BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens

Exhaustive capture of MAPs RNA expression

Résumé

MHC-I-associated peptides deriving from non-coding genomic regions and mutations can generate tumor-specific antigens, including neoantigens. Quantifying tumor-specific antigens’ RNA expression in malignant and benign tissues is critical for discriminating actionable targets. We present BamQuery, a tool attributing an exhaustive RNA expression to MHC-I-associated peptides of any origin from bulk and single-cell RNA-sequencing data. We show that many cryptic and mutated tumor-specific antigens can derive from multiple discrete genomic regions, abundantly expressed in normal tissues. BamQuery can also be used to predict MHC-I-associated peptides immunogenicity and identify actionable tumor-specific antigens de novo.

Publication
Genome Biology
Maria Virginia Ruiz Cuevas
Maria Virginia Ruiz Cuevas
Étudiante au doctorat en bio-informatique (2018-2023)

Detection of Cryptic protein source of MHC-I associated peptides

Sébastien Lemieux
Sébastien Lemieux
Chercheur principal

Chercheur principal, Unité de recherche en bio-informatique fonctionnelle et structurale, IRIC | Direction scientifique de la plateforme de Bio-informatique | Professeur agrégé, Département de biochimie et médecine moléculaire, Université de Montréal