---
title: "Receptor-guided targeting of a melanoma-enriched noncanonical antigen (EVA003)"
id: "pubmed-42706244"
canonical_url: "https://medichelpline.com/clinical-feed/pubmed-42706244"
content_type: "clinical_feed_article"
specialty: "Pharmacology"
source_name: "PubMed / NCBI"
source_url: "https://pubmed.ncbi.nlm.nih.gov/42706244/"
doi: "10.1038/s41392-026-02961-5"
published_at: "2026-09-08T00:00:00.000Z"
evidence_level: "Journal Article"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Receptor-guided targeting of a melanoma-enriched noncanonical antigen (EVA003)
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/pubmed-42706244
- **Specialty:** [Pharmacology](https://medichelpline.com/clinical-feed/pharmacology.md)
- **Primary Source:** PubMed / NCBI
- **Source URL:** [Original Journal Publication](https://pubmed.ncbi.nlm.nih.gov/42706244/)
- **DOI:** [10.1038/s41392-026-02961-5](https://doi.org/10.1038%2Fs41392-026-02961-5)
- **Published At:** 2026-09-08T00:00:00.000Z
- **Evidence Rating:** Journal Article
## Executive GIST (TL;DR)
- The study integrates de novo transcriptome assembly, exon-resolved quantification, RNA in situ hybridization, and **immunopeptidomics** to discover melanoma-associated **noncanonical peptides** arising from transcription outside annotated protein-coding regions. - Three recurrent melanoma-associated noncanonical transcripts were identified; one, named **EVA003**, was prioritized because of a repeat-enriched genomic architecture and a genomically unique immunogenic core sequence. - EVA003 showed tumor-enriched exon-level expression across independent datasets and was validated by RNA in situ hybridization. - Peptides derived from EVA003 were shown to be endogenously presented on **HLA-A*03:01** molecules and elicited specific reactivity in patient-derived **tumor-infiltrating lymphocytes (TILs)**. - Single-cell transcriptomics of reactive TILs identified a dominant peptide-reactive clonotype, which allowed isolation of a naturally occurring **T cell receptor (TCR)** specific for the EVA003-derived peptide. - Transfer of this naturally occurring TCR into healthy donor T cells conferred antigen-dependent activation and cytotoxicity against peptide-pulsed target cells and melanoma cells expressing EVA003 endogenously. - The work establishes a biologically informed pipeline to prioritize and validate **noncanonical tumor antigens** at the receptor level and demonstrates that genomically unique, tumor-enriched noncanonical peptides can be targeted by engineered T cells. - The findings support integrating prioritized noncanonical antigens into engineered T cell therapeutic strategies but specific clinical outcomes, broader patient coverage, safety data, and scalability were not reported in the abstract. - Competing-interest disclosures note involvement by Enara Bio in antigen discovery and validation; several authors report advisory roles, proprietary data access, honoraria, or grants from industry and public funders as detailed in the conflict of interest statement.
## Clinical Analysis & Structured Key Points
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Ozcan.Met@regionh.dk.")[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42706244/#full-view-affiliation-4 "Department of Health Technology, Technical University of Denmark, Lyngby, Denmark. Ozcan.Met@regionh.dk.") Affiliations Expand ### Affiliations * 1 National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark. * 2 Department of Immunology and Microbiology, Copenhagen University, Copenhagen, Denmark. * 3 National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark. Ozcan.Met@regionh.dk. * 4 Department of Health Technology, Technical University of Denmark, Lyngby, Denmark. Ozcan.Met@regionh.dk. * PMID: **42706244** * DOI: [ 10.1038/s41392-026-02961-5 ](https://doi.org/10.1038/s41392-026-02961-5) Item in Clipboard # Receptor-defined targeting of a genomically unique melanoma-enriched noncanonical antigen Thomas Morgan Hulen et al. Signal Transduct Target Ther. 2026. Show details Display options Display options Format Abstract PubMed PMID Signal Transduct Target Ther Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Signal+Transduct+Target+Ther%22%5Bjour%5D&sort=date&sort_order=desc) * [ Search in NLM Catalog ](https://www.ncbi.nlm.nih.gov/nlmcatalog?term=%22Signal+Transduct+Target+Ther%22%5BTitle+Abbreviation%5D) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42706244/) . 