Date of Award
Spring 2026
Language
English
Embargo Period
4-27-2028
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
College/School/Department
Department of Biological Sciences
Program
Biology
First Advisor
J. Andrew Berglund
Committee Members
J. Andrew Berglund, Marlene Belfort, Hannah Shorrock, Gaby Fuchs, Kaalak Reddy
Keywords
spinocerebellar ataxias, CAG repeat expansion diseases, alternative splicing, myotonic dystrophy, Huntington's disease, microsatellite diseases
Subject Categories
Biology
Abstract
Spinocerebellar ataxias (SCAs) are a genetically heterogeneous group of dominantly inherited neurodegenerative disorders characterized by progressive motor dysfunction driven by cerebellar degeneration and Purkinje neuron loss. Among the more than 50 identified SCA subtypes, several of the most prevalent, including SCA1, SCA2, SCA3, SCA6, SCA7, SCA12 and SCA17, are caused by CAG repeat expansions that encode polyglutamine (polyQ) tracts, with the exception of SCA12, where the CAG repeat is located within 5’ untranslated region (UTR) of a disease-causing gene. Despite extensive investigation into transcriptional dysregulation, protein aggregation, and cellular stress pathways, the molecular mechanisms linking CAG repeat expansions to early neuronal dysfunction and disease onset remain poorly understood, particularly at presymptomatic stages.
Alternative splicing is a highly regulated process essential for neuronal function and proteomic diversity. Dysregulation of alternative splicing is a well-established pathogenic mechanism in other microsatellite expansion disorders, such as myotonic dystrophy (DM), and has emerged as an early molecular feature in Huntington’s disease (HD). However, whether alternative splicing dysregulation contributes to disease pathogenesis in CAG expansion SCAs had not been systematically examined prior to this work.
To address this gap, our group conducted a comprehensive analysis of transcriptomic splicing changes across 29 publicly available RNA sequencing (RNASeq) datasets derived from mouse models of SCA1, SCA3, and SCA7. This analysis revealed widespread dysregulation of alternative splicing across all three CAG expansion SCAs. Importantly, these splicing changes were detected presymptomatically, persisted throughout disease progression, were CAG repeat length dependent, and were present in brain regions central to SCA pathology, including the cerebellum, pons, and medulla. Dysregulated splicing events affected genes involved in pathways known to be disrupted in SCAs, including ion channel function, synaptic signaling, transcriptional regulation, and cytoskeletal organization. As part of my project, I validated several disease-relevant splicing events with known functional consequences, including Trpc3, Kcnma1, Cacna2d2 in the Atxn1154Q/2Q SCA1 mouse model.
Following the identification of alternative splicing dysregulation as a shared hallmark in mouse models, as part of my primary research, I next investigated whether similar transcriptomic changes occur in patient-derived cellular models. Using RNASeq of fibroblast lines from individuals with SCA1, SCA3, and SCA7, I identified robust and reproducible dysregulation of alternative splicing across all CAG expansion SCA patient lines examined. Dysregulated splicing events affected disease-relevant pathways, including microtubule-based processes, transcriptional regulation, and DNA damage and repair. Several novel alternative splicing events were validated across multiple patient-derived lines, demonstrating that these changes are conserved across genotypes and disease contexts.
To determine whether CAG repeats themselves contribute to splicing dysregulation independently of gene context, I analyzed CAG-containing reporter cell lines. These experiments revealed widespread alternative splicing changes even when the repeat expansion was outside of any SCA-associated gene context, suggesting that expanded CAG repeats alone are sufficient to lead to splicing changes. Importantly, several of these events were responsive to therapeutic intervention, supporting their potential utility as molecular readouts for treatment response. Together, these findings establish alternative splicing dysregulation as a shared pathogenic mechanism across SCA1, SCA3, and SCA7 patient models.
As a secondary project, I contributed to a small-molecule screening effort aimed at identifying therapeutic compounds with efficacy across multiple CAG expansion SCAs. This work identified a novel CAG-repeat binding compound, Hit 2, that selectively reduced expression of disease-associated transcripts in SCA1, SCA3, and SCA7 patient-derived fibroblasts, as well as in the Atxn1154Q/2Q mouse model. Notably, our lead compound also rescued dysregulated alternative splicing events in vivo, providing the first evidence that small molecules can target a shared molecular mechanism across multiple CAG expansion SCAs.
Finally, I extended this work to iPSC-derived cortical neurons, a more disease-relevant neuronal model. These studies revealed widespread alternative splicing dysregulation affecting neuronal pathways, with splicing changes exceeding differential gene expression in sensitivity, a common theme in all analyzed cell lines. I identified and validated disease-relevant splicing events, including SCAPER and SNHG14, further supporting the relevance of alternative splicing dysregulation in human neuronal contexts.
In summary, the work presented in this dissertation identifies alternative splicing dysregulation as a novel, early, and shared molecular feature of CAG expansion SCAs. The exon-specific and tissue-sensitive nature of alternative splicing makes it a particularly powerful candidate for non-invasive biomarkers of disease onset, progression, and therapeutic response. These findings provide a framework for leveraging splicing-based readouts in the development and evaluation of future therapies for this devastating group of neurodegenerative disorders.
License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Recommended Citation
Aliyeva, Asmar, "Dysregulation of Alternative Splicing Is a Transcriptomic Feature of CAG Repeat Expansion Spinocerebellar Ataxias" (2026). Electronic Theses & Dissertations (2024 - present). 405.
https://scholarsarchive.library.albany.edu/etd/405