Cancer-associated DDX3X mutations drive stress granule assembly and impair global translation

Abstract

DDX3X is a DEAD-box RNA helicase that has been implicated in multiple aspects of RNA metabolism including translation initiation and the assembly of stress granules (SGs). Recent genomic studies have reported recurrent DDX3X mutations in numerous tumors including medulloblastoma (MB), but the physiological impact of these mutations is poorly understood. Here we show that a consistent feature of MB-associated mutations is SG hyper-assembly and concomitant translation impairment. We used CLIP-seq to obtain a comprehensive assessment of DDX3X binding targets and ribosome profiling for high-resolution assessment of global translation. Surprisingly, mutant DDX3X expression caused broad inhibition of translation that impacted DDX3X targeted and non-targeted mRNAs alike. Assessment of translation efficiency with single-cell resolution revealed that SG hyper-assembly correlated precisely with impaired global translation. SG hyper-assembly and translation impairment driven by mutant DDX3X were rescued by a genetic approach that limited SG assembly and by deletion of the N-terminal low complexity domain within DDX3X. Thus, in addition to a primary defect at the level of translation initiation caused by DDX3X mutation, SG assembly itself contributes to global translation inhibition. This work provides mechanistic insights into the consequences of cancer-related DDX3X mutations, suggesting that globally reduced translation may provide a context-dependent survival advantage that must be considered as a possible contributor to tumorigenesis.

DDX 3X and specific initiation factors modulate FMR 1 repeat‐associated non‐AUG‐initiated translation

“…This indicates that DDX3X knockdown does not lead to global inhibition of mRNA translation, again highlighting the role of DDX3X in the expression of select genes. This finding is consistent with previous work demonstrating that the expression of only a specific subset of mRNAs—those with long and/or secondary‐structured 5′ UTRs—is reduced following DDX3X / Ded1 disruption .…”

Targeting RNA helicases in cancer: The translation trap

“…However, more recent reports have found that the mutations have inhibitory effects on mRNA translation. Specific mutations occurring in medulloblastoma were found to result in reduced RNA unwinding activity[44], defects in RNA-stimulated ATP hydrolysis[45] and hyper-assembly of RNA stress granules, which have a general inhibitory effect on translation[46]. It was proposed that inhibition of translation potentially provides a survival advantage to medulloblastoma cells during progression.…”

Biomolecular condensates in neurodegeneration and cancer

“…RNA splicing, secondary structure and modifications have been shown to modulate cellular condensate assembly and composition . Similarly, various protein modifications have been shown to modulate condensate assembly (reviewed in Reference ), composition (reviewed in Reference ) and material properties . Second, association to nearby structures, such as membranes, can also promote condensate assembly (eg, actin or Ras signaling cluster assembly).…”

“…Both the helicase core of DDX3X (mediating RNA binding) and N‐terminal IDRs (mediating DDX3X phase separation) contribute to its partitioning into SGs . Cancer‐associated DDX3X mutations are mostly found in the helicase core and induce SG assembly in an eIF2a‐independent manner, possibly by inhibiting the translational activity of DDX3X . In each of these cases, it is unclear whether heightened SG assembly is causal or a consequence of cancer development.…”