Abstract
IFNγ signaling in melanoma cells caused tryptophan depletion, resulting in frameshifted polypeptides.
Major Finding: IFNγ signaling in melanoma cells caused tryptophan depletion, resulting in frameshifted polypeptides.
Concept: Aberrant peptides were displayed on cell surfaces by HLA-I and elicted specific CD8+ T-cell responses.
Impact: This work highlights the complexity of IFNγ signaling and shows how cells cope with tryptophan depletion.
High IFN signaling is associated with tumor inflammation and has been correlated with favorable responses to immune checkpoint blockade in melanoma. However, some tumors co-opt IFNγ, taking advantage of the fact that IFNγ induces the transcription of IDO1, encoding an enzyme in the kynurenine pathway, which uses tryptophan to generate NAD+ for cellular energy needs. Because this may lead to tryptophan depletion, Bartok, Pataskar, Nagel, and colleagues performed ribosome profiling on melanoma cells treated with IFNγ to determine the ribosome occupancy on mRNAs in these cells. As predicted, ribosome stalling occurred at tryptophan codons; unexpectedly, though, marked accumulation of ribosomes was also observed approximately 20 codons downstream of tryptophan codons. These ribosome pileups, termed W-bumps, most often occurred when multiple in-frame tryptophan codons coexisted in regions of eight codons. Further, there was an inverse association between protein expression level and tryptophan content in the IFNγ-treated cells. An in silico investigation suggested that W-bumps occurring downstream of ribosomal frameshifts caused by tryptophan-codon skipping may lead to the presence of disordered, out-of-frame peptides in the lower exit tunnel of the ribosomes (which could cause ribosome stalling), a finding corroborated by in vitro studies. Correspondingly, proteomic analyses showed that IFNγ-treated melanoma cells produced the frameshifted aberrant polypeptides. Further, peptides derived from these frameshifted polypeptides were displayed on cell surfaces by HLA-I, and these displayed peptides were sufficient to elicit peptide-specific responses from naïve CD8+ T cells derived from healthy donors following coculture. Collectively, these results provide insight into the role of IFNγ-mediated IDO1 induction and the subsequent tryptophan depletion in melanoma, illustrating the complexity of the role of IFNγ signaling in cancer.
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