Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames

Céline M. Laumont, Tariq Daouda, Jean-Philippe Laverdure, Éric Bonneil, Olivier Caron-Lizotte, Marie-Pierre Hardy, Diana P. Granados, Chantal Durette, Sébastien Lemieux, Pierre Thibault and Claude Perreault ()
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Céline M. Laumont: Institute for Research in Immunology and Cancer, Université de Montréal
Tariq Daouda: Institute for Research in Immunology and Cancer, Université de Montréal
Jean-Philippe Laverdure: Institute for Research in Immunology and Cancer, Université de Montréal
Éric Bonneil: Institute for Research in Immunology and Cancer, Université de Montréal
Olivier Caron-Lizotte: Institute for Research in Immunology and Cancer, Université de Montréal
Marie-Pierre Hardy: Institute for Research in Immunology and Cancer, Université de Montréal
Diana P. Granados: Institute for Research in Immunology and Cancer, Université de Montréal
Chantal Durette: Institute for Research in Immunology and Cancer, Université de Montréal
Sébastien Lemieux: Institute for Research in Immunology and Cancer, Université de Montréal
Pierre Thibault: Institute for Research in Immunology and Cancer, Université de Montréal
Claude Perreault: Institute for Research in Immunology and Cancer, Université de Montréal

Nature Communications, 2016, vol. 7, issue 1, 1-12

Abstract: Abstract In view of recent reports documenting pervasive translation outside of canonical protein-coding sequences, we wished to determine the proportion of major histocompatibility complex (MHC) class I-associated peptides (MAPs) derived from non-canonical reading frames. Here we perform proteogenomic analyses of MAPs eluted from human B cells using high-throughput mass spectrometry to probe the six-frame translation of the B-cell transcriptome. We report that ∼10% of MAPs originate from allegedly noncoding genomic sequences or exonic out-of-frame translation. The biogenesis and properties of these ‘cryptic MAPs’ differ from those of conventional MAPs. Cryptic MAPs come from very short proteins with atypical C termini, and are coded by transcripts bearing long 3′UTRs enriched in destabilizing elements. Relative to conventional MAPs, cryptic MAPs display different MHC class I-binding preferences and harbour more genomic polymorphisms, some of which are immunogenic. Cryptic MAPs increase the complexity of the MAP repertoire and enhance the scope of CD8 T-cell immunosurveillance.

Date: 2016
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms10238

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DOI: 10.1038/ncomms10238

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