1
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Rosenberg AM, Ayres CM, Medina-Cucurella AV, Whitehead TA, Baker BM. Enhanced T cell receptor specificity through framework engineering. Front Immunol 2024; 15:1345368. [PMID: 38545094 PMCID: PMC10967027 DOI: 10.3389/fimmu.2024.1345368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/15/2024] [Indexed: 04/12/2024] Open
Abstract
Development of T cell receptors (TCRs) as immunotherapeutics is hindered by inherent TCR cross-reactivity. Engineering more specific TCRs has proven challenging, as unlike antibodies, improving TCR affinity does not usually improve specificity. Although various protein design approaches have been explored to surmount this, mutations in TCR binding interfaces risk broadening specificity or introducing new reactivities. Here we explored if TCR specificity could alternatively be tuned through framework mutations distant from the interface. Studying the 868 TCR specific for the HIV SL9 epitope presented by HLA-A2, we used deep mutational scanning to identify a framework mutation above the mobile CDR3β loop. This glycine to proline mutation had no discernable impact on binding affinity or functional avidity towards the SL9 epitope but weakened recognition of SL9 escape variants and led to fewer responses in a SL9-derived positional scanning library. In contrast, an interfacial mutation near the tip of CDR3α that also did not impact affinity or functional avidity towards SL9 weakened specificity. Simulations indicated that the specificity-enhancing mutation functions by reducing the range of loop motions, limiting the ability of the TCR to adjust to different ligands. Although our results are likely to be TCR dependent, using framework engineering to control TCR loop motions may be a viable strategy for improving the specificity of TCR-based immunotherapies.
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Affiliation(s)
- Aaron M. Rosenberg
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | | | - Timothy A. Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
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2
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Antunes DA, Baker BM, Cornberg M, Selin LK. Editorial: Quantification and prediction of T-cell cross-reactivity through experimental and computational methods. Front Immunol 2024; 15:1377259. [PMID: 38444853 PMCID: PMC10912571 DOI: 10.3389/fimmu.2024.1377259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Affiliation(s)
- Dinler A. Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - Markus Cornberg
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
- Centre for Individualized Infection Medicine (CiiM), c/o CRC Hannover, Hannover, Germany
- German Center for Infection Research (DZIF), Partner-site Hannover-Braunschweig, Hannover, Germany
| | - Liisa K. Selin
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, United States
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3
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Adams AC, Macy AM, Borden ES, Herrmann LM, Brambley CA, Ma T, Li X, Hughes A, Roe DJ, Mangold AR, Buetow KH, Wilson MA, Baker BM, Hastings KT. Distinct sets of molecular characteristics define tumor-rejecting neoantigens. bioRxiv 2024:2024.02.13.579546. [PMID: 38405868 PMCID: PMC10888839 DOI: 10.1101/2024.02.13.579546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Challenges in identifying tumor-rejecting neoantigens limit the efficacy of neoantigen vaccines to treat cancers, including cutaneous squamous cell carcinoma (cSCC). A minority of human cSCC tumors shared neoantigens, supporting the need for personalized vaccines. Using a UV-induced mouse cSCC model which recapitulated the mutational signature and driver mutations found in human disease, we found that CD8 T cells constrain cSCC. Two MHC class I neoantigens were identified that constrained cSCC growth. Compared to the wild-type peptides, one tumor-rejecting neoantigen exhibited improved MHC binding and the other had increased solvent accessibility of the mutated residue. Across known neoantigens that do not impact MHC binding, structural modeling of the peptide/MHC complexes indicated that increased solvent accessibility, which will facilitate TCR recognition of the neoantigen, distinguished tumor-rejecting from non-immunogenic neoantigens. This work reveals characteristics of tumor-rejecting neoantigens that may be of considerable importance in identifying optimal vaccine candidates in cSCC and other cancers.
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4
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Mikhaylov V, Brambley CA, Keller GLJ, Arbuiso AG, Weiss LI, Baker BM, Levine AJ. Accurate modeling of peptide-MHC structures with AlphaFold. Structure 2024; 32:228-241.e4. [PMID: 38113889 PMCID: PMC10872456 DOI: 10.1016/j.str.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/17/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023]
Abstract
Major histocompatibility complex (MHC) proteins present peptides on the cell surface for T cell surveillance. Reliable in silico prediction of which peptides would be presented and which T cell receptors would recognize them is an important problem in structural immunology. Here, we introduce an AlphaFold-based pipeline for predicting the three-dimensional structures of peptide-MHC complexes for class I and class II MHC molecules. Our method demonstrates high accuracy, outperforming existing tools in class I modeling accuracy and class II peptide register prediction. We validate its performance and utility with new experimental data on a recently described cancer neoantigen/wild-type peptide pair and explore applications toward improving peptide-MHC binding prediction.
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Affiliation(s)
- Victor Mikhaylov
- The Simons Center for Systems Biology, Institute for Advanced Study, 1 Einstein Drive, Princeton, NJ 08540, USA.
| | - Chad A Brambley
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Grant L J Keller
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Alyssa G Arbuiso
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Laura I Weiss
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Arnold J Levine
- The Simons Center for Systems Biology, Institute for Advanced Study, 1 Einstein Drive, Princeton, NJ 08540, USA
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5
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Custodio JM, Ayres CM, Rosales TJ, Brambley CA, Arbuiso AG, Landau LM, Keller GLJ, Srivastava PK, Baker BM. Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes. Proc Natl Acad Sci U S A 2023; 120:e2312057120. [PMID: 38085776 PMCID: PMC10742377 DOI: 10.1073/pnas.2312057120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/23/2023] [Indexed: 12/18/2023] Open
Abstract
Neoepitopes arising from amino acid substitutions due to single nucleotide polymorphisms are targets of T cell immune responses to cancer and are of significant interest in the development of cancer vaccines. However, understanding the characteristics of rare protective neoepitopes that truly control tumor growth has been a challenge, due to their scarcity as well as the challenge of verifying true, neoepitope-dependent tumor control in humans. Taking advantage of recent work in mouse models that circumvented these challenges, here, we compared the structural and physical properties of neoepitopes that range from fully protective to immunologically inactive. As neoepitopes are derived from self-peptides that can induce immune tolerance, we studied not only how the various neoepitopes differ from each other but also from their wild-type counterparts. We identified multiple features associated with protection, including features that describe how neoepitopes differ from self as well as features associated with recognition by diverse T cell receptor repertoires. We demonstrate both the promise and limitations of neoepitope structural analysis and predictive modeling and illustrate important aspects that can be incorporated into neoepitope prediction pipelines.
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Affiliation(s)
- Jean M. Custodio
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Tatiana J. Rosales
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Chad A. Brambley
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Alyssa G. Arbuiso
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Lauren M. Landau
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Grant L. J. Keller
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
| | - Pramod K. Srivastava
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT06030
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN46556
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6
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Khorki ME, Shi T, Cianciolo EE, Burg AR, Chukwuma PC, Picarsic JL, Morrice MK, Woodle ES, Maltzman JS, Ferguson A, Katz JD, Baker BM, Hildeman DA. Prior viral infection primes cross-reactive CD8+ T cells that respond to mouse heart allografts. Front Immunol 2023; 14:1287546. [PMID: 38143762 PMCID: PMC10748599 DOI: 10.3389/fimmu.2023.1287546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
Introduction Significant evidence suggests a connection between transplant rejection and the presence of high levels of pre-existing memory T cells. Viral infection can elicit viral-specific memory T cells that cross-react with allo-MHC capable of driving allograft rejection in mice. Despite these advances, and despite their critical role in transplant rejection, a systematic study of allo-reactive memory T cells, their specificities, and the role of cross-reactivity with viral antigens has not been performed. Methods Here, we established a model to identify, isolate, and characterize cross-reactive T cells using Nur77 reporter mice (C57BL/6 background), which transiently express GFP exclusively upon TCR engagement. We infected Nur77 mice with lymphocytic choriomeningitis virus (LCMV-Armstrong) to generate a robust memory compartment, where quiescent LCMV-specific memory CD8+ T cells could be readily tracked with MHC tetramer staining. Then, we transplanted LCMV immune mice with allogeneic hearts and monitored expression of GFP within MHC-tetramer defined viral-specific T cells as an indicator of their ability to cross-react with alloantigens. Results Strikingly, prior LCMV infection significantly increased the kinetics and magnitude of rejection as well as CD8+ T cell recruitment into allogeneic, but not syngeneic, transplanted hearts, relative to non-infected controls. Interestingly, as early as day 1 after allogeneic heart transplant an average of ~8% of MHC-tetramer+ CD8+ T cells expressed GFP, in contrast to syngeneic heart transplants, where the frequency of viral-specific CD8+ T cells that were GFP+ was <1%. These data show that a significant percentage of viral-specific memory CD8+ T cells expressed T cell receptors that also recognized alloantigens in vivo. Notably, the frequency of cross-reactive CD8+ T cells differed depending upon the viral epitope. Further, TCR sequences derived from cross-reactive T cells harbored distinctive motifs that may provide insight into cross-reactivity and allo-specificity. Discussion In sum, we have established a mouse model to track viral-specific, allo-specific, and cross-reactive T cells; revealing that prior infection elicits substantial numbers of viral-specific T cells that cross-react to alloantigen, respond very early after transplant, and may promote rapid rejection.
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Affiliation(s)
- M. Eyad Khorki
- Division of Nephrology & Hypertension, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Tiffany Shi
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Eileen E. Cianciolo
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Ashley R. Burg
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - P. Chukwunalu Chukwuma
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - Jennifer L. Picarsic
- Division of Pathology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pathology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Mary K. Morrice
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - E. Steve Woodle
- Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Jonathan S. Maltzman
- Department of Medicine, Stanford University, Palo Alto, CA, United States
- Geriatric Research and Education Clinical Center, Veterans Affairs (VA) Palo Alto Health Care System, Palo Alto, CA, United States
| | - Autumn Ferguson
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Jonathan D. Katz
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Brian M. Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - David A. Hildeman
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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7
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Klebanoff CA, Chandran SS, Baker BM, Quezada SA, Ribas A. T cell receptor therapeutics: immunological targeting of the intracellular cancer proteome. Nat Rev Drug Discov 2023; 22:996-1017. [PMID: 37891435 PMCID: PMC10947610 DOI: 10.1038/s41573-023-00809-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 10/29/2023]
Abstract
The T cell receptor (TCR) complex is a naturally occurring antigen sensor that detects, amplifies and coordinates cellular immune responses to epitopes derived from cell surface and intracellular proteins. Thus, TCRs enable the targeting of proteins selectively expressed by cancer cells, including neoantigens, cancer germline antigens and viral oncoproteins. As such, TCRs have provided the basis for an emerging class of oncology therapeutics. Herein, we review the current cancer treatment landscape using TCRs and TCR-like molecules. This includes adoptive cell transfer of T cells expressing endogenous or engineered TCRs, TCR bispecific engagers and antibodies specific for human leukocyte antigen (HLA)-bound peptides (TCR mimics). We discuss the unique complexities associated with the clinical development of these therapeutics, such as HLA restriction, TCR retrieval, potency assessment and the potential for cross-reactivity. In addition, we highlight emerging clinical data that establish the antitumour potential of TCR-based therapies, including tumour-infiltrating lymphocytes, for the treatment of diverse human malignancies. Finally, we explore the future of TCR therapeutics, including emerging genome editing methods to safely enhance potency and strategies to streamline patient identification.
