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      MHC-II neoantigens shape tumor immunity and response to immunotherapy

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          Abstract

          The ability of the immune system to eliminate and shape the immunogenicity of tumors defines the process of cancer immunoediting 1 . Immunotherapies such as those that target immune checkpoint molecules can be used to augment immune-mediated elimination of tumors and have resulted in durable responses in cancer patients that did not respond to previous treatments. However, only a subset of patients benefit from immunotherapy and more knowledge about what is required for successful treatment is needed 24 . While the role of tumor neoantigen-specific CD8 + T cells in tumor rejection is well established 59 , the roles played by other T cell subsets have received less attention. Here we show spontaneous and immunotherapy-induced anti-tumor responses require the activity of both tumor antigen specific CD8 + and CD4 + T cells, even in tumors that do not express MHC class II. Additionally, tumor cell expression of MHC class II-restricted antigens is required at the site of successful rejection, indicating that CD4 + T cell activation must also occur in the tumor microenvironment. These findings suggest that MHC class II-restricted neoantigens have a key function in the anti-tumor response that is nonoverlapping with that of MHC class I-restricted neoantigens and therefore need to be considered when identifying patients who will most benefit from immunotherapy.

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          Most cited references19

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          NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data.

          Cytotoxic T cells are of central importance in the immune system's response to disease. They recognize defective cells by binding to peptides presented on the cell surface by MHC class I molecules. Peptide binding to MHC molecules is the single most selective step in the Ag-presentation pathway. Therefore, in the quest for T cell epitopes, the prediction of peptide binding to MHC molecules has attracted widespread attention. In the past, predictors of peptide-MHC interactions have primarily been trained on binding affinity data. Recently, an increasing number of MHC-presented peptides identified by mass spectrometry have been reported containing information about peptide-processing steps in the presentation pathway and the length distribution of naturally presented peptides. In this article, we present NetMHCpan-4.0, a method trained on binding affinity and eluted ligand data leveraging the information from both data types. Large-scale benchmarking of the method demonstrates an increase in predictive performance compared with state-of-the-art methods when it comes to identification of naturally processed ligands, cancer neoantigens, and T cell epitopes.
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            CD4+ T-cell help in the tumor milieu is required for recruitment and cytolytic function of CD8+ T lymphocytes.

            CD4 help for CD8(+) T lymphocytes prevents tolerance and promotes the survival of effector and memory CD8(+) T cells. Here, we describe additional helper functions that require CD4(+) T cells within the tumor environment. CD8(+) T-cell recruitment, proliferation, and effector function within the tumor were greatly enhanced by tumor-specific CD4(+) T cells. Recruitment of CD8(+) T cells was accelerated by IFN-γ-dependent production of chemokines. Production of interleukin-2 by tumor resident CD4(+) T cells enhanced CD8(+) T-cell proliferation and upregulated expression of granzyme B. These results highlight a novel role for tumor-specific CD4(+) T cells in promoting CD8(+) T-cell recruitment and cytolytic function, two previously unappreciated aspects of tumor-specific CD4 help. ©2010 AACR.
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              Induction of a CD8+ Cytotoxic T Lymphocyte Response by Cross-priming Requires Cognate CD4+ T Cell Help

              Class I–restricted presentation is usually associated with cytoplasmic degradation of cellular proteins and is often considered inaccessible to exogenous antigens. Nonetheless, certain exogenous elements can gain entry into this so-called endogenous pathway by a mechanism termed cross-presentation. This is known to be effective for class I–restricted cytotoxic T lymphocyte (CTL) cross-priming directed against a variety of exogenous tumor, viral, and minor transplantation antigens. The related effect of cross-tolerance can also effectively eliminate responses to selected self components. In both cases, this presentation appears to require the active involvement of a bone marrow–derived antigen presenting cell (APC). Here, we show that CTL induction by cross-priming with cell-associated ovalbumin requires the active involvement of CD4+ helper T cells. Importantly, this CD4+ population is only effective when both the helper and CTL determinants are recognized on the same APC. Moreover, we would argue that the cognitive nature of this event suggests that the CD4+ T cell actively modifies the APC, converting it into an effective stimulator for the successful priming of the CTL precursor.

                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                17 September 2019
                23 October 2019
                October 2019
                23 April 2020
                : 574
                : 7780
                : 696-701
                Affiliations
                [1 ]Department of Pathology and Immunology, Washington University School of Medicine
                [2 ]The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine
                [3 ]Division of Oncology, Department of Medicine, Washington University School of Medicine
                [4 ]Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute
                [5 ]David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology
                [6 ]Howard Hughes Medical Institute, Massachusetts Institute of Technology
                Author notes
                [#]

                Current address: Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.

                [* ]Correspondence and requests for materials should be addressed to rdschreiber@ 123456wustl.edu .

                AUTHOR CONTRIBUTIONS

                E.A. conceived and designed the experiments, collected the data, performed and interpreted the analyses, and wrote the manuscript. D.M.L and A.P.M planned experiments, and collected and analyzed data. I.K. conceived of and designed the hmMHC algorithm and performed analyses using it, and wrote the methodological description found in this manuscript. M.D. generated the KP9025 sarcoma cell line. A.M.L provided technical assistance and helped plan experiments using MHC class II tetramers. W.M. and C.F.L. planned, performed and analyzed mass spectrometry experiments. E.E. assisted with bioinformatics analyses. A.N.V. assisted with the generation of the CD4 + T cell hybridomas, and helped design and perform experiments using them. D.R. designed, collected, and analyzed data for experiments involving multi-color flow cytometry. J.P.W. provided technical support for MHC class I tetramer staining. M.M.G assisted in experiment planning. R.F.V.M. collected and analyzed data for experiments involving multi-color flow cytometry. C.D.A., K.C.F.S. and J.M.W. provided technical assistance throughout the study. A.C. collected data. K.W.W. provided mITGB1-MHC class II monomers and provided assistance in experimental design. T.J. provided support in experimental design and data analysis regarding the KP9025 sarcoma line. M.N.A. conceived and designed the hmMHC algorithm and provided bioinformatics support. E.R.U. provided assistance in experimental design. R.D.S. conceived experiments, interpreted data, and wrote the manuscript. All authors contributed to manuscript revision.

                R.D.S. is a cofounder, scientific advisory board member, stockholder, and royalty recipient of Jounce Therapeutics and Neon Therapeutics and is a scientific advisory board member for A2 Biotherapeutics, BioLegend, Codiak Biosciences, Constellation Pharmaceuticals, NGM Biopharmaceuticals and Sensei Biotherapeutics. K.W.W. serves on the scientific advisory board of Tscan Therapeutics and Nextechinvest and receives sponsored research funding from Bristol-Myers Squibb and Novartis; these activities are not related to the findings described in this publication. T.J. is a member of the Board of Directors of Amgen and Thermo Fisher Scientific. He is also a co-Founder of Dragonfly Therapeutics and T2 Biosystems. T.J. serves on the Scientific Advisory Board of Dragonfly Therapeutics, SQZ Biotech, and Skyhawk Therapeutics. None of these affiliations represent a conflict of interest with respect to the design or execution of this study or interpretation of data presented in this manuscript. Dr. Jacks’s laboratory currently also receives funding from the Johnson & Johnson Lung Cancer Initiative and Calico, but this funding did not support the research described in this manuscript.

                Article
                NIHMS1539806
                10.1038/s41586-019-1671-8
                6858572
                31645760
                1f16130f-8606-46d5-90cb-608b3a2957c3

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