A Drosophila model of Pontocerebellar Hypoplasia reveals a critical role for the RNA exosome in neurons
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Abstract
Abstract The RNA exosome is an evolutionarily-conserved ribonuclease complex critically important for precise processing and/or complete degradation of a variety of cellular RNAs. The recent discovery that mutations in genes encoding structural RNA exosome subunits cause tissue-specific diseases makes defining the role of this complex within specific tissues critically important. Mutations in the RNA exosome component 3 ( EXOSC3 ) gene cause Pontocerebellar Hypoplasia Type 1b (PCH1b), an autosomal recessive neurologic disorder. The majority of disease-linked mutations are missense mutations that alter evolutionarily-conserved regions of EXOSC3. The tissue-specific defects caused by these amino acid changes in EXOSC3 are challenging to understand based on current models of RNA exosome function with only limited analysis of the complex in any multicellular model in vivo . The goal of this study is to provide insight into how mutations in EXOSC3 impact the function of the RNA exosome. To assess the tissue-specific roles and requirements for the Drosophila ortholog of EXOSC3 termed Rrp40, we utilized tissue-specific RNAi drivers. Depletion of Rrp40 in different tissues reveals a general requirement for Rrp40 in the development of many tissues including the brain, but also highlight an agedependent requirement for Rrp40 in neurons. To assess the functional consequences of the specific amino acid substitutions in EXOSC3 that cause PCH1b, we used CRISPR/Cas9 gene editing technology to generate flies that model this RNA exosome-linked disease. These flies show reduced viability; however, the surviving animals exhibit a spectrum of behavioral and morphological phenotypes. RNA-seq analysis of these Drosophila Rrp40 mutants reveals increases in the steady-state levels of specific mRNAs and ncRNAs, some of which are central to neuronal function. In particular, Arc1 mRNA, which encodes a key regulator of synaptic plasticity, is increased in the Drosophila Rrp40 mutants. Taken together, this study defines a requirement for the RNA exosome in specific tissues/cell types and provides insight into how defects in RNA exosome function caused by specific amino acid substitutions that occur in PCH1b can contribute to neuronal dysfunction. Author Summary Pontocerebellar Hypoplasia Type 1b (PCH1b) is a devastating genetic neurological disorder that preferentially affects specific regions of the brain. Typically, children born with PCH1b have structural defects in regions of the brain including those associated with key autonomic functions. Currently, there is no cure or treatment for the disease. PCH1b is caused by mutations in the RNA exosome component 3 ( EXOSC3 ) gene, which encodes a structural component of the ubiquitous and essential multi-subunit RNA exosome complex. The RNA exosome is critical for both precise processing and turnover of multiple classes of RNAs. To elucidate the functional consequences of amino acid changes in EXOSC3 that cause PCH1b, we exploited well-established genetic approaches in Drosophila melanogaster that model EXOSC3 mutations found in individuals with PCH1b. Using this system, we find that the Drosophila EXOSC3 homolog (termed Rrp40) is essential for normal development and has an important function in neurons. Furthermore, PCH1b missense mutations modeled in Rrp40 cause reduced viability and produce neuronal-specific phenotypes that correlate with altered levels of target RNAs that encode factors with key roles in neurons. These results provide a basis for understanding how amino acid changes that occur in the RNA exosome contribute to neuronal dysfunction and disease.
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Variants in genes encoding several subunits of the RNA exosome complex have been linked to PCH, including EXOSC3 (PCH1B), EXOSC8 (PCH1C), EXOSC9 (PCH1D), and provisionally EXOSC1 (PCH1F).
“variants in genes encoding several subunits of the RNA exosome complex have been linked to PCH, including EXOSC3 (PCH1B), EXOSC8 (PCH1C), EXOSC9 (PCH1D), and provisionally EXOSC1 (PCH1F)15–25.”
From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [18]
The Introduction links EXOSC3 mutations to PCH1b. The References list studies concerning EXOSC8-associated cerebellar hypoplasia and EXOSC9-associated PCH1D, but the passages do not identify EXOSC8 as PCH1C or mention a provisional EXOSC1–PCH1F link. Those specific parts of the attributed list are not supported by our copy. (LLM, conf=0.85)
Experimental — accuracy not yet measuredPCH1B is characterized by marked hypotonia, progressive cerebellar atrophy, and motor neuron dysfunction.
