1
|
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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [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.
Collapse
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
| |
Collapse
|
2
|
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: 3] [Impact Index Per Article: 3.0] [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.
Collapse
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
| |
Collapse
|
3
|
Müller TR, Sekine T, Trubach D, Niessl J, Chen P, Bergman P, Blennow O, Hansson L, Mielke S, Nowak P, Vesterbacka J, Akber M, Olofsson A, Amaya Hernandez SP, Gao Y, Cai C, Söderdahl G, Smith CIE, Österborg A, Loré K, Sällberg Chen M, Ljungman P, Ljunggren HG, Karlsson AC, Saini SK, Aleman S, Buggert M. Additive effects of booster mRNA vaccination and SARS-CoV-2 Omicron infection on T cell immunity across immunocompromised states. Sci Transl Med 2023; 15:eadg9452. [PMID: 37437015 PMCID: PMC7615622 DOI: 10.1126/scitranslmed.adg9452] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/23/2023] [Indexed: 07/14/2023]
Abstract
Suboptimal immunity to SARS-CoV-2 mRNA vaccination has frequently been observed in individuals with various immunodeficiencies. Given the increased antibody evasion properties of emerging SARS-CoV-2 subvariants, it is necessary to assess whether other components of adaptive immunity generate resilient and protective responses against infection. We assessed T cell responses in 279 individuals, covering five different immunodeficiencies and healthy controls, before and after booster mRNA vaccination, as well as after Omicron infection in a subset of patients. We observed robust and persistent Omicron-reactive T cell responses that increased markedly upon booster vaccination and correlated directly with antibody titers across all patient groups. Poor vaccination responsiveness in immunocompromised or elderly individuals was effectively counteracted by the administration of additional vaccine doses. Functionally, Omicron-reactive T cell responses exhibited a pronounced cytotoxic profile and signs of longevity, characterized by CD45RA+ effector memory subpopulations with stem cell-like properties and increased proliferative capacity. Regardless of underlying immunodeficiency, booster-vaccinated and Omicron-infected individuals appeared protected against severe disease and exhibited enhanced and diversified T cell responses against conserved and Omicron-specific epitopes. Our findings indicate that T cells retain the ability to generate highly functional responses against newly emerging variants, even after repeated antigen exposure and a robust immunological imprint from ancestral SARS-CoV-2 mRNA vaccination.
Collapse
Affiliation(s)
- Thomas R. Müller
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Takuya Sekine
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Darya Trubach
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julia Niessl
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Puran Chen
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Peter Bergman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Clinical Immunology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Ola Blennow
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Transplantation, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
| | - Lotta Hansson
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Stephan Mielke
- Department of Laboratory Medicine, Biomolecular and Cellular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Cellular Therapy and Allogeneic Stem Cell Transplantation (CAST), Karolinska Comprehensive Cancer Center, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Piotr Nowak
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Sweden
| | - Jan Vesterbacka
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
| | - Mira Akber
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Olofsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Susana Patricia Amaya Hernandez
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Yu Gao
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Curtis Cai
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gunnar Söderdahl
- Department of Transplantation, Karolinska University Hospital, Stockholm, Sweden
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - C. I. Edvard Smith
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Biomolecular and Cellular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Cellular Therapy and Allogeneic Stem Cell Transplantation (CAST), Karolinska Comprehensive Cancer Center, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Anders Österborg
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Karin Loré
- Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Per Ljungman
- Department of Cellular Therapy and Allogeneic Stem Cell Transplantation (CAST), Karolinska Comprehensive Cancer Center, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Department of Medicine Huddinge, Hematology, Karolinska Institutet, Stockholm
| | - Hans-Gustaf Ljunggren
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Annika C. Karlsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Karolinska University Laboratory, Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Sunil Kumar Saini
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Soo Aleman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine Huddinge, Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
4
|
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: 0] [Impact Index Per Article: 0] [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.
Collapse
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
| |
Collapse
|
5
|
Povlsen HR, Bentzen AK, Kadivar M, Jessen LE, Hadrup SR, Nielsen M. Improved T cell receptor antigen pairing through data-driven filtering of sequencing information from single cells. eLife 2023; 12:e81810. [PMID: 37133356 PMCID: PMC10156162 DOI: 10.7554/elife.81810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/13/2023] [Indexed: 05/04/2023] Open
Abstract
Novel single-cell-based technologies hold the promise of matching T cell receptor (TCR) sequences with their cognate peptide-MHC recognition motif in a high-throughput manner. Parallel capture of TCR transcripts and peptide-MHC is enabled through the use of reagents labeled with DNA barcodes. However, analysis and annotation of such single-cell sequencing (SCseq) data are challenged by dropout, random noise, and other technical artifacts that must be carefully handled in the downstream processing steps. We here propose a rational, data-driven method termed ITRAP (improved T cell Receptor Antigen Paring) to deal with these challenges, filtering away likely artifacts, and enable the generation of large sets of TCR-pMHC sequence data with a high degree of specificity and sensitivity, thus outputting the most likely pMHC target per T cell. We have validated this approach across 10 different virus-specific T cell responses in 16 healthy donors. Across these samples, we have identified up to 1494 high-confident TCR-pMHC pairs derived from 4135 single cells.
Collapse
Affiliation(s)
- Helle Rus Povlsen
- Department of Health Technology at Technical University of DenmarkKongens LyngbyDenmark
| | - Amalie Kai Bentzen
- Department of Health Technology at Technical University of DenmarkKongens LyngbyDenmark
| | - Mohammad Kadivar
- Department of Health Technology at Technical University of DenmarkKongens LyngbyDenmark
| | - Leon Eyrich Jessen
- Department of Health Technology at Technical University of DenmarkKongens LyngbyDenmark
| | - Sine Reker Hadrup
- Department of Health Technology at Technical University of DenmarkKongens LyngbyDenmark
| | - Morten Nielsen
- Department of Health Technology at Technical University of DenmarkKongens LyngbyDenmark
| |
Collapse
|
6
|
Sun Y, Young MC, Woodward CH, Danon JN, Truong H, Gupta S, Winters TJ, Burslem G, Sgourakis NG. Universal open MHC-I molecules for rapid peptide loading and enhanced complex stability across HLA allotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.533266. [PMID: 36993702 PMCID: PMC10055308 DOI: 10.1101/2023.03.18.533266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The polymorphic nature and intrinsic instability of class I major histocompatibility complex (MHC-I) and MHC-like molecules loaded with suboptimal peptides, metabolites, or glycolipids presents a fundamental challenge for identifying disease-relevant antigens and antigen-specific T cell receptors (TCRs), hindering the development of autologous therapeutics. Here, we leverage the positive allosteric coupling between the peptide and light chain (β 2 microglobulin, β 2 m) subunits for binding to the MHC-I heavy chain (HC) through an engineered disulfide bond bridging conserved epitopes across the HC/β 2 m interface, to generate conformationally stable, open MHC-I molecules. Biophysical characterization shows that open MHC-I molecules are properly folded protein complexes of enhanced thermal stability compared to the wild type, when loaded with low- to intermediate-affinity peptides. Using solution NMR, we characterize the effects of the disulfide bond on the conformation and dynamics of the MHC-I structure, ranging from local changes in β 2 m interacting sites of the peptide binding groove to long-range effects on the α 2-1 helix and α 3 domain. The interchain disulfide bond stabilizes empty MHC-I molecules in a peptide-receptive, open conformation to promote peptide exchange across multiple human leucocyte antigen (HLA) allotypes, covering representatives from five HLA-A, six HLA-B supertypes, and oligomorphic HLA-Ib molecules. Our structural design, combined with conditional β-peptide ligands, provides a universal platform for generating ready-to-load MHC-I systems of enhanced stability, enabling a range of approaches to screen antigenic epitope libraries and probe polyclonal TCR repertoires in the context of highly polymorphic HLA-I allotypes, as well as oligomorphic nonclassical molecules. Significance Statement We outline a structure-guided approach for generating conformationally stable, open MHC-I molecules with enhanced ligand exchange kinetics spanning five HLA-A, all HLA-B supertypes, and oligomorphic HLA-Ib allotypes. We present direct evidence of positive allosteric cooperativity between peptide binding and β 2 m association with the heavy chain by solution NMR and HDX-MS spectroscopy. We demonstrate that covalently linked β 2 m serves as a conformational chaperone to stabilize empty MHC-I molecules in a peptide-receptive state, by inducing an open conformation and preventing intrinsically unstable heterodimers from irreversible aggregation. Our study provides structural and biophysical insights into the conformational properties of MHC-I ternary complexes, which can be further applied to improve the design of ultra-stable, universal ligand exchange systems in a pan-HLA allelic setting.
Collapse
|
7
|
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: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [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.
Collapse
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,
| |
Collapse
|
8
|
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: 42] [Impact Index Per Article: 21.0] [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.
Collapse
|
9
|
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: 3.5] [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:
| |
Collapse
|
10
|
Reguzova A, Fischer N, Müller M, Salomon F, Jaenisch T, Amann R. A Novel Orf Virus D1701-VrV-Based Dengue Virus (DENV) Vaccine Candidate Expressing HLA-Specific T Cell Epitopes: A Proof-of-Concept Study. Biomedicines 2021; 9:biomedicines9121862. [PMID: 34944678 PMCID: PMC8698572 DOI: 10.3390/biomedicines9121862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/02/2022] Open
Abstract
Although dengue virus (DENV) affects almost half of the world’s population there are neither preventive treatments nor any long-lasting and protective vaccines available at this time. The complexity of the protective immune response to DENV is still not fully understood. The most advanced vaccine candidates focus specifically on humoral immune responses and the production of virus-neutralizing antibodies. However, results from several recent studies have revealed the protective role of T cells in the immune response to DENV. Hence, in this study, we generated a novel and potent DENV vaccine candidate based on an Orf virus (ORFV, genus Parapoxvirus) vector platform engineered to encode five highly conserved or cross-reactive DENV human leukocyte antigen (HLA)-A*02- or HLA-B*07-restricted epitopes as minigenes (ORFV-DENV). We showed that ORFV-DENV facilitates the in vitro priming of CD8+ T cells from healthy blood donors based on responses to each of the encoded immunogenic peptides. Moreover, we demonstrated that peripheral blood mononuclear cells isolated from clinically confirmed DENV-positive donors stimulated with ORFV-DENV generate cytotoxic T cell responses to at least three of the expressed DENV peptides. Finally, we showed that ORFV-DENV could activate CD8+ T cells isolated from donors who had recovered from Zika virus (ZIKV) infection. ZIKV belongs to the same virus family (Flaviviridae) and has epitope sequences that are homologous to those of DENV. We found that highly conserved HLA-B*07-restricted ZIKV and DENV epitopes induced functional CD8+ T cell responses in PBMCs isolated from confirmed ZIKV-positive donors. In summary, this proof-of-concept study characterizes a promising new ORFV D1701-VrV-based DENV vaccine candidate that induces broad and functional epitope-specific CD8+ T cell responses.
