Tryptophan-to-phenylalanine codon reassignment (W>F) occurs after tryptophan depletion.

  • Major Finding: Tryptophan-to-phenylalanine codon reassignment (W>F) occurs after tryptophan depletion.

  • Concept: IFNγ-mediated IDO1 induction depletes tryptophan and increases W>F substitutants through WARS1.

  • Impact: Pan-cancer enrichment of these inducible substitutants increases antigen presentation and T-cell activity.


Expression of the enzyme indoleamine 2,3-dioxygenase 1 (IDO1) can be induced by secretion of IFNγ, leading to reduction of intracellular tryptophan and inhibition of T-cell immunity. Pataskar, Champagne, Nagel, and colleagues sought to investigate how this depletion of tryptophan can affect in-frame protein synthesis following IFNγ induction and revealed that, upon IFNγ treatment, there was a tryptophan-to-phenylalanine codon reassignment (W>F) that could still generate a full-length protein. Investigation into the induction of these codon reassignments demonstrated that tryptophanyl-tRNA synthetase (WARS1) can activate both tryptophan and phenylalanine, suggesting this may be the source of W>F. This type of codon reassignment was entitled “substitutants” to distinguish them from genetically encoded mutants. Using the Clinical Proteomic Tumor Analysis Consortium dataset, these W>F substitutants were shown to be more enriched than other W>X possibilities in squamous cell lung cancer tissues. Tissue stratification based on IDO1 expression indicated an induction of W>F substitutants in tumor tissue compared to adjacent normal tissue. Additionally, examination of gene signatures revealed that high numbers of these substitutants correlated with a high immune response and peptide presentation signature, whereas those with low expression displayed a gene signature enriched for chromatin, p53 activity, and SUMOylation. Control W>Y substitutants had no specific gene expression cluster. Further analyses showed that W>F substitutants are present in many different cancer types and are linked to tumors with a high number of infiltrating T cells. Furthermore, W>F substitutant antigens were found to be presented at the cell surface to induce T-cell recognition and cytotoxicity against tumor cells, demonstrating potential immunogenicity. Therefore, this study exposes the occurrence of codon reassignment after amino acid deprivation—specifically the presence of W>F substitutants after tryptophan depletion—and denotes their effect on immunoreactivity in cancer.

Pataskar A, Champagne J, Nagel R, Kenski J, Laos M, Michaux J, et al. Tryptophan depletion results in tryptophan-to-phenylalanine substitutants. Nature 2022;603:721–7.

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