“PCH1B is a subtype characterized by marked hypotonia, progressive cerebellar atrophy, and motor neuron dysfunction and caused by variants in the EXOSC3 gene15,18,21–23,25.”
From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [18]
The Introduction (page not provided) describes PCH1b as caused by EXOSC3 mutations and characterized by cerebellar atrophy and spinal motor neuron degeneration. It does not specify marked hypotonia or say that the cerebellar atrophy is progressive. (LLM, conf=0.86)
Experimental — accuracy not yet measuredPathogenic variants in EXOSC3 cause pontocerebellar hypoplasia type 1B (PCH1B).
“Pathogenic variants in EXOSC3, a noncatalytic subunit of the RNA exosome, cause pontocerebellar hypoplasia type 1B (PCH1B)”
From EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery (2026) · cites this paper as [18]
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Wijeratne, H. R. S., Runnebohm, A. M., Barron, M. P., Hampton, A. J., Li, R., Peck Justice, S. A., Lenceski, S. H., Rooney, J. D., Smith-Kinnaman, W. R., Chang, G. S., et al. (2026) · doi:10.64898/2026.01.26.701775 · Cited by 1 · see citing works
“Within the PCH spectrum, PCH1B is a subtype characterized by marked hypotonia, progressive cerebellar atrophy, and motor neuron dysfunction and caused by variants in the EXOSC3 gene 15,18,21-23 , 25 .”
Lancaster, C. L., Yalamanchili, P. S., Goldy, J. N., Leung, S. W., Corbett, A. H., & Moberg, K. H. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.05.588324 · Cited by 1 · see citing works
Self-citationRNA Exosome-Mediated RNA Surveillance Governs Developmental Timing in the Human CerebellumPreprint
Barr, N. A., Baltov, B., Kang, R. E., Gada, J. J., Wade, M. J., Tjoa, E. N., Lee, V. H., Seth, A., Dzirasa, K., Schaffer, A. E., et al. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.6921929 · Cited by 1 · see citing works
Self-citationSterrett, M. C., Farchi, D., Strassler, S. E., Boise, L., Fasken, M. B., & Corbett, A. H. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.31.514520
Self-citationThe RNA exosome: mechanisms of RNA surveillance, regulation, and disease
Upadhyai, P., Quadri, N., & Chandran, D. (2026) · RNA Biology · doi:10.1080/15476286.2026.2685379
Biallelic pathogenic variants in EXOSC3 mediate thrombotic microangiopathy of the kidney
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Self-citationFasken, M. B., Leung, S. W., Serafim, L. F., Yan, C., Intemann, M. L., Gable, D. L., Baranano, K. W., Ivanov, I. N., Ghalei, H., & Corbett, A. H. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.29.741578
Self-citation
- Authors
- Morton, D. J., Jalloh, B., Kim, L., Kremsky, I., Nair, R. J., Nguyen, K. B., Rounds, J. C., Sterrett, M. C., Brown, B., Le, T., Karkare, M. C., McGaughey, K. D., Sheng, S., Leung, S. W., Fasken, M. B., Moberg, K. H., & Corbett, A. H.
- Affiliations
- Emory University (US)
- Corresponding author
- Morton, Derrick J.
- Corbett, Anita H.
- ORCID
- Venue
- PLOS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2020-07-09
- Volume
- 16
- Issue
- 7
- Pages
- e1008901
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC7373318
- OpenAlex
- W3042059188
- Cited by
- 24
- References
- 60
- Citations by year
- 2026: 6 · 2025: 4 · 2024: 4 · 2023: 4 · 2022: 3 · 2021: 2 · 2020: 1
- FWCI
- 0.81
- Type
- journal article
- Language
- en
- Update notices
- new_version (2020-07-21)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institute of General Medical Sciences (GM125350, GM130147)
- Burroughs Wellcome Fund (PDEP)
- National Institute of Mental Health (MH107305, NS103595)
- National Institutes of Health (HD088043, GM000680)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- RNA exosome, EXOSC3, Drosophila model, missense mutations, neurons, synaptic plasticity, non-coding RNA, neurological disorders
- MeSH terms
- Animals, Cerebellar Diseases, Cerebellum, Cytoskeletal Proteins, Disease Models, Animal, Drosophila melanogaster, Humans, Mutation, Nerve Tissue Proteins, Neurons, RNA, RNA-Binding Proteins, Amino Acid Substitution, Exosomes, Exosome Multienzyme Ribonuclease Complex, CRISPR-Cas Systems
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