1
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Lo WL, Huseby ES. The partitioning of TCR repertoires by thymic selection. J Exp Med 2024; 221:e20230897. [PMID: 39167074 PMCID: PMC11338286 DOI: 10.1084/jem.20230897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/22/2024] [Accepted: 07/09/2024] [Indexed: 08/23/2024] Open
Abstract
αβ T cells are critical components of the adaptive immune system; they maintain tissue and immune homeostasis during health, provide sterilizing immunity after pathogen infection, and are capable of eliminating transformed tumor cells. Fundamental to these distinct functions is the ligand specificity of the unique antigen receptor expressed on each mature T cell (TCR), which endows lymphocytes with the ability to behave in a cell-autonomous, disease context-specific manner. Clone-specific behavioral properties are initially established during T cell development when thymocytes use TCR recognition of major histocompatibility complex (MHC) and MHC-like ligands to instruct survival versus death and to differentiate into a plethora of inflammatory and regulatory T cell lineages. Here, we review the ligand specificity of the preselection thymocyte repertoire and argue that developmental stage-specific alterations in TCR signaling control cross-reactivity and foreign versus self-specificity of T cell sublineages.
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Affiliation(s)
- Wan-Lin Lo
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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2
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Pourhashem Z, Nourani L, Pirahmadi S, Yousefi H, J. Sani J, Raz A, Zakeri S, Dinparast Djadid N, Abouie Mehrizi A. Malaria transmission blocking activity of Anopheles stephensi alanyl aminopeptidase N antigen formulated with MPL, CpG, and QS21 adjuvants. PLoS One 2024; 19:e0306664. [PMID: 38968270 PMCID: PMC11226095 DOI: 10.1371/journal.pone.0306664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/29/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUNDS Malaria, a preventive and treatable disease, is still responsible for annual deaths reported in most tropical regions, principally in sub-Saharan Africa. Subunit recombinant transmission-blocking vaccines (TBVs) have been proposed as promising vaccines to succeed in malaria elimination and eradication. Here, a provisional study was designed to assess the immunogenicity and functional activity of alanyl aminopeptidase N (APN1) of Anopheles stephensi, as a TBV candidate, administered with MPL, CpG, and QS21 adjuvants in the murine model. METHODOLOGY/PRINCIPAL FINDINGS The mouse groups were immunized with recombinant APN1 (rAPN1) alone or formulated with CpG, MPL, QS-21, or a combination of adjuvants (CMQ), and the elicited immune responses were evaluated after the third immunization. The standard membrane feeding assay (SMFA) measured the functional activity of antibodies against bacterial-expressed APN1 protein in adjuvanted vaccine groups on transmission of P. falciparum (NF54) to An. stephensi mosquitoes. Evaluation of mice vaccinated with rAPN1 formulated with distinct adjuvants manifested a significant increase in the high-avidity level of anti-APN1 IgG and IgG subclasses; however, rAPN1 induced the highest level of high-avidity anti-APN1 IgG1, IgG2a, and IgG2b antibodies in the immunized vaccine group 5 (APN1/CMQ). In addition, vaccine group 5 (receiving APN1/CMQ), had still the highest level of anti-APN1 IgG antibodies relative to other immunized groups after six months, on day 180. The SMFA data indicates a trend towards higher transmission-reducing activity in groups 2 and 5, which received the antigen formulated with CpG or a combination of three adjuvants. CONCLUSIONS/SIGNIFICANCE The results have shown the capability of admixture to stimulate high-affinity and long-lasting antibodies against the target antigen to hinder Plasmodium parasite development in the mid-gut of An. stephensi. The attained results authenticated APN1/CMQ and APN1/CpG as a potent APN1-based TBV formulation which will be helpful in designing a vaccine in the future.
