RNA helicases to combat RNA phase transitions in repeat expansion disorders

Abstract Repeat-expansion disorders are a collection of more than 40 rare but devastating diseases that largely effect the central nervous system. Currently, they are incurable. The genetic basis for these disorders is repeat expansions, the length of which determines disease severity and age of onset. In these disorders, repeat sequences cause pathology in a multimodal fashion. The translation of repeats located in coding regions can disrupt normal protein function and produce toxic repeat peptides. These neurotoxic peptides can be produced even when the repeats are in noncoding regions via repeat associated non-AUG translation. Another agent of pathology is the repeat RNA transcript itself, where aberrant binding of the repeat RNA to RNA-binding proteins leads to issues like deregulation of the miRNA machinery, aberrant translation, and mis-splicing events. Repeat RNAs also enable transcripts to undergo liquid-liquid phase separation (LLPS) and form nuclear RNA foci in cells. These foci can sequester RNA-binding proteins, which may contribute to the observed repeat RNA toxicity. It has been well established that RNA helicases regulate the formation of phase separated ribonucleoprotein (RNP) granules in cells, but no work exists to understand how helicases affect the RNA foci in repeat-expansion disorders. Considering first that repeat RNAs cause potentially pathological RNA foci and that second, helicases are important for the formation of other cellular RNP granules, we hypothesize that RNA helicases can also modulate the formation of RNA foci in repeat-expansion disorders. The proposed work is focused on the deleterious RNA foci that form in the repeat-expansion disorders caused by CAG trinucleotide expansions like Huntington’s Disease and several spinocerebellar ataxias. This proposed study aims to identify RNA helicases that modulate these deleterious RNA foci and understand the mechanism by which they do so. Knockout screens in human HAP1 cells expressing CAG repeat constructs which form RNA foci have identified candidate RNA helicases that affect RNA foci size and number. This work will utilize in vitro approaches to understand the mechanism underlying how these candidate helicases effect RNA foci. After the recent failure of two candidate therapies for Huntington’s Disease in clinical trials, it is especially necessary to consider new therapeutic targets for these disorders. This work will expand our understanding of RNA helicase function in repeat-expansion disorders and offer a new therapeutic tool to explore for combatting these diseases. The proposed fellowship will be conducted at the University of Pennsylvania in the lab of Dr. James Shorter, a leading researcher in the molecular basis of neurodegenerative diseases and protein disaggregases. Completion of the proposal in this lab will provide rigorous training in biochemical assay design and in vitro protein and RNA handling techniques.