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      Novel and shared neoantigen derived from histone 3 variant H3.3K27M mutation for glioma T cell therapy

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          Abstract

          Chheda et al. have identified an HLA-A2–restricted CD8 + T cell epitope encompassing the H3.3K27M mutation and a corresponding TCR that specifically recognizes the H3.3K27M epitope in glioma cells. These data establish a preclinical basis for T cell–based therapy for HLA-A2 + patients with H3.3K27M + glioma.

          Abstract

          The median overall survival for children with diffuse intrinsic pontine glioma (DIPG) is less than one year. The majority of diffuse midline gliomas, including more than 70% of DIPGs, harbor an amino acid substitution from lysine (K) to methionine (M) at position 27 of histone 3 variant 3 (H3.3). From a CD8 + T cell clone established by stimulation of HLA-A2 + CD8 + T cells with synthetic peptide encompassing the H3.3K27M mutation, complementary DNA for T cell receptor (TCR) α- and β-chains were cloned into a retroviral vector. TCR-transduced HLA-A2 + T cells efficiently killed HLA-A2 +H3.3K27M + glioma cells in an antigen- and HLA-specific manner. Adoptive transfer of TCR-transduced T cells significantly suppressed the progression of glioma xenografts in mice. Alanine-scanning assays suggested the absence of known human proteins sharing the key amino acid residues required for recognition by the TCR, suggesting that the TCR could be safely used in patients. These data provide us with a strong basis for developing T cell–based therapy targeting this shared neoepitope.

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          Most cited references37

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          Immunogenicity of somatic mutations in human gastrointestinal cancers.

          It is unknown whether the human immune system frequently mounts a T cell response against mutations expressed by common epithelial cancers. Using a next-generation sequencing approach combined with high-throughput immunologic screening, we demonstrated that tumor-infiltrating lymphocytes (TILs) from 9 out of 10 patients with metastatic gastrointestinal cancers contained CD4(+) and/or CD8(+) T cells that recognized one to three neo-epitopes derived from somatic mutations expressed by the patient's own tumor. There were no immunogenic epitopes shared between these patients. However, we identified in one patient a human leukocyte antigen-C*08:02-restricted T cell receptor from CD8(+) TILs that targeted the KRAS(G12D) hotspot driver mutation found in many human cancers. Thus, a high frequency of patients with common gastrointestinal cancers harbor immunogenic mutations that can potentially be exploited for the development of highly personalized immunotherapies.
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            Identification of a Titin-derived HLA-A1-presented peptide as a cross-reactive target for engineered MAGE A3-directed T cells.

            MAGE A3, which belongs to the family of cancer-testis antigens, is an attractive target for adoptive therapy given its reactivation in various tumors and limited expression in normal tissues. We developed an affinity-enhanced T cell receptor (TCR) directed to a human leukocyte antigen (HLA)-A*01-restricted MAGE A3 antigen (EVDPIGHLY) for use in adoptive therapy. Extensive preclinical investigations revealed no off-target antigen recognition concerns; nonetheless, administration to patients of T cells expressing the affinity-enhanced MAGE A3 TCR resulted in a serious adverse event (SAE) and fatal toxicity against cardiac tissue. We present a description of the preclinical in vitro functional analysis of the MAGE A3 TCR, which failed to reveal any evidence of off-target activity, and a full analysis of the post-SAE in vitro investigations, which reveal cross-recognition of an off-target peptide. Using an amino acid scanning approach, a peptide from the muscle protein Titin (ESDPIVAQY) was identified as an alternative target for the MAGE A3 TCR and the most likely cause of in vivo toxicity. These results demonstrate that affinity-enhanced TCRs have considerable effector functions in vivo and highlight the potential safety concerns for TCR-engineered T cells. Strategies such as peptide scanning and the use of more complex cell cultures are recommended in preclinical studies to mitigate the risk of off-target toxicity in future clinical investigations.
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              Deconstructing the peptide-MHC specificity of T cell recognition.

