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Wu Y, Liang X, Sun Y, Ning J, Dai Y, Jin S, Xu Y, Chen S, Pan L. A general pHLA-CD80 scaffold fusion protein to promote efficient antigen-specific T cell-based immunotherapy. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200827. [PMID: 39027379 PMCID: PMC11255371 DOI: 10.1016/j.omton.2024.200827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/23/2024] [Accepted: 06/07/2024] [Indexed: 07/20/2024]
Abstract
Inadequate antigen-specific T cells activation hampers immunotherapy due to complex antigen presentation. In addition, therapeutic in vivo T cell expansion is constrained by slow expansion rates and limited functionality. Herein, we introduce a model fusion protein termed antigen-presenting cell-mimic fusion protein (APC-mimic), designed to greatly mimicking the natural antigen presentation pattern of antigen-presenting cells and directly expand T cells both in vitro and in vivo. The APC-mimic comprises the cognate peptide-human leukocyte antigen (pHLA) complex and the co-stimulatory marker CD80, which are natural ligands on APCs. Following a single stimulation, APC-mimic leads to an approximately 400-fold increase in the polyclonal expansion of antigen-specific T cells compared with the untreated group in vitro without the requirement for specialized antigen-presenting cells. Through the combination of single-cell TCR sequencing (scTCR-seq) and single-cell RNA sequencing (scRNA-seq), we identify an approximately 600-fold monoclonal expansion clonotype among these polyclonal clonotypes. It also exhibits suitability for in vivo applications confirmed in the OT-1 mouse model. Furthermore, T cells expanded by APC-mimic effectively inhibits tumor growth in adoptive cell transfer (ACT) murine models. These findings pave the way for the versatile APC-mimic platform for personalized therapeutics, enabling direct expansion of polyfunctional antigen-specific T cell subsets in vitro and in vivo.
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Affiliation(s)
- Yue Wu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiao Liang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanping Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiangtao Ning
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yukun Dai
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shijie Jin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingchun Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuqing Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Precision Medicine on Tumor Therapeutics, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Liqiang Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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2
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Santamorena MM, Tischer-Zimmermann S, Bonifacius A, Mireisz CNM, Costa B, Khan F, Kulkarni U, Lauruschkat CD, Sampaio KL, Stripecke R, Blasczyk R, Maecker-Kolhoff B, Kraus S, Schlosser A, Cicin-Sain L, Kalinke U, Eiz-Vesper B. Engineered HCMV-infected APCs enable the identification of new immunodominant HLA-restricted epitopes of anti-HCMV T-cell immunity. HLA 2024; 103:e15541. [PMID: 38923358 DOI: 10.1111/tan.15541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 06/28/2024]
Abstract
Complications due to HCMV infection or reactivation remain a challenging clinical problem in immunocompromised patients, mainly due to insufficient or absent T-cell functionality. Knowledge of viral targets is crucial to improve monitoring of high-risk patients and optimise antiviral T-cell therapy. To expand the epitope spectrum, genetically-engineered dendritic cells (DCs) and fibroblasts were designed to secrete soluble (s)HLA-A*11:01 and infected with an HCMV mutant lacking immune evasion molecules (US2-6 + 11). More than 700 HLA-A*11:01-restricted epitopes, including more than 50 epitopes derived from a broad range of HCMV open-reading-frames (ORFs) were identified by mass spectrometry and screened for HLA-A*11:01-binding using established prediction tools. The immunogenicity of the 24 highest scoring new candidates was evaluated in vitro in healthy HLA-A*11:01+/HCMV+ donors. Thus, four subdominant epitopes and one immunodominant epitope, derived from the anti-apoptotic protein UL36 and ORFL101C (A11SAL), were identified. Their HLA-A*11:01 complex stability was verified in vitro. In depth analyses revealed highly proliferative and cytotoxic memory T-cell responses against A11SAL, with T-cell responses comparable to the immunodominant HLA-A*02:01-restricted HCMVpp65NLV epitope. A11SAL-specific T cells were also detectable in vivo in immunosuppressed transplant patients and shown to be effective in an in vitro HCMV-infection model, suggesting their crucial role in inhibiting viral replication and improvement of patient's outcome. The developed in vitro pipeline is the first to utilise genetically-engineered DCs to identify naturally presented immunodominant HCMV-derived epitopes. It therefore offers advantages over in silico predictions, is transferable to other HLA alleles, and will significantly expand the repertoire of viral targets to improve therapeutic options.
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Affiliation(s)
- Maria Michela Santamorena
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School (MHH), Hannover, Germany
| | - Sabine Tischer-Zimmermann
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School (MHH), Hannover, Germany
| | - Agnes Bonifacius
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School (MHH), Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
| | - Chiara Noemi-Marie Mireisz
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg, Germany
| | - Bibiana Costa
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Fawad Khan
- Immune Ageing and Chronic Infection, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Upasana Kulkarni
- Immune Ageing and Chronic Infection, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | | | - Renata Stripecke
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf, Center for Molecular Medicine Cologne (CMMC), Institute of Translational Immuno-oncology, Cologne, Germany
- German Center for Infections Research (DZIF) Bonn-Cologne, Cologne, Germany
| | - Rainer Blasczyk
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School (MHH), Hannover, Germany
| | - Britta Maecker-Kolhoff
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
- German Center for Infections Research (DZIF) Bonn-Cologne, Cologne, Germany
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Sabrina Kraus
- Department of Internal Medicine II, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Wuerzburg, Wuerzburg, Germany
| | - Luka Cicin-Sain
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
- Immune Ageing and Chronic Infection, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Cluster of Excellence - Resolving Infection Susceptibility (RESIST, EXC 2155), Hannover Medical School, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany
- Cluster of Excellence - Resolving Infection Susceptibility (RESIST, EXC 2155), Hannover Medical School, Hannover, Germany
| | - Britta Eiz-Vesper
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School (MHH), Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover-Braunschweig, Hannover, Germany
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3
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Kouro T, Higashijima N, Horaguchi S, Mano Y, Kasajima R, Xiang H, Fujimoto Y, Kishi H, Hamana H, Hoshino D, Himuro H, Matsuura R, Tsuji S, Imai K, Sasada T. Novel chimeric antigen receptor-expressing T cells targeting the malignant mesothelioma-specific antigen sialylated HEG1. Int J Cancer 2024; 154:1828-1841. [PMID: 38212893 DOI: 10.1002/ijc.34843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/13/2024]
Abstract
The selection of highly specific target antigens is critical for the development of clinically efficient and safe chimeric antigen receptors (CARs). In search of diagnostic marker for malignant mesothelioma (MM), we have established SKM9-2 monoclonal antibody (mAb) which recognizes a MM-specific molecule, sialylated Protein HEG homolog 1 (HEG1), with high specificity and sensitivity. In this study, to develop a novel therapeutic approach against MM, we generated SKM9-2 mAb-derived CARs that included the CD28 (SKM-28z) or 4-1BB (SKM-BBz) costimulatory domain. SKM-28z CAR-T cells showed continuous growth and enhanced Tim-3, LAG-3, and PD-1 expression in vitro, which might be induced by tonic signaling caused by self-activation; however, these phenotypes were not observed in SKM-BBz CAR-T cells. In addition, SKM-BBz CAR-T cells exhibited slightly stronger in vitro killing activity against MM cell lines than SKM-28z CAR-T cells. More importantly, only SKM-BBz CAR-T cells, but not SKM-28z CAR-T cells, significantly inhibited tumor growth in vivo in a MM cell line xenograft mouse model. Gene expression profiling and reporter assays revealed differential signaling pathway activation; in particular, SKM-BBz CAR-T cells exhibited enhanced NF-kB signaling and reduced NFAT activation. In addition, SKM-BBz CAR-T cells showed upregulation of early memory markers, such as TCF7 and CCR7, as well as downregulation of pro-apoptotic proteins, such as BAK1 and BID, which may be associated with phenotypical and functional differences between SKM-BBz and SKM-28z CAR-T cells. In conclusion, we developed novel SKM9-2-derived CAR-T cells with the 4-1BB costimulatory domain, which could provide a promising therapeutic approach against refractory MM.