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Affiliation(s)
- Christopher A Klebanoff
- Memorial Sloan Kettering Cancer Center (MSKCC), Human Oncology and Pathogenesis Program, New York, NY, USA.
| | - Smita S Chandran
- Memorial Sloan Kettering Cancer Center (MSKCC), Human Oncology and Pathogenesis Program, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, ID, USA
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, ID, USA
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Achilles Therapeutics, London, UK
| | - Antoni Ribas
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
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8
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Gillig MA, Brennick CA, George MM, Balsbaugh JL, Shcheglova TV, Mandoiu II, Rosales T, Baker BM, Srivastava PK, Karandikar SH. CD8+ T Cell-Dependent Antitumor Activity In Vivo of a Mass Spectrometry-Identified Neoepitope despite Undetectable CD8+ Immunogenicity In Vitro. J Immunol 2023; 211:ji2300356. [PMID: 37966257 PMCID: PMC10694033 DOI: 10.4049/jimmunol.2300356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/15/2023] [Indexed: 11/16/2023]
Abstract
Identification of neoepitopes that can control tumor growth in vivo remains a challenge even 10 y after the first genomics-defined cancer neoepitopes were identified. In this study, we identify a neoepitope, resulting from a mutation in the junction plakoglobin (Jup) gene (chromosome 11), from the mouse colon cancer line MC38-FABF (C57BL/6). This neoepitope, Jup mutant (JupMUT), was detected during mass spectrometry of MHC class I-eluted peptides from the tumor. JupMUT has a predicted binding affinity of 564 nM for the Kb molecule and a higher predicted affinity of 82 nM for Db. However, whereas structural modeling of JupMUT and its unmutated counterpart Jup wild-type indicates that there are little conformational differences between the two epitopes bound to Db, large structural divergences are predicted between the two epitopes bound to Kb. Together with in vitro binding data with RMA-S cells, these data suggest that Kb rather than Db is the relevant MHC class I molecule of JupMUT. Immunization of naive C57BL/6 mice with JupMUT elicits CD8-dependent tumor control of a MC38-FABF challenge. Despite the CD8 dependence of JupMUT-mediated tumor control in vivo, CD8+ T cells from JupMUT-immunized mice do not produce higher levels of IFN-γ than do naive mice. The structural and immunological characteristics of JupMUT are substantially different from those of many other neoepitopes that have been shown to mediate tumor control.
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Affiliation(s)
- Marc A. Gillig
- Department of Immunology, Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT
| | - Cory A. Brennick
- Department of Immunology, Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT
| | - Mariam M. George
- Department of Immunology, Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources and Equipment, University of Connecticut, Storrs, CT
| | - Tatiana V. Shcheglova
- Department of Immunology, Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT
| | - Ion I. Mandoiu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT
| | - Tatiana Rosales
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN
| | - Pramod K. Srivastava
- Department of Immunology, Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT
| | - Sukrut H. Karandikar
- Department of Immunology, Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT
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9
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Ayres CM, Corcelli SA, Baker BM. The Energetic Landscape of Catch Bonds in TCR Interfaces. J Immunol 2023; 211:325-332. [PMID: 37459192 PMCID: PMC10361606 DOI: 10.4049/jimmunol.2300121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/14/2023] [Indexed: 07/20/2023]
Abstract
Recognition of peptide/MHC complexes by αβ TCRs has traditionally been viewed through the lens of conventional receptor-ligand theory. Recent work, however, has shown that TCR recognition and T cell signaling can be profoundly influenced and tuned by mechanical forces. One outcome of applied force is the catch bond, where TCR dissociation rates decrease (half-lives increase) when limited force is applied. Although catch bond behavior is believed to be widespread in biology, its counterintuitive nature coupled with the difficulties of describing mechanisms at the structural level have resulted in considerable mystique. In this review, we demonstrate that viewing catch bonds through the lens of energy landscapes, barriers, and the ensuing reaction rates can help demystify catch bonding and provide a foundation on which atomic-level TCR catch bond mechanisms can be built.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN
| | - Steve A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN
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10
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Shi T, Burg AR, Caldwell JT, Roskin KM, Castro-Rojas CM, Chukwuma PC, Gray GI, Foote SG, Alonso JA, Cuda CM, Allman DA, Rush JS, Regnier CH, Wieczorek G, Alloway RR, Shields AR, Baker BM, Woodle ES, Hildeman DA. Single cell transcriptomic analysis of renal allograft rejection reveals insights into intragraft TCR clonality. J Clin Invest 2023:170191. [PMID: 37227784 DOI: 10.1172/jci170191] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
Bulk analysis of renal allograft biopsies (rBx) identified RNA transcripts associated with acute cellular rejection (ACR); however, these lacked cellular context critical to mechanistic understanding of how rejection occurs despite immunosuppression (IS). We performed combined single cell RNA transcriptomic and TCRα/β sequencing on rBx from patients with ACR under differing IS: tacrolimus, iscalimab, and belatacept. We found distinct CD8+ T cell phenotypes (e.g., effector, memory, exhausted) depending upon IS type, particularly within clonally expanded cells (CD8EXP). Gene expression of CD8EXP identified therapeutic targets that were influenced by IS type. TCR analysis revealed a highly restricted number of CD8EXP, independent of HLA mismatch or IS type. Subcloning of TCRα/β cDNAs from CD8EXP into Jurkat76 cells (TCR-/-) conferred alloreactivity by mixed lymphocyte reaction. Analysis of sequential rBx samples revealed persistence of CD8EXP that decreased, but were not eliminated, after successful anti-rejection therapy. In contrast, CD8EXP were maintained in treatment-refractory rejection. Finally, most rBx-derived CD8EXP were also observed in matching urine samples, providing precedent for using urine-derived CD8EXP as a surrogate for those found in the rejecting allograft. Overall, our data define the clonal CD8+ T cell response to ACR, paving the next steps to improve detection, assessment, and treatment of rejection.
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Affiliation(s)
- Tiffany Shi
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Ashley R Burg
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - J Timothy Caldwell
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Krishna M Roskin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - Cyd M Castro-Rojas
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
| | - P Chukwunalu Chukwuma
- Department of Chemistry and Biochemistry and the Harper Cancer Research Ins, University of Notre Dame, South Bend, United States of America
| | - George I Gray
- Department of Chemistry and Biochemistry and the Harper Cancer Research Ins, University of Notre Dame, South Bend, United States of America
| | - Sara G Foote
- Department of Chemistry and Biochemistry and the Harper Cancer Research Ins, University of Notre Dame, South Bend, United States of America
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry and the Harper Cancer Research Ins, University of Notre Dame, South Bend, United States of America
| | - Carla M Cuda
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, United States of America
| | - David A Allman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States of America
| | - James S Rush
- Immunology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Catherine H Regnier
- Immunology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Grazyna Wieczorek
- Immunology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Rita R Alloway
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - Adele R Shields
- Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Ins, University of Notre Dame, South Bend, United States of America
| | - E Steve Woodle
- Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, United States of America
| | - David A Hildeman
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, United States of America
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11
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Shi T, Burg AR, Caldwell JT, Roskin K, Castro-Rojas CM, Chukwuma PC, Gray GI, Foote SG, Alonso J, Cuda CM, Allman DA, Rush JS, Regnier CH, Wieczorek G, Alloway RR, Shields AR, Baker BM, Woodle ES, Hildeman DA. Single cell transcriptomic analysis of renal allograft rejection reveals novel insights into intragraft TCR clonality. bioRxiv 2023:2023.02.08.524808. [PMID: 36798151 PMCID: PMC9934650 DOI: 10.1101/2023.02.08.524808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Bulk analysis of renal allograft biopsies (rBx) identified RNA transcripts associated with acute cellular rejection (ACR); however, these lacked cellular context critical to mechanistic understanding. We performed combined single cell RNA transcriptomic and TCRα/β sequencing on rBx from patients with ACR under differing immunosuppression (IS): tacrolimus, iscalimab, and belatacept. TCR analysis revealed a highly restricted CD8 + T cell clonal expansion (CD8 EXP ), independent of HLA mismatch or IS type. Subcloning of TCRα/β cDNAs from CD8 EXP into Jurkat76 cells (TCR -/- ) conferred alloreactivity by mixed lymphocyte reaction. scRNAseq analysis of CD8 EXP revealed effector, memory, and exhausted phenotypes that were influenced by IS type. Successful anti-rejection treatment decreased, but did not eliminate, CD8 EXP , while CD8 EXP were maintained during treatment-refractory rejection. Finally, most rBx-derived CD8 EXP were also observed in matching urine samples. Overall, our data define the clonal CD8 + T cell response to ACR, providing novel insights to improve detection, assessment, and treatment of rejection.
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12
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Liu C, Liu H, Dasgupta M, Hellman LM, Zhang X, Qu K, Xue H, Wang Y, Fan F, Chang Q, Yu D, Ge L, Zhang Y, Cui Z, Zhang P, Heller B, Zhang H, Shi B, Baker BM, Liu C. Validation and promise of a TCR mimic antibody for cancer immunotherapy of hepatocellular carcinoma. Sci Rep 2022; 12:12068. [PMID: 35840635 PMCID: PMC9287321 DOI: 10.1038/s41598-022-15946-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022] Open
Abstract
Monoclonal antibodies are at the vanguard of the most promising cancer treatments. Whereas traditional therapeutic antibodies have been limited to extracellular antigens, T cell receptor mimic (TCRm) antibodies can target intracellular antigens presented by cell surface major histocompatibility complex (MHC) proteins. TCRm antibodies can therefore target a repertoire of otherwise undruggable cancer antigens. However, the consequences of off-target peptide/MHC recognition with engineered T cell therapies are severe, and thus there are significant safety concerns with TCRm antibodies. Here we explored the specificity and safety profile of a new TCRm-based T cell therapy for hepatocellular carcinoma (HCC), a solid tumor for which no effective treatment exists. We targeted an alpha-fetoprotein peptide presented by HLA-A*02 with a highly specific TCRm, which crystallographic structural analysis showed binds directly over the HLA protein and interfaces with the full length of the peptide. We fused the TCRm to the γ and δ subunits of a TCR, producing a signaling AbTCR construct. This was combined with an scFv/CD28 co-stimulatory molecule targeting glypican-3 for increased efficacy towards tumor cells. This AbTCR + co-stimulatory T cell therapy showed potent activity against AFP-positive cancer cell lines in vitro and an in an in vivo model and undetectable activity against AFP-negative cells. In an in-human safety assessment, no significant adverse events or cytokine release syndrome were observed and evidence of efficacy was seen. Remarkably, one patient with metastatic HCC achieved a complete remission after nine months and ultimately qualified for a liver transplant.
