RNA-Mediated Toxicity In Neurodegeneration: The Mechanistic Role Of The C9ORF72 Repeat Expansion In ALS Molecular Pathogenesis

Citation

Bhattacharya, Paulomi (2025) RNA-Mediated Toxicity In Neurodegeneration: The Mechanistic Role Of The C9ORF72 Repeat Expansion In ALS Molecular Pathogenesis. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/2ywx-7a47. https://resolver.caltech.edu/CaltechTHESIS:03182025-023751137

Abstract

The G4C2 hexanucleotide repeat expansion in the first intron of the C9ORF72 gene is the most common genetic mutation linked to ALS, accounting for ~40 percent of familial and 10 percent of sporadic cases. Yet, its functional contribution to molecular pathogenesis remains unknown. The prevailing model is that this expansion leads to transcription of a novel RNA (C9-repeat RNA) that leads to disease either through its RNA product or translation of dipeptide repeat proteins it encodes (“gain-of-function”). However, recent attempts to degrade the C9-repeat RNA in several major clinical trials have failed to show any improvement in C9-ALS patients, raising questions about what role, if any, the C9-repeat RNA plays in ALS pathogenesis. Here, we demonstrate that the C9-repeat RNA is not detectable in C9-ALS patient-derived iPSNs or postmortem brain tissue. We show that transcription of the C9ORF72 gene initiates downstream of the G4C2 repeat sequence with the repeat expansion residing at a promoter-proximal region and displaying chromatin signatures of an enhancer. Because this region is GC-rich and has been reported to be preferentially methylated in C9-ALS patients, we explored whether this repeat expansion might lead to reduced C9ORF72 gene expression. We show that the C9-repeat is associated with reduced allele-specific expression of the C9ORF72 gene, consistent with the GC-rich features of the repeat expansion and previous reports of preferential DNA methylation in C9-ALS patients. Taken together, our findings challenge the prevailing gain-of-function models in C9-ALS and instead suggest that the repeat expansion region may function as a regulatory element that silences C9ORF72 expression from the mutant allele.

Item Type:

Thesis (Dissertation (Ph.D.))

Subject Keywords:

ALS, C9ORF72, repeat expansion mutation

Degree Grantor:

California Institute of Technology

Division:

Biology and Biological Engineering

Major Option:

Biological Engineering

Awards:

Eli and Edythe Broad Innovation Award in Stem Cell Biology and Regenerative Medicine, 2022.

Thesis Availability:

Not set

Research Advisor(s):

Guttman, Mitchell

Thesis Committee:

Shapiro, Mikhail G. (chair)
Ichida, Justin K.
Lester, Henry A.
Thomson, Matthew

Defense Date:

15 August 2024

Funders:

Funding Agency	Grant Number
Chan Zuckerburg Initiative (CZI)	CZI 2018-191923

Record Number:

CaltechTHESIS:03182025-023751137

Persistent URL:

https://resolver.caltech.edu/CaltechTHESIS:03182025-023751137

DOI:

10.7907/2ywx-7a47

Default Usage Policy:

No commercial reproduction, distribution, display or performance rights in this work are provided.

ID Code:

17070

Collection:

CaltechTHESIS

Deposited By:

Paulomi Bhattacharya

Deposited On:

15 Apr 2025 18:46

Last Modified:

15 Apr 2025 18:46

Full text not available from this repository.

Repository Staff Only: item control page