51
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Alba J, Di Rienzo L, Milanetti E, Acuto O, D’Abramo M. Molecular Dynamics Simulations Reveal Canonical Conformations in Different pMHC/TCR Interactions. Cells 2020; 9:E942. [PMID: 32290289 PMCID: PMC7226950 DOI: 10.3390/cells9040942] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 01/14/2023] Open
Abstract
The major defense system against microbial pathogens in vertebrates is the adaptive immune response and represents an effective mechanism in cancer surveillance. T cells represent an essential component of this complex system. They can recognize myriads of antigens as short peptides (p) originated from the intracellular degradation of foreign proteins presented by major histocompatibility complex (MHC) proteins. The clonotypic T-cell antigen receptor (TCR) is specialized in recognizing pMHC and triggering T cells immune response. It is still unclear how TCR engagement to pMHC is translated into the intracellular signal that initiates T-cell immune response. Some work has suggested the possibility that pMHC binding induces in the TCR conformational changes transmitted to its companion CD3 subunits that govern signaling. The conformational changes would promote phosphorylation of the CD3 complex ζ chain that initiates signal propagation intracellularly. Here, we used all-atom molecular dynamics simulations (MDs) of 500 ns to analyze the conformational behavior of three TCRs (1G4, ILA1 and ILA1α1β1) interacting with the same MHC class I (HLA-A*02:01) bound to different peptides, and modelled in the presence of a lipid bilayer. Our data suggest a correlation between the conformations explored by the β-chain constant regions and the T-cell response experimentally determined. In particular, independently by the TCR type involved in the interaction, the TCR activation seems to be linked to a specific zone of the conformational space explored by the β-chain constant region. Moreover, TCR ligation restricts the conformational space the MHC class I groove.
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Affiliation(s)
- Josephine Alba
- Department of Chemistry, University of Rome Sapienza, P.le A.Moro 5-00185 Rome, Italy
| | - Lorenzo Di Rienzo
- Department of Physics, University of Rome Sapienza, 5-00185 Rome Italy; (L.D.R.); (E.M.)
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 000161 Rome, Italy
| | - Edoardo Milanetti
- Department of Physics, University of Rome Sapienza, 5-00185 Rome Italy; (L.D.R.); (E.M.)
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 000161 Rome, Italy
| | - Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK;
| | - Marco D’Abramo
- Department of Chemistry, University of Rome Sapienza, P.le A.Moro 5-00185 Rome, Italy
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52
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Coles CH, Mulvaney RM, Malla S, Walker A, Smith KJ, Lloyd A, Lowe KL, McCully ML, Martinez Hague R, Aleksic M, Harper J, Paston SJ, Donnellan Z, Chester F, Wiederhold K, Robinson RA, Knox A, Stacey AR, Dukes J, Baston E, Griffin S, Jakobsen BK, Vuidepot A, Harper S. TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex. THE JOURNAL OF IMMUNOLOGY 2020; 204:1943-1953. [PMID: 32102902 DOI: 10.4049/jimmunol.1900915] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/29/2019] [Indexed: 12/18/2022]
Abstract
The molecular rules driving TCR cross-reactivity are poorly understood and, consequently, it is unclear the extent to which TCRs targeting the same Ag recognize the same off-target peptides. We determined TCR-peptide-HLA crystal structures and, using a single-chain peptide-HLA phage library, we generated peptide specificity profiles for three newly identified human TCRs specific for the cancer testis Ag NY-ESO-1157-165-HLA-A2. Two TCRs engaged the same central peptide feature, although were more permissive at peripheral peptide positions and, accordingly, possessed partially overlapping peptide specificity profiles. The third TCR engaged a flipped peptide conformation, leading to the recognition of off-target peptides sharing little similarity with the cognate peptide. These data show that TCRs specific for a cognate peptide recognize discrete peptide repertoires and reconciles how an individual's limited TCR repertoire following negative selection in the thymus is able to recognize a vastly larger antigenic pool.
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Affiliation(s)
- Charlotte H Coles
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Rachel M Mulvaney
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Sunir Malla
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrew Walker
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Kathrine J Smith
- GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Angharad Lloyd
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Kate L Lowe
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | | | | | - Milos Aleksic
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Jane Harper
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Samantha J Paston
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Zoe Donnellan
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Fiona Chester
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Katrin Wiederhold
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Ross A Robinson
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrew Knox
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrea R Stacey
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Joseph Dukes
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Emma Baston
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Sue Griffin
- GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Bent K Jakobsen
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Annelise Vuidepot
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Stephen Harper
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
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53
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Tripathi SK, Salunke DM. Exploring the different states of wild-type T-cell receptor and mutant conformational changes towards understanding the antigen recognition. J Biomol Struct Dyn 2020; 39:188-201. [PMID: 31870204 DOI: 10.1080/07391102.2019.1708795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Recognition of proteolytic peptide fragments presented by major histocompatibility complex (MHC) on target cells by T-cell receptor (TCR) is among the most important interactions in the adaptive immune system. Several computational studies have been performed to investigate conformational and dynamical properties of TCRs for enhanced immunogenicity. Here, we present the large-scale molecular dynamics (MD) simulation studies of the two comprehensive systems consisting of the wild-type and mutant IG4 TCR in complex with the tumor epitope NY-ESO peptide (SLLMWITQC) and analyzed for mapping conformational changes of TCR in the states prior to antigen binding, upon antigen binding and after the antigen was released. All of the simulations were performed with different states of TCRs for each 1000 ns of simulation time, providing six simulations for time duration of 6000 ns (6µs). We show that rather than undergoing most critical conformational changes upon antigen binding, the high proportion of complementarity-determining region (CDR) loops change by comparatively small amount. The hypervariable CDRα3 and CDRβ3 loops showed significant structural changes. Interestingly, the TCR β chain loops showed the least changes, which is reliable with recent implications that β domain of TCR may propel antigen interaction. The mutant shows higher rigidity than wild-type even in released state; expose an induced fit mechanism occurring from the re-structuring of CDRα3 loop and can allow enhanced binding affinity of the peptide antigen. Additionally, we show that CDRα3 loop and peptide contacts are an adaptive feature of affinity enhanced mutant TCR.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunil Kumar Tripathi
- Structural Immunology Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Dinakar M Salunke
- Structural Immunology Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India.,Structural Immunology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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54
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Denham EM, Barton MI, Black SM, Bridge MJ, de Wet B, Paterson RL, van der Merwe PA, Goyette J. A generic cell surface ligand system for studying cell-cell recognition. PLoS Biol 2019; 17:e3000549. [PMID: 31815943 PMCID: PMC6922461 DOI: 10.1371/journal.pbio.3000549] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/19/2019] [Accepted: 11/12/2019] [Indexed: 01/11/2023] Open
Abstract
Dose-response experiments are a mainstay of receptor biology studies and can reveal valuable insights into receptor function. Such studies of receptors that bind cell surface ligands are currently limited by the difficulty in manipulating the surface density of ligands at a cell–cell interface. Here, we describe a generic cell surface ligand system that allows precise manipulation of cell surface ligand densities over several orders of magnitude. These densities are robustly quantifiable, a major advance over previous studies. We validate the system for a range of immunoreceptors, including the T-cell receptor (TCR), and show that this generic ligand stimulates via the TCR at a similar surface density as its native ligand. We also extend our work to the activation of chimeric antigen receptors. This novel system allows the effect of varying the surface density, valency, dimensions, and affinity of the ligand to be investigated. It can be readily broadened to other receptor–cell surface ligand interactions and will facilitate investigation into the activation of, and signal integration between, cell surface receptors. This study describes a generic cell-surface ligand system that allows precise manipulation of ligand densities, valency, dimensions, and affinity. The system is validated for a range of immunoreceptors, including the T-cell receptor, and can be readily broadened to other cell-surface receptor-ligand interactions.
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Affiliation(s)
- Eleanor M. Denham
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Michael I. Barton
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Susannah M. Black
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Marcus J. Bridge
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Ben de Wet
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Rachel L. Paterson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - P. Anton van der Merwe
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
- * E-mail: (JG); (PAvdM)
| | - Jesse Goyette
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, United Kingdom
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail: (JG); (PAvdM)
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55
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Karapetyan AR, Chaipan C, Winkelbach K, Wimberger S, Jeong JS, Joshi B, Stein RB, Underwood D, Castle JC, van Dijk M, Seibert V. TCR Fingerprinting and Off-Target Peptide Identification. Front Immunol 2019; 10:2501. [PMID: 31695703 PMCID: PMC6817589 DOI: 10.3389/fimmu.2019.02501] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/07/2019] [Indexed: 01/06/2023] Open
Abstract
Adoptive T cell therapy using patient T cells redirected to recognize tumor-specific antigens by expressing genetically engineered high-affinity T-cell receptors (TCRs) has therapeutic potential for melanoma and other solid tumors. Clinical trials implementing genetically modified TCRs in melanoma patients have raised concerns regarding off-target toxicities resulting in lethal destruction of healthy tissue, highlighting the urgency of assessing which off-target peptides can be recognized by a TCR. As a model system we used the clinically efficacious NY-ESO-1-specific TCR C259, which recognizes the peptide epitope SLLMWITQC presented by HLA-A*02:01. We investigated which amino acids at each position enable a TCR interaction by sequentially replacing every amino acid position outside of anchor positions 2 and 9 with all 19 possible alternative amino acids, resulting in 134 peptides (133 altered peptides plus epitope peptide). Each peptide was individually evaluated using three different in vitro assays: binding of the NY-ESOc259 TCR to the peptide, peptide-dependent activation of TCR-expressing cells, and killing of peptide-presenting target cells. To represent the TCR recognition kernel, we defined Position Weight Matrices (PWMs) for each assay by assigning normalized measurements to each of the 20 amino acids in each position. To predict potential off-target peptides, we applied a novel algorithm projecting the PWM-defined kernel into the human proteome, scoring NY-ESOc259 TCR recognition of 336,921 predicted human HLA-A*02:01 binding 9-mer peptides. Of the 12 peptides with high predicted score, we confirmed 7 (including NY-ESO-1 antigen SLLMWITQC) strongly activate human primary NY-ESOc259-expressing T cells. These off-target peptides include peptides with up to 7 amino acid changes (of 9 possible), which could not be predicted using the recognition motif as determined by alanine scans. Thus, this replacement scan assay determines the “TCR fingerprint” and, when coupled with the algorithm applied to the database of human 9-mer peptides binding to HLA-A*02:01, enables the identification of potential off-target antigens and the tissues where they are expressed. This platform enables both screening of multiple TCRs to identify the best candidate for clinical development and identification of TCR-specific cross-reactive peptide recognition and constitutes an improved methodology for the identification of potential off-target peptides presented on MHC class I molecules.
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56
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Jensen KK, Rantos V, Jappe EC, Olsen TH, Jespersen MC, Jurtz V, Jessen LE, Lanzarotti E, Mahajan S, Peters B, Nielsen M, Marcatili P. TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes. Sci Rep 2019; 9:14530. [PMID: 31601838 PMCID: PMC6787230 DOI: 10.1038/s41598-019-50932-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 09/09/2019] [Indexed: 01/30/2023] Open
Abstract
The interaction between the class I major histocompatibility complex (MHC), the peptide presented by the MHC and the T-cell receptor (TCR) is a key determinant of the cellular immune response. Here, we present TCRpMHCmodels, a method for accurate structural modelling of the TCR-peptide-MHC (TCR-pMHC) complex. This TCR-pMHC modelling pipeline takes as input the amino acid sequence and generates models of the TCR-pMHC complex, with a median Cα RMSD of 2.31 Å. TCRpMHCmodels significantly outperforms TCRFlexDock, a specialised method for docking pMHC and TCR structures. TCRpMHCmodels is simple to use and the modelling pipeline takes, on average, only two minutes. Thanks to its ease of use and high modelling accuracy, we expect TCRpMHCmodels to provide insights into the underlying mechanisms of TCR and pMHC interactions and aid in the development of advanced T-cell-based immunotherapies and rational design of vaccines. The TCRpMHCmodels tool is available at http://www.cbs.dtu.dk/services/TCRpMHCmodels/.