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Affiliation(s)
- Taku Kouro
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Naoko Higashijima
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Shun Horaguchi
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
- Department of Pediatric Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Yasunobu Mano
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Rika Kasajima
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Huihui Xiang
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Yuki Fujimoto
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Hiroshi Hamana
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Daisuke Hoshino
- Cancer Biology Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Hidetomo Himuro
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
| | - Rieko Matsuura
- Division of Cancer Therapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Shoutaro Tsuji
- Division of Cancer Therapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Department of Medical Technology & Clinical Engineering, Gunma University of Health and Welfare, Maebashi, Japan
| | - Kohzoh Imai
- Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Tetsuro Sasada
- Division of Cancer Immunotherapy, Kanagawa Cancer Center Research Institute, Yokohama, Japan
- Cancer Vaccine and Immunotherapy Center, Kanagawa Cancer Center, Yokohama, Japan
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4
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Jin Y, Miyama T, Brown A, Hayase T, Song X, Singh AK, Huang L, Flores II, McDaniel LK, Glover I, Halsey TM, Prasad R, Chapa V, Ahmed S, Zhang J, Rai K, Peterson CB, Lizee G, Karmouch J, Hayase E, Molldrem JJ, Chang CC, Tsai WB, Jenq RR. Tsyn-Seq: a T-cell Synapse-Based Antigen Identification Platform. Cancer Immunol Res 2024; 12:530-543. [PMID: 38363296 PMCID: PMC11065584 DOI: 10.1158/2326-6066.cir-23-0467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/02/2023] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Tools for genome-wide rapid identification of peptide-major histocompatibility complex targets of T-cell receptors (TCR) are not yet universally available. We present a new antigen screening method, the T-synapse (Tsyn) reporter system, which includes antigen-presenting cells (APC) with a Fas-inducible NF-κB reporter and T cells with a nuclear factor of activated T cells (NFAT) reporter. To functionally screen for target antigens from a cDNA library, productively interacting T cell-APC aggregates were detected by dual-reporter activity and enriched by flow sorting followed by antigen identification quantified by deep sequencing (Tsyn-seq). When applied to a previously characterized TCR specific for the E7 antigen derived from human papillomavirus type 16 (HPV16), Tsyn-seq successfully enriched the correct cognate antigen from a cDNA library derived from an HPV16-positive cervical cancer cell line. Tsyn-seq provides a method for rapidly identifying antigens recognized by TCRs of interest from a tumor cDNA library. See related Spotlight by Makani and Joglekar, p. 515.
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Affiliation(s)
- Yimei Jin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Takahiko Miyama
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Alexandria Brown
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Tomo Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Anand K. Singh
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Licai Huang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ivonne I. Flores
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Lauren K. McDaniel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Israel Glover
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Taylor M. Halsey
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Rishika Prasad
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Valerie Chapa
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Saira Ahmed
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Gregory Lizee
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jennifer Karmouch
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Eiko Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Jeffrey J. Molldrem
- Department of Hematopoietic Biology & Malignancy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Wen-Bin Tsai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Robert R. Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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5
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Li D, Pavlovitch-Bedzyk AJ, Ebinger JE, Khan A, Hamideh M, Merchant A, Figueiredo JC, Cheng S, Davis MM, McGovern DPB, Melmed GY, Xu AM, Braun J. A Paratope-Enhanced Method to Determine Breadth and Depth TCR Clonal Metrics of the Private Human T-Cell Vaccine Response after SARS-CoV-2 Vaccination. Int J Mol Sci 2023; 24:14223. [PMID: 37762524 PMCID: PMC10531868 DOI: 10.3390/ijms241814223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Quantitative metrics for vaccine-induced T-cell responses are an important need for developing correlates of protection and their use in vaccine-based medical management and population health. Molecular TCR analysis is an appealing strategy but currently requires a targeted methodology involving complex integration of ex vivo data (antigen-specific functional T-cell cytokine responses and TCR molecular responses) that uncover only public antigen-specific metrics. Here, we describe an untargeted private TCR method that measures breadth and depth metrics of the T-cell response to vaccine challenge using a simple pre- and post-vaccine subject sampling, TCR immunoseq analysis, and a bioinformatic approach using self-organizing maps and GLIPH2. Among 515 subjects undergoing SARS-CoV-2 mRNA vaccination, we found that breadth and depth metrics were moderately correlated between the targeted public TCR response and untargeted private TCR response methods. The untargeted private TCR method was sufficiently sensitive to distinguish subgroups of potential clinical significance also observed using public TCR methods (the reduced T-cell vaccine response with age and the paradoxically elevated T-cell vaccine response of patients on anti-TNF immunotherapy). These observations suggest the promise of this untargeted private TCR method to produce T-cell vaccine-response metrics in an antigen-agnostic and individual-autonomous context.
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Affiliation(s)
- Dalin Li
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Ana Jimena Pavlovitch-Bedzyk
- Computational and Systems Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; (A.J.P.-B.); (M.M.D.)
| | - Joseph E. Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (J.E.E.); (S.C.)
| | - Abdul Khan
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Mohamed Hamideh
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Akil Merchant
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.M.); (J.C.F.); (A.M.X.)
| | - Jane C. Figueiredo
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.M.); (J.C.F.); (A.M.X.)
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (J.E.E.); (S.C.)
| | - Mark M. Davis
- Computational and Systems Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; (A.J.P.-B.); (M.M.D.)
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dermot P. B. McGovern
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Gil Y. Melmed
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
| | - Alexander M. Xu
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.M.); (J.C.F.); (A.M.X.)
| | - Jonathan Braun
- Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (D.L.); (A.K.); (M.H.); (D.P.B.M.); (G.Y.M.)
