Bartok, Pataskar, and Nagel et al. showed that prolonged in vitro IFNγ treatment of melanoma cells stimulated indoleamine 2,3-dioxygenase 1 (IDO1)-induced tryptophan (W) depletion. This caused ribosomes to globally stall at translation start sites to reduce protein synthesis, and at W codons. Stalling at W codons resulted in reading frame shifts and production of chimeric ‘trans’ out-of-frame peptides with altered secondary structure. Aberrant peptides were detected in the full HLA-I immunoproteome of IFNγ-treated melanoma cells and were presented by peptide-loaded DCs to prime naive CD8+ T cells. Tyrosine (Y)-deprivation induced comparable frameshifting at Y codons.
Contributed by Paula Hochman
ABSTRACT: Extensive tumour inflammation, which is reflected by high levels of infiltrating T cells and interferon-_ (IFN_) signalling, improves the response of patients with melanoma to checkpoint immunotherapy(1,2). Many tumours, however, escape by activating cellular pathways that lead to immunosuppression. One such mechanism is the production of tryptophan metabolites along the kynurenine pathway by the enzyme indoleamine 2,3-dioxygenase 1 (IDO1), which is induced by IFN_(3-5). However, clinical trials using inhibition of IDO1 in combination with blockade of the PD1 pathway in patients with melanoma did not improve the efficacy of treatment compared to PD1 pathway blockade alone(6,7), pointing to an incomplete understanding of the role of IDO1 and the consequent degradation of tryptophan in mRNA translation and cancer progression. Here we used ribosome profiling in melanoma cells to investigate the effects of prolonged IFN_ treatment on mRNA translation. Notably, we observed accumulations of ribosomes downstream of tryptophan codons, along with their expected stalling at the tryptophan codon. This suggested that ribosomes bypass tryptophan codons in the absence of tryptophan. A detailed examination of these tryptophan-associated accumulations of ribosomes-which we term 'W-bumps'-showed that they were characterized by ribosomal frameshifting events. Consistently, reporter assays combined with proteomic and immunopeptidomic analyses demonstrated the induction of ribosomal frameshifting, and the generation and presentation of aberrant trans-frame peptides at the cell surface after treatment with IFN_. Priming of naive T cells from healthy donors with aberrant peptides induced peptide-specific T cells. Together, our results suggest that IDO1-mediated depletion of tryptophan, which is induced by IFN_, has a role in the immune recognition of melanoma cells by contributing to diversification of the peptidome landscape.
Author Info: (1) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. (2) Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterda
Author Info: (1) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. (2) Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. (3) Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. (4) Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway. Institute of Clinical Medicine, University of Oslo, Oslo, Norway. (5) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. (6) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. (7) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. (8) Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. (9) Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. (10) Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. (11) Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands. Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands. (12) Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands. (13) Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. (14) Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. (15) Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. (16) Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel. (17) The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel. (18) Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. (19) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. (20) Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel. (21) Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway. Institute of Clinical Medicine, University of Oslo, Oslo, Norway. (22) Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway. Institute of Clinical Medicine, University of Oslo, Oslo, Norway. (23) Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. (24) Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands. Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands. (25) Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Utrecht, The Netherlands. Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands. (26) Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel. (27) Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. (28) Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway. Institute of Clinical Medicine, University of Oslo, Oslo, Norway. (29) Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. Yardena.Samuels@weizmann.ac.il. (30) Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands. r.agami@nki.nl. Erasmus MC, Rotterdam University, Rotterdam, The Netherlands. r.agami@nki.nl.
