BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens
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 Bam...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-08-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-023-03029-1 |
| _version_ | 1797559385066569728 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Maria Virginia Ruiz Cuevas |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T17:44:36Z |
| format | Article |
| id | doaj.art-23d904d29bc341d1bcfd3983798d9305 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-03-10T17:44:36Z |
| publishDate | 2023-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-23d904d29bc341d1bcfd3983798d93052023-11-20T09:35:10ZengBMCGenome Biology1474-760X2023-08-0124113310.1186/s13059-023-03029-1BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigensMaria Virginia Ruiz Cuevas0Marie-Pierre Hardy1Jean-David Larouche2Anca Apavaloaei3Eralda Kina4Krystel Vincent5Patrick Gendron6Jean-Philippe Laverdure7Chantal Durette8Pierre Thibault9Sébastien Lemieux10Claude Perreault11Grégory Ehx12Institute for Research in Immunology and Cancer (IRIC), Université de MontréalInstitute for Research in Immunology and Cancer (IRIC), Université de MontréalInstitute for Research in Immunology and Cancer (IRIC), Université de MontréalInstitute for Research in Immunology and Cancer (IRIC), Université de MontréalInstitute for Research in Immunology and Cancer (IRIC), Université de MontréalInstitute for Research in Immunology and Cancer (IRIC), Université de MontréalInstitute for Research in Immunology and Cancer (IRIC), Université de MontréalInstitute for Research in Immunology and Cancer (IRIC), Université de MontréalInstitute for Research in Immunology and Cancer (IRIC), Université de MontréalInstitute for Research in Immunology and Cancer (IRIC), Université de MontréalInstitute for Research in Immunology and Cancer (IRIC), Université de MontréalInstitute for Research in Immunology and Cancer (IRIC), Université de MontréalInstitute for Research in Immunology and Cancer (IRIC), Université de MontréalAbstract 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.https://doi.org/10.1186/s13059-023-03029-1ImmunopeptidomeComputational biologyMajor histocompatibility complexTumor antigens |
| spellingShingle | 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 BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens Genome Biology Immunopeptidome Computational biology Major histocompatibility complex Tumor antigens |
| title | BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens |
| title_full | BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens |
| title_fullStr | BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens |
| title_full_unstemmed | BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens |
| title_short | BamQuery: a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens |
| title_sort | bamquery a proteogenomic tool to explore the immunopeptidome and prioritize actionable tumor antigens |
| topic | Immunopeptidome Computational biology Major histocompatibility complex Tumor antigens |
| url | https://doi.org/10.1186/s13059-023-03029-1 |
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