Investigating Circular RNAs in Humans: Their Roles and Interactome in Parkinson’s Disease Progression

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