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Affiliation(s)
- Chang Liu
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Hong Liu
- Eureka Therapeutics Inc., 5858 Horton Street, Suite 170, Emeryville, CA, USA
| | - Moumita Dasgupta
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, USA
| | - Lance M Hellman
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, USA
| | - Xiaogang Zhang
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Kai Qu
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Hui Xue
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Yun Wang
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Fenling Fan
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Qi Chang
- Eureka Therapeutics Inc., 5858 Horton Street, Suite 170, Emeryville, CA, USA
| | - Duo Yu
- Eureka Therapeutics Inc., 5858 Horton Street, Suite 170, Emeryville, CA, USA
| | - Linhu Ge
- Eureka Therapeutics Inc., 5858 Horton Street, Suite 170, Emeryville, CA, USA
| | - Yu Zhang
- Eureka Therapeutics Inc., 5858 Horton Street, Suite 170, Emeryville, CA, USA
| | - Ziyou Cui
- Eureka Therapeutics Inc., 5858 Horton Street, Suite 170, Emeryville, CA, USA
| | - Pengbo Zhang
- Eureka Therapeutics Inc., 5858 Horton Street, Suite 170, Emeryville, CA, USA
| | - Bradley Heller
- Eureka Therapeutics Inc., 5858 Horton Street, Suite 170, Emeryville, CA, USA
| | - Hongbing Zhang
- Eureka Therapeutics Inc., 5858 Horton Street, Suite 170, Emeryville, CA, USA
| | - Bingyin Shi
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, USA.
| | - Cheng Liu
- Eureka Therapeutics Inc., 5858 Horton Street, Suite 170, Emeryville, CA, USA.
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13
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Rosales TJ, Baker BM. Chaperoning the dance of antigen presentation. Nat Chem Biol 2022; 18:796-797. [PMID: 35725942 DOI: 10.1038/s41589-022-01069-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tatiana J Rosales
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
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14
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Ayres CM, Baker BM. Peptide-dependent tuning of major histocompatibility complex motional properties and the consequences for cellular immunity. Curr Opin Immunol 2022; 76:102184. [PMID: 35550277 PMCID: PMC10052791 DOI: 10.1016/j.coi.2022.102184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 12/22/2022]
Abstract
T cell receptors (TCRs) and other receptors of the immune system recognize peptides presented by class I or class II major histocompatibility complex (MHC) proteins. Although we generally distinguish between the MHC protein and its peptide, at an atomic level the two form a structural composite, which allows peptides to influence MHC properties and vice versa. One consequence is the peptide-dependent tuning of MHC structural dynamics, which contributes to protein structural adaptability and influences how receptors identify and bind targets. Peptide-dependent tuning of MHC protein dynamics can impact processes such as antigenicity, TCR cross-reactivity, and T cell repertoire selection. Motional tuning extends beyond the binding groove, influencing peptide selection and exchange, as well as interactions with other immune receptors. Here, we review recent findings showing how peptides can affect the dynamic and adaptable nature of MHC proteins. We highlight consequences for immunity and demonstrate how MHC proteins have evolved to be highly sensitive dynamic reporters, with broad immunological consequences.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
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15
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Keller GLJ, Weiss LI, Baker BM. Physicochemical Heuristics for Identifying High Fidelity, Near-Native Structural Models of Peptide/MHC Complexes. Front Immunol 2022; 13:887759. [PMID: 35547730 PMCID: PMC9084917 DOI: 10.3389/fimmu.2022.887759] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
There is long-standing interest in accurately modeling the structural features of peptides bound and presented by class I MHC proteins. This interest has grown with the advent of rapid genome sequencing and the prospect of personalized, peptide-based cancer vaccines, as well as the development of molecular and cellular therapeutics based on T cell receptor recognition of peptide-MHC. However, while the speed and accessibility of peptide-MHC modeling has improved substantially over the years, improvements in accuracy have been modest. Accuracy is crucial in peptide-MHC modeling, as T cell receptors are highly sensitive to peptide conformation and capturing fine details is therefore necessary for useful models. Studying nonameric peptides presented by the common class I MHC protein HLA-A*02:01, here we addressed a key question common to modern modeling efforts: from a set of models (or decoys) generated through conformational sampling, which is best? We found that the common strategy of decoy selection by lowest energy can lead to substantial errors in predicted structures. We therefore adopted a data-driven approach and trained functions capable of predicting near native decoys with exceptionally high accuracy. Although our implementation is limited to nonamer/HLA-A*02:01 complexes, our results serve as an important proof of concept from which improvements can be made and, given the significance of HLA-A*02:01 and its preference for nonameric peptides, should have immediate utility in select immunotherapeutic and other efforts for which structural information would be advantageous.
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Affiliation(s)
- Grant L J Keller
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - Laura I Weiss
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
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16
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Chandran SS, Ma J, Klatt MG, Dündar F, Bandlamudi C, Razavi P, Wen HY, Weigelt B, Zumbo P, Fu SN, Banks LB, Yi F, Vercher E, Etxeberria I, Bestman WD, Da Cruz Paula A, Aricescu IS, Drilon A, Betel D, Scheinberg DA, Baker BM, Klebanoff CA. Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA. Nat Med 2022; 28:946-957. [PMID: 35484264 PMCID: PMC9117146 DOI: 10.1038/s41591-022-01786-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 03/16/2022] [Indexed: 01/05/2023]
Abstract
Public neoantigens (NeoAgs) represent an elite class of shared cancer-specific epitopes derived from recurrently mutated driver genes. Here we describe a high-throughput platform combining single-cell transcriptomic and T cell receptor (TCR) sequencing to establish whether mutant PIK3CA, among the most frequently genomically altered driver oncogenes, generates an immunogenic public NeoAg. Using this strategy, we developed a panel of TCRs that recognize an endogenously processed neopeptide encompassing a common PIK3CA hotspot mutation restricted by the prevalent human leukocyte antigen (HLA)-A*03:01 allele. Mechanistically, immunogenicity to this public NeoAg arises from enhanced neopeptide/HLA complex stability caused by a preferred HLA anchor substitution. Structural studies indicated that the HLA-bound neopeptide presents a comparatively 'featureless' surface dominated by the peptide's backbone. To bind this epitope with high specificity and affinity, we discovered that a lead TCR clinical candidate engages the neopeptide through an extended interface facilitated by an unusually long CDR3β loop. In patients with diverse malignancies, we observed NeoAg clonal conservation and spontaneous immunogenicity to the neoepitope. Finally, adoptive transfer of TCR-engineered T cells led to tumor regression in vivo in mice bearing PIK3CA-mutant tumors but not wild-type PIK3CA tumors. Together, these findings establish the immunogenicity and therapeutic potential of a mutant PIK3CA-derived public NeoAg.
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Affiliation(s)
- Smita S Chandran
- Human Oncology and Pathogenesis Program (HOPP), Immuno-Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Parker Institute for Cancer Immunotherapy, New York, NY, USA.
| | - Jiaqi Ma
- Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, IN, USA
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, USA
| | - Martin G Klatt
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Human Oncology and Pathogenesis Program (HOPP), Immuno-Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
| | - Si Ning Fu
- Human Oncology and Pathogenesis Program (HOPP), Immuno-Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lauren B Banks
- Human Oncology and Pathogenesis Program (HOPP), Immuno-Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fei Yi
- Human Oncology and Pathogenesis Program (HOPP), Immuno-Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Enric Vercher
- Human Oncology and Pathogenesis Program (HOPP), Immuno-Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Inaki Etxeberria
- Human Oncology and Pathogenesis Program (HOPP), Immuno-Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Watchain D Bestman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ilinca S Aricescu
- Human Oncology and Pathogenesis Program (HOPP), Immuno-Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Early Drug Development Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - David A Scheinberg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, IN, USA
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, USA
| | - Christopher A Klebanoff
- Human Oncology and Pathogenesis Program (HOPP), Immuno-Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Parker Institute for Cancer Immunotherapy, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA.
- Early Drug Development Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Cell Therapy Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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17
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Ebrahimi-Nik H, Moussa M, Englander RP, Singhaviranon S, Michaux J, Pak H, Miyadera H, Corwin WL, Keller GLJ, Hagymasi AT, Shcheglova TV, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, Srivastava PK. Reversion analysis reveals the in vivo immunogenicity of a poorly MHC I-binding cancer neoepitope. Nat Commun 2021; 12:6423. [PMID: 34741035 PMCID: PMC8571378 DOI: 10.1038/s41467-021-26646-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 09/27/2021] [Indexed: 12/30/2022] Open
Abstract
High-affinity MHC I-peptide interactions are considered essential for immunogenicity. However, some neo-epitopes with low affinity for MHC I have been reported to elicit CD8 T cell dependent tumor rejection in immunization-challenge studies. Here we show in a mouse model that a neo-epitope that poorly binds to MHC I is able to enhance the immunogenicity of a tumor in the absence of immunization. Fibrosarcoma cells with a naturally occurring mutation are edited to their wild type counterpart; the mutation is then re-introduced in order to obtain a cell line that is genetically identical to the wild type except for the neo-epitope-encoding mutation. Upon transplantation into syngeneic mice, all three cell lines form tumors that are infiltrated with activated T cells. However, lymphocytes from the two tumors that harbor the mutation show significantly stronger transcriptional signatures of cytotoxicity and TCR engagement, and induce greater breadth of TCR reactivity than those of the wild type tumors. Structural modeling of the neo-epitope peptide/MHC I pairs suggests increased hydrophobicity of the neo-epitope surface, consistent with higher TCR reactivity. These results confirm the in vivo immunogenicity of low affinity or ‘non-binding’ epitopes that do not follow the canonical concept of MHC I-peptide recognition. The immunogenicity of peptides is believed to be determined by their high-affinity binding to MHC I. Here authors show that low-affinity MHC I-peptide interactions are also able to trigger robust T cell response and anti-tumour immunity in vivo.
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Affiliation(s)
- Hakimeh Ebrahimi-Nik
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA.,Broad Institute of MIT and Harvard, 105 Broadway, Cambridge, MA, USA
| | - Marmar Moussa
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Ryan P Englander
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Summit Singhaviranon
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Justine Michaux
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - HuiSong Pak
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - Hiroko Miyadera
- Department of Medical Genetics, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Chiba, Japan
| | - William L Corwin
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA.,Arvinas, 5 science park, 395 Winchester Ave, New Haven, CT, USA
| | - Grant L J Keller
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Adam T Hagymasi
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Tatiana V Shcheglova
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA
| | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - Brian M Baker
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Ion I Mandoiu
- Department of Computer Sciences, University of Connecticut School of Engineering, Storrs, CT, USA
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.,Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), Lausanne, Switzerland
| | - Pramod K Srivastava
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, CT, USA.
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18
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Shi T, Roskin K, Baker BM, Woodle ES, Hildeman D. Advanced Genomics-Based Approaches for Defining Allograft Rejection With Single Cell Resolution. Front Immunol 2021; 12:750754. [PMID: 34721421 PMCID: PMC8551864 DOI: 10.3389/fimmu.2021.750754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Solid organ transplant recipients require long-term immunosuppression for prevention of rejection. Calcineurin inhibitor (CNI)-based immunosuppressive regimens have remained the primary means for immunosuppression for four decades now, yet little is known about their effects on graft resident and infiltrating immune cell populations. Similarly, the understanding of rejection biology under specific types of immunosuppression remains to be defined. Furthermore, development of innovative, rationally designed targeted therapeutics for mitigating or preventing rejection requires a fundamental understanding of the immunobiology that underlies the rejection process. The established use of microarray technologies in transplantation has provided great insight into gene transcripts associated with allograft rejection but does not characterize rejection on a single cell level. Therefore, the development of novel genomics tools, such as single cell sequencing techniques, combined with powerful bioinformatics approaches, has enabled characterization of immune processes at the single cell level. This can provide profound insights into the rejection process, including identification of resident and infiltrating cell transcriptomes, cell-cell interactions, and T cell receptor α/β repertoires. In this review, we discuss genomic analysis techniques, including microarray, bulk RNAseq (bulkSeq), single-cell RNAseq (scRNAseq), and spatial transcriptomic (ST) techniques, including considerations of their benefits and limitations. Further, other techniques, such as chromatin analysis via assay for transposase-accessible chromatin sequencing (ATACseq), bioinformatic regulatory network analyses, and protein-based approaches are also examined. Application of these tools will play a crucial role in redefining transplant rejection with single cell resolution and likely aid in the development of future immunomodulatory therapies in solid organ transplantation.
