Poster Presentation Australasian RNA Biology and Biotechnology Association 2026 Conference

Dicodon organization links tRNA modifications to cancer cell proteome (#131)

Kiana H Moghaddam 1 , Clelia Timpone 2 3 , Laasya N Gowda 2 3 , Candani A Tutuka 3 , Gail P Risbridger 4 , Joel Steele 5 , Ralf Schittenhelm 5 , Eric P Kusnadi 2 3 , Luc Furic 2 3 , Ola Larsson 1
  1. Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
  2. Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
  3. Peter MacCallum Cancer Center, Melbourne, VIC, Australia
  4. Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
  5. Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria, Australia

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 the estrogen receptor alpha network [1]. Here, we evaluated how ELP3 regulates proteome composition and thereby cellular phenotype. 

We first demonstrated that CRISPR/Cas9-mediated depletion of ELP3 significantly decreases proliferation and clonogenic potential in the prostate cancer cell lines DU145 and LNCaP, but not in the non-transformed, prostate-derived cell line PNT1A. Importantly, integration of translatomic and proteomic datasets suggested that mRNAs encoding downregulated proteins were highly associated with polysomes. While single-codon analysis was insufficient to explain ELP3-sensitive protein expression, we identified six codon pairs (dicodons) significantly associated with reduced protein output despite increased ribosome association. This highlights that specific combinations of codons provide unique information not captured by individual codons alone. Functionally, enrichment analysis and subsequent validation experiments demonstrated that ELP3 depletion caused mitotic defects, including lagging chromosomes and micronuclei formation. Furthermore, although the Integrated Stress Response (ISR) pathway was activated, as indicated by increased eIF2α phosphorylation, its typical translational program was unaffected. As proteins associated with ISR-sensitive translation also encoded by mRNAs with high frequencies of the identified dicodons, ELP3 appears to interfere with ISR. 

In summary, we demonstrate that loss of U34 tRNA modifications impairs translation elongation at specific dicodon contexts, whose cumulative presence and spatial distribution within gene sequences were independent predictors of ELP3-dependent changes in protein levels. Our findings indicate that the identified dicodons act as translational traps, slowing down elongation and thereby affecting protein fate under ELP3 depletion. Our data identify U34 tRNA modification as a cancer-selective, targetable vulnerability that links coding features to translational control, mitotic fidelity and cellular stress response.

  1. Lorent J*, Kusnadi EP*, van Hoef V, Rebello RJ, Leibovitch M, Ristau J, Chen S, Lawrence MG, Szkop KJ, Samreen B, Balanathan P, Rapino F, Close P, Bukczynska P, Scharmann K, Takizawa I, Risbridger GP, Selth LA, Leidel SA, Lin Q, Topisirovic I^, Larsson O^, Furic L^. Translational offsetting as a mode of estrogen receptor α-dependent regulation of gene expression. EMBO J. 2019 Dec 2;38(23):e101323. doi: 10.15252/embj.2018101323.