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Affiliation(s)
| | - Vasileios Rantos
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark.,Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory, Notkestrasse 85, 22607, Hamburg, Germany
| | - Emma Christine Jappe
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark.,Evaxion Biotech, Bredgade 34E, 1260, Copenhagen, Denmark
| | - Tobias Hegelund Olsen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Vanessa Jurtz
- Department of Bioinformatics and Data Mining, Novo Nordisk A/S, 2760, Måløv, Denmark
| | - Leon Eyrich Jessen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Esteban Lanzarotti
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Swapnil Mahajan
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,University of California San Diego, Department of Medicine, La Jolla, CA 92037, USA
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Paolo Marcatili
- Department of Bio and Health Informatics, Technical University of Denmark, Kgs. Lyngby, Denmark.
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57
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Impact of epitope density on CD8+ T cell development and function. Mol Immunol 2019; 113:120-125. [DOI: 10.1016/j.molimm.2019.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/17/2019] [Accepted: 03/21/2019] [Indexed: 11/23/2022]
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58
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Gao K, Chen L, Zhang Y, Zhao Y, Wan Z, Wu J, Lin L, Kuang Y, Lu J, Zhang X, Tian L, Liu X, Qiu X. Germline-Encoded TCR-MHC Contacts Promote TCR V Gene Bias in Umbilical Cord Blood T Cell Repertoire. Front Immunol 2019; 10:2064. [PMID: 31543879 PMCID: PMC6730489 DOI: 10.3389/fimmu.2019.02064] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
T cells recognize antigens as peptides bound to major histocompatibility complex (MHC) proteins through T cell receptors (TCRs) on their surface. To recognize a wide range of pathogens, each individual possesses a substantial number of TCRs with an extremely high degree of variability. It remains controversial whether germline-encoded TCR repertoire is shaped by MHC polymorphism and, if so, what is the preference between MHC genetic variants and TCR V gene compatibility. To investigate the "net" genetic association between MHC variations and TRBV genes, we applied quantitative trait locus (QTL) mapping to test the associations between MHC polymorphism and TCR β chain V (TRBV) genes usage using umbilical cord blood (UCB) samples of 201 Chinese newborns. We found TRBV gene and MHC loci that are predisposed to interact with one another differ from previous conclusions. The majority of MHC amino acid residues associated with the TRBV gene usage show spatial proximities in known structures of TCR-pMHC complexes. These results show for the first time that MHC variants bias TRBV gene usage in UCB of Chinese ancestry and indicate that germline-encoded contacts influence TCR-MHC interactions in intact T cell repertoires.
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Affiliation(s)
- Kai Gao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | | | | | - Yi Zhao
- BGI-Shenzhen, Shenzhen, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | | | | | | | - Yashu Kuang
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jinhua Lu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Women and Children's Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiuqing Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | | | - Xiao Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Xiu Qiu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Women and Children's Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Obstetrics and Gynecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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59
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Madura F, Rizkallah PJ, Legut M, Holland CJ, Fuller A, Bulek A, Schauenburg AJ, Trimby A, Hopkins JR, Wells SA, Godkin A, Miles JJ, Sami M, Li Y, Liddy N, Jakobsen BK, Loveridge EJ, Cole DK, Sewell AK. TCR-induced alteration of primary MHC peptide anchor residue. Eur J Immunol 2019; 49:1052-1066. [PMID: 31091334 PMCID: PMC6618058 DOI: 10.1002/eji.201948085] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/21/2019] [Accepted: 05/14/2019] [Indexed: 12/12/2022]
Abstract
The HLA-A*02:01-restricted decapeptide EAAGIGILTV, derived from melanoma antigen recognized by T-cells-1 (MART-1) protein, represents one of the best-studied tumor associated T-cell epitopes, but clinical results targeting this peptide have been disappointing. This limitation may reflect the dominance of the nonapeptide, AAGIGILTV, at the melanoma cell surface. The decapeptide and nonapeptide are presented in distinct conformations by HLA-A*02:01 and TCRs from clinically relevant T-cell clones recognize the nonapeptide poorly. Here, we studied the MEL5 TCR that potently recognizes the nonapeptide. The structure of the MEL5-HLA-A*02:01-AAGIGILTV complex revealed an induced fit mechanism of antigen recognition involving altered peptide-MHC anchoring. This "flexing" at the TCR-peptide-MHC interface to accommodate the peptide antigen explains previously observed incongruences in this well-studied system and has important implications for future therapeutic approaches. Finally, this study expands upon the mechanisms by which molecular plasticity can influence antigen recognition by T cells.
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Affiliation(s)
| | | | | | | | - Anna Fuller
- School of MedicineCardiff UniversityCardiffUK
| | - Anna Bulek
- School of MedicineCardiff UniversityCardiffUK
| | | | | | | | | | | | - John J. Miles
- School of MedicineCardiff UniversityCardiffUK
- Centre for Biodiscovery and Molecular Development of TherapeuticsAustralian Institute of Tropical Health and MedicineJames Cook UniversityCairnsQueenslandAustralia
| | | | - Yi Li
- Immunocore Ltd.AbingdonUK
| | | | | | - E. Joel Loveridge
- School of ChemistryCardiff UniversityCardiffUK
- Department of ChemistrySwansea UniversitySwanseaUK
| | - David K. Cole
- School of MedicineCardiff UniversityCardiffUK
- Immunocore Ltd.AbingdonUK
| | - Andrew K. Sewell
- School of MedicineCardiff UniversityCardiffUK
- Systems Immunity Research InstituteCardiff UniversityCardiffUK
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60
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Thakkar N, Bailey-Kellogg C. Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity. BMC Bioinformatics 2019; 20:241. [PMID: 31092185 PMCID: PMC6521430 DOI: 10.1186/s12859-019-2864-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/29/2019] [Indexed: 12/18/2022] Open
Abstract
Background Repertoire sequencing is enabling deep explorations into the cellular immune response, including the characterization of commonalities and differences among T cell receptor (TCR) repertoires from different individuals, pathologies, and antigen specificities. In seeking to understand the generality of patterns observed in different groups of TCRs, it is necessary to balance how well each pattern represents the diversity among TCRs from one group (sensitivity) vs. how many TCRs from other groups it also represents (specificity). The variable complementarity determining regions (CDRs), particularly the third CDRs (CDR3s) interact with major histocompatibility complex (MHC)-presented epitopes from putative antigens, and thus encode the determinants of recognition. Results We here systematically characterize the predictive power that can be obtained from CDR3 sequences, using representative, readily interpretable methods for evaluating CDR sequence similarity and then clustering and classifying sequences based on similarity. An initial analysis of CDR3s of known structure, clustered by structural similarity, helps calibrate the limits of sequence diversity among CDRs that might have a common mode of interaction with presented epitopes. Subsequent analyses demonstrate that this same range of sequence similarity strikes a favorable specificity/sensitivity balance in distinguishing twins from non-twins based on overall CDR3 repertoires, classifying CDR3 repertoires by antigen specificity, and distinguishing general pathologies. Conclusion We conclude that within a fairly broad range of sequence similarity, matching CDR3 sequences are likely to share specificities. Electronic supplementary material The online version of this article (10.1186/s12859-019-2864-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Neerja Thakkar
- Department of Computer Science, Dartmouth, Hanover, NH, USA
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61
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Corridoni D, Shiraishi S, Chapman T, Steevels T, Muraro D, Thézénas ML, Prota G, Chen JL, Gileadi U, Ternette N, Cerundolo V, Simmons A. NOD2 and TLR2 Signal via TBK1 and PI31 to Direct Cross-Presentation and CD8 T Cell Responses. Front Immunol 2019; 10:958. [PMID: 31114588 PMCID: PMC6503738 DOI: 10.3389/fimmu.2019.00958] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 04/15/2019] [Indexed: 12/16/2022] Open
Abstract
NOD2 and TLR2 recognize components of bacterial cell wall peptidoglycan and direct defense against enteric pathogens. CD8+ T cells are important for immunity to such pathogens but how NOD2 and TLR2 induce antigen specific CD8+ T cell responses is unknown. Here, we define how these pattern recognition receptors (PRRs) signal in primary dendritic cells (DCs) to influence MHC class I antigen presentation. We show NOD2 and TLR2 phosphorylate PI31 via TBK1 following activation in DCs. PI31 interacts with TBK1 and Sec16A at endoplasmic reticulum exit sites (ERES), which positively regulates MHC class I peptide loading and immunoproteasome stability. Following NOD2 and TLR2 stimulation, depletion of PI31 or inhibition of TBK1 activity in vivo impairs DC cross-presentation and CD8+ T cell activation. DCs from Crohn's patients expressing NOD2 polymorphisms show dysregulated cross-presentation and CD8+ T cell responses. Our findings reveal unidentified mechanisms that underlie CD8+ T cell responses to bacteria in health and in Crohn's.
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Affiliation(s)
- Daniele Corridoni
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Seiji Shiraishi
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Thomas Chapman
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Tessa Steevels
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Daniele Muraro
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Marie-Laëtitia Thézénas
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Gennaro Prota
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Ji-Li Chen
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Uzi Gileadi
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Nicola Ternette
- The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Alison Simmons
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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62
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Colin-York H, Javanmardi Y, Skamrahl M, Kumari S, Chang VT, Khuon S, Taylor A, Chew TL, Betzig E, Moeendarbary E, Cerundolo V, Eggeling C, Fritzsche M. Cytoskeletal Control of Antigen-Dependent T Cell Activation. Cell Rep 2019; 26:3369-3379.e5. [PMID: 30893608 PMCID: PMC6426652 DOI: 10.1016/j.celrep.2019.02.074] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 08/06/2018] [Accepted: 02/20/2019] [Indexed: 11/23/2022] Open
Abstract
Cytoskeletal actin dynamics is essential for T cell activation. Here, we show evidence that the binding kinetics of the antigen engaging the T cell receptor influences the nanoscale actin organization and mechanics of the immune synapse. Using an engineered T cell system expressing a specific T cell receptor and stimulated by a range of antigens, we found that the peak force experienced by the T cell receptor during activation was independent of the unbinding kinetics of the stimulating antigen. Conversely, quantification of the actin retrograde flow velocity at the synapse revealed a striking dependence on the antigen unbinding kinetics. These findings suggest that the dynamics of the actin cytoskeleton actively adjusted to normalize the force experienced by the T cell receptor in an antigen-specific manner. Consequently, tuning actin dynamics in response to antigen kinetics may thus be a mechanism that allows T cells to adjust the lengthscale and timescale of T cell receptor signaling.
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Affiliation(s)
- Huw Colin-York
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Yousef Javanmardi
- Department of Mechanical Engineering, University College London, London WC1E 7JE, UK
| | - Mark Skamrahl
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Sudha Kumari
- Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Veronica T Chang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Satya Khuon
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Aaron Taylor
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Teng-Leong Chew
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Emad Moeendarbary
- Department of Mechanical Engineering, University College London, London WC1E 7JE, UK; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Marco Fritzsche
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK; Kennedy Institute for Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7LF, UK.
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63
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Wu P, Zhang T, Liu B, Fei P, Cui L, Qin R, Zhu H, Yao D, Martinez RJ, Hu W, An C, Zhang Y, Liu J, Shi J, Fan J, Yin W, Sun J, Zhou C, Zeng X, Xu C, Wang J, Evavold BD, Zhu C, Chen W, Lou J. Mechano-regulation of Peptide-MHC Class I Conformations Determines TCR Antigen Recognition. Mol Cell 2019; 73:1015-1027.e7. [PMID: 30711376 PMCID: PMC6408234 DOI: 10.1016/j.molcel.2018.12.018] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/27/2018] [Accepted: 12/20/2018] [Indexed: 01/08/2023]
Abstract
TCRs recognize cognate pMHCs to initiate T cell signaling and adaptive immunity. Mechanical force strengthens TCR-pMHC interactions to elicit agonist-specific catch bonds to trigger TCR signaling, but the underlying dynamic structural mechanism is unclear. We combined steered molecular dynamics (SMD) simulation, single-molecule biophysical approaches, and functional assays to collectively demonstrate that mechanical force induces conformational changes in pMHCs to enhance pre-existing contacts and activates new interactions at the TCR-pMHC binding interface to resist bond dissociation under force, resulting in TCR-pMHC catch bonds and T cell activation. Intriguingly, cancer-associated somatic mutations in HLA-A2 that may restrict these conformational changes suppressed TCR-pMHC catch bonds. Structural analysis also indicated that HLA polymorphism might alter the equilibrium of these conformational changes. Our findings not only reveal critical roles of force-induced conformational changes in pMHCs for activating TCR-pMHC catch bonds but also have implications for T cell-based immunotherapy.
