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Camarena ME, Theunissen P, Ruiz M, Ruiz-Orera J, Calvo-Serra B, Castelo R, Castro C, Sarobe P, Fortes P, Perera-Bel J, Albà MM. Microproteins encoded by noncanonical ORFs are a major source of tumor-specific antigens in a liver cancer patient meta-cohort. SCIENCE ADVANCES 2024; 10:eadn3628. [PMID: 38985879 DOI: 10.1126/sciadv.adn3628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
Abstract
The expression of tumor-specific antigens during cancer progression can trigger an immune response against the tumor. Here, we investigate if microproteins encoded by noncanonical open reading frames (ncORFs) are a relevant source of tumor-specific antigens. We analyze RNA sequencing data from 117 hepatocellular carcinoma (HCC) tumors and matched healthy tissue together with ribosome profiling and immunopeptidomics data. Combining human leukocyte antigen-epitope binding predictions and experimental validation experiments, we conclude that around 40% of the tumor-specific antigens in HCC are likely to be derived from ncORFs, including two peptides that can trigger an immune response in humanized mice. We identify a subset of 33 tumor-specific long noncoding RNAs expressing novel cancer antigens shared by more than 10% of the HCC samples analyzed, which, when combined, cover a large proportion of the patients. The results of the study open avenues for extending the range of anticancer vaccines.
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Affiliation(s)
| | - Patrick Theunissen
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Marta Ruiz
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Jorge Ruiz-Orera
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Beatriz Calvo-Serra
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Robert Castelo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carla Castro
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Pablo Sarobe
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
- Cancer Clinic University of Navarra (CCUN), Pamplona, Spain
| | - Puri Fortes
- Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
- Cancer Clinic University of Navarra (CCUN), Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid, Spain
| | | | - M Mar Albà
- Hospital del Mar Research Institute, Barcelona, Spain
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
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2
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Dréno B, Khammari A, Fortun A, Vignard V, Saiagh S, Beauvais T, Jouand N, Bercegay S, Simon S, Lang F, Labarrière N. Phase I/II clinical trial of adoptive cell transfer of sorted specific T cells for metastatic melanoma patients. Cancer Immunol Immunother 2021; 70:3015-3030. [PMID: 34120214 PMCID: PMC8423703 DOI: 10.1007/s00262-021-02961-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023]
Abstract
Adoptive cell transfer (ACT) of tumor-specific T lymphocytes represents a relevant therapeutic strategy to treat metastatic melanoma patients. Ideal T-cells should combine tumor specificity and reactivity with survival in vivo, while avoiding autoimmune side effects. Here we report results from a Phase I/II clinical trial (NCT02424916, performed between 2015 and 2018) in which 6 metastatic HLA-A2 melanoma patients received autologous antigen-specific T-cells produced from PBMC, after peptide stimulation in vitro, followed by sorting with HLA-peptide multimers and amplification. Each patient received a combination of Melan-A and MELOE-1 polyclonal specific T-cells, whose specificity and anti-tumor reactivity were checked prior to injection, with subcutaneous IL-2. Transferred T-cells were also characterized in terms of functional avidity, diversity and phenotype and their blood persistence was evaluated. An increase in specific T-cells was detected in the blood of all patients at day 1 and progressively disappeared from day 7 onwards. No serious adverse events occurred after this ACT. Clinically, five patients progressed and one patient experienced a partial response following therapy. Melan-A and MELOE-1 specific T-cells infused to this patient were diverse, of high avidity, with a high proportion of T lymphocytes co-expressing PD-1 and TIGIT but few other exhaustion markers. In conclusion, we demonstrated the feasibility and safety of ACT with multimer-sorted Melan-A and MELOE-1 specific T cells to metastatic melanoma patients. The clinical efficacy of such therapeutic strategy could be further enhanced by the selection of highly reactive T-cells, based on PD-1 and TIGIT co-expression, and a combination with ICI, such as anti-PD-1.
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Affiliation(s)
- Brigitte Dréno
- Dermato-Cancerology Department, CIC 1413, CHU Nantes, Nantes, France.,UTCG, CHU Nantes, Nantes, France.,CRCINA, Inserm, Université de Nantes, 44000, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Nantes, France
| | - Amir Khammari
- Dermato-Cancerology Department, CIC 1413, CHU Nantes, Nantes, France.,CRCINA, Inserm, Université de Nantes, 44000, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Nantes, France
| | - Agnès Fortun
- CRCINA, Inserm, Université de Nantes, 44000, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Virginie Vignard
- CRCINA, Inserm, Université de Nantes, 44000, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Nantes, France
| | | | - Tiffany Beauvais
- CRCINA, Inserm, Université de Nantes, 44000, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Nantes, France
| | - Nicolas Jouand
- LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,SFR Santé, CNRS, Inserm, Inserm UMS 016, CNRS UMS 3556, Université de Nantes, CHU Nantes, 44000, Nantes, France
| | | | - Sylvain Simon
- CRCINA, Inserm, Université de Nantes, 44000, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - François Lang
- CRCINA, Inserm, Université de Nantes, 44000, Nantes, France. .,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.
| | - Nathalie Labarrière
- CRCINA, Inserm, Université de Nantes, 44000, Nantes, France. .,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France. .,SFR Santé, CNRS, Inserm, Inserm UMS 016, CNRS UMS 3556, Université de Nantes, CHU Nantes, 44000, Nantes, France.
