Investigating Circular RNAs in Humans: Their Roles and Interactome in Parkinson’s Disease Progression
Creators: name: Van Horn, Megan
Publisher: name: Carnegie Mellon University
Year: 2023
Subjects: subject: Biochemistry
subject: Bioinformatics
subject: FOS: Computer and information sciences

description: Circular RNAs (circRNA) are products of alternative splicing that consist of a closed circular structure through a covalent 3′-5′ phosphodiester linkage. Their unique structure lends itself to a variety of physical properties and functions, including increased half-life within the cellular environment and the ability to sponge microRNA (miRNA) and RNA-binding proteins (RBPs). Through sponging, circRNA can directly affect networks of interaction by reducing the levels of available miRNA or RBPs through sequestration. Additionally, circRNA have been demonstrated to be cargo within extracellular vesicles known as exosomes, allowing them to spread their effects throughout the body. 
CircRNA in brain and blood tissue samples from PD patients are identified and analyzed for significant differential expression (DE) to better understand their influence and relationship within Parkinson’s disease (PD) pathology. PD is a neurodegenerative disease affecting millions of people with no current cure, only symptomatic treatment. Through previous studies, circRNA have been shown to have significant changes in expression in neurodegenerative conditions, indicating a potential role in pathology or as a biomarker of parkinsonism. Also included within this thesis is a study on the relationship between circRNA expression and the early stages of HIV infection. 
To investigate the presence and relationship between circRNA and PD, a bioinformatics pipeline is constructed and implemented. RNA-sequencing sets for each of the areas of interest are analyzed using the pipeline to identify three DE circRNA present in brain samples and ten DE circRNA present across all blood samples. An age- and gender-based analysis is conducted on the blood sample circRNA to determine if distribution of circRNA is biased towards a certain time period of disease progression or particular demographic characteristic. Each group of DE circRNA is further explored for secondary structure features, binding to miRNA and RBPs, and known carriage by exosomes. Further, RNA-sequencing data from each study is re-analyzed for mRNA transcript isoforms for determination of competitive or non-competitive expression between circRNA and mRNA produced from the same genomic locus. 
Further analysis shows minor overlap between the two DE circRNA populations, indicating that there may be exosomal transfer of PD-related circRNA. Many of the DE circRNA show links to PD pathology, primarily through genomic origin, and also contain binding sites for miRNA and RBPs previously implicated in PD progression. A large number of circRNA interactomes interface with pathways affecting mitochondrial dysfunction, neuronal degradation, and neuroinflammation, all characteristics of PD pathology. This thesis proposes various novel circRNA as putative biomarkers for PD progression and suggests new networks of interaction as their modes of action.