Collapse
Affiliation(s)
- Alena Reguzova
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.M.); (F.S.)
| | - Nico Fischer
- Department of Infectious Diseases, Heidelberg Institute of Global Health (HIGH) & Tropical Medicine, Heidelberg University Hospital, 69120 Heidelberg, Germany; (N.F.); (T.J.)
| | - Melanie Müller
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.M.); (F.S.)
| | - Ferdinand Salomon
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.M.); (F.S.)
| | - Thomas Jaenisch
- Department of Infectious Diseases, Heidelberg Institute of Global Health (HIGH) & Tropical Medicine, Heidelberg University Hospital, 69120 Heidelberg, Germany; (N.F.); (T.J.)
| | - Ralf Amann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Germany; (A.R.); (M.M.); (F.S.)
- Correspondence: ; Tel.: +49-707-1298-7614
| |
Collapse
|
11
|
Brunk F, Moritz A, Nelde A, Bilich T, Casadei N, Fraschka SAK, Heitmann JS, Hörber S, Peter A, Rammensee H, Singh H, Walz J, Maurer D, Wagner C. SARS-CoV-2-reactive T-cell receptors isolated from convalescent COVID-19 patients confer potent T-cell effector function. Eur J Immunol 2021; 51:2651-2664. [PMID: 34424997 PMCID: PMC8646365 DOI: 10.1002/eji.202149290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/25/2021] [Indexed: 11/25/2022]
Abstract
Both B cells and T cells are involved in an effective immune response to SARS-CoV-2, the disease-causing virus of COVID-19. While B cells-with the indispensable help of CD4+ T cells-are essential to generate neutralizing antibodies, T cells on their own have been recognized as another major player in effective anti-SARS-CoV-2 immunity. In this report, we provide insights into the characteristics of individual HLA-A*02:01- and HLA-A*24:02-restricted SARS-CoV-2-reactive TCRs, isolated from convalescent COVID-19 patients. We observed that SARS-CoV-2-reactive T-cell populations were clearly detectable in convalescent samples and that TCRs isolated from these T cell clones were highly functional upon ectopic re-expression. The SARS-CoV-2-reactive TCRs described in this report mediated potent TCR signaling in reporter assays with low nanomolar EC50 values. We further demonstrate that these SARS-CoV-2-reactive TCRs conferred powerful T-cell effector function to primary CD8+ T cells as evident by a robust anti-SARS-CoV-2 IFN-γ response and in vitro cytotoxicity. We also provide an example of a long-lasting anti-SARS-CoV-2 memory response by reisolation of one of the retrieved TCRs 5 months after initial sampling. Taken together, these findings contribute to a better understanding of anti-SARS-CoV-2 T-cell immunity and may contribute to paving the way toward immunotherapeutics approaches targeting SARS-CoV-2.
Collapse
Affiliation(s)
| | | | - Annika Nelde
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TübingenTübingenGermany
- Department of ImmunologyInstitute for Cell BiologyUniversity of TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
| | - Tatjana Bilich
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TübingenTübingenGermany
- Department of ImmunologyInstitute for Cell BiologyUniversity of TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
| | - Nicolas Casadei
- NGS Competence Center TübingenTübingenGermany
- Institute of Medical Genetics and Applied GenomicsUniversity Hospital TübingenTübingenGermany
| | - Sabine A. K. Fraschka
- NGS Competence Center TübingenTübingenGermany
- Institute of Medical Genetics and Applied GenomicsUniversity Hospital TübingenTübingenGermany
| | - Jonas S. Heitmann
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
| | - Sebastian Hörber
- Department for Diagnostic Laboratory MedicineInstitute for Clinical Chemistry and PathobiochemistryUniversity Hospital TübingenTübingenGermany
| | - Andreas Peter
- Department for Diagnostic Laboratory MedicineInstitute for Clinical Chemistry and PathobiochemistryUniversity Hospital TübingenTübingenGermany
| | - Hans‐Georg Rammensee
- Department of ImmunologyInstitute for Cell BiologyUniversity of TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ)Partner Site TübingenTübingenGermany
| | | | - Juliane Walz
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TübingenTübingenGermany
- Department of ImmunologyInstitute for Cell BiologyUniversity of TübingenTübingenGermany
- Cluster of Excellence iFIT (EXC2180) ‘Image‐Guided and Functionally Instructed Tumor Therapies,’University of TübingenTübingenGermany
- Dr. Margarete Fischer‐Bosch Institute of Clinical Pharmacology, Robert Bosch Center for Tumor Diseases (RBCT)StuttgartGermany
| | | | | |
Collapse
|
12
|
Darwish M, Wichner S, Li J, Chang JC, Tam C, Franke Y, Li H, Chan P, Blanchette C. High-throughput identification of conditional MHCI ligands and scaled-up production of conditional MHCI complexes. Protein Sci 2021; 30:1169-1183. [PMID: 33840137 PMCID: PMC8138534 DOI: 10.1002/pro.4082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 01/28/2023]
Abstract
Despite the need to monitor the impact of Cancer Immunotherapy (CI)/Immuno-Oncology (IO) therapeutics on neoantigen-specific T-cell responses, very few clinical programs incorporate this aspect of immune monitoring due to the challenges in high-throughput (HTP) generation of Major Histocompatibility Complex Class I (MHCI) tetramers across a wide range of HLA alleles. This limitation was recently addressed through the development of MHCI complexes with peptides containing a nonnatural UV cleavable amino acid (conditional MHCI ligands) that enabled HTP peptide exchange upon UV exposure. Despite this advancement, the number of alleles with known conditional MHCI ligands is limited. We developed a novel workflow to enable identification and validation of conditional MHCI ligands across a range of HLA alleles. First, known peptide binders were screened via an enzyme-linked immunosorbent assay (ELISA) assay. Conditional MHCI ligands were designed using the highest-performing peptides and evaluated in the same ELISA assay. The top performers were then selected for scale-up production. Next-generation analytical techniques (LC/MS, SEC-MALS, and 2D LC/MS) were used to characterize the complex after refolding with the conditional MHCI ligands. Finally, we used 2D LC/MS to evaluate peptide exchange with these scaled-up conditional MHCI complexes after UV exposure with validated peptide binders. Successful peptide exchange was observed for all conditional MHCI ligands upon UV exposure, validating our screening approach. This approach has the potential to be broadly applied and enable HTP generation of MHCI monomers and tetramers across a wider range of HLA alleles, which could be critical to enabling the use of MHCI tetramers to monitor neoantigen-specific T-cells in the clinic.
Collapse
Affiliation(s)
| | - Sara Wichner
- Protein ChemistryGenentech IncSan FranciscoCaliforniaUSA
| | - Jenny Li
- Biochemical and Cellular PharmacologyGenentech IncSan FranciscoCaliforniaUSA
| | | | - Christine Tam
- BioMolecular ResourcesGenentech IncSan FranciscoCaliforniaUSA
| | - Yvonne Franke
- BioMolecular ResourcesGenentech IncSan FranciscoCaliforniaUSA
| | - Hong Li
- Protein ChemistryGenentech IncSan FranciscoCaliforniaUSA
| | - Pamela Chan
- Biochemical and Cellular PharmacologyGenentech IncSan FranciscoCaliforniaUSA
| | | |
Collapse
|
13
|
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: 145] [Impact Index Per Article: 48.3] [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.
Collapse
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.
| |
Collapse
|
14
|
Saini SK, Ørskov AD, Bjerregaard AM, Unnikrishnan A, Holmberg-Thydén S, Borch A, Jensen KV, Anande G, Bentzen AK, Marquard AM, Tamhane T, Treppendahl MB, Gang AO, Dufva IH, Szallasi Z, Ternette N, Pedersen AG, Eklund AC, Pimanda J, Grønbæk K, Hadrup SR. Human endogenous retroviruses form a reservoir of T cell targets in hematological cancers. Nat Commun 2020; 11:5660. [PMID: 33168830 PMCID: PMC7653045 DOI: 10.1038/s41467-020-19464-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 10/10/2020] [Indexed: 01/03/2023] Open
Abstract
Human endogenous retroviruses (HERV) form a substantial part of the human genome, but mostly remain transcriptionally silent under strict epigenetic regulation, yet can potentially be reactivated by malignant transformation or epigenetic therapies. Here, we evaluate the potential for T cell recognition of HERV elements in myeloid malignancies by mapping transcribed HERV genes and generating a library of 1169 potential antigenic HERV-derived peptides predicted for presentation by 4 HLA class I molecules. Using DNA barcode-labeled MHC-I multimers, we find CD8+ T cell populations recognizing 29 HERV-derived peptides representing 18 different HERV loci, of which HERVH-5, HERVW-1, and HERVE-3 have more profound responses; such HERV-specific T cells are present in 17 of the 34 patients, but less frequently in healthy donors. Transcriptomic analyses reveal enhanced transcription of the HERVs in patients; meanwhile DNA-demethylating therapy causes a small and heterogeneous enhancement in HERV transcription without altering T cell recognition. Our study thus uncovers T cell recognition of HERVs in myeloid malignancies, thereby implicating HERVs as potential targets for immunotherapeutic therapies.