              In order to survey a universe of major histocompatibility complex (MHC)-presented peptide antigens whose numbers greatly exceed the diversity of the T cell repertoire, T cell receptors (TCRs) are thought to be cross-reactive. However, the nature and extent of TCR cross-reactivity has not been conclusively measured experimentally. We developed a system to identify MHC-presented peptide ligands by combining TCR selection of highly diverse yeast-displayed peptide-MHC libraries with deep sequencing. Although we identified hundreds of peptides reactive with each of five different mouse and human TCRs, the selected peptides possessed TCR recognition motifs that bore a close resemblance to their known antigens. This structural conservation of the TCR interaction surface allowed us to exploit deep-sequencing information to computationally identify activating microbial and self-ligands for human autoimmune TCRs. The mechanistic basis of TCR cross-reactivity described here enables effective surveillance of diverse self and foreign antigens without necessitating degenerate recognition of nonhomologous peptides. Copyright © 2014 Elsevier Inc. All rights reserved.
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                Author and article information

                Journal
                J Exp Med
                J. Exp. Med
                jem
                jem
                The Journal of Experimental Medicine
                The Rockefeller University Press
                0022-1007
                1540-9538
                02 January 2018
                : 215
                : 1
                : 141-157
                Affiliations
                [1 ]Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA
                [2 ]Department of Surgery, Immunogenetics and Transplantation Laboratory, University of California, San Francisco, San Francisco, CA
                [3 ]Cancer Immunotherapy Program, University of California, San Francisco, San Francisco, CA
                [4 ]Center for Infectious Disease, Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA
                [5 ]Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
                [6 ]Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA
                [7 ]Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
                [8 ]Department of Structural Biology, Stanford University School of Medicine, Stanford, CA
                [9 ]Department of Public Health, University of California, Berkeley, Berkeley, CA
                [10 ]Department of Neurosurgery, University of Pittsburgh School of Medicine, Pittsburgh, PA
                [11 ]Institut de Recerca Sant Joan de Deu, Barcelona, Spain
                [12 ]The Parker Institute for Cancer Immunotherapy, San Francisco, CA
                Author notes
                Correspondence to Hideho Okada: hideho.okada@ 123456ucsf.edu
                [*]

                Z.S. Chheda and G. Kohanbash contributed equally to this paper.

                Author information
                http://orcid.org/0000-0002-3953-8022
                http://orcid.org/0000-0002-7310-3890
                http://orcid.org/0000-0002-4799-9056
                http://orcid.org/0000-0003-2587-2617
                http://orcid.org/0000-0001-5780-3830
                http://orcid.org/0000-0003-1765-357X
                http://orcid.org/0000-0001-8821-7877
                http://orcid.org/0000-0002-8485-426X
                http://orcid.org/0000-0003-0076-9920
                Article
                20171046
                10.1084/jem.20171046
                5748856
                29203539
                ef748252-f579-4365-a958-ecd30cf911cc
                © 2018 Chheda et al.

                This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/).

                History
                : 08 June 2017
                : 01 October 2017
                : 23 October 2017
                Funding
                Funded by: NIH, DOI https://doi.org/10.13039/100000002;
                Funded by: National Institute of Neurological Disorders and Stroke, DOI https://doi.org/10.13039/100000065;
                Award ID: R01NS096954
                Funded by: NIH, DOI https://doi.org/10.13039/100000002;
                Funded by: NINDS, DOI https://doi.org/10.13039/100000065;
                Award ID: 2R01NS055140
                Funded by: National Center for Advancing Translational Sciences, DOI https://doi.org/10.13039/100006108;
                Funded by: NIH, DOI https://doi.org/10.13039/100000002;
                Funded by: University of California, San Francisco, DOI https://doi.org/10.13039/100008069;
                Funded by: Clinical & Translational Science Institute
                Funded by: V Foundation for Cancer Research, DOI https://doi.org/10.13039/100001368;
                Award ID: D2015-018
                Funded by: Parker Institute for Cancer Immunotherapy
                Funded by: NIH, DOI https://doi.org/10.13039/100000002;
                Funded by: National Cancer Institute, DOI https://doi.org/10.13039/100000054;
                Award ID: 1T32CA151022
                Funded by: Fondo Alicia Pueyo
                Award ID: CP13/00189
                Funded by: Instituto de Salud Carlos III, DOI https://doi.org/10.13039/501100004587;
                Funded by: Fondo Europeo de Desarrollo Regional, DOI https://doi.org/10.13039/501100008530;
                Award ID: PI15/01161
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                Medicine
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