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Missense mutations in the RNA exosome component exosome component 2 (EXOSC2), also known as ribosomal RNA-processing protein 4 (RRP4), were recently identified in two unrelated families with a novel syndrome known as Short stature, Hearing loss, Retinitis pigmentosa and distinctive Facies (SHRF, #OMIM 617763). Little is known about the mechanism of the SHRF pathogenesis. Here we have studied the effect of mutations in  EXOSC2/RRP4  in patient-derived lymphoblasts, clustered regularly interspaced short palindromic repeats (CRISPR)-generated mutant fetal keratinocytes and  Drosophila . We determined that human  EXOSC2  is an essential gene and that the pathogenic G198D mutation prevents binding to other RNA exosome components, resulting in protein and complex instability and altered expression and/or activities of critical genes, including those in the autophagy pathway. In parallel, we generated multiple CRISPR knockouts of the fly  rrp4  gene. Using these flies, as well as  rrp4  mutants with Piggy Bac (PBac) transposon insertion in the 3′UTR and RNAi flies, we determined that fly  rrp4  was also essential, that fly  rrp4  phenotypes could be rescued by wild-type human  EXOSC2  but not the pathogenic form and that fly  rrp4  is critical for eye development and maintenance, muscle ultrastructure and wing vein development. We found that overexpression of the transcription factor MITF was sufficient to rescue the small eye and adult lethal phenotypes caused by  rrp4  inhibition. The autophagy genes  ATG1  and  ATG17 , which are regulated by MITF, had similar effect. Pharmacological stimulation of autophagy with rapamycin also rescued the lethality caused by  rrp4  inactivation. Our results implicate defective autophagy in SHRF pathogenesis and suggest therapeutic strategies.

Genetic and genomic studies of pathogenic EXOSC2 mutations in the newly described disease SHRF implicate the autophagy pathway in disease pathogenesis