Investigating RNA Dysfunction of Inherited Neuromuscular and Neurodevelopmental Disease

Author

Jacob H. Schroader, University at Albany, State University of New YorkFollow

ORCID

https://orcid.org/0000-0002-7702-1016

Date of Award

Summer 2025

Language

English

Embargo Period

8-1-2026

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

College/School/Department

Department of Biological Sciences

Program

Biology

First Advisor

Kaalak Reddy

Second Advisor

John Andrew Berglund

Committee Members

Kaalak Reddy, John Andrew Berglund, Gabriele Fuchs, Thomas Begley, Eric Wang

Keywords

ITPase deficiency, Inosine misincorporation, Noncanonical nucleotides, Inherited neurodevelopmental disease, Inherited neuromuscular disease, Myotonic dystrophy type 1

Subject Categories

Bioinformatics | Congenital, Hereditary, and Neonatal Diseases and Abnormalities | Molecular Biology | Musculoskeletal Diseases

Abstract

ITPase deficiency is a rare but fatal, autosomal recessive enzyme deficiency involving encephalopathy, microcephaly, congenital cataracts, hypotonia, developmental delay, and dilated cardiomyopathy. Within a decade since the original description of the severe form in humans, there are huge gaps in the field regarding the underlying molecular mechanisms driving pathogenesis resulting from ITPase deficiency. Past studies have focused on characterization of the organism level ITPase-deficient phenotype, but the molecular and cellular characterization remains to be fully described. Due to the biochemical function and established biological role of the ITPase enzyme, investigation into the consequences of inosine accumulation and misincorporation into RNA represents a promising research avenue. To address the open questions, I used RNA sequencing approaches to determine base pair preferences and establish a stochastic model of inosine misincorporation. I determined the molecular effects of this inosine misincorporation on the fate of RNA containing inosine. I tested the molecular and cellular responses to introduction of inosine-containing RNAs and how these responses are tied to inosine levels. Specifically, I uncovered that inosine misincorporation into mRNA leads to translation disruption and basic activation of the integrated stress response with an innate immune gene expression signature. I identified factors that respond to inosine levels and/or activate the ISR including protein kinase R (PKR) in cellular models of ITPase deficiency. Beyond the functional, mechanistic investigation, I also characterized the transcriptomes of several model systems of ITPase deficiency currently in use with modern RNA sequencing techniques. The majority of the work presented in the dissertation pertains to severe ITPase deficiency reflecting the collective time spent on the subject. As a secondary project, I contributed to a study on myotonic dystrophy type 1, a multisystemic disease and the most common adult muscular dystrophy, that is featured here as part of the dissertation. Myotonic dystrophy type 1 or DM1 is an autosomal dominant genetic disorder caused by excessive CTG repeats in the 3’UTR of the DMPK gene that leads to production of toxic CUG RNA. These toxic CUG RNAs sequester the muscleblind-like (MBNL) family of alternative splicing regulators leading to global spliceopathy that is linked to the various symptoms of disease. I was involved in a genome-scale screen for modifiers of toxic CUG RNA, leading to the identification of core components of the spliceosome including SNRPD2. My contribution was in characterizing transcriptomic changes resulting from altered SNRPD2 levels in control and DM1 patient cells using RNA sequencing. Taken together, my thesis uncovers novel RNA dysfunction processes underlying inherited neurodevelopmental and neuromuscular disease.

License

This work is licensed under the University at Albany Standard Author Agreement.

Recommended Citation

Schroader, Jacob H., "Investigating RNA Dysfunction of Inherited Neuromuscular and Neurodevelopmental Disease" (2025). Electronic Theses & Dissertations (2024 - present). 289.
https://scholarsarchive.library.albany.edu/etd/289