A common germline variant in the 3’UTR controls DDIT4 translation efficiency and stress responses in cancer cells
Description
Systematic strategies for identifying and classifying variants that directly modulate ribosome engagement are lacking. Here, we develop and extensively validate a pipeline to identify translation-associated single-nucleotide polymorphisms (tranSNPs) by integrating allele-specific analysis of total and polysome-associated mRNAs. By applying this approach, we uncovered multiple common variants showing allele-specific enrichment in polysomes, without corresponding changes in mRNA levels, which is indicative of differential translational efficiency. We focused on rs1053639, a frequent germline SNP located in the 3′UTR of DDIT4, a key stress-responsive regulator of mTORC1 signaling. Using edited cell models, we showed that this variant controls DDIT4 protein output through allele-specific differences in mRNA translation. Mechanistically, the two alleles differ in their interaction with the RNA-binding protein RBMX, leading to altered mRNA subcellular localization and translation, independently of transcription. Functionally, allele-specific regulation of DDIT4 translation impacts stress-dependent mTORC1 repression and autophagy, resulting in divergent competitive fitness in prolonged co-culture, in vivo xenograft assays, and response to therapeutic perturbations. Consistent with these findings, analysis of cancer patient datasets revealed an association between rs1053639 genotype and clinical outcome in colorectal cancer. Together, our study establishes tranSNPs as a previously underappreciated class of functional genetic variants that modulate gene expression at the level of translation.
Files
Steps to reproduce
Uncropped images of the western blot data that are included in the manuscript. Methods are described in the manuscript as well as in the preprint version bioRxiv 2025.04.02.646512; doi: https://doi.org/10.1101/2025.04.02.646512
Institutions
- University of TrentoTrentino-Alto Adige, Trento