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Affiliation(s)
- Tiffany Shi
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Krishna Roskin
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - E Steve Woodle
- Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - David Hildeman
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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19
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Brennick CA, George MM, Moussa MM, Hagymasi AT, Seesi SA, Shcheglova TV, Englander RP, Keller GL, Balsbaugh JL, Baker BM, Schietinger A, Mandoiu II, Srivastava PK. An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection. J Clin Invest 2021; 131:142823. [PMID: 33320837 PMCID: PMC7843235 DOI: 10.1172/jci142823] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/04/2020] [Indexed: 01/01/2023] Open
Abstract
Identification of neoepitopes that are effective in cancer therapy is a major challenge in creating cancer vaccines. Here, using an entirely unbiased approach, we queried all possible neoepitopes in a mouse cancer model and asked which of those are effective in mediating tumor rejection and, independently, in eliciting a measurable CD8 response. This analysis uncovered a large trove of effective anticancer neoepitopes that have strikingly different properties from conventional epitopes and suggested an algorithm to predict them. It also revealed that our current methods of prediction discard the overwhelming majority of true anticancer neoepitopes. These results from a single mouse model were validated in another antigenically distinct mouse cancer model and are consistent with data reported in human studies. Structural modeling showed how the MHC I-presented neoepitopes had an altered conformation, higher stability, or increased exposure to T cell receptors as compared with the unmutated counterparts. T cells elicited by the active neoepitopes identified here demonstrated a stem-like early dysfunctional phenotype associated with effective responses against viruses and tumors of transgenic mice. These abundant anticancer neoepitopes, which have not been tested in human studies thus far, can be exploited for generation of personalized human cancer vaccines.
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Affiliation(s)
- Cory A Brennick
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Mariam M George
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Marmar M Moussa
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Adam T Hagymasi
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Sahar Al Seesi
- Computer Science Department, Smith College, Northampton, Massachusetts, USA
| | - Tatiana V Shcheglova
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Ryan P Englander
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Grant Lj Keller
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jeremy L Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources and Equipment, University of Connecticut, Storrs, Connecticut, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Ion I Mandoiu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, USA
| | - Pramod K Srivastava
- Department of Immunology, and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
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20
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Kaseke C, Park RJ, Singh NK, Koundakjian D, Bashirova A, Garcia Beltran WF, Takou Mbah OC, Ma J, Senjobe F, Urbach JM, Nathan A, Rossin EJ, Tano-Menka R, Khatri A, Piechocka-Trocha A, Waring MT, Birnbaum ME, Baker BM, Carrington M, Walker BD, Gaiha GD. HLA class-I-peptide stability mediates CD8 + T cell immunodominance hierarchies and facilitates HLA-associated immune control of HIV. Cell Rep 2021; 36:109378. [PMID: 34260940 PMCID: PMC8293625 DOI: 10.1016/j.celrep.2021.109378] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/24/2021] [Accepted: 06/18/2021] [Indexed: 11/29/2022] Open
Abstract
Defining factors that govern CD8+ T cell immunodominance is critical for the rational design of vaccines for viral pathogens. Here, we assess the contribution of human leukocyte antigen (HLA) class-I-peptide stability for 186 optimal HIV epitopes across 18 HLA alleles using transporter associated with antigen processing (TAP)-deficient mono-allelic HLA-expressing cell lines. We find that immunodominant HIV epitopes increase surface stabilization of HLA class-I molecules in comparison to subdominant epitopes. HLA class-I-peptide stability is also strongly correlated with overall immunodominance hierarchies, particularly for epitopes from high-abundance proteins (e.g., Gag). Moreover, HLA alleles associated with HIV protection are preferentially stabilized by epitopes derived from topologically important viral regions at a greater frequency than neutral and risk alleles. These findings indicate that relative stabilization of HLA class-I is a key factor for CD8+ T cell epitope immunodominance hierarchies, with implications for HIV control and the design of T-cell-based vaccines. TAP-deficient HLA-expressing cells provide rapid assessment of HLA-peptide stability Immunodominant HIV CD8+ T cell epitopes are superior stabilizers of HLA molecules HLA class-I-peptide stability correlates with overall immunodominance hierarchies Protective HLA alleles are preferentially stabilized by highly networked epitopes
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Affiliation(s)
- Clarety Kaseke
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ryan J Park
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Harvard Radiation Oncology Program, Boston, MA 02114, USA
| | - Nishant K Singh
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Wilfredo F Garcia Beltran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Jiaqi Ma
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46556, USA
| | - Fernando Senjobe
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Program in Virology, Harvard Medical School, Boston, MA 02114, USA
| | | | - Anusha Nathan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elizabeth J Rossin
- Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA 02114, USA; The Broad Institute, Cambridge, MA 02142, USA
| | - Rhoda Tano-Menka
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashok Khatri
- Massachusetts General Hospital Endocrine Unit and Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Michael T Waring
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Michael E Birnbaum
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46556, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; The Broad Institute, Cambridge, MA 02142, USA; Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa; Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.
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21
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Alonso JA, Smith AR, Baker BM. Tumor rejection properties of gp100 209-specific T cells correlate with T cell receptor binding affinity towards the wild type rather than anchor-modified antigen. Mol Immunol 2021; 135:365-372. [PMID: 33990005 DOI: 10.1016/j.molimm.2021.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/03/2021] [Indexed: 10/21/2022]
Abstract
Although there are exceptions and outliers, T cell functional responses generally correlate with the affinity of a TCR for a peptide/MHC complex. In one recently described outlier case, the most promising clinical candidate in a series of TCRs specific for the gp100209 melanoma antigen bound with the weakest solution affinity and produced the least amount of cytokine in vitro. Hypotheses for this outlier behavior included unusual cytokine expression patterns arising from an atypical TCR binding geometry. Studying this instance in more detail, we found here that outlier behavior is attributable not to unusual cytokine patterns or TCR binding, but the use of a position 2 anchor-modified peptide variant in in vitro experiments instead of the wild type antigen that is present in vivo. Although the anchor-modified variant has been widely used in basic and clinical immunology as a surrogate for the wild type peptide, prior work has shown that TCRs can clearly distinguish between the two. We show that when this differential recognition is accounted for, the functional properties of gp100209-specific TCRs track with their affinity towards the peptide/MHC complex. Beyond demonstrating the correlates with T cell function for a clinically relevant TCR, our results provide important considerations for selection of TCRs for immunotherapy and the use of modified peptides in immunology.
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Affiliation(s)
- Jesus A Alonso
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Angela R Smith
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
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22
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Ma J, Ayres CM, Hellman LM, Devlin JR, Baker BM. Dynamic allostery controls the peptide sensitivity of the Ly49C natural killer receptor. J Biol Chem 2021; 296:100686. [PMID: 33891944 PMCID: PMC8138769 DOI: 10.1016/j.jbc.2021.100686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 11/30/2022] Open
Abstract
Using a variety of activating and inhibitory receptors, natural killer (NK) cells protect against disease by eliminating cells that have downregulated class I major histocompatibility complex (MHC) proteins, such as in response to cell transformation or viral infection. The inhibitory murine NK receptor Ly49C specifically recognizes the class I MHC protein H-2Kb. Unusual among NK receptors, Ly49C exhibits a peptide-dependent sensitivity to H-2Kb recognition, which has not been explained despite detailed structural studies. To gain further insight into Ly49C peptide sensitivity, we examined Ly49C recognition biochemically and through the lens of dynamic allostery. We found that the peptide sensitivity of Ly49C arises through small differences in H-2Kb-binding affinity. Although molecular dynamics simulations supported a role for peptide-dependent protein dynamics in producing these differences in binding affinity, calorimetric measurements indicated an enthalpically as opposed to entropically driven process. A quantitative linkage analysis showed that this emerges from peptide-dependent dynamic tuning of electrostatic interactions across the Ly49C–H-2Kb interface. We propose a model whereby different peptides alter the flexibility of H-2Kb, which in turn changes the strength of electrostatic interactions across the protein–protein interface. Our results provide a quantitative assessment of how peptides alter Ly49C-binding affinity, suggest the underlying mechanism, and demonstrate peptide-driven allostery at work in class I MHC proteins. Lastly, our model provides a solution for how dynamic allostery could impact binding of some, but not all, class I MHC partners depending on the structural and chemical composition of the interfaces.
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Affiliation(s)
- Jiaqi Ma
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Cory M Ayres
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Lance M Hellman
- Department of Physical and Life Sciences, Nevada State College, Henderson, Nevada, USA
| | - Jason R Devlin
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA.
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23
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McGrath E, Waschbüsch D, Baker BM, Khan AR. LRRK2 binds to the Rab32 subfamily in a GTP-dependent manner via its armadillo domain. Small GTPases 2021; 12:133-146. [PMID: 31552791 PMCID: PMC7849779 DOI: 10.1080/21541248.2019.1666623] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/26/2019] [Accepted: 09/02/2019] [Indexed: 12/31/2022] Open
Abstract
LRRK2 is a multi-domain Ser/Thr kinase that is associated with inherited and sporadic cases of Parkinson's disease. Many mutations linked to disease are associated within a central ROC-COR regulatory region and the subsequent kinase domain, leading to enhanced catalytic activity. The N-terminus of human LRRK2 consists of armadillo repeat motifs (ARMs) followed by ankyrin repeats (ANKs). Recently, Rab GTPases have emerged as key players in LRRK2 function, both as substrates of the kinase, and as regulators of the catalytic activity. Rabs recruit effector proteins via their GTP-dependent switch 1 and 2 regions to distinct sub-cellular compartments to regulate membrane trafficking. LRRK2 phosphorylates Rab8, Rab10 and Rab12 in switch 2, and this activity is regulated via interactions with Rab29. Furthermore, the related Rab32-subfamily GTPases, Rab32 and Rab38, have also been shown to interact with LRRK2. Here, we have mapped the interactions of the Rab32-subfamily to the ARM domain of LRRK2. The complexes are dependent on the GTP state of the Rabs in vitro, implying that LRRK2 may be an effector of the Rab32-subfamily of small GTPases. X-ray crystal structures of the Rab32-family GTPases and subsequent mutational studies reveal that a positively charged residue in switch 1 is critical for binding of Rab32/38 to LRRK2. Homology modelling and mutational analyses of the ARM domain point to a patch of negatively charged residues that contribute to complex formation. These structural and biochemical studies provide a framework for understanding the molecular basis for Rab regulation of LRRK2 and its role in Parkinson's disease.