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6
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Xu AM, Chour W, DeLucia DC, Su Y, Pavlovitch-Bedzyk AJ, Ng R, Rasheed Y, Davis MM, Lee JK, Heath JR. Entropic analysis of antigen-specific CDR3 domains identifies essential binding motifs shared by CDR3s with different antigen specificities. Cell Syst 2023; 14:273-284.e5. [PMID: 37001518 PMCID: PMC10355346 DOI: 10.1016/j.cels.2023.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 09/01/2022] [Accepted: 03/01/2023] [Indexed: 04/22/2023]
Abstract
Antigen-specific T cell receptor (TCR) sequences can have prognostic, predictive, and therapeutic value, but decoding the specificity of TCR recognition remains challenging. Unlike DNA strands that base pair, TCRs bind to their targets with different orientations and different lengths, which complicates comparisons. We present scanning parametrized by normalized TCR length (SPAN-TCR) to analyze antigen-specific TCR CDR3 sequences and identify patterns driving TCR-pMHC specificity. Using entropic analysis, SPAN-TCR identifies 2-mer motifs that decrease the diversity (entropy) of CDR3s. These motifs are the most common patterns that can predict CDR3 composition, and we identify "essential" motifs that decrease entropy in the same CDR3 α or β chain containing the 2-mer, and "super-essential" motifs that decrease entropy in both chains. Molecular dynamics analysis further suggests that these motifs may play important roles in binding. We then employ SPAN-TCR to resolve similarities in TCR repertoires against different antigens using public databases of TCR sequences.
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Affiliation(s)
- Alexander M Xu
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | - William Chour
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 91125, USA
| | - Diana C DeLucia
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Rachel Ng
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Yusuf Rasheed
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Mark M Davis
- Computational and Systems Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John K Lee
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - James R Heath
- Institute for Systems Biology, Seattle, WA 98109, USA.
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7
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Features of repertoire diversity and gene expression in human cytotoxic T cells following allogeneic hematopoietic cell transplantation. Commun Biol 2021; 4:1177. [PMID: 34635773 PMCID: PMC8505416 DOI: 10.1038/s42003-021-02709-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 09/21/2021] [Indexed: 11/09/2022] Open
Abstract
Cytomegalovirus reactivation is still a critical concern following allogeneic hematopoietic cell transplantation, and cellular immune reconstitution of cytomegalovirus-specific cytotoxic T-cells is necessary for the long-term control of cytomegalovirus reactivation after allogeneic hematopoietic cell transplantation. Here we show the features of repertoire diversity and the gene expression profile of HLA-A24 cytomegalovirus-specific cytotoxic T-cells in actual recipients according to the cytomegalovirus reactivation pattern. A skewed preference for BV7 genes and sequential “G” amino acids motif is observed in complementarity-determining region-3 of T cell receptor-β. Increased binding scores are observed in T-cell clones with complementarity-determining region-3 of T cell receptor-β with a “(G)GG” motif. Single-cell RNA-sequence analyses demonstrate the homogenous distribution of the gene expression profile in individual cytomegalovirus-specific cytotoxic T-cells within each recipient. On the other hand, bulk RNA-sequence analyses reveal that gene expression profiles among patients are different according to the cytomegalovirus reactivation pattern, and are associated with cytokine production or cell division. These methods and results can help us to better understand immune reconstitution following hematopoietic cell transplantation, leading to future studies on the clinical application of adoptive T-cell therapies. Cytomegalovirus reactivation is an important concern after allogeneic stem cell transplantation (allo-HCT) or organ transplantation. Here, Hideki Nakasone et al. investigate changes in repertoire diversity and gene expression among clinically-transferred T cells to improve our understanding of immune reconstitution following allo-HCT.
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8
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Public and private human T-cell clones respond differentially to HCMV antigen when boosted by CD3 copotentiation. Blood Adv 2021; 4:5343-5356. [PMID: 33125463 DOI: 10.1182/bloodadvances.2020002255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/17/2020] [Indexed: 12/16/2022] Open
Abstract
Human cytomegalovirus (HCMV) induces long-lasting T-cell immune responses that control but do not clear infection. Typical responses involve private T-cell clones, expressing T-cell antigen receptors (TCRs) unique to a person, and public T-cell clones with identical TCRs active in different people. Here, we report the development of a pretherapeutic immunostimulation modality against HCMV for human T cells, CD3 copotentiation, and the clonal analysis of its effects in recall assays at single-cell resolution. CD3 copotentiation of human T cells required identification of an intrinsically inert anti-CD3 Fab fragment that conditionally augmented signaling only when TCR was coengaged with antigen. When applied in recall assays, CD3 copotentiation enhanced the expansion of both public and private T-cell clones responding to autologous HLA-A2(+) antigen-presenting cells and immunodominant NLVPMVATV (NLV) peptide from HCMV pp65 protein. Interestingly, public vs private TCR expression was associated with distinct clonal expansion signatures in response to recall stimulus. This implied that besides possible differences in their generation and selection in an immune response, public and private T cells may respond differently to pharmacoimmunomodulation. Furthermore, a third clonal expansion profile was observed upon CD3 copotentiation of T-cell clones from HLA-A2(-) donors and 1 HLA-A2(+) presumed-uninfected donor, where NLV was of low intrinsic potency. We conclude that human T-cell copotentiation can increase the expansion of different classes of T-cell clones responding to recall antigens of different strengths, and this may be exploitable for therapeutic development against chronic, persistent infections such as HCMV.
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9
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T-cell receptor repertoire of cytomegalovirus-specific cytotoxic T-cells after allogeneic stem cell transplantation. Sci Rep 2020; 10:22218. [PMID: 33335252 PMCID: PMC7747720 DOI: 10.1038/s41598-020-79363-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023] Open
Abstract
Cytomegalovirus (CMV) infection is a major complication during allogeneic stem cell transplantation (allo-SCT). However, mechanisms of adaptive immunity that drive this remain unclear. To define early immunological responses to CMV after transplantation, we using next-generation sequencing to examine the repertoire of T-cell receptors in CD8+/CMV pp65 tetramer+ cells (CMV-CTLs) in peripheral blood samples obtained from 16 allo-SCT recipients with HLA-A*24:02 at the time of CMV reactivation. In most patients, TCR beta repertoire of CMV-CTLs was highly skewed (median Inverse Simpson's index: 1.595) and, 15 of 16 patients shared at least one TCR-beta clonotype with ≥ 2 patients. The shared TCRs were dominant in 12 patients and, two clonotypes were shared by about half of the patients. Similarity analysis showed that CDR3 sequences of shared TCRs were more similar than unshared TCRs. TCR beta repertoires of CMV-CTLs in 12 patients were also analyzed after 2-4 weeks to characterize the short-term dynamics of TCR repertoires. In ten patients, we observed persistence of prevailing clones. In the other two patients, TCR repertoires became more diverse, major clones declined, and new private clones subsequently emerged. These results provided the substantive clue to understand the immunological behavior against CMV reactivation after allo-SCT.
