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

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...

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Detalles Bibliográficos
Autores principales: Cuevas, Maria Virginia Ruiz, Hardy, Marie-Pierre, Larouche, Jean-David, Apavaloaei, Anca, Kina, Eralda, Vincent, Krystel, Gendron, Patrick, Laverdure, Jean-Philippe, Durette, Chantal, Thibault, Pierre, Lemieux, Sébastien, Perreault, Claude, Ehx, Grégory
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10426134/
https://www.ncbi.nlm.nih.gov/pubmed/37582761
http://dx.doi.org/10.1186/s13059-023-03029-1
Descripción
Sumario: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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-03029-1.

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