Tryptophan depletion results in tryptophan-to-phenylalanine substitutants

Activated T cells secrete interferon-gamma, which triggers intracellular tryptophan shortage by upregulating the indoleamine 2,3-dioxygenase 1(IDO1) enzyme(1-4). Here we showthat despite tryptophan depletion, in-frame protein synthesis continues across tryptophan codons. We identified tryptophan-to-phenylalanine codon reassignment (W>F) asthe major event facilitating this process, and pinpointed tryptophanyl-tRNA synthetase (WARS1) as its source. We call these W>F peptides 'substitutants' to distinguish them from genetically encoded mutants. Using large-scale proteomics analyses, we demonstrate W>F substitutants to be highly abundant in multiple cancer types. W>F substitutants were enriched in tumours relative to matching adjacent normal tissues, and were associated with increased IDO1 expression, oncogenic signalling and the tumour-immune microenvironment. Functionally, W>F substitutants can impair protein activity, but also expand the landscape of antigens presented at the cell surface to activate T cell responses. Thus, substitutants are generated by an alternative decoding mechanism with potential effects on gene function and tumour immunoreactivity.

Automated summary

Activated T cells secrete interferon-gamma to trigger tryptophan depletion by increasing the activity of IDO1 enzyme. However, in-frame protein synthesis continues across tryptophan codons due to the reassignment of tryptophan-to-phenylalanine codons. These substitutants are highly abundant in multiple cancer types and are associated with increased IDO1 expression, oncogenic signaling, and the tumor-immune microenvironment.