Potential shared neoantigens from pan-cancer transcript isoforms
Abstract Isoform switching in cancer is a prevalent phenomenon with significant implications for immunotherapy, as actionable neoantigens derived from these cancer-specific events would be applicable to broad categories of patients, reducing the necessity for personalized treatments. By integrating...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-05-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-025-00817-6 |
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| author | Jirapat Techachakrit Aijaz Ahmad Malik Trairak Pisitkun Sira Sriswasdi |
| author_facet | Jirapat Techachakrit Aijaz Ahmad Malik Trairak Pisitkun Sira Sriswasdi |
| author_sort | Jirapat Techachakrit |
| collection | DOAJ |
| description | Abstract Isoform switching in cancer is a prevalent phenomenon with significant implications for immunotherapy, as actionable neoantigens derived from these cancer-specific events would be applicable to broad categories of patients, reducing the necessity for personalized treatments. By integrating five large-scale transcriptomic datasets comprising over 19,500 samples across 29 cancer and 54 normal tissue types, we identified cancer-associated isoform switching events common to multiple cancer types, several of which involve genes with established mechanistic roles in oncogenesis. The presence of neoantigen-containing peptides derived from these transcripts was confirmed in broad cancer and normal tissue proteome datasets and the binding affinity of predicted neoantigens to the human leukocyte antigen (HLA) complex via molecular dynamics simulations. The study presents strong evidence that isoform switching in cancer is a significant source of actionable neoantigens that have the capability to trigger an immune response. These findings suggest that isoform switching events could potentially be leveraged for broad immunotherapeutic strategies across various cancer types. |
| format | Article |
| id | doaj-art-b07e76142167415dabc458d00d7e7490 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-b07e76142167415dabc458d00d7e74902025-08-20T03:53:12ZengNature PortfolioScientific Reports2045-23222025-05-0115111510.1038/s41598-025-00817-6Potential shared neoantigens from pan-cancer transcript isoformsJirapat Techachakrit0Aijaz Ahmad Malik1Trairak Pisitkun2Sira Sriswasdi3Center of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn UniversityCenter of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn UniversityCenter of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn UniversityCenter of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn UniversityAbstract Isoform switching in cancer is a prevalent phenomenon with significant implications for immunotherapy, as actionable neoantigens derived from these cancer-specific events would be applicable to broad categories of patients, reducing the necessity for personalized treatments. By integrating five large-scale transcriptomic datasets comprising over 19,500 samples across 29 cancer and 54 normal tissue types, we identified cancer-associated isoform switching events common to multiple cancer types, several of which involve genes with established mechanistic roles in oncogenesis. The presence of neoantigen-containing peptides derived from these transcripts was confirmed in broad cancer and normal tissue proteome datasets and the binding affinity of predicted neoantigens to the human leukocyte antigen (HLA) complex via molecular dynamics simulations. The study presents strong evidence that isoform switching in cancer is a significant source of actionable neoantigens that have the capability to trigger an immune response. These findings suggest that isoform switching events could potentially be leveraged for broad immunotherapeutic strategies across various cancer types.https://doi.org/10.1038/s41598-025-00817-6Shared pan-cancer neoantigensIsoform switchingImmunotherapy targets |
| spellingShingle | Jirapat Techachakrit Aijaz Ahmad Malik Trairak Pisitkun Sira Sriswasdi Potential shared neoantigens from pan-cancer transcript isoforms Scientific Reports Shared pan-cancer neoantigens Isoform switching Immunotherapy targets |
| title | Potential shared neoantigens from pan-cancer transcript isoforms |
| title_full | Potential shared neoantigens from pan-cancer transcript isoforms |
| title_fullStr | Potential shared neoantigens from pan-cancer transcript isoforms |
| title_full_unstemmed | Potential shared neoantigens from pan-cancer transcript isoforms |
| title_short | Potential shared neoantigens from pan-cancer transcript isoforms |
| title_sort | potential shared neoantigens from pan cancer transcript isoforms |
| topic | Shared pan-cancer neoantigens Isoform switching Immunotherapy targets |
| url | https://doi.org/10.1038/s41598-025-00817-6 |
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