Humanized Saccharomyces cerevisiae provides a facile and effective tool to identify damaging human variants that cause exosomopathies

Abstract The RNA exosome is an evolutionarily conserved, multiprotein complex that is the major RNase in 3′ processing and degradation of a wide range of RNAs in eukaryotes. Single amino acid changes in RNA exosome subunits cause rare genetic diseases collectively called exosomopathies. However, distinguishing disease-causing variants from nonpathogenic ones remains challenging, and the mechanism by which these variants cause disease is largely unknown. Previous studies have employed a budding yeast model of RNA exosome-linked diseases that relies on mutating the orthologous yeast genes. Here, we develop a humanized yeast model of exosomopathies that allows us to unambiguously assess damaging effects of the exact patient variant in budding yeast. Individual replacement of the yeast subunits with corresponding mammalian orthologs identified 6 out of 9 noncatalytic core subunits of the budding yeast RNA exosome that can be replaced by a mammalian subunit, with 3 of the replacements supporting close to normal growth. Further analysis of the disease-associated variants utilizing the hybrid yeast/mammalian RNA exosome revealed functional defects caused by both previously characterized and uncharacterized variants of EXOSC2, EXOSC4, EXOSC7, and EXOSC9. Analysis of the protein levels of these variants indicates that a subset of the patient-derived variants causes reduced protein levels, while other variants are defective but are expressed as well as the reference allele, suggesting a more direct contribution of these residues to RNA exosome function. This humanized yeast model of exosomopathies provides a convenient and sensitive genetic tool to help distinguish damaging RNA exosome variants from benign variants. This disease model can be further exploited to uncover the underpinning mechanism of RNA exosome defects.