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10
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Sukegawa K, Shitaoka K, Hamana H, Kobayashi E, Miyahara Y, Fujii K, Tsuda K, Saeki S, Nagata T, Ozawa T, Saito S, Fujii T, Muraguchi A, Shiku H, Kishi H. Relationship between T cell receptor clonotype and PD‐1 expression of tumor‐infiltrating lymphocytes in colorectal cancer. Eur J Immunol 2020; 50:1580-1590. [DOI: 10.1002/eji.201948399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Kenta Sukegawa
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
- Department of Surgery and Science, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Kiyomi Shitaoka
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Hiroshi Hamana
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Eiji Kobayashi
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Yoshihiro Miyahara
- Department of Personalized Cancer Immunotherapy Mie University Graduate School of Medicine Mie Japan
| | - Keisuke Fujii
- Department of Immuno‐Gene Therapy Mie University Graduate School of Medicine Mie Japan
| | - Kei Tsuda
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
- Department of Obstetrics and Gynecology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Shiori Saeki
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
- Department of Surgery and Science, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Takuya Nagata
- Department of Surgery and Science, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Tatsuhiko Ozawa
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Shigeru Saito
- Department of Obstetrics and Gynecology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Tsutomu Fujii
- Department of Surgery and Science, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Atsushi Muraguchi
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
| | - Hiroshi Shiku
- Department of Personalized Cancer Immunotherapy Mie University Graduate School of Medicine Mie Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly University of Toyama Toyama Japan
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11
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Kared H, Tan SW, Lau MC, Chevrier M, Tan C, How W, Wong G, Strickland M, Malleret B, Amoah A, Pilipow K, Zanon V, Govern NM, Lum J, Chen JM, Lee B, Florian MC, Geiger H, Ginhoux F, Ruiz-Mateos E, Fulop T, Rajasuriar R, Kamarulzaman A, Ng TP, Lugli E, Larbi A. Immunological history governs human stem cell memory CD4 heterogeneity via the Wnt signaling pathway. Nat Commun 2020; 11:821. [PMID: 32041953 PMCID: PMC7010798 DOI: 10.1038/s41467-020-14442-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 01/09/2020] [Indexed: 12/21/2022] Open
Abstract
The diversity of the naïve T cell repertoire drives the replenishment potential and capacity of memory T cells to respond to immune challenges. Attrition of the immune system is associated with an increased prevalence of pathologies in aged individuals, but whether stem cell memory T lymphocytes (TSCM) contribute to such attrition is still unclear. Using single cells RNA sequencing and high-dimensional flow cytometry, we demonstrate that TSCM heterogeneity results from differential engagement of Wnt signaling. In humans, aging is associated with the coupled loss of Wnt/β-catenin signature in CD4 TSCM and systemic increase in the levels of Dickkopf-related protein 1, a natural inhibitor of the Wnt/β-catenin pathway. Functional assays support recent thymic emigrants as the precursors of CD4 TSCM. Our data thus hint that reversing TSCM defects by metabolic targeting of the Wnt/β-catenin pathway may be a viable approach to restore and preserve immune homeostasis in the context of immunological history.
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Affiliation(s)
- Hassen Kared
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore.
| | - Shu Wen Tan
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
| | - Mai Chan Lau
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
| | - Marion Chevrier
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
| | - Crystal Tan
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
| | - Wilson How
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
| | - Glenn Wong
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
| | - Marie Strickland
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Benoit Malleret
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Amanda Amoah
- Institute of Molecular Medicine, University of Ulm, Ulm, Germany
| | - Karolina Pilipow
- Humanitas Clinical and Research Center, Laboratory of Translational Immunology (LTI), Rozzano, Italy
| | - Veronica Zanon
- Humanitas Clinical and Research Center, Laboratory of Translational Immunology (LTI), Rozzano, Italy
| | - Naomi Mc Govern
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
| | - Josephine Lum
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
| | - Jin Miao Chen
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
| | - Bernett Lee
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
| | | | - Hartmut Geiger
- Institute of Molecular Medicine, University of Ulm, Ulm, Germany
- Experimental Hematology and Cancer Biology, CCHMC, Cincinnati, OH, USA
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore
| | - Ezequiel Ruiz-Mateos
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville, Spain
| | - Tamas Fulop
- Department of Medicine, Faculty of Medicine, University of Sherbrooke, Sherbrooke, Quebec, Canada
| | - Reena Rajasuriar
- Centre of Excellence for Research in AIDS (CERiA), University of Malaya, Kuala Lumpur, Malaysia
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Centre of Excellence for Research in AIDS (CERiA), University of Malaya, Kuala Lumpur, Malaysia
- Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tze Pin Ng
- Gerontology Research Programme and Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Enrico Lugli
- Humanitas Clinical and Research Center, Laboratory of Translational Immunology (LTI), Rozzano, Italy
| | - Anis Larbi
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Immunos Building, 8A Biomedical Grove, Biopolis, Republic of Singapore.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore.
- Department of Medicine, Faculty of Medicine, University of Sherbrooke, Sherbrooke, Quebec, Canada.
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12
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High-throughput sequencing reveals the diversity of TCR β chain CDR3 repertoire in patients with severe acne. Mol Immunol 2020; 120:23-31. [PMID: 32045771 DOI: 10.1016/j.molimm.2020.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 01/16/2020] [Accepted: 01/31/2020] [Indexed: 02/08/2023]
Abstract
Acne is a common chronic inflammatory skin disease, and the inflammation immune response runs through all stages of acne lesions. In this study, we use a combination of multiplex-PCR and high-throughput sequencing technologies to analyze T cell receptor β chain CDR3 (complementarity-determining region 3) in peripheral blood isolated from severe acne patients. Once compared with healthy controls, we propose to identify acne-relevant CDR3 peptides. Our results reveal that the diversity of T cell receptor β chain (TRB) CDR3 sequences in the peripheral blood of the severe acne vulgaris (SA) group differed from that of the control group. In addition, we find 10 TRB CDR3 sequences, amino acid sequences and V-J combinations with significantly different expressions between the SA group and the non-acne (NA) group (P < 0.0001). These findings may contribute to a better understanding of the role of immunity in the pathogenesis of acne and may serve as biomarkers for evaluating risk or prognosis of severe acne disease in future.
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13
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Smith CJ, Venturi V, Quigley MF, Turula H, Gostick E, Ladell K, Hill BJ, Himelfarb D, Quinn KM, Greenaway HY, Dang THY, Seder RA, Douek DC, Hill AB, Davenport MP, Price DA, Snyder CM. Stochastic Expansions Maintain the Clonal Stability of CD8 + T Cell Populations Undergoing Memory Inflation Driven by Murine Cytomegalovirus. THE JOURNAL OF IMMUNOLOGY 2019; 204:112-121. [PMID: 31818981 PMCID: PMC6920548 DOI: 10.4049/jimmunol.1900455] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 10/16/2019] [Indexed: 11/19/2022]
Abstract
Clonal stability is a feature of memory inflation. Stochastic expansions maintain clonal stability during memory inflation. Persistent clonotypes are often public in the context of memory inflation.