2026 Sep 8;11(1):370. doi: 10.1038/s41392-026-02961-5. ### Authors [Thomas Morgan Hulen](https://pubmed.ncbi.nlm.nih.gov/?term=Hulen+TM&cauthor_id=42706244)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42706244/#short-view-affiliation-1 "National Center for Cancer Immune Therapy \(CCIT-DK\), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark."), [Michael Douglas Crowther](https://pubmed.ncbi.nlm.nih.gov/?term=Crowther+MD&cauthor_id=42706244)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42706244/#short-view-affiliation-1 "National Center for Cancer Immune Therapy \(CCIT-DK\), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark."), [Luke Alexander Schuster](https://pubmed.ncbi.nlm.nih.gov/?term=Schuster+LA&cauthor_id=42706244)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42706244/#short-view-affiliation-1 "National Center for Cancer Immune Therapy \(CCIT-DK\), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark."), [Shawez Khan](https://pubmed.ncbi.nlm.nih.gov/?term=Khan+S&cauthor_id=42706244)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42706244/#short-view-affiliation-1 "National Center for Cancer Immune Therapy \(CCIT-DK\), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark."), [Aimilia Schina](https://pubmed.ncbi.nlm.nih.gov/?term=Schina+A&cauthor_id=42706244)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42706244/#short-view-affiliation-1 "National Center for Cancer Immune Therapy \(CCIT-DK\), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark."), [Marco Donia](https://pubmed.ncbi.nlm.nih.gov/?term=Donia+M&cauthor_id=42706244)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42706244/#short-view-affiliation-1 "National Center for Cancer Immune Therapy \(CCIT-DK\), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark."), [Mads Hald Andersen](https://pubmed.ncbi.nlm.nih.gov/?term=Andersen+MH&cauthor_id=42706244)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42706244/#short-view-affiliation-1 "National Center for Cancer Immune Therapy \(CCIT-DK\), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark.")[ 2 ](https://pubmed.ncbi.nlm.nih.gov/42706244/#short-view-affiliation-2 "Department of Immunology and Microbiology, Copenhagen University, Copenhagen, Denmark."), [Inge Marie Svane](https://pubmed.ncbi.nlm.nih.gov/?term=Svane+IM&cauthor_id=42706244)[ 1 ](https://pubmed.ncbi.nlm.nih.gov/42706244/#short-view-affiliation-1 "National Center for Cancer Immune Therapy \(CCIT-DK\), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark."), [Özcan Met](https://pubmed.ncbi.nlm.nih.gov/?term=Met+%C3%96&cauthor_id=42706244)[ 3 ](https://pubmed.ncbi.nlm.nih.gov/42706244/#short-view-affiliation-3 "National Center for Cancer Immune Therapy \(CCIT-DK\), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark. Ozcan.Met@regionh.dk.")[ 4 ](https://pubmed.ncbi.nlm.nih.gov/42706244/#short-view-affiliation-4 "Department of Health Technology, Technical University of Denmark, Lyngby, Denmark. Ozcan.Met@regionh.dk.") ### Affiliations * 1 National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark. * 2 Department of Immunology and Microbiology, Copenhagen University, Copenhagen, Denmark. * 3 National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark. Ozcan.Met@regionh.dk. * 4 Department of Health Technology, Technical University of Denmark, Lyngby, Denmark. Ozcan.Met@regionh.dk. * PMID: **42706244** * DOI: [ 10.1038/s41392-026-02961-5 ](https://doi.org/10.1038/s41392-026-02961-5) Item in Clipboard Cite Display options Display options Format Abstract PubMed PMID ## Abstract Effective T cell-based immunotherapies require functional receptors that can be engineered and redeployed to recognize tumor-restricted antigens. Noncanonical peptides arising from transcription outside annotated protein-coding regions expand the antigenic landscape of cancer; however, systematic strategies to biologically prioritize and functionally validate such targets remain underdeveloped. Here, we integrated de novo transcript analysis, exon-resolved quantification, RNA in situ hybridization, and immunopeptidomics to identify melanoma-associated noncanonical transcripts and advance candidates through receptor-level validation. Among three recurrent melanoma-associated transcripts, EVA003 emerged as a lead target based on its distinct repeat-enriched genomic architecture, consistent tumor-enriched exon-level expression across independent datasets, and a genomically unique immunogenic core sequence. We demonstrate endogenous presentation of EVA003-derived peptides on HLA-A*03:01 