Collapse
Affiliation(s)
- Sunil Kumar Saini
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andreas Due Ørskov
- Department of Haematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Anne-Mette Bjerregaard
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ashwin Unnikrishnan
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
- Prince of Wales Clinical School, UNSW, Sydney, NSW, 2052, Australia
| | - Staffan Holmberg-Thydén
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Haematology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Annie Borch
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Kathrine Valentini Jensen
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Govardhan Anande
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
- Prince of Wales Clinical School, UNSW, Sydney, NSW, 2052, Australia
| | - Amalie Kai Bentzen
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Andrea Marion Marquard
- 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
| | | | - Anne Ortved Gang
- Department of Haematology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Inge Høgh Dufva
- Department of Haematology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Zoltan Szallasi
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicola Ternette
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anders Gorm Pedersen
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aron Charles Eklund
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - John Pimanda
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
- Prince of Wales Clinical School, UNSW, Sydney, NSW, 2052, Australia
- Haematology Department, South Eastern Area Laboratory Services, Prince of Wales Hospital, Randwick, NSW, 2031, Australia
| | - Kirsten Grønbæk
- Department of Haematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Section of Experimental and Translational Immunology, Technical University of Denmark, Kongens Lyngby, Denmark.
| |
Collapse
|
15
|
Moritz A, Anjanappa R, Wagner C, Bunk S, Hofmann M, Pszolla G, Saikia A, Garcia-Alai M, Meijers R, Rammensee HG, Springer S, Maurer D. High-throughput peptide-MHC complex generation and kinetic screenings of TCRs with peptide-receptive HLA-A*02:01 molecules. Sci Immunol 2020; 4:4/37/eaav0860. [PMID: 31324691 DOI: 10.1126/sciimmunol.aav0860] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 06/21/2019] [Indexed: 12/26/2022]
Abstract
Major histocompatibility complex (MHC) class I molecules present short peptide ligands on the cell surface for interrogation by cytotoxic CD8+ T cells. MHC class I complexes presenting tumor-associated peptides such as neoantigens represent key targets of cancer immunotherapy approaches currently in development, making them important for efficacy and safety screenings. Without peptide ligand, MHC class I complexes are unstable and decay quickly, making the production of soluble monomers for analytical purposes labor intensive. We have developed a disulfide-stabilized HLA-A*02:01 molecule that is stable without peptide but can form peptide-MHC complexes (pMHCs) with ligands of choice in a one-step loading procedure. We illustrate the similarity between the engineered mutant and the wild-type molecule with respect to affinity of wild-type or affinity-matured T cell receptors (TCRs) and present a crystal structure corroborating the binding kinetics measurements. In addition, we demonstrate a high-throughput binding kinetics measurement platform to analyze the binding characteristics of bispecific TCR (bsTCR) molecules against diverse pMHC libraries produced with the disulfide-stabilized HLA-A*02:01 molecule. We show that bsTCR affinities for pMHCs are indicative of in vitro function and generate a bsTCR binding motif to identify potential off-target interactions in the human proteome. These findings showcase the potential of the platform and the engineered HLA-A*02:01 molecule in the emerging field of pMHC-targeting biologics.
Collapse
Affiliation(s)
- Andreas Moritz
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany. .,Immatics Biotechnologies GmbH, Tübingen, Germany
| | | | | | | | | | | | - Ankur Saikia
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Maria Garcia-Alai
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | | |
Collapse
|
16
|
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: 26] [Impact Index Per Article: 6.5] [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.
Collapse
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
| |
Collapse
|
17
|
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: 5] [Impact Index Per Article: 1.0] [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.
Collapse
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
| |
Collapse
|
18
|
Abstract
Malignant transformation of cells depends on accumulation of DNA damage. Over the past years we have learned that the T cell-based immune system frequently responds to the neoantigens that arise as a consequence of this DNA damage. Furthermore, recognition of neoantigens appears an important driver of the clinical activity of both T cell checkpoint blockade and adoptive T cell therapy as cancer immunotherapies. Here we review the evidence for the relevance of cancer neoantigens in tumor control and the biological properties of these antigens. We discuss recent technological advances utilized to identify neoantigens, and the T cells that recognize them, in individual patients. Finally, we discuss strategies that can be employed to exploit cancer neoantigens in clinical interventions.
Collapse
Affiliation(s)
- Ton N Schumacher
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; , .,Oncode Institute, 3521AL Utrecht, The Netherlands
| | - Wouter Scheper
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; , .,Oncode Institute, 3521AL Utrecht, The Netherlands
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; ,
| |
Collapse
|
19
|
Bentzen AK, Such L, Jensen KK, Marquard AM, Jessen LE, Miller NJ, Church CD, Lyngaa R, Koelle DM, Becker JC, Linnemann C, Schumacher TNM, Marcatili P, Nghiem P, Nielsen M, Hadrup SR. T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide-MHC complexes. Nat Biotechnol 2018; 36:nbt.4303. [PMID: 30451992 PMCID: PMC9452375 DOI: 10.1038/nbt.4303] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/24/2018] [Indexed: 02/08/2023]
Abstract
The promiscuous nature of T-cell receptors (TCRs) allows T cells to recognize a large variety of pathogens, but makes it challenging to understand and control T-cell recognition. Existing technologies provide limited information about the key requirements for T-cell recognition and the ability of TCRs to cross-recognize structurally related elements. Here we present a 'one-pot' strategy for determining the interactions that govern TCR recognition of peptide-major histocompatibility complex (pMHC). We measured the relative affinities of TCRs to libraries of barcoded peptide-MHC variants and applied this knowledge to understand the recognition motif, here termed the TCR fingerprint. The TCR fingerprints of 16 different TCRs were identified and used to predict and validate cross-recognized peptides from the human proteome. The identified fingerprints differed among TCRs recognizing the same epitope, demonstrating the value of this strategy for understanding T-cell interactions and assessing potential cross-recognition before selection of TCRs for clinical development.
Collapse
Affiliation(s)
- Amalie K Bentzen
- Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
| | - Lina Such
- Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
| | - Kamilla K Jensen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Andrea M Marquard
- Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
| | - Leon E Jessen
- Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Natalie J Miller
- Department of Medicine, Divisions of Dermatology, University of Washington, Seattle, Washington, USA
| | - Candice D Church
- Department of Medicine, Divisions of Dermatology, University of Washington, Seattle, Washington, USA
| | - Rikke Lyngaa
- Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Division of Vaccine and Infectious Diseases, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jürgen C Becker
- Translational Skin Cancer Research, University Hospital Essen and University of Duisburg-Essen, Essen, Germany
| | - Carsten Linnemann
- Department of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ton N M Schumacher
- Department of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paolo Marcatili
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Paul Nghiem
- Department of Medicine, Divisions of Dermatology, University of Washington, Seattle, Washington, USA
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Sine R Hadrup
- Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
20
|
Gfeller D, Bassani-Sternberg M. Predicting Antigen Presentation-What Could We Learn From a Million Peptides? Front Immunol 2018; 9:1716. [PMID: 30090105 PMCID: PMC6068240 DOI: 10.3389/fimmu.2018.01716] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/12/2018] [Indexed: 12/30/2022] Open
Abstract
Antigen presentation lies at the heart of immune recognition of infected or malignant cells. For this reason, important efforts have been made to predict which peptides are more likely to bind and be presented by the human leukocyte antigen (HLA) complex at the surface of cells. These predictions have become even more important with the advent of next-generation sequencing technologies that enable researchers and clinicians to rapidly determine the sequences of pathogens (and their multiple variants) or identify non-synonymous genetic alterations in cancer cells. Here, we review recent advances in predicting HLA binding and antigen presentation in human cells. We argue that the very large amount of high-quality mass spectrometry data of eluted (mainly self) HLA ligands generated in the last few years provides unprecedented opportunities to improve our ability to predict antigen presentation and learn new properties of HLA molecules, as demonstrated in many recent studies of naturally presented HLA-I ligands. Although major challenges still lie on the road toward the ultimate goal of predicting immunogenicity, these experimental and computational developments will facilitate screening of putative epitopes, which may eventually help decipher the rules governing T cell recognition.
Collapse
Affiliation(s)
- David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, Ludwig Institute for Cancer Research, University Hospital of Lausanne, Lausanne, Switzerland
| |
Collapse
|
21
|
MHC class I presented antigens from malignancies: A perspective on analytical characterization & immunogenicity. J Proteomics 2018; 191:48-57. [PMID: 29698800 DOI: 10.1016/j.jprot.2018.04.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/10/2018] [Accepted: 04/14/2018] [Indexed: 12/17/2022]
Abstract
The field of cancer immunotherapy has expanded rapidly in the past few years, with many new approaches entering the clinic for T cell mediated killing of tumors. Several of these clinical approaches involve the exploitation of a CD8 + T cell response against MHC I presented tumor antigens. Here, we describe the types of tumor antigens which are considered as targets in the design of T cell based therapeutic approaches, the rationale for targeting MHC I antigens and the analytical tools commonly employed for the discovery of MHC I presented peptides. The advantages and disadvantages of each approach are discussed and a perspective on the future directions of the MHC I peptide exploration field and biotherapeutic strategies is given. SIGNIFICANCE: This work is the first time a review article has been written to summarize all the various types of tumor antigens, and the analytical tools employed to discover and characterize them.
Collapse
|
22
|
Abstract
The interrogation of cell surface-presented immunogenic epitopes is of great importance to differentiate diseased cells in consequence to malignant transformation or viral infections. On the basis of this knowledge, next-generation immunotherapies against cancers, autoimmunity, or infectious diseases can be developed. The identification of altered peptide repertoires of transformed cells renders mass spectrometry-based analysis indispensable. This is evident considering the low correlation of gene or protein expression alterations, respectively, with changes in the peptide repertoire rendering those analyses less informative. Nevertheless, immunogenicity of peptides appearing to be exclusively found on diseased cells has to be finally proven in T cell-based assays. This review highlights the capabilities and limitations of mass spectrometry in the identification of entire immunopeptidomes, as well as individual potential immunogenic epitopes with a strong focus on cancer. Furthermore, an overview of state-of-the-art immunogenicity screens is presented.
