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Ma J, Ayres CM, Brambley CA, Chandran SS, Rosales TJ, Corcelli SA, Kovrigin EL, Klebanoff CA, Baker BM. Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity. RESEARCH SQUARE 2024:rs.3.rs-4457195. [PMID: 38854019 PMCID: PMC11160895 DOI: 10.21203/rs.3.rs-4457195/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The inherent cross-reactivity of the T cell receptor (TCR) is balanced by high specificity, which often manifests in confounding ways not easily interpretable from static structures. We show here that TCR discrimination between an HLA-A*03:01 (HLA-A3)-restricted public neoantigen derived from mutant PIK3CA and its wild-type (WT) counterpart emerges from motions within the HLA binding groove that vary with the identity of the peptide's first primary anchor. The motions form a dynamic gate that in the complex with the WT peptide impedes a large conformational change required for TCR binding. The more rigid neoantigen is insusceptible to this limiting dynamic, and with the gate open, is able to transit its central tryptophan residue underneath the peptide backbone to the contralateral side of the HLA-A3 peptide binding groove, facilitating TCR binding. Our findings reveal a novel mechanism driving TCR specificity for a cancer neoantigen that is rooted in the dynamic and allosteric nature of peptide/MHC-I complexes, with implications for resolving long-standing and often confounding questions about the determinants of T cell specificity.
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Affiliation(s)
- Jiaqi Ma
- 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
| | - Cory M Ayres
- 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
| | - Chad A Brambley
- 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
| | - Smita S Chandran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
- Center for Cell Engineering, MSKCC, New York, NY, USA
| | - Tatiana J Rosales
- 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
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Evgenii L Kovrigin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Christopher A Klebanoff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
- Center for Cell Engineering, MSKCC, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, New York, NY, 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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2
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A class-mismatched TCR bypasses MHC restriction via an unorthodox but fully functional binding geometry. Nat Commun 2022; 13:7189. [PMID: 36424374 PMCID: PMC9691722 DOI: 10.1038/s41467-022-34896-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
MHC restriction, which describes the binding of TCRs from CD4+ T cells to class II MHC proteins and TCRs from CD8+ T cells to class I MHC proteins, is a hallmark of immunology. Seemingly rare TCRs that break this paradigm exist, but mechanistic insight into their behavior is lacking. TIL1383I is a prototypical class-mismatched TCR, cloned from a CD4+ T cell but recognizing the tyrosinase tumor antigen presented by the class I MHC HLA-A2 in a fully functional manner. Here we find that TIL1383I binds this class I target with a highly atypical geometry. Despite unorthodox binding, TCR signaling, antigen specificity, and the ability to use CD8 are maintained. Structurally, a key feature of TIL1383I is an exceptionally long CDR3β loop that mediates functions that are traditionally performed separately by hypervariable and germline loops in canonical TCR structures. Our findings thus expand the range of known TCR binding geometries compatible with normal function and specificity, provide insight into the determinants of MHC restriction, and may help guide TCR selection and engineering for immunotherapy.
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3
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Wegrecki M, Ocampo TA, Gunasinghe SD, von Borstel A, Tin SY, Reijneveld JF, Cao TP, Gully BS, Le Nours J, Moody DB, Van Rhijn I, Rossjohn J. Atypical sideways recognition of CD1a by autoreactive γδ T cell receptors. Nat Commun 2022; 13:3872. [PMID: 35790773 PMCID: PMC9256601 DOI: 10.1038/s41467-022-31443-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/16/2022] [Indexed: 01/04/2023] Open
Abstract
CD1a is a monomorphic antigen-presenting molecule on dendritic cells that presents lipids to αβ T cells. Whether CD1a represents a ligand for other immune receptors remains unknown. Here we use CD1a tetramers to show that CD1a is a ligand for Vδ1+ γδ T cells. Functional studies suggest that two γδ T cell receptors (TCRs) bound CD1a in a lipid-independent manner. The crystal structures of three Vγ4Vδ1 TCR-CD1a-lipid complexes reveal that the γδ TCR binds at the extreme far side and parallel to the long axis of the β-sheet floor of CD1a's antigen-binding cleft. Here, the γδ TCR co-recognises the CD1a heavy chain and β2 microglobulin in a manner that is distinct from all other previously observed γδ TCR docking modalities. The 'sideways' and lipid antigen independent mode of autoreactive CD1a recognition induces TCR clustering on the cell surface and proximal T cell signalling as measured by CD3ζ phosphorylation. In contrast with the 'end to end' binding of αβ TCRs that typically contact carried antigens, autoreactive γδ TCRs support geometrically diverse approaches to CD1a, as well as antigen independent recognition.
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Affiliation(s)
- Marcin Wegrecki
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Tonatiuh A Ocampo
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, US
| | - Sachith D Gunasinghe
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- European Molecular Biology Laboratory (EMBL) Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Anouk von Borstel
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Shin Yi Tin
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Josephine F Reijneveld
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, US
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Thinh-Phat Cao
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Benjamin S Gully
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jérôme Le Nours
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - D Branch Moody
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, US.
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, US.
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK.
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4
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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] [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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5
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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] [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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6
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Abstract
T cell activation is a critical event in the adaptive immune response, indispensable for cell-mediated and humoral immunity as well as for immune regulation. Recent years have witnessed an emerging trend emphasizing the essential role that physical force and mechanical properties play at the T cell interface. In this review, we integrate current knowledge of T cell antigen recognition and the different models of T cell activation from the perspective of mechanobiology, focusing on the interaction between the T cell receptor (TCR) and the peptide-major histocompatibility complex (pMHC) antigen. We address the shortcomings of TCR affinity alone in explaining T cell functional outcomes and the rising status of force-regulated TCR bond lifetimes, most notably the TCR catch bond. Ultimately, T cell activation and the ensuing physiological responses result from mechanical interaction between TCRs and the pMHC. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Baoyu Liu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; , ,
| | - Elizabeth M Kolawole
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; , ,
| | - Brian D Evavold
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; , ,
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7
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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] [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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