CMV is an obligate and persistent intracellular pathogen that continually drives the production of highly differentiated virus-specific CD8+ T cells in an Ag-dependent manner, a phenomenon known as memory inflation. Extensive proliferation is required to generate and maintain inflationary CD8+ T cell populations, which are counterintuitively short-lived and typically exposed to limited amounts of Ag during the chronic phase of infection. An apparent discrepancy therefore exists between the magnitude of expansion and the requirement for ongoing immunogenic stimulation. To address this issue, we explored the clonal dynamics of memory inflation. First, we tracked congenically marked OT-I cell populations in recipient mice infected with murine CMV (MCMV) expressing the cognate Ag OVA. Irrespective of numerical dominance, stochastic expansions were observed in each population, such that dominant and subdominant OT-I cells were maintained at stable frequencies over time. Second, we characterized endogenous CD8+ T cell populations specific for two classic inflationary epitopes, M38 and IE3. Multiple clonotypes simultaneously underwent Ag-driven proliferation during latent infection with MCMV. In addition, the corresponding CD8+ T cell repertoires were stable over time and dominated by persistent clonotypes, many of which also occurred in more than one mouse. Collectively, these data suggest that stochastic encounters with Ag occur frequently enough to maintain oligoclonal populations of inflationary CD8+ T cells, despite intrinsic constraints on epitope display at individual sites of infection with MCMV.
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Affiliation(s)
- Corinne J Smith
- Department of Microbiology and Immunology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107
| | - Vanessa Venturi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Maire F Quigley
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Holly Turula
- Department of Microbiology and Immunology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107
| | - Emma Gostick
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, United Kingdom
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, United Kingdom
| | - Brenna J Hill
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Danielle Himelfarb
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Kylie M Quinn
- Cellular Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Hui Yee Greenaway
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Thurston H Y Dang
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Robert A Seder
- Cellular Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Ann B Hill
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR 97239
| | - Miles P Davenport
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - David A Price
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; .,Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, United Kingdom
| | - Christopher M Snyder
- Department of Microbiology and Immunology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107;
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14
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Meier JA, Haque M, Fawaz M, Abdeen H, Coffey D, Towlerton A, Abdeen A, Toor A, Warren E, Reed J, Kanakry CG, Keating A, Luznik L, Toor AA. T Cell Repertoire Evolution after Allogeneic Bone Marrow Transplantation: An Organizational Perspective. Biol Blood Marrow Transplant 2019; 25:868-882. [PMID: 30677510 DOI: 10.1016/j.bbmt.2019.01.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/11/2019] [Indexed: 12/31/2022]
Abstract
High-throughput sequencing (HTS) of human T cell receptors has revealed a high level of complexity in the T cell repertoire, which makes it difficult to correlate T cell reconstitution with clinical outcomes. The associations identified thus far are of a broadly statistical nature, precluding precise modeling of outcomes based on T cell repertoire development following bone marrow transplantation (BMT). Previous work has demonstrated an inherent, mathematically definable order observed in the T cells from a diverse group of donors, which is perturbed in recipients following BMT. In this study, T cell receptor (TCR)-β sequences from HLA-matched related donor and recipient pairs are analyzed to further develop this methodology. TCR-β sequencing from unsorted and sorted T cell subsets isolated from the peripheral blood samples of BMT donors and recipients show conservation and symmetry of VJ segment usage in the clonal frequencies, linked to the organization of the gene segments along the TCR locus. This TCR-β VJ segment translational symmetry is preserved post-transplantation and even in cases of acute graft-versus-host disease (aGVHD), suggesting that GVHD occurrence represents a polyclonal donor T cell response to recipient antigens. The complexity of the repertoire is significantly diminished after BMT, and the T cell clonal hierarchy is altered post-transplantation. Low-frequency donor clones tended to take on a higher rank in the recipients following BMT, especially in patients with aGVHD. Over time, the repertoire evolves to a more donor-like state in the recipients who did not develop GVHD as opposed to those who did. The results presented here support new methods of quantifying and characterizing post-transplantation T cell repertoire reconstitution.
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Affiliation(s)
- Jeremy A Meier
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Mahdee Haque
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Mohamed Fawaz
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Hamdi Abdeen
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - David Coffey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Andrea Towlerton
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ahmed Abdeen
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Abdullah Toor
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia
| | - Edus Warren
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jason Reed
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia
| | - Christopher G Kanakry
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Armand Keating
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Leo Luznik
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Amir A Toor
- Bone Marrow Transplant Program, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia.
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15
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Keskin DB, Anandappa AJ, Sun J, Tirosh I, Mathewson ND, Li S, Oliveira G, Giobbie-Hurder A, Felt K, Gjini E, Shukla SA, Hu Z, Li L, Le PM, Allesøe RL, Richman AR, Kowalczyk MS, Abdelrahman S, Geduldig JE, Charbonneau S, Pelton K, Iorgulescu JB, Elagina L, Zhang W, Olive O, McCluskey C, Olsen LR, Stevens J, Lane WJ, Salazar AM, Daley H, Wen PY, Chiocca EA, Harden M, Lennon NJ, Gabriel S, Getz G, Lander ES, Regev A, Ritz J, Neuberg D, Rodig SJ, Ligon KL, Suvà ML, Wucherpfennig KW, Hacohen N, Fritsch EF, Livak KJ, Ott PA, Wu CJ, Reardon DA. Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial. Nature 2019; 565:234-239. [PMID: 30568305 PMCID: PMC6546179 DOI: 10.1038/s41586-018-0792-9] [Citation(s) in RCA: 847] [Impact Index Per Article: 169.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 10/01/2018] [Indexed: 12/14/2022]
Abstract
Neoantigens, which are derived from tumour-specific protein-coding mutations, are exempt from central tolerance, can generate robust immune responses1,2 and can function as bona fide antigens that facilitate tumour rejection3. Here we demonstrate that a strategy that uses multi-epitope, personalized neoantigen vaccination, which has previously been tested in patients with high-risk melanoma4-6, is feasible for tumours such as glioblastoma, which typically have a relatively low mutation load1,7 and an immunologically 'cold' tumour microenvironment8. We used personalized neoantigen-targeting vaccines to immunize patients newly diagnosed with glioblastoma following surgical resection and conventional radiotherapy in a phase I/Ib study. Patients who did not receive dexamethasone-a highly potent corticosteroid that is frequently prescribed to treat cerebral oedema in patients with glioblastoma-generated circulating polyfunctional neoantigen-specific CD4+ and CD8+ T cell responses that were enriched in a memory phenotype and showed an increase in the number of tumour-infiltrating T cells. Using single-cell T cell receptor analysis, we provide evidence that neoantigen-specific T cells from the peripheral blood can migrate into an intracranial glioblastoma tumour. Neoantigen-targeting vaccines thus have the potential to favourably alter the immune milieu of glioblastoma.
