BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens
Maria Virginia Ruiz Cuevas, Marie‐Pierre Hardy, Jean‐David Larouche, Anca Apavaloaei, Eralda Kina, Krystel Vincent, Patrick Gendron, Jean‐Philippe Laverdure, Chantal Durette, Pierre Thibault, Sébastien Lemieux, Claude Perreault, Grégory Ehx
Abstract
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.