Collapse
|
23
|
Chandran PA, Heidu S, Zelba H, Schmid-Horch B, Rammensee HG, Pascolo S, Gouttefangeas C. A Simple and Rapid Method for Quality Control of Major Histocompatibility Complex-Peptide Monomers by Flow Cytometry. Front Immunol 2017; 8:96. [PMID: 28228758 PMCID: PMC5296342 DOI: 10.3389/fimmu.2017.00096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/19/2017] [Indexed: 11/29/2022] Open
Abstract
Major histocompatibility complex (MHC) multimers are essential tools in T cell immunomonitoring, which are employed both in basic and clinical research, as well as for assessing clinical samples during therapy. The generation of MHC monomers loaded with synthetic peptides is an elaborate and time-consuming process. It would be beneficial to assess the quality of these monomers prior to downstream applications. In this technical note, we describe a novel flow cytometry-based, cell-free, quick, and robust assay to check the quality of MHC monomers directly after refolding or after long-term storage.
Collapse
Affiliation(s)
- P. Anoop Chandran
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Tuebingen, Tuebingen, Germany
| | - Sonja Heidu
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Tuebingen, Tuebingen, Germany
| | - Henning Zelba
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Tuebingen, Tuebingen, Germany
| | - Barbara Schmid-Horch
- Center for Clinical Transfusion Medicine GmbH, University Hospital, Tuebingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Tuebingen, Tuebingen, Germany
| | - Steve Pascolo
- Department of Dermatology, University Hospital, Zürich, Switzerland
| | - Cécile Gouttefangeas
- Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University and German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) Partner Site Tuebingen, Tuebingen, Germany
| |
Collapse
|
24
|
Bentzen AK, Marquard AM, Lyngaa R, Saini SK, Ramskov S, Donia M, Such L, Furness AJS, McGranahan N, Rosenthal R, Straten PT, Szallasi Z, Svane IM, Swanton C, Quezada SA, Jakobsen SN, Eklund AC, Hadrup SR. Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes. Nat Biotechnol 2016; 34:1037-1045. [PMID: 27571370 DOI: 10.1038/nbt.3662] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 08/04/2016] [Indexed: 01/17/2023]
Abstract
Identification of the peptides recognized by individual T cells is important for understanding and treating immune-related diseases. Current cytometry-based approaches are limited to the simultaneous screening of 10-100 distinct T-cell specificities in one sample. Here we use peptide-major histocompatibility complex (MHC) multimers labeled with individual DNA barcodes to screen >1,000 peptide specificities in a single sample, and detect low-frequency CD8 T cells specific for virus- or cancer-restricted antigens. When analyzing T-cell recognition of shared melanoma antigens before and after adoptive cell therapy in melanoma patients, we observe a greater number of melanoma-specific T-cell populations compared with cytometry-based approaches. Furthermore, we detect neoepitope-specific T cells in tumor-infiltrating lymphocytes and peripheral blood from patients with non-small cell lung cancer. Barcode-labeled pMHC multimers enable the combination of functional T-cell analysis with large-scale epitope recognition profiling for the characterization of T-cell recognition in various diseases, including in small clinical samples.
Collapse
Affiliation(s)
- Amalie Kai Bentzen
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Andrea Marion Marquard
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Rikke Lyngaa
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Sunil Kumar Saini
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Sofie Ramskov
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Marco Donia
- Center for Cancer Immune Therapy, Department of Hematology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Oncology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Lina Such
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Andrew J S Furness
- CRUK Lung Cancer Center of Excellence, UCL Cancer Institute, London, UK
- Cancer Immunology Unit, UCL Cancer Institute, University College London, London, UK
| | - Nicholas McGranahan
- CRUK Lung Cancer Center of Excellence, UCL Cancer Institute, London, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK
| | - Rachel Rosenthal
- CRUK Lung Cancer Center of Excellence, UCL Cancer Institute, London, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK
| | - Per Thor Straten
- Center for Cancer Immune Therapy, Department of Hematology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Zoltan Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Inge Marie Svane
- Center for Cancer Immune Therapy, Department of Hematology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Oncology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Charles Swanton
- CRUK Lung Cancer Center of Excellence, UCL Cancer Institute, London, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK
| | - Sergio A Quezada
- CRUK Lung Cancer Center of Excellence, UCL Cancer Institute, London, UK
- Cancer Immunology Unit, UCL Cancer Institute, University College London, London, UK
| | - Søren Nyboe Jakobsen
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
- Immudex, Copenhagen, Denmark
| | - Aron Charles Eklund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Sine Reker Hadrup
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| |
Collapse
|
25
|
Gfeller D, Bassani-Sternberg M, Schmidt J, Luescher IF. Current tools for predicting cancer-specific T cell immunity. Oncoimmunology 2016; 5:e1177691. [PMID: 27622028 DOI: 10.1080/2162402x.2016.1177691] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/06/2016] [Accepted: 04/06/2016] [Indexed: 12/20/2022] Open
Abstract
Tumor exome and RNA sequencing data provide a systematic and unbiased view on cancer-specific expression, over-expression, and mutations of genes, which can be mined for personalized cancer vaccines and other immunotherapies. Of key interest are tumor-specific mutations, because T cells recognizing neoepitopes have the potential to be highly tumoricidal. Here, we review recent developments and technical advances in identifying MHC class I and class II-restricted tumor antigens, especially neoantigen derived MHC ligands, including in silico predictions, immune-peptidome analysis by mass spectrometry, and MHC ligand validation by biochemical methods on T cells.
Collapse
Affiliation(s)
- David Gfeller
- Ludwig Center for Cancer Research, University of Lausanne, Epalinges, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Julien Schmidt
- Ludwig Center for Cancer Research, University of Lausanne , Epalinges, Switzerland
| | - Immanuel F Luescher
- Ludwig Center for Cancer Research, University of Lausanne , Epalinges, Switzerland
| |
Collapse
|
26
|
Hastings AK, Gilchuk P, Joyce S, Williams JV. Novel HLA-A2-restricted human metapneumovirus epitopes reduce viral titers in mice and are recognized by human T cells. Vaccine 2016; 34:2663-70. [PMID: 27105560 DOI: 10.1016/j.vaccine.2016.04.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/12/2016] [Accepted: 04/13/2016] [Indexed: 11/25/2022]
Abstract
Human metapneumovirus (HMPV) is a major cause of morbidity and mortality from acute lower respiratory tract illness, with most individuals seropositive by age five. Despite the presence of neutralizing antibodies, secondary infections are common and can be severe in young, elderly, and immunocompromised persons. Preclinical vaccine studies for HMPV have suggested a need for a balanced antibody and T cell immune response to enhance protection and avoid lung immunopathology. We infected transgenic mice expressing human HLA-A*0201 with HMPV and used ELISPOT to screen overlapping and predicted epitope peptides. We identified six novel HLA-A2 restricted CD8(+) T cell (TCD8) epitopes, with M39-47 (M39) immunodominant. Tetramer staining detected M39-specific TCD8 in lungs and spleen of HMPV-immune mice. Immunization with adjuvant-formulated M39 peptide reduced lung virus titers upon challenge. Finally, we show that TCD8 from HLA-A*0201 positive humans recognize M39 by IFNγ ELISPOT and tetramer staining. These results will facilitate HMPV vaccine development and human studies.
Collapse
Affiliation(s)
- Andrew K Hastings
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Pavlo Gilchuk
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Sebastian Joyce
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Veterans Administration Tennessee Valley Healthcare System, Nashville, TN 37332, USA
| | - John V Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, USA.
| |
Collapse
|
27
|
Alanio C, Nicoli F, Sultanik P, Flecken T, Perot B, Duffy D, Bianchi E, Lim A, Clave E, van Buuren MM, Schnuriger A, Johnsson K, Boussier J, Garbarg-Chenon A, Bousquet L, Mottez E, Schumacher TN, Toubert A, Appay V, Heshmati F, Thimme R, Pol S, Mallet V, Albert ML. Bystander hyperactivation of preimmune CD8+ T cells in chronic HCV patients. eLife 2015; 4. [PMID: 26568315 PMCID: PMC4752008 DOI: 10.7554/elife.07916] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 11/12/2015] [Indexed: 01/21/2023] Open
Abstract
Chronic infection perturbs immune homeostasis. While prior studies have reported dysregulation of effector and memory cells, little is known about the effects on naïve T cell populations. We performed a cross-sectional study of chronic hepatitis C (cHCV) patients using tetramer-associated magnetic enrichment to study antigen-specific inexperienced CD8(+) T cells (i.e., tumor or unrelated virus-specific populations in tumor-free and sero-negative individuals). cHCV showed normal precursor frequencies, but increased proportions of memory-phenotype inexperienced cells, as compared to healthy donors or cured HCV patients. These observations could be explained by low surface expression of CD5, a negative regulator of TCR signaling. Accordingly, we demonstrated TCR hyperactivation and generation of potent CD8(+) T cell responses from the altered T cell repertoire of cHCV patients. In sum, we provide the first evidence that naïve CD8(+) T cells are dysregulated during cHCV infection, and establish a new mechanism of immune perturbation secondary to chronic infection.
