ArticleNature communications2023
Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Preclinical proof of concept for a personalized SNAP™-TIL (Specific Neo-Antigen Peptides-TIL) therapy platform.Oncoimmunology · 2026Article
- Review
- Non-canonical and induced neoantigens as emerging sources of cancer-specific immunotherapy targets.Frontiers in immunology · 2026Review
- Unlocking the undruggable spliceosome: generative AI and structural dynamics in cancer therapy.Frontiers in cell and developmental biology · 2026Review
- Artificial Intelligence and the Evolving Landscape of Immunopeptidomics.Proteomics. Clinical applications · 2025Review
- Engineering adoptive cell therapy for solid tumors.Medical oncology (Northwood, London, England) · 2025Review
- Neoantigen-Driven Immunotherapy in Triple-Negative Breast Cancer: Emerging Strategies and Clinical Potential.Biomedicines · 2025Review
- The role of neoantigens and tumor mutational burden in cancer immunotherapy: advances, mechanisms, and perspectives.Journal of hematology & oncology · 2025Review
- Efficient and effective identification of cancer neoantigens from tumor only RNA-seq.NAR genomics and bioinformatics · 2025Article
- Immunopeptidomics-guided discovery and characterization of neoantigens for personalized cancer immunotherapy.Science advances · 2025Article
- Multi-omics in immunotherapy research for HNSCC: present situation and future perspectives.NPJ precision oncology · 2025Review
- Article
- Predictive marker for response to trifluridine/tipiracil plus bevacizumab in metastatic colorectal cancer patients.BMC cancer · 2025Article
- Advances in neoantigen-based immunotherapy for head and neck squamous cell carcinoma: a comprehensive review.Frontiers in oncology · 2025Review
- The 2024 Report on the Human Proteome from the HUPO Human Proteome Project.Journal of proteome research · 2024Review
- Immune evasion: An imperative and consequence of MYC deregulation.Molecular oncology · 2024Review
- Targeting Neoantigens in Cancer: Possibilities and Opportunities in Breast Cancer.Antibodies (Basel, Switzerland) · 2024Review
- Gene network-based and ensemble modeling-based selection of tumor-associated antigens with a predicted low risk of tissue damage for targeted immunotherapy.Journal for immunotherapy of cancer · 2024Article
- Novel insights into TCR-T cell therapy in solid neoplasms: optimizing adoptive immunotherapy.Experimental hematology & oncology · 2024Review
- RBPs: an RNA editor's choice.Frontiers in molecular biosciences · 2024Review
Corrections and comments
- Erratum issued
Authors and funding
39 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Systemic pan-tumor analyses may reveal the significance of common features implicated in cancer immunogenicity and patient survival. Here, we provide a comprehensive multi-omics data set for 32 patients across 25 tumor types for proteogenomic-based discovery of neoantigens. By using an optimized computational approach, we discover a large number of tumor-specific and tumor-associated antigens. To create a pipeline for the identification of neoantigens in our cohort, we combine DNA and RNA sequencing with MS-based immunopeptidomics of tumor specimens, followed by the assessment of their immunogenicity and an in-depth validation process. We detect a broad variety of non-canonical HLA-binding peptides in the majority of patients demonstrating partially immunogenicity. Our validation process allows for the selection of 32 potential neoantigen candidates. The majority of neoantigen candidates originates from variants identified in the RNA data set, illustrating the relevance of RNA as a still understudied source of cancer antigens. This study underlines the importance of RNA-centered variant detection for the identification of shared biomarkers and potentially relevant neoantigen candidates.
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