C9ORF72 ALS/FTD MOLECULAR DISEASE MECHANISM AND NUCLEIC ACID THERAPEUTICS

Author

Katy Ovington, Southern Illinois University CarbondaleFollow

Date of Award

8-1-2022

Degree Name

Doctor of Philosophy

Department

Molecular Biology, Microbiology and Biochemistry

First Advisor

Gagnon, Keith

Abstract

More than 40 neurological diseases are known to be caused by large expansions oftandem repeat sequences scattered throughout the human genome in introns, exons and untranslated regions. The GGGGCC (G4C2) repeat expansion located in the first intron of the C9ORF72 gene is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). In C9 FTD/ALS, expanded transcripts are known to aggregate and accumulate in the cell nucleus, sequestering RNA binding proteins. Other expanded RNA species are exported to the cytoplasm to undergo a non-canonical form of translation termed ‘repeat-associated non-AUG (RAN) translation’. RAN translation leads to the production of toxic polydipeptide repeat proteins in the absence of a canonical AUG start codon. This dissertation will highlight new mechanistic features of translation across the G4C2 repeat expansion, identify a potential therapeutic for C9 FTD/ALS using RNAi and develop a cellular system to explore the G4C2 repeat RNA lifecycle. First, we demonstrate that increasing G4C2 repeat expansion size results in suppression of translation from both canonical and non-canonical start codons, suggesting that large polydipeptide repeats are rarely fully translated. We further find that initiation does not occur from within the repeat expansion, relying on upstream sequence for initiation. However, some reading frames are prone to substantial frameshifting, such as poly-GA. We also show that a bias in ii codon usage efficiency contributes to previously observed variations in the levels of each polydipeptide. Our results support and extend previous studies by identifying two new mechanisms that bias production of poly-dipeptides toward poly-GA in C9 FTD/ALS. Further, we generated central mismatch-containing short hairpin RNAs (shRNAs) targeting the G4C2 repeat expansion to reduce aggregation or block translation of repeatcontaining transcripts. Iterative design was able to improve shRNA processing efficiency and cellular abundance, yet they were unable to reduce nuclear RNA foci in patient-derived cells. Despite this, we show preliminary data suggesting that these shRNAs are able to target cytoplasmic repeat-containing transcripts and resulting in a reduced translation of poly-GP. Finally, we optimized the previously published RNA-protein interaction detection (RaPID) technique, which uses proximity dependent labelling by a mutant biotin ligase and mass spectrometry for protein identification in living cells, to identify proteins interacting with the G4C2 repeat expansion. We embedded the box B RNA hairpin between G4C2 repeats and tested the ability for λN fused to a biotin ligase mutant, BASU, to specifically bind the box B hairpin in vitro. We show that 6 repeats each side of the hairpin combined with an extended hairpin stem promotes specific binding of the λN-BASU fusion protein and is likely to be successful in cells. C9 FTD/ALS is a currently incurable neurodegenerative disorder largely due to the limited understanding of disease mechanism. This dissertation demonstrates new mechanisms of translation across the G4C2 repeat expansion that results in toxic DPR production while also developing a nucleic acid therapeutic for long-term treatment of C9 FTD/ALS and further developing systems to explore RNA-mediated toxicity in cells.