Collapse
Affiliation(s)
- Cécile Alanio
- Unités de Recherche Internationales Mixtes Pasteur, Institut Pasteur, Paris, France.,Centre d'Immunologie Humaine, Institut Pasteur, Paris, France.,Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
| | - Francesco Nicoli
- Sorbonne Universités, UPMC Univ Paris 06, DNU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France.,Emory, , United States
| | - Philippe Sultanik
- Unités de Recherche Internationales Mixtes Pasteur, Institut Pasteur, Paris, France.,Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
| | - Tobias Flecken
- The University Medical Center Freiburg, Department of Internal Medicine II, Albert-Ludwigs-Universität, Freiberg, Germany
| | - Brieuc Perot
- Unités de Recherche Internationales Mixtes Pasteur, Institut Pasteur, Paris, France.,Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
| | - Darragh Duffy
- Unités de Recherche Internationales Mixtes Pasteur, Institut Pasteur, Paris, France.,Centre d'Immunologie Humaine, Institut Pasteur, Paris, France.,Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
| | | | - Annick Lim
- Plateforme d'Immunoscope, Institut Pasteur, Paris, France
| | - Emmanuel Clave
- Hôpital Saint-Louis, Assistance publique - hôpitaux de Paris, Paris, France
| | - Marit M van Buuren
- Department of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aurélie Schnuriger
- Laboratoire de virologie, Hôpital Armand-Trousseau, Assistance publique - hôpitaux de Paris, Paris, France
| | - Kerstin Johnsson
- Mathematics, Faculty of Engineering, Lunds University, Lund, Sweden
| | - Jeremy Boussier
- Unités de Recherche Internationales Mixtes Pasteur, Institut Pasteur, Paris, France.,Centre d'Immunologie Humaine, Institut Pasteur, Paris, France.,Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
| | - Antoine Garbarg-Chenon
- Laboratoire de virologie, Hôpital Armand-Trousseau, Assistance publique - hôpitaux de Paris, Paris, France
| | | | - Estelle Mottez
- Centre d'Immunologie Humaine, Institut Pasteur, Paris, France
| | - Ton N Schumacher
- Department of Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Antoine Toubert
- Hôpital Saint-Louis, Assistance publique - hôpitaux de Paris, Paris, France
| | - Victor Appay
- Sorbonne Universités, UPMC Univ Paris 06, DNU FAST, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France.,Emory, , United States
| | | | - Robert Thimme
- The University Medical Center Freiburg, Department of Internal Medicine II, Albert-Ludwigs-Universität, Freiberg, Germany
| | | | | | - Matthew L Albert
- Unités de Recherche Internationales Mixtes Pasteur, Institut Pasteur, Paris, France.,Centre d'Immunologie Humaine, Institut Pasteur, Paris, France.,Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
| |
Collapse
|
28
|
Brooks SE, Bonney SA, Lee C, Publicover A, Khan G, Smits EL, Sigurdardottir D, Arno M, Li D, Mills KI, Pulford K, Banham AH, van Tendeloo V, Mufti GJ, Rammensee HG, Elliott TJ, Orchard KH, Guinn BA. Application of the pMHC Array to Characterise Tumour Antigen Specific T Cell Populations in Leukaemia Patients at Disease Diagnosis. PLoS One 2015; 10:e0140483. [PMID: 26492414 PMCID: PMC4619595 DOI: 10.1371/journal.pone.0140483] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/25/2015] [Indexed: 01/03/2023] Open
Abstract
Immunotherapy treatments for cancer are becoming increasingly successful, however to further improve our understanding of the T-cell recognition involved in effective responses and to encourage moves towards the development of personalised treatments for leukaemia immunotherapy, precise antigenic targets in individual patients have been identified. Cellular arrays using peptide-MHC (pMHC) tetramers allow the simultaneous detection of different antigen specific T-cell populations naturally circulating in patients and normal donors. We have developed the pMHC array to detect CD8+ T-cell populations in leukaemia patients that recognise epitopes within viral antigens (cytomegalovirus (CMV) and influenza (Flu)) and leukaemia antigens (including Per Arnt Sim domain 1 (PASD1), MelanA, Wilms' Tumour (WT1) and tyrosinase). We show that the pMHC array is at least as sensitive as flow cytometry and has the potential to rapidly identify more than 40 specific T-cell populations in a small sample of T-cells (0.8-1.4 x 10(6)). Fourteen of the twenty-six acute myeloid leukaemia (AML) patients analysed had T cells that recognised tumour antigen epitopes, and eight of these recognised PASD1 epitopes. Other tumour epitopes recognised were MelanA (n = 3), tyrosinase (n = 3) and WT1(126-134) (n = 1). One of the seven acute lymphocytic leukaemia (ALL) patients analysed had T cells that recognised the MUC1(950-958) epitope. In the future the pMHC array may be used provide point of care T-cell analyses, predict patient response to conventional therapy and direct personalised immunotherapy for patients.
Collapse
MESH Headings
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/metabolism
- Antigens, Nuclear/metabolism
- CD8-Positive T-Lymphocytes/immunology
- Cell Separation
- Epitopes/immunology
- Flow Cytometry
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/immunology
- Major Histocompatibility Complex/immunology
- Peptides/immunology
- Reproducibility of Results
Collapse
Affiliation(s)
- Suzanne E. Brooks
- Cancer Sciences Unit (MP824), Somers Cancer Sciences Building, University of Southampton, Southampton, United Kingdom
| | - Stephanie A. Bonney
- Cancer Sciences Unit (MP824), Somers Cancer Sciences Building, University of Southampton, Southampton, United Kingdom
| | - Cindy Lee
- Cancer Sciences Unit (MP824), Somers Cancer Sciences Building, University of Southampton, Southampton, United Kingdom
- Department of Haematology, Southampton University Hospitals Trust, University of Southampton, Southampton, United Kingdom
| | - Amy Publicover
- Department of Haematology, Southampton University Hospitals Trust, University of Southampton, Southampton, United Kingdom
| | - Ghazala Khan
- Department of Life Sciences, University of Bedfordshire, Park Square, Luton, United Kingdom
| | - Evelien L. Smits
- Laboratory of Experimental Haematology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijkstraat 10, B-2650 Antwerp, Belgium
| | - Dagmar Sigurdardottir
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Matthew Arno
- King’s Genomics Centre, School of Biomedical and Health Sciences, King's College London, London, United Kingdom
| | - Demin Li
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Ken I. Mills
- Blood Cancer Research Group, Centre for Cancer Research and Cell Biology (CCRCB), Queen’s University Belfast, Belfast, United Kingdom
| | - Karen Pulford
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Alison H. Banham
- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Viggo van Tendeloo
- Laboratory of Experimental Haematology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijkstraat 10, B-2650 Antwerp, Belgium
| | - Ghulam J. Mufti
- Department of Haematological Medicine, King's College London School of Medicine, London, United Kingdom
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Tim J. Elliott
- Cancer Sciences Unit (MP824), Somers Cancer Sciences Building, University of Southampton, Southampton, United Kingdom
| | - Kim H. Orchard
- Department of Haematology, Southampton University Hospitals Trust, University of Southampton, Southampton, United Kingdom
| | - Barbara-ann Guinn
- Cancer Sciences Unit (MP824), Somers Cancer Sciences Building, University of Southampton, Southampton, United Kingdom
- Department of Life Sciences, University of Bedfordshire, Park Square, Luton, United Kingdom
- Department of Haematological Medicine, King's College London School of Medicine, London, United Kingdom
| |
Collapse
|
29
|
Phetsouphanh C, Zaunders JJ, Kelleher AD. Detecting Antigen-Specific T Cell Responses: From Bulk Populations to Single Cells. Int J Mol Sci 2015; 16:18878-93. [PMID: 26274954 PMCID: PMC4581277 DOI: 10.3390/ijms160818878] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 07/29/2015] [Accepted: 08/03/2015] [Indexed: 12/18/2022] Open
Abstract
A new generation of sensitive T cell-based assays facilitates the direct quantitation and characterization of antigen-specific T cell responses. Single-cell analyses have focused on measuring the quality and breadth of a response. Accumulating data from these studies demonstrate that there is considerable, previously-unrecognized, heterogeneity. Standard assays, such as the ICS, are often insufficient for characterization of rare subsets of cells. Enhanced flow cytometry with imaging capabilities enables the determination of cell morphology, as well as the spatial localization of the protein molecules within a single cell. Advances in both microfluidics and digital PCR have improved the efficiency of single-cell sorting and allowed multiplexed gene detection at the single-cell level. Delving further into the transcriptome of single-cells using RNA-seq is likely to reveal the fine-specificity of cellular events such as alternative splicing (i.e., splice variants) and allele-specific expression, and will also define the roles of new genes. Finally, detailed analysis of clonally related antigen-specific T cells using single-cell TCR RNA-seq will provide information on pathways of differentiation of memory T cells. With these state of the art technologies the transcriptomics and genomics of Ag-specific T cells can be more definitively elucidated.
Collapse
Affiliation(s)
| | - John James Zaunders
- Kirby Institute, University of New South Wales, 2031 Sydney, Australia.
- Centre for Applied Medical Research, St. Vincent's Hospital, 2010 Sydney, Australia.
| | - Anthony Dominic Kelleher
- Kirby Institute, University of New South Wales, 2031 Sydney, Australia.
- Centre for Applied Medical Research, St. Vincent's Hospital, 2010 Sydney, Australia.
| |
Collapse
|
30
|
Frøsig TM, Yap J, Seremet T, Lyngaa R, Svane IM, Thor Straten P, Heemskerk MHM, Grotenbreg GM, Hadrup SR. Design and validation of conditional ligands for HLA-B*08:01, HLA-B*15:01, HLA-B*35:01, and HLA-B*44:05. Cytometry A 2015; 87:967-75. [PMID: 26033882 DOI: 10.1002/cyto.a.22689] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/25/2015] [Accepted: 04/23/2015] [Indexed: 11/08/2022]
Abstract
We designed conditional ligands restricted to HLA-B*08:01, -B*35:01, and -B*44:05 and proved the use of a conditional ligand previously designed for HLA-B*15:02 together with HLA-B*15:01. Furthermore, we compared the detection capabilities of specific HLA-B*15:01-restricted T cells using the HLA-B*15:01 and HLA-B*15:02 major histocompatibility complex (MHC) multimers and found remarkable differences in the staining patterns detected by flow cytometry. These new conditional ligands greatly add to the application of MHC-based technologies in the analyses of T-cell recognition as they represent frequently expressed HLA-B molecules. This expansion of conditional ligands is important to allow T-cell detection over a wide range of HLA restrictions, and provide comprehensive understanding of the T-cell recognition in a given context.