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Affiliation(s)
- Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Annabelle J Anandappa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jing Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Itay Tirosh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nathan D Mathewson
- Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shuqiang Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anita Giobbie-Hurder
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristen Felt
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Evisa Gjini
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sachet A Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zhuting Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Letitia Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Phuong M Le
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rosa L Allesøe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Bio- and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alyssa R Richman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | | | - Sara Abdelrahman
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jack E Geduldig
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sarah Charbonneau
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristine Pelton
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - J Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Oriol Olive
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christine McCluskey
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lars R Olsen
- Department of Bio- and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jonathan Stevens
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - William J Lane
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Heather Daley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick Y Wen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - E Antonio Chiocca
- Harvard Medical School, Boston, MA, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Maegan Harden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott J Rodig
- Harvard Medical School, Boston, MA, USA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Mario L Suvà
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Kai W Wucherpfennig
- Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Edward F Fritsch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Neon Therapeutics Inc, Cambridge, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - David A Reardon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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16
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CDR3 repertoire diversity of CD8+ T lymphocytes in patients with HCV. Cell Immunol 2018; 336:34-39. [PMID: 30591202 DOI: 10.1016/j.cellimm.2018.12.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 12/10/2018] [Accepted: 12/19/2018] [Indexed: 12/25/2022]
Abstract
T cell receptors (TCR) diversity is known to serve as a defining hallmark of the antigen-reactive T cell repertoire. Complementarity determining region 3 (CDR3) was the most important region for the recognition of peptide-major histocompatibility complex (MHC) complexes and represented the diversity of TCR repertoire. In this study, we detected the CDR3 spectratypes by complexity scoring system to assess TCR repertoire diversity and further analyzed the correlation of CDR3 score with CD8+ T cell function and with the prognosis of chronic hepatitis C virus (HCV)-infected patients. The results demonstrated that CDR3 score was related to CD8+ T cell function and prognosis by analyzing the clinical indicators such as viral load (VL), rapid virologic response (RVR), early virologic response (EVR) and sustained virologic response (SVR). Importantly, we found that Vβ27, a member of CDR3 subfamily, might play an important role in the clearance of HCV. These findings indicate that TCR diversity maybe serve as a biomarker to predict the clinical parameters of HCV-infected patients.
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17
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Bak S, Tischer S, Dragon A, Ravens S, Pape L, Koenecke C, Oelke M, Blasczyk R, Maecker-Kolhoff B, Eiz-Vesper B. Selective Effects of mTOR Inhibitor Sirolimus on Naïve and CMV-Specific T Cells Extending Its Applicable Range Beyond Immunosuppression. Front Immunol 2018; 9:2953. [PMID: 30619313 PMCID: PMC6304429 DOI: 10.3389/fimmu.2018.02953] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/30/2018] [Indexed: 12/13/2022] Open
Abstract
Cytomegalovirus (CMV) infection/reactivation remains among the most important complications of immunosuppression after transplantation. However, recent clinical observations indicate that mammalian target of rapamycin (mTOR) inhibition with sirolimus may improve the outcome of CMV complications. Underlying mechanisms of this observation, particularly the effect of sirolimus on naïve- and CMV-specific cytotoxic CD8+ T-cell (CMV-CTL) functionality is still undiscovered. Here, the influence of sirolimus on naïve and memory CMV-CTLs was determined by CD3/CD28 crosslinking and alloreactivity assays. After stimulating CMV-CTL with HLA-A*02:01-restricted CMVpp65-peptide loaded artificial antigen-presenting cells (aAPCs), we measured the effect of sirolimus on T-cell proliferation, phenotype, and functionality. Sirolimus significantly improved CMV-specific effector memory T-cell function and negatively influenced naïve T cells. This unique mechanism of action was further characterized by increased secretion of interferon-gamma (IFN-γ), granzyme B (GzB) and enhanced target-cell-dependent cytotoxic capacity of activated CMV-CTLs. Next-generation-sequencing (NGS) was applied to monitor T-cell receptor (TCR)-repertoire dynamics and to verify, that the increased functionality was not related to sirolimus-resistant CTL-clones. Instead, modulation of environmental cues during CMV-CTL development via IL-2 receptor (IL-2R)-driven signal transducer and activator of transcription-5 (STAT-5) signaling under mTOR inhibition allowed fine-tuning of T-cell programming for enhanced antiviral response with stable TCR-repertoire dynamics. We show for the first time that sirolimus acts selectively on human naïve and memory T cells and improves CMV-specific T-cell function via modulation of the environmental milieu. The data emphasize the importance to extend immune monitoring including cytokine levels and T-cell functionality which will help to identify patients who may benefit from individually tailored immunosuppression.
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Affiliation(s)
- Szilvia Bak
- Hannover Medical School, Institute for Transfusion Medicine, Hannover, Germany
| | - Sabine Tischer
- Hannover Medical School, Institute for Transfusion Medicine, Hannover, Germany
| | - Anna Dragon
- Hannover Medical School, Institute for Transfusion Medicine, Hannover, Germany
| | - Sarina Ravens
- Hannover Medical School, Institute of Immunology, Hannover, Germany
| | - Lars Pape
- Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | - Christian Koenecke
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Mathias Oelke
- Department of Pathology, John Hopkins School of Medicine, Baltimore, MD, United States.,NexImmune Inc., Gaithersburg, MD, United States
| | - Rainer Blasczyk
- Hannover Medical School, Institute for Transfusion Medicine, Hannover, Germany
| | - Britta Maecker-Kolhoff
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Britta Eiz-Vesper
- Hannover Medical School, Institute for Transfusion Medicine, Hannover, Germany
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18
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Caccamo N, Joosten SA, Ottenhoff THM, Dieli F. Atypical Human Effector/Memory CD4 + T Cells With a Naive-Like Phenotype. Front Immunol 2018; 9:2832. [PMID: 30559746 PMCID: PMC6287111 DOI: 10.3389/fimmu.2018.02832] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/16/2018] [Indexed: 12/21/2022] Open
Abstract
The induction of adaptive immunological memory, mediated by T and B cells, plays an important role in protective immunity to pathogens induced by previous infections or vaccination. Naive CD4+ T cells that have been primed by antigen develop into memory or effector cells, which may be distinguished by their capability to exert a long-term and rapid response upon re-challenge by antigen, to produce distinct cytokines and surface marker expression phenotypes such as CD45RA/RO, CD27, CD62L, and CCR7. Moreover, a distinct lineage of memory T cells populates tissues (tissue-resident memory T cells or TRM cells) which orchestratea the response to pathogens re encountered at tissue sites. Recent evidence, however, has highlighted that CD4+ naive T cells are much more heterogeneous that previously thought, and that they harbor diversity in phenotypes, differentiation stages, persistence, functions, and anatomic localizations. These cells represent cellular subsets that are extremely heterogeneous and multifunctional at their very initial stages of differentiation, with the potential to become "atypical" memory and effector cells. In this mini review, we focus on recently obtained data from studies in humans, in which this newly recognized heterogeneity in the naive T cell pool was discovered in terms of surface marker expression, cytokine production, or transcriptomic profiles. The deep analysis of immune functions at the single cell level combined with a better understanding of the generation and maintenance of the various atypical memory CD4+ T cell subsets with a naive-like phenotype will be important in immune-monitoring of vaccination and immunotherapies in infectious diseases.
