Abstract SY24-02: Di-codon organization links tRNA modifications to cancer cell proteome composition

Abstract mRNA translation is commonly dysregulated in cancer at both initiation and elongation phases. We previously showed that tRNA-modifying enzymes, including ELP3, coordinate transcriptional and translational programs in prostate cancer cells downstream of estrogen receptor alpha. Here, we asked how ELP3 regulates proteome composition and thereby downstream cellular functions. ELP3 depletion significantly decreased proliferation and clonogenic potential in prostate cancer cell lines, but not in a non-transformed cell line. Consistent with regulation of gene expression at the elongation phase of mRNA translation, mRNAs encoding proteins that were reduced upon ELP3 depletion were highly associated with polysomes. While single-codon composition was insufficient to explain ELP3-sensitive protein expression, we identified six codon pairs (di-codons) that associated with reduced protein output. Intriguingly, although the Integrated Stress Response (ISR) was activated upon ELP3 depletion, as indicated by increased p-eIF2α, its translational program was unaffected. As proteins with ISR-sensitive translation also showed high frequencies of identified di-codons, ELP3 appears to interfere with the ISR. Di-codons were also enriched in mRNAs encoding proliferation-associated proteins. Consistently, ELP3 depletion caused mitotic defects, including lagging chromosomes and micronuclei formation. In summary, ELP3 appears to regulate proteome composition via di-codons that slow down elongation and thereby determine protein fate. Citation Format: Kiana H. Moghaddam, Clelia Timpone, Laasya N. Gowda, Dani Tutuka, Gail P. Risbridger, Qishan Lin, Ralf B. Schittenhelm, Ivan Topisirovic, Eric P. Kusnadi, Luc Furic, Ola Larsson. Di-codon organization links tRNA modifications to cancer cell proteome composition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(8_Suppl):Abstract nr SY24-02.