ABPEPserver: a web application for documentation and analysis of substitutants
Abstract Background Cancer immunotherapy is implemented by identifying antigens that are presented on the cell surface of cancer cells and illicit T-cell response (Schumacher and Schreiber, Science 348:69–74, 2015; Waldman et al., Nat Rev Immunol 20:651–668, 2020; Zhang et al., Front Immunol 12:672,...
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| Format: | Article |
| Language: | English |
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BMC
2023-06-01
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| Series: | BMC Cancer |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12885-023-10970-8 |
| _version_ | 1797811434486235136 |
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| author | Abhijeet Pataskar Jasmine Montenegro Navarro Reuven Agami |
| author_facet | Abhijeet Pataskar Jasmine Montenegro Navarro Reuven Agami |
| author_sort | Abhijeet Pataskar |
| collection | DOAJ |
| description | Abstract Background Cancer immunotherapy is implemented by identifying antigens that are presented on the cell surface of cancer cells and illicit T-cell response (Schumacher and Schreiber, Science 348:69–74, 2015; Waldman et al., Nat Rev Immunol 20:651–668, 2020; Zhang et al., Front Immunol 12:672,356, 2021b). Classical candidates of such antigens are the peptides resulting from genetic alterations and are named “neoantigen" (Schumacher and Schreiber, Science 348:69–74, 2015). Neoantigens have been widely catalogued across several human cancer types (Tan et al., Database (Oxford) 2020;2020b; Vigneron et al., Cancer Immun 13:15, 2013; Yi et al., iScience 24:103,107, 2021; Zhang et al., BMC Bioinformatics 22:40, 2021a). Recently, a new class of inducible antigens has been identified, namely Substitutants, that are produced as a result of aberrant protein translation (Pataskar et al., Nature 603:721–727, 2022). Main Catalogues of Substitutant expression across human cancer types, their specificity and association to gene expression signatures remain elusive for the scientific community's access. As a solution, we present ABPEPserver, an online database and analytical platform that can visualize a large-scale tumour proteomics analysis of Substitutant expression across eight tumour types sourced from the CPTAC database (Edwards et al., J Proteome Res 14:2707–2713, 2015). Functionally, ABPEPserver offers the analysis of gene-association signatures of Substitutant peptides, a comparison of enrichment between tumour and tumour-adjacent normal tissues, and a list of peptides that serve as candidates for immunotherapy design. ABPEPserver will significantly enhance the exploration of aberrant protein production in human cancer, as exemplified in a case study. Conclusion ABPEPserver is designed on an R SHINY platform to catalogue Substitutant peptides in human cancer. The application is available at https://rhpc.nki.nl/sites/shiny/ABPEP/ . The code is available under GNU General public license from GitHub ( https://github.com/jasminesmn/ABPEPserver ). |
| first_indexed | 2024-03-13T07:23:39Z |
| format | Article |
| id | doaj.art-c5a6a4a75bd54206b000c3841378bdf7 |
| institution | Directory Open Access Journal |
| issn | 1471-2407 |
| language | English |
| last_indexed | 2024-03-13T07:23:39Z |
| publishDate | 2023-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Cancer |
| spelling | doaj.art-c5a6a4a75bd54206b000c3841378bdf72023-06-04T11:31:27ZengBMCBMC Cancer1471-24072023-06-012311710.1186/s12885-023-10970-8ABPEPserver: a web application for documentation and analysis of substitutantsAbhijeet Pataskar0Jasmine Montenegro Navarro1Reuven Agami2Division of Oncogenomics, Oncode Institute, The Netherlands Cancer InstituteDivision of Oncogenomics, Oncode Institute, The Netherlands Cancer InstituteDivision of Oncogenomics, Oncode Institute, The Netherlands Cancer InstituteAbstract Background Cancer immunotherapy is implemented by identifying antigens that are presented on the cell surface of cancer cells and illicit T-cell response (Schumacher and Schreiber, Science 348:69–74, 2015; Waldman et al., Nat Rev Immunol 20:651–668, 2020; Zhang et al., Front Immunol 12:672,356, 2021b). Classical candidates of such antigens are the peptides resulting from genetic alterations and are named “neoantigen" (Schumacher and Schreiber, Science 348:69–74, 2015). Neoantigens have been widely catalogued across several human cancer types (Tan et al., Database (Oxford) 2020;2020b; Vigneron et al., Cancer Immun 13:15, 2013; Yi et al., iScience 24:103,107, 2021; Zhang et al., BMC Bioinformatics 22:40, 2021a). Recently, a new class of inducible antigens has been identified, namely Substitutants, that are produced as a result of aberrant protein translation (Pataskar et al., Nature 603:721–727, 2022). Main Catalogues of Substitutant expression across human cancer types, their specificity and association to gene expression signatures remain elusive for the scientific community's access. As a solution, we present ABPEPserver, an online database and analytical platform that can visualize a large-scale tumour proteomics analysis of Substitutant expression across eight tumour types sourced from the CPTAC database (Edwards et al., J Proteome Res 14:2707–2713, 2015). Functionally, ABPEPserver offers the analysis of gene-association signatures of Substitutant peptides, a comparison of enrichment between tumour and tumour-adjacent normal tissues, and a list of peptides that serve as candidates for immunotherapy design. ABPEPserver will significantly enhance the exploration of aberrant protein production in human cancer, as exemplified in a case study. Conclusion ABPEPserver is designed on an R SHINY platform to catalogue Substitutant peptides in human cancer. The application is available at https://rhpc.nki.nl/sites/shiny/ABPEP/ . The code is available under GNU General public license from GitHub ( https://github.com/jasminesmn/ABPEPserver ).https://doi.org/10.1186/s12885-023-10970-8SubstitutantsCodon reassignmentTranslationCancerImmunotherapy |
| spellingShingle | Abhijeet Pataskar Jasmine Montenegro Navarro Reuven Agami ABPEPserver: a web application for documentation and analysis of substitutants BMC Cancer Substitutants Codon reassignment Translation Cancer Immunotherapy |
| title | ABPEPserver: a web application for documentation and analysis of substitutants |
| title_full | ABPEPserver: a web application for documentation and analysis of substitutants |
| title_fullStr | ABPEPserver: a web application for documentation and analysis of substitutants |
| title_full_unstemmed | ABPEPserver: a web application for documentation and analysis of substitutants |
| title_short | ABPEPserver: a web application for documentation and analysis of substitutants |
| title_sort | abpepserver a web application for documentation and analysis of substitutants |
| topic | Substitutants Codon reassignment Translation Cancer Immunotherapy |
| url | https://doi.org/10.1186/s12885-023-10970-8 |
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