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Burbage M, Rocañín-Arjó A, Baudon B, Arribas YA, Merlotti A, Rookhuizen DC, Heurtebise-Chrétien S, Ye M, Houy A, Burgdorf N, Suarez G, Gros M, Sadacca B, Carrascal M, Garmilla A, Bohec M, Baulande S, Lombard B, Loew D, Waterfall JJ, Stern MH, Goudot C, Amigorena S. Epigenetically controlled tumor antigens derived from splice junctions between exons and transposable elements. Sci Immunol 2023; 8:eabm6360. [PMID: 36735776 DOI: 10.1126/sciimmunol.abm6360] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/12/2023] [Indexed: 02/05/2023]
Abstract
Oncogenesis often implicates epigenetic alterations, including derepression of transposable elements (TEs) and defects in alternative splicing. Here, we explore the possibility that noncanonical splice junctions between exons and TEs represent a source of tumor-specific antigens. We show that mouse normal tissues and tumor cell lines express wide but distinct ranges of mRNA junctions between exons and TEs, some of which are tumor specific. Immunopeptidome analyses in tumor cell lines identified peptides derived from exon-TE splicing junctions associated to MHC-I molecules. Exon-TE junction-derived peptides were immunogenic in tumor-bearing mice. Both prophylactic and therapeutic vaccinations with junction-derived peptides delayed tumor growth in vivo. Inactivation of the TE-silencing histone 3-lysine 9 methyltransferase Setdb1 caused overexpression of new immunogenic junctions in tumor cells. Our results identify exon-TE splicing junctions as epigenetically controlled, immunogenic, and protective tumor antigens in mice, opening possibilities for tumor targeting and vaccination in patients with cancer.
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Affiliation(s)
- Marianne Burbage
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Ares Rocañín-Arjó
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Blandine Baudon
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Yago A Arribas
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Antonela Merlotti
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Derek C Rookhuizen
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | | | - Mengliang Ye
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Alexandre Houy
- Institut Curie, Université Paris Sciences et Lettres, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, 75005 Paris, France
| | - Nina Burgdorf
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Guadalupe Suarez
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Marine Gros
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Benjamin Sadacca
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Montserrat Carrascal
- Biological and Environmental Proteomics, Institut d'Investigacions Biomèdiques de Barcelona-CSIC, IDIBAPS, Roselló 161, 6a planta, 08036 Barcelona, Spain
| | - Andrea Garmilla
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
| | - Mylène Bohec
- Institut Curie, Centre de Recherche, Genomics of Excellence Platform, PSL Research University, Paris cedex 05, France
| | - Sylvain Baulande
- Institut Curie, Centre de Recherche, Genomics of Excellence Platform, PSL Research University, Paris cedex 05, France
| | - Bérangère Lombard
- Institut Curie, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Paris cedex 05, France
| | - Damarys Loew
- Institut Curie, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Paris cedex 05, France
| | - Joshua J Waterfall
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Marc-Henri Stern
- Institut Curie, Université Paris Sciences et Lettres, INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe labellisée par la Ligue Nationale Contre le Cancer, 75005 Paris, France
| | - Christel Goudot
- Institut Curie, Université Paris Sciences et Lettres, 75005 Paris, France
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Merlotti A, Sadacca B, Arribas YA, Ngoma M, Burbage M, Goudot C, Houy A, Rocañín-Arjó A, Lalanne A, Seguin-Givelet A, Lefevre M, Heurtebise-Chrétien S, Baudon B, Oliveira G, Loew D, Carrascal M, Wu CJ, Lantz O, Stern MH, Girard N, Waterfall JJ, Amigorena S. Noncanonical splicing junctions between exons and transposable elements represent a source of immunogenic recurrent neo-antigens in patients with lung cancer. Sci Immunol 2023; 8:eabm6359. [PMID: 36735774 DOI: 10.1126/sciimmunol.abm6359] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/12/2023] [Indexed: 02/05/2023]
Abstract
Although most characterized tumor antigens are encoded by canonical transcripts (such as differentiation or tumor-testis antigens) or mutations (both driver and passenger mutations), recent results have shown that noncanonical transcripts including long noncoding RNAs and transposable elements (TEs) can also encode tumor-specific neo-antigens. Here, we investigate the presentation and immunogenicity of tumor antigens derived from noncanonical mRNA splicing events between coding exons and TEs. Comparing human non-small cell lung cancer (NSCLC) and diverse healthy tissues, we identified a subset of splicing junctions that is both tumor specific and shared across patients. We used HLA-I peptidomics to identify peptides encoded by tumor-specific junctions in primary NSCLC samples and lung tumor cell lines. Recurrent junction-encoded peptides were immunogenic in vitro, and CD8+ T cells specific for junction-encoded epitopes were present in tumors and tumor-draining lymph nodes from patients with NSCLC. We conclude that noncanonical splicing junctions between exons and TEs represent a source of recurrent, immunogenic tumor-specific antigens in patients with NSCLC.