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Affiliation(s)
- Zeinab Pourhashem
- Pasteur Institute of Iran, Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Tehran, Iran
| | - Leila Nourani
- Pasteur Institute of Iran, Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Tehran, Iran
| | - Sakineh Pirahmadi
- Pasteur Institute of Iran, Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Tehran, Iran
| | - Hemn Yousefi
- Pasteur Institute of Iran, Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Tehran, Iran
| | - Jafar J. Sani
- Pasteur Institute of Iran, Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Tehran, Iran
| | - Abbasali Raz
- Pasteur Institute of Iran, Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Tehran, Iran
| | - Sedigheh Zakeri
- Pasteur Institute of Iran, Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Tehran, Iran
| | - Navid Dinparast Djadid
- Pasteur Institute of Iran, Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Tehran, Iran
| | - Akram Abouie Mehrizi
- Pasteur Institute of Iran, Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Tehran, Iran
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3
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Boyd LF, Jiang J, Ahmad J, Natarajan K, Margulies DH. Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1366-1380. [PMID: 38456672 PMCID: PMC10982845 DOI: 10.4049/jimmunol.2300839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
mAbs to MHC class I (MHC-I) molecules have proved to be crucial reagents for tissue typing and fundamental studies of immune recognition. To augment our understanding of epitopic sites seen by a set of anti-MHC-I mAb, we determined X-ray crystal structures of four complexes of anti-MHC-I Fabs bound to peptide/MHC-I/β2-microglobulin (pMHC-I). An anti-H2-Dd mAb, two anti-MHC-I α3 domain mAbs, and an anti-β2-microglobulin mAb bind pMHC-I at sites consistent with earlier mutational and functional experiments, and the structures explain allelomorph specificity. Comparison of the experimentally determined structures with computationally derived models using AlphaFold Multimer showed that although predictions of the individual pMHC-I heterodimers were quite acceptable, the computational models failed to properly identify the docking sites of the mAb on pMHC-I. The experimental and predicted structures provide insight into strengths and weaknesses of purely computational approaches and suggest areas that merit additional attention.
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Affiliation(s)
- Lisa F. Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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4
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Acuto O. T-cell virtuosity in ''knowing thyself". Front Immunol 2024; 15:1343575. [PMID: 38415261 PMCID: PMC10896960 DOI: 10.3389/fimmu.2024.1343575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/17/2024] [Indexed: 02/29/2024] Open
Abstract
Major Histocompatibility Complex (MHC) I and II and the αβ T-cell antigen receptor (TCRαβ) govern fundamental traits of adaptive immunity. They form a membrane-borne ligand-receptor system weighing host proteome integrity to detect contamination by nonself proteins. MHC-I and -II exhibit the "MHC-fold", which is able to bind a large assortment of short peptides as proxies for self and nonself proteins. The ensuing varying surfaces are mandatory ligands for Ig-like TCRαβ highly mutable binding sites. Conserved molecular signatures guide TCRαβ ligand binding sites to focus on the MHC-fold (MHC-restriction) while leaving many opportunities for its most hypervariable determinants to contact the peptide. This riveting molecular strategy affords many options for binding energy compatible with specific recognition and signalling aimed to eradicated microbial pathogens and cancer cells. While the molecular foundations of αβ T-cell adaptive immunity are largely understood, uncertainty persists on how peptide-MHC binding induces the TCRαβ signals that instruct cell-fate decisions. Solving this mystery is another milestone for understanding αβ T-cells' self/nonself discrimination. Recent developments revealing the innermost links between TCRαβ structural dynamics and signalling modality should help dissipate this long-sought-after enigma.
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Affiliation(s)
- Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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5
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Boyd LF, Jiang J, Ahmad J, Natarajan K, Margulies DH. Experimental structures of antibody/MHC-I complexes reveal details of epitopes overlooked by computational prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569627. [PMID: 38106040 PMCID: PMC10723347 DOI: 10.1101/2023.12.01.569627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Monoclonal antibodies (mAb) to major histocompatibility complex class I (MHC-I) molecules have proved to be crucial reagents for tissue typing and fundamental studies of immune recognition. To augment our understanding of epitopic sites seen by a set of anti-MHC-I mAb, we determined X-ray crystal structures of four complexes of anti-MHC-I antigen-binding fragments (Fab) bound to peptide/MHC-I/β2m (pMHC-I). An anti-H2-Dd mAb, two anti-MHC-I α3 domain mAb, and an anti-β2-microglobulin (β2m) mAb bind pMHC-I at sites consistent with earlier mutational and functional experiments, and the structures explain allelomorph specificity. Comparison of the experimentally determined structures with computationally derived models using AlphaFold Multimer (AF-M) showed that although predictions of the individual pMHC-I heterodimers were quite acceptable, the computational models failed to properly identify the docking sites of the mAb on pMHC-I. The experimental and predicted structures provide insight into strengths and weaknesses of purely computational approaches and suggest areas that merit additional attention.
