Dataset Information

Oncogene-dependent sloppiness in mRNA translation

ABSTRACT: mRNA translation is a highly conserved and tightly-controlled mechanism for protein synthesis. However, despite protein quality control mechanisms, amino-acid shortage in melanoma induces aberrant proteins by ribosomal frameshifting. The extent and the underlying mechanisms related to this phenomenon are yet unknown. Here, we show that tryptophan-depletion-induced ribosomal frameshifting is a widespread phenomenon in cancer. We termed this event sloppiness and strikingly observed its association with MAPK pathway hyperactivation. Indeed, sloppiness is stimulated by RAS activation in primary cells, suppressed by pharmacological inhibition of the oncogenic MAPK pathway in sloppy cells, and is restored in cells with acquired resistance to MAPK pathway inhibition. Interestingly, sloppiness causes aberrant peptide presentation at the cell surface, allowing recognition and specific killing of drug-resistant cancer cells by T lymphocytes. Thus, while oncogenes empower cancer progression and aggressiveness, they also expose a vulnerability by provoking the production of aberrant peptides through sloppiness.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Melanocyte, Epithelial Cell, Cell Culture, Colon Epithelial Cell, Fibroblast

DISEASE(S): Skin Cancer,Carcinoma,Colon Cancer

SUBMITTER: Onno Bleijerveld

LAB HEAD: Reuven Agami

PROVIDER: PXD022707 | Pride | 2021-09-28

REPOSITORIES: pride

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			Action	DRS
	20200306_Fusion_Agami_Remco_ATF4GFP_Ctrl_01.raw	Raw
	20200306_Fusion_Agami_Remco_ATF4GFP_Ctrl_02.raw	Raw
	20200306_Fusion_Agami_Remco_ATF4GFP_Ctrl_03.raw	Raw
	20200306_Fusion_Agami_Remco_ATF4GFP_IFN_01.raw	Raw
	20200306_Fusion_Agami_Remco_ATF4GFP_IFN_02.raw	Raw

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Publications

Oncogene-dependent sloppiness in mRNA translation.

Champagne Julien J Pataskar Abhijeet A Blommaert Naomi N Nagel Remco R Wernaart Demi D Ramalho Sofia S Kenski Juliana J Bleijerveld Onno B OB Zaal Esther A EA Berkers Celia R CR Altelaar Maarten M Peeper Daniel S DS Faller William J WJ Agami Reuven R

Molecular cell 20210924 22

mRNA translation is a highly conserved and tightly controlled mechanism for protein synthesis. Despite protein quality control mechanisms, amino acid shortage in melanoma induces aberrant proteins by ribosomal frameshifting. The extent and the underlying mechanisms related to this phenomenon are yet unknown. Here, we show that tryptophan depletion-induced ribosomal frameshifting is a widespread phenomenon in cancer. We termed this event sloppiness and strikingly observed its association with MAP ...[more]

PMID: 34562372

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Project description:Many tumors escape by activating multiple cellular pathways that induce immunosuppression. One pivotal immune-suppressive mechanism is the production of tryptophan metabolites along the kynurenine pathway by IFNγ-induced IDO1 enzyme production 4-8. Phase III clinical trials using chemical inhibition of IDO1 in combination with PD1 pathway blockade, however, failed to improve melanoma treatment 9-12. This points at an incomplete understanding of the role of IDO1 and the consequent tryptophan degradation on mRNA translation and cancer progression. Here, we investigated the effects of prolonged IFNγ treatment on mRNA translation in melanoma cells by ribosome profiling. Surprisingly, we observed a massive accumulation of ribosomes ~20 amino acids downstream of tryptophan codons (termed here as W-Bumps) along with their expected stalling at the tryptophan codon itself. This indicated ribosomal bypass of the tryptophan codons in the absence of tryptophan. Detailed examination of W-Bumps position and its corresponding peptide sequences pinpointed towards ribosomal frameshifting events and their effects in the ribosome exit tunnel. In particular, W-Bumps strength was associated with the disorderedness level of potential out-of-frame peptides predicted downstream of tryptophan codons. Indeed, reporter assays demonstrated the induction of ribosomal frameshifting, and the generation of trans-frame proteins and their presentation at the cell surface after IFNγ treatment. Proteomics and immunopeptidomics analyses verified the production of IFNγ-induced trans-frame and out-of-frame aberrant peptides and their presentation on HLA class I molecules. Priming of naïve T cells from healthy donors with aberrant peptides resulted in identification of reactive, peptide-specific T cells. Altogether, our results suggest that IFNγ-induced IDO1-mediated tryptophan depletion plays a role in the immune recognition of melanoma cells by contributing to the diversity of the peptidome landscape, and by inducing the presentation of aberrant peptides.

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