and detect specific reactivity in patient-derived tumor-infiltrating lymphocytes. Single-cell transcriptomic profiling identified a dominant peptide-reactive clonotype, enabling isolation of a naturally occurring T cell receptor. Transfer of this receptor into healthy donor T cells conferred antigen-dependent activation and cytotoxicity against both peptide-pulsed targets and melanoma cells expressing EVA003 endogenously. Together, these findings establish a biologically informed strategy for prioritizing noncanonical tumor antigens and demonstrate that genomically unique, tumor-enriched noncanonical peptides can be presented to molecularly defined receptors capable of mediating cancer cell killing. These findings support the integration of prioritized noncanonical antigens into engineered T cell therapeutic strategies. © 2026. The Author(s). [PubMed Disclaimer](https://pubmed.ncbi.nlm.nih.gov/disclaimer/) ## Conflict of interest statement Competing interests: Enara Bio contributed to the antigen discovery and validation experiments in this study. The authors declare that they have no financial, commercial, or professional affiliations with Enara Bio. M.D. has received proprietary data access from Bristol Myers Squibb and Genentech and is an advisor of Achilles Therapeutics. MHA is an advisor and shareholder at IO Biotech. I.M.S. has received honoraria for consultancies and lectures from Novartis, Roche, Merck, and Bristol Myers Squibb; a restricted research grant from Novartis; and financial support for attending symposia from Bristol Myers Squibb, Merck, Novartis, Pfizer, and Roche. ÖM reports grants from public funding sources to institution from the Danish Cancer Society, Novo Nordisk Foundation, and Independent Research Fund Denmark. All other authors declare no competing interests. ## References 1. 1. Rohaan, M. W. et al. Tumor-infiltrating lymphocyte therapy or ipilimumab in advanced melanoma. N. Engl. J. Med. 387, 2113–2125 (2022). - [DOI](https://doi.org/10.1056/nejmoa2210233) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/36477031/) 2. 1. Borch, T. H. et al. Future role for adoptive T-cell therapy in checkpoint inhibitor-resistant metastatic melanoma. J. Immunother. Cancer 8, 1–7 (2020). - [DOI](https://doi.org/10.1136/jitc-2020-000668) 3. 1. Tumeh, P. C. et al. PD-1 blockade induces responses by inhibiting adaptive immune resistance. Nature 515, 568–571 (2014). - [DOI](https://doi.org/10.1038/nature13954) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/25428505/) - [PMC](https://pmc.ncbi.nlm.nih.gov/articles/4246418/) 4. 1. Labanieh, L. & Mackall, C. L. CAR immune cells: Design principles, resistance and the next generation. Nature 614, 635–648 (2023). - [DOI](https://doi.org/10.1038/s41586-023-05707-3) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/36813894/) 5. 1. Atilla, P. A. & Atilla, E. Resistance against anti-CD19 and anti-BCMA CAR T cells: Recent advances and coping strategies. Transl. Oncol. 22, 101459 (2022). - [DOI](https://doi.org/10.1016/j.tranon.2022.101459) - [PubMed](https://pubmed.ncbi.nlm.nih.gov/35617812/) - [PMC](https://pmc.ncbi.nlm.nih.gov/articles/9136177/) Show all 49 references ## MeSH terms * Antigens, Neoplasm* / genetics Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Antigens%2C+Neoplasm%2Fgenetics%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Antigens%2C+Neoplasm) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42706244/) * Antigens, Neoplasm* / immunology Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Antigens%2C+Neoplasm%2Fimmunology%22%5BMAJR%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Antigens%2C+Neoplasm) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42706244/) * Cell Line, Tumor Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Cell+Line%2C+Tumor%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Cell+Line%2C+Tumor) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42706244/) * Humans Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Humans%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Humans) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42706244/) * Immunotherapy Actions * [ Search in PubMed ](https://pubmed.ncbi.nlm.nih.gov/?term=%22Immunotherapy%22%5BMeSH%5D&sort=date&sort_order=desc) * [ Search in MeSH ](https://www.ncbi.nlm.nih.gov/mesh?term=Immunotherapy) * [ Add to Search ](https://pubmed.ncbi.nlm.nih.gov/42706244/) * Lymphocytes, Tumor-Infiltrating / immunology Actions *
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