Collapse
Affiliation(s)
- Thomas Mørch Frøsig
- Department of Hematology, Center for Cancer Immune Therapy, Herlev University Hospital, Copenhagen, Denmark.,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Jiawei Yap
- Department of Microbiology, National University of Singapore, Singapore.,Department of Biological Sciences and the Immunology Program, National University of Singapore, Singapore
| | - Tina Seremet
- Department of Hematology, Center for Cancer Immune Therapy, Herlev University Hospital, Copenhagen, Denmark
| | - Rikke Lyngaa
- Department of Hematology, Center for Cancer Immune Therapy, Herlev University Hospital, Copenhagen, Denmark.,Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Inge Marie Svane
- Department of Hematology, Center for Cancer Immune Therapy, Herlev University Hospital, Copenhagen, Denmark.,Department of Oncology, Herlev University Hospital, Copenhagen, Denmark
| | - Per Thor Straten
- Department of Hematology, Center for Cancer Immune Therapy, Herlev University Hospital, Copenhagen, Denmark
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gijsbert M Grotenbreg
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark.,Department of Microbiology, National University of Singapore, Singapore
| | - Sine Reker Hadrup
- Department of Hematology, Center for Cancer Immune Therapy, Herlev University Hospital, Copenhagen, Denmark.,Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| |
Collapse
|
31
|
Broadening the repertoire of melanoma-associated T-cell epitopes. Cancer Immunol Immunother 2015; 64:609-20. [PMID: 25854582 PMCID: PMC4412285 DOI: 10.1007/s00262-015-1664-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 02/02/2015] [Indexed: 12/13/2022]
Abstract
Immune therapy has provided a significant breakthrough in the treatment of metastatic melanoma. Despite the remarkable clinical efficacy and established involvement of effector CD8 T cells, the knowledge of the exact peptide-MHC complexes recognized by T cells on the tumor cell surface is limited. Many melanoma-associated T-cell epitopes have been described, but this knowledge remains largely restricted to HLA-A2, and we lack understanding of the T-cell recognition in the context of other HLA molecules. We selected six melanoma-associated antigens (MAGE-A3, NY-ESO-1, gp100, Mart1, tyrosinase and TRP-2) that are frequently recognized in patients with the aim of identifying novel T-cell epitopes restricted to HLA-A1, -A3, -A11 and -B7. Using in silico prediction and in vitro confirmation, we identified 127 MHC ligands and analyzed the T-cell responses against these ligands via the MHC multimer-based enrichment of peripheral blood from 39 melanoma patients and 10 healthy donors. To dissect the T-cell reactivity against this large peptide library, we used combinatorial-encoded MHC multimers and observed the T-cell responses against 17 different peptide-MHC complexes in the patient group and four in the healthy donor group. We confirmed the processing and presentation of HLA-A3-restricted T-cell epitopes from tyrosinase (TQYESGSMDK) and gp100 (LIYRRRLMK) and an HLA-A11-restricted T-cell epitope from gp100 (AVGATKVPR) via the cytolytic T-cell recognition of melanoma cell lines and/or K562 cells expressing the appropriate antigen and HLA molecule. We further found T-cell reactivity against two of the identified sequences among tumor-infiltrating lymphocytes from melanoma patients, suggesting a potential clinical relevance of these sequences.
Collapse
|
32
|
Hadrup SR, Maurer D, Laske K, Frøsig TM, Andersen SR, Britten CM, van der Burg SH, Walter S, Gouttefangeas C. Cryopreservation of MHC multimers: Recommendations for quality assurance in detection of antigen specific T cells. Cytometry A 2015; 87:37-48. [PMID: 25297339 PMCID: PMC4309491 DOI: 10.1002/cyto.a.22575] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 08/24/2014] [Accepted: 09/24/2014] [Indexed: 11/16/2022]
Abstract
Fluorescence-labeled peptide-MHC class I multimers serve as ideal tools for the detection of antigen-specific T cells by flow cytometry, enabling functional and phenotypical characterization of specific T cells at the single cell level. While this technique offers a number of unique advantages, MHC multimer reagents can be difficult to handle in terms of stability and quality assurance. The stability of a given fluorescence-labeled MHC multimer complex depends on both the stability of the peptide-MHC complex itself and the stability of the fluorochrome. Consequently, stability is difficult to predict and long-term storage is generally not recommended. We investigated here the possibility of cryopreserving MHC multimers, both in-house produced and commercially available, using a wide range of peptide-MHC class I multimers comprising virus and cancer-associated epitopes of different affinities presented by various HLA-class I molecules. Cryopreservation of MHC multimers was feasible for at least 6 months, when they were dissolved in buffer containing 5-16% glycerol (v/v) and 0.5% serum albumin (w/v). The addition of cryoprotectants was tolerated across three different T-cell staining protocols for all fluorescence labels tested (PE, APC, PE-Cy7 and Quantum dots). We propose cryopreservation as an easily implementable method for stable storage of MHC multimers and recommend the use of cryopreservation in long-term immunomonitoring projects, thereby eliminating the variability introduced by different batches and inconsistent stability.
Collapse
Affiliation(s)
- Sine Reker Hadrup
- Department of Hematology, Center for Cancer Immune Therapy (CCIT), University Hospital HerlevHerlev, Denmark
| | | | - Karoline Laske
- Department of Immunology, Institute for Cell Biology, University of TübingenGermany and DKTK, DKFZ partner site Tübingen, Germany
| | - Thomas Mørch Frøsig
- Department of Hematology, Center for Cancer Immune Therapy (CCIT), University Hospital HerlevHerlev, Denmark
| | - Sofie Ramskov Andersen
- Department of Hematology, Center for Cancer Immune Therapy (CCIT), University Hospital HerlevHerlev, Denmark
| | - Cedrik M Britten
- Translational Oncology, University Medical Center, Johannes Gutenberg-University Mainz gGmbHMainz, Germany
| | - Sjoerd H van der Burg
- Department of Clinical Oncology, Leiden University Medical CenterLeiden, The Netherlands
| | | | - Cécile Gouttefangeas
- Department of Immunology, Institute for Cell Biology, University of TübingenGermany and DKTK, DKFZ partner site Tübingen, Germany
| |
Collapse
|
33
|
Lyngaa R, Pedersen NW, Schrama D, Thrue CA, Ibrani D, Met O, Thor Straten P, Nghiem P, Becker JC, Hadrup SR. T-cell responses to oncogenic merkel cell polyomavirus proteins distinguish patients with merkel cell carcinoma from healthy donors. Clin Cancer Res 2014; 20:1768-78. [PMID: 24526738 DOI: 10.1158/1078-0432.ccr-13-2697] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE Merkel cell carcinoma (MCC) is a highly aggressive skin cancer with strong evidence of viral carcinogenesis. The association of MCC with the Merkel cell polyomavirus (MCPyV) may explain the explicit immunogenicity of MCC. Indeed, MCPyV-encoded proteins are likely targets for cytotoxic immune responses to MCC as they are both foreign to the host and necessary to maintain the oncogenic phenotype. However, to date only a single MCPyV-derived CD8 T-cell epitope has been described, thus impeding specific monitoring of T-cell responses to MCC. METHOD To overcome this limitation, we scanned the MCPyV oncoprotein large T and small T antigens and the virus capsid protein VP1 for potential T-cell epitopes, and tested for MHC class I affinity. We confirmed the relevance of these epitopes using a high-throughput platform for T-cell enrichment and combinatorial encoding of MHC class I multimers. RESULTS In peripheral blood from 38 patients with MCC and 30 healthy donors, we identified 53 MCPyV-directed CD8 T-cell responses against 35 different peptide sequences. Strikingly, T-cell responses against oncoproteins were exclusively present in patients with MCC, but not in healthy donors. We further demonstrate both the processing and presentation of the oncoprotein-derived epitopes, as well as the lytic activity of oncoprotein-specific T cells toward MHC-matched MCC cells. Demonstrating the presence of oncoprotein-specific T cells among tumor-infiltrating lymphocytes further substantiated the relevance of the identified epitopes. CONCLUSION These T-cell epitopes represent ideal targets for antigen-specific immune therapy of MCC, and enable tracking and characterization of MCPyV-specific immune responses.
Collapse
Affiliation(s)
- Rikke Lyngaa
- Authors' Affiliations: Center for Cancer Immune Therapy (CCIT), Department of Hematology, University Hospital Herlev, Herlev, Denmark; General Dermatology, Medical University of Graz, Graz, Austria; Departments of Medicine/Dermatology, Pathology, University of Washington; Fred Hutchinson Cancer Research Center, Seattle Cancer Center Care Alliance, Seattle, Washington; and Department of Oncology, University Hospital Herlev, Herlev, Denmark
| | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Chang CXL, Tan AT, Or MY, Toh KY, Lim PY, Chia ASE, Froesig TM, Nadua KD, Oh HLJ, Leong HN, Hadrup SR, Gehring AJ, Tan YJ, Bertoletti A, Grotenbreg GM. Conditional ligands for Asian HLA variants facilitate the definition of CD8+ T-cell responses in acute and chronic viral diseases. Eur J Immunol 2013; 43:1109-20. [PMID: 23280567 PMCID: PMC3655610 DOI: 10.1002/eji.201243088] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/07/2012] [Accepted: 12/21/2012] [Indexed: 01/02/2023]
Abstract
Conditional ligands have enabled the high-throughput production of human leukocyte antigen (HLA) libraries that present defined peptides. Immunomonitoring platforms typically concentrate on restriction elements associated with European ancestry, and such tools are scarce for Asian HLA variants. We report 30 novel irradiation-sensitive ligands, specifically targeting South East Asian populations, which provide 93, 63, and 79% coverage for HLA-A, -B, and -C, respectively. Unique ligands for all 16 HLA types were constructed to provide the desired soluble HLA product in sufficient yield. Peptide exchange was accomplished for all variants as demonstrated by an ELISA-based MHC stability assay. HLA tetramers with redirected specificity could detect antigen-specific CD8(+) T-cell responses against human cytomegalovirus, hepatitis B (HBV), dengue virus (DENV), and Epstein-Barr virus (EBV) infections. The potential of this population-centric HLA library was demonstrated with the characterization of seven novel T-cell epitopes from severe acute respiratory syndrome coronavirus, HBV, and DENV. Posthoc analysis revealed that the majority of responses would be more readily identified by our unbiased discovery approach than through the application of state-of-the-art epitope prediction. This flow cytometry-based technology therefore holds considerable promise for monitoring clinically relevant antigen-specific T-cell responses in populations of distinct ethnicity.