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Affiliation(s)
- Nadia Caccamo
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), University of Palermo, Palermo, Italy.,Department of Biopathology and Medical Biotechnologies, University of Palermo, Palermo, Italy
| | - Simone A Joosten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Francesco Dieli
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), University of Palermo, Palermo, Italy.,Department of Biopathology and Medical Biotechnologies, University of Palermo, Palermo, Italy
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19
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Hu Z, Anandappa AJ, Sun J, Kim J, Leet DE, Bozym DJ, Chen C, Williams L, Shukla SA, Zhang W, Tabbaa D, Steelman S, Olive O, Livak KJ, Kishi H, Muraguchi A, Guleria I, Stevens J, Lane WJ, Burkhardt UE, Fritsch EF, Neuberg D, Ott PA, Keskin DB, Hacohen N, Wu CJ. A cloning and expression system to probe T-cell receptor specificity and assess functional avidity to neoantigens. Blood 2018; 132:1911-1921. [PMID: 30150207 PMCID: PMC6213317 DOI: 10.1182/blood-2018-04-843763] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/19/2018] [Indexed: 12/23/2022] Open
Abstract
Recent studies have highlighted the promise of targeting tumor neoantigens to generate potent antitumor immune responses and provide strong motivation for improving our understanding of antigen-T-cell receptor (TCR) interactions. Advances in single-cell sequencing technologies have opened the door for detailed investigation of the TCR repertoire, providing paired information from TCRα and TCRβ, which together determine specificity. However, a need remains for efficient methods to assess the specificity of discovered TCRs. We developed a streamlined approach for matching TCR sequences with cognate antigen through on-demand cloning and expression of TCRs and screening against candidate antigens. Here, we first demonstrate the system's capacity to identify viral-antigen-specific TCRs and compare the functional avidity of TCRs specific for a given antigen target. We then apply this system to identify neoantigen-specific TCR sequences from patients with melanoma treated with personalized neoantigen vaccines and characterize functional avidity of neoantigen-specific TCRs. Furthermore, we use a neoantigen-prediction pipeline to show that an insertion-deletion mutation in a putative chronic lymphocytic leukemia (CLL) driver gives rise to an immunogenic neoantigen mut-MGA, and use this approach to identify the mut-MGA-specific TCR sequence. This approach provides a means to identify and express TCRs, and then rapidly assess antigen specificity and functional avidity of a reconstructed TCR, which can be applied for monitoring antigen-specific T-cell responses, and potentially for guiding the design of effective T-cell-based immunotherapies.
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MESH Headings
- Antigens, Neoplasm/immunology
- Cancer Vaccines/therapeutic use
- Cells, Cultured
- Cloning, Molecular/methods
- HEK293 Cells
- Humans
- Jurkat Cells
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Melanoma/immunology
- Melanoma/therapy
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- T-Cell Antigen Receptor Specificity
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Affiliation(s)
- Zhuting Hu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Annabelle J Anandappa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Jing Sun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jintaek Kim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Donna E Leet
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - David J Bozym
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Christina Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Sachet A Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA
| | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Diana Tabbaa
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Oriol Olive
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Kenneth J Livak
- Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA
| | - Hiroyuki Kishi
- Department of Immunology, University of Toyama, Toyama, Japan
| | | | - Indira Guleria
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Jonathan Stevens
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - William J Lane
- Harvard Medical School, Boston, MA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Ute E Burkhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Edward F Fritsch
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA; and
| | - Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA; and
| | - Nir Hacohen
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Massachusetts General Hospital, Boston, MA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA; and
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20
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Jiang Q, Zhao T, Zheng W, Zhou J, Wang H, Dong H, Chen Y, Tang X, Liu C, Ye L, Mao Q, Wang C, Han J, Shang X, Wu Y. Patient-shared TCRβ-CDR3 clonotypes correlate with favorable prognosis in chronic hepatitis B. Eur J Immunol 2018; 48:1539-1549. [PMID: 29856484 DOI: 10.1002/eji.201747327] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 03/22/2018] [Accepted: 05/24/2018] [Indexed: 01/12/2023]
Abstract
The presence of shared T-cell clonotypes was found in several different diseases, but its relationship with the progression of disease remains unclear. By sequencing the complementary determining region 3 of T-cell receptor (TCR) β chains from the purified antigen-experienced CD8+ T cells, we characterized the T-cell repertoire in a prospective cohort study among 75 patients with chronic hepatitis B in China, as well as a healthy control and a validation cohort. We found that most T-cell clones from patients harbored the "patient-specific" TCR sequences. However, "patient-shared" TCR clonotypes were also widely found, which correlated with the favorable turnover of disease. Interestingly, the frequency of the "patient-shared" clonotypes can serve as a biomarker for favorable prognosis. Based on the clonotypes in those patients with favorable outcomes, we created a database including several clusters of protective anti-HBV CD8+ T-cell clonotypes that might be a reasonable target for therapeutic vaccine development or adoptive cell transfer therapy. These findings were validated in an additional independent cohort of patients. These results suggest that the "patient-shared" TCR clonotypes may serve as a valuable prognostic tool in the treatment of chronic hepatitis B and possibly other chronic viral diseases.
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Affiliation(s)
- Qiong Jiang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Tingting Zhao
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Wenhong Zheng
- Department of Health, Third Military Medical University, Chongqing, P. R. China
| | - Jijun Zhou
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Haoliang Wang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Hui Dong
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Yongwen Chen
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Xiaoqin Tang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Cong Liu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Lilin Ye
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Qing Mao
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing, P. R. China
| | - Chunlin Wang
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Jian Han
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Xiaoyun Shang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, P. R. China
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21
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Induction of oligoclonal CD8 T cell responses against pulmonary metastatic cancer by a phospholipid-conjugated TLR7 agonist. Proc Natl Acad Sci U S A 2018; 115:E6836-E6844. [PMID: 29967183 DOI: 10.1073/pnas.1803281115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recent advances in cancer immunotherapy have improved patient survival. However, only a minority of patients with pulmonary metastatic disease respond to treatment with checkpoint inhibitors. As an alternate approach, we have tested the ability of systemically administered 1V270, a toll-like receptor 7 (TLR7) agonist conjugated to a phospholipid, to inhibit lung metastases in two variant murine 4T1 breast cancer models, as well as in B16 melanoma, and Lewis lung carcinoma models. In the 4T1 breast cancer models, 1V270 therapy inhibited lung metastases if given up to a week after primary tumor initiation. The treatment protocol was facilitated by the minimal toxic effects exerted by the phospholipid TLR7 agonist compared with the unconjugated agonist. 1V270 exhibited a wide therapeutic window and minimal off-target receptor binding. The 1V270 therapy inhibited colonization by tumor cells in the lungs in an NK cell dependent manner. Additional experiments revealed that single administration of 1V270 led to tumor-specific CD8+ cell-dependent adaptive immune responses that suppressed late-stage metastatic tumor growth in the lungs. T cell receptor (TCR) repertoire analyses showed that 1V270 therapy induced oligoclonal T cells in the lungs and mediastinal lymph nodes. Different animals displayed commonly shared TCR clones following 1V270 therapy. Intranasal administration of 1V270 also suppressed lung metastasis and induced tumor-specific adaptive immune responses. These results indicate that systemic 1V270 therapy can induce tumor-specific cytotoxic T cell responses to pulmonary metastatic cancers and that TCR repertoire analyses can be used to monitor, and to predict, the response to therapy.
