The Inherited MDS Gene DDX41 Is Essential for Ribosomal RNA Processing through Regulation of Snorna Biogenesis

Germline mutations in the DEAD-box RNA helicase gene DDX41 cause inherited susceptibility to Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML). These patients have normal hematopoietic indices into adulthood and present with MDS at a median age of 61 years, slightly younger than the general MDS patient population (71 years). Germline DDX41 mutations are always heterozygous and are typically frame-shift mutations, causing loss of function of the protein. More than half of these patients acquire a second-hit mutation in the healthy DDX41 allele in their disease clones. Greater than 80% of the second-hit mutations cause the amino acid substitution R525H, which results in loss of helicase activity. Multiple functions have been ascribed to DDX41, such as functioning as an innate immune sensor, a component of the RNA spliceosome, and a regulator of ribosomal RNA processing; however, its role in the pathogenesis of MDS remains poorly understood. To mimic the DDX41 mutations in human patients, we generated conditional mouse models of the most common DDX41 mutations, D140fs and R525H. We found that DDX41 is essential for the viability and function of hematopoietic stem and progenitor cells (HSPCs) and that R525H mutations render DDX41 inactive. We have also reported that mice with biallelic DDX41 mutations develop progressive anemia, dysplasia, and marrow failure. HSPCs lacking wild-type Ddx41 have dysfunctional ribosomes and reduced protein translation, leading to cycle arrest and apoptosis. As a mechanistic basis for the ribosome defect in Ddx41-deficient HSPCs, we found that loss of Ddx41 causes a profound increase in unprocessed snoRNA transcripts, which likely interrupts their cellular function. Importantly, we did not observe a change in host gene transcript abundance, and thus it is unlikely that the defects observed in Ddx41-deficient cells are caused by loss of the protein products of the host genes. SnoRNAs regulate ribosomal RNA (rRNA) by catalyzing post-transcriptional modifications, including methylation and pseudouridylation. Since the majority of the snoRNAs that were found to be unprocessed in Ddx41-deficient HSPCs were from the SNORA family, which is involved in pseudouridylation, we quantified the abundance of pseudouridine at specific sites in ribosomal RNA and found it to be reduced in Ddx41-deficient HSPCs. Utilizing global high-throughput sequencing approaches to analyze DDX41 binding to RNAs, we found that DDX41 preferentially binds to snoRNAs relative to all other types of RNA in the cells. Thus, DDX41 binds to snoRNAs and is essential for snoRNA processing, snoRNA-mediated rRNA pseudouridylation, and protein translation in HSPCs. These findings provide critical mechanistic insight into the protein translation defect that we and others have observed in DDX41-deficient cells and uncover the basis of ineffective hematopoiesis in MDS patients with DDX41 mutations.