Date of Award

2019

Degree Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Cell & Molecular Biology

First Advisor

Edward B. Lee

Abstract

Repeat expansion mutations in the gene C9orf72 are the most common cause of the fatal neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). The molecular mechanisms that contribute to these diseases are still not fully understood. In this dissertation, we explore mechanisms associated with repeat expansions in C9orf72 that alter gene expression and contribute to disease. In chapter 2, we develop a novel method of targeted DNA methylation in order to study how epigenetic changes in C9orf72 expansion carriers contribute to disease pathways. We find that C9orf72 promoter hypermethylation is sufficient to reduce gene expression and induce heterochromatin silencing of this locus in ALS patient derived cells. We also uncover a link between DNA damage repair pathways and DNA methylation where a double strand break in CpG islands can promote DNA methylation. Furthermore, we have taken advantage of these findings to develop and optimize a novel targeted DNA methylation method that utilizes homology directed repair for precise methylation editing in the absence of off-target effects. In chapter 3, we ask whether intermediate length repeat expansions in C9orf72 are associated with a different neurodegenerative disease, corticobasal degeneration (CBD). CBD shares similar clinical symptoms with Parkinson’s disease but exhibits distinct tau pathology in neurons and glial cells. We find that intermediate C9orf72 repeat expansion carriers (17-30 repeats) are three times more likely to develop CBD than those with smaller repeats. While full expansion carriers with ALS/FTD tend to have reduced C9orf72 expression, we show that intermediate expansion carriers actually have increased C9orf72 mRNA and protein levels. This increase in C9orf72 expression drives aberrant gene expression profiles in vesicle trafficking, stress response and autophagy pathways. Furthermore, we find that autophagy initiated by nutrient starvation is deficient in cells that over-express C9orf72. In sum, this thesis contributes a novel method of targeted DNA methylation to the research community and shows how DNA methylation alters expression of a disease relevant gene. This work also highlights how variable lengths of the repeat expansion in C9orf72 can lead to distinctive underlying molecular mechanisms and ultimately drive risk for different neurodegenerative diseases.

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