diseases. Importantly, as we showed for yeast prions, TDP-43 and other disease proteins can misfold into different self-seeding aggregate variants/strains (not due to alterations in their primary sequence), that have distinct characteristics. Thus, different variants of TDP-43 could affect neurons differently, causing e.g. ALS vs. LATE. TDP-43 variants established in yeast would be important tools to iden- tify disease specific variants and facilitate development of variant specific treatments. We will also investigate the premise that entry into liquid-like granules is an upstream trigger of toxic species formation to learn if liquid- like granules are therapeutic targets. Our approach will be to quantify the relationship between entry of prion proteins into liquid condensates and stochastic formation of prions in yeast. Finally, we will examine the new area of disease associated metabolite amyloid-like aggregates and the hypothesis that they nucleate prion- like/disease protein misfolding, similar to our early demonstration of cross-seeding between yeast prions. This work is expected to lead to new treatment approaches for protein misfolding diseases.