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Affiliation(s)
| | | | - Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD, 20892-1892
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD, 20892-1892
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD, 20892-1892
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6
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McElwee MK, Dileepan T, Mahmud SA, Jenkins MK. The CD4+ T cell repertoire specific for citrullinated peptides shows evidence of immune tolerance. J Exp Med 2023; 220:e20230209. [PMID: 37831103 PMCID: PMC10570851 DOI: 10.1084/jem.20230209] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/27/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
Rheumatoid arthritis occurs most often in people who express HLA-DR molecules containing a five aa "shared epitope" in the β chain. These MHCII molecules preferentially bind citrullinated peptides formed by posttranslational modification of arginine. Citrullinated peptide:HLA-DR complexes may act as arthritis-initiating neo-antigens for CD4+ T cells. Here, we used fluorophore-conjugated HLA-DR tetramers containing citrullinated peptides from human cartilage intermediate layer protein, fibrinogen, vimentin, or enolase 1 to track cognate CD4+ T cells. Immunization of HLA-DR transgenic mice with citrullinated peptides from vimentin or enolase 1 failed to cause any expansion of tetramer-binding cells, whereas immunization with citrullinated peptides from cartilage intermediate layer protein or fibrinogen elicited some expansion. The expanded tetramer-binding populations, however, had lower T helper 1 and higher regulatory T cell frequencies than populations elicited by viral peptides. These results indicate that HLA-DR-bound citrullinated peptides are not neo-antigens and induce varying degrees of immune tolerance that could pose a barrier to rheumatoid arthritis.
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Affiliation(s)
- Matthew K. McElwee
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
- Division of Rheumatic and Autoimmune Diseases, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Thamotharampillai Dileepan
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Shawn A. Mahmud
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
- Division of Pediatric Rheumatology, Allergy and Immunology, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Marc K. Jenkins
- Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
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7
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Levi R, Levi L, Louzoun Y. Bw4 ligand and direct T-cell receptor binding induced selection on HLA A and B alleles. Front Immunol 2023; 14:1236080. [PMID: 38077375 PMCID: PMC10703150 DOI: 10.3389/fimmu.2023.1236080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction The HLA region is the hallmark of balancing selection, argued to be driven by the pressure to present a wide variety of viral epitopes. As such selection on the peptide-binding positions has been proposed to drive HLA population genetics. MHC molecules also directly binds to the T-Cell Receptor and killer cell immunoglobulin-like receptors (KIR). Methods We here combine the HLA allele frequencies in over six-million Hematopoietic Stem Cells (HSC) donors with a novel machine-learning-based method to predict allele frequency. Results We show for the first time that allele frequency can be predicted from their sequences. This prediction yields a natural measure for selection. The strongest selection is affecting KIR binding regions, followed by the peptide-binding cleft. The selection from the direct interaction with the KIR and TCR is centered on positively charged residues (mainly Arginine), and some positions in the peptide-binding cleft are not associated with the allele frequency, especially Tyrosine residues. Discussion These results suggest that the balancing selection for peptide presentation is combined with a positive selection for KIR and TCR binding.