Collapse
Affiliation(s)
- Cynthia X L Chang
- Department of Microbiology, National University of Singapore, Singapore
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Alanio C, Bouvier I, Jusforgues-Saklani H, Albert ML. Tracking antigen-specific CD8⁺ T cells using MHC class I multimers. Methods Mol Biol 2013; 960:309-326. [PMID: 23329496 DOI: 10.1007/978-1-62703-218-6_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The tracking of epitope-specific T cells is a useful approach for the study of adaptive immune responses. This protocol describes how Major Histocompatibility Complex Class I (MHC-I) multimers can be used to stain, enrich, and enumerate (rare) populations of CD8(+) T cells specific for a given antigen. It provides the detailed steps for multimer labeling, magnetic enrichment, and cytometric analysis. Additionally, it provides informations for multiplexing experiments in order to achieve simultaneous detection of multiple antigenic specificities, and strategies for coupling the protocol with functional assays (e.g., intracellular cytokine staining). Future developments in cytometric systems (e.g., mass spectroscopy-based cytometry) and gene expression studies (e.g., single cell PCR) will extend these approaches and provide an unprecedented assessment of the immune repertoire.
Collapse
Affiliation(s)
- Cécile Alanio
- Immunobiologie des cellules dendritiques, Unité Mixte Pasteur/Inserm U818, Institut Pasteur and Centre d'Immunologie Humaine, Institut Pasteur, Paris, France
| | - Isabelle Bouvier
- Immunobiologie des cellules dendritiques, Unité Mixte Pasteur/Inserm U818, Institut Pasteur and Centre d'Immunologie Humaine, Institut Pasteur, Paris, France
| | - Hélène Jusforgues-Saklani
- Immunobiologie des cellules dendritiques, Unité Mixte Pasteur/Inserm U818, Institut Pasteur and Centre d'Immunologie Humaine, Institut Pasteur, Paris, France
| | - Matthew L Albert
- Immunobiologie des cellules dendritiques, Unité Mixte Pasteur/Inserm U818, Institut Pasteur and Centre d'Immunologie Humaine, Institut Pasteur, Paris, France.
| |
Collapse
|
36
|
Ellebaek E, Iversen TZ, Junker N, Donia M, Engell-Noerregaard L, Met Ö, Hölmich LR, Andersen RS, Hadrup SR, Andersen MH, thor Straten P, Svane IM. Adoptive cell therapy with autologous tumor infiltrating lymphocytes and low-dose Interleukin-2 in metastatic melanoma patients. J Transl Med 2012; 10:169. [PMID: 22909342 PMCID: PMC3514199 DOI: 10.1186/1479-5876-10-169] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 08/14/2012] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Adoptive cell therapy may be based on isolation of tumor-specific T cells, e.g. autologous tumor infiltrating lymphocytes (TIL), in vitro activation and expansion and the reinfusion of these cells into patients upon chemotherapy induced lymphodepletion. Together with high-dose interleukin (IL)-2 this treatment has been given to patients with advanced malignant melanoma and impressive response rates but also significant IL-2 associated toxicity have been observed. Here we present data from a feasibility study at a Danish Translational Research Center using TIL adoptive transfer in combination with low-dose subcutaneous IL-2 injections. METHODS This is a pilot trial (ClinicalTrials.gov identifier: NCT00937625) including patients with metastatic melanoma, PS ≤1, age <70, measurable and progressive disease and no involvement of the central nervous system. Six patients were treated with lymphodepleting chemotherapy, TIL infusion, and 14 days of subcutaneous low-dose IL-2 injections, 2 MIU/day. RESULTS Low-dose IL-2 considerably decreased the treatment related toxicity with no grade 3-4 IL-2 related adverse events. Objective clinical responses were seen in 2 of 6 treated patients with ongoing complete responses (30+ and 10+ months), 2 patients had stable disease (4 and 5 months) and 2 patients progressed shortly after treatment. Tumor-reactivity of the infused cells and peripheral lymphocytes before and after therapy were analyzed. Absolute number of tumor specific T cells in the infusion product tended to correlate with clinical response and also, an induction of peripheral tumor reactive T cells was observed for 1 patient in complete remission. CONCLUSION Complete and durable responses were induced after treatment with adoptive cell therapy in combination with low-dose IL-2 which significantly decreased toxicity of this therapy.
Collapse
Affiliation(s)
- Eva Ellebaek
- CCIT, Center for Cancer Immune Therapy, Department of Hematology, Copenhagen University Hospital, Herlev, Denmark
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Brimnes MK, Gang AO, Donia M, thor Straten P, Svane IM, Hadrup SR. Generation of autologous tumor-specific T cells for adoptive transfer based on vaccination, in vitro restimulation and CD3/CD28 dynabead-induced T cell expansion. Cancer Immunol Immunother 2012; 61:1221-31. [PMID: 22237888 PMCID: PMC11029656 DOI: 10.1007/s00262-011-1199-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 12/25/2011] [Indexed: 10/14/2022]
Abstract
Adoptive cell transfer (ACT) of in vitro expanded autologous tumor-infiltrating lymphocytes (TIL) has been shown to exert therapeutic efficacy in melanoma patients. We aimed to develop an ACT protocol based on tumor-specific T cells isolated from peripheral blood and in vitro expanded by Dynabeads® ClinExVivo™CD3/CD28. We show here that the addition of an in vitro restimulation step with relevant peptides prior to bead expansion dramatically increased the proportion of tumor-specific T cells in PBMC-cultures. Importantly, peptide-pulsed dendritic cells (DCs) as well as allogeneic tumor lysate-pulsed DCs from the DC vaccine preparation could be used with comparable efficiency to peptides for in vitro restimulation, to increase the tumor-specific T-cell response. Furthermore, we tested the use of different ratios and different types of Dynabeads® CD3/CD28 and CD3/CD28/CD137 T-cell expander, for optimized expansion of tumor-specific T cells. A ratio of 1:3 of Dynabeads® CD3/CD28 T-cell expander to T cells resulted in the maximum number of tumor-specific T cells. The addition of CD137 did not improve functionality or fold expansion. Both T-cell expansion systems could generate tumor-specific T cells that were both cytotoxic and effective cytokine producers upon antigen recognition. Dynabeads®-expanded T-cell cultures shows phenotypical characteristics of memory T cells with potential to migrate and expand in vivo. In addition, they possess longer telomeres compared to TIL cultures. Taken together, we demonstrate that in vitro restimulation of tumor-specific T cells prior to bead expansion is necessary to achieve high numbers of tumor-specific T cells. This is effective and easily applicable in combination with DC vaccination, by use of vaccine-generated DCs, either pulsed with peptide or tumor-lysate.
Collapse
Affiliation(s)
- Marie Klinge Brimnes
- Department of Hematology 54P4, Center for Cancer Immune Therapy (CCIT), University Hospital Herlev, 2730 Herlev, Denmark
| | - Anne Ortved Gang
- Department of Hematology 54P4, Center for Cancer Immune Therapy (CCIT), University Hospital Herlev, 2730 Herlev, Denmark
| | - Marco Donia
- Department of Hematology 54P4, Center for Cancer Immune Therapy (CCIT), University Hospital Herlev, 2730 Herlev, Denmark
- Department of Biomedical Sciences, University of Catania, Catania, Italy
| | - Per thor Straten
- Department of Hematology 54P4, Center for Cancer Immune Therapy (CCIT), University Hospital Herlev, 2730 Herlev, Denmark
| | - Inge Marie Svane
- Department of Hematology 54P4, Center for Cancer Immune Therapy (CCIT), University Hospital Herlev, 2730 Herlev, Denmark
- Department of Oncology, University Hospital Herlev, Herlev, Denmark
| | - Sine Reker Hadrup
- Department of Hematology 54P4, Center for Cancer Immune Therapy (CCIT), University Hospital Herlev, 2730 Herlev, Denmark
- Institute for International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
38
|
Erickson JJ, Gilchuk P, Hastings AK, Tollefson SJ, Johnson M, Downing MB, Boyd KL, Johnson JE, Kim AS, Joyce S, Williams JV. Viral acute lower respiratory infections impair CD8+ T cells through PD-1. J Clin Invest 2012; 122:2967-82. [PMID: 22797302 DOI: 10.1172/jci62860] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 06/07/2012] [Indexed: 12/25/2022] Open
Abstract
Viruses are leading causes of severe acute lower respiratory infections (LRIs). These infections evoke incomplete immunity, as individuals can be repeatedly reinfected throughout life. We report that acute viral LRI causes rapid pulmonary CD8+ cytotoxic T lymphocyte (TCD8) functional impairment via programmed death-1/programmed death ligand-1 (PD-1/PD-L1) signaling, a pathway previously associated with prolonged antigenic stimulation during chronic infections and cancer. PD-1-mediated TCD8 impairment occurred acutely in mice following infection with human metapneumovirus or influenza virus. Viral antigen was sufficient for PD-1 upregulation, but induction of PD-L1 was required for impairment. During secondary viral infection or epitope-only challenge, memory TCD8 rapidly reexpressed PD-1 and exhibited severe functional impairment. Inhibition of PD-1 signaling using monoclonal antibody blockade prevented TCD8 impairment, reduced viral titers during primary infection, and enhanced protection of immunized mice against challenge infection. Additionally, PD-1 and PD-L1 were upregulated in the lungs of patients with 2009 H1N1 influenza virus, respiratory syncytial virus, or parainfluenza virus infection. These results indicate that PD-1 mediates TCD8 functional impairment during acute viral infection and may contribute to recurrent viral LRIs. Therefore, the PD-1/PD-L1 pathway may represent a therapeutic target in the treatment of respiratory viruses.
Collapse
Affiliation(s)
- John J Erickson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Andersen RS, Thrue CA, Junker N, Lyngaa R, Donia M, Ellebæk E, Svane IM, Schumacher TN, Thor Straten P, Hadrup SR. Dissection of T-cell antigen specificity in human melanoma. Cancer Res 2012; 72:1642-50. [PMID: 22311675 DOI: 10.1158/0008-5472.can-11-2614] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tumor-infiltrating lymphocytes (TIL) isolated from melanoma patients and expanded in vitro by interleukin (IL)-2 treatment can elicit therapeutic response after adoptive transfer, but the antigen specificities of the T cells transferred have not been determined. By compiling all known melanoma-associated antigens and applying a novel technology for high-throughput analysis of T-cell responses, we dissected the composition of melanoma-restricted T-cell responses in 63 TIL cultures. T-cell reactivity screens against 175 melanoma-associated epitopes detected 90 responses against 18 different epitopes predominantly from differentiation and cancer-testis antigens. Notably, the majority of these responses were of low frequency and tumor-specific T-cell frequencies decreased during rapid expansion. A further notable observation was a large variation in the T-cell specificities detected in cultures established from different fragments of resected melanoma lesions. In summary, our findings provide an initial definition of T-cell populations contributing to tumor recognition in TILs although the specificity of many tumor-reactive TILs remains undefined.