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3
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Charpentier M, Croyal M, Carbonnelle D, Fortun A, Florenceau L, Rabu C, Krempf M, Labarrière N, Lang F. IRES-dependent translation of the long non coding RNA meloe in melanoma cells produces the most immunogenic MELOE antigens. Oncotarget 2018; 7:59704-59713. [PMID: 27486971 PMCID: PMC5312342 DOI: 10.18632/oncotarget.10923] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 07/20/2016] [Indexed: 01/14/2023] Open
Abstract
MELOE-1 and MELOE-2, two highly specific melanoma antigens involved in T cell immunosurveillance are produced by IRES-dependent translation of the long « non coding » and polycistronic RNA, meloe. In the present study, we document the expression of an additional ORF, MELOE-3, located in the 5' region of meloe. Data from in vitro translation experiments and transfection of melanoma cells with bicistronic vectors documented that MELOE-3 is exclusively translated by the classical cap-dependent pathway. Using a sensitive tandem mass spectrometry technique, we detected the presence of MELOE-3 in total lysates of both melanoma cells and normal melanocytes. This contrasts with our previous observation of the melanoma-restricted expression of MELOE-1 and MELOE-2. Furthermore, in vitro stimulation of PBMC from 6 healthy donors with overlapping peptides from MELOE-1 or MELOE-3 revealed a very scarce MELOE-3 specific T cell repertoire as compared to the abundant repertoire observed against MELOE-1. The poor immunogenicity of MELOE-3 and its expression in melanocytes is consistent with an immune tolerance towards a physiologically expressed protein. In contrast, melanoma-restricted expression of IRES-dependent MELOE-1 may explain its high immunogenicity. In conclusion, within the MELOE family, IRES-dependent antigens represent the best T cell targets for immunotherapy of melanoma.
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Affiliation(s)
- Maud Charpentier
- CRCNA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Mikael Croyal
- UMR INRA 1280, CHU, Nantes, France.,West Human Nutrition Research Center, CHU, Nantes, France
| | | | - Agnès Fortun
- CRCNA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Laetitia Florenceau
- CRCNA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France.,CHU, Nantes, France
| | - Catherine Rabu
- CRCNA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Michel Krempf
- UMR INRA 1280, CHU, Nantes, France.,West Human Nutrition Research Center, CHU, Nantes, France.,CHU, Nantes, France
| | - Nathalie Labarrière
- CRCNA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France.,CHU, Nantes, France
| | - François Lang
- CRCNA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
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Geukes Foppen MH, Donia M, Svane IM, Haanen JBAG. Tumor-infiltrating lymphocytes for the treatment of metastatic cancer. Mol Oncol 2015; 9:1918-35. [PMID: 26578452 DOI: 10.1016/j.molonc.2015.10.018] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 10/20/2015] [Indexed: 12/15/2022] Open
Abstract
Over the past few years melanoma incidence has been rising steadily, resulting in an increase in melanoma related mortality. Until recently, therapeutic options for metastatic melanoma were scarce. Chemotherapy and, in some countries, IL-2 were the only registered treatment modalities. In the last five years, treatment with immunotherapy (anti CTLA-4, anti PD-1, or the combination of these antibodies) has shown very promising results and was able to improve survival in patients with metastatic melanoma. Adoptive cell therapy using tumor-infiltrating lymphocytes is yet another, but highly promising, immunotherapeutic strategy for patients with metastatic melanoma. This review will discuss the development of TIL as a treatment option for melanoma, its mode of action and simplification over time, and the possibilities to expand this therapy to other types of cancer. Also, the future directions of TIL based therapies will be highlighted.
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Affiliation(s)
- M H Geukes Foppen
- Department of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
| | - M Donia
- Center for Cancer Immune Therapy, Department of Haematology and Oncology, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, 2730 Herlev, Denmark.
| | - I M Svane
- Center for Cancer Immune Therapy, Department of Haematology and Oncology, Herlev Hospital, University of Copenhagen, Herlev Ringvej 75, 2730 Herlev, Denmark.
| | - J B A G Haanen
- Department of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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