Assessment of microexon-associated junction usage in Parkinson's disease and spinocerebellar Ataxia type 3

Microexons are short exonic sequences of 3-30 nucleotides that undergo alternative splicing and have been implicated in several neurodevelopmental disorders. However, their contribution to neurodegenerative diseases remains insufficiently characterized.

We analyzed microexon-associated junction usage in the frontal cortex of Parkinson's disease (PD) patients and in the cerebellum of Spinocerebellar Ataxia Type 3 (SCA3) patients using deep RNA-Sequencing of human postmortem brain tissue and corresponding SH-SY5Y cellular models. Microexon-associated junction usage was quantified based on splice junction reads derived from STAR alignments, followed by statistical testing with false discovery rate (FDR) correction for multiple testing and visualization using Sashimi plots. Selected candidate events in the cellular datasets were assessed by PCR.

Across all datasets, 19 microexon-associated junction candidate events were identified but did not survive FDR correction. Human brain tissue exhibited substantially more detectable microexons compared to cellular models, which may reflect differences in splicing complexity between differentiated tissue and neuroblastoma-derived cells. While visual inspection suggested that effect sizes were generally small and variable across samples, the majority of microexon-containing genes were expressed in both systems. PCR confirmed detection of the selected microexons but did not validate differences in microexon-associated junction usage between experimental groups.

Our findings provide an overview of microexon landscapes in PD and SCA3 and an exploratory statistical analysis. Although large and consistent disease-specific patterns of microexon-associated junction usage were not observed, our findings suggest that microexon regulation in neurodegeneration may involve subtle and context-dependent alterations that warrant further investigation in larger cohorts.