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Affiliation(s)
| | | | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
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8
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Choy C, Chen J, Li J, Gallagher DT, Lu J, Wu D, Zou A, Hemani H, Baptiste BA, Wichmann E, Yang Q, Ciffelo J, Yin R, McKelvy J, Melvin D, Wallace T, Dunn C, Nguyen C, Chia CW, Fan J, Ruffolo J, Zukley L, Shi G, Amano T, An Y, Meirelles O, Wu WW, Chou CK, Shen RF, Willis RA, Ko MSH, Liu YT, De S, Pierce BG, Ferrucci L, Egan J, Mariuzza R, Weng NP. SARS-CoV-2 infection establishes a stable and age-independent CD8 + T cell response against a dominant nucleocapsid epitope using restricted T cell receptors. Nat Commun 2023; 14:6725. [PMID: 37872153 PMCID: PMC10593757 DOI: 10.1038/s41467-023-42430-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
The resolution of SARS-CoV-2 replication hinges on cell-mediated immunity, wherein CD8+ T cells play a vital role. Nonetheless, the characterization of the specificity and TCR composition of CD8+ T cells targeting non-spike protein of SARS-CoV-2 before and after infection remains incomplete. Here, we analyzed CD8+ T cells recognizing six epitopes from the SARS-CoV-2 nucleocapsid (N) protein and found that SARS-CoV-2 infection slightly increased the frequencies of N-recognizing CD8+ T cells but significantly enhanced activation-induced proliferation compared to that of the uninfected donors. The frequencies of N-specific CD8+ T cells and their proliferative response to stimulation did not decrease over one year. We identified the N222-230 peptide (LLLDRLNQL, referred to as LLL thereafter) as a dominant epitope that elicited the greatest proliferative response from both convalescent and uninfected donors. Single-cell sequencing of T cell receptors (TCR) from LLL-specific CD8+ T cells revealed highly restricted Vα gene usage (TRAV12-2) with limited CDR3α motifs, supported by structural characterization of the TCR-LLL-HLA-A2 complex. Lastly, transcriptome analysis of LLL-specific CD8+ T cells from donors who had expansion (expanders) or no expansion (non-expanders) after in vitro stimulation identified increased chromatin modification and innate immune functions of CD8+ T cells in non-expanders. These results suggests that SARS-CoV-2 infection induces LLL-specific CD8+ T cell responses with a restricted TCR repertoire.
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Affiliation(s)
- Cecily Choy
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Joseph Chen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jiangyuan Li
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - D Travis Gallagher
- National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA
| | - Jian Lu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Daichao Wu
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Ainslee Zou
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Humza Hemani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Beverly A Baptiste
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Emily Wichmann
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Qian Yang
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jeffrey Ciffelo
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Rui Yin
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Julia McKelvy
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Denise Melvin
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Tonya Wallace
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Christopher Dunn
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Cuong Nguyen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Chee W Chia
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jinshui Fan
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jeannie Ruffolo
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Linda Zukley
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | | | | | - Yang An
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Osorio Meirelles
- Laboratory of Epidemiology & Population Sciences, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Wells W Wu
- Facility for Biotechnology Resources, CBER, Food and Drug Administration, Silver Spring, MD, USA
| | - Chao-Kai Chou
- Facility for Biotechnology Resources, CBER, Food and Drug Administration, Silver Spring, MD, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, CBER, Food and Drug Administration, Silver Spring, MD, USA
| | - Richard A Willis
- NIH Tetramer Core Facility at Emory University, Atlanta, GA, USA
| | | | | | - Supriyo De
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Brian G Pierce
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Josephine Egan
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Roy Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Nan-Ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA.
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9
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Trier NH, Houen G. Antibody Cross-Reactivity in Auto-Immune Diseases. Int J Mol Sci 2023; 24:13609. [PMID: 37686415 PMCID: PMC10487534 DOI: 10.3390/ijms241713609] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Autoimmunity is defined by the presence of antibodies and/or T cells directed against self-components. Although of unknown etiology, autoimmunity commonly is associated with environmental factors such as infections, which have been reported to increase the risk of developing autoimmune diseases. Occasionally, similarities between infectious non-self and self-tissue antigens may contribute to immunological cross-reactivity in autoimmune diseases. These reactions may be interpreted as molecular mimicry, which describes cross-reactivity between foreign pathogens and self-antigens that have been reported to cause tissue damage and to contribute to the development of autoimmunity. By focusing on the nature of antibodies, cross-reactivity in general, and antibody-antigen interactions, this review aims to characterize the nature of potential cross-reactive immune reactions between infectious non-self and self-tissue antigens which may be associated with autoimmunity but may not actually be the cause of disease onset.
