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Aronson SL, Thijssen B, Lopez-Yurda M, Koole SN, van der Leest P, León-Castillo A, Harkes R, Seignette IM, Sanders J, Alkemade M, Kemper I, Holtkamp MJ, Mandjes IAM, Broeks A, Lahaye MJ, Rijlaarsdam MA, van den Broek D, Wessels LFA, Horlings HM, van Driel WJ, Sonke GS. Neo-adjuvant pembrolizumab in stage IV high-grade serous ovarian cancer: the phase II Neo-Pembro trial. Nat Commun 2025; 16:3520. [PMID: 40229272 PMCID: PMC11997049 DOI: 10.1038/s41467-025-58440-y] [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: 10/22/2024] [Accepted: 03/24/2025] [Indexed: 04/16/2025] Open
Abstract
While immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment, their efficacy in high-grade serous ovarian cancer (HGSOC) remains limited. Some patients, however, achieve lasting responses, emphasizing the need to understand how tumor microenvironment and molecular characteristics influence ICI response. The phase 2 Neo-Pembro study (NCT03126812) included 33 untreated stage IV HGSOC patients, who were scheduled for 6 cycles of carboplatin-paclitaxel and interval cytoreductive surgery. Pembrolizumab (pembro) was added from cycle two and continued for one year. The primary objective was to assess intratumoral immune activation using multiplexed immunofluorescence and immune-related gene expression. Our findings show immune activation, evidenced by an increase in CD3 + , CD8 + , CD8 + /FOXP3+ ratio, TNF-α and interferon-γ signaling. Treatment was well-tolerated. We observed major pathologic responses in 9/33 patients (27%, 95%CI 14-46), with pathologic response strongly associated with immune activation and OS. At a median follow-up of 52.8 months, 8/9 major responders were alive, with 6 patients recurrence-free. In contrast, 4/24 minor responders survived, including one recurrence-free. ctDNA clearance was observed in all major responders and was associated with prolonged PFS and OS. PD-L1 expression and homologous recombination deficiency were predictive of major response and may serve as biomarkers, warranting further exploration. These results suggest major responders may benefit from neo-adjuvant pembro.
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Affiliation(s)
- S L Aronson
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Center for Gynecologic Oncology Amsterdam, Department of Gynecologic Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - B Thijssen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - M Lopez-Yurda
- Department of Biometrics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - S N Koole
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Center for Gynecologic Oncology Amsterdam, Department of Gynecologic Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - P van der Leest
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - A León-Castillo
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - R Harkes
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - I M Seignette
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - J Sanders
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - M Alkemade
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - I Kemper
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - M J Holtkamp
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - I A M Mandjes
- Department of Biometrics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - A Broeks
- Core Facility Molecular Pathology & Biobanking, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - M J Lahaye
- Department of Radiology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- GROW Research Institute for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - M A Rijlaarsdam
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - D van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - L F A Wessels
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - H M Horlings
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - W J van Driel
- Center for Gynecologic Oncology Amsterdam, Department of Gynecologic Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - G S Sonke
- Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
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2
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Borgers JSW, Lenkala D, Kohler V, Jackson EK, Linssen MD, Hymson S, McCarthy B, O'Reilly Cosgrove E, Balogh KN, Esaulova E, Starr K, Ware Y, Klobuch S, Sciuto T, Chen X, Mahimkar G, Sheen JHF, Ramesh S, Wilgenhof S, van Thienen JV, Scheiner KC, Jedema I, Rooney M, Dong JZ, Srouji JR, Juneja VR, Arieta CM, Nuijen B, Gottstein C, Finney OC, Manson K, Nijenhuis CM, Gaynor RB, DeMario M, Haanen JB, van Buuren MM. Personalized, autologous neoantigen-specific T cell therapy in metastatic melanoma: a phase 1 trial. Nat Med 2025; 31:881-893. [PMID: 39753970 PMCID: PMC11922764 DOI: 10.1038/s41591-024-03418-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 11/13/2024] [Indexed: 03/21/2025]
Abstract
New treatment approaches are warranted for patients with advanced melanoma refractory to immune checkpoint blockade (ICB) or BRAF-targeted therapy. We designed BNT221, a personalized, neoantigen-specific autologous T cell product derived from peripheral blood, and tested this in a 3 + 3 dose-finding study with two dose levels (DLs) in patients with locally advanced or metastatic melanoma, disease progression after ICB, measurable disease (Response Evaluation Criteria in Solid Tumors version 1.1) and, where appropriate, BRAF-targeted therapy. Primary and secondary objectives were evaluation of safety, highest tolerated dose and anti-tumor activity. We report here the non-pre-specified, final results of the completed monotherapy arm consisting of nine patients: three at DL1 (1 × 108-1 × 109 cells) and six at DL2 (2 × 109-1 × 1010 cells). Drug products (DPs) were generated for all enrolled patients. BNT221 was well tolerated across both DLs, with no dose-limiting toxicities of grade 3 or higher attributed to the T cell product observed. Specifically, no cytokine release, immune effector cell-associated neurotoxicity or macrophage activation syndromes were reported. A dose of 5.0 × 108-1.0 × 1010 cells was identified for further study conduct. Six patients showed stable disease as best overall response, and tumor reductions (≤20%) were reported for four of these patients. In exploratory analyses, multiple mutant-specific CD4+ and CD8+ T cell responses were generated in each DP. These were cytotoxic, polyfunctional and expressed T cell receptors with broad functional avidities. Neoantigen-specific clonotypes were detected after treatment in blood and tumor. Our results provide key insights into this neoantigen-specific adoptive T cell therapy and demonstrate proof of concept for this new therapeutic approach. ClinicalTrials.gov registration: NCT04625205 .
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Affiliation(s)
- Jessica S W Borgers
- Department of Medical Oncology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | | | | | | | - Matthijs D Linssen
- BioTherapeutics Unit, Division of Pharmacy and Pharmacology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | - Sebastian Klobuch
- Department of Medical Oncology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | | | - Xi Chen
- BioNTech US, Cambridge, MA, USA
| | | | | | | | - Sofie Wilgenhof
- Department of Medical Oncology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | - Johannes V van Thienen
- Department of Medical Oncology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | - Karina C Scheiner
- BioTherapeutics Unit, Division of Pharmacy and Pharmacology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | - Inge Jedema
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | | | | | | | | | | | - Bastiaan Nuijen
- BioTherapeutics Unit, Division of Pharmacy and Pharmacology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | | | | | | | - Cynthia M Nijenhuis
- BioTherapeutics Unit, Division of Pharmacy and Pharmacology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands
| | | | | | - John B Haanen
- Department of Medical Oncology, Netherlands Cancer Institute (NKI), Amsterdam, The Netherlands.
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3
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Mühlenbruch L, Rieger D, Becker H, Santos Leite AM, Mäurer I, Schittenhelm J, Dubbelaar M, Bichmann L, Kohlbacher O, Rammensee HG, Gouttefangeas C, Tatagiba M, Walz JS, Tabatabai G. The immunopeptidomic landscape of ependymomas provides actionable antigens for T-cell-based immunotherapy. Neurooncol Adv 2025; 7:vdae226. [PMID: 40376681 PMCID: PMC12080555 DOI: 10.1093/noajnl/vdae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2025] Open
Abstract
Background Ependymoma are primary tumors of the nervous system. Due to their growth pattern, many ependymomas can be managed with neurosurgical resection alone. A substantial proportion of these tumors recurs or displays infiltrative growth patterns. Further established therapeutic options include radiation therapy. Systemic treatment options include platinum-based therapeutic regimes or a combination of lapatinib and temozolomide. Peptide-based immunotherapy represents a promising therapeutic strategy relying on the induction of tumor-specific T cells targeting human leukocyte antigens (HLA)-presented peptides. Our work aimed to analyze the landscape of naturally presented HLA class I and II ligands of primary ependymomas (EPN) to delineate EPN-associated antigens. Methods We investigated 22 EPN tissue samples using a comparative mass spectrometry-based immunopeptidomic approach. Additionally, EPN-specific antigens were functionally characterized in T-cell-based immunogenicity assays. Results We discovered a subset of EPN-exclusive peptides including HLA-A*02 and HLA-A*25/HLA-A*26-restricted HLA ligands and identified a small panel of cancer/testis antigens (CTAs)-derived HLA ligands. Furthermore, we outlined immunopeptidomic alterations in different ependymoma subgroups and progressive ependymoma. Subsequently, we performed functional characterization of the previously identified HLA-A*02:01 restricted peptide FLDS to demonstrate immunogenicity in vitro. Conclusion The immunopeptidome landscape of EPNs provides actionable targets that could further be explored as a T cell-based immunotherapeutic strategy in this tumor entity.
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Affiliation(s)
- Lena Mühlenbruch
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Department of Peptide-based Immunotherapy, Institute of Immunology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - David Rieger
- Center for Personalized Medicine, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Center for Neuro-Oncology, Comprehensive Cancer Center Tuebingen-Stuttgart, University Hospital Tuebingen, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Department of Neurology and Interdisciplinary Neuro-Oncology, University Hospital Tuebingen, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - Hannes Becker
- Department of Neurosurgery, University Hospital Tuebingen, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Center for Personalized Medicine, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Center for Neuro-Oncology, Comprehensive Cancer Center Tuebingen-Stuttgart, University Hospital Tuebingen, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Department of Neurology and Interdisciplinary Neuro-Oncology, University Hospital Tuebingen, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - Ana Maia Santos Leite
- Institute for Immunology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - Irina Mäurer
- Center for Personalized Medicine, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Center for Neuro-Oncology, Comprehensive Cancer Center Tuebingen-Stuttgart, University Hospital Tuebingen, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Department of Neurology and Interdisciplinary Neuro-Oncology, University Hospital Tuebingen, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - Jens Schittenhelm
- German Cancer Consortium (DKTK), Partner Site Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Department of Neuropathology, University Hospital Tuebingen, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Center for Personalized Medicine, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Center for Neuro-Oncology, Comprehensive Cancer Center Tuebingen-Stuttgart, University Hospital Tuebingen, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - Marissa Dubbelaar
- Quantitative Biology Center (QBiC), Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Institute for Immunology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Department of Peptide-based Immunotherapy, Institute of Immunology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - Leon Bichmann
- Applied Bioinformatics, Department of Computer Science, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Institute for Immunology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - Oliver Kohlbacher
- Institute for Bioinformatics and Medical Informatics, University of Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Institute for Translational Bioinformatics, University Hospital Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Cluster of Excellence Machine Learning in the Sciences (EXC2064), University of Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Applied Bioinformatics, Department of Computer Science, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - Hans-Georg Rammensee
- German Cancer Consortium (DKTK), Partner Site Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Institute for Immunology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - Cécile Gouttefangeas
- German Cancer Consortium (DKTK), Partner Site Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Institute for Immunology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - Marcos Tatagiba
- German Cancer Consortium (DKTK), Partner Site Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Department of Neurosurgery, University Hospital Tuebingen, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Center for Personalized Medicine, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Center for Neuro-Oncology, Comprehensive Cancer Center Tuebingen-Stuttgart, University Hospital Tuebingen, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- German Cancer Consortium (DKTK), Partner Site Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Department of Peptide-based Immunotherapy, Institute of Immunology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
| | - Ghazaleh Tabatabai
- German Cancer Consortium (DKTK), Partner Site Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Center for Personalized Medicine, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Center for Neuro-Oncology, Comprehensive Cancer Center Tuebingen-Stuttgart, University Hospital Tuebingen, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Department of Neurology and Interdisciplinary Neuro-Oncology, University Hospital Tuebingen, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” Eberhard Karls University Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany
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4
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Alban TJ, Riaz N, Parthasarathy P, Makarov V, Kendall S, Yoo SK, Shah R, Weinhold N, Srivastava R, Ma X, Krishna C, Mok JY, van Esch WJE, Garon E, Akerley W, Creelan B, Aanur N, Chowell D, Geese WJ, Rizvi NA, Chan TA. Neoantigen immunogenicity landscapes and evolution of tumor ecosystems during immunotherapy with nivolumab. Nat Med 2024; 30:3209-3222. [PMID: 39349627 PMCID: PMC12066197 DOI: 10.1038/s41591-024-03240-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 08/08/2024] [Indexed: 11/16/2024]
Abstract
Neoantigen immunoediting drives immune checkpoint blockade efficacy, yet the molecular features of neoantigens and how neoantigen immunogenicity shapes treatment response remain poorly understood. To address these questions, 80 patients with non-small cell lung cancer were enrolled in the biomarker cohort of CheckMate 153 (CA209-153), which collected radiographic guided biopsy samples before treatment and during treatment with nivolumab. Early loss of mutations and neoantigens during therapy are both associated with clinical benefit. We examined 1,453 candidate neoantigens, including many of which that had reduced cancer cell fraction after treatment with nivolumab, and identified 196 neopeptides that were recognized by T cells. Mapping these neoantigens to clonal dynamics, evolutionary trajectories and clinical response revealed a strong selection against immunogenic neoantigen-harboring clones. We identified position-specific amino acid and physiochemical features related to immunogenicity and developed an immunogenicity score. Nivolumab-induced microenvironmental evolution in non-small cell lung cancer shared some similarities with melanoma, yet critical differences were apparent. This study provides unprecedented molecular portraits of neoantigen landscapes underlying nivolumab's mechanism of action.
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Affiliation(s)
- Tyler J Alban
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Prerana Parthasarathy
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Vladimir Makarov
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Sviatoslav Kendall
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Seong-Keun Yoo
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Rachna Shah
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nils Weinhold
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raghvendra Srivastava
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiaoxiao Ma
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | | | | | - Edward Garon
- Department of Thoracic Medical Oncology, University of California Los Angeles, Los Angeles, CA, USA
| | - Wallace Akerley
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Benjamin Creelan
- Department of Thoracic Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Diego Chowell
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Naiyer A Rizvi
- Synthekine, Menlo Park, CA, USA
- Thoracic Oncology, Columbia University, New York, NY, USA
| | - Timothy A Chan
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA.
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.
- National Center for Regenerative Medicine, Cleveland Clinic, Cleveland, OH, USA.
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5
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Zhang T, Zhang X, Chen J, Zhang X, Zhang Y. Harnessing microbial antigens as cancer antigens: a promising avenue for cancer immunotherapy. Front Immunol 2024; 15:1411490. [PMID: 39139570 PMCID: PMC11319170 DOI: 10.3389/fimmu.2024.1411490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/16/2024] [Indexed: 08/15/2024] Open
Abstract
Immunotherapy has revolutionized cancer treatment by leveraging the immune system's innate capabilities to combat malignancies. Despite the promise of tumor antigens in stimulating anti-tumor immune responses, their clinical utility is hampered by limitations in eliciting robust and durable immune reactions, exacerbated by tumor heterogeneity and immune evasion mechanisms. Recent insights into the immunogenic properties of host homologous microbial antigens have sparked interest in their potential for augmenting anti-tumor immunity while minimizing off-target effects. This review explores the therapeutic potential of microbial antigen peptides in tumor immunotherapy, beginning with an overview of tumor antigens and their challenges in clinical translation. We further explore the intricate relationship between microorganisms and tumor development, elucidating the concept of molecular mimicry and its implications for immune recognition of tumor-associated antigens. Finally, we discuss methodologies for identifying and characterizing microbial antigen peptides, highlighting their immunogenicity and prospects for therapeutic application.
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Affiliation(s)
- Tao Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Xilong Zhang
- Department of Burns and Plastic Surgery, First People’s Hospital of Xuzhou City, Xuzhou, China
| | - Jianquan Chen
- Central Laboratory, Translational Medicine Research Center, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Xiuwei Zhang
- Department of Burns and Plastic Surgery, First People’s Hospital of Xuzhou City, Xuzhou, China
| | - Yunlei Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
- Central Laboratory, Translational Medicine Research Center, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
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6
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Lucibello F, Lalanne AI, Le Gac AL, Soumare A, Aflaki S, Cyrta J, Dubreuil L, Mestdagh M, Salou M, Houy A, Ekwegbara C, Jamet C, Gardrat S, Le Ven A, Bernardeau K, Cassoux N, Matet A, Malaise D, Pierron G, Piperno-Neumann S, Stern MH, Rodrigues M, Lantz O. Divergent local and systemic antitumor response in primary uveal melanomas. J Exp Med 2024; 221:e20232094. [PMID: 38563818 PMCID: PMC10986814 DOI: 10.1084/jem.20232094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/08/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Uveal melanoma (UM) is the most common cancer of the eye. The loss of chromosome 3 (M3) is associated with a high risk of metastases. M3 tumors are more infiltrated by T-lymphocytes than low-risk disomic-3 (D3) tumors, contrasting with other tumor types in which T cell infiltration correlates with better prognosis. Whether these T cells represent an antitumor response and how these T cells would be primed in the eye are both unknown. Herein, we characterized the T cells infiltrating primary UMs. CD8+ and Treg cells were more abundant in M3 than in D3 tumors. CD39+PD-1+CD8+ T cells were enriched in M3 tumors, suggesting specific responses to tumor antigen (Ag) as confirmed using HLA-A2:Melan-A tetramers. scRNAseq-VDJ analysis of T cells evidenced high numbers of proliferating CD39+PD1+CD8+ clonal expansions, suggesting in situ antitumor Ag responses. TCRseq and tumor-Ag tetramer staining characterized the recirculation pattern of the antitumor responses in M3 and D3 tumors. Thus, tumor-Ag responses occur in localized UMs, raising the question of the priming mechanisms in the absence of known lymphatic drainage.