Collapse
Affiliation(s)
- Rikke Sick Andersen
- Department of Hematology, Center for Cancer Immune Therapy and Oncology, University Hospital Herlev, Herlev, Denmark
| | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Blank CU, Hooijkaas AI, Haanen JB, Schumacher TN. Combination of targeted therapy and immunotherapy in melanoma. Cancer Immunol Immunother 2011; 60:1359-71. [PMID: 21847631 PMCID: PMC11028983 DOI: 10.1007/s00262-011-1079-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 07/17/2011] [Indexed: 12/18/2022]
Abstract
The treatment of human melanoma has progressed markedly in recent years. Building on the observation that immune recognition is a frequent event in melanoma, a series of immunotherapeutic approaches have been evaluated in clinical trials, culminating in the first phase III study improving overall survival of melanoma patients since 20 years. However, the response rates seen upon immunotherapeutic interventions such as anti-CTLA4 treatment are often low. Furthermore, clinical responses can take several weeks to develop, during which time stage IV melanoma patients often deteriorate. Recent advances in our understanding of the genetic lesions in human melanoma now also allow the specific targeting of the signaling pathway alterations in this disease. Such targeted therapies can lead to high response rates, although the duration of these responses is thus far relatively short. We suggest that the combination of immuno and targeted therapy offers potential for synergy for both conceptual and practical reasons. In this review, we will discuss the potential and possible limitations for such combination therapy, and we describe the most promising combinations of targeted therapy and immunotherapy that can be tested in the clinic in the coming years. The concept of induction therapy by small molecule administration and consolidation by immunotherapeutics also has potential for the treatment of other human cancers.
Collapse
Affiliation(s)
- Christian U. Blank
- Division of Immunology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Ziekenhuis, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Division of Medical Oncology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Ziekenhuis, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Anna I. Hooijkaas
- Division of Immunology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Ziekenhuis, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - John B. Haanen
- Division of Immunology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Ziekenhuis, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Division of Medical Oncology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Ziekenhuis, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Ton N. Schumacher
- Division of Immunology, The Netherlands Cancer Institute, Antoni van Leeuwenhoek Ziekenhuis, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| |
Collapse
|
41
|
Hombrink P, Hadrup SR, Bakker A, Kester MGD, Falkenburg JHF, von dem Borne PA, Schumacher TNM, Heemskerk MHM. High-throughput identification of potential minor histocompatibility antigens by MHC tetramer-based screening: feasibility and limitations. PLoS One 2011; 6:e22523. [PMID: 21850230 PMCID: PMC3151248 DOI: 10.1371/journal.pone.0022523] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 06/22/2011] [Indexed: 11/28/2022] Open
Abstract
T-cell recognition of minor histocompatibility antigens (MiHA) plays an important role in the graft-versus-tumor (GVT) effect of allogeneic stem cell transplantation (allo-SCT). However, the number of MiHA identified to date remains limited, making clinical application of MiHA reactive T-cell infusion difficult. This study represents the first attempt of genome-wide prediction of MiHA, coupled to the isolation of T-cell populations that react with these antigens. In this unbiased high-throughput MiHA screen, both the possibilities and pitfalls of this approach were investigated. First, 973 polymorphic peptides expressed by hematopoietic stem cells were predicted and screened for HLA-A2 binding. Subsequently a set of 333 high affinity HLA-A2 ligands was identified and post transplantation samples from allo-SCT patients were screened for T-cell reactivity by a combination of pMHC-tetramer-based enrichment and multi-color flow cytometry. Using this approach, 71 peptide-reactive T-cell populations were generated. The isolation of a T-cell line specifically recognizing target cells expressing the MAP4K1IMA antigen demonstrates that identification of MiHA through this approach is in principle feasible. However, with the exception of the known MiHA HMHA1, none of the other T-cell populations that were generated demonstrated recognition of endogenously MiHA expressing target cells, even though recognition of peptide-loaded targets was often apparent. Collectively these results demonstrate the technical feasibility of high-throughput analysis of antigen-specific T-cell responses in small patient samples. However, the high-sensitivity of this approach requires the use of potential epitope sets that are not solely based on MHC binding, to prevent the frequent detection of T-cell responses that lack biological relevance.
Collapse
Affiliation(s)
- Pleun Hombrink
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands.
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Chew SL, Or MY, Chang CXL, Gehring AJ, Bertoletti A, Grotenbreg GM. Stability screening of arrays of major histocompatibility complexes on combinatorially encoded flow cytometry beads. J Biol Chem 2011; 286:28466-75. [PMID: 21680737 DOI: 10.1074/jbc.m111.262691] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The binding and stabilization capacity of potential T cell epitopes to class I MHC molecules form the basis for their immunogenicity and provide fundamental insight into factors that dictate cellular immune responses. We have developed a versatile high throughput cell-free method to measure MHC stability by capturing a variety of MHC products on the surface of streptavidin-coated particles followed by flow cytometry analysis. Arrays of peptide-MHC combinations, generated by exchanging conditional ligand-loaded MHC, could be probed in a single experiment, thus combining the molecular precision of biochemically purified MHCs with high content multiparametric flow cytometry-based assays. Semiquantitative determination of the peptide affinity for the restriction element could also be accomplished through competition experiments using this bead-based assay. Furthermore, the generated peptide-MHC reagents could directly be applied to antigen-specific CD8(+) T lymphocyte analysis. The combinatorial labeling of beads allowed straightforward identification by their unique fluorescent signatures and provided a convenient means for extended assay multiplexing.
Collapse
Affiliation(s)
- Shi Ling Chew
- Department of Microbiology, Department of Biological Sciences, and Immunology Programme, Life Sciences Institute, National University of Singapore, 117456 Singapore
| | | | | | | | | | | |
Collapse
|
43
|
Hadrup SR, Schumacher TN. MHC-based detection of antigen-specific CD8+ T cell responses. Cancer Immunol Immunother 2010; 59:1425-33. [PMID: 20177676 PMCID: PMC2892606 DOI: 10.1007/s00262-010-0824-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 01/30/2010] [Indexed: 12/05/2022]
Abstract
The hallmark of adaptive immunity is its ability to recognise a wide range of antigens and technologies that capture this diversity are therefore of substantial interest. New methods have recently been developed that allow the parallel analysis of T cell reactivity against vast numbers of different epitopes in limited biological material. These technologies are based on the joint binding of differentially labelled MHC multimers on the T cell surface, thereby providing each antigen-specific T cell population with a unique multicolour code. This strategy of 'combinatorial encoding' enables detection of many (at least 25) different T cell populations per sample and should be of broad value for both T cell epitope identification and immunomonitoring.
Collapse
Affiliation(s)
- Sine Reker Hadrup
- Department of Hematology, Center for Cancer Immune Therapy, CCIT, University Hospital Herlev, Herlev, Denmark.
| | | |
Collapse
|
44
|
Hoppes R, Ekkebus R, Schumacher TN, Ovaa H. Technologies for MHC class I immunoproteomics. J Proteomics 2010; 73:1945-53. [DOI: 10.1016/j.jprot.2010.05.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 05/06/2010] [Accepted: 05/16/2010] [Indexed: 11/29/2022]
|
45
|
Casalegno-Garduño R, Schmitt A, Yao J, Wang X, Xu X, Freund M, Schmitt M. Multimer technologies for detection and adoptive transfer of antigen-specific T cells. Cancer Immunol Immunother 2010; 59:195-202. [PMID: 19847424 PMCID: PMC11030699 DOI: 10.1007/s00262-009-0778-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 09/24/2009] [Indexed: 10/20/2022]
Abstract
Identification and purification of antigen-specific T cells without altering their functional status are of high scientific and clinical interest. Staining with major histocompatibility complex (MHC)-peptide multimers constitutes a very powerful method to study antigen-specific T-cell subpopulations, allowing their direct visualization and quantification. MHC-peptide multimers, such as dimers, tetramers, pentamers, streptamers, dextramers and octamers have been used to evaluate the frequency of CD8(+) T cells, specific for tumor/leukemia-associated antigens as well as for viral antigens, e.g., CMVpp65 and EBV-EBNA. Moreover, MHC-peptide multimers have been used for rapid and efficient ex vivo isolation and expansion of T cells. A recent development in the field of MHC-peptide multimers led to the purification of CD8(+) T cells specific for leukemia antigens. This might help to select leukemia-specific donor lymphocyte infusions (DLIs), thus allowing dissection of the noxious graft-versus-host disease (GvHD) from beneficial anti-viral and even anti-leukemic effects. This review covers different types of MHC-peptide multimers and their applications, as well as the impact that multimers might have on further development of DLIs.
Collapse
Affiliation(s)
- Rosaely Casalegno-Garduño
- Department of Internal Medicine III, Clinical Stem Cell Transplantation and Immunotherapy, University Clinic Rostock, 18055 Rostock, Germany
| | - Anita Schmitt
- Department of Internal Medicine III, Clinical Stem Cell Transplantation and Immunotherapy, University Clinic Rostock, 18055 Rostock, Germany
| | - Junxia Yao
- Center for Stem Cell Research and Application, Institute of Hematology, Union Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Xinchao Wang
- Department of Internal Medicine III, Clinical Stem Cell Transplantation and Immunotherapy, University Clinic Rostock, 18055 Rostock, Germany
- Department of Oncology and Hematology, Zhongda Hospital, Southeast University, Nanjing, China
| | - Xun Xu
- Department of Internal Medicine III, Clinical Stem Cell Transplantation and Immunotherapy, University Clinic Rostock, 18055 Rostock, Germany
- Department of Immunology, Jiangsu University, Zhenjiang, China
| | - Mathias Freund
- Department of Internal Medicine III, Clinical Stem Cell Transplantation and Immunotherapy, University Clinic Rostock, 18055 Rostock, Germany
| | - Michael Schmitt
- Department of Internal Medicine III, Clinical Stem Cell Transplantation and Immunotherapy, University Clinic Rostock, 18055 Rostock, Germany
| |
Collapse
|