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Ebrahimi-Nik H, Moussa M, Englander RP, Singhaviranon S, Michaux J, Pak H, Miyadera H, Corwin WL, Keller GLJ, Hagymasi AT, Shcheglova TV, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, Srivastava PK. Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope. Nat Commun 2021; 12:6423. [PMID: 34741035 PMCID: PMC8571378 DOI: 10.1038/s41467-021-26646-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 09/27/2021] [Indexed: 12/30/2022] Open
Abstract
High-affinity MHC I-peptide interactions are considered essential for immunogenicity. However, some neo-epitopes with low affinity for MHC I have been reported to elicit CD8 T cell dependent tumor rejection in immunization-challenge studies. Here we show in a mouse model that a neo-epitope that poorly binds to MHC I is able to enhance the immunogenicity of a tumor in the absence of immunization. Fibrosarcoma cells with a naturally occurring mutation are edited to their wild type counterpart; the mutation is then re-introduced in order to obtain a cell line that is genetically identical to the wild type except for the neo-epitope-encoding mutation. Upon transplantation into syngeneic mice, all three cell lines form tumors that are infiltrated with activated T cells. However, lymphocytes from the two tumors that harbor the mutation show significantly stronger transcriptional signatures of cytotoxicity and TCR engagement, and induce greater breadth of TCR reactivity than those of the wild type tumors. Structural modeling of the neo-epitope peptide/MHC I pairs suggests increased hydrophobicity of the neo-epitope surface, consistent with higher TCR reactivity. These results confirm the in vivo immunogenicity of low affinity or ‘non-binding’ epitopes that do not follow the canonical concept of MHC I-peptide recognition. The immunogenicity of peptides is believed to be determined by their high-affinity binding to MHC I. Here authors show that low-affinity MHC I-peptide interactions are also able to trigger robust T cell response and anti-tumour immunity in vivo.
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Affiliation(s)
- Hakimeh Ebrahimi-Nik
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA.,Broad Institute of MIT and Harvard, 105 Broadway, Cambridge, MA, USA
| | - Marmar Moussa
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Ryan P Englander
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Summit Singhaviranon
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Justine Michaux
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - HuiSong Pak
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - Hiroko Miyadera
- Department of Medical Genetics, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
| | - William L Corwin
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA.,Arvinas, 5 science park, 395 Winchester Ave, New Haven, CT, USA
| | - Grant L J Keller
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Adam T Hagymasi
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Tatiana V Shcheglova
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - Brian M Baker
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Ion I Mandoiu
- Department of Computer Sciences, University of Connecticut School of Engineering, Storrs, CT, USA
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - Pramod K Srivastava
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA.
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Brennick CA, George MM, Moussa MM, Hagymasi AT, Seesi SA, Shcheglova TV, Englander RP, Keller GL, Balsbaugh JL, Baker BM, Schietinger A, Mandoiu II, Srivastava PK. An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection. J Clin Invest 2021; 131:142823. [PMID: 33320837 PMCID: PMC7843235 DOI: 10.1172/jci142823] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/04/2020] [Indexed: 01/01/2023] Open
Abstract
Identification of neoepitopes that are effective in cancer therapy is a major challenge in creating cancer vaccines. Here, using an entirely unbiased approach, we queried all possible neoepitopes in a mouse cancer model and asked which of those are effective in mediating tumor rejection and, independently, in eliciting a measurable CD8 response. This analysis uncovered a large trove of effective anticancer neoepitopes that have strikingly different properties from conventional epitopes and suggested an algorithm to predict them. It also revealed that our current methods of prediction discard the overwhelming majority of true anticancer neoepitopes. These results from a single mouse model were validated in another antigenically distinct mouse cancer model and are consistent with data reported in human studies. Structural modeling showed how the MHC I-presented neoepitopes had an altered conformation, higher stability, or increased exposure to T cell receptors as compared with the unmutated counterparts. T cells elicited by the active neoepitopes identified here demonstrated a stem-like early dysfunctional phenotype associated with effective responses against viruses and tumors of transgenic mice. These abundant anticancer neoepitopes, which have not been tested in human studies thus far, can be exploited for generation of personalized human cancer vaccines.
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Affiliation(s)
- Cory A Brennick
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Mariam M George
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Marmar M Moussa
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Adam T Hagymasi
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Sahar Al Seesi
- Computer Science Department, Smith College, Northampton, Massachusetts, USA
| | - Tatiana V Shcheglova
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Ryan P Englander
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Grant Lj Keller
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jeremy L Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources and Equipment, University of Connecticut, Storrs, Connecticut, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Ion I Mandoiu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, USA
| | - Pramod K Srivastava
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
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George MM, Brennick CA, Moussa MM, Hagymasi AT, Seesi SA, Shcheglova TV, Englander RP, Keller GL, Balsbaugh JL, Baker BM, Mandoiu II, Srivastava PK. Unbiased analysis of all possible neoepitopes of MC38-FABF tumor reveals a new universe of cancer neoepitopes with unexpected properties. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.239.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Cancer neoepitopes are the only truly tumor-specific antigens and therefore, the most suitable as cancer vaccines. Current methods to predict neoepitopes, based on studies of viral epitopes, emphasize high affinity MHC-peptide interactions. Increasing evidence in human and murine models indicates that the present neoepitope prediction methods are mostly inaccurate in predicting true MHC I-restricted cancer neoepitopes. Here, in a completely unbiased approach, all possible neoepitopes in a mouse tumor model were tested for their ability to mediate tumor rejection and also CD8+ T cell responses. These studies show that the true tumor rejecting neoepitopes have different properties from those of viral epitopes. Further, CD8+ T cell responses elicited by these neoepitopes possess a more plastic chromatin phenotype with stem-like properties that is known to be associated with anti-viral and anti-tumor immune responses. Such cancer neoepitopes can be exploited for generation of personalized cancer vaccines.
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Affiliation(s)
| | | | - Marmar M Moussa
- 1University of Connecticut, Health Center
- 2Department of Computer Sciences, University of Connecticut
| | | | | | | | | | | | | | | | - Ion I. Mandoiu
- 2Department of Computer Sciences, University of Connecticut
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