BamQuery: a Proteogenomic Tool to Explore the Immunopeptidome and Prioritize Actionable Tumor Antigens

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2023 Aug 15

PMID 37582761

Authors

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

Sebastien Lemieux

Claude Perreault

Gregory Ehx

Affiliations

Soon will be listed here.

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.

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