The somatic hotspot mutation of DDX41 (p.R525H) elicits dominant-negative effects upon non-truncating germline variants, explaining similar disease risk as truncating variants.

Abstract Heterozygous germline variants of DDX41 occur in 2-4% of adult Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML) cases, making them the most prevalent cause of inherited predisposition to these diseases. Homozygous deleterious variants are never observed in the germline, and loss of both DDX41 alleles causes apoptosis of proliferative cells, consistent with essentiality. Most disease-associated germline variants cause loss of full-length protein expression (truncating). However, 30-40% are missense (non-truncating) and their role in disease risk compared to truncating variants remains in question. Previous reports have shown that both truncating and non-truncating Pathogenic/Likely Pathogenic (P/LP) variants (defined by ACMG scoring) are associated with DDX41-specific disease features, including co-mutation of the contralateral allele of DDX41. In contrast, variants of unknown significance (VUS) are less associated with these features. Acquired co-mutations of DDX41, of which p.R525H accounts for 50-70%, are restricted to DDX41-mutated patients and are always missense. Our previous studies indicated that p.R525H lacks the essential DDX41 function and cannot support hematopoietic progenitor proliferation. However, the frequency with which this mutation occurs and the absence of acquired truncating mutations suggest that p.R525H has a specific effect on DDX41 function that is distinct from complete loss and promotes pathogenesis specifically in the context of existing P/LP DDX41 mutation. To understand how germline non-truncating variants predispose to disease, we characterized the effect of six recurrent non-truncating P/LP variants (p.G173R, p.R219H, p.P258L, p.Y259C, p.K331del, and p.I396T) and three VUS (p.K9E, p.Y33H, and p.M155H) on DDX41 function. We utilized a genetic complementation approach in murine lineage-negative (Linneg) bone marrow cells with inducible deletion of DDX41. We found that all non-truncating P/LP and VUS forms of DDX41 could fully rescue the colony forming potential of Ddx41-deficient cells to a similar level as wild-type protein, whereas the p.R525H variant completely failed to rescue. To determine the effect of the non-truncating variants on DDX41 function at endogenous expression levels, we utilized CRISPR to modify the DDX41 alleles in MOLM13 human AML cells. We produced viable, proliferating cell lines with homozygous mutations for all 3 VUS and 4/6 P/LP variants. For p.P258L and p.K331del, like p.R525H, we could not produce homozygous mutant cell lines despite screening hundreds of clones and finding several with heterozygosity. To further study the P/LP variants that were functional in the cell line, we generated C57Bl/6 mouse lines harboring p.G173R, p.Y259C, and p.I396T mutations in the endogenous Ddx41 alleles. Heterozygous mutant mice were phenotypically normal in all three strains. However, we could not obtain homozygous mutant mice for p.G173R or p.Y259C, indicating these cannot support embryonic/fetal development. In contrast, p.I396T-homozygous mutant mice were born at Mendelian ratios and were phenotypically normal until at least 15 months of age. Since p.R525H mutation is common in patients with non-truncating P/LP variants, we sought to model the combined effect of these mutations. We utilized the Linneg cells with inducible knockout of Ddx41, co-expressed each non-truncating variant with p.R525H by viral transduction, and monitored the colony formation potential. Remarkably, cultures expressing P/LP variants or M155I combined with p.R525H had dramatically reduced colony formation, while wild-type DDX41 and the other 2 VUS supported normal colony formation when co-expressed with p.R525H. Thus, we conclude p.R525H has a dominant-negative effect on certain non-truncating DDX41 variants. This is consistent with the emerging idea that the presence of an acquired hotspot DDX41 co-mutation is sufficient to classify a non-truncating DDX41 variant as pathogenic.Our results demonstrate that many DDX41 missense variants retain protein function when overexpressed. However, at endogenous expression levels, some P/LP variants are unable to support cell proliferation, indicative of hypomorphic effects on protein function. In patients, acquisition of the p.R525H mutation in the contralateral allele disrupts the functionality of P/LP variants through dominant-negative effects, leading to hematopoietic progenitor defects that are hallmark of the DDX41 pathogenesis.