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Affiliation(s)
- Antonela Merlotti
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Benjamin Sadacca
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Yago A Arribas
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Mercia Ngoma
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Marianne Burbage
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Christel Goudot
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Alexandre Houy
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
| | - Ares Rocañín-Arjó
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Ana Lalanne
- Institut Curie, Laboratory of Clinical immunology, 75005 Paris, France
- Institut Curie, CIC-BT1428, 75005 Paris, France
| | - Agathe Seguin-Givelet
- Thoracic Surgery Department, Curie-Montsouris Thorax Institute - Institut Mutualiste Montsouris, Paris, France
- Paris 13 University, Sorbonne Paris Cité, Faculty of Medicine SMBH, Bobigny, France
| | - Marine Lefevre
- Department of Pathology, Institute Mutualiste Montsouris, Paris, France
| | | | - Blandine Baudon
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Damarys Loew
- Institut Curie, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Paris cedex 05, France
| | - Montserrat Carrascal
- Biological and Environmental Proteomics, Institut d'Investigacions Biomèdiques de Barcelona-CSIC, IDIBAPS, Roselló 161, 6a planta, 08036 Barcelona, Spain
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Olivier Lantz
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
- Institut Curie, Laboratory of Clinical immunology, 75005 Paris, France
- Institut Curie, CIC-BT1428, 75005 Paris, France
| | - Marc-Henri Stern
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
| | - Nicolas Girard
- Thoracic Surgery Department, Curie-Montsouris Thorax Institute - Institut Mutualiste Montsouris, Paris, France
| | - Joshua J Waterfall
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Sebastian Amigorena
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
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Rocañín-Arjó A, Rodríguez-Botigué L, Esteban E, Theves C, Evdokimova LE, Fedorova SA, Gibert M, Crubezy E, Moral P. Close genetic relationships in vast territories: autosomal and X chromosome Alu diversity in Yakuts from Siberia. Anthropol Anz 2014; 70:309-17. [PMID: 24466640 DOI: 10.1127/0003-5548/2013/0296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Twelve autosomal and 8 X chromosome Alu markers were genotyped for the first time in 161 Central and West Yakuts to test their ability to reconstruct the genetic history of these populations, the northernmost Turkic-speaker ethnic group living in Siberia. Autosomal data revealed that both groups showed extremely close genetic distances to other populations of Siberian origins that occupied areas from Lake Baikal, the ancestral place of origin of Yakuts, to North Siberia, their current territories. Autosomal and X chromosome data revealed some discrepancies on the genetic differentiation and the effective sizes of Central and West Yakuts. Such discrepancies could be related to the patrilineal and occasionally polygamous structure of these populations. Autosomal and X Alu markers are informative markers to reconstruct population past demography and history, but their utility is limited by the available data. This study represents a contribution for further investigations on these populations.
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Affiliation(s)
- Ares Rocañín-Arjó
- Secció d'Antropologia, Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
| | - Laura Rodríguez-Botigué
- Institut de Biologia Evolutiva (CSIC-UPF), Department de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Esther Esteban
- Secció d'Antropologia, Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
| | - Catherine Theves
- Laboratory AMIS, UMR 5288, CNRS-Université de Toulouse III-Paul Sabatier, Université de Strasbourg, France
| | | | - Sardana A Fedorova
- North-Eastern Federal University and Yakut Research Centre of Complex Medical Problems, Russian Academy of Medical Sciences, Republic of Sakha, Russian Federation
| | - Morgane Gibert
- Laboratory AMIS, UMR 5288, CNRS-Université de Toulouse III-Paul Sabatier, Université de Strasbourg, France
| | - Eric Crubezy
- Laboratory AMIS, UMR 5288, CNRS-Université de Toulouse III-Paul Sabatier, Université de Strasbourg, France
| | - Pedro Moral
- Secció d'Antropologia, Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
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