A RiboCancer cell line panel reveals that CLL-associated Rps15 mutations translationally rewire transcription through codon-specific tRNA accommodation defects

Various somatic deletions and point mutations targeting ribosomal proteins (RPs) have been identified in cancer. To assess how these affect ribosomal translation, we applied genomewide translatome analysis (proteome, Ribo-seq and total RNA-seq) on an isogenic cell line library modeling the most recurrent RP defects (Rpl5+/-, Rpl11+/- , Rpl22+/- , Rpl22-/-, Rpl10 R98S, Rps15 P131S and Rps15 H137Y). We detected little translational changes in the RP knock-out models. In contrast, RP point mutations were associated with a significant number of translation efficiency changes, reaching up to 10% of expressed genes in Rps15 mutants associated with Chronic Lymphocytic Leukemia (CLL). Further cryo-electron microscopy and biochemical analyses revealed that these Rps15 mutations alter the stability of the C-terminal Rps15 domain, affecting the translation elongation cycle dynamics of these mutant ribosomes, and deregulating accommodation of aminoacylated tRNAs at the ribosomal A-site. Using Ribo-seq and translation reporter assays, we show that this accommodation defect shows codon specificity, explaining the reduced translation efficiency of genes enriched for these codons in Rps15 mutant cells, such as histones. Finally, the genes presenting reduced translation efficiency in Rps15 mutants are enriched for transcriptional regulators such as transcription factor Runx3, resulting in downregulation of Runx3 target genes involved in immune regulation. Overall, this study compares the translational rewiring imposed by the most frequent somatic RP mutations. We provide unprecedented mechanistic insights in the translation defects induced by CLL-associated Rps15 mutations, and reveal an unappreciated cross-talk between translational and transcriptional dysregulation in these RP mutant cells.