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Affiliation(s)
- Emma McGrath
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
| | - Dieter Waschbüsch
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
| | - Amir R. Khan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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24
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Schmidt J, Smith AR, Magnin M, Racle J, Devlin JR, Bobisse S, Cesbron J, Bonnet V, Carmona SJ, Huber F, Ciriello G, Speiser DE, Bassani-Sternberg M, Coukos G, Baker BM, Harari A, Gfeller D. Prediction of neo-epitope immunogenicity reveals TCR recognition determinants and provides insight into immunoediting. Cell Rep Med 2021; 2:100194. [PMID: 33665637 PMCID: PMC7897774 DOI: 10.1016/j.xcrm.2021.100194] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 12/11/2020] [Accepted: 01/11/2021] [Indexed: 02/07/2023]
Abstract
CD8+ T cell recognition of peptide epitopes plays a central role in immune responses against pathogens and tumors. However, the rules that govern which peptides are truly recognized by existing T cell receptors (TCRs) remain poorly understood, precluding accurate predictions of neo-epitopes for cancer immunotherapy. Here, we capitalize on recent (neo-)epitope data to train a predictor of immunogenic epitopes (PRIME), which captures molecular properties of both antigen presentation and TCR recognition. PRIME not only improves prioritization of neo-epitopes but also correlates with T cell potency and unravels biophysical determinants of TCR recognition that we experimentally validate. Analysis of cancer genomics data reveals that recurrent mutations tend to be less frequent in patients where they are predicted to be immunogenic, providing further evidence for immunoediting in human cancer. PRIME will facilitate identification of pathogen epitopes in infectious diseases and neo-epitopes in cancer immunotherapy.
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Affiliation(s)
- Julien Schmidt
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - Angela R Smith
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Morgane Magnin
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - Julien Racle
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Jason R Devlin
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Sara Bobisse
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - Julien Cesbron
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | | | - Santiago J Carmona
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Florian Huber
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - Giovanni Ciriello
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Daniel E Speiser
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Alexandre Harari
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland.,Center of Experimental Therapeutics, Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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25
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Smith AR, Alonso JA, Ayres CM, Singh NK, Hellman LM, Baker BM. Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner. Proc Natl Acad Sci U S A 2021; 118:e2018125118. [PMID: 33468649 PMCID: PMC7848747 DOI: 10.1073/pnas.2018125118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Presentation of peptides by class I MHC proteins underlies T cell immune responses to pathogens and cancer. The association between peptide binding affinity and immunogenicity has led to the engineering of modified peptides with improved MHC binding, with the hope that these peptides would be useful for eliciting cross-reactive immune responses directed toward their weak binding, unmodified counterparts. Increasing evidence, however, indicates that T cell receptors (TCRs) can perceive such anchor-modified peptides differently than wild-type (WT) peptides, although the scope of discrimination is unclear. We show here that even modifications at primary anchors that have no discernible structural impact can lead to substantially stronger or weaker T cell recognition depending on the TCR. Surprisingly, the effect of peptide anchor modification can be sensed by a TCR at regions distant from the site of modification, indicating a through-protein mechanism in which the anchor residue serves as an allosteric modulator for TCR binding. Our findings emphasize caution in the use and interpretation of results from anchor-modified peptides and have implications for how anchor modifications are accounted for in other circumstances, such as predicting the immunogenicity of tumor neoantigens. Our data also highlight an important need to better understand the highly tunable dynamic nature of class I MHC proteins and the impact this has on various forms of immune recognition.
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MESH Headings
- Allosteric Regulation
- Binding Sites
- Cloning, Molecular
- Crystallography, X-Ray
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/immunology
- Humans
- Jurkat Cells
- Kinetics
- Models, Molecular
- Peptides/chemistry
- Peptides/genetics
- Peptides/immunology
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Engineering
- 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
- Th2 Cells/cytology
- Th2 Cells/immunology
- Thermodynamics
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Affiliation(s)
- Angela R Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Nishant K Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Lance M Hellman
- Department of Physical and Life Sciences, Nevada State College, Henderson, NV 89002
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556;
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
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26
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Borrman T, Pierce BG, Vreven T, Baker BM, Weng Z. High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. Bioinformatics 2020; 36:5377-5385. [PMID: 33355667 PMCID: PMC8016493 DOI: 10.1093/bioinformatics/btaa1050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 11/23/2020] [Accepted: 12/08/2020] [Indexed: 01/14/2023] Open
Abstract
MOTIVATION The binding of T cell receptors (TCRs) to their target peptide MHC (pMHC) ligands initializes the cell-mediated immune response. In autoimmune diseases such as multiple sclerosis, the TCR erroneously recognizes self-peptides as foreign and activates an immune response against healthy cells. Such responses can be triggered by cross-recognition of the autoreactive TCR with foreign peptides. Hence, it would be desirable to identify such foreign-antigen triggers to provide a mechanistic understanding of autoimmune diseases. However, the large sequence space of foreign antigens presents an obstacle in the identification of cross-reactive peptides. RESULTS Here, we present an in silico modeling and scoring method which exploits the structural properties of TCR-pMHC complexes to predict the binding of cross-reactive peptides. We analyzed three mouse TCRs and one human TCR isolated from a patient with multiple sclerosis. Cross-reactive peptides for these TCRs were previously identified via yeast display coupled with deep sequencing, providing a robust dataset for evaluating our method. Modeling query peptides in their associated TCR-pMHC crystal structures, our method accurately selected the top binding peptides from sets containing more than a hundred thousand unique peptides. AVAILABILITY AND IMPLEMENTATION Analyses were performed using custom Python and R scripts available at https://github.com/tborrman/antigen-predict. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Thom Vreven
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
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27
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Singh NK, Alonso JA, Harris DT, Anderson SD, Ma J, Hellman LM, Rosenberg AM, Kolawole EM, Evavold BD, Kranz DM, Baker BM. An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding Modes. Biochemistry 2020; 59:4163-4175. [PMID: 33074657 DOI: 10.1021/acs.biochem.0c00689] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
T cell receptors (TCRs) orchestrate cellular immunity by recognizing peptides presented by a range of major histocompatibility complex (MHC) proteins. Naturally occurring TCRs bind the composite peptide/MHC surface, recognizing peptides that are structurally and chemically compatible with the TCR binding site. Here we describe a molecularly evolved TCR variant that binds the human class I MHC protein HLA-A2 independent of the bound peptide, achieved by a drastic perturbation of the TCR binding geometry that places the molecule far from the peptide binding groove. This unique geometry is unsupportive of normal T cell signaling. A substantial divergence between affinity measurements in solution and in two dimensions between proximal cell membranes leads us to attribute the lack of signaling to steric hindrance that limits binding in the confines of a cell-cell interface. Our results provide an example of how receptor binding geometry can impact T cell function and provide further support for the view that germline-encoded residues in TCR binding loops evolved to drive productive TCR recognition and signaling.
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Affiliation(s)
- Nishant K Singh
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Daniel T Harris
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Scott D Anderson
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Jiaqi Ma
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Lance M Hellman
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Aaron M Rosenberg
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Elizabeth M Kolawole
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, Utah 84112, United States
| | - Brian D Evavold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, Utah 84112, United States
| | - David M Kranz
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
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28
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Tarbe M, Miles JJ, Edwards ESJ, Miles KM, Sewell AK, Baker BM, Quideau S. Synthesis and Biological Evaluation of Hapten-Clicked Analogues of The Antigenic Peptide Melan-A/MART-1 26(27L)-35. ChemMedChem 2020; 15:799-807. [PMID: 32162475 PMCID: PMC7473458 DOI: 10.1002/cmdc.202000038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/03/2020] [Indexed: 11/12/2022]
Abstract
A click-chemistry-based approach was implemented to prepare peptidomimetics designed in silico and made from aromatic azides and a propargylated GIGI-mimicking platform derived from the altered Melan-A/MART-126(27L)-35 antigenic peptide ELAGIGILTV. The CuI -catalyzed Huisgen cycloaddition was carried out on solid support to generate rapidly a first series of peptidomimetics, which were evaluated for their capacity to dock at the interface between the major histocompatibility complex class-I (MHC-I) human leucocyte antigen (HLA)-A2 and T-cell receptors (TCRs). Despite being a weak HLA-A2 ligand, one of these 11 first synthetic compounds bearing a p-nitrobenzyl-triazole side chain was recognized by the receptor proteins of Melan-A/MART-1-specific T-cells. After modification of the N and C termini of this agonist, which was intended to enhance HLA-A2 binding, one of the resulting seven additional compounds triggered significant T-cell responses. Thus, these results highlight the capacity of naturally circulating human TCRs that are specific for the native Melan-A/MART-126-35 peptide to cross-react with peptidomimetics bearing organic motifs structurally different from the native central amino acids.
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Affiliation(s)
- Marion Tarbe
- Université de Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - John J Miles
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Emily S J Edwards
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
- Department of Immunology and Pathology, Central Clinical School, Monash University, Level 6, 89 Commercial Road, Melbourne, Victoria, 3004, Australia
| | - Kim M Miles
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Brian M Baker
- Department of Chemistry & Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Stéphane Quideau
- Université de Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
- Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France
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29
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Alonso JA, Singh NK, Kranz DM, Evavold BD, Baker BM. Insights from an in vitro derived T cell receptor. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.80.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Heterodimeric alpha-beta T cell receptors (TCRs) play a key role in cell-mediated immune responses of adaptive immunity. T cells continuously probe peptides presented by major histocompatibility complex (MHC) found on the cell surface. T cell activation initiates through the binding of antigenic peptides on MHCs. Yeast display technology has proven an effective way to gain insight into the underpinnings of peptide-MHC specificity enabling the switching of TCR affinity and specificity to unrelated antigens through directed evolution. Interestingly, in vitro directed evolution also generates mutants that lose peptide specificity. Here, we provide further detail of one of these cross-reactive TCRs, S3–4, which binds tightly but with a highly unusual geometry. Despite binding with an affinity that is characteristic of a strong agonist, S3–4’s odd binding geometry does not support T cell signaling. Further investigation with functional experiments and 2D kinetics shows that lack of signaling by S3–4 is ultimately attributable to the TCR’s inability to reach ligand. Although S3–4 is an example from a constrained system generated outside the bounds of usual immune function, our results show how unusual binding can influence T cell function and further demonstrate how divergences between 3D and 2D binding parameters can emerge.
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Affiliation(s)
| | | | - David M Kranz
- 4Department of Pathobiology, University of Illinois at Urbana-Champaign
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30
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George MM, Brennick CA, Moussa MM, Hagymasi AT, Seesi SA, Shcheglova TV, Englander RP, Keller GL, Balsbaugh JL, Baker BM, Mandoiu II, Srivastava PK. Unbiased analysis of all possible neoepitopes of MC38-FABF tumor reveals a new universe of cancer neoepitopes with unexpected properties. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.239.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Cancer neoepitopes are the only truly tumor-specific antigens and therefore, the most suitable as cancer vaccines. Current methods to predict neoepitopes, based on studies of viral epitopes, emphasize high affinity MHC-peptide interactions. Increasing evidence in human and murine models indicates that the present neoepitope prediction methods are mostly inaccurate in predicting true MHC I-restricted cancer neoepitopes. Here, in a completely unbiased approach, all possible neoepitopes in a mouse tumor model were tested for their ability to mediate tumor rejection and also CD8+ T cell responses. These studies show that the true tumor rejecting neoepitopes have different properties from those of viral epitopes. Further, CD8+ T cell responses elicited by these neoepitopes possess a more plastic chromatin phenotype with stem-like properties that is known to be associated with anti-viral and anti-tumor immune responses. Such cancer neoepitopes can be exploited for generation of personalized cancer vaccines.
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Affiliation(s)
| | | | - Marmar M Moussa
- 1University of Connecticut, Health Center
- 2Department of Computer Sciences, University of Connecticut
| | | | | | | | | | | | | | | | - Ion I. Mandoiu
- 2Department of Computer Sciences, University of Connecticut
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31
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Alonso JA, Singh NK, Devancaze L, Devlin J, Baker BM. Structure-guided design of the TIL1383I T cell receptor. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.80.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
T cell therapy is an exciting form of cancer immunotherapy in which T cells are engineered to target specific tumor antigens. We employed a structure-guided design approach with the goal of engineering a safer and more effective variant of the TIL1383I T cell receptor (TCR) currently under study in clinical trials for malignant melanoma. Using our unpublished structure of TIL1383I we are in process of designing a panel of TCR variants with the goal of identifying candidates that improve “focus” towards the tyrosinase antigen presented on the MHC class I molecule HLA-A2. Structural analysis of TIL1383I revealed key residues, particularly beta-chain residues E97, G101, L102, responsible for engaging the tyrosinase peptide bound to HLA-A2. The crystal structure of TIL1383I in complex with tyrosinase-HLA-A2 also highlighted its uncharacteristic binding geometry and we therefore hypothesize that this binding orientation is associated with the observed CD8 co-receptor independence of TIL1383I. Indeed, functional analysis with TIL1383I-transduced CD8-positive and CD8-negative T cells, transduced T cells expressing a truncated CD8 lacking the intracellular LCK signaling domain, and tyrosinase peptide variants presented by HLA-A2 mutants outline this co-receptor independence. Combined with our interrogation of tyrosinase peptide cross-reactivity via a peptide positional scanning library approach, structure-guided design resulted in the identification of TIL1383I variants with improved binding affinities to the tyrosinase peptide as well as an understanding of structural characteristics that may contribute to TIL1383I’s co-receptor independence.
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32
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Singh NK, Abualrous ET, Ayres CM, Noé F, Gowthaman R, Pierce BG, Baker BM. Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen. Proteins 2020; 88:503-513. [PMID: 31589793 PMCID: PMC6982585 DOI: 10.1002/prot.25829] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 11/11/2022]
Abstract
Recognition of antigenic peptides bound to major histocompatibility complex (MHC) proteins by αβ T cell receptors (TCRs) is a hallmark of T cell mediated immunity. Recent data suggest that variations in TCR binding geometry may influence T cell signaling, which could help explain outliers in relationships between physical parameters such as TCR-pMHC binding affinity and T cell function. Traditionally, TCR binding geometry has been described with simple descriptors such as the crossing angle, which quantifies what has become known as the TCR's diagonal binding mode. However, these descriptors often fail to reveal distinctions in binding geometry that are apparent through visual inspection. To provide a better framework for relating TCR structure to T cell function, we developed a comprehensive system for quantifying the geometries of how TCRs bind peptide/MHC complexes. We show that our system can discern differences not clearly revealed by more common methods. As an example of its potential to impact biology, we used it to reveal differences in how TCRs bind class I and class II peptide/MHC complexes, which we show allow the TCR to maximize access to and "read out" the peptide antigen. We anticipate our system will be of use in not only exploring these and other details of TCR-peptide/MHC binding interactions, but also addressing questions about how TCR binding geometry relates to T cell function, as well as modeling structural properties of class I and class II TCR-peptide/MHC complexes from sequence information. The system is available at https://tcr3d.ibbr.umd.edu/tcr_com or for download as a script.
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MESH Headings
- Binding Sites
- Crystallography, X-Ray
- Histocompatibility Antigens Class I/chemistry
- Histocompatibility Antigens Class I/immunology
- Histocompatibility Antigens Class I/metabolism
- Histocompatibility Antigens Class II/chemistry
- Histocompatibility Antigens Class II/immunology
- Histocompatibility Antigens Class II/metabolism
- Humans
- Models, Molecular
- Principal Component Analysis
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocytes/chemistry
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Thermodynamics
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Affiliation(s)
- Nishant K. Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Esam T. Abualrous
- Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Frank Noé
- Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Ragul Gowthaman
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Brian G. Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
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33
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Groth E, Ayres CM, Baker BM, Corcelli SA. Modeling the Binding Mechanism of a T Cell Receptor and Major Histocompatibility Complex. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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34
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Spear TT, Evavold BD, Baker BM, Nishimura MI. Understanding TCR affinity, antigen specificity, and cross-reactivity to improve TCR gene-modified T cells for cancer immunotherapy. Cancer Immunol Immunother 2019; 68:1881-1889. [PMID: 31595324 PMCID: PMC11028285 DOI: 10.1007/s00262-019-02401-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022]
Abstract
Adoptive cell transfer (ACT) using T cell receptor (TCR) gene-modified T cells is an exciting and rapidly evolving field. Numerous preclinical and clinical studies have demonstrated various levels of feasibility, safety, and efficacy using TCR-engineered T cells to treat cancer and viral infections. Although evidence suggests their use can be effective, to what extent and how to improve these therapeutics are still matters of investigation. As TCR affinity has been generally accepted as the central role in defining T cell specificity and sensitivity, selection for and generation of high affinity TCRs has remained a fundamental approach to design more potent T cells. However, traditional methods for affinity-enhancement by random mutagenesis can induce undesirable cross-reactivity causing on- and off-target adverse events, generate exhausted effectors by overstimulation, and ignore other kinetic and cellular parameters that have been shown to impact antigen specificity. In this Focussed Research Review, we comment on the preclinical and clinical potential of TCR gene-modified T cells, summarize our contributions challenging the role TCR affinity plays in antigen recognition, and explore how structure-guided design can be used to manipulate antigen specificity and TCR cross-reactivity to improve the safety and efficacy of TCR gene-modified T cells used in ACT.
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Affiliation(s)
- Timothy T Spear
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, 2160 S. 1st Ave, Bldg 112, Room 308, Maywood, IL, 60153, USA.
| | - Brian D Evavold
- Department of Pathology, Microbiology and Immunology, University of Utah, Salt Lake City, UT, 84112, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, 46530, USA
| | - Michael I Nishimura
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, 2160 S. 1st Ave, Bldg 112, Room 308, Maywood, IL, 60153, USA
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35
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Riley TP, Keller GLJ, Smith AR, Davancaze LM, Arbuiso AG, Devlin JR, Baker BM. Structure Based Prediction of Neoantigen Immunogenicity. Front Immunol 2019; 10:2047. [PMID: 31555277 PMCID: PMC6724579 DOI: 10.3389/fimmu.2019.02047] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/13/2019] [Indexed: 12/30/2022] Open
Abstract
The development of immunological therapies that incorporate peptide antigens presented to T cells by MHC proteins is a long sought-after goal, particularly for cancer, where mutated neoantigens are being explored as personalized cancer vaccines. Although neoantigens can be identified through sequencing, bioinformatics and mass spectrometry, identifying those which are immunogenic and able to promote tumor rejection remains a significant challenge. Here we examined the potential of high-resolution structural modeling followed by energetic scoring of structural features for predicting neoantigen immunogenicity. After developing a strategy to rapidly and accurately model nonameric peptides bound to the common class I MHC protein HLA-A2, we trained a neural network on structural features that influence T cell receptor (TCR) and peptide binding energies. The resulting structurally-parameterized neural network outperformed methods that do not incorporate explicit structural or energetic properties in predicting CD8+ T cell responses of HLA-A2 presented nonameric peptides, while also providing insight into the underlying structural and biophysical mechanisms governing immunogenicity. Our proof-of-concept study demonstrates the potential for structure-based immunogenicity predictions in the development of personalized peptide-based vaccines.
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Affiliation(s)
| | | | | | | | | | | | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
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36
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Ebrahimi-Nik H, Michaux J, Corwin WL, Keller GL, Shcheglova T, Pak H, Coukos G, Baker BM, Mandoiu II, Bassani-Sternberg M, Srivastava PK. Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejection. JCI Insight 2019; 5:129152. [PMID: 31219806 PMCID: PMC6675551 DOI: 10.1172/jci.insight.129152] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Neoepitopes are the only truly tumor-specific antigens. Although potential neoepitopes can be readily identified using genomics, the neoepitopes that mediate tumor rejection constitute a small minority, and there is little consensus on how to identify them. Here, for the first time to our knowledge, we use a combination of genomics, unbiased discovery mass spectrometry (MS) immunopeptidomics, and targeted MS to directly identify neoepitopes that elicit actual tumor rejection in mice. We report that MS-identified neoepitopes are an astonishingly rich source of tumor rejection-mediating neoepitopes (TRMNs). MS has also demonstrated unambiguously the presentation by MHC I, of confirmed tumor rejection neoepitopes that bind weakly to MHC I; this was done using DCs exogenously loaded with long peptides containing the weakly binding neoepitopes. Such weakly MHC I–binding neoepitopes are routinely excluded from analysis, and our demonstration of their presentation, and their activity in tumor rejection, reveals a broader universe of tumor-rejection neoepitopes than presently imagined. Modeling studies show that a mutation in the active neoepitope alters its conformation such that its T cell receptor–facing surface is substantially altered, increasing its exposed hydrophobicity. No such changes are observed in the inactive neoepitope. These results broaden our understanding of antigen presentation and help prioritize neoepitopes for personalized cancer immunotherapy. Neoepitopes identified by mass spectrometry are a rich source of tumor rejection antigens, including those with a weak binding to MHC I.
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Affiliation(s)
- Hakimeh Ebrahimi-Nik
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Justine Michaux
- University of Lausanne, Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - William L Corwin
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Grant Lj Keller
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Tatiana Shcheglova
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - HuiSong Pak
- University of Lausanne, Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - George Coukos
- University of Lausanne, Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Brian M Baker
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Ion I Mandoiu
- Department of Computer Sciences, University of Connecticut School of Engineering, Storrs, Connecticut, USA
| | - Michal Bassani-Sternberg
- University of Lausanne, Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Pramod K Srivastava
- Department of Immunology and Carole and Ray Neag Comprehensive Cancer Center, University of Connecticut School of Medicine, Farmington, Connecticut, USA
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37
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Ayres CM, Abualrous ET, Bailey A, Abraham C, Hellman LM, Corcelli SA, Noé F, Elliott T, Baker BM. Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility. Front Immunol 2019; 10:966. [PMID: 31130956 PMCID: PMC6509175 DOI: 10.3389/fimmu.2019.00966] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/15/2019] [Indexed: 11/21/2022] Open
Abstract
T cell receptor (TCR) recognition of antigenic peptides bound and presented by class I major histocompatibility complex (MHC) proteins underlies the cytotoxic immune response to diseased cells. Crystallographic structures of TCR-peptide/MHC complexes have demonstrated how TCRs simultaneously interact with both the peptide and the MHC protein. However, it is increasingly recognized that, beyond serving as a static platform for peptide presentation, the physical properties of class I MHC proteins are tuned by different peptides in ways that are not always structurally visible. These include MHC protein motions, or dynamics, which are believed to influence interactions with a variety of MHC-binding proteins, including not only TCRs, but other activating and inhibitory receptors as well as components of the peptide loading machinery. Here, we investigated the mechanisms by which peptides tune the dynamics of the common class I MHC protein HLA-A2. By examining more than 50 lengthy molecular dynamics simulations of HLA-A2 presenting different peptides, we identified regions susceptible to dynamic tuning, including regions in the peptide binding domain as well as the distal α3 domain. Further analyses of the simulations illuminated mechanisms by which the influences of different peptides are communicated throughout the protein, and involve regions of the peptide binding groove, the β2-microglobulin subunit, and the α3 domain. Overall, our results demonstrate that the class I MHC protein is a highly tunable peptide sensor whose physical properties vary considerably with bound peptide. Our data provides insight into the underlying principles and suggest a role for dynamically driven allostery in the immunological function of MHC proteins.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Esam T Abualrous
- Computational Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Alistair Bailey
- Institute for Life Sciences and Centre for Cancer Immunology, University of Southampton, Southampton, United Kingdom
| | - Christian Abraham
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Lance M Hellman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Frank Noé
- Computational Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Tim Elliott
- Institute for Life Sciences and Centre for Cancer Immunology, University of Southampton, Southampton, United Kingdom
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
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38
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Hellman LM, Foley KC, Singh NK, Alonso JA, Riley TP, Devlin JR, Ayres CM, Keller GLJ, Zhang Y, Vander Kooi CW, Nishimura MI, Baker BM. Improving T Cell Receptor On-Target Specificity via Structure-Guided Design. Mol Ther 2018; 27:300-313. [PMID: 30617019 DOI: 10.1016/j.ymthe.2018.12.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/05/2018] [Accepted: 12/08/2018] [Indexed: 12/30/2022] Open
Abstract
T cell receptors (TCRs) have emerged as a new class of immunological therapeutics. However, though antigen specificity is a hallmark of adaptive immunity, TCRs themselves do not possess the high specificity of monoclonal antibodies. Although a necessary function of T cell biology, the resulting cross-reactivity presents a significant challenge for TCR-based therapeutic development, as it creates the potential for off-target recognition and immune toxicity. Efforts to enhance TCR specificity by mimicking the antibody maturation process and enhancing affinity can inadvertently exacerbate TCR cross-reactivity. Here we demonstrate this concern by showing that even peptide-targeted mutations in the TCR can introduce new reactivities against peptides that bear similarity to the original target. To counteract this, we explored a novel structure-guided approach for enhancing TCR specificity independent of affinity. Tested with the MART-1-specific TCR DMF5, our approach had a small but discernible impact on cross-reactivity toward MART-1 homologs yet was able to eliminate DMF5 cross-recognition of more divergent, unrelated epitopes. Our study provides a proof of principle for the use of advanced structure-guided design techniques for improving TCR specificity, and it suggests new ways forward for enhancing TCRs for therapeutic use.
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Affiliation(s)
- Lance M Hellman
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Kendra C Foley
- Department of Surgery and the Cardinal Bernardin Cancer Center, Loyola University of Chicago, Maywood, IL, USA
| | - Nishant K Singh
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Timothy P Riley
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Jason R Devlin
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Cory M Ayres
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Grant L J Keller
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Yuting Zhang
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Craig W Vander Kooi
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Michael I Nishimura
- Department of Surgery and the Cardinal Bernardin Cancer Center, Loyola University of Chicago, Maywood, IL, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
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39
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Riley TP, Baker BM. The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeutics. Semin Cell Dev Biol 2018; 84:30-41. [DOI: 10.1016/j.semcdb.2017.10.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/07/2017] [Accepted: 10/17/2017] [Indexed: 12/29/2022]
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40
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Riley TP, Hellman LM, Gee MH, Mendoza JL, Alonso JA, Foley KC, Nishimura MI, Vander Kooi CW, Garcia KC, Baker BM. T cell receptor cross-reactivity expanded by dramatic peptide-MHC adaptability. Nat Chem Biol 2018; 14:934-942. [PMID: 30224695 PMCID: PMC6371774 DOI: 10.1038/s41589-018-0130-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/25/2018] [Indexed: 12/31/2022]
Abstract
T cell receptor cross-reactivity allows a fixed T cell repertoire to respond to a much larger universe of potential antigens. Recent work has emphasized the importance of peptide structural and chemical homology, as opposed to sequence similarity, in T cell receptor cross-reactivity. Surprisingly though, T cell receptors can also cross-react between ligands with little physiochemical commonalities. Studying the clinically relevant receptor DMF5, we demonstrate that cross-recognition of such divergent antigens can occur through mechanisms that involve heretofore unanticipated rearrangements in the peptide and presenting MHC protein, including binding-induced peptide register shifts and extensions from MHC peptide binding grooves. Moreover, cross-reactivity can proceed even when such dramatic rearrangements do not translate into structural or chemical molecular mimicry. Beyond demonstrating new principles of T cell receptor cross-reactivity, our results have implications for efforts to predict and control T cell specificity and cross-reactivity, and highlight challenges associated with predicting T cell reactivities.
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Affiliation(s)
- Timothy P Riley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Lance M Hellman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Marvin H Gee
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Juan L Mendoza
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jesus A Alonso
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kendra C Foley
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - Michael I Nishimura
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL, USA
| | - Craig W Vander Kooi
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA. .,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
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41
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Eby JM, Smith AR, Riley TP, Cosgrove C, Ankney CM, Henning SW, Paulos CM, Garrett-Mayer E, Luiten RM, Nishimura MI, Baker BM, Le Poole IC. Molecular properties of gp100-reactive T-cell receptors drive the cytokine profile and antitumor efficacy of transgenic host T cells. Pigment Cell Melanoma Res 2018; 32:68-78. [PMID: 30009548 DOI: 10.1111/pcmr.12724] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/04/2018] [Accepted: 07/11/2018] [Indexed: 11/27/2022]
Abstract
To study the contribution of T-cell receptors (TCR) to resulting T-cell responses, we studied three different human αβ TCRs, reactive to the same gp100-derived peptide presented in the context of HLA-A*0201. When expressed in primary CD8 T cells, all receptors elicited classic antigen-induced IFN-γ responses, which correlated with TCR affinity for peptide-MHC in the order T4H2 > R6C12 > SILv44. However, SILv44 elicited superior IL-17A release. Importantly, in vivo, SILv44-transgenic T cells mediated superior antitumor responses to 888-A2 + human melanoma tumor cells upon adoptive transfer into tumor-challenged mice while maintaining IL-17 expression. Modeling of the TCR ternary complexes suggested architectural differences between SILv44 and the other complexes, providing a potential structural basis for the observed differences. Overall, the data reveal a more prominent role for the T-cell receptor in defining host T-cell physiology than traditionally assumed, while parameters beyond IFN-γ secretion and TCR affinity ultimately determine the reactivity of tumor-reactive T cells.
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Affiliation(s)
- Jonathan M Eby
- Oncology Research Institute, Loyola University Chicago, Maywood, Illinois
| | - Angela R Smith
- Department of Chemistry and Biochemistry, The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana
| | - Timothy P Riley
- Department of Chemistry and Biochemistry, The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana
| | - Cormac Cosgrove
- Department of Dermatology, Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - Christian M Ankney
- Oncology Research Institute, Loyola University Chicago, Maywood, Illinois
| | - Steven W Henning
- Department of Dermatology, Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois
| | - Chrystal M Paulos
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina
| | - Elizabeth Garrett-Mayer
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Rosalie M Luiten
- Netherlands Institute for Pigment Disorders, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Dermatology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Michael I Nishimura
- Oncology Research Institute, Loyola University Chicago, Maywood, Illinois.,Department of Surgery, Medical University of South Carolina, Charleston, South Carolina
| | - Brian M Baker
- Department of Chemistry and Biochemistry, The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana
| | - I Caroline Le Poole
- Oncology Research Institute, Loyola University Chicago, Maywood, Illinois.,Department of Dermatology, Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois.,Department of Microbiology and Immunology, Northwestern University, Chicago, Illinois
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42
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Smith AR, Eby JM, Ankney CM, Cosgrove C, Henning SW, Nishimura MI, Le Poole C, Baker BM. Structural Characterization of Vitiligo Associated T Cell Receptor: Towards the Development of Improved Melanoma Immunotherapy. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.lb38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Angela R Smith
- Department of Chemistry and Biochemistry and the Harper Cancer Research InstituteUniversity of Notre DameNotre DameIN
| | - Jonathan M Eby
- Oncology Research Institute, Loyola University ChicagoMaywoodIL
| | | | - Cormac Cosgrove
- Department of DermatologyLurie Comprehensive Cancer CenterChicagoIL
| | - Steven W Henning
- Department of DermatologyLurie Comprehensive Cancer CenterChicagoIL
| | - Michael I Nishimura
- Oncology Research Institute, Loyola University ChicagoMaywoodIL
- Department of SurgeryLoyola University ChicagoMaywoodIL
| | - Caroline Le Poole
- Oncology Research Institute, Loyola University ChicagoMaywoodIL
- Departments of Pathology, Microbiology and InmmunologyLoyola University ChicagoMaywoodIL
- Department of DermatologyLurie Comprehensive Cancer CenterChicagoIL
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research InstituteUniversity of Notre DameNotre DameIN
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43
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Davancaze LM, Singh NK, Anderson MJ, Huyke FA, Nishimura MI, Baker BM. Structural Characterization of the TIL 1383I T Cell Receptor. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.806.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lauren M. Davancaze
- Department of Chemistry & Biochemistry and the Harper Cancer Research InstituteUniversity of Notre DameSouth BendIN
| | - Nishant K. Singh
- Department of Chemistry & Biochemistry and the Harper Cancer Research InstituteUniversity of Notre DameSouth BendIN
| | - Michael J. Anderson
- Department of Chemistry & Biochemistry and the Harper Cancer Research InstituteUniversity of Notre DameSouth BendIN
| | - Fernando A. Huyke
- Department of Chemistry & Biochemistry and the Harper Cancer Research InstituteUniversity of Notre DameSouth BendIN
| | | | - Brian M. Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research InstituteUniversity of Notre DameSouth BendIN
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44
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Spear TT, Wang Y, Smith TW, Simms PE, Garrett-Mayer E, Hellman LM, Baker BM, Nishimura MI. Altered Peptide Ligands Impact the Diversity of Polyfunctional Phenotypes in T Cell Receptor Gene-Modified T Cells. Mol Ther 2018; 26:996-1007. [PMID: 29503203 DOI: 10.1016/j.ymthe.2018.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 01/10/2018] [Accepted: 01/16/2018] [Indexed: 12/23/2022] Open
Abstract
The use of T cell receptor (TCR) gene-modified T cells in adoptive cell transfer has had promising clinical success, but often, simple preclinical evaluation does not necessarily accurately predict treatment efficacy or safety. Preclinical studies generally evaluate one or a limited number of type 1 cytokines to assess antigen recognition. However, recent studies have implicated other "typed" T cells in effective anti-tumor/viral immunity, and limited functional evaluations may underestimate cross-reactivity. In this study, we use an altered peptide ligand (APL) model and multi-dimensional flow cytometry to evaluate polyfunctionality of TCR gene-modified T cells. Evaluating six cytokines and the lytic marker CD107a on a per cell basis revealed remarkably diverse polyfunctional phenotypes within a single T cell culture and among peripheral blood lymphocyte (PBL) donors. This polyfunctional assessment identified unexpected phenotypes, including cells producing both type 1 and type 2 cytokines, and highlighted interferon γneg (IFNγneg) antigen-reactive populations overlooked in our previous studies. Additionally, APLs skewed functional phenotypes to be less polyfunctional, which was not necessarily related to changes in TCR-peptide-major histocompatibility complex (pMHC) affinity. A better understanding of gene-modified T cell functional diversity may help identify optimal therapeutic phenotypes, predict clinical responses, anticipate off-target recognition, and improve the design and delivery of TCR gene-modified T cells.
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Affiliation(s)
- Timothy T Spear
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL 60153, USA.
| | - Yuan Wang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Thomas W Smith
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Patricia E Simms
- Flow Cytometry Core Facility, Office of Research Services, Loyola University Chicago, Maywood, IL, 60153 USA
| | - Elizabeth Garrett-Mayer
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29415, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29415, USA
| | - Lance M Hellman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Michael I Nishimura
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, Maywood, IL 60153, USA
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45
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Baker BM. Accounting for Specificity and Cross-Reactivity in T Cell Receptor Molecular Recognition. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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46
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Spear TT, Wang Y, Foley KC, Murray DC, Scurti GM, Simms PE, Garrett-Mayer E, Hellman LM, Baker BM, Nishimura MI. Critical biological parameters modulate affinity as a determinant of function in T-cell receptor gene-modified T-cells. Cancer Immunol Immunother 2017; 66:1411-1424. [PMID: 28634816 PMCID: PMC5647210 DOI: 10.1007/s00262-017-2032-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 06/11/2017] [Indexed: 12/26/2022]
Abstract
T-cell receptor (TCR)-pMHC affinity has been generally accepted to be the most important factor dictating antigen recognition in gene-modified T-cells. As such, there is great interest in optimizing TCR-based immunotherapies by enhancing TCR affinity to augment the therapeutic benefit of TCR gene-modified T-cells in cancer patients. However, recent clinical trials using affinity-enhanced TCRs in adoptive cell transfer (ACT) have observed unintended and serious adverse events, including death, attributed to unpredicted off-tumor or off-target cross-reactivity. It is critical to re-evaluate the importance of other biophysical, structural, or cellular factors that drive the reactivity of TCR gene-modified T-cells. Using a model for altered antigen recognition, we determined how TCR-pMHC affinity influenced the reactivity of hepatitis C virus (HCV) TCR gene-modified T-cells against a panel of naturally occurring HCV peptides and HCV-expressing tumor targets. The impact of other factors, such as TCR-pMHC stabilization and signaling contributions by the CD8 co-receptor, as well as antigen and TCR density were also evaluated. We found that changes in TCR-pMHC affinity did not always predict or dictate IFNγ release or degranulation by TCR gene-modified T-cells, suggesting that less emphasis might need to be placed on TCR-pMHC affinity as a means of predicting or augmenting the therapeutic potential of TCR gene-modified T-cells used in ACT. A more complete understanding of antigen recognition by gene-modified T-cells and a more rational approach to improve the design and implementation of novel TCR-based immunotherapies is necessary to enhance efficacy and maximize safety in patients.
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Affiliation(s)
- Timothy T Spear
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, 2160 S. 1st Ave, Bldg 112, Room 308, Maywood, IL, 60153, USA.
| | - Yuan Wang
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Kendra C Foley
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, 2160 S. 1st Ave, Bldg 112, Room 308, Maywood, IL, 60153, USA
| | - David C Murray
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, 2160 S. 1st Ave, Bldg 112, Room 308, Maywood, IL, 60153, USA
| | - Gina M Scurti
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, 2160 S. 1st Ave, Bldg 112, Room 308, Maywood, IL, 60153, USA
| | - Patricia E Simms
- Flow Cytometry Core Facility, Office of Research Services, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Elizabeth Garrett-Mayer
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, 29415, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29415, USA
| | - Lance M Hellman
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Michael I Nishimura
- Department of Surgery, Cardinal Bernardin Cancer Center, Loyola University Chicago, 2160 S. 1st Ave, Bldg 112, Room 308, Maywood, IL, 60153, USA
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47
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Singh NK, Riley TP, Baker SCB, Borrman T, Weng Z, Baker BM. Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes. J Immunol 2017; 199:2203-2213. [PMID: 28923982 DOI: 10.4049/jimmunol.1700744] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/10/2017] [Indexed: 12/14/2022]
Abstract
T cell specificity emerges from a myriad of processes, ranging from the biological pathways that control T cell signaling to the structural and physical mechanisms that influence how TCRs bind peptides and MHC proteins. Of these processes, the binding specificity of the TCR is a key component. However, TCR specificity is enigmatic: TCRs are at once specific but also cross-reactive. Although long appreciated, this duality continues to puzzle immunologists and has implications for the development of TCR-based therapeutics. In this review, we discuss TCR specificity, emphasizing results that have emerged from structural and physical studies of TCR binding. We show how the TCR specificity/cross-reactivity duality can be rationalized from structural and biophysical principles. There is excellent agreement between predictions from these principles and classic predictions about the scope of TCR cross-reactivity. We demonstrate how these same principles can also explain amino acid preferences in immunogenic epitopes and highlight opportunities for structural considerations in predictive immunology.
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Affiliation(s)
- Nishant K Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556; and
| | - Timothy P Riley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556; and
| | - Sarah Catherine B Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556; and
| | - Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556; .,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556; and
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48
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Moore T, Wagner CR, Scurti GM, Hutchens KA, Godellas C, Clark AL, Kolawole EM, Hellman LM, Singh NK, Huyke FA, Wang SY, Calabrese KM, Embree HD, Orentas R, Shirai K, Dellacecca E, Garrett-Mayer E, Li M, Eby JM, Stiff PJ, Evavold BD, Baker BM, Le Poole IC, Dropulic B, Clark JI, Nishimura MI. Clinical and immunologic evaluation of three metastatic melanoma patients treated with autologous melanoma-reactive TCR-transduced T cells. Cancer Immunol Immunother 2017; 67:311-325. [PMID: 29052782 DOI: 10.1007/s00262-017-2073-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 10/03/2017] [Indexed: 11/24/2022]
Abstract
Malignant melanoma incidence has been increasing for over 30 years, and despite promising new therapies, metastatic disease remains difficult to treat. We describe preliminary results from a Phase I clinical trial (NCT01586403) of adoptive cell therapy in which three patients received autologous CD4+ and CD8+ T cells transduced with a lentivirus carrying a tyrosinase-specific TCR and a marker protein, truncated CD34 (CD34t). This unusual MHC Class I-restricted TCR produces functional responses in both CD4+ and CD8+ T cells. Parameters monitored on transduced T cells included activation (CD25, CD69), inhibitory (PD-1, TIM-3, CTLA-4), costimulatory (OX40), and memory (CCR7) markers. For the clinical trial, T cells were activated, transduced, selected for CD34t+ cells, then re-activated, and expanded in IL-2 and IL-15. After lymphodepleting chemotherapy, patients were given transduced T cells and IL-2, and were followed for clinical and biological responses. Transduced T cells were detected in the circulation of three treated patients for the duration of observation (42, 523, and 255 days). Patient 1 tolerated the infusion well but died from progressive disease after 6 weeks. Patient 2 had a partial response by RECIST criteria then progressed. After progressing, Patient 2 was given high-dose IL-2 and subsequently achieved complete remission, coinciding with the development of vitiligo. Patient 3 had a mixed response that did not meet RECIST criteria for a clinical response and developed vitiligo. In two of these three patients, adoptive transfer of tyrosinase-reactive TCR-transduced T cells into metastatic melanoma patients had clinical and/or biological activity without serious adverse events.
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Affiliation(s)
- Tamson Moore
- Department of Surgery, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA.
| | - Courtney Regan Wagner
- Department of Medicine, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
| | - Gina M Scurti
- Department of Surgery, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
| | - Kelli A Hutchens
- Department of Pathology, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
- Forefront Dermatology, 801 York St, Manitowoc, WI, 54220, USA
| | - Constantine Godellas
- Department of Surgery, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
| | - Ann Lau Clark
- Department of Medicine, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
| | | | - Lance M Hellman
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46656, USA
| | - Nishant K Singh
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46656, USA
| | - Fernando A Huyke
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46656, USA
| | - Siao-Yi Wang
- Department of Surgery, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
| | - Kelly M Calabrese
- Department of Surgery, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
- Abbvie, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Heather D Embree
- Lentigen Technology Inc, A Miltenyi Biotec Company, 910 Clopper Road Suite 200S, Gaithersburg, MD, 20878, USA
| | - Rimas Orentas
- Lentigen Technology Inc, A Miltenyi Biotec Company, 910 Clopper Road Suite 200S, Gaithersburg, MD, 20878, USA
| | - Keisuke Shirai
- Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas St, Charleston, SC, 29425, USA
- Dartmouth-Hitchcock, Norris Cotton Cancer Center, One Medical Center Dr, Lebanon, NH, 03756, USA
| | - Emilia Dellacecca
- Department of Pathology, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
- Department of Microbiology, and Immunology, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, USA
| | - Elizabeth Garrett-Mayer
- Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas St, Charleston, SC, 29425, USA
| | - Mingli Li
- Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas St, Charleston, SC, 29425, USA
- Bluebird Biology, 60 Binney St., Cambridge, MA, 02142, USA
| | - Jonathan M Eby
- Department of Pathology, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
- Department of Microbiology, and Immunology, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, USA
| | - Patrick J Stiff
- Department of Medicine, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
| | - Brian D Evavold
- O. Wayne Rollins Research Center, Emory University, Room 3127, 1510 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46656, USA
| | - I Caroline Le Poole
- Department of Pathology, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
- Department of Microbiology, and Immunology, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, USA
- Lurie Comprehensive Cancer Center, Department of Dermatology, Northwestern University at Chicago, Room 5-113, 303 East Superior Street, Chicago, IL, 60611, USA
| | - Boro Dropulic
- Lentigen Technology Inc, A Miltenyi Biotec Company, 910 Clopper Road Suite 200S, Gaithersburg, MD, 20878, USA
| | - Joseph I Clark
- Department of Medicine, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
| | - Michael I Nishimura
- Department of Surgery, Loyola University Chicago, 2160 S. 1st Avenue, Maywood, IL, 60153, USA
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49
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Abstract
Recognition of antigens by T cell receptors (TCRs) underlies cellular immunity. By comparing how different TCRs recognize the key antigens associated with celiac disease, Petersen et al. (2016), in this issue of Structure, show how celiac antigen properties select immunologically distinct yet structurally and physically compatible TCRs, ultimately driving autoimmunity.
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Affiliation(s)
- Nishant K Singh
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA.
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA.
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50
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Ayres CM, Corcelli SA, Baker BM. Peptide and Peptide-Dependent Motions in MHC Proteins: Immunological Implications and Biophysical Underpinnings. Front Immunol 2017; 8:935. [PMID: 28824655 PMCID: PMC5545744 DOI: 10.3389/fimmu.2017.00935] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/21/2017] [Indexed: 01/28/2023] Open
Abstract
Structural biology of peptides presented by class I and class II MHC proteins has transformed immunology, impacting our understanding of fundamental immune mechanisms and allowing researchers to rationalize immunogenicity and design novel vaccines. However, proteins are not static structures as often inferred from crystallographic structures. Their components move and breathe individually and collectively over a range of timescales. Peptides bound within MHC peptide-binding grooves are no exception and their motions have been shown to impact recognition by T cell and other receptors in ways that influence function. Furthermore, peptides tune the motions of MHC proteins themselves, which impacts recognition of peptide/MHC complexes by other proteins. Here, we review the motional properties of peptides in MHC binding grooves and discuss how peptide properties can influence MHC motions. We briefly review theoretical concepts about protein motion and highlight key data that illustrate immunological consequences. We focus primarily on class I systems due to greater availability of data, but segue into class II systems as the concepts and consequences overlap. We suggest that characterization of the dynamic “energy landscapes” of peptide/MHC complexes and the resulting functional consequences is one of the next frontiers in structural immunology.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
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