Biallelic variants in the RNA exosome geneEXOSC5are associated with developmental delays, short stature, cerebellar hypoplasia and motor weakness

Abstract

The RNA exosome is an essential ribonuclease complex involved in the processing and degradation of both coding and noncoding RNAs. We present three patients with biallelic variants in EXOSC5, which encodes a structural subunit of the RNA exosome. The common clinical features of these patients comprise failure to thrive, short stature, feeding difficulties, developmental delays that affect motor skills, hypotonia and esotropia. Brain MRI revealed cerebellar hypoplasia and ventriculomegaly. The first patient had a deletion involving exons 5-6 of EXOSC5 and a missense variant, p.Thr114Ile, that were inherited in trans, the second patient was homozygous for p.Leu206His, and the third patient had paternal isodisomy for chromosome 19 and was homozygous for p.Met148Thr. We employed three complementary approaches to explore the requirement for EXOSC5 in brain development and assess the functional consequences of pathogenic variants in EXOSC5. Loss of function for the zebrafish ortholog results in shortened and curved tails and bodies, reduced eye and head size and edema. We modeled pathogenic EXOSC5 variants in both budding yeast and mammalian cells. Some of these variants show defects in RNA exosome function as well as altered interactions with other RNA exosome subunits. Overall, these findings expand the number of genes encoding RNA exosome components that have been implicated in human disease, while also suggesting that disease mechanism varies depending on the specific pathogenic variant. IntroductionThe RNA exosome is a ribonuclease complex composed of ten, evolutionarily conserved subunits that form a ring-like structure with 3'-5' exonuclease activity that is critical for the processing and degradation of a variety of RNAs both in the nucleus and cytoplasm (1-3). The exosome subunits are designated as exosome component (EXOSC) proteins in humans, mice (M. musculus) and other mammals and ribosomal RNA processing (Rrp) proteins in zebrafish (D. rerio), fruit flies (D. melanogaster) and budding yeast (S. cerevisiae), where the complex was first identified and studied (4, 5). The EXOSC4-9 subunits and their orthologs form a central, six-subunit ring that is covered by a three-subunit cap composed of EXOSC1-3. The ring-like complex creates a central channel through which RNA substrates are threaded to the catalytic subunit, DIS3 or DIS3L, at the base (6-10). In addition to DIS3 or DIS3L, the 9-subunit exosome complex also associates with another catalytic subunit, EXOSC10 at the cap. Notably, DIS3 and EXOSC10 are predominantly nuclear (7,(9)(10)(11), whereas DIS3L is mostly cytoplasmic (12).Although all six structural core ring subunits contain an RNase PH-like domain, they are all catalytically inactive due to amino acid substitutions that replace key catalytic residues (13). Thus, RNA substrates of the RNA exosome access the DIS3 catalytic subunit primarily via interactions with the non-catalytic core channel (14-16). Consistent with the critical function of the RNA exosome in the processing and decay of numerous ce...

A budding yeast model for human disease mutations in the EXOSC2 cap subunit of the RNA exosome complex

“…Recent studies have linked missense mutations in EXOSC genes encoding the structural subunits of the RNA exosome to various human pathologies, which comprise a growing family of diseases termed "RNA exosomopathies" (Wan et al 2012;Biancheri et al 2013;Boczonadi et al 2014;Eggens et al 2014;Di Donato et al 2016;Schottmann et al 2017;Burns et al 2018;Fasken et al 2020;Slavotinek et al 2020). Intriguingly, these single amino acid substitutions often occur in highly conserved domains of the RNA exosome subunits.…”

“…Mutations in the cap subunit gene EXOSC3 and the core subunit gene EXOSC8 cause forms of pontocerebellar hypoplasia (PCH1b and PCH1c, respectively), neurological disorders characterized by atrophy of the pons and cerebellum (Wan et al 2012;Biancheri et al 2013;Boczonadi et al 2014;Eggens et al 2014;Schottmann et al 2017;Morton et al 2018), while mutations in the core subunit genes EXOSC5 and EXOSC9 have been linked to similar neurological defects including cerebellar degeneration, neuronopathy and neurodevelopmental delays (Burns et al 2017;Burns et al 2018;Slavotinek et al 2020). In contrast to the other exosomopathy mutations described thus far, missense mutations in the cap subunit gene EXOSC2 have been linked to a novel, complex syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt (Di Donato et al 2016), later named SHRF (Short stature, Hearing loss, Retinitis pigmentosa and distinctive Facies) (OMIM #617763) (Yang et al 2019).…”

A Budding Yeast Model for Human Disease Mutations in theEXOSC2Cap Subunit of the RNA Exosome

“…The copyright holder for this preprint this version posted December 7, 2020. ; https://doi.org/10.1101/2020.12.06.413658 doi: bioRxiv preprint Sterrett Enyenihi et al 4 2017; BURNS, DONKERVOORT et al 2018;FASKEN et al 2020;SLAVOTINEK, MISCEO et al 2020). Intriguingly, these single amino acid substitutions often occur in highly conserved domains of the exosome subunits.…”

“…and EXOSC9 have been linked to similar neurological defects including cerebellar degeneration, neuronopathy and neurodevelopmental delays (BURNS, DONKERVOORT et al 2017;BURNS et al 2018;SLAVOTINEK et al 2020). In contrast to the other exosomopathy mutations described thus far, missense mutations in the cap subunit gene EXOSC2 have been linked to a novel, complex disorder characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt (DI DONATO et al 2016), later named SHRF (Short stature, Hearing loss, Retinitis pigmentosa and distinctive Facies) (OMIM #617763) (YANG, BAYAT et al 2019).…”

“…Given that this diverse class of RNA exosomopathies arises from amino acid substitutions in structural subunits of a singular complex, assessing defects in RNA exosome function in vivo is critical for a holistic understanding of the molecular and functional consequences underlying each disease phenotype. Previous studies have assessed the functional and molecular consequences of exosomopathy-linked EXOSC3 and EXOSC5 mutations in vivo using yeast and fly genetic model systems (FASKEN, LOSH et al 2017;GILLESPIE, GABUNILAS et al 2017;DE AMORIM 2020;MORTON, JALLOH et al 2020;SLAVOTINEK et al 2020). Utilizing a genetic model system to explore the (which was not certified by peer review) is the author/funder.…”