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Affiliation(s)
- Peng Wu
- Department of Neurobiology, Institute of Neuroscience, and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Tongtong Zhang
- Department of Neurobiology, Institute of Neuroscience, and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Baoyu Liu
- Coulter Department of Biomedical Engineering, Woodruff School of Mechanical Engineering, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA; Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Panyu Fei
- School of Mechanical Engineering, Zhejiang University, Hangzhou 310058, China
| | - Lei Cui
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rui Qin
- Department of Neurobiology, Institute of Neuroscience, and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Huaying Zhu
- Department of Neurobiology, Institute of Neuroscience, and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Danmei Yao
- Department of Neurobiology, Institute of Neuroscience, and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ryan J Martinez
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Wei Hu
- Department of Neurobiology, Institute of Neuroscience, and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chenyi An
- School of Mechanical Engineering, Zhejiang University, Hangzhou 310058, China
| | - Yong Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Junwei Liu
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310058, China
| | - Jiawei Shi
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310058, China
| | - Juan Fan
- Department of Neurobiology, Institute of Neuroscience, and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Weiwei Yin
- Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310058, China
| | - Jie Sun
- Department of Cell Biology and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Chun Zhou
- School of Public Health and Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xun Zeng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, and First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Chenqi Xu
- State Key Laboratory of Molecular Biology, Chinese Academy Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai 200031, China
| | - Jianan Wang
- Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Brian D Evavold
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Cheng Zhu
- Coulter Department of Biomedical Engineering, Woodruff School of Mechanical Engineering, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Wei Chen
- Department of Neurobiology, Institute of Neuroscience, and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310058, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Modern Optical Instrumentation, Zhejiang University, Hangzhou 310058, China.
| | - Jizhong Lou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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64
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Clancy-Thompson E, Devlin CA, Tyler PM, Servos MM, Ali LR, Ventre KS, Bhuiyan MA, Bruck PT, Birnbaum ME, Dougan SK. Altered Binding of Tumor Antigenic Peptides to MHC Class I Affects CD8 + T Cell-Effector Responses. Cancer Immunol Res 2018; 6:1524-1536. [PMID: 30352798 DOI: 10.1158/2326-6066.cir-18-0348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/03/2018] [Accepted: 10/18/2018] [Indexed: 12/12/2022]
Abstract
T-cell priming occurs when a naïve T cell recognizes cognate peptide-MHC complexes on an activated antigen-presenting cell. The circumstances of this initial priming have ramifications on the fate of the newly primed T cell. Newly primed CD8+ T cells can embark onto different trajectories, with some becoming short-lived effector cells and others adopting a tissue resident or memory cell fate. To determine whether T-cell priming influences the quality of the effector T-cell response to tumors, we used transnuclear CD8+ T cells that recognize the melanoma antigen TRP1 using TRP1high or TRP1low TCRs that differ in both affinity and fine specificity. From a series of altered peptide ligands, we identified a point mutation (K8) in a nonanchor residue that, when analyzed crystallographically and biophysically, destabilized the peptide interaction with the MHC binding groove. In vitro, the K8 peptide induced robust proliferation of both TRP1high and TRP1low CD8+ T cells but did not induce expression of PD-1. Cytokine production from K8-stimulated TRP1 cells was minimal, whereas cytotoxicity was increased. Upon transfer into B16 tumor-bearing mice, the reference peptide (TRP1-M9)- and K8-stimulated TRP1 cells were equally effective at controlling tumor growth but accomplished this through different mechanisms. TRP1-M9-stimulated cells produced more IFNγ, whereas K8-stimulated cells accumulated to higher numbers and were more cytotoxic. We, therefore, conclude that TCR recognition of weakly binding peptides during priming can skew the effector function of tumor-specific CD8+ T cells.
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Affiliation(s)
- Eleanor Clancy-Thompson
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Christine A Devlin
- Department of Biological Engineering, Massachusetts Institute of Technology, Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts
| | - Paul M Tyler
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mariah M Servos
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lestat R Ali
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Katherine S Ventre
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - M Aladdin Bhuiyan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Patrick T Bruck
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michael E Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Koch Institute for Integrative Cancer Research, Cambridge, Massachusetts.
| | - Stephanie K Dougan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
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65
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Jenkins E, Santos AM, O'Brien-Ball C, Felce JH, Wilcock MJ, Hatherley D, Dustin ML, Davis SJ, Eggeling C, Sezgin E. Reconstitution of immune cell interactions in free-standing membranes. J Cell Sci 2018; 132:jcs219709. [PMID: 30209137 PMCID: PMC6398472 DOI: 10.1242/jcs.219709] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/04/2018] [Indexed: 12/28/2022] Open
Abstract
The spatiotemporal regulation of signalling proteins at the contacts formed between immune cells and their targets determines how and when immune responses begin and end. Therapeutic control of immune responses therefore relies on thorough elucidation of the molecular processes occurring at these interfaces. However, the detailed investigation of each component's contribution to the formation and regulation of the contact is hampered by the complexities of cell composition and architecture. Moreover, the transient nature of these interactions creates additional challenges, especially in the use of advanced imaging technology. One approach that circumvents these problems is to establish in vitro systems that faithfully mimic immune cell interactions, but allow complexity to be 'dialled-in' as needed. Here, we present an in vitro system that makes use of synthetic vesicles that mimic important aspects of immune cell surfaces. Using this system, we began to explore the spatial distribution of signalling molecules (receptors, kinases and phosphatases) and how this changes during the initiation of signalling. The GUV/cell system presented here is expected to be widely applicable.
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Affiliation(s)
- Edward Jenkins
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ana Mafalda Santos
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Caitlin O'Brien-Ball
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - James H Felce
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
| | - Martin J Wilcock
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Deborah Hatherley
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
| | - Simon J Davis
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Institute of Applied Optics Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Erdinc Sezgin
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
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66
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Dolton G, Zervoudi E, Rius C, Wall A, Thomas HL, Fuller A, Yeo L, Legut M, Wheeler S, Attaf M, Chudakov DM, Choy E, Peakman M, Sewell AK. Optimized Peptide-MHC Multimer Protocols for Detection and Isolation of Autoimmune T-Cells. Front Immunol 2018; 9:1378. [PMID: 30008714 PMCID: PMC6034003 DOI: 10.3389/fimmu.2018.01378] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/04/2018] [Indexed: 12/14/2022] Open
Abstract
Peptide–MHC (pMHC) multimers have become the “gold standard” for the detection and isolation of antigen-specific T-cells but recent evidence shows that normal use of these reagents can miss fully functional T-cells that bear T-cell receptors (TCRs) with low affinity for cognate antigen. This issue is particularly pronounced for anticancer and autoimmune T-cells as self-reactive T-cell populations are enriched for low-affinity TCRs due to the removal of cells with higher affinity receptors by immune tolerance mechanisms. Here, we stained a wide variety of self-reactive human T-cells using regular pMHC staining and an optimized technique that included: (i) protein kinase inhibitor (PKI), to prevent TCR triggering and internalization, and (ii) anti-fluorochrome antibody, to reduce reagent dissociation during washing steps. Lymphocytes derived from the peripheral blood of type 1 diabetes patients were stained with pMHC multimers made with epitopes from preproinsulin (PPI), insulin-β chain, glutamic acid decarboxylase 65 (GAD65), or glucose-6-phospate catalytic subunit-related protein (IGRP) presented by disease-risk allelles HLA A*02:01 or HLA*24:02. Samples from ankylosing spondylitis patients were stained with a multimerized epitope from vasoactive intestinal polypeptide receptor 1 (VIPR1) presented by HLA B*27:05. Optimized procedures stained an average of 40.5-fold (p = 0.01, range between 1.4 and 198) more cells than could be detected without the inclusion of PKI and cross-linking anti-fluorochrome antibody. Higher order pMHC dextramers recovered more cells than pMHC tetramers in parallel assays, and standard staining protocols with pMHC tetramers routinely recovered less cells than functional assays. HLA A*02:01-restricted PPI-specific and HLA B*27:05-restricted VIPR1-specific T-cell clones generated using the optimized procedure could not be stained by standard pMHC tetramer staining. However, these clones responded well to exogenously supplied peptide and endogenously processed and presented epitopes. We also showed that anti-fluorochrome antibody-conjugated magnetic beads enhanced staining of self-reactive T-cells that could not be stained using standard protocols, thus enabling rapid ex vivo isolation of autoimmune T-cells. We, therefore, conclude that regular pMHC tetramer staining is generally unsuitable for recovering self-reactive T-cells from clinical samples and recommend the use of the optimized protocols described herein.
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Affiliation(s)
- Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Efthalia Zervoudi
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Cristina Rius
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Aaron Wall
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Hannah L Thomas
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Anna Fuller
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Lorraine Yeo
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London, London, United Kingdom
| | - Mateusz Legut
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Sophie Wheeler
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Meriem Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Dmitriy M Chudakov
- Pirogov Russian National Research Medical University, Moscow, Russia.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ernest Choy
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Mark Peakman
- Department of Immunobiology, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.,NIHR Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London, London, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
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67
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Dib L, Salamin N, Gfeller D. Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins. PLoS Comput Biol 2018; 14:e1006188. [PMID: 29782520 PMCID: PMC5983860 DOI: 10.1371/journal.pcbi.1006188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 06/01/2018] [Accepted: 05/09/2018] [Indexed: 01/11/2023] Open
Abstract
Major histocompatibility complex class I (MHC-I) molecules are critical to adaptive immune defence mechanisms in vertebrate species and are encoded by highly polymorphic genes. Polymorphic sites are located close to the ligand-binding groove and entail MHC-I alleles with distinct binding specificities. Some efforts have been made to investigate the relationship between polymorphism and protein stability. However, less is known about the relationship between polymorphism and MHC-I co-evolutionary constraints. Using Direct Coupling Analysis (DCA) we found that co-evolution analysis accurately pinpoints structural contacts, although the protein family is restricted to vertebrates and comprises less than five hundred species, and that the co-evolutionary signal is mainly driven by inter-species changes, and not intra-species polymorphism. Moreover, we show that polymorphic sites in human preferentially avoid co-evolving residues, as well as residues involved in protein stability. These results suggest that sites displaying high polymorphism may have been selected during vertebrates’ evolution to avoid co-evolutionary constraints and thereby maximize their mutability. Amino acid co-evolution represents cases of simultaneous substitution of amino acids at distinct positions in protein sequences. In the MHC-I protein family, such co-evolution could result from either amino acid changes across species or changes within species due to the high polymorphism of MHC-I molecules. Here we show that signals captured by global methods such as Direct Coupling Analysis (DCA) to estimate co-evolution primarily result from changes across species. Moreover, our results indicate that polymorphic sites in MHC-I molecules tend to be decoupled from co-evolving ones. This could suggest that they have been selected to maximize their mutability, which is known to be functionally important to entail MHC-I molecules with a wide repertoire of binding specificities for antigen presentation.