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Affiliation(s)
- Nicole Hartwig Trier
- Department of Neurology, Rigshospitalet Glostrup, Valdemar Hansens Vej 1-23, 2600 Glostrup, Denmark
| | - Gunnar Houen
- Department of Neurology, Rigshospitalet Glostrup, Valdemar Hansens Vej 1-23, 2600 Glostrup, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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10
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Papadaki GF, Ani O, Florio TJ, Young MC, Danon JN, Sun Y, Dersh D, Sgourakis NG. Decoupling peptide binding from T cell receptor recognition with engineered chimeric MHC-I molecules. Front Immunol 2023; 14:1116906. [PMID: 36761745 PMCID: PMC9905809 DOI: 10.3389/fimmu.2023.1116906] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
Major Histocompatibility Complex class I (MHC-I) molecules display self, viral or aberrant epitopic peptides to T cell receptors (TCRs), which employ interactions between complementarity-determining regions with both peptide and MHC-I heavy chain 'framework' residues to recognize specific Human Leucocyte Antigens (HLAs). The highly polymorphic nature of the HLA peptide-binding groove suggests a malleability of interactions within a common structural scaffold. Here, using structural data from peptide:MHC-I and pMHC:TCR structures, we first identify residues important for peptide and/or TCR binding. We then outline a fixed-backbone computational design approach for engineering synthetic molecules that combine peptide binding and TCR recognition surfaces from existing HLA allotypes. X-ray crystallography demonstrates that chimeric molecules bridging divergent HLA alleles can bind selected peptide antigens in a specified backbone conformation. Finally, in vitro tetramer staining and biophysical binding experiments using chimeric pMHC-I molecules presenting established antigens further demonstrate the requirement of TCR recognition on interactions with HLA framework residues, as opposed to interactions with peptide-centric Chimeric Antigen Receptors (CARs). Our results underscore a novel, structure-guided platform for developing synthetic HLA molecules with desired properties as screening probes for peptide-centric interactions with TCRs and other therapeutic modalities.
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Affiliation(s)
- Georgia F. Papadaki
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Omar Ani
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Tyler J. Florio
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Michael C. Young
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Julia N. Danon
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Yi Sun
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Devin Dersh
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nikolaos G. Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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11
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Bosselut R. A Beginner's Guide to T Cell Development. Methods Mol Biol 2023; 2580:3-24. [PMID: 36374448 DOI: 10.1007/978-1-0716-2740-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
T lymphocytes (T cells) are essential components of the adaptive immune system; they serve multiple functions in responses to pathogens and to ensure immune homeostasis. Written for readers first entering this field of study, this chapter is a brief overview of the development of T cells in the thymus, from the entry of thymus-settling bone marrow-derived precursors to the egress of mature T cells. Surveyed topics include the differentiation and expansion of early precursors, the generation of the T cell antigen receptor repertoire, the selection of αβ T cell precursors, and their acquisition of functional competency.
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Affiliation(s)
- Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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12
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Li W, Zhu X, Xu Y, Chen J, Zhang H, Yang Z, Qi Y, Hong J, Li Y, Wang G, Shen J, Qian C. Simultaneous editing of TCR, HLA-I/II and HLA-E resulted in enhanced universal CAR-T resistance to allo-rejection. Front Immunol 2022; 13:1052717. [PMID: 36532006 PMCID: PMC9757162 DOI: 10.3389/fimmu.2022.1052717] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
Introduction The major challenge for universal chimeric antigen receptor T cell (UCAR-T) therapy is the inability to persist for a long time in patients leading to inferior efficacy clinically. The objective of this study was to design a novel UCAR-T cell that could avoid the occurrence of allo-rejection and provide effective resistance to allogeneic Natural Killer (NK) cell rejection, together with the validation of its safety and efficacy ex vivo and in vivo. Methods We prepared T-cell receptor (TCR), Human leukocyte antigen (HLA)-I/II triple-edited (TUCAR-T) cells and evaluated the anti-tumor efficacy ex vivo and in vivo. We measured the resistance of exogenous HLA-E expressing TUCAR-T (ETUCAR-T) to NK rejection by using an enhanced NK. Furthermore, we established the safety and efficacy of this regimen by treating Nalm6 tumor-bearing mice with a repeated high-dose infusion of ETUCAR-T. Moreover, we analyzed the effects of individual gene deficiency CAR-T on treated mice and the changes in the transcriptional profiles of different gene-edited T cells via RNA-Seq. Results Data showed that HLA-II editing didn't impair the anti-tumor efficacy of TUCAR-T ex vivo and in vivo and we found for the first time that HLA-II deficiency could facilitate the persistence of CAR-T. Contrastively, as the most commonly eliminated target in UCAR-T, TCR deficiency was found to be a key disadvantageous factor for the shorter-term anti-tumor efficacy in vivo. Our study demonstrated ETUCAR-T could effectively resist allogeneic NK rejection ex vivo and in vivo. Discussion Our research provided a potential and effective strