4.5 Article

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

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GENOME BIOLOGY
卷 24, 期 1, 页码 -

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BMC
DOI: 10.1186/s13059-023-03029-1

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Immunopeptidome; Computational biology; Major histocompatibility complex; Tumor antigens

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A tool called BamQuery has been developed to determine the expression of MHC-I-associated peptides deriving from non-coding genomic regions and mutations from RNA sequencing data. It can also predict their immunogenicity and identify specific 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 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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