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Affiliation(s)
- Francesca Lucibello
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Ana I. Lalanne
- Laboratoire d’Immunologie Clinique, Institut Curie, Paris, France
- Centre d’investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Paris, France
| | - Anne-Laure Le Gac
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Abdoulaye Soumare
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Setareh Aflaki
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Joanna Cyrta
- Departments of Pathology, Institut Curie, Paris, France
| | - Lea Dubreuil
- Laboratoire d’Immunologie Clinique, Institut Curie, Paris, France
| | - Martin Mestdagh
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Marion Salou
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | - Alexandre Houy
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Christina Ekwegbara
- Laboratoire d’Immunologie Clinique, Institut Curie, Paris, France
- Centre d’investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Paris, France
| | - Camille Jamet
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
| | | | - Anais Le Ven
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Karine Bernardeau
- Centre Hospitalier Universitaire (CHU) Nantes, Centre National de la Recherche Scientifique, Inserm, BioCore, US16, Nantes Université, Nantes, France
| | - Nathalie Cassoux
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | - Alexandre Matet
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | - Denis Malaise
- Department of Surgical Oncology, University of Paris, Institut Curie, Paris, France
| | | | | | - Marc-Henri Stern
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
| | - Manuel Rodrigues
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, PSL University, Institut Curie, Paris, France
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Olivier Lantz
- Department of Immunity and Cancer, Inserm U932, Paris Sciences et Lettres (PSL) University, Institut Curie, Paris, France
- Laboratoire d’Immunologie Clinique, Institut Curie, Paris, France
- Centre d’investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Paris, France
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7
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Sundebo Meldgaard T, Viborg N, Suarez Hernandez S, Vazquez Albacete D, Tamhane T, Reker Hadrup S. Validation of novel conditional ligands and large-scale detection of antigen-specific T cells for H-2D d and H-2K d. Sci Rep 2024; 14:12292. [PMID: 38811654 PMCID: PMC11136991 DOI: 10.1038/s41598-024-62938-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024] Open
Abstract
The UV-mediated peptide exchange has enabled the generation of multiple different MHC multimer specificities in parallel, surpassing tedious individual refolding of MHC molecules with peptide ligands. Murine models are acknowledged as an effective tool for preclinical research to advance our understanding of immunological mechanisms, with the potential translatability of key learnings from mouse models to the clinic. The common inbred mouse strain BALB/c is frequently used in immunological research. However, for the BALB/c histocompatibility (H)-2 alleles availability of conditional ligand has been limited. To overcome this challenge, we design and experimentally validate conditional ligands restricted to murine MHC class I alleles H2Dd and H2Kd. In addition, we demonstrate the ability of the three H2d molecules and two additional C57BL/6 H2b molecules folded in-house with conditional ligands to generate fluorescently labeled peptide-H2 tetramers that allow staining of antigen-specific CD8+ T cells in splenocyte samples. Finally, we generate large peptide-H-2 multimer libraries with a DNA-barcode labeling system for high-throughput interrogation of CD8+ T cell specificity in murine splenocyte samples. Consequently, the described techniques will contribute to our understanding of the antigen-specific CD8+ T cell repertoire in murine preclinical models of various diseases.
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Affiliation(s)
- Trine Sundebo Meldgaard
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
- Novo Nordisk, Copenhagen, Denmark
| | - Nadia Viborg
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
- Evaxion Biotech, Hørsholm, Denmark
| | - Sara Suarez Hernandez
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
- RIVM National Institute for Public Health and the Environment, Utrecht, The Netherlands
| | - Dario Vazquez Albacete
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
- Novonesis, Copenhagen, Denmark
| | - Tripti Tamhane
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Sine Reker Hadrup
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark.
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8
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Mørk SK, Skadborg SK, Albieri B, Draghi A, Bol K, Kadivar M, Westergaard MCW, Stoltenborg Granhøj J, Borch A, Petersen NV, Thuesen N, Rasmussen IS, Andreasen LV, Dohn RB, Yde CW, Noergaard N, Lorentzen T, Soerensen AB, Kleine-Kohlbrecher D, Jespersen A, Christensen D, Kringelum J, Donia M, Hadrup SR, Marie Svane I. Dose escalation study of a personalized peptide-based neoantigen vaccine (EVX-01) in patients with metastatic melanoma. J Immunother Cancer 2024; 12:e008817. [PMID: 38782542 PMCID: PMC11116868 DOI: 10.1136/jitc-2024-008817] [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] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Neoantigens can serve as targets for T cell-mediated antitumor immunity via personalized neopeptide vaccines. Interim data from our clinical study NCT03715985 showed that the personalized peptide-based neoantigen vaccine EVX-01, formulated in the liposomal adjuvant, CAF09b, was safe and able to elicit EVX-01-specific T cell responses in patients with metastatic melanoma. Here, we present results from the dose-escalation part of the study, evaluating the feasibility, safety, efficacy, and immunogenicity of EVX-01 in addition to anti-PD-1 therapy. METHODS Patients with metastatic melanoma on anti-PD-1 therapy were treated in three cohorts with increasing vaccine dosages (twofold and fourfold). Tumor-derived neoantigens were selected by the AI platform PIONEER and used in personalized therapeutic cancer peptide vaccines EVX-01. Vaccines were administered at 2-week intervals for a total of three intraperitoneal and three intramuscular injections. The study's primary endpoint was safety and tolerability. Additional endpoints were immunological responses, survival, and objective response rates. RESULTS Compared with the base dose level previously reported, no new vaccine-related serious adverse events were observed during dose escalation of EVX-01 in combination with an anti-PD-1 agent given according to local guidelines. Two patients at the third dose level (fourfold dose) developed grade 3 toxicity, most likely related to pembrolizumab. Overall, 8 out of the 12 patients had objective clinical responses (6 partial response (PR) and 2 CR), with all 4 patients at the highest dose level having a CR (1 CR, 3 PR). EVX-01 induced peptide-specific CD4+ and/or CD8+T cell responses in all treated patients, with CD4+T cells as the dominating responses. The magnitude of immune responses measured by IFN-γ ELISpot assay correlated with individual peptide doses. A significant correlation between the PIONEER quality score and induced T cell immunogenicity was detected, while better CRs correlated with both the number of immunogenic EVX-01 peptides and the PIONEER quality score. CONCLUSION Immunization with EVX-01-CAF09b in addition to anti-PD-1 therapy was shown to be safe and well tolerated and elicit vaccine neoantigen-specific CD4+and CD8+ T cell responses at all dose levels. In addition, objective tumor responses were observed in 67% of patients. The results encourage further assessment of the antitumor efficacy of EVX-01 in combination with anti-PD-1 therapy.
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Affiliation(s)
- Sofie Kirial Mørk
- Department of Oncology, Copenhagen University Hospital, National Center for Cancer Immune Therapy (CCIT-DK), Herlev, Denmark
| | | | - Benedetta Albieri
- Department of Oncology, Copenhagen University Hospital, National Center for Cancer Immune Therapy (CCIT-DK), Herlev, Denmark
| | - Arianna Draghi
- Department of Oncology, Copenhagen University Hospital, National Center for Cancer Immune Therapy (CCIT-DK), Herlev, Denmark
| | - Kalijn Bol
- Medical Oncology, Radboudumc, Nijmegen, The Netherlands
| | - Mohammad Kadivar
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Joachim Stoltenborg Granhøj
- Department of Oncology, Copenhagen University Hospital, National Center for Cancer Immune Therapy (CCIT-DK), Herlev, Denmark
| | - Annie Borch
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | | | | | | | - Rebecca Bach Dohn
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Nis Noergaard
- Department of Urology, Copenhagen University Hospital, Herlev, Denmark
| | - Torben Lorentzen
- Department of Gastroenterology, Copenhagen University Hospital, Herlev, Denmark
| | | | | | | | - Dennis Christensen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Marco Donia
- Department of Oncology, Copenhagen University Hospital, National Center for Cancer Immune Therapy (CCIT-DK), Herlev, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Inge Marie Svane
- Department of Oncology, Copenhagen University Hospital, National Center for Cancer Immune Therapy (CCIT-DK), Herlev, Denmark
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9
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Kristensen NP, Dionisio E, Bentzen AK, Tamhane T, Kemming JS, Nos G, Voss LF, Hansen UK, Lauer GM, Hadrup SR. Simultaneous analysis of pMHC binding and reactivity unveils virus-specific CD8 T cell immunity to a concise epitope set. SCIENCE ADVANCES 2024; 10:eadm8951. [PMID: 38608022 PMCID: PMC11014448 DOI: 10.1126/sciadv.adm8951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/12/2024] [Indexed: 04/14/2024]
Abstract
CD8 T cells provide immunity to virus infection through recognition of epitopes presented by peptide major histocompatibility complexes (pMHCs). To establish a concise panel of widely recognized T cell epitopes from common viruses, we combined analysis of TCR down-regulation upon stimulation with epitope-specific enumeration based on barcode-labeled pMHC multimers. We assess CD8 T cell binding and reactivity for 929 previously reported epitopes in the context of 1 of 25 HLA alleles representing 29 viruses. The prevalence and magnitude of CD8 T cell responses were evaluated in 48 donors and reported along with 137 frequently recognized virus epitopes, many of which were underrepresented in the public domain. Eighty-four percent of epitope-specific CD8 T cell populations demonstrated reactivity to peptide stimulation, which was associated with effector and long-term memory phenotypes. Conversely, nonreactive T cell populations were associated primarily with naive phenotypes. Our analysis provides a reference map of epitopes for characterizing CD8 T cell responses toward common human virus infections.
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Affiliation(s)
- Nikolaj Pagh Kristensen
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Edoardo Dionisio
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Amalie Kai Bentzen
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Tripti Tamhane
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Janine Sophie Kemming
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Grigorii Nos
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Lasse Frank Voss
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Ulla Kring Hansen
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Georg Michael Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Sine Reker Hadrup
- Section for Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
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10
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Cavalluzzo B, Viuff MC, Tvingsholm SA, Ragone C, Manolio C, Mauriello A, Buonaguro FM, Tornesello ML, Izzo F, Morabito A, Hadrup SR, Tagliamonte M, Buonaguro L. Cross-reactive CD8 + T cell responses to tumor-associated antigens (TAAs) and homologous microbiota-derived antigens (MoAs). J Exp Clin Cancer Res 2024; 43:87. [PMID: 38509571 PMCID: PMC10953141 DOI: 10.1186/s13046-024-03004-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND We have recently shown extensive sequence and conformational homology between tumor-associated antigens (TAAs) and antigens derived from microorganisms (MoAs). The present study aimed to assess the breadth of T-cell recognition specific to MoAs and the corresponding TAAs in healthy subjects (HS) and patients with cancer (CP). METHOD A library of > 100 peptide-MHC (pMHC) combinations was used to generate DNA-barcode labelled multimers. Homologous peptides were selected from the Cancer Antigenic Peptide Database, as well as Bacteroidetes/Firmicutes-derived peptides. They were incubated with CD8 + T cells from the peripheral blood of HLA-A*02:01 healthy individuals (n = 10) and cancer patients (n = 16). T cell recognition was identified using tetramer-staining analysis. Cytotoxicity assay was performed using as target cells TAP-deficient T2 cells loaded with MoA or the paired TuA. RESULTS A total of 66 unique pMHC recognized by CD8+ T cells across all groups were identified. Of these, 21 epitopes from microbiota were identified as novel immunological targets. Reactivity against selected TAAs was observed for both HS and CP. pMHC tetramer staining confirmed CD8+ T cell populations cross-reacting with CTA SSX2 and paired microbiota epitopes. Moreover, PBMCs activated with the MoA where shown to release IFNγ as well as to exert cytotoxic activity against cells presenting the paired TuA. CONCLUSIONS Several predicted microbiota-derived MoAs are recognized by T cells in HS and CP. Reactivity against TAAs was observed also in HS, primed by the homologous bacterial antigens. CD8+ T cells cross-reacting with MAGE-A1 and paired microbiota epitopes were identified in three subjects. Therefore, the microbiota can elicit an extensive repertoire of natural memory T cells to TAAs, possibly able to control tumor growth ("natural anti-cancer vaccination"). In addition, non-self MoAs can be included in preventive/therapeutic off-the-shelf cancer vaccines with more potent anti-tumor efficacy than those based on TAAs.
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Affiliation(s)
- Beatrice Cavalluzzo
- Innovative Immunological Models Unit, Istituto Nazionale Tumori - IRCCS - "Fond G. Pascale", Via Mariano Semmola, 52, Naples, Italy
| | - Marie Christine Viuff
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Siri Amanda Tvingsholm
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Concetta Ragone
- Innovative Immunological Models Unit, Istituto Nazionale Tumori - IRCCS - "Fond G. Pascale", Via Mariano Semmola, 52, Naples, Italy
| | - Carmen Manolio
- Innovative Immunological Models Unit, Istituto Nazionale Tumori - IRCCS - "Fond G. Pascale", Via Mariano Semmola, 52, Naples, Italy
| | - Angela Mauriello
- Innovative Immunological Models Unit, Istituto Nazionale Tumori - IRCCS - "Fond G. Pascale", Via Mariano Semmola, 52, Naples, Italy
| | - Franco M Buonaguro
- Molecular Biology and Viral Oncogenesis Unit, Istituto Nazionale Tumori - IRCCS - "Fond G. Pascale", Naples, Italy
| | - Maria Lina Tornesello
- Molecular Biology and Viral Oncogenesis Unit, Istituto Nazionale Tumori - IRCCS - "Fond G. Pascale", Naples, Italy
| | - Francesco Izzo
- Hepatobiliary Surgical Oncology Unit, Istituto Nazionale Tumori - IRCCS - "Fond. G. Pascale", Naples, Italy
| | - Alessandro Morabito
- Thoracic Medical Oncology, Istituto Nazionale Tumori - IRCCS - "Fond G. Pascale", Naples, Italy
| | - Sine Reker Hadrup
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Maria Tagliamonte
- Innovative Immunological Models Unit, Istituto Nazionale Tumori - IRCCS - "Fond G. Pascale", Via Mariano Semmola, 52, Naples, Italy.
| | - Luigi Buonaguro
- Innovative Immunological Models Unit, Istituto Nazionale Tumori - IRCCS - "Fond G. Pascale", Via Mariano Semmola, 52, Naples, Italy.
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11
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Hansen UK, Church CD, Carnaz Simões AM, Frej MS, Bentzen AK, Tvingsholm SA, Becker JC, Fling SP, Ramchurren N, Topalian SL, Nghiem PT, Hadrup SR. T antigen-specific CD8+ T cells associate with PD-1 blockade response in virus-positive Merkel cell carcinoma. J Clin Invest 2024; 134:e177082. [PMID: 38618958 PMCID: PMC11014655 DOI: 10.1172/jci177082] [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: 10/31/2023] [Accepted: 01/23/2024] [Indexed: 04/16/2024] Open
Abstract
Merkel cell carcinoma (MCC) is a highly immunogenic skin cancer primarily induced by Merkel cell polyomavirus, which is driven by the expression of the oncogenic T antigens (T-Ags). Blockade of the programmed cell death protein-1 (PD-1) pathway has shown remarkable response rates, but evidence for therapy-associated T-Ag-specific immune response and therapeutic strategies for the nonresponding fraction are both limited. We tracked T-Ag-reactive CD8+ T cells in peripheral blood of 26 MCC patients under anti-PD1 therapy, using DNA-barcoded pMHC multimers, displaying all peptides from the predicted HLA ligandome of the oncoproteins, covering 33 class I haplotypes. We observed a broad T cell recognition of T-Ags, including identification of 20 T-Ag-derived epitopes we believe to be novel. Broadening of the T-Ag recognition profile and increased T cell frequencies during therapy were strongly associated with clinical response and prolonged progression-free survival. T-Ag-specific T cells could be further boosted and expanded directly from peripheral blood using artificial antigen-presenting scaffolds, even in patients with no detectable T-Ag-specific T cells. These T cells provided strong tumor-rejection capacity while retaining a favorable phenotype for adoptive cell transfer. These findings demonstrate that T-Ag-specific T cells are associated with the clinical outcome to PD-1 blockade and that Ag-presenting scaffolds can be used to boost such responses.