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22
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Ichinohe T, Miyama T, Kawase T, Honjo Y, Kitaura K, Sato H, Shin-I T, Suzuki R. Next-Generation Immune Repertoire Sequencing as a Clue to Elucidate the Landscape of Immune Modulation by Host-Gut Microbiome Interactions. Front Immunol 2018; 9:668. [PMID: 29666626 PMCID: PMC5891584 DOI: 10.3389/fimmu.2018.00668] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 03/19/2018] [Indexed: 12/23/2022] Open
Abstract
The human immune system is a fine network consisted of the innumerable numbers of functional cells that balance the immunity and tolerance against various endogenous and environmental challenges. Although advances in modern immunology have revealed a role of many unique immune cell subsets, technologies that enable us to capture the whole landscape of immune responses against specific antigens have been not available to date. Acquired immunity against various microorganisms including host microbiome is principally founded on T cell and B cell populations, each of which expresses antigen-specific receptors that define a unique clonotype. Over the past several years, high-throughput next-generation sequencing has been developed as a powerful tool to profile T- and B-cell receptor repertoires in a given individual at the single-cell level. Sophisticated immuno-bioinformatic analyses by use of this innovative methodology have been already implemented in clinical development of antibody engineering, vaccine design, and cellular immunotherapy. In this article, we aim to discuss the possible application of high-throughput immune receptor sequencing in the field of nutritional and intestinal immunology. Although there are still unsolved caveats, this emerging technology combined with single-cell transcriptomics/proteomics provides a critical tool to unveil the previously unrecognized principle of host–microbiome immune homeostasis. Accumulation of such knowledge will lead to the development of effective ways for personalized immune modulation through deeper understanding of the mechanisms by which the intestinal environment affects our immune ecosystem.
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Affiliation(s)
- Tatsuo Ichinohe
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | - Takahiko Miyama
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | - Takakazu Kawase
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | - Yasuko Honjo
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | | | | | | | - Ryuji Suzuki
- Repertoire Genesis Incorporation, Ibaraki, Japan.,Department of Rheumatology and Clinical Immunology, Clinical Research Center for Rheumatology and Allergy, National Hospital Organization Sagamihara Hospital, Sagamihara, Japan
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23
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24
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Tsuruta M, Ueda S, Yew PY, Fukuda I, Yoshimura S, Kishi H, Hamana H, Hirayama M, Yatsuda J, Irie A, Senju S, Yuba E, Kamba T, Eto M, Nakayama H, Nishimura Y. Bladder cancer-associated cancer-testis antigen-derived long peptides encompassing both CTL and promiscuous HLA class II-restricted Th cell epitopes induced CD4 + T cells expressing converged T-cell receptor genes in vitro. Oncoimmunology 2018; 7:e1415687. [PMID: 29632734 DOI: 10.1080/2162402x.2017.1415687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/02/2017] [Accepted: 12/04/2017] [Indexed: 10/18/2022] Open
Abstract
DEP domain containing 1 (DEPDC1) and M-phase phosphoprotein 1 (MPHOSPH1) are human cancer testis antigens that are frequently overexpressed in urinary bladder cancer. In a phase I/II clinical trial, a DEPDC1- and MPHOSPH1-derived short peptide vaccine demonstrated promising efficacy in preventing bladder cancer recurrence. Here, we aimed to identify long peptides (LPs) derived from DEPDC1 and MPHOSPH1 that induced both T-helper (Th) cells and tumor-reactive cytotoxic T lymphocytes (CTLs). Stimulation of peripheral blood mononuclear cells (PBMCs) from healthy donors with the synthetic DEPDC1- and MPHOSPH1-LPs predicted to bind to promiscuous human leukocyte antigen (HLA) class II molecules by a computer algorithm induced specific CD4+ T cells as revealed by interferon-γ enzyme-linked immunospot assays. Three of six LPs encompassed HLA-A2- or -A24-restricted CTL epitopes or both, and all six LPs stimulated DEPDC1- or MPHOSPH1-specific Th cells restricted by promiscuous and frequently observed HLA class II molecules in the Japanese population. Some LPs are naturally processed from the proteins in DCs, and the capacity of these LPs to cross-prime CTLs was confirmed in vivo using HLA-A2 or -A24 transgenic mice. The LP-specific and HLA class II-restricted T-cell responses were also observed in PBMCs from patients with bladder cancer. Repeated stimulation of PBMCs with DEPDC1-LPs and MPHOSPH1-LPs yielded clonal Th cells expressing specific T-cell receptor (TCR)-α and β genes. These DEPDC1- or MPHOSPH1-derived LPs may have applications in immunotherapy in patients with bladder cancer, and the TCR genes identified may be useful for monitoring of Th cells specific to LPs in vivo.
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Affiliation(s)
- Miki Tsuruta
- Department of Immunogenetics, Graduate School of Medical Sciences, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan.,Department of Oral and Maxillofacial Surgery, Graduate School of Medical Sciences, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan
| | - Shohei Ueda
- Department of Immunogenetics, Graduate School of Medical Sciences, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan.,Department of Urology, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Poh Yin Yew
- Tumor Immunoanalysis Department, OncoTherapy Science, Inc., Sakado, Takatsu-ku, Kawasaki, Kanagawa, Japan
| | - Isao Fukuda
- Tumor Immunoanalysis Department, OncoTherapy Science, Inc., Sakado, Takatsu-ku, Kawasaki, Kanagawa, Japan
| | - Sachiko Yoshimura
- Tumor Immunoanalysis Department, OncoTherapy Science, Inc., Sakado, Takatsu-ku, Kawasaki, Kanagawa, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences (Medicine), University of Toyama, Sugitani, Toyama, Toyama, Japan
| | - Hiroshi Hamana
- Department of Innovative Cancer Immunotherapy, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Sugitani, Toyama, Toyama, Japan
| | - Masatoshi Hirayama
- Department of Immunogenetics, Graduate School of Medical Sciences, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan.,Department of Oral and Maxillofacial Surgery, Graduate School of Medical Sciences, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan
| | - Junji Yatsuda
- Department of Urology, Graduate School of Medical Sciences, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan
| | - Atsushi Irie
- Department of Immunogenetics, Graduate School of Medical Sciences, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan
| | - Satoru Senju
- Department of Immunogenetics, Graduate School of Medical Sciences, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan
| | - Eiji Yuba
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, Gakuen-cho, Naka-ku, Sakai, Osaka, Japan
| | - Tomomi Kamba
- Department of Urology, Graduate School of Medical Sciences, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan
| | - Masatoshi Eto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan.,Department of Urology, Graduate School of Medical Sciences, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan
| | - Hideki Nakayama
- Department of Oral and Maxillofacial Surgery, Graduate School of Medical Sciences, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan
| | - Yasuharu Nishimura
- Department of Immunogenetics, Graduate School of Medical Sciences, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan.,Nishimura Project Laboratory, Center for Resource Development and Analysis, Kumamoto University, Honjo, Chuo-ku, Kumamoto, Japan
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