Sterile alpha motif domain-containing protein 9 is an RNA binding protein impacting ribosome biogenesis and interferon signaling
Inherited bone marrow failure syndromes 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 were identified in recent years as a frequent genetic lesion resulting in inherited bone marrow failure and monosomy 7, some patients even have severe multisystem syndromes that include myelodysplasia such as MIRAGE and ataxia-pancytopenia syndromes. 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. Here, we used a SAMD9-targeted, inducible CRISPRa/i system to better understand the transcriptional changes that result from SAMD9 transcriptional manipulation. We also used cross-linking and solid phase purification to demonstrate that SAMD9 is an RNA binding protein, and that it is likely through this RNA binding function that SAMD9 affects ribosome biogenesis and subsequently global protein translation and cell proliferation. Thus, ribosome dysfunction contributes to SAMD9-related bone marrow failure like other classical inherited bone marrow failure syndromes. Overall design: Three different isogenic K562 cell lines (parental, [VPR]-D9, [KRAB]-D9) were analyzed by RNA sequencing. Comparisons were made between no treatment conditions and IFN, doxycycline, or a combination of both.