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Affiliation(s)
- Linda Dib
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Switzerland
- Swiss Institutes of Bioinformatics, Quartier Sorge, Lausanne, Switzerland
| | - Nicolas Salamin
- Swiss Institutes of Bioinformatics, Quartier Sorge, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Switzerland
- Swiss Institutes of Bioinformatics, Quartier Sorge, Lausanne, Switzerland
- * E-mail:
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68
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Chen L, Tian Y, Zhan K, Chen A, Weng Z, Huang J, Li Y, Sun Y, Zheng H, Li Y. A humanized TCR retaining authentic specificity and affinity conferred potent anti-tumour cytotoxicity. Immunology 2018; 155:123-136. [PMID: 29645087 DOI: 10.1111/imm.12935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 03/05/2018] [Accepted: 03/28/2018] [Indexed: 12/14/2022] Open
Abstract
The affinity of T-cell receptor (TCR) determines the efficacy of TCR-based immunotherapy. By using human leucocyte antigen (HLA)-A*02 transgenic mice, a TCR was generated previously specific for human tumour testis antigen peptide MAGE-A3112-120 (KVAELVHFL) HLA-A*02 complex. We developed an approach to humanize the murine TCR by replacing the mouse framework with sequences of folding optimized human TCR variable domains for retaining binding affinity. The resultant humanized TCR exhibited higher affinity and conferred better anti-tumour activity than its parent murine MAGE-A3 TCR (SRm1). In addition, the affinity of humanized TCR was enhanced further to achieve improved T-cell activation. Our studies demonstrated that the human TCR variable domain frameworks could provide support for complementarity-determining regions from a murine TCR, and retain the original binding activity. It could be used as a generic approach of TCR humanization.
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Affiliation(s)
- Lin Chen
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ye Tian
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Kai Zhan
- XiangXue Life Sciences Research Center, XiangXue Pharmaceutical Co. Ltd, Guangzhou, China
| | - Anan Chen
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhiming Weng
- XiangXue Life Sciences Research Center, XiangXue Pharmaceutical Co. Ltd, Guangzhou, China
| | - Jiao Huang
- XiangXue Life Sciences Research Center, XiangXue Pharmaceutical Co. Ltd, Guangzhou, China
| | - Yanyan Li
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yongjie Sun
- Institute of Health Sciences, Anhui University, Hefei, China
| | - Hongjun Zheng
- XiangXue Life Sciences Research Center, XiangXue Pharmaceutical Co. Ltd, Guangzhou, China
| | - Yi Li
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,XiangXue Life Sciences Research Center, XiangXue Pharmaceutical Co. Ltd, Guangzhou, China
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69
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70
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Abstract
Human leukocyte antigen (HLA)-I molecules generally bind short peptides (8–10 amino acids), although extended HLA-I restricted peptides (>10 amino acids) can be presented to T cells. However, the function of such extended HLA-I epitopes in tumour immunity, and how they would be recognised by T-cell receptors (TCR) remains unclear. Here we show that the structures of two distinct TCRs (TRAV4+TRAJ21+-TRBV28+TRBJ2-3+ and TRAV4+TRAJ8+-TRBV9+TRBJ2-1+), originating from a polyclonal T-cell repertoire, bind to HLA-B*07:02, presenting a 13-amino-acid-long tumour-associated peptide, NY-ESO-160–72. Comparison of the structures reveals that the two TCRs differentially binds NY-ESO-160–72–HLA-B*07:02 complex, and induces differing extent of conformational change of the NY-ESO-160–72 epitope. Accordingly, polyclonal TCR usage towards an extended HLA-I restricted tumour epitope translates to differing TCR recognition modes, whereby extensive flexibility at the TCR–pHLA-I interface engenders recognition. Human leukocyte antigen (HLA) presents peptides to activate T cells, but many aspects in the T cell receptor (TCR)/HLA interaction remain unclear. Here the authors show, via structural data, that two TCRs differentially recognize the same tumour peptide/HLA complex and induce contrasting conformation changes of the peptide.
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71
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Hafstrand I, Doorduijn EM, Sun R, Talyzina A, Sluijter M, Pellegrino S, Sandalova T, Duru AD, van Hall T, Achour A. The Immunogenicity of a Proline-Substituted Altered Peptide Ligand toward the Cancer-Associated TEIPP Neoepitope Trh4 Is Unrelated to Complex Stability. THE JOURNAL OF IMMUNOLOGY 2018; 200:2860-2868. [PMID: 29507106 DOI: 10.4049/jimmunol.1700228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 02/07/2018] [Indexed: 01/05/2023]
Abstract
Human cancers frequently display defects in Ag processing and presentation allowing for immune evasion, and they therefore constitute a significant challenge for T cell-based immunotherapy. We have previously demonstrated that the antigenicity of tumor-associated Ags can be significantly enhanced through unconventional residue modifications as a novel tool for MHC class I (MHC-I)-based immunotherapy approaches. We have also previously identified a novel category of cancer neo-epitopes, that is, T cell epitopes associated with impaired peptide processing (TEIPP), that are selectively presented by MHC-I on cells lacking the peptide transporter TAP. In this study, we demonstrate that substitution of the nonanchoring position 3 into a proline residue of the first identified TEIPP peptide, the murine Trh4, results in significantly enhanced recognition by antitumor CTLs toward the wild-type epitope. Although higher immunogenicity has in most cases been associated with increased MHC/peptide complex stability, our results demonstrate that the overall stability of H-2Db in complex with the highly immunogenic altered peptide ligand Trh4-p3P is significantly reduced compared with wild-type H-2Db/Trh4. Comparison of the crystal structures of the H-2Db/Trh4-p3P and H-2Db/Trh4 complexes revealed that the conformation of the nonconventional methionine anchor residue p5M is altered, deleting its capacity to form adequate sulfur-π interactions with H-2Db residues, thus reducing the overall longevity of the complex. Collectively, our results indicate that vaccination with Thr4-p3P significantly enhances T cell recognition of targets presenting the wild-type TEIPP epitope and that higher immunogenicity is not necessarily directly related to MHC/peptide complex stability, opening for the possibility to design novel peptide vaccines with reduced MHC/peptide complex stability.
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Affiliation(s)
- Ida Hafstrand
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Elien M Doorduijn
- Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Anna Talyzina
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Marjolein Sluijter
- Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Sara Pellegrino
- Department of Pharmaceutical Science, General and Organic Chemistry Section, University of Milan, 20133 Milan, Italy
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Adil Doganay Duru
- Cell Therapy Institute, Nova Southeastern University, Fort Lauderdale, FL 33314; and.,College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328
| | - Thorbald van Hall
- Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands;
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden; .,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
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72
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Ahmed M, Lopez-Albaitero A, Pankov D, Santich BH, Liu H, Yan S, Xiang J, Wang P, Hasan AN, Selvakumar A, O'Reilly RJ, Liu C, Cheung NKV. TCR-mimic bispecific antibodies targeting LMP2A show potent activity against EBV malignancies. JCI Insight 2018; 3:97805. [PMID: 29467338 DOI: 10.1172/jci.insight.97805] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/10/2018] [Indexed: 12/14/2022] Open
Abstract
EBV infection is associated with a number of malignancies of clinical unmet need, including Hodgkin lymphoma, nasopharyngeal carcinoma, gastric cancer, and posttransplant lymphoproliferative disease (PTLD), all of which express the EBV protein latent membrane protein 2A (LMP2A), an antigen that is difficult to target by conventional antibody approaches. To overcome this, we utilized phage display technology and a structure-guided selection strategy to generate human T cell receptor-like (TCR-like) monoclonal antibodies with exquisite specificity for the LMP2A-derived nonamer peptide, C426LGGLLTMV434 (CLG), as presented on HLA-A*02:01. Our lead construct, clone 38, closely mimics the native binding mode of a TCR, recognizing residues at position P3-P8 of the CLG peptide. To enhance antitumor potency, we constructed dimeric T cell engaging bispecific antibodies (DiBsAb) of clone 38 and an affinity-matured version clone 38-2. Both DiBsAb showed potent antitumor properties in vitro and in immunodeficient mice implanted with EBV transformed B lymphoblastoid cell lines and human T cell effectors. Clone 38 DiBsAb showed a stronger safety profile compared with its affinity-matured variant, with no activity against EBV- tumor cell lines and a panel of normal tissues, and was less cross-reactive against HLA-A*02:01 cells pulsed with a panel of CLG-like peptides predicted from a proteomic analysis. Clone 38 was also shown to recognize the CLG peptide on other HLA-A*02 suballeles, including HLA-A*02:02, HLA-A*02:04, and HLA-A*02:06, allowing for its potential use in additional populations. Clone 38 DiBsAb is a lead candidate to treat EBV malignancies with one of the strongest safety profiles documented for TCR-like mAbs.
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Affiliation(s)
- Mahiuddin Ahmed
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Andres Lopez-Albaitero
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dmitry Pankov
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Brian H Santich
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hong Liu
- Eureka Therapeutics, Emeryville, California, USA
| | - Su Yan
- Eureka Therapeutics, Emeryville, California, USA
| | - Jingyi Xiang
- Eureka Therapeutics, Emeryville, California, USA
| | - Pei Wang
- Eureka Therapeutics, Emeryville, California, USA
| | - Aisha N Hasan
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Annamalai Selvakumar
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Richard J O'Reilly
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Cheng Liu
- Eureka Therapeutics, Emeryville, California, USA
| | - Nai-Kong V Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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73
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Zhang SQ, Parker P, Ma KY, He C, Shi Q, Cui Z, Williams CM, Wendel BS, Meriwether AI, Salazar MA, Jiang N. Direct measurement of T cell receptor affinity and sequence from naïve antiviral T cells. Sci Transl Med 2017; 8:341ra77. [PMID: 27252176 DOI: 10.1126/scitranslmed.aaf1278] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/09/2016] [Indexed: 12/26/2022]
Abstract
T cells recognize and kill a myriad of pathogen-infected or cancer cells using a diverse set of T cell receptors (TCRs). The affinity of TCR to cognate antigen is of high interest in adoptive T cell transfer immunotherapy and antigen-specific T cell repertoire immune profiling because it is widely known to correlate with downstream T cell responses. We introduce the in situ TCR affinity and sequence test (iTAST) for simultaneous measurement of TCR affinity and sequence from single primary CD8(+) T cells in human blood. We demonstrate that the repertoire of primary antigen-specific T cells from pathogen-inexperienced individuals has a surprisingly broad affinity range of 1000-fold composed of diverse TCR sequences. Within this range, samples from older individuals contained a reduced frequency of high-affinity T cells compared to young individuals, demonstrating an age-related effect of T cell attrition that could cause holes in the repertoire. iTAST should enable the rapid selection of high-affinity TCRs ex vivo for adoptive immunotherapy and measurement of T cell response for immune monitoring applications.
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Affiliation(s)
- Shu-Qi Zhang
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Patricia Parker
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Ke-Yue Ma
- Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Chenfeng He
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Qian Shi
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Zhonghao Cui
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Chad M Williams
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Ben S Wendel
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Amanda I Meriwether
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Mary Alice Salazar
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Ning Jiang
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA. Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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74
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Diller KI, Bayden AS, Audie J, Diller DJ. PeptideNavigator: An interactive tool for exploring large and complex data sets generated during peptide-based drug design projects. Comput Biol Med 2017; 92:176-187. [PMID: 29207334 DOI: 10.1016/j.compbiomed.2017.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/18/2017] [Accepted: 11/18/2017] [Indexed: 01/01/2023]
Abstract
There is growing interest in peptide-based drug design and discovery. Due to their relatively large size, polymeric nature, and chemical complexity, the design of peptide-based drugs presents an interesting "big data" challenge. Here, we describe an interactive computational environment, PeptideNavigator, for naturally exploring the tremendous amount of information generated during a peptide drug design project. The purpose of PeptideNavigator is the presentation of large and complex experimental and computational data sets, particularly 3D data, so as to enable multidisciplinary scientists to make optimal decisions during a peptide drug discovery project. PeptideNavigator provides users with numerous viewing options, such as scatter plots, sequence views, and sequence frequency diagrams. These views allow for the collective visualization and exploration of many peptides and their properties, ultimately enabling the user to focus on a small number of peptides of interest. To drill down into the details of individual peptides, PeptideNavigator provides users with a Ramachandran plot viewer and a fully featured 3D visualization tool. Each view is linked, allowing the user to seamlessly navigate from collective views of large peptide data sets to the details of individual peptides with promising property profiles. Two case studies, based on MHC-1A activating peptides and MDM2 scaffold design, are presented to demonstrate the utility of PeptideNavigator in the context of disparate peptide-design projects.
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Affiliation(s)
- Kyle I Diller
- CMDBioscience Inc., 5 Science Park, New Haven, CT 06511, United States
| | - Alexander S Bayden
- CMDBioscience Inc., 5 Science Park, New Haven, CT 06511, United States; IDEAYA Biosciences Inc., 7000 Shoreline Court, Suite 350, South San Francisco, CA 94080, United States
| | - Joseph Audie
- CMDBioscience Inc., 5 Science Park, New Haven, CT 06511, United States; Chemistry Department, Sacred Heart University, 5151 Park Avenue, Fairfield, CT 06825, United States
| | - David J Diller
- CMDBioscience Inc., 5 Science Park, New Haven, CT 06511, United States.
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75
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Yang X, Chen G, Weng NP, Mariuzza RA. Structural basis for clonal diversity of the human T-cell response to a dominant influenza virus epitope. J Biol Chem 2017; 292:18618-18627. [PMID: 28931605 DOI: 10.1074/jbc.m117.810382] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/08/2017] [Indexed: 12/20/2022] Open
Abstract
Influenza A virus (IAV) causes an acute infection in humans that is normally eliminated by CD8+ cytotoxic T lymphocytes. Individuals expressing the MHC class I molecule HLA-A2 produce cytotoxic T lymphocytes bearing T-cell receptors (TCRs) that recognize the immunodominant IAV epitope GILGFVFTL (GIL). Most GIL-specific TCRs utilize α/β chain pairs encoded by the TRAV27/TRBV19 gene combination to recognize this relatively featureless peptide epitope (canonical TCRs). However, ∼40% of GIL-specific TCRs express a wide variety of other TRAV/TRBV combinations (non-canonical TCRs). To investigate the structural underpinnings of this remarkable diversity, we determined the crystal structure of a non-canonical GIL-specific TCR (F50) expressing the TRAV13-1/TRBV27 gene combination bound to GIL-HLA-A2 to 1.7 Å resolution. Comparison of the F50-GIL-HLA-A2 complex with the previously published complex formed by a canonical TCR (JM22) revealed that F50 and JM22 engage GIL-HLA-A2 in markedly different orientations. These orientations are distinguished by crossing angles of TCR to peptide-MHC of 29° for F50 versus 69° for JM22 and by a focus by F50 on the C terminus rather than the center of the MHC α1 helix for JM22. In addition, F50, unlike JM22, uses a tryptophan instead of an arginine to fill a critical notch between GIL and the HLA-A2 α2 helix. The F50-GIL-HLA-A2 complex shows that there are multiple structurally distinct solutions to recognizing an identical peptide-MHC ligand with sufficient affinity to elicit a broad anti-IAV response that protects against viral escape and T-cell clonal loss.
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Affiliation(s)
- Xinbo Yang
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850.,the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, and
| | - Guobing Chen
- the Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - Nan-Ping Weng
- the Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - Roy A Mariuzza
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850, .,the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, and
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76
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Bassani-Sternberg M, Chong C, Guillaume P, Solleder M, Pak H, Gannon PO, Kandalaft LE, Coukos G, Gfeller D. Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity. PLoS Comput Biol 2017; 13:e1005725. [PMID: 28832583 PMCID: PMC5584980 DOI: 10.1371/journal.pcbi.1005725] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 09/05/2017] [Accepted: 08/17/2017] [Indexed: 01/01/2023] Open
Abstract
The precise identification of Human Leukocyte Antigen class I (HLA-I) binding motifs plays a central role in our ability to understand and predict (neo-)antigen presentation in infectious diseases and cancer. Here, by exploiting co-occurrence of HLA-I alleles across ten newly generated as well as forty public HLA peptidomics datasets comprising more than 115,000 unique peptides, we show that we can rapidly and accurately identify many HLA-I binding motifs and map them to their corresponding alleles without any a priori knowledge of HLA-I binding specificity. Our approach recapitulates and refines known motifs for 43 of the most frequent alleles, uncovers new motifs for 9 alleles that up to now had less than five known ligands and provides a scalable framework to incorporate additional HLA peptidomics studies in the future. The refined motifs improve neo-antigen and cancer testis antigen predictions, indicating that unbiased HLA peptidomics data are ideal for in silico predictions of neo-antigens from tumor exome sequencing data. The new motifs further reveal distant modulation of the binding specificity at P2 for some HLA-I alleles by residues in the HLA-I binding site but outside of the B-pocket and we unravel the underlying mechanisms by protein structure analysis, mutagenesis and in vitro binding assays. Predicting the differences between cancer and normal cells that are visible to the immune system is of central importance for cancer immunotherapy. Here we introduce a novel computational framework to harness the wealth of data from in-depth HLA peptidomics studies, including ten novel high quality (<1% FDR) datasets generated for this work, to improve predictions of peptides displayed on HLA-I molecules. These high-throughput and unbiased data enable us to refine models of HLA-I binding specificity for many alleles (including some that had no ligand until this study) and improve predictions of neo-antigens from exome sequencing data in melanoma and lung cancer samples. Moreover, the refined description of HLA-I binding specificity reveals cases of allosteric modulation of HLA-I binding specificity at the second amino acid position (P2) of their ligands by residues that are part of the HLA-I binding site but outside of the B pocket.
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Affiliation(s)
- Michal Bassani-Sternberg
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
- * E-mail: (DG); (MBS)
| | - Chloé Chong
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Philippe Guillaume
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Marthe Solleder
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - HuiSong Pak
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Philippe O. Gannon
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Lana E. Kandalaft
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - David Gfeller
- Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland
- Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- * E-mail: (DG); (MBS)
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77
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Merkle PS, Irving M, Hongjian S, Ferber M, Jørgensen TJD, Scholten K, Luescher I, Coukos G, Zoete V, Cuendet MA, Michielin O, Rand KD. The T-Cell Receptor Can Bind to the Peptide-Bound Major Histocompatibility Complex and Uncomplexed β2-Microglobulin through Distinct Binding Sites. Biochemistry 2017; 56:3945-3961. [DOI: 10.1021/acs.biochem.7b00385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Patrick S. Merkle
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Melita Irving
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - Song Hongjian
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mathias Ferber
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Kirsten Scholten
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - Immanuel Luescher
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - George Coukos
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Michel A. Cuendet
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Department
of Physiology and Biophysics, Weill Cornell Medical College, 1300
York Avenue, New York, New
York 10065, United States
| | - Olivier Michielin
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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78
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Schmidt J, Guillaume P, Dojcinovic D, Karbach J, Coukos G, Luescher I. In silico and cell-based analyses reveal strong divergence between prediction and observation of T-cell-recognized tumor antigen T-cell epitopes. J Biol Chem 2017; 292:11840-11849. [PMID: 28536262 DOI: 10.1074/jbc.m117.789511] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/11/2017] [Indexed: 11/06/2022] Open
Abstract
Tumor exomes provide comprehensive information on mutated, overexpressed genes and aberrant splicing, which can be exploited for personalized cancer immunotherapy. Of particular interest are mutated tumor antigen T-cell epitopes, because neoepitope-specific T cells often are tumoricidal. However, identifying tumor-specific T-cell epitopes is a major challenge. A widely used strategy relies on initial prediction of human leukocyte antigen-binding peptides by in silico algorithms, but the predictive power of this approach is unclear. Here, we used the human tumor antigen NY-ESO-1 (ESO) and the human leukocyte antigen variant HLA-A*0201 (A2) as a model and predicted in silico the 41 highest-affinity, A2-binding 8-11-mer peptides and assessed their binding, kinetic complex stability, and immunogenicity in A2-transgenic mice and on peripheral blood mononuclear cells from ESO-vaccinated melanoma patients. We found that 19 of the peptides strongly bound to A2, 10 of which formed stable A2-peptide complexes and induced CD8+ T cells in A2-transgenic mice. However, only 5 of the peptides induced cognate T cells in humans; these peptides exhibited strong binding and complex stability and contained multiple large hydrophobic and aromatic amino acids. These results were not predicted by in silico algorithms and provide new clues to improving T-cell epitope identification. In conclusion, our findings indicate that only a small fraction of in silico-predicted A2-binding ESO peptides are immunogenic in humans, namely those that have high peptide-binding strength and complex stability. This observation highlights the need for improving in silico predictions of peptide immunogenicity.
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Affiliation(s)
- Julien Schmidt
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | - Danijel Dojcinovic
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | | | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland; Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Immanuel Luescher
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland.
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79
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Preparation of peptide-MHC and T-cell receptor dextramers by biotinylated dextran doping. Biotechniques 2017; 62:123-130. [PMID: 28298179 DOI: 10.2144/000114525] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/25/2017] [Indexed: 11/23/2022] Open
Abstract
Peptide-major histocompatibility complex (pMHC) multimers enable the detection, characterization, and isolation of antigen-specific T-cell subsets at the single-cell level via flow cytometry and fluorescence microscopy. These labeling reagents exploit a multivalent scaffold to increase the avidity of individually weak T-cell receptor (TCR)-pMHC interactions. Dextramers are an improvement over the original streptavidin-based tetramer technology because they are more multivalent, improving sensitivity for rare, low-avidity T cells, including self/tumor-reactive clones. However, commercial pMHC dextramers are expensive, and in-house production is very involved for a typical biology research laboratory. Here, we present a simple, inexpensive protocol for preparing pMHC dextramers by doping in biotinylated dextran during conventional tetramer preparation. We use these pMHC dextramers to identify patient-derived, tumor-reactive T cells. We apply the same dextran doping technique to prepare TCR dextramers and use these novel reagents to yield new insight into MHC I-mediated antigen presentation.
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80
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Borrman T, Cimons J, Cosiano M, Purcaro M, Pierce BG, Baker BM, Weng Z. ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes. Proteins 2017; 85:908-916. [PMID: 28160322 DOI: 10.1002/prot.25260] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/17/2017] [Accepted: 01/23/2017] [Indexed: 11/07/2022]
Abstract
The ATLAS (Altered TCR Ligand Affinities and Structures) database (https://zlab.umassmed.edu/atlas/web/) is a manually curated repository containing the binding affinities for wild-type and mutant T cell receptors (TCRs) and their antigens, peptides presented by the major histocompatibility complex (pMHC). The database links experimentally measured binding affinities with the corresponding three dimensional (3D) structures for TCR-pMHC complexes. The user can browse and search affinities, structures, and experimental details for TCRs, peptides, and MHCs of interest. We expect this database to facilitate the development of next-generation protein design algorithms targeting TCR-pMHC interactions. ATLAS can be easily parsed using modeling software that builds protein structures for training and testing. As an example, we provide structural models for all mutant TCRs in ATLAS, built using the Rosetta program. Utilizing these structures, we report a correlation of 0.63 between experimentally measured changes in binding energies and our predicted changes. Proteins 2017; 85:908-916. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605
| | - Jennifer Cimons
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, 46556
| | - Michael Cosiano
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, 46556
| | - Michael Purcaro
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, 20850
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, 46556
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605
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81
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Hoffmann T, Marion A, Antes I. DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles. BMC STRUCTURAL BIOLOGY 2017; 17:2. [PMID: 28148269 PMCID: PMC5289058 DOI: 10.1186/s12900-016-0071-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 12/29/2016] [Indexed: 11/22/2022]
Abstract
Background T cell receptor (TCR) molecules are involved in the adaptive immune response as they distinguish between self- and foreign-peptides, presented in major histocompatibility complex molecules (pMHC). Former studies showed that the association angles of the TCR variable domains (Vα/Vβ) can differ significantly and change upon binding to the pMHC complex. These changes can be described as a rotation of the domains around a general Center of Rotation, characterized by the interaction of two highly conserved glutamine residues. Methods We developed a computational method, DynaDom, for the prediction of TCR Vα/Vβ inter-domain and TCR/pMHC orientations in TCRpMHC complexes, which allows predicting the orientation of multiple protein-domains. In addition, we implemented a new approach to predict the correct orientation of the carboxamide endgroups in glutamine and asparagine residues, which can also be used as an external, independent tool. Results The approach was evaluated for the remodeling of 75 and 53 experimental structures of TCR and TCRpMHC (class I) complexes, respectively. We show that the DynaDom method predicts the correct orientation of the TCR Vα/Vβ angles in 96 and 89% of the cases, for the poses with the best RMSD and best interaction energy, respectively. For the concurrent prediction of the TCR Vα/Vβ and pMHC orientations, the respective rates reached 74 and 72%. Through an exhaustive analysis, we could show that the pMHC placement can be further improved by a straightforward, yet very time intensive extension of the current approach. Conclusions The results obtained in the present remodeling study prove the suitability of our approach for interdomain-angle optimization. In addition, the high prediction rate obtained specifically for the energetically highest ranked poses further demonstrates that our method is a powerful candidate for blind prediction. Therefore it should be well suited as part of any accurate atomistic modeling pipeline for TCRpMHC complexes and potentially other large molecular assemblies. Electronic supplementary material The online version of this article (doi:10.1186/s12900-016-0071-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Hoffmann
- Department of Biosciences and Center for Integrated Protein Science Munich, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany
| | - Antoine Marion
- Department of Biosciences and Center for Integrated Protein Science Munich, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany
| | - Iris Antes
- Department of Biosciences and Center for Integrated Protein Science Munich, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany.
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82
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Maus MV, Plotkin J, Jakka G, Stewart-Jones G, Rivière I, Merghoub T, Wolchok J, Renner C, Sadelain M. An MHC-restricted antibody-based chimeric antigen receptor requires TCR-like affinity to maintain antigen specificity. MOLECULAR THERAPY-ONCOLYTICS 2017; 3:1-9. [PMID: 29675462 PMCID: PMC5904357 DOI: 10.1038/mto.2016.23] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/23/2016] [Indexed: 01/09/2023]
Abstract
Chimeric antigen receptors (CARs) are synthetic receptors that usually redirect T cells to surface antigens independent of human leukocyte antigen (HLA). Here, we investigated a T cell receptor-like CAR based on an antibody that recognizes HLA-A*0201 presenting a peptide epitope derived from the cancer-testis antigen NY-ESO-1. We hypothesized that this CAR would efficiently redirect transduced T cells in an HLA-restricted, antigen-specific manner. However, we found that despite the specificity of the soluble Fab, the same antibody in the form of a CAR caused moderate lysis of HLA-A2 expressing targets independent of antigen owing to T cell avidity. We hypothesized that lowering the affinity of the CAR for HLA-A2 would improve its specificity. We undertook a rational approach of mutating residues that, in the crystal structure, were predicted to stabilize binding to HLA-A2. We found that one mutation (DN) lowered the affinity of the Fab to T cell receptor-range and restored the epitope specificity of the CAR. DN CAR T cells lysed native tumor targets in vitro, and, in a xenogeneic mouse model implanted with two human melanoma lines (A2+/NYESO+ and A2+/NYESO−), DN CAR T cells specifically migrated to, and delayed progression of, only the HLA-A2+/NY-ESO-1+ melanoma. Thus, although maintaining MHC-restricted antigen specificity required T cell receptor-like affinity that decreased potency, there is exciting potential for CARs to expand their repertoire to include a broad range of intracellular antigens.
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Affiliation(s)
- Marcela V Maus
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jason Plotkin
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gopinadh Jakka
- Department of Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Guillaume Stewart-Jones
- Division of Structural Biology, Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Isabelle Rivière
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Taha Merghoub
- Ludwig Center for Cancer Immunotherapy, Swim Across America Laboratory, MSKCC, New York, New York, USA
| | - Jedd Wolchok
- Ludwig Center for Cancer Immunotherapy, Swim Across America Laboratory, MSKCC, New York, New York, USA
| | - Christoph Renner
- Department of Oncology, University Hospital Zurich, Zurich, Switzerland.,Department of Oncology, University Hospital Basel, Basel, Switzerland
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill-Cornell Medical College, New York, New York, USA
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83
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Ren J, Liu X, Fang C, Jiang S, June CH, Zhao Y. Multiplex Genome Editing to Generate Universal CAR T Cells Resistant to PD1 Inhibition. Clin Cancer Res 2016; 23:2255-2266. [PMID: 27815355 DOI: 10.1158/1078-0432.ccr-16-1300] [Citation(s) in RCA: 648] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/27/2016] [Accepted: 10/23/2016] [Indexed: 11/16/2022]
Abstract
Purpose: Using gene-disrupted allogeneic T cells as universal effector cells provides an alternative and potentially improves current chimeric antigen receptor (CAR) T-cell therapy against cancers and infectious diseases.Experimental Design: The CRISPR/Cas9 system has recently emerged as a simple and efficient way for multiplex genome engineering. By combining lentiviral delivery of CAR and electro-transfer of Cas9 mRNA and gRNAs targeting endogenous TCR, β-2 microglobulin (B2M) and PD1 simultaneously, to generate gene-disrupted allogeneic CAR T cells deficient of TCR, HLA class I molecule and PD1.Results: The CRISPR gene-edited CAR T cells showed potent antitumor activities, both in vitro and in animal models and were as potent as non-gene-edited CAR T cells. In addition, the TCR and HLA class I double deficient T cells had reduced alloreactivity and did not cause graft-versus-host disease. Finally, simultaneous triple genome editing by adding the disruption of PD1 led to enhanced in vivo antitumor activity of the gene-disrupted CAR T cells.Conclusions: Gene-disrupted allogeneic CAR and TCR T cells could provide an alternative as a universal donor to autologous T cells, which carry difficulties and high production costs. Gene-disrupted CAR and TCR T cells with disabled checkpoint molecules may be potent effector cells against cancers and infectious diseases. Clin Cancer Res; 23(9); 2255-66. ©2016 AACR.
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Affiliation(s)
- Jiangtao Ren
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xiaojun Liu
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Chongyun Fang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Shuguang Jiang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Carl H June
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yangbing Zhao
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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84
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Zhang H, Lim HS, Knapp B, Deane CM, Aleksic M, Dushek O, van der Merwe PA. The contribution of major histocompatibility complex contacts to the affinity and kinetics of T cell receptor binding. Sci Rep 2016; 6:35326. [PMID: 27734930 PMCID: PMC5062128 DOI: 10.1038/srep35326] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/28/2016] [Indexed: 11/09/2022] Open
Abstract
The interaction between the T cell antigen receptor (TCR) and antigenic peptide in complex with major histocompatibility complex (MHC) molecules is a crucial step in T cell activation. The relative contributions of TCR:peptide and TCR:MHC contacts to the overall binding energy remain unclear. This has important implications for our understanding of T cell development and function. In this study we used site directed mutagenesis to estimate the contribution of HLA-A2 side-chains to the binding of four TCRs. Our results show that these TCRs have very different energetic ‘footprints’ on HLA-A2, with no residues contributing to all TCR interactions. The estimated overall contribution of MHC side-chains to the total interaction energy was variable, with lower limits ranging from 11% to 50%. Kinetic analysis suggested a minor and variable contribution of MHC side-chains to the transition state complex, arguing against a two-step mechanism for TCR binding.
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Affiliation(s)
- Hao Zhang
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Hong-Sheng Lim
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Berhard Knapp
- Department of Statistics, University of Oxford, United Kingdom
| | | | - Milos Aleksic
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
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85
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Toughiri R, Wu X, Ruiz D, Huang F, Crissman JW, Dickey M, Froning K, Conner EM, Cujec TP, Demarest SJ. Comparing domain interactions within antibody Fabs with kappa and lambda light chains. MAbs 2016; 8:1276-1285. [PMID: 27454112 PMCID: PMC5058631 DOI: 10.1080/19420862.2016.1214785] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
IgG antibodies are multi-domain proteins with complex inter-domain interactions. Human IgG heavy chains (HCs) associate with light chains (LCs) of the κ or λ isotype to form mature antibodies capable of binding antigen. The HC/LC interaction involves 4 domains: VH and CH1 from the HC and VL and CL from the LC. Human Fabs with κ LCs have been well characterized for their unfolding behaviors and demonstrate a significant level of cooperativity and stabilization when all 4 domains are intact. Very little is known regarding the thermodynamic properties of human Fabs with λ LCs. Here, we dissect the domain contributions to Fab stability for both κ and λ LC-containing Fabs. We find the cooperativity of unfolding between the constant domains, CH1/Cλ, and variable domains, VH/Vλ, within λ LC-containing Fabs is significantly weaker than that of κ LC-containing Fabs. The data suggests there may not be an evolutionary necessity for strong variable/constant domain cooperativity within λ LC-containing Fabs. After investigating the biophysical properties of Fabs with mismatched variable and constant domain subunits (e.g., VH/Vκ paired with CH1/Cλ or T cell receptor Cα/Cβ), the major role of the constant domains for both κ- and λ-containing Fabs may be to reduce the hydrophobic exposure at the VH/VL interface. Even though Fabs with these non-native pairings were thermodynamically less stable, they secreted well from mammalian cells as well behaved monodisperse proteins, which was in contrast to what was observed with the VH/Vκ and VH/Vλ scFvs that secreted as a mixture of monomer and aggregates.
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Affiliation(s)
- Raheleh Toughiri
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Xiufeng Wu
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Diana Ruiz
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Flora Huang
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - John W Crissman
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Mark Dickey
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Karen Froning
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Elaine M Conner
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Thomas P Cujec
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Stephen J Demarest
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
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86
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Aberrant Glycosylation of Anchor-Optimized MUC1 Peptides Can Enhance Antigen Binding Affinity and Reverse Tolerance to Cytotoxic T Lymphocytes. Biomolecules 2016; 6:biom6030031. [PMID: 27367740 PMCID: PMC5039417 DOI: 10.3390/biom6030031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 06/07/2016] [Accepted: 06/07/2016] [Indexed: 12/22/2022] Open
Abstract
Cancer vaccines have often failed to live up to their promise, although recent results with checkpoint inhibitors are reviving hopes that they will soon fulfill their promise. Although mutation-specific vaccines are under development, there is still high interest in an off-the-shelf vaccine to a ubiquitous antigen, such as MUC1, which is aberrantly expressed on most solid and many hematological tumors, including more than 90% of breast carcinomas. Clinical trials for MUC1 have shown variable success, likely because of immunological tolerance to a self-antigen and to poor immunogenicity of tandem repeat peptides. We hypothesized that MUC1 peptides could be optimized, relying on heteroclitic optimizations of potential anchor amino acids with and without tumor-specific glycosylation of the peptides. We have identified novel MUC1 class I peptides that bind to HLA-A*0201 molecules with significantly higher affinity and function than the native MUC1 peptides. These peptides elicited CTLs from normal donors, as well as breast cancer patients, which were highly effective in killing MUC1-expressing MCF-7 breast cancer cells. Each peptide elicited lytic responses in greater than 6/8 of normal individuals and 3/3 breast cancer patients. The CTLs generated against the glycosylated-anchor modified peptides cross reacted with the native MUC1 peptide, STAPPVHNV, suggesting these analog peptides may offer substantial improvement in the design of epitope-based vaccines.
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87
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Bianchi V, Bulek A, Fuller A, Lloyd A, Attaf M, Rizkallah PJ, Dolton G, Sewell AK, Cole DK. A Molecular Switch Abrogates Glycoprotein 100 (gp100) T-cell Receptor (TCR) Targeting of a Human Melanoma Antigen. J Biol Chem 2016; 291:8951-9. [PMID: 26917722 PMCID: PMC4861463 DOI: 10.1074/jbc.m115.707414] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/09/2016] [Indexed: 11/06/2022] Open
Abstract
Human CD8(+) cytotoxic T lymphocytes can mediate tumor regression in melanoma through the specific recognition of HLA-restricted peptides. Because of the relatively weak affinity of most anti-cancer T-cell receptors (TCRs), there is growing emphasis on immunizing melanoma patients with altered peptide ligands in order to induce strong anti-tumor immunity capable of breaking tolerance toward these self-antigens. However, previous studies have shown that these immunogenic designer peptides are not always effective. The melanocyte differentiation protein, glycoprotein 100 (gp100), encodes a naturally processed epitope that is an attractive target for melanoma immunotherapies, in particular peptide-based vaccines. Previous studies have shown that substitutions at peptide residue Glu(3) have a broad negative impact on polyclonal T-cell responses. Here, we describe the first atomic structure of a natural cognate TCR in complex with this gp100 epitope and highlight the relatively high affinity of the interaction. Alanine scan mutagenesis performed across the gp100(280-288) peptide showed that Glu(3) was critically important for TCR binding. Unexpectedly, structural analysis demonstrated that the Glu(3) → Ala substitution resulted in a molecular switch that was transmitted to adjacent residues, abrogating TCR binding and T-cell recognition. These findings help to clarify the mechanism of T-cell recognition of gp100 during melanoma responses and could direct the development of altered peptides for vaccination.
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Affiliation(s)
- Valentina Bianchi
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Anna Bulek
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Anna Fuller
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Angharad Lloyd
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Meriem Attaf
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Pierre J Rizkallah
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Garry Dolton
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Andrew K Sewell
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - David K Cole
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
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88
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Bello M, Correa-Basurto J. Energetic and flexibility properties captured by long molecular dynamics simulations of a membrane-embedded pMHCII-TCR complex. MOLECULAR BIOSYSTEMS 2016; 12:1350-66. [PMID: 26926952 DOI: 10.1039/c6mb00058d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although crystallographic data have provided important molecular insight into the interactions in the pMHC-TCR complex, the inherent features of this structural approach cause it to only provide a static picture of the interactions. While unbiased molecular dynamics simulations (UMDSs) have provided important information about the dynamic structural behavior of the pMHC-TCR complex, most of them have modeled the pMHC-TCR complex as soluble, when in physiological conditions, this complex is membrane bound; therefore, following this latter UMDS protocol might hamper important dynamic results. In this contribution, we performed three independent 300 ns-long UMDSs of the pMHCII-TCR complex anchored in two opposing membranes to explore the structural and energetic properties of the recognition of pMHCII by the TCR. The conformational ensemble generated through UMDSs was subjected to clustering and Cartesian principal component analyses (cPCA) to explore the dynamical behavior of the pMHCII-TCR association. Furthermore, based on the conformational population sampled through UMDSs, the effective binding free energy, per-residue free energy decomposition, and alanine scanning mutations were explored for the native pMHCII-TCR complex, as well as for 12 mutations (p1-p12MHCII-TCR) introduced in the native peptide. Clustering analyses and cPCA provide insight into the rocking motion of the TCR onto pMHCII, together with the presence of new electrostatic interactions not observed through crystallographic methods. Energetic results provide evidence of the main contributors to the pMHC-TCR complex formation as well as the key residues involved in this molecular recognition process.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico City, CP: 11340, Mexico.
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89
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How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire. Proc Natl Acad Sci U S A 2016; 113:E1276-85. [PMID: 26884163 DOI: 10.1073/pnas.1522069113] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining αβ TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged "hot-spot" region that is almost exclusive to the α1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Vα and Vβ genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs.
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90
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Abstract
T-cell receptor (TCR) binding to peptide/MHC determines specificity and initiates signaling in antigen-specific cellular immune responses. Structures of TCR-pMHC complexes have provided enormous insight to cellular immune functions, permitted a rational understanding of processes such as pathogen escape, and led to the development of novel approaches for the design of vaccines and other therapeutics. As production, crystallization, and structure determination of TCR-pMHC complexes can be challenging, there is considerable interest in modeling new complexes. Here we describe a rapid approach to TCR-pMHC modeling that takes advantage of structural features conserved in known complexes, such as the restricted TCR binding site and the generally conserved diagonal docking mode. The approach relies on the powerful Rosetta suite and is implemented using the PyRosetta scripting environment. We show how the approach can recapitulate changes in TCR binding angles and other structural details, and highlight areas where careful evaluation of parameters is needed and alternative choices might be made. As TCRs are highly sensitive to subtle structural perturbations, there is room for improvement. Our method nonetheless generates high-quality models that can be foundational for structure-based hypotheses regarding TCR recognition.
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Affiliation(s)
- Timothy P Riley
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556, USA
- Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556, USA
| | - Nishant K Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556, USA
- Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556, USA
| | - Brian G Pierce
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556, USA.
- Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556, USA.
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91
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Hofmann S, Mead A, Malinovskis A, Hardwick NR, Guinn BA. Analogue peptides for the immunotherapy of human acute myeloid leukemia. Cancer Immunol Immunother 2015; 64:1357-67. [PMID: 26438084 PMCID: PMC11029593 DOI: 10.1007/s00262-015-1762-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 09/27/2015] [Indexed: 12/14/2022]
Abstract
The use of peptide vaccines, enhanced by adjuvants, has shown some efficacy in clinical trials. However, responses are often short-lived and rarely induce notable memory responses. The reason is that self-antigens have already been presented to the immune system as the tumor develops, leading to tolerance or some degree of host tumor cell destruction. To try to break tolerance against self-antigens, one of the methods employed has been to modify peptides at the anchor residues to enhance their ability to bind major histocompatibility complex molecules, extending their exposure to the T-cell receptor. These modified or analogue peptides have been investigated as stimulators of the immune system in patients with different cancers with variable but sometimes notable success. In this review we describe the background and recent developments in the use of analogue peptides for the immunotherapy of acute myeloid leukemia describing knowledge useful for the application of analogue peptide treatments for other malignancies.
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Affiliation(s)
- Susanne Hofmann
- Third Clinic for Internal Medicine, University of Ulm, Ulm, Germany
| | - Andrew Mead
- Department of Life Sciences, University of Bedfordshire, Park Square, Luton, LU1 3JU, UK
| | - Aleksandrs Malinovskis
- Department of Life Sciences, University of Bedfordshire, Park Square, Luton, LU1 3JU, UK
| | - Nicola R Hardwick
- Division of Translational Vaccine Research, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
- Department of Haematological Medicine, Guy's, King's & St. Thomas' School of Medicine, The Rayne Institute, King's College London, 123 Coldharbour Lane, London, UK
| | - Barbara-Ann Guinn
- Department of Life Sciences, University of Bedfordshire, Park Square, Luton, LU1 3JU, UK.
- Department of Haematological Medicine, Guy's, King's & St. Thomas' School of Medicine, The Rayne Institute, King's College London, 123 Coldharbour Lane, London, UK.
- Cancer Sciences Unit, Southampton University Hospitals Trust, University of Southampton, Southampton, UK.
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92
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Motozono C, Pearson JA, De Leenheer E, Rizkallah PJ, Beck K, Trimby A, Sewell AK, Wong FS, Cole DK. Distortion of the Major Histocompatibility Complex Class I Binding Groove to Accommodate an Insulin-derived 10-Mer Peptide. J Biol Chem 2015; 290:18924-33. [PMID: 26085090 PMCID: PMC4521012 DOI: 10.1074/jbc.m114.622522] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 06/12/2015] [Indexed: 01/23/2023] Open
Abstract
The non-obese diabetic mouse model of type 1 diabetes continues to be an important tool for delineating the role of T-cell-mediated destruction of pancreatic β-cells. However, little is known about the molecular mechanisms that enable this disease pathway. We show that insulin reactivity by a CD8(+) T-cell clone, known to induce type 1 diabetes, is characterized by weak T-cell antigen receptor binding to a relatively unstable peptide-MHC. The structure of the native 9- and 10-mer insulin epitopes demonstrated that peptide residues 7 and 8 form a prominent solvent-exposed bulge that could potentially be the main focus of T-cell receptor binding. The C terminus of the peptide governed peptide-MHC stability. Unexpectedly, we further demonstrate a novel mode of flexible peptide presentation in which the MHC peptide-binding groove is able to "open the back door" to accommodate extra C-terminal peptide residues.
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Affiliation(s)
- Chihiro Motozono
- From the Division of Infection and Immunity and the Department of Immunology, Kinki University School of Medicine, Osaka 589-8511, Japan, and
| | - James A Pearson
- the Institute of Molecular and Experimental Medicine, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Evy De Leenheer
- the Institute of Molecular and Experimental Medicine, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | | | - Konrad Beck
- the Cardiff University School of Dentistry, Heath Park, Cardiff CF14 4XY, United Kingdom
| | | | | | - F Susan Wong
- the Institute of Molecular and Experimental Medicine, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom,
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93
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Hoffmann T, Krackhardt AM, Antes I. Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition. PLoS Comput Biol 2015; 11:e1004244. [PMID: 26185983 PMCID: PMC4505886 DOI: 10.1371/journal.pcbi.1004244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/17/2015] [Indexed: 02/01/2023] Open
Abstract
T-cell receptors (TCR) play an important role in the adaptive immune system as they recognize pathogen- or cancer-based epitopes and thus initiate the cell-mediated immune response. Therefore there exists a growing interest in the optimization of TCRs for medical purposes like adoptive T-cell therapy. However, the molecular mechanisms behind T-cell signaling are still predominantly unknown. For small sets of TCRs it was observed that the angle between their Vα- and Vβ-domains, which bind the epitope, can vary and might be important for epitope recognition. Here we present a comprehensive, quantitative study of the variation in the Vα/Vβ interdomain-angle and its influence on epitope recognition, performing a systematic bioinformatics analysis based on a representative set of experimental TCR structures. For this purpose we developed a new, cuboid-based superpositioning method, which allows a unique, quantitative analysis of the Vα/Vβ-angles. Angle-based clustering led to six significantly different clusters. Analysis of these clusters revealed the unexpected result that the angle is predominantly influenced by the TCR-clonotype, whereas the bound epitope has only a minor influence. Furthermore we could identify a previously unknown center of rotation (CoR), which is shared by all TCRs. All TCR geometries can be obtained by rotation around this center, rendering it a new, common TCR feature with the potential of improving the accuracy of TCR structure prediction considerably. The importance of Vα/Vβ rotation for signaling was confirmed as we observed larger variances in the Vα/Vβ-angles in unbound TCRs compared to epitope-bound TCRs. Our results strongly support a two-step mechanism for TCR-epitope: First, preformation of a flexible TCR geometry in the unbound state and second, locking of the Vα/Vβ-angle in a TCR-type specific geometry upon epitope-MHC association, the latter being driven by rotation around the unique center of rotation. The recognition of antigenic peptides by cytotoxic T-cells is one of the crucial steps during the adaptive immune response. Thus a detailed understanding of this process is not only important for elucidating the mechanism behind T-cell signaling, but also for various emerging new medical applications like T-cell based immunotherapies and designed bio-therapeutics. However, despite the fast growing interest in this field, the mechanistic basis of the immune response is still largely unknown. Previous qualitative studies suggested that the T-cell receptor (TCR) Vα/Vβ-interdomain angle plays a crucial role in epitope recognition as it predetermines the relative position of its antigen-recognizing CDR1-3 loops and thus TCR specificity. In the manuscript we present a systematic bioinformatic analysis of the structural characteristics of bound and unbound TCR molecules focusing on the Vα/Vβ-angle. Our results demonstrate the importance of this angle for signaling, as several distinct Vα/Vβ-angle based structural clusters could be observed and larger angle flexibilities exist for unbound TCRs than for bound TCRs, providing quantitative proof for a two-step locking mechanism upon epitope recognition. In this context, we could identify a unique rotational point, which allows a quantitative, yet intuitive description of all observed angle variations and the structural changes upon epitope binding.
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MESH Headings
- Binding Sites
- Computer Simulation
- Epitope Mapping/methods
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/ultrastructure
- Models, Chemical
- Models, Immunological
- Models, Molecular
- Protein Binding
- Protein Conformation
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/ultrastructure
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Affiliation(s)
- Thomas Hoffmann
- Department of Biosciences and Center for Integrated Protein Science Munich,Technische Universität München, Freising-Weihenstephan, Germany
| | - Angela M. Krackhardt
- Medizinische Klinik III, Innere Medizin mit Schwerpunkt Hämatologie und Onkologie, Technische Universität München, Munich, Germany
- Clinical Cooperation Group, Antigen specific T cell therapy, Helmholtz Zentrum München (GmbH), German Center for Environmental Health, Munich, Germany
- German Cancer Consortium (DKTK), Munich, Germany
| | - Iris Antes
- Department of Biosciences and Center for Integrated Protein Science Munich,Technische Universität München, Freising-Weihenstephan, Germany
- * E-mail:
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94
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Obenaus M, Leitão C, Leisegang M, Chen X, Gavvovidis I, van der Bruggen P, Uckert W, Schendel DJ, Blankenstein T. Identification of human T-cell receptors with optimal affinity to cancer antigens using antigen-negative humanized mice. Nat Biotechnol 2015; 33:402-7. [PMID: 25774714 DOI: 10.1038/nbt.3147] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/12/2015] [Indexed: 12/21/2022]
Abstract
Identifying T-cell receptors (TCRs) that bind tumor-associated antigens (TAAs) with optimal affinity is a key bottleneck in the development of adoptive T-cell therapy of cancer. TAAs are unmutated self proteins, and T cells bearing high-affinity TCRs specific for such antigens are commonly deleted in the thymus. To identify optimal-affinity TCRs, we generated antigen-negative humanized mice with a diverse human TCR repertoire restricted to the human leukocyte antigen (HLA) A*02:01 (ref. 3). These mice were immunized with human TAAs, for which they are not tolerant, allowing induction of CD8⁺ T cells with optimal-affinity TCRs. We isolate TCRs specific for the cancer/testis (CT) antigen MAGE-A1 (ref. 4) and show that two of them have an anti-tumor effect in vivo. By comparison, human-derived TCRs have lower affinity and do not mediate substantial therapeutic effects. We also identify optimal-affinity TCRs specific for the CT antigen NY-ESO. Our humanized mouse model provides a useful tool for the generation of optimal-affinity TCRs for T-cell therapy.
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Affiliation(s)
| | | | | | - Xiaojing Chen
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | | | - Pierre van der Bruggen
- 1] Ludwig Institute for Cancer Research and WELBIO, Brussels, Belgium. [2] De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Wolfgang Uckert
- 1] Max-Delbrück-Center for Molecular Medicine, Berlin, Germany. [2] Institute of Biology, Humboldt University, Berlin, Germany
| | | | - Thomas Blankenstein
- 1] Max-Delbrück-Center for Molecular Medicine, Berlin, Germany. [2] Institute of Immunology, Charité Campus Buch, Berlin, Germany
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95
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Madura F, Rizkallah PJ, Holland CJ, Fuller A, Bulek A, Godkin AJ, Schauenburg AJ, Cole DK, Sewell AK. Structural basis for ineffective T-cell responses to MHC anchor residue-improved "heteroclitic" peptides. Eur J Immunol 2015; 45:584-91. [PMID: 25471691 PMCID: PMC4357396 DOI: 10.1002/eji.201445114] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 10/03/2014] [Accepted: 11/26/2014] [Indexed: 12/11/2022]
Abstract
MHC anchor residue-modified "heteroclitic" peptides have been used in many cancer vaccine trials and often induce greater immune responses than the wild-type peptide. The best-studied system to date is the decamer MART-1/Melan-A26-35 peptide, EAAGIGILTV, where the natural alanine at position 2 has been modified to leucine to improve human leukocyte antigen (HLA)-A*0201 anchoring. The resulting ELAGIGILTV peptide has been used in many studies. We recently showed that T cells primed with the ELAGIGILTV peptide can fail to recognize the natural tumor-expressed peptide efficiently, thereby providing a potential molecular reason for why clinical trials of this peptide have been unsuccessful. Here, we solved the structure of a TCR in complex with HLA-A*0201-EAAGIGILTV peptide and compared it with its heteroclitic counterpart , HLA-A*0201-ELAGIGILTV. The data demonstrate that a suboptimal anchor residue at position 2 enables the TCR to "pull" the peptide away from the MHC binding groove, facilitating extra contacts with both the peptide and MHC surface. These data explain how a TCR can distinguish between two epitopes that differ by only a single MHC anchor residue and demonstrate how weak MHC anchoring can enable an induced-fit interaction with the TCR. Our findings constitute a novel demonstration of the extreme sensitivity of the TCR to minor alterations in peptide conformation.
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MESH Headings
- Alanine/chemistry
- Alanine/genetics
- Amino Acid Sequence
- Amino Acid Substitution
- Crystallography, X-Ray
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/immunology
- Humans
- Leucine/chemistry
- Leucine/genetics
- MART-1 Antigen/chemistry
- MART-1 Antigen/genetics
- MART-1 Antigen/immunology
- Models, Molecular
- Molecular Sequence Data
- Peptides/chemistry
- Peptides/genetics
- Peptides/immunology
- Protein Binding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- T-Lymphocytes, Cytotoxic/cytology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
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Affiliation(s)
- Florian Madura
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Pierre J Rizkallah
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Christopher J Holland
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Anna Fuller
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Anna Bulek
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Andrew J Godkin
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Andrea J Schauenburg
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - David K Cole
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
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96
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Miles JJ, McCluskey J, Rossjohn J, Gras S. Understanding the complexity and malleability of T-cell recognition. Immunol Cell Biol 2015; 93:433-41. [PMID: 25582337 DOI: 10.1038/icb.2014.112] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/21/2014] [Accepted: 11/23/2014] [Indexed: 12/15/2022]
Abstract
T cells are the master regulators of immune system function, continually walking the biological tightrope between adequate host defence and accidental host pathology. Tolerance is maintained or broken through an intricate structural interplay between the T-cell receptor (TCR) and major histocompatibility complex (MHC) molecule cradling peptide antigens (p). Recent advances in structural biology have shown that the TCR/pMHC interface is surprising precise and extraordinarily malleable. We have seen that seemingly minor changes in the TCR/pMHC interface can abrogate function, as well as substantial conformational changes before and after TCR docking. Our understanding of T-cell biology has also been altered with the knowledge that MHC molecules can bind not only peptides, but also an array of natural and synthetic compounds. Here, we review some examples of the precision and flexibility intrinsic to the TCR/p/MHCI axis.
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Affiliation(s)
- John J Miles
- 1] QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland, Australia [2] School of Medicine, The University of Queensland, Brisbane, Queensland, Australia [3] Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Jamie Rossjohn
- 1] Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK [2] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia [3] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Stephanie Gras
- 1] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia [2] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
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97
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Rossjohn J, Gras S, Miles JJ, Turner SJ, Godfrey DI, McCluskey J. T cell antigen receptor recognition of antigen-presenting molecules. Annu Rev Immunol 2014; 33:169-200. [PMID: 25493333 DOI: 10.1146/annurev-immunol-032414-112334] [Citation(s) in RCA: 508] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Major Histocompatibility Complex (MHC) locus encodes classical MHC class I and MHC class II molecules and nonclassical MHC-I molecules. The architecture of these molecules is ideally suited to capture and present an array of peptide antigens (Ags). In addition, the CD1 family members and MR1 are MHC class I-like molecules that bind lipid-based Ags and vitamin B precursors, respectively. These Ag-bound molecules are subsequently recognized by T cell antigen receptors (TCRs) expressed on the surface of T lymphocytes. Structural and associated functional studies have been highly informative in providing insight into these interactions, which are crucial to immunity, and how they can lead to aberrant T cell reactivity. Investigators have determined over thirty unique TCR-peptide-MHC-I complex structures and twenty unique TCR-peptide-MHC-II complex structures. These investigations have shown a broad consensus in docking geometry and provided insight into MHC restriction. Structural studies on TCR-mediated recognition of lipid and metabolite Ags have been mostly confined to TCRs from innate-like natural killer T cells and mucosal-associated invariant T cells, respectively. These studies revealed clear differences between TCR-lipid-CD1, TCR-metabolite-MR1, and TCR-peptide-MHC recognition. Accordingly, TCRs show remarkable structural and biological versatility in engaging different classes of Ag that are presented by polymorphic and monomorphic Ag-presenting molecules of the immune system.
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Affiliation(s)
- Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia; ,
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98
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Understanding the structural dynamics of TCR-pMHC interactions. Trends Immunol 2014; 35:604-612. [DOI: 10.1016/j.it.2014.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/20/2014] [Accepted: 10/20/2014] [Indexed: 12/23/2022]
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99
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Abstract
αβ T-cell receptor (TCR) activation plays a crucial role for T-cell function. However, the TCR itself does not possess signaling domains. Instead, the TCR is noncovalently coupled to a conserved multisubunit signaling apparatus, the CD3 complex, that comprises the CD3εγ, CD3εδ, and CD3ζζ dimers. How antigen ligation by the TCR triggers CD3 activation and what structural role the CD3 extracellular domains (ECDs) play in the assembled TCR-CD3 complex remain unclear. Here, we use two complementary structural approaches to gain insight into the overall organization of the TCR-CD3 complex. Small-angle X-ray scattering of the soluble TCR-CD3εδ complex reveals the CD3εδ ECDs to sit underneath the TCR α-chain. The observed arrangement is consistent with EM images of the entire TCR-CD3 integral membrane complex, in which the CD3εδ and CD3εγ subunits were situated underneath the TCR α-chain and TCR β-chain, respectively. Interestingly, the TCR-CD3 transmembrane complex bound to peptide-MHC is a dimer in which two TCRs project outward from a central core composed of the CD3 ECDs and the TCR and CD3 transmembrane domains. This arrangement suggests a potential ligand-dependent dimerization mechanism for TCR signaling. Collectively, our data advance our understanding of the molecular organization of the TCR-CD3 complex, and provides a conceptual framework for the TCR activation mechanism.
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100
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Hoppes R, Oostvogels R, Luimstra JJ, Wals K, Toebes M, Bies L, Ekkebus R, Rijal P, Celie PHN, Huang JH, Emmelot ME, Spaapen RM, Lokhorst H, Schumacher TNM, Mutis T, Rodenko B, Ovaa H. Altered peptide ligands revisited: vaccine design through chemically modified HLA-A2-restricted T cell epitopes. THE JOURNAL OF IMMUNOLOGY 2014; 193:4803-13. [PMID: 25311806 DOI: 10.4049/jimmunol.1400800] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Virus or tumor Ag-derived peptides that are displayed by MHC class I molecules are attractive starting points for vaccine development because they induce strong protective and therapeutic cytotoxic T cell responses. In thus study, we show that the MHC binding and consequent T cell reactivity against several HLA-A*02 restricted epitopes can be further improved through the incorporation of nonproteogenic amino acids at primary and secondary anchor positions. We screened more than 90 nonproteogenic, synthetic amino acids through a range of epitopes and tested more than 3000 chemically enhanced altered peptide ligands (CPLs) for binding affinity to HLA-A*0201. With this approach, we designed CPLs of viral epitopes, of melanoma-associated Ags, and of the minor histocompatibility Ag UTA2-1, which is currently being evaluated for its antileukemic activity in clinical dendritic cell vaccination trials. The crystal structure of one of the CPLs in complex with HLA-A*0201 revealed the molecular interactions likely responsible for improved binding. The best CPLs displayed enhanced affinity for MHC, increasing MHC stability and prolonging recognition by Ag-specific T cells and, most importantly, they induced accelerated expansion of antitumor T cell frequencies in vitro and in vivo as compared with the native epitope. Eventually, we were able to construct a toolbox of preferred nonproteogenic residues with which practically any given HLA-A*02 restricted epitope can be readily optimized. These CPLs could improve the therapeutic outcome of vaccination strategies or can be used for ex vivo enrichment and faster expansion of Ag-specific T cells for transfer into patients.
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Affiliation(s)
- Rieuwert Hoppes
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Rimke Oostvogels
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands Department of Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Jolien J Luimstra
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Kim Wals
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Mireille Toebes
- Division of Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Laura Bies
- Division of Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Reggy Ekkebus
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Pramila Rijal
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Patrick H N Celie
- Division of Biochemistry, The Netherlands Cancer Institute Protein Facility, 1066 CX Amsterdam, the Netherlands; and
| | - Julie H Huang
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Maarten E Emmelot
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Robbert M Spaapen
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Henk Lokhorst
- Department of Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Ton N M Schumacher
- Division of Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Tuna Mutis
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Boris Rodenko
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Huib Ovaa
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
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