Overexpression of human SAMD9 inhibits protein translation and alters MYC signaling resulting in cell cycle arrest

Inherited bone marrow failure syndromes (iBMFS) often result from pathogenic mutations in genes that are important for ribosome function, namely, Diamond-Blackfan anemia, Shwachman-Diamond syndrome, and dyskeratosis congenita. Germline mutations in SAMD9 are a frequent genetic lesion resulting in an iBMFS with monosomy 7; some patients have severe multisystem syndromes that include myelodysplasia. The association of germline SAMD9 mutations and bone marrow failure is clear, but to date, there is no reliable method to predict if a novel SAMD9 mutation is pathogenic unless it is accompanied by an obvious family history and/or clinical syndrome. The difficulty with pathogenicity prediction is, in part, due to the incomplete understanding of the biological functions of SAMD9. We used a SAMD9-targeted, inducible CRISPRa system and RNA sequencing to better understand the global transcriptional changes that result from transcriptional manipulation of SAMD9. Supporting recent discoveries that SAMD9 acts as a ACNase specific for phenylalanine tRNA (tRNA-Phe), we confirmed with crosslinking and solid-phase purification (CLASP) that SAMD9 is an RNA binding protein and analyzed how overexpression of tRNA-Phe may reverse transcriptomic changes caused by SAMD9 activation. Our data show that overexpression of SAMD9 from the endogenous locus results in decreased cell proliferation, cell cycle progression, and global protein translation. When SAMD9 contains a gain-of-function mutation (p.E1136Q) these functional phenotypes are exacerbated, but only partially rescued with tRNA-Phe overexpression suggesting additional molecular actions of SAMD9. Additionally, we demonstrate that gene expression pathways important for ribosome biogenesis and MYC signaling are the most significantly impacted by SAMD9 overexpression.