Systematic analysis of RNA exosome mutations reveals global transcriptomic dysregulation and morphological abnormalities in the brain

Intracellular ribonucleases (RNases) are critically important for all aspects of RNA metabolism, ensuring proper steady-state RNA levels and accurate gene expression. Intriguingly, inherited mutations in genes encoding ubiquitous RNases are associated with tissue-specific human diseases, primarily affecting the nervous system. Specifically, recessive missense mutations in genes encoding structural subunits of the RNA exosome RNase complex lead to syndromic neurodevelopmental disorders characterized by progressive neurodegeneration, such as Pontocerebellar Hypoplasia Type 1b (PCH1b). PCH1b is characterized by atrophy of the brain and motor neuropathologies. We employ a comprehensive approach to begin to uncover the basis for tissue-specific pathology observed in individuals with RNA exosome-linked PCH1b by utilizing high-throughput genomic and standard brain and behavioral phenotyping assays in Drosophila. We generated mutant flies modeling pathogenic RNA exosome mutations in EXOSC3/Rrp40 via CRISPR/Cas9 engineering to investigate the functional consequences of Rrp40 mutations on cell-type-specific brain transcriptomes, as well as brain morphology and behavior. High throughput genomic sequencing of brain-enriched tissue from Rrp40 mutant flies reveals distinct widespread cell-type-specific transcriptomic dysregulation. Moreover, Rrp40 mutant flies exhibit brain morphological and behavioral defects indicative of neurodegeneration. These findings highlight the critical role of RNase function in maintaining neuronal homeostasis and provide insights into the mechanisms underlying RNA exosome-linked neuropathology.