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Affiliation(s)
- Ulla Kring Hansen
- Section of Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- PokeAcell Aps, BioInnovation Institute, Copenhagen, Denmark
| | - Candice D. Church
- Department of Dermatology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Marcus Svensson Frej
- Section of Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- PokeAcell Aps, BioInnovation Institute, Copenhagen, Denmark
| | - Amalie Kai Bentzen
- Section of Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Siri A. Tvingsholm
- Section of Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jürgen C. Becker
- Department of Translational Skin Cancer Research, University Hospital Essen and German Cancer Consortium (DKTK), Essen, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | | | | | - Suzanne L. Topalian
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Paul T. Nghiem
- Department of Dermatology, Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Sine Reker Hadrup
- Section of Experimental and Translational Immunology, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
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12
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Meyer M, Parpoulas C, Barthélémy T, Becker JP, Charoentong P, Lyu Y, Börsig S, Bulbuc N, Tessmer C, Weinacht L, Ibberson D, Schmidt P, Pipkorn R, Eichmüller SB, Steinberger P, Lindner K, Poschke I, Platten M, Fröhling S, Riemer AB, Hassel JC, Roberti MP, Jäger D, Zörnig I, Momburg F. MediMer: a versatile do-it-yourself peptide-receptive MHC class I multimer platform for tumor neoantigen-specific T cell detection. Front Immunol 2024; 14:1294565. [PMID: 38239352 PMCID: PMC10794645 DOI: 10.3389/fimmu.2023.1294565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/28/2023] [Indexed: 01/22/2024] Open
Abstract
Peptide-loaded MHC class I (pMHC-I) multimers have revolutionized our capabilities to monitor disease-associated T cell responses with high sensitivity and specificity. To improve the discovery of T cell receptors (TCR) targeting neoantigens of individual tumor patients with recombinant MHC molecules, we developed a peptide-loadable MHC class I platform termed MediMer. MediMers are based on soluble disulfide-stabilized β2-microglobulin/heavy chain ectodomain single-chain dimers (dsSCD) that can be easily produced in large quantities in eukaryotic cells and tailored to individual patients' HLA allotypes with only little hands-on time. Upon transient expression in CHO-S cells together with ER-targeted BirA biotin ligase, biotinylated dsSCD are purified from the cell supernatant and are ready to use. We show that CHO-produced dsSCD are free of endogenous peptide ligands. Empty dsSCD from more than 30 different HLA-A,B,C allotypes, that were produced and validated so far, can be loaded with synthetic peptides matching the known binding criteria of the respective allotypes, and stored at low temperature without loss of binding activity. We demonstrate the usability of peptide-loaded dsSCD multimers for the detection of human antigen-specific T cells with comparable sensitivities as multimers generated with peptide-tethered β2m-HLA heavy chain single-chain trimers (SCT) and wild-type peptide-MHC-I complexes prior formed in small-scale refolding reactions. Using allotype-specific, fluorophore-labeled competitor peptides, we present a novel dsSCD-based peptide binding assay capable of interrogating large libraries of in silico predicted neoepitope peptides by flow cytometry in a high-throughput and rapid format. We discovered rare T cell populations with specificity for tumor neoepitopes and epitopes from shared tumor-associated antigens in peripheral blood of a melanoma patient including a so far unreported HLA-C*08:02-restricted NY-ESO-1-specific CD8+ T cell population. Two representative TCR of this T cell population, which could be of potential value for a broader spectrum of patients, were identified by dsSCD-guided single-cell sequencing and were validated by cognate pMHC-I multimer staining and functional responses to autologous peptide-pulsed antigen presenting cells. By deploying the technically accessible dsSCD MHC-I MediMer platform, we hope to significantly improve success rates for the discovery of personalized neoepitope-specific TCR in the future by being able to also cover rare HLA allotypes.
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Affiliation(s)
- Marten Meyer
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Christina Parpoulas
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Titouan Barthélémy
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonas P. Becker
- Division of Immunotherapy and Immunoprevention, DKFZ, Heidelberg, Germany
- German Center for Infection Research (DZIF) Partner Site Heidelberg, Heidelberg, Germany
| | - Pornpimol Charoentong
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany
| | - Yanhong Lyu
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
| | - Selina Börsig
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Nadja Bulbuc
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Tessmer
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
| | - Lisa Weinacht
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, Heidelberg University, Heidelberg, Germany
| | - Patrick Schmidt
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
- GMP and T Cell Therapy, DKFZ, Heidelberg, Germany
| | | | | | - Peter Steinberger
- Division of Immune Receptors and T Cell Activation, Center for Pathophysiology, Infectiology, Medical University of Vienna, Vienna, Austria
| | - Katharina Lindner
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Isabel Poschke
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), DKFZ, Core Center, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience (MCTN), Heidelberg University, Mannheim, Germany
- DKFZ Hector Cancer Institute at the University Medical Center, Mannheim, Germany
- Helmholtz Institute for Translational Oncology, Mainz (HI-TRON Mainz), Mainz, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), DKFZ, Core Center, Heidelberg, Germany
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Angelika B. Riemer
- Division of Immunotherapy and Immunoprevention, DKFZ, Heidelberg, Germany
- German Center for Infection Research (DZIF) Partner Site Heidelberg, Heidelberg, Germany
| | - Jessica C. Hassel
- Section of DermatoOncology, Department of Dermatology and NCT, Heidelberg University Hospital, Heidelberg, Germany
| | - Maria Paula Roberti
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Dirk Jäger
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Inka Zörnig
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Momburg
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
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13
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Tvingsholm SA, Frej MS, Rafa VM, Hansen UK, Ormhøj M, Tyron A, Jensen AWP, Kadivar M, Bentzen AK, Munk KK, Aasbjerg GN, Ternander JSH, Heeke C, Tamhane T, Schmess C, Funt SA, Kjeldsen JW, Kverneland AH, Met Ö, Draghi A, Jakobsen SN, Donia M, Marie Svane I, Hadrup SR. TCR-engaging scaffolds selectively expand antigen-specific T-cells with a favorable phenotype for adoptive cell therapy. J Immunother Cancer 2023; 11:e006847. [PMID: 37586765 PMCID: PMC10432666 DOI: 10.1136/jitc-2023-006847] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Adoptive cell therapy (ACT) has shown promising results for the treatment of cancer and viral infections. Successful ACT relies on ex vivo expansion of large numbers of desired T-cells with strong cytotoxic capacity and in vivo persistence, which constitutes the greatest challenge to current ACT strategies. Here, in this study, we present a novel technology for ex vivo expansion of antigen-specific T-cells; artificial antigen-presenting scaffolds (Ag-scaffolds) consisting of a dextran-polysaccharide backbone, decorated with combinations of peptide-Major Histocompatibility Complex (pMHC), cytokines and co-stimulatory molecules, enabling coordinated stimulation of antigen-specific T-cells. METHODS The capacity of Ag-scaffolds to expand antigen-specific T-cells was explored in ex vivo cultures with peripheral blood mononuclear cells from healthy donors and patients with metastatic melanoma. The resulting T-cell products were assessed for phenotypic and functional characteristics. RESULTS We identified an optimal Ag-scaffold for expansion of T-cells for ACT, carrying pMHC and interleukin-2 (IL-2) and IL-21, with which we efficiently expanded both virus-specific and tumor-specific CD8+ T cells from peripheral blood of healthy donors and patients, respectively. The resulting T-cell products were characterized by a high frequency of antigen-specific cells with high self-renewal capacity, low exhaustion, a multifunctional cytokine profile upon antigen-challenge and superior tumor killing capacity. This demonstrates that the coordinated stimuli provided by an optimized stoichiometry of TCR engaging (pMHC) and stimulatory (cytokine) moieties is essential to obtain desired T-cell characteristics. To generate an 'off-the-shelf' multitargeting Ag-scaffold product of relevance to patients with metastatic melanoma, we identified the 30 most frequently recognized shared HLA-A0201-restricted melanoma epitopes in a cohort of 87 patients. By combining these in an Ag-scaffold product, we were able to expand tumor-specific T-cells from 60-70% of patients with melanoma, yielding a multitargeted T-cell product with up to 25% specific and phenotypically and functionally improved T cells. CONCLUSIONS Taken together, the Ag-scaffold represents a promising new technology for selective expansion of antigen-specific CD8+ T cells directly from blood, yielding a highly specific and functionally enhanced T-cell product for ACT.
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Affiliation(s)
| | | | - Vibeke Mindahl Rafa
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | - Maria Ormhøj
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Alexander Tyron
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Agnete W P Jensen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Herlev, Denmark
| | - Mohammad Kadivar
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Amalie Kai Bentzen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Kamilla K Munk
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Gitte N Aasbjerg
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | - Christina Heeke
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Tripti Tamhane
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Christian Schmess
- NMI Natural and Medical Science Institute, University of Tübingen, Tubingen, Germany
| | - Samuel A Funt
- Deptartment of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Julie Westerlin Kjeldsen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Herlev, Denmark
| | - Anders Handrup Kverneland
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Herlev, Denmark
| | - Özcan Met
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Copenhagen, Denmark
| | - Arianna Draghi
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Herlev, Denmark
| | - Søren Nyboe Jakobsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Herlev, Denmark
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Herlev Hospital, Herlev, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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14
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Tsimberidou AM, Guenther K, Andersson BS, Mendrzyk R, Alpert A, Wagner C, Nowak A, Aslan K, Satelli A, Richter F, Kuttruff-Coqui S, Schoor O, Fritsche J, Coughlin Z, Mohamed AS, Sieger K, Norris B, Ort R, Beck J, Vo HH, Hoffgaard F, Ruh M, Backert L, Wistuba II, Fuhrmann D, Ibrahim NK, Morris VK, Kee BK, Halperin DM, Nogueras-Gonzalez GM, Kebriaei P, Shpall EJ, Vining D, Hwu P, Singh H, Reinhardt C, Britten CM, Hilf N, Weinschenk T, Maurer D, Walter S. Feasibility and Safety of Personalized, Multi-Target, Adoptive Cell Therapy (IMA101): First-in-Human Clinical Trial in Patients with Advanced Metastatic Cancer. Cancer Immunol Res 2023; 11:925-945. [PMID: 37172100 PMCID: PMC10330623 DOI: 10.1158/2326-6066.cir-22-0444] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/15/2022] [Accepted: 05/11/2023] [Indexed: 05/14/2023]
Abstract
IMA101 is an actively personalized, multi-targeted adoptive cell therapy (ACT), whereby autologous T cells are directed against multiple novel defined peptide-HLA (pHLA) cancer targets. HLA-A*02:01-positive patients with relapsed/refractory solid tumors expressing ≥1 of 8 predefined targets underwent leukapheresis. Endogenous T cells specific for up to 4 targets were primed and expanded in vitro. Patients received lymphodepletion (fludarabine, cyclophosphamide), followed by T-cell infusion and low-dose IL2 (Cohort 1). Patients in Cohort 2 received atezolizumab for up to 1 year (NCT02876510). Overall, 214 patients were screened, 15 received lymphodepletion (13 women, 2 men; median age, 44 years), and 14 were treated with T-cell products. IMA101 treatment was feasible and well tolerated. The most common adverse events were cytokine release syndrome (Grade 1, n = 6; Grade 2, n = 4) and expected cytopenias. No patient died during the first 100 days after T-cell therapy. No neurotoxicity was observed. No objective responses were noted. Prolonged disease stabilization was noted in three patients lasting for 13.7, 12.9, and 7.3 months. High frequencies of target-specific T cells (up to 78.7% of CD8+ cells) were detected in the blood of treated patients, persisted for >1 year, and were detectable in posttreatment tumor tissue. Individual T-cell receptors (TCR) contained in T-cell products exhibited broad variation in TCR avidity, with the majority being low avidity. High-avidity TCRs were identified in some patients' products. This study demonstrates the feasibility and tolerability of an actively personalized ACT directed to multiple defined pHLA cancer targets. Results warrant further evaluation of multi-target ACT approaches using potent high-avidity TCRs. See related Spotlight by Uslu and June, p. 865.
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Affiliation(s)
- Apostolia M Tsimberidou
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Borje S Andersson
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | - Anna Nowak
- Immatics Biotechnologies GmbH, Tuebingen, Germany
| | - Katrin Aslan
- Immatics Biotechnologies GmbH, Tuebingen, Germany
| | | | | | | | | | | | | | | | | | - Becky Norris
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rita Ort
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer Beck
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Henry Hiep Vo
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Manuel Ruh
- Immatics Biotechnologies GmbH, Tuebingen, Germany
| | | | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Nuhad K Ibrahim
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Van Karlyle Morris
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Texas
| | - Bryan K Kee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Texas
| | - Daniel M Halperin
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Texas
| | | | - Partow Kebriaei
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David Vining
- Department of Abdominal Imaging, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | - Norbert Hilf
- Immatics Biotechnologies GmbH, Tuebingen, Germany
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15
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Hulen TM, Friese C, Kristensen NP, Granhøj JS, Borch TH, Peeters MJW, Donia M, Andersen MH, Hadrup SR, Svane IM, Met Ö. Ex vivo modulation of intact tumor fragments with anti-PD-1 and anti-CTLA-4 influences the expansion and specificity of tumor-infiltrating lymphocytes. Front Immunol 2023; 14:1180997. [PMID: 37359554 PMCID: PMC10285209 DOI: 10.3389/fimmu.2023.1180997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
Checkpoint inhibition (CPI) therapy and adoptive cell therapy with autologous tumor-infiltrating lymphocytes (TIL-based ACT) are the two most effective immunotherapies for the treatment of metastatic melanoma. While CPI has been the dominating therapy in the past decade, TIL-based ACT is beneficial for individuals even after progression on previous immunotherapies. Given that notable differences in response have been made when used as a subsequent treatment, we investigated how the qualities of TILs changed when the ex vivo microenvironment of intact tumor fragments were modulated with checkpoint inhibitors targeting programmed death receptor 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4). Initially, we show that unmodified TILs from CPI-resistant individuals can be produced, are overwhelmingly terminally differentiated, and are capable of responding to tumor. We then investigate these properties in ex vivo checkpoint modulated TILs finding that that they retain these qualities. Lastly, we confirmed the specificity of the TILs to the highest responding tumor antigens, and identified this reactivity resides largely in CD39+CD69+ terminally differentiated populations. Overall, we found that anti-PD-1 will alter the proliferative capacity while anti-CTLA4 will influence breadth of antigen specificity.
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Affiliation(s)
- Thomas Morgan Hulen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Christina Friese
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | | | - Joachim Stoltenborg Granhøj
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Troels Holz Borch
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Marlies J. W. Peeters
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Mads Hald Andersen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Özcan Met
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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16
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Puig-Saus C, Sennino B, Peng S, Wang CL, Pan Z, Yuen B, Purandare B, An D, Quach BB, Nguyen D, Xia H, Jilani S, Shao K, McHugh C, Greer J, Peabody P, Nayak S, Hoover J, Said S, Jacoby K, Dalmas O, Foy SP, Conroy A, Yi MC, Shieh C, Lu W, Heeringa K, Ma Y, Chizari S, Pilling MJ, Ting M, Tunuguntla R, Sandoval S, Moot R, Hunter T, Zhao S, Saco JD, Perez-Garcilazo I, Medina E, Vega-Crespo A, Baselga-Carretero I, Abril-Rodriguez G, Cherry G, Wong DJ, Hundal J, Chmielowski B, Speiser DE, Bethune MT, Bao XR, Gros A, Griffith OL, Griffith M, Heath JR, Franzusoff A, Mandl SJ, Ribas A. Neoantigen-targeted CD8 + T cell responses with PD-1 blockade therapy. Nature 2023; 615:697-704. [PMID: 36890230 PMCID: PMC10441586 DOI: 10.1038/s41586-023-05787-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/02/2023] [Indexed: 03/10/2023]
Abstract
Neoantigens are peptides derived from non-synonymous mutations presented by human leukocyte antigens (HLAs), which are recognized by antitumour T cells1-14. The large HLA allele diversity and limiting clinical samples have restricted the study of the landscape of neoantigen-targeted T cell responses in patients over their treatment course. Here we applied recently developed technologies15-17 to capture neoantigen-specific T cells from blood and tumours from patients with metastatic melanoma with or without response to anti-programmed death receptor 1 (PD-1) immunotherapy. We generated personalized libraries of neoantigen-HLA capture reagents to single-cell isolate the T cells and clone their T cell receptors (neoTCRs). Multiple T cells with different neoTCR sequences (T cell clonotypes) recognized a limited number of mutations in samples from seven patients with long-lasting clinical responses. These neoTCR clonotypes were recurrently detected over time in the blood and tumour. Samples from four patients with no response to anti-PD-1 also demonstrated neoantigen-specific T cell responses in the blood and tumour to a restricted number of mutations with lower TCR polyclonality and were not recurrently detected in sequential samples. Reconstitution of the neoTCRs in donor T cells using non-viral CRISPR-Cas9 gene editing demonstrated specific recognition and cytotoxicity to patient-matched melanoma cell lines. Thus, effective anti-PD-1 immunotherapy is associated with the presence of polyclonal CD8+ T cells in the tumour and blood specific for a limited number of immunodominant mutations, which are recurrently recognized over time.
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Affiliation(s)
- Cristina Puig-Saus
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA.
| | | | | | | | | | | | | | - Duo An
- PACT Pharma, San Francisco, CA, USA
| | | | | | - Huiming Xia
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Sameeha Jilani
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yan Ma
- PACT Pharma, San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Sidi Zhao
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Justin D Saco
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ivan Perez-Garcilazo
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Egmidio Medina
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Agustin Vega-Crespo
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ignacio Baselga-Carretero
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Gabriel Abril-Rodriguez
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Grace Cherry
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Deborah J Wong
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jasreet Hundal
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Bartosz Chmielowski
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
| | - Daniel E Speiser
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Alena Gros
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | - Antoni Ribas
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA.
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17
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Merlotti A, Sadacca B, Arribas YA, Ngoma M, Burbage M, Goudot C, Houy A, Rocañín-Arjó A, Lalanne A, Seguin-Givelet A, Lefevre M, Heurtebise-Chrétien S, Baudon B, Oliveira G, Loew D, Carrascal M, Wu CJ, Lantz O, Stern MH, Girard N, Waterfall JJ, Amigorena S. Noncanonical splicing junctions between exons and transposable elements represent a source of immunogenic recurrent neo-antigens in patients with lung cancer. Sci Immunol 2023; 8:eabm6359. [PMID: 36735774 DOI: 10.1126/sciimmunol.abm6359] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/12/2023] [Indexed: 02/05/2023]
Abstract
Although most characterized tumor antigens are encoded by canonical transcripts (such as differentiation or tumor-testis antigens) or mutations (both driver and passenger mutations), recent results have shown that noncanonical transcripts including long noncoding RNAs and transposable elements (TEs) can also encode tumor-specific neo-antigens. Here, we investigate the presentation and immunogenicity of tumor antigens derived from noncanonical mRNA splicing events between coding exons and TEs. Comparing human non-small cell lung cancer (NSCLC) and diverse healthy tissues, we identified a subset of splicing junctions that is both tumor specific and shared across patients. We used HLA-I peptidomics to identify peptides encoded by tumor-specific junctions in primary NSCLC samples and lung tumor cell lines. Recurrent junction-encoded peptides were immunogenic in vitro, and CD8+ T cells specific for junction-encoded epitopes were present in tumors and tumor-draining lymph nodes from patients with NSCLC. We conclude that noncanonical splicing junctions between exons and TEs represent a source of recurrent, immunogenic tumor-specific antigens in patients with NSCLC.
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Affiliation(s)
- Antonela Merlotti
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Benjamin Sadacca
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Yago A Arribas
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Mercia Ngoma
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Marianne Burbage
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Christel Goudot
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Alexandre Houy
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
| | - Ares Rocañín-Arjó
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Ana Lalanne
- Institut Curie, Laboratory of Clinical immunology, 75005 Paris, France
- Institut Curie, CIC-BT1428, 75005 Paris, France
| | - Agathe Seguin-Givelet
- Thoracic Surgery Department, Curie-Montsouris Thorax Institute - Institut Mutualiste Montsouris, Paris, France
- Paris 13 University, Sorbonne Paris Cité, Faculty of Medicine SMBH, Bobigny, France
| | - Marine Lefevre
- Department of Pathology, Institute Mutualiste Montsouris, Paris, France
| | | | - Blandine Baudon
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Damarys Loew
- Institut Curie, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Paris cedex 05, France
| | - Montserrat Carrascal
- Biological and Environmental Proteomics, Institut d'Investigacions Biomèdiques de Barcelona-CSIC, IDIBAPS, Roselló 161, 6a planta, 08036 Barcelona, Spain
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Olivier Lantz
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
- Institut Curie, Laboratory of Clinical immunology, 75005 Paris, France
- Institut Curie, CIC-BT1428, 75005 Paris, France
| | - Marc-Henri Stern
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
| | - Nicolas Girard
- Thoracic Surgery Department, Curie-Montsouris Thorax Institute - Institut Mutualiste Montsouris, Paris, France
| | - Joshua J Waterfall
- INSERM U830, PSL Research University, Institute Curie Research Center, Paris, France
- Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Sebastian Amigorena
- Institut Curie, Université Paris Sciences et Lettres, INSERM U932, 75005 Paris, France
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18
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Hernandez SPA, Hersby DS, Munk KK, Tamhane T, Trubach D, Tagliamonte M, Buonaguro L, Gang AO, Hadrup SR, Saini SK. Three doses of BNT162b2 COVID-19 mRNA vaccine establish long-lasting CD8 + T cell immunity in CLL and MDS patients. Front Immunol 2023; 13:1035344. [PMID: 36703960 PMCID: PMC9873231 DOI: 10.3389/fimmu.2022.1035344] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Patients with hematological malignancies are prioritized for COVID-19 vaccine due to their high risk for severe SARS-CoV-2 infection-related disease and mortality. To understand T cell immunity, its long-term persistence, and its correlation with antibody response, we evaluated the BNT162b2 COVID-19 mRNA vaccine-specific immune response in chronic lymphocytic leukemia (CLL) and myeloid dysplastic syndrome (MDS) patients. Longitudinal analysis of CD8+ T cells using DNA-barcoded peptide-MHC multimers covering the full SARS-CoV-2 Spike-protein (415 peptides) showed vaccine-specific T cell activation and persistence of memory T cells up to six months post-vaccination. Surprisingly, a higher frequency of vaccine-induced antigen-specific CD8+ T cells was observed in the patient group compared to a healthy donor group. Furthermore, and importantly, immunization with the second booster dose significantly increased the frequency of antigen-specific CD8+ T cells as well as the total number of T cell specificities. Altogether 59 BNT162b2 mRNA vaccine-derived immunogenic responses were identified, of which 23 established long-term CD8+ T cell memory response with a strong immunodominance for NYNYLYRLF (HLA-A24:02) and YLQPRTFLL (HLA-A02:01) epitopes. In summary, we mapped the vaccine-induced antigen-specific CD8+ T cells and showed a booster-specific activation and enrichment of memory T cells that could be important for long-term disease protection in this patient group.
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Affiliation(s)
- Susana Patricia Amaya Hernandez
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ditte Stampe Hersby
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Kamilla Kjærgaard Munk
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tripti Tamhane
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Darya Trubach
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Maria Tagliamonte
- Innovative Immunological Models Unit, National Cancer Institute Pascale Foundation – IRCCS, Napoli, Italy
| | - Luigi Buonaguro
- Innovative Immunological Models Unit, National Cancer Institute Pascale Foundation – IRCCS, Napoli, Italy
| | - Anne Ortved Gang
- Department of Hematology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sunil Kumar Saini
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark,*Correspondence: Sunil Kumar Saini,
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19
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The common HLA class I-restricted tumor-infiltrating T cell response in HPV16-induced cancer. Cancer Immunol Immunother 2022; 72:1553-1565. [DOI: 10.1007/s00262-022-03350-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
AbstractImmunotherapies targeting truly tumor-specific targets focus on the expansion and activation of T cells against neoantigens or oncogenic viruses. One target is the human papilloma virus type 16 (HPV16), responsible for several anogenital cancers and oropharyngeal carcinomas. Spontaneous and vaccine-induced HPV-specific T cells have been associated with better clinical outcome. However, the epitopes and restriction elements to which these T cells respond remained elusive. To identify CD8+ T cell epitopes in cultures of tumor infiltrating lymphocytes, we here used multimers and/or a functional screening platform exploiting single HLA class I allele-engineered antigen presenting cells. This resulted in the detection of 20 CD8+ T cell responses to 11 different endogenously processed HLA-peptide combinations within 12 HPV16-induced tumors. Specific HLA-peptide combinations dominated the response in patients expressing these HLA alleles. T cell receptors (TCRs) reactive to seven different HLA class I-restricted peptides could be isolated and analysis revealed tumor reactivity for five of the six TCRs analyzed. The tumor reactive TCRs to these dominant HLA class I peptide combinations can potentially be used to engineer tumor-specific T cells for adoptive cell transfer approaches to treat HPV16-induced cancers.
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Clarkson BDS, Johnson RK, Bingel C, Lothaller C, Howe CL. Preservation of antigen-specific responses in cryopreserved CD4 + and CD8 + T cells expanded with IL-2 and IL-7. J Transl Autoimmun 2022; 5:100173. [PMID: 36467614 PMCID: PMC9713293 DOI: 10.1016/j.jtauto.2022.100173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/31/2022] [Accepted: 11/20/2022] [Indexed: 11/27/2022] Open
Abstract
Objectives We sought to develop medium throughput standard operating procedures for screening cryopreserved human peripheral blood mononuclear cells (PBMCs) for CD4+ and CD8+ T cell responses to potential autoantigens. Methods Dendritic cells were loaded with a peptide cocktail from ubiquitous viruses or full-length viral protein antigens and cocultured with autologous T cells. We measured expression of surface activation markers on T cells by flow cytometry and cytometry by time of flight 24-72 h later. We tested responses among T cells freshly isolated from healthy control PBMCs, cryopreserved T cells, and T cells derived from a variety of T cell expansion protocols. We also compared the transcriptional profile of CD8+ T cells rested with interleukin (IL)7 for 48 h after 1) initial thawing, 2) expansion, and 3) secondary cryopreservation/thawing of expanded cells. To generate competent antigen presenting cells from PBMCs, we promoted differentiation of PBMCs into dendritic cells with granulocyte macrophage colony stimulating factor and IL-4. Results We observed robust dendritic cell differentiation from human PBMCs treated with 50 ng/mL GM-CSF and 20 ng/mL IL-4 in as little as 3 days. Dendritic cell purity was substantially increased by magnetically enriching for CD14+ monocytes prior to differentiation. We also measured antigen-dependent T cell activation in DC-T cell cocultures. However, polyclonal expansion of T cells with anti-CD3/antiCD28 abolished antigen-dependent upregulation of CD69 in our assay despite minimal transcriptional differences between rested CD8+ T cells before and after expansion. Furthermore, resting these expanded T cells in IL-2, IL-7 or IL-15 did not restore the antigen dependent responses. In contrast, T cells that were initially expanded with IL-2 + IL-7 rather than plate bound anti-CD3 + anti-CD28 retained responsiveness to antigen stimulation and these responses strongly correlated with responses measured at initial thawing. Significance While screening techniques for potential pathological autoantibodies have come a long way, comparable full-length protein target assays for screening patient T cells at medium throughput are noticeably lacking due to technical hurdles. Here we advance techniques that should have broad applicability to translational studies investigating cell mediated immunity in infectious or autoimmune diseases. Future studies are aimed at investigating possible CD8+ T cell autoantigens in MS and other CNS autoimmune diseases.
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Affiliation(s)
- Benjamin DS. Clarkson
- Department of Neurology, Mayo Clinic, Rochester, MN, 55905, USA,Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, 55905, USA,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA,Corresponding author. Mayo Clinic, Guggenheim 1521C, 200 First Street SW, Rochester, MN, 55905.
| | | | - Corinna Bingel
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center, Heidelberg, Germany
| | | | - Charles L. Howe
- Department of Neurology, Mayo Clinic, Rochester, MN, 55905, USA,Center for Multiple Sclerosis and Autoimmune Neurology, Mayo Clinic, Rochester, MN, 55905, USA,Division of Experimental Neurology, Mayo Clinic, Rochester, MN, 55905, USA,Department of Immunology, Mayo Clinic, Rochester, MN, 55905, USA
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21
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Mechanisms of CD40-dependent cDC1 licensing beyond costimulation. Nat Immunol 2022; 23:1536-1550. [PMID: 36271147 PMCID: PMC9896965 DOI: 10.1038/s41590-022-01324-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 09/07/2022] [Indexed: 02/08/2023]
Abstract
CD40 signaling in classical type 1 dendritic cells (cDC1s) is required for CD8 T cell-mediated tumor rejection, but the underlying mechanisms are incompletely understood. Here, we identified CD40-induced genes in cDC1s, including Cd70, Tnfsf9, Ptgs2 and Bcl2l1, and examined their contributions to anti-tumor immunity. cDC1-specific inactivation of CD70 and COX-2, and global CD27 inactivation, only partially impaired tumor rejection or tumor-specific CD8 T cell expansion. Loss of 4-1BB, alone or in Cd27-/- mice, did not further impair anti-tumor immunity. However, cDC1-specific CD40 inactivation reduced cDC1 mitochondrial transmembrane potential and increased caspase activation in tumor-draining lymph nodes, reducing migratory cDC1 numbers in vivo. Similar impairments occurred during in vitro antigen presentation by Cd40-/- cDC1s to CD8+ T cells, which were reversed by re-expression of Bcl2l1. Thus, CD40 signaling in cDC1s not only induces costimulatory ligands for CD8+ T cells but also induces Bcl2l1 that sustains cDC1 survival during priming of anti-tumor responses.
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22
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Ferris ST, Ohara RA, Ou F, Wu R, Huang X, Kim S, Chen J, Liu TT, Schreiber RD, Murphy TL, Murphy KM. cDC1 Vaccines Drive Tumor Rejection by Direct Presentation Independently of Host cDC1. Cancer Immunol Res 2022; 10:920-931. [PMID: 35648641 PMCID: PMC9357132 DOI: 10.1158/2326-6066.cir-21-0865] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 04/07/2022] [Accepted: 05/24/2022] [Indexed: 02/05/2023]
Abstract
As a cell-based cancer vaccine, dendritic cells (DC), derived from peripheral blood monocytes or bone marrow (BM) treated with GM-CSF (GMDC), were initially thought to induce antitumor immunity by presenting tumor antigens directly to host T cells. Subsequent work revealed that GMDCs do not directly prime tumor-specific T cells, but must transfer their antigens to host DCs. This reduces their advantage over strictly antigen-based strategies proposed as cancer vaccines. Type 1 conventional DCs (cDC1) have been reported to be superior to GMDCs as a cancer vaccine, but whether they act by transferring antigens to host DCs is unknown. To test this, we compared antitumor responses induced by GMDCs and cDC1 in Irf8 +32-/- mice, which lack endogenous cDC1 and cannot reject immunogenic fibrosarcomas. Both GMDCs and cDC1 could cross-present cell-associated antigens to CD8+ T cells in vitro. However, injection of GMDCs into tumors in Irf8 +32-/- mice did not induce antitumor immunity, consistent with their reported dependence on host cDC1. In contrast, injection of cDC1s into tumors in Irf8 +32-/- mice resulted in their migration to tumor-draining lymph nodes, activation of tumor-specific CD8+ T cells, and rejection of the tumors. Tumor rejection did not require the in vitro loading of cDC1 with antigens, indicating that acquisition of antigens in vivo is sufficient to induce antitumor responses. Finally, cDC1 vaccination showed abscopal effects, with rejection of untreated tumors growing concurrently on the opposite flank. These results suggest that cDC1 may be a useful future avenue to explore for antitumor therapy. See related Spotlight by Hubert et al., p. 918.
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Affiliation(s)
- Stephen T. Ferris
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
| | - Ray A. Ohara
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
| | - Feiya Ou
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
| | - Renee Wu
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
| | - Xiao Huang
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
| | - Sunkyung Kim
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
| | - Jing Chen
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
| | - Tian-Tian Liu
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
| | - Robert D. Schreiber
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Theresa L. Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
| | - Kenneth M. Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, MO, 63110, USA
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Bonté PE, Arribas YA, Merlotti A, Carrascal M, Zhang JV, Zueva E, Binder ZA, Alanio C, Goudot C, Amigorena S. Single-cell RNA-seq-based proteogenomics identifies glioblastoma-specific transposable elements encoding HLA-I-presented peptides. Cell Rep 2022; 39:110916. [PMID: 35675780 DOI: 10.1016/j.celrep.2022.110916] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/22/2022] [Accepted: 05/12/2022] [Indexed: 11/03/2022] Open
Abstract
We analyze transposable elements (TEs) in glioblastoma (GBM) patients using a proteogenomic pipeline that combines single-cell transcriptomics, bulk RNA sequencing (RNA-seq) samples from tumors and healthy-tissue cohorts, and immunopeptidomic samples. We thus identify 370 human leukocyte antigen (HLA)-I-bound peptides encoded by TEs differentially expressed in GBM. Some of the peptides are encoded by repeat sequences from intact open reading frames (ORFs) present in up to several hundred TEs from recent long interspersed nuclear element (LINE)-1, long terminal repeat (LTR), and SVA subfamilies. Other HLA-I-bound peptides are encoded by single copies of TEs from old subfamilies that are expressed recurrently in GBM tumors and not expressed, or very infrequently and at low levels, in healthy tissues (including brain). These peptide-coding, GBM-specific, highly recurrent TEs represent potential tumor-specific targets for cancer immunotherapies.
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Affiliation(s)
- Pierre-Emmanuel Bonté
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Yago A Arribas
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Antonela Merlotti
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Montserrat Carrascal
- Biological and Environmental Proteomics, Institut d'Investigacions Biomèdiques de Barcelona-CSIC, IDIBAPS, Roselló 161, 6a planta, 08036 Barcelona, Spain
| | - Jiasi Vicky Zhang
- GBM Translational Center of Excellence, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elina Zueva
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Zev A Binder
- GBM Translational Center of Excellence, Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cécile Alanio
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France; Laboratoire d'Immunologie Clinique, Institut Curie, Paris 75005, France; Parker Institute of Cancer Immunotherapy, San Francisco, CA, USA
| | - Christel Goudot
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France.
| | - Sebastian Amigorena
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France.
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Neoantigen-specific CD8 T cell responses in the peripheral blood following PD-L1 blockade might predict therapy outcome in metastatic urothelial carcinoma. Nat Commun 2022; 13:1935. [PMID: 35410325 PMCID: PMC9001725 DOI: 10.1038/s41467-022-29342-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/07/2022] [Indexed: 12/14/2022] Open
Abstract
CD8+ T cell reactivity towards tumor mutation-derived neoantigens is widely believed to facilitate the antitumor immunity induced by immune checkpoint blockade (ICB). Here we show that broadening in the number of neoantigen-reactive CD8+ T cell (NART) populations between pre-treatment to 3-weeks post-treatment distinguishes patients with controlled disease compared to patients with progressive disease in metastatic urothelial carcinoma (mUC) treated with PD-L1-blockade. The longitudinal analysis of peripheral CD8+ T cell recognition of patient-specific neopeptide libraries consisting of DNA barcode-labelled pMHC multimers in a cohort of 24 patients from the clinical trial NCT02108652 also shows that peripheral NARTs derived from patients with disease control are characterised by a PD1+ Ki67+ effector phenotype and increased CD39 levels compared to bystander bulk- and virus-antigen reactive CD8+ T cells. The study provides insights into NART characteristics following ICB and suggests that early-stage NART expansion and activation are associated with response to ICB in patients with mUC. Immune checkpoint blockade therapy is successful in a high proportion of cancer patients, but others remain unresponsive. Authors here show that therapeutic success might be predictable in metastatic bladder cancer by longitudinal analysis of the early neoantigen-specific CD8 T cell response in peripheral blood.
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25
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Koch EAT, Schaft N, Kummer M, Berking C, Schuler G, Hasumi K, Dörrie J, Schuler-Thurner B. A One-Armed Phase I Dose Escalation Trial Design: Personalized Vaccination with IKKβ-Matured, RNA-Loaded Dendritic Cells for Metastatic Uveal Melanoma. Front Immunol 2022; 13:785231. [PMID: 35185883 PMCID: PMC8854646 DOI: 10.3389/fimmu.2022.785231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/14/2022] [Indexed: 11/19/2022] Open
Abstract
Uveal melanoma (UM) is an orphan disease with a mortality of 80% within one year upon the development of metastatic disease. UM does hardly respond to chemotherapy and kinase inhibitors and is largely resistant to checkpoint inhibition. Hence, further therapy approaches are urgently needed. To improve clinical outcome, we designed a trial employing the 3rd generation personalized IKKβ-matured RNA-transfected dendritic cell (DC) vaccine which primes T cells and in addition activates NK cells. This ongoing phase I trial [NCT04335890 (www.clinicaltrials.gov), Eudract: 2018-004390-28 (www.clinicaltrialsregister.eu)] investigates patients with treatment-naive metastatic UM. Monocytes are isolated by leukapheresis, differentiated to immature DCs, matured with a cytokine cocktail, and activated via the NF-κB pathway by electroporation with RNA encoding a constitutively active mutant of IKKβ. Three types of antigen-RNA are co-electroporated: i) amplified mRNA of the tumor representing the whole transcriptome, ii) RNA encoding driver mutations identified by exome sequencing, and iii) overexpressed non-mutated tumor antigens detected by transcriptome sequencing. This highly personalized DC vaccine is applied by 9 intravenous infusions in a staggered schedule over one year. Parallel to the vaccination, standard therapy, usually an immune checkpoint blockade (ICB) as mono (anti-PD-1) or combined (anti-CTLA4 and anti-PD-1) regimen is initiated. The coordinated vaccine-induced immune response encompassing tumor-specific T cells and innate NK cells should synergize with ICB, perhaps resulting in measurable clinical responses in this resistant tumor entity. Primary outcome measures of this trial are safety, tolerability and toxicity; secondary outcome measures comprise overall survival and induction of antigen-specific T cells.
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Affiliation(s)
- Elias A. T. Koch
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg (CCC ER-EMN), Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Niels Schaft
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg (CCC ER-EMN), Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- *Correspondence: Niels Schaft,
| | - Mirko Kummer
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg (CCC ER-EMN), Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Carola Berking
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg (CCC ER-EMN), Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Gerold Schuler
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg (CCC ER-EMN), Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | | | - Jan Dörrie
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg (CCC ER-EMN), Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Beatrice Schuler-Thurner
- Department of Dermatology, Universitätsklinikum Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg (CCC ER-EMN), Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
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26
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Bystander T cells in cancer immunology and therapy. NATURE CANCER 2022; 3:143-155. [PMID: 35228747 DOI: 10.1038/s43018-022-00335-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/11/2022] [Indexed: 01/10/2023]
Abstract
Cancer-specific T cells are required for effective anti-cancer immunity and have a central role in cancer immunotherapy. However, emerging evidence suggests that only a small fraction of tumor-infiltrating T cells are cancer specific, and T cells that recognize cancer-unrelated antigens (so-called 'bystanders') are abundant. Although the role of cancer-specific T cells in anti-cancer immunity has been well established, the implications of bystander T cells in tumors are only beginning to be understood. It is becoming increasingly clear that bystander T cells are not a homogeneous group of cells but, instead, they differ in their specificities, their activation states and effector functions. In this Perspective, we discuss recent studies of bystander T cells in tumors, including experimental and computational approaches that enable their identification and functional analysis and viewpoints on how these insights could be used to develop new therapeutic approaches for cancer immunotherapy.
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27
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Hansen UK, Lyngaa R, Ibrani D, Church C, Verhaegen M, Dlugosz AA, Becker JC, Straten PT, Nghiem P, Hadrup SR. Extended T-Cell Epitope Landscape in Merkel Cell Polyomavirus Large T and Small T Oncoproteins Identified Uniquely in Patients with Cancer. J Invest Dermatol 2022; 142:239-243.e13. [PMID: 34298058 PMCID: PMC9413685 DOI: 10.1016/j.jid.2021.06.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 01/03/2023]
Affiliation(s)
- Ulla Kring Hansen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Rikke Lyngaa
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Dafina Ibrani
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington, USA;,Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington, USA
| | - Candice Church
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington, USA;,Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington, USA
| | - Monique Verhaegen
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Andrzej Antoni Dlugosz
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA;,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jürgen Christian Becker
- Department of Translational Skin Cancer Research, University Hospital Essen, Essen, Germany;,German Cancer Consortium (DKTK), Essen, Germany;,German Cancer Research Center (DKFZ), Heidelberg, Germany;,Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Per thor Straten
- National Center for Cancer Immune Therapy, Copenhagen University Hospital, Herlev, Denmark
| | - Paul Nghiem
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, Washington, USA;,Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington, USA;,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA;,Seattle Cancer Care Alliance Center, Seattle, Washington, USA
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark;,Corresponding author:
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Cossarizza A, Chang HD, Radbruch A, Abrignani S, Addo R, Akdis M, Andrä I, Andreata F, Annunziato F, Arranz E, Bacher P, Bari S, Barnaba V, Barros-Martins J, Baumjohann D, Beccaria CG, Bernardo D, Boardman DA, Borger J, Böttcher C, Brockmann L, Burns M, Busch DH, Cameron G, Cammarata I, Cassotta A, Chang Y, Chirdo FG, Christakou E, Čičin-Šain L, Cook L, Corbett AJ, Cornelis R, Cosmi L, Davey MS, De Biasi S, De Simone G, del Zotto G, Delacher M, Di Rosa F, Di Santo J, Diefenbach A, Dong J, Dörner T, Dress RJ, Dutertre CA, Eckle SBG, Eede P, Evrard M, Falk CS, Feuerer M, Fillatreau S, Fiz-Lopez A, Follo M, Foulds GA, Fröbel J, Gagliani N, Galletti G, Gangaev A, Garbi N, Garrote JA, Geginat J, Gherardin NA, Gibellini L, Ginhoux F, Godfrey DI, Gruarin P, Haftmann C, Hansmann L, Harpur CM, Hayday AC, Heine G, Hernández DC, Herrmann M, Hoelsken O, Huang Q, Huber S, Huber JE, Huehn J, Hundemer M, Hwang WYK, Iannacone M, Ivison SM, Jäck HM, Jani PK, Keller B, Kessler N, Ketelaars S, Knop L, Knopf J, Koay HF, Kobow K, Kriegsmann K, Kristyanto H, Krueger A, Kuehne JF, Kunze-Schumacher H, Kvistborg P, Kwok I, Latorre D, et alCossarizza A, Chang HD, Radbruch A, Abrignani S, Addo R, Akdis M, Andrä I, Andreata F, Annunziato F, Arranz E, Bacher P, Bari S, Barnaba V, Barros-Martins J, Baumjohann D, Beccaria CG, Bernardo D, Boardman DA, Borger J, Böttcher C, Brockmann L, Burns M, Busch DH, Cameron G, Cammarata I, Cassotta A, Chang Y, Chirdo FG, Christakou E, Čičin-Šain L, Cook L, Corbett AJ, Cornelis R, Cosmi L, Davey MS, De Biasi S, De Simone G, del Zotto G, Delacher M, Di Rosa F, Di Santo J, Diefenbach A, Dong J, Dörner T, Dress RJ, Dutertre CA, Eckle SBG, Eede P, Evrard M, Falk CS, Feuerer M, Fillatreau S, Fiz-Lopez A, Follo M, Foulds GA, Fröbel J, Gagliani N, Galletti G, Gangaev A, Garbi N, Garrote JA, Geginat J, Gherardin NA, Gibellini L, Ginhoux F, Godfrey DI, Gruarin P, Haftmann C, Hansmann L, Harpur CM, Hayday AC, Heine G, Hernández DC, Herrmann M, Hoelsken O, Huang Q, Huber S, Huber JE, Huehn J, Hundemer M, Hwang WYK, Iannacone M, Ivison SM, Jäck HM, Jani PK, Keller B, Kessler N, Ketelaars S, Knop L, Knopf J, Koay HF, Kobow K, Kriegsmann K, Kristyanto H, Krueger A, Kuehne JF, Kunze-Schumacher H, Kvistborg P, Kwok I, Latorre D, Lenz D, Levings MK, Lino AC, Liotta F, Long HM, Lugli E, MacDonald KN, Maggi L, Maini MK, Mair F, Manta C, Manz RA, Mashreghi MF, Mazzoni A, McCluskey J, Mei HE, Melchers F, Melzer S, Mielenz D, Monin L, Moretta L, Multhoff G, Muñoz LE, Muñoz-Ruiz M, Muscate F, Natalini A, Neumann K, Ng LG, Niedobitek A, Niemz J, Almeida LN, Notarbartolo S, Ostendorf L, Pallett LJ, Patel AA, Percin GI, Peruzzi G, Pinti M, Pockley AG, Pracht K, Prinz I, Pujol-Autonell I, Pulvirenti N, Quatrini L, Quinn KM, Radbruch H, Rhys H, Rodrigo MB, Romagnani C, Saggau C, Sakaguchi S, Sallusto F, Sanderink L, Sandrock I, Schauer C, Scheffold A, Scherer HU, Schiemann M, Schildberg FA, Schober K, Schoen J, Schuh W, Schüler T, Schulz AR, Schulz S, Schulze J, Simonetti S, Singh J, Sitnik KM, Stark R, Starossom S, Stehle C, Szelinski F, Tan L, Tarnok A, Tornack J, Tree TIM, van Beek JJP, van de Veen W, van Gisbergen K, Vasco C, Verheyden NA, von Borstel A, Ward-Hartstonge KA, Warnatz K, Waskow C, Wiedemann A, Wilharm A, Wing J, Wirz O, Wittner J, Yang JHM, Yang J. Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition). Eur J Immunol 2021; 51:2708-3145. [PMID: 34910301 PMCID: PMC11115438 DOI: 10.1002/eji.202170126] [Show More Authors] [Citation(s) in RCA: 274] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The third edition of Flow Cytometry Guidelines provides the key aspects to consider when performing flow cytometry experiments and includes comprehensive sections describing phenotypes and functional assays of all major human and murine immune cell subsets. Notably, the Guidelines contain helpful tables highlighting phenotypes and key differences between human and murine cells. Another useful feature of this edition is the flow cytometry analysis of clinical samples with examples of flow cytometry applications in the context of autoimmune diseases, cancers as well as acute and chronic infectious diseases. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid. All sections are written and peer-reviewed by leading flow cytometry experts and immunologists, making this edition an essential and state-of-the-art handbook for basic and clinical researchers.
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Affiliation(s)
- Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Hyun-Dong Chang
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Institute for Biotechnology, Technische Universität, Berlin, Germany
| | - Andreas Radbruch
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Sergio Abrignani
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Richard Addo
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Immanuel Andrä
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Francesco Andreata
- Division of Immunology, Transplantation and Infectious Diseases, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Eduardo Arranz
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
| | - Petra Bacher
- Institute of Immunology, Christian-Albrechts Universität zu Kiel & Universitätsklinik Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Sudipto Bari
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Vincenzo Barnaba
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
- Center for Life Nano & Neuro Science@Sapienza, Istituto Italiano di Tecnologia (IIT), Rome, Italy
- Istituto Pasteur - Fondazione Cenci Bolognetti, Rome, Italy
| | | | - Dirk Baumjohann
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Cristian G. Beccaria
- Division of Immunology, Transplantation and Infectious Diseases, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - David Bernardo
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Dominic A. Boardman
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Jessica Borger
- Department of Immunology and Pathology, Monash University, Melbourne, Victoria, Australia
| | - Chotima Böttcher
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leonie Brockmann
- Department of Microbiology & Immunology, Columbia University, New York City, USA
| | - Marie Burns
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Dirk H. Busch
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Garth Cameron
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Ilenia Cammarata
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Yinshui Chang
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Fernando Gabriel Chirdo
- Instituto de Estudios Inmunológicos y Fisiopatológicos - IIFP (UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Eleni Christakou
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Laura Cook
- BC Children’s Hospital Research Institute, Vancouver, Canada
- Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Alexandra J. Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca Cornelis
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Lorenzo Cosmi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Martin S. Davey
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Sara De Biasi
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Gabriele De Simone
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Michael Delacher
- Institute for Immunology, University Medical Center Mainz, Mainz, Germany
- Research Centre for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Francesca Di Rosa
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - James Di Santo
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France
- Inserm U1223, Paris, France
| | - Andreas Diefenbach
- Laboratory of Innate Immunity, Department of Microbiology, Infectious Diseases and Immunology, Charité – Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
- Mucosal and Developmental Immunology, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Jun Dong
- Cell Biology, German Rheumatism Research Center Berlin (DRFZ), An Institute of the Leibniz Association, Berlin, Germany
| | - Thomas Dörner
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Department of Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Regine J. Dress
- Institute of Systems Immunology, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Charles-Antoine Dutertre
- Institut National de la Sante Et de la Recherce Medicale (INSERM) U1015, Equipe Labellisee-Ligue Nationale contre le Cancer, Villejuif, France
| | - Sidonia B. G. Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Pascale Eede
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Maximilien Evrard
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Christine S. Falk
- Institute of Transplant Immunology, Hannover Medical School, Hannover, Germany
| | - Markus Feuerer
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Chair for Immunology, University Regensburg, Regensburg, Germany
| | - Simon Fillatreau
- Institut Necker Enfants Malades, INSERM U1151-CNRS, UMR8253, Paris, France
- Université de Paris, Paris Descartes, Faculté de Médecine, Paris, France
- AP-HP, Hôpital Necker Enfants Malades, Paris, France
| | - Aida Fiz-Lopez
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
| | - Marie Follo
- Department of Medicine I, Lighthouse Core Facility, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gemma A. Foulds
- John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Centre for Health, Ageing and Understanding Disease (CHAUD), School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Julia Fröbel
- Immunology of Aging, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Nicola Gagliani
- Department of Medicine, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Germany
| | - Giovanni Galletti
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Anastasia Gangaev
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Natalio Garbi
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, Germany
| | - José Antonio Garrote
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
- Laboratory of Molecular Genetics, Servicio de Análisis Clínicos, Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - Jens Geginat
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Nicholas A. Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Lara Gibellini
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Paola Gruarin
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
| | - Claudia Haftmann
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Leo Hansmann
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin (CVK), Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, Germany
| | - Christopher M. Harpur
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
| | - Adrian C. Hayday
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - Guido Heine
- Division of Allergy, Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Daniela Carolina Hernández
- Innate Immunity, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Gastroenterology, Infectious Diseases, Rheumatology, Berlin, Germany
| | - Martin Herrmann
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Oliver Hoelsken
- Laboratory of Innate Immunity, Department of Microbiology, Infectious Diseases and Immunology, Charité – Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
- Mucosal and Developmental Immunology, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Qing Huang
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Samuel Huber
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johanna E. Huber
- Institute for Immunology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Jochen Huehn
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Hundemer
- Department of Hematology, Oncology and Rheumatology, University Heidelberg, Heidelberg, Germany
| | - William Y. K. Hwang
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
- Executive Offices, National Cancer Centre Singapore, Singapore
| | - Matteo Iannacone
- Division of Immunology, Transplantation and Infectious Diseases, IRCSS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sabine M. Ivison
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Peter K. Jani
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Baerbel Keller
- Department of Rheumatology and Clinical Immunology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nina Kessler
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, Germany
| | - Steven Ketelaars
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Laura Knop
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
| | - Jasmin Knopf
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Hui-Fern Koay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Katja Kobow
- Department of Neuropathology, Universitätsklinikum Erlangen, Germany
| | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, University Heidelberg, Heidelberg, Germany
| | - H. Kristyanto
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Andreas Krueger
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jenny F. Kuehne
- Institute of Transplant Immunology, Hannover Medical School, Hannover, Germany
| | - Heike Kunze-Schumacher
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Immanuel Kwok
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Daniel Lenz
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Megan K. Levings
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
- School of Biomedical Engineering, The University of British Columbia, Vancouver, Canada
| | - Andreia C. Lino
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Francesco Liotta
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Heather M. Long
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Enrico Lugli
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Katherine N. MacDonald
- BC Children’s Hospital Research Institute, Vancouver, Canada
- School of Biomedical Engineering, The University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, The University of British Columbia, Vancouver, Canada
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Mala K. Maini
- Division of Infection & Immunity, Institute of Immunity & Transplantation, University College London, London, UK
| | - Florian Mair
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Calin Manta
- Department of Hematology, Oncology and Rheumatology, University Heidelberg, Heidelberg, Germany
| | - Rudolf Armin Manz
- Institute for Systemic Inflammation Research, University of Luebeck, Luebeck, Germany
| | | | - Alessio Mazzoni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Henrik E. Mei
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Fritz Melchers
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Susanne Melzer
- Clinical Trial Center Leipzig, Leipzig University, Härtelstr.16, −18, Leipzig, 04107, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Leticia Monin
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - Lorenzo Moretta
- Department of Immunology, IRCCS Bambino Gesù Children’s Hospital, Rome, Italy
| | - Gabriele Multhoff
- Radiation Immuno-Oncology Group, Center for Translational Cancer Research (TranslaTUM), Technical University of Munich (TUM), Klinikum rechts der Isar, Munich, Germany
- Department of Radiation Oncology, Technical University of Munich (TUM), Klinikum rechts der Isar, Munich, Germany
| | - Luis Enrique Muñoz
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Miguel Muñoz-Ruiz
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - Franziska Muscate
- Department of Medicine, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ambra Natalini
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
| | - Katrin Neumann
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lai Guan Ng
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Jana Niemz
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Samuele Notarbartolo
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
| | - Lennard Ostendorf
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Laura J. Pallett
- Division of Infection & Immunity, Institute of Immunity & Transplantation, University College London, London, UK
| | - Amit A. Patel
- Institut National de la Sante Et de la Recherce Medicale (INSERM) U1015, Equipe Labellisee-Ligue Nationale contre le Cancer, Villejuif, France
| | - Gulce Itir Percin
- Immunology of Aging, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Giovanna Peruzzi
- Center for Life Nano & Neuro Science@Sapienza, Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Marcello Pinti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - A. Graham Pockley
- John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Centre for Health, Ageing and Understanding Disease (CHAUD), School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Katharina Pracht
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Immo Prinz
- Institute of Immunology, Hannover Medical School, Hannover, Germany
- Institute of Systems Immunology, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Irma Pujol-Autonell
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
- Peter Gorer Department of Immunobiology, King’s College London, London, UK
| | - Nadia Pulvirenti
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
| | - Linda Quatrini
- Department of Immunology, IRCCS Bambino Gesù Children’s Hospital, Rome, Italy
| | - Kylie M. Quinn
- School of Biomedical and Health Sciences, RMIT University, Bundorra, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Helena Radbruch
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Hefin Rhys
- Flow Cytometry Science Technology Platform, The Francis Crick Institute, London, UK
| | - Maria B. Rodrigo
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, Germany
| | - Chiara Romagnani
- Innate Immunity, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Gastroenterology, Infectious Diseases, Rheumatology, Berlin, Germany
| | - Carina Saggau
- Institute of Immunology, Christian-Albrechts Universität zu Kiel & Universitätsklinik Schleswig-Holstein, Kiel, Germany
| | | | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Lieke Sanderink
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Chair for Immunology, University Regensburg, Regensburg, Germany
| | - Inga Sandrock
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Christine Schauer
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts Universität zu Kiel & Universitätsklinik Schleswig-Holstein, Kiel, Germany
| | - Hans U. Scherer
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthias Schiemann
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Frank A. Schildberg
- Clinic for Orthopedics and Trauma Surgery, University Hospital Bonn, Bonn, Germany
| | - Kilian Schober
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Germany
| | - Janina Schoen
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Wolfgang Schuh
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Schüler
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
| | - Axel R. Schulz
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Sebastian Schulz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Julia Schulze
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Sonia Simonetti
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
| | - Jeeshan Singh
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Katarzyna M. Sitnik
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Regina Stark
- Charité Universitätsmedizin Berlin – BIH Center for Regenerative Therapies, Berlin, Germany
- Sanquin Research – Adaptive Immunity, Amsterdam, The Netherlands
| | - Sarah Starossom
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christina Stehle
- Innate Immunity, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Gastroenterology, Infectious Diseases, Rheumatology, Berlin, Germany
| | - Franziska Szelinski
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Department of Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Leonard Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Attila Tarnok
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
- Department of Precision Instrument, Tsinghua University, Beijing, China
- Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Julia Tornack
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Timothy I. M. Tree
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
| | - Jasper J. P. van Beek
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | | | - Chiara Vasco
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
| | - Nikita A. Verheyden
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anouk von Borstel
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kirsten A. Ward-Hartstonge
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Claudia Waskow
- Immunology of Aging, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich-Schiller-University Jena, Jena, Germany
- Department of Medicine III, Technical University Dresden, Dresden, Germany
| | - Annika Wiedemann
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Department of Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Anneke Wilharm
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - James Wing
- Immunology Frontier Research Center, Osaka University, Japan
| | - Oliver Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jens Wittner
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Jennie H. M. Yang
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
| | - Juhao Yang
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Differential effects of PD-1 and CTLA-4 blockade on the melanoma-reactive CD8 T cell response. Proc Natl Acad Sci U S A 2021; 118:2102849118. [PMID: 34670835 DOI: 10.1073/pnas.2102849118] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2021] [Indexed: 01/05/2023] Open
Abstract
Immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte-associated protein 4 (CTLA-4) have revolutionized the treatment of melanoma patients. Based on early studies addressing the mechanism of action, it was assumed that PD-1 blockade mostly influences T cell responses at the tumor site. However, recent work has demonstrated that PD-1 blockade can influence the T cell compartment in peripheral blood. If the activation of circulating, tumor-reactive T cells would form an important mechanism of action of PD-1 blockade, it may be predicted that such blockade would alter either the frequency and/or the breadth of the tumor-reactive CD8 T cell response. To address this question, we analyzed CD8 T cell responses toward 71 melanoma-associated epitopes in peripheral blood of 24 melanoma patients. We show that both the frequency and the breadth of the circulating melanoma-reactive CD8 T cell response was unaltered upon PD-1 blockade. In contrast, a broadening of the circulating melanoma-reactive CD8 T cell response was observed upon CTLA-4 blockade, in concordance with our prior data. Based on these results, we conclude that PD-1 and CTLA-4 blockade have distinct mechanisms of action. In addition, the data provide an argument in favor of the hypothesis that anti-PD-1 therapy may primarily act at the tumor site.
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30
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Vaurs J, Douchin G, Echasserieau K, Oger R, Jouand N, Fortun A, Hesnard L, Croyal M, Pecorari F, Gervois N, Bernardeau K. A novel and efficient approach to high-throughput production of HLA-E/peptide monomer for T-cell epitope screening. Sci Rep 2021; 11:17234. [PMID: 34446788 PMCID: PMC8390762 DOI: 10.1038/s41598-021-96560-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/10/2021] [Indexed: 12/05/2022] Open
Abstract
Over the past two decades, there has been a great interest in the study of HLA-E-restricted αβ T cells during bacterial and viral infections, including recently SARS-CoV-2 infection. Phenotyping of these specific HLA-E-restricted T cells requires new tools such as tetramers for rapid cell staining or sorting, as well as for the identification of new peptides capable to bind to the HLA-E pocket. To this aim, we have developed an optimal photosensitive peptide to generate stable HLA-E/pUV complexes allowing high-throughput production of new HLA-E/peptide complexes by peptide exchange. We characterized the UV exchange by ELISA and improved the peptide exchange readout using size exclusion chromatography. This novel approach for complex quantification is indeed very important to perform tetramerization of MHC/peptide complexes with the high quality required for detection of specific T cells. Our approach allows the rapid screening of peptides capable of binding to the non-classical human HLA-E allele, paving the way for the development of new therapeutic approaches based on the detection of HLA-E-restricted T cells.
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Affiliation(s)
- Juliette Vaurs
- P2R "Production de Protéines Recombinantes", Université de Nantes, CRCINA, SFR-Santé, INSERM, CNRS, CHU Nantes, Nantes, France
| | - Gaël Douchin
- P2R "Production de Protéines Recombinantes", Université de Nantes, CRCINA, SFR-Santé, INSERM, CNRS, CHU Nantes, Nantes, France
| | - Klara Echasserieau
- P2R "Production de Protéines Recombinantes", Université de Nantes, CRCINA, SFR-Santé, INSERM, CNRS, CHU Nantes, Nantes, France
- Université de Nantes, Inserm, CRCINA, 44000, Nantes, France
| | - Romain Oger
- Université de Nantes, Inserm, CRCINA, 44000, Nantes, France
- LabEx IGO «Immunotherapy, Graft, Oncology», Nantes, France
| | - Nicolas Jouand
- Université de Nantes, Inserm, CRCINA, 44000, Nantes, France
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, 44000, Nantes, France
| | - Agnès Fortun
- P2R "Production de Protéines Recombinantes", Université de Nantes, CRCINA, SFR-Santé, INSERM, CNRS, CHU Nantes, Nantes, France
- Université de Nantes, CHU de Nantes, Cibles et médicaments des infections et du cancer, IICiMed, EA 1155, 44000, Nantes, France
| | - Leslie Hesnard
- Université de Nantes, Inserm, CRCINA, 44000, Nantes, France
| | - Mikaël Croyal
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, Inserm UMS 016, CNRS UMS 3556, 44000, Nantes, France
- Université de Nantes, CHU Nantes, CNRS, INSERM, l'institut du thorax, 44000, Nantes, France
- CRNH-Ouest Mass Spectrometry Core Facility, 44000, Nantes, France
| | - Frédéric Pecorari
- P2R "Production de Protéines Recombinantes", Université de Nantes, CRCINA, SFR-Santé, INSERM, CNRS, CHU Nantes, Nantes, France
- Université de Nantes, Inserm, CRCINA, 44000, Nantes, France
| | - Nadine Gervois
- Université de Nantes, Inserm, CRCINA, 44000, Nantes, France.
- LabEx IGO «Immunotherapy, Graft, Oncology», Nantes, France.
| | - Karine Bernardeau
- P2R "Production de Protéines Recombinantes", Université de Nantes, CRCINA, SFR-Santé, INSERM, CNRS, CHU Nantes, Nantes, France.
- Université de Nantes, Inserm, CRCINA, 44000, Nantes, France.
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31
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Bagadia P, O'Connor KW, Wu R, Ferris ST, Ward JP, Schreiber RD, Murphy TL, Murphy KM. Bcl6-Independent In Vivo Development of Functional Type 1 Classical Dendritic Cells Supporting Tumor Rejection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:125-132. [PMID: 34135058 PMCID: PMC8797952 DOI: 10.4049/jimmunol.1901010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 04/16/2021] [Indexed: 11/19/2022]
Abstract
The transcriptional repressor Bcl6 has been reported as required for development of a subset of classical dendritic cell (cDCs) called cDC1, which is responsible for cross-presentation. However, mechanisms and in vivo functional analysis have been lacking. We generated a system for conditional deletion of Bcl6 in mouse cDCs. We confirmed the reported in vitro requirement for Bcl6 in cDC1 development and the general role for Bcl6 in cDC development in competitive settings. However, deletion of Bcl6 did not abrogate the in vivo development of cDC1. Instead, Bcl6 deficiency caused only a selective reduction in CD8α expression by cDC1 without affecting XCR1 or CD24 expression. Normal cDC1 development was confirmed in Bcl6cKO mice by development of XCR1+ Zbtb46-GFP+ cDC1 by rejection of syngeneic tumors and by priming of tumor-specific CD8 T cells. In summary, Bcl6 regulates a subset of cDC1-specific markers and is required in vitro but not in vivo for cDC1 development.
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Affiliation(s)
- Prachi Bagadia
- Department of Oncology, Amgen Inc., South San Francisco, CA
| | - Kevin W O'Connor
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Renee Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Stephen T Ferris
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Jeffrey P Ward
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO; and
| | - Robert D Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO;
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32
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Wennhold K, Thelen M, Lehmann J, Schran S, Preugszat E, Garcia-Marquez M, Lechner A, Shimabukuro-Vornhagen A, Ercanoglu MS, Klein F, Thangarajah F, Eidt S, Löser H, Bruns C, Quaas A, von Bergwelt-Baildon M, Schlößer HA. CD86 + Antigen-Presenting B Cells Are Increased in Cancer, Localize in Tertiary Lymphoid Structures, and Induce Specific T-cell Responses. Cancer Immunol Res 2021; 9:1098-1108. [PMID: 34155067 DOI: 10.1158/2326-6066.cir-20-0949] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 02/22/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022]
Abstract
The role of B cells in antitumor immunity and their impact on emerging immunotherapies is increasingly gaining attention. B-cell effector functions include not only secretion of antibodies, but also presentation of antigens to T cells. A physiologic B-cell subset with immunostimulatory properties was described in humans, defined by a high expression of CD86 and downregulation of CD21. We used multicolor flow cytometry and IHC to elucidate abundance and spatial distribution of these antigen-presenting B cells (BAPC) in blood (peripheral blood mononuclear cells, PBMC) and tumor samples of 237 patients with cancer. Antigen-specific T-cell responses to cancer testis antigens were determined using tetramer staining and sorted BAPCs in FluoroSpot assays for selected patients. We found that BAPCs were increased in the tumor microenvironment of 9 of 10 analyzed cancer types with site-specific variation. BAPCs were not increased in renal cell carcinoma, whereas we found a systemic increase with elevated fractions in tumor-infiltrating lymphocytes (TIL) and PBMCs of patients with colorectal cancer and gastroesophageal adenocarcinoma. BAPCs were localized in lymphoid follicles of tertiary lymphoid structures (TLS) and were enriched in tumors with increased numbers of TLSs. BAPCs isolated from tumor-draining lymph nodes of patients with cancer showed increased percentages of tumor antigen-specific B cells and induced responses of autologous T cells in vitro. Our results highlight the relevance of BAPCs as professional antigen-presenting cells in tumor immunity and provide a mechanistic rationale for the observed correlation of B-cell abundance and response to immune checkpoint inhibition.
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Affiliation(s)
- Kerstin Wennhold
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Martin Thelen
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Jonas Lehmann
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Simon Schran
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Ella Preugszat
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Maria Garcia-Marquez
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Axel Lechner
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig Maximilians University, Munich, Germany.,Gene Center, Ludwig Maximilians University, Munich, Germany
| | - Alexander Shimabukuro-Vornhagen
- Department I for Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Meryem S Ercanoglu
- Institute of Virology, Laboratory of Experimental Immunology, University of Cologne, Cologne, Germany
| | - Florian Klein
- Institute of Virology, Laboratory of Experimental Immunology, University of Cologne, Cologne, Germany
| | - Fabinshy Thangarajah
- Department of Gynecology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Sebastian Eidt
- Institute of Pathology, St. Elisabeth Hospital, Cologne, Germany
| | - Heike Löser
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Christiane Bruns
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, University of Cologne, Cologne, Germany
| | - Michael von Bergwelt-Baildon
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Gene Center, Ludwig Maximilians University, Munich, Germany.,Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Hans A Schlößer
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany. .,Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
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33
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Saini SK, Hersby DS, Tamhane T, Povlsen HR, Amaya Hernandez SP, Nielsen M, Gang AO, Hadrup SR. SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8 + T cell activation in COVID-19 patients. Sci Immunol 2021; 6:eabf7550. [PMID: 33853928 PMCID: PMC8139428 DOI: 10.1126/sciimmunol.abf7550] [Citation(s) in RCA: 170] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/08/2021] [Indexed: 12/11/2022]
Abstract
T cells are important for effective viral clearance, elimination of virus-infected cells and long-term disease protection. To examine the full-spectrum of CD8+ T cell immunity in COVID-19, we experimentally evaluated 3141 major histocompatibility (MHC) class I-binding peptides covering the complete SARS-CoV-2 genome. Using DNA-barcoded peptide-MHC complex (pMHC) multimers combined with a T cell phenotype panel, we report a comprehensive list of 122 immunogenic and a subset of immunodominant SARS-CoV-2 T cell epitopes. Substantial CD8+ T cell recognition was observed in COVID-19 patients, with up to 27% of all CD8+ lymphocytes interacting with SARS-CoV-2-derived epitopes. Most immunogenic regions were derived from open reading frame (ORF) 1 and ORF3, with ORF1 containing most of the immunodominant epitopes. CD8+ T cell recognition of lower affinity was also observed in healthy donors toward SARS-CoV-2-derived epitopes. This pre-existing T cell recognition signature was partially overlapping with the epitope landscape observed in COVID-19 patients and may drive the further expansion of T cell responses to SARS-CoV-2 infection. Importantly the phenotype of the SARS-CoV-2-specific CD8+ T cells, revealed a strong T cell activation in COVID-19 patients, while minimal T cell activation was seen in healthy individuals. We found that patients with severe disease displayed significantly larger SARS-CoV-2-specific T cell populations compared to patients with mild diseases and these T cells displayed a robust activation profile. These results further our understanding of T cell immunity to SARS-CoV-2 infection and hypothesize that strong antigen-specific T cell responses are associated with different disease outcomes.
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Affiliation(s)
- Sunil Kumar Saini
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Ditte Stampe Hersby
- Department of Haematology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Tripti Tamhane
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Helle Rus Povlsen
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Susana Patricia Amaya Hernandez
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Morten Nielsen
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anne Ortved Gang
- Department of Haematology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark.
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34
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Donia M, Fagone P, Nicoletti F, Andersen RS, Høgdall E, Straten PT, Andersen MH, Svane IM. BRAF inhibition improves tumor recognition by the immune system: Potential implications for combinatorial therapies against melanoma involving adoptive T-cell transfer. Oncoimmunology 2021; 1:1476-1483. [PMID: 23264894 PMCID: PMC3525603 DOI: 10.4161/onci.21940] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In spite of the fact that they occur at high rates, the clinical responses of BRAFV600 mutant metastatic melanoma to BRAF inhibitors are usually short-lasting, with most cases progressing within less than 8 mo. Immunomodulatory strategies initiated after progression have recently been reported to be poorly efficient. By characterizing the immunological interactions between T cells and cancer cells in clinical material as well as the influence of the FDA-approved BRAF inhibitor vemurafenib on the immune system, we aimed at unraveling new strategies to expand the efficacy of adoptive T-cell transfer, which represents one of the most promising approaches currently in clinical development for the treatment of metastatic melanoma. Here we show that blocking the BRAF-MAPK pathway in BRAF signaling-addicted melanoma cells significantly increases the ability of T cells contained in clinical grade tumor-infiltrating lymphocytes to recognize autologous BRAFV600 mutant melanoma cell lines in vitro. Antitumor reactivity was improved regardless of the class of antigen recognized by tumor-specific CD8+ T cells. Microarray data suggests that improved tumor recognition is associated with modified expression of MHC Class I-associated proteins as well as of heat-shock proteins. In conclusion, our preclinical data suggest that an appropriately timed sequential treatment of BRAFV600 mutant melanoma with vemurafenib and adoptive T-cell transfer might result in synergistic antineoplastic effects owing to an increased immunogenicity of cancer cells.
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Affiliation(s)
- Marco Donia
- Center for Cancer Immune Therapy; Department of Haematology; Copenhagen University Hospital at Herlev; Herlev, Denmark ; Department of Biomedical Sciences; University of Catania; Catania, Italy
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35
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Bousbaine D, Ploegh HL. Antigen discovery tools for adaptive immune receptor repertoire research. CURRENT OPINION IN SYSTEMS BIOLOGY 2020; 24:64-70. [PMID: 33195881 PMCID: PMC7665270 DOI: 10.1016/j.coisb.2020.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The adaptive immune system has evolved to recognize with incredible precision a large diversity of molecules. Innovations in high-throughput sequencing and bioinformatics have accelerated large-scale immune repertoire analyses and given us important insights into the behavior of the adaptive immune system. However, establishing a connection between receptor sequence and its antigen-specificity remains a challenge despite its central role in determining T and B cell fate. We discuss recent large-scale antigen discovery technologies which can be combined with adaptive immune receptor repertoire (AIRR) studies. We highlight important discoveries made using repertoire analyses in the field of host-microbe interactions.
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Affiliation(s)
- Djenet Bousbaine
- Department of Bioengineering and ChEM-H, Stanford University, Stanford CA, USA
| | - Hidde L. Ploegh
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston MA, USA
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36
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Wells DK, van Buuren MM, Dang KK, Hubbard-Lucey VM, Sheehan KCF, Campbell KM, Lamb A, Ward JP, Sidney J, Blazquez AB, Rech AJ, Zaretsky JM, Comin-Anduix B, Ng AHC, Chour W, Yu TV, Rizvi H, Chen JM, Manning P, Steiner GM, Doan XC, Merghoub T, Guinney J, Kolom A, Selinsky C, Ribas A, Hellmann MD, Hacohen N, Sette A, Heath JR, Bhardwaj N, Ramsdell F, Schreiber RD, Schumacher TN, Kvistborg P, Defranoux NA. Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction. Cell 2020; 183:818-834.e13. [PMID: 33038342 DOI: 10.1016/j.cell.2020.09.015] [Citation(s) in RCA: 314] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/08/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022]
Abstract
Many approaches to identify therapeutically relevant neoantigens couple tumor sequencing with bioinformatic algorithms and inferred rules of tumor epitope immunogenicity. However, there are no reference data to compare these approaches, and the parameters governing tumor epitope immunogenicity remain unclear. Here, we assembled a global consortium wherein each participant predicted immunogenic epitopes from shared tumor sequencing data. 608 epitopes were subsequently assessed for T cell binding in patient-matched samples. By integrating peptide features associated with presentation and recognition, we developed a model of tumor epitope immunogenicity that filtered out 98% of non-immunogenic peptides with a precision above 0.70. Pipelines prioritizing model features had superior performance, and pipeline alterations leveraging them improved prediction performance. These findings were validated in an independent cohort of 310 epitopes prioritized from tumor sequencing data and assessed for T cell binding. This data resource enables identification of parameters underlying effective anti-tumor immunity and is available to the research community.
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Affiliation(s)
- Daniel K Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
| | - Marit M van Buuren
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands; T Cell Immunology, Biopharmaceutical New Technologies (BioNTech) Corporation, BioNTech US, Cambridge, MA, USA
| | - Kristen K Dang
- Computational Oncology, Sage Bionetworks, Seattle, WA, USA
| | | | - Kathleen C F Sheehan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Katie M Campbell
- Division of Hematology and Oncology, Department of Medicine, Johnson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrew Lamb
- Computational Oncology, Sage Bionetworks, Seattle, WA, USA
| | - Jeffrey P Ward
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Ana B Blazquez
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew J Rech
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Jesse M Zaretsky
- Division of Hematology and Oncology, Department of Medicine, Johnson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Begonya Comin-Anduix
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Surgery, David Geffen School of Medicine, Johnson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - William Chour
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thomas V Yu
- Computational Oncology, Sage Bionetworks, Seattle, WA, USA
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, MSKCC, New York, NY, USA
| | - Jia M Chen
- Division of Hematology and Oncology, Department of Medicine, Johnson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Patrice Manning
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | | | - Xengie C Doan
- Computational Oncology, Sage Bionetworks, Seattle, WA, USA
| | - Taha Merghoub
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Medicine, MSKCC, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Justin Guinney
- Computational Oncology, Sage Bionetworks, Seattle, WA, USA; Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Adam Kolom
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Anna-Maria Kellen Clinical Accelerator, Cancer Research Institute, New York, NY, USA
| | - Cheryl Selinsky
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Antoni Ribas
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Division of Hematology and Oncology, Department of Medicine, Johnson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew D Hellmann
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Druckenmiller Center for Lung Cancer Research, MSKCC, New York, NY, USA; Department of Medicine, MSKCC, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Alessandro Sette
- Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - James R Heath
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Institute for Systems Biology, Seattle, WA, USA
| | - Nina Bhardwaj
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fred Ramsdell
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Robert D Schreiber
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, St. Louis, MO, USA; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Ton N Schumacher
- Division of Molecular Oncology and Immunology, Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, the Netherlands
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37
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Biotechnologies to tackle the challenge of neoantigen identification. Curr Opin Biotechnol 2020; 65:52-59. [DOI: 10.1016/j.copbio.2019.12.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 02/06/2023]
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38
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Vujovic M, Degn KF, Marin FI, Schaap-Johansen AL, Chain B, Andresen TL, Kaplinsky J, Marcatili P. T cell receptor sequence clustering and antigen specificity. Comput Struct Biotechnol J 2020; 18:2166-2173. [PMID: 32952933 PMCID: PMC7473833 DOI: 10.1016/j.csbj.2020.06.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/25/2020] [Accepted: 06/27/2020] [Indexed: 11/17/2022] Open
Abstract
There has been increasing interest in the role of T cells and their involvement in cancer, autoimmune and infectious diseases. However, the nature of T cell receptor (TCR) epitope recognition at a repertoire level is not yet fully understood. Due to technological advances a plethora of TCR sequences from a variety of disease and treatment settings has become readily available. Current efforts in TCR specificity analysis focus on identifying characteristics in immune repertoires which can explain or predict disease outcome or progression, or can be used to monitor the efficacy of disease therapy. In this context, clustering of TCRs by sequence to reflect biological similarity, and especially to reflect antigen specificity have become of paramount importance. We review the main TCR sequence clustering methods and the different similarity measures they use, and discuss their performance and possible improvement. We aim to provide guidance for non-specialists who wish to use TCR repertoire sequencing for disease tracking, patient stratification or therapy prediction, and to provide a starting point for those aiming to develop novel techniques for TCR annotation through clustering.
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Affiliation(s)
- Milena Vujovic
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark
| | - Kristine Fredlund Degn
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark
| | - Frederikke Isa Marin
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark
| | - Anna-Lisa Schaap-Johansen
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark
| | - Benny Chain
- UCL Division of Infection and Immunity, University College London, Wing 3.2, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Thomas Lars Andresen
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark
| | - Joseph Kaplinsky
- Ludwig Institute for Cancer Research Ltd, University of Oxford, Nuffield Department of Medicine, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Paolo Marcatili
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark
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39
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Ferris ST, Durai V, Wu R, Theisen DJ, Ward JP, Bern MD, Davidson JT, Bagadia P, Liu T, Briseño CG, Li L, Gillanders WE, Wu GF, Yokoyama WM, Murphy TL, Schreiber RD, Murphy KM. cDC1 prime and are licensed by CD4 + T cells to induce anti-tumour immunity. Nature 2020; 584:624-629. [PMID: 32788723 PMCID: PMC7469755 DOI: 10.1038/s41586-020-2611-3] [Citation(s) in RCA: 366] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/23/2020] [Indexed: 12/15/2022]
Abstract
Conventional type 1 dendritic cells (cDC1)1 are thought to perform antigen cross-presentation, which is required to prime CD8+ T cells2,3, whereas cDC2 are specialized for priming CD4+ T cells4,5. CD4+ T cells are also considered to help CD8+ T cell responses through a variety of mechanisms6-11, including a process whereby CD4+ T cells 'license' cDC1 for CD8+ T cell priming12. However, this model has not been directly tested in vivo or in the setting of help-dependent tumour rejection. Here we generated an Xcr1Cre mouse strain to evaluate the cellular interactions that mediate tumour rejection in a model requiring CD4+ and CD8+ T cells. As expected, tumour rejection required cDC1 and CD8+ T cell priming required the expression of major histocompatibility class I molecules by cDC1. Unexpectedly, early priming of CD4+ T cells against tumour-derived antigens also required cDC1, and this was not simply because they transport antigens to lymph nodes for processing by cDC2, as selective deletion of major histocompatibility class II molecules in cDC1 also prevented early CD4+ T cell priming. Furthermore, deletion of either major histocompatibility class II or CD40 in cDC1 impaired tumour rejection, consistent with a role for cognate CD4+ T cell interactions and CD40 signalling in cDC1 licensing. Finally, CD40 signalling in cDC1 was critical not only for CD8+ T cell priming, but also for initial CD4+ T cell activation. Thus, in the setting of tumour-derived antigens, cDC1 function as an autonomous platform capable of antigen processing and priming for both CD4+ and CD8+ T cells and of the direct orchestration of their cross-talk that is required for optimal anti-tumour immunity.
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Affiliation(s)
- Stephen T Ferris
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Vivek Durai
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Renee Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Derek J Theisen
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey P Ward
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Michael D Bern
- Division of Rheumatology, Washington University School of Medicine, St Louis, MO, USA
| | - Jesse T Davidson
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Prachi Bagadia
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Tiantian Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Carlos G Briseño
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Lijin Li
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - William E Gillanders
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
- The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St Louis, MO, USA
| | - Gregory F Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Wayne M Yokoyama
- Division of Rheumatology, Washington University School of Medicine, St Louis, MO, USA
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Robert D Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Howard Hughes Medical Institute, Washington University School of Medicine, St Louis, MO, USA.
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40
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Assessment of TCR signal strength of antigen-specific memory CD8 + T cells in human blood. Blood Adv 2020; 3:2153-2163. [PMID: 31320320 DOI: 10.1182/bloodadvances.2019000292] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 05/24/2019] [Indexed: 02/07/2023] Open
Abstract
Assessment of the quality and the breadth of antigen (Ag)-specific memory T cells in human samples is of paramount importance to elucidate the pathogenesis and to develop new treatments in various diseases. T-cell receptor (TCR) signal strength, primarily controlled by TCR affinity, affects many fundamental aspects of T-cell biology; however, no current assays for detection of Ag-specific CD8+ T cells can assess their TCR signal strength in human samples. Here, we provide evidence that interferon regulatory factor 4 (IRF4), a transcription factor rapidly upregulated in correlation with TCR signal strength, permits the assessment of the TCR signal strength of Ag-specific CD8+ T cells in human peripheral blood mononuclear cells (PBMCs). Coexpression of IRF4 and CD137 sensitively detected peptide-specific CD8+ T cells with extremely low background in PBMCs stimulated for 18 hours with MHC class I peptides. Our assay revealed that human memory CD8+ T cells with high-affinity TCRs have an intrinsic ability to highly express CD25. Furthermore, HIV-specific CD8+ T cells in chronic HIV+ subjects were found to display primarily low-affinity TCRs with low CD25 expression capacity. Impairment in the functions of HIV-specific CD8+ T cells might be associated with their suboptimal TCR signals, as well as impaired responsiveness to interleukin-2.
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41
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Hansen UK, Ramskov S, Bjerregaard AM, Borch A, Andersen R, Draghi A, Donia M, Bentzen AK, Marquard AM, Szallasi Z, Eklund AC, Svane IM, Hadrup SR. Tumor-Infiltrating T Cells From Clear Cell Renal Cell Carcinoma Patients Recognize Neoepitopes Derived From Point and Frameshift Mutations. Front Immunol 2020; 11:373. [PMID: 32226429 PMCID: PMC7080703 DOI: 10.3389/fimmu.2020.00373] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Mutation-derived neoantigens are important targets for T cell-mediated reactivity toward tumors and, due to their unique tumor expression, an attractive target for immunotherapy. Neoepitope-specific T cells have been detected across a number of solid cancers with high mutational burden tumors, but neoepitopes have been mostly selected from single nucleotide variations (SNVs), and little focus has been given to neoepitopes derived from in-frame and frameshift indels, which might be equally important and potentially highly immunogenic. Clear cell renal cell carcinomas (ccRCCs) are medium-range mutational burden tumors with a high pan-cancer proportion of frameshift mutations. In this study, the mutational landscape of tumors from six RCC patients was analyzed by whole-exome sequencing (WES) of DNA from tumor fragments (TFs), autologous tumor cell lines (TCLs), and tumor-infiltrating lymphocytes (TILs, germline reference). Neopeptides were predicted using MuPeXI, and patient-specific peptide–MHC (pMHC) libraries were created for all neopeptides with a rank score < 2 for binding to the patient's HLAs. T cell recognition toward neoepitopes in TILs was evaluated using the high-throughput technology of DNA barcode-labeled pMHC multimers. The patient-specific libraries consisted of, on average, 258 putative neopeptides (range, 103–397, n = 6). In four patients, WES was performed on two different sources (TF and TCL), whereas in two patients, WES was performed only on TF. Most of the peptides were predicted from both sources. However, a fraction was predicted from one source only. Among the total predicted neopeptides, 16% were derived from frameshift indels. T cell recognition of 52 neoepitopes was detected across all patients (range, 4–18, n = 6) and spanning two to five HLA restrictions per patient. On average, 21% of the recognized neoepitopes were derived from frameshift indels (range, 0–43%, n = 6). Thus, frameshift indels are equally represented in the pool of immunogenic neoepitopes as SNV-derived neoepitopes. This suggests the importance of a broad neopeptide prediction strategy covering multiple sources of tumor material, and including different genetic alterations. This study, for the first time, describes the T cell recognition of frameshift-derived neoepitopes in RCC and determines their immunogenic profile.
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Affiliation(s)
- Ulla Kring Hansen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Sofie Ramskov
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | - Annie Borch
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Rikke Andersen
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Copenhagen, Denmark
| | - Arianna Draghi
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marco Donia
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Copenhagen, Denmark
| | - Amalie Kai Bentzen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Aron Charles Eklund
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.,Clinical Microbiomics A/S, Copenhagen, Denmark
| | - Inge Marie Svane
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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42
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Pedersen NW, Laske K, Maurer D, Welters M, Walter S, Gouttefangeas C, Hadrup SR. Optimization in Detection of Antigen-Specific T Cells Through Differentially Labeled MHC Multimers. Cytometry A 2019; 97:955-964. [PMID: 31808999 PMCID: PMC7540688 DOI: 10.1002/cyto.a.23942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/15/2019] [Accepted: 11/19/2019] [Indexed: 11/09/2022]
Abstract
A large variety of fluorescent molecules are used on a regular basis to tag major histocompatibility complex (MHC) multimers for detection of antigen-specific T cells. We have evaluated the way in which the choice of fluorescent label can impact the detection of MHC multimer binding T cells in an exploratory proficiency panel where detection of MHC multimer binding T cells was assessed across 16 different laboratories. We found that the staining index (SI) of the multimer reagent provided the best direct correlation with the value of a given fluorochrome for T cell detection studies. The SI is dependent on flow cytometer settings and chosen antibody panel; hence, the optimal fluorochrome selection may differ from lab to lab. Consequently, we describe a strategy to evaluate performance of the detection channels and optimize the SI for selected fluorescent molecules. This approach can easily be used to test and optimize fluorescence detection in relation to MHC multimer staining and in general, for antibody-based identification of rare cell populations. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
| | - Karoline Laske
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen, Germany.,Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | - Marij Welters
- Department of Clinical Oncology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Cécile Gouttefangeas
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
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43
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Anti-CD20 therapy depletes activated myelin-specific CD8 + T cells in multiple sclerosis. Proc Natl Acad Sci U S A 2019; 116:25800-25807. [PMID: 31748274 PMCID: PMC6926057 DOI: 10.1073/pnas.1915309116] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system. CD8+ T cells have been strongly implicated in MS pathogenesis, but it is unclear whether myelin is a CD8+ T cell autoantigenic target in MS. This study demonstrated that while myelin-specific CD8+ T cells are present at similar frequencies in untreated MS patients and healthy subjects, the proportion of memory and CD20-expressing myelin-specific CD8+ T cells was increased in MS patients, suggesting prior antigen encounter. This activated phenotype was reversible as the memory and CD20-expressing populations of certain myelin-specific CD8+ T cells were reduced following anti-CD20 treatment. CD8+ T cells are believed to play an important role in multiple sclerosis (MS), yet their role in MS pathogenesis remains poorly defined. Although myelin proteins are considered potential autoantigenic targets, prior studies of myelin-reactive CD8+ T cells in MS have relied on in vitro stimulation, thereby limiting accurate measurement of their ex vivo precursor frequencies and phenotypes. Peptide:MHC I tetramers were used to identify and validate 5 myelin CD8+ T cell epitopes, including 2 newly described determinants in humans. The validated tetramers were used to measure the ex vivo precursor frequencies and phenotypes of myelin-specific CD8+ T cells in the peripheral blood of untreated MS patients and HLA allele-matched healthy controls. In parallel, CD8+ T cell responses against immunodominant influenza epitopes were also measured. There were no differences in ex vivo frequencies of tetramer-positive myelin-specific CD8+ T cells between MS patients and control subjects. An increased proportion of myelin-specific CD8+ T cells in MS patients exhibited a memory phenotype and expressed CD20 compared to control subjects, while there were no phenotypic differences observed among influenza-specific CD8+ T cells. Longitudinal assessments were also measured in a subset of MS patients subsequently treated with anti-CD20 monoclonal antibody therapy. The proportion of memory and CD20+ CD8+ T cells specific for certain myelin but not influenza epitopes was significantly reduced following anti-CD20 treatment. This study, representing a characterization of unmanipulated myelin-reactive CD8+ T cells in MS, indicates these cells may be attractive targets in MS therapy.
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44
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Fuchs YF, Sharma V, Eugster A, Kraus G, Morgenstern R, Dahl A, Reinhardt S, Petzold A, Lindner A, Löbel D, Bonifacio E. Gene Expression-Based Identification of Antigen-Responsive CD8 + T Cells on a Single-Cell Level. Front Immunol 2019; 10:2568. [PMID: 31781096 PMCID: PMC6851025 DOI: 10.3389/fimmu.2019.02568] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/16/2019] [Indexed: 12/31/2022] Open
Abstract
CD8+ T cells are important effectors of adaptive immunity against pathogens, tumors, and self antigens. Here, we asked how human cognate antigen-responsive CD8+ T cells and their receptors could be identified in unselected single-cell gene expression data. Single-cell RNA sequencing and qPCR of dye-labeled antigen-specific cells identified large gene sets that were congruently up- or downregulated in virus-responsive CD8+ T cells under different antigen presentation conditions. Combined expression of TNFRSF9, XCL1, XCL2, and CRTAM was the most distinct marker of virus-responsive cells on a single-cell level. Using transcriptomic data, we developed a machine learning-based classifier that provides sensitive and specific detection of virus-responsive CD8+ T cells from unselected populations. Gene response profiles of CD8+ T cells specific for the autoantigen islet-specific glucose-6-phosphatase catalytic subunit-related protein differed markedly from virus-specific cells. These findings provide single-cell gene expression parameters for comprehensive identification of rare antigen-responsive cells and T cell receptors.
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Affiliation(s)
- Yannick F Fuchs
- Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Virag Sharma
- Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany.,German Center for Diabetes Research (DZD), Paul Langerhans Institute Dresden, Technische Universität Dresden, Dresden, Germany
| | - Anne Eugster
- Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Gloria Kraus
- Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Robert Morgenstern
- Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Andreas Dahl
- DRESDEN-Concept Genome Center c/o Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Susanne Reinhardt
- DRESDEN-Concept Genome Center c/o Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Andreas Petzold
- DRESDEN-Concept Genome Center c/o Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Annett Lindner
- Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Doreen Löbel
- Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Ezio Bonifacio
- Faculty of Medicine, DFG Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany.,German Center for Diabetes Research (DZD), Paul Langerhans Institute Dresden, Technische Universität Dresden, Dresden, Germany.,Institute of Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
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45
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Gouttefangeas C, Schuhmacher J, Dimitrov S. Adhering to adhesion: assessing integrin conformation to monitor T cells. Cancer Immunol Immunother 2019; 68:1855-1863. [PMID: 31309255 PMCID: PMC11028104 DOI: 10.1007/s00262-019-02365-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/02/2019] [Indexed: 11/27/2022]
Abstract
Monitoring T cells is of major importance for the development of immunotherapies. Recent sophisticated assays can address particular aspects of the anti-tumor T-cell repertoire or support very large-scale immune screening for biomarker discovery. Robust methods for the routine assessment of the quantity and quality of antigen-specific T cells remain, however, essential. This review discusses selected methods that are commonly used for T-cell monitoring and summarizes the advantages and limitations of these assays. We also present a new functional assay, which specifically detects activated β2 integrins within a very short time following CD8+ T-cell stimulation. Because of its unique and favorable characteristics, this assay could be useful for implementation into our T-cell monitoring toolbox.
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Affiliation(s)
- Cécile Gouttefangeas
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University, Auf der Morgenstelle 15, 72076, Tübingen, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany.
| | - Juliane Schuhmacher
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University, Auf der Morgenstelle 15, 72076, Tübingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Stoyan Dimitrov
- Institute of Medical Psychology and Behavioral Neurobiology, Eberhard Karls University, Otfried-Müller Straße 25, 72076, Tübingen, Germany.
- German Center for Diabetes Research, 72076, Tübingen, Germany.
- Institute for Diabetes Research and Metabolic Diseases, Helmholtz Center Munich at the University of Tübingen (IDM), Otfried-Müller Straße 10, 72076, Tübingen, Germany.
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46
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Viborg N, Ramskov S, Andersen RS, Sturm T, Fugmann T, Bentzen AK, Rafa VM, Straten PT, Svane IM, Met Ö, Hadrup SR. T cell recognition of novel shared breast cancer antigens is frequently observed in peripheral blood of breast cancer patients. Oncoimmunology 2019; 8:e1663107. [PMID: 31741759 PMCID: PMC6844330 DOI: 10.1080/2162402x.2019.1663107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/25/2022] Open
Abstract
Advances within cancer immunotherapy have fueled a paradigm shift in cancer treatment, resulting in increasing numbers of cancer types benefitting from novel treatment options. Despite originally being considered an immunologically silent malignancy, recent studies encourage the research of breast cancer immunogenicity to evaluate immunotherapy as a treatment strategy. However, the epitope landscape in breast cancer is minimally described, limiting the options for antigen-specific, targeted strategies. Aromatase, never in mitosis A-related kinase 3 (NEK3), protein inhibitor of activated STAT3 (PIAS3), and prolactin are known as upregulated proteins in breast cancer. In the present study, these four proteins are identified as novel T cell targets in breast cancer. From the four proteins, 147 peptides were determined to bind HLA-A*0201 and -B*0702 using a combined in silico/in vitro affinity screening. T cell recognition of all 147 peptide-HLA-A*0201/-B*0702 combinations was assessed through the use of a novel high-throughput method utilizing DNA barcode labeled multimers. T cell recognition of sequences within all four proteins was demonstrated in peripheral blood of patients, and significantly more T cell responses were detected in patients compared to healthy donors for both HLA-A*0201 and -B*0702. Notably, several of the identified responses were directed toward peptides, with a predicted low or intermediate binding affinity. This demonstrates the importance of including low-affinity binders in the search for epitopes within shared tumor associated antigens (TAAs), as these might be less subject to immune tolerance mechanisms. The study presents four novel TAAs containing multiple possible targets for immunotherapy of breast cancer.
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Affiliation(s)
- Nadia Viborg
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Sofie Ramskov
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Rikke Sick Andersen
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Herlev, Denmark
| | | | | | - Amalie Kai Bentzen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Vibeke Mindahl Rafa
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Per Thor Straten
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Herlev, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Inge Marie Svane
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Herlev, Denmark
| | - Özcan Met
- Center for Cancer Immune Therapy, Copenhagen University Hospital, Herlev, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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47
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Ng AHC, Peng S, Xu AM, Noh WJ, Guo K, Bethune MT, Chour W, Choi J, Yang S, Baltimore D, Heath JR. MATE-Seq: microfluidic antigen-TCR engagement sequencing. LAB ON A CHIP 2019; 19:3011-3021. [PMID: 31502632 DOI: 10.1039/c9lc00538b] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Adaptive immunity is based on peptide antigen recognition. Our ability to harness the immune system for therapeutic gain relies on the discovery of the T cell receptor (TCR) genes that selectively target antigens from infections, mutated proteins, and foreign agents. Here we present a method that selectively labels peptide antigen-specific CD8+ T cells using magnetic nanoparticles functionalized with peptide-MHC tetramers, isolates these specific cells within an integrated microfluidic device, and directly amplifies the TCR genes for sequencing. Critically, the identity of the peptide recognized by the TCR is preserved, providing the link between peptide and gene. The platform requires inputs on the order of just 100 000 CD8+ T cells, can be multiplexed for simultaneous analysis of multiple peptides, and performs sorting and isolation on chip. We demonstrate 1000-fold sensitivity enhancement of detecting antigen-specific TCRs relative to bulk analysis and simultaneous capture of two virus antigen-specific TCRs from a population of T cells.
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Affiliation(s)
- Alphonsus H C Ng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd, Pasadena, CA 91125, USA
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48
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Peng S, Zaretsky JM, Ng AHC, Chour W, Bethune MT, Choi J, Hsu A, Holman E, Ding X, Guo K, Kim J, Xu AM, Heath JE, Noh WJ, Zhou J, Su Y, Lu Y, McLaughlin J, Cheng D, Witte ON, Baltimore D, Ribas A, Heath JR. Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood. Cell Rep 2019; 28:2728-2738.e7. [PMID: 31484081 PMCID: PMC6774618 DOI: 10.1016/j.celrep.2019.07.106] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 05/04/2019] [Accepted: 07/29/2019] [Indexed: 12/30/2022] Open
Abstract
Neoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanoparticles that present neoantigen-loaded major histocompatibility complex (MHC) tetramers at high avidity by barcoded DNA linkers. The magnetic particles provide a convenient handle to isolate the desired cell populations, and the barcoded DNA enables multiplexed analysis. The method exhibits superior recovery of antigen-specific T cell populations relative to literature approaches. We applied the method to profile neoantigen-specific T cell populations in the tumor and blood of patients with metastatic melanoma over the course of anti-PD1 checkpoint inhibitor therapy. We show that the method has value for monitoring clinical responses to cancer immunotherapy and might help guide the development of personalized mutational neoantigen-specific T cell therapies and cancer vaccines.
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Affiliation(s)
- Songming Peng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Jesse M Zaretsky
- Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Alphonsus H C Ng
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - William Chour
- Institute for Systems Biology, Seattle, WA 98109, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Michael T Bethune
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Jongchan Choi
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Alice Hsu
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Elizabeth Holman
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Xiaozhe Ding
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Katherine Guo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Jungwoo Kim
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Alexander M Xu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - John E Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Won Jun Noh
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Jing Zhou
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Yapeng Su
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Yue Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jami McLaughlin
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Owen N Witte
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Antoni Ribas
- Department of Medicine, University of California Los Angeles and Jonsson Comprehensive Cancer Center, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA; Institute for Systems Biology, Seattle, WA 98109, USA.
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49
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Khalil DN, Suek N, Campesato LF, Budhu S, Redmond D, Samstein RM, Krishna C, Panageas KS, Capanu M, Houghton S, Hirschhorn D, Zappasodi R, Giese R, Gasmi B, Schneider M, Gupta A, Harding JJ, Moral JA, Balachandran VP, Wolchok JD, Merghoub T. In situ vaccination with defined factors overcomes T cell exhaustion in distant tumors. J Clin Invest 2019; 129:3435-3447. [PMID: 31329159 DOI: 10.1172/jci128562] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022] Open
Abstract
Irreversible T cell exhaustion limits the efficacy of programmed cell death 1 (PD-1) blockade. We observed that dual CD40-TLR4 stimulation within a single tumor restored PD-1 sensitivity and that this regimen triggered a systemic tumor-specific CD8+ T cell response. This approach effectively treated established tumors in diverse syngeneic cancer models, and the systemic effect was dependent on the injected tumor, indicating that treated tumors were converted into necessary components of this therapy. Strikingly, this approach was associated with the absence of exhausted PD-1hi T cells in treated and distant tumors, while sparing the intervening draining lymph node and spleen. Furthermore, patients with transcription changes like those induced by this therapy experienced improved progression-free survival with anti-PD-1 treatment. Dual CD40-TLR4 activation within a single tumor is thus an approach for overcoming resistance to PD-1 blockade that is unique in its ability to cause the loss of exhausted T cells within tumors while sparing nonmalignant tissues.
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Affiliation(s)
- Danny N Khalil
- Ludwig Collaborative and Swim Across America Laboratory.,Parker Institute for Cancer Immunotherapy, and.,Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medicine, New York, New York, USA
| | - Nathan Suek
- Ludwig Collaborative and Swim Across America Laboratory
| | | | - Sadna Budhu
- Ludwig Collaborative and Swim Across America Laboratory
| | - David Redmond
- Ludwig Collaborative and Swim Across America Laboratory
| | | | | | | | - Marinela Capanu
- Department of Epidemiology and Biostatistics, MSKCC, New York, New York, USA
| | - Sean Houghton
- Ludwig Collaborative and Swim Across America Laboratory
| | | | - Roberta Zappasodi
- Ludwig Collaborative and Swim Across America Laboratory.,Parker Institute for Cancer Immunotherapy, and
| | - Rachel Giese
- Ludwig Collaborative and Swim Across America Laboratory.,Department of Surgery, MSKCC, New York, New York, USA
| | - Billel Gasmi
- National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | | | - Aditi Gupta
- Ludwig Collaborative and Swim Across America Laboratory
| | - James J Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medicine, New York, New York, USA
| | | | - Vinod P Balachandran
- Parker Institute for Cancer Immunotherapy, and.,Hepatopancreatobiliary Service, Department of Surgery and David M. Rubenstein Center for Pancreatic Cancer Research, MSKCC, New York, New York, USA
| | - Jedd D Wolchok
- Ludwig Collaborative and Swim Across America Laboratory.,Parker Institute for Cancer Immunotherapy, and.,Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medicine, New York, New York, USA
| | - Taha Merghoub
- Ludwig Collaborative and Swim Across America Laboratory.,Parker Institute for Cancer Immunotherapy, and.,Department of Medicine, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medicine, New York, New York, USA
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50
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Saini SK, Tamhane T, Anjanappa R, Saikia A, Ramskov S, Donia M, Svane IM, Jakobsen SN, Garcia-Alai M, Zacharias M, Meijers R, Springer S, Hadrup SR. Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells. Sci Immunol 2019; 4:4/37/eaau9039. [DOI: 10.1126/sciimmunol.aau9039] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/20/2019] [Indexed: 12/17/2022]
Abstract
The peptide-dependent stability of MHC class I molecules poses a substantial challenge for their use in peptide-MHC multimer–based approaches to comprehensively analyze T cell immunity. To overcome this challenge, we demonstrate the use of functionally empty MHC class I molecules stabilized by a disulfide bond to link the α1and α2helices close to the F pocket. Peptide-loaded disulfide-stabilized HLA-A*02:01 shows complete structural overlap with wild-type HLA-A*02:01. Peptide-MHC multimers prepared using disulfide-stabilized HLA-A*02:01, HLA-A*24:02, and H-2Kbcan be used to identify antigen-specific T cells, and they provide a better staining index for antigen-specific T cell detection compared with multimers prepared with wild-type MHC class I molecules. Disulfide-stabilized MHC class I molecules can be loaded with peptide in the multimerized form without affecting their capacity to stain T cells. We demonstrate the value of empty-loadable tetramers that are converted to antigen-specific tetramers by a single-step peptide addition through their use to identify T cells specific for mutation-derived neoantigens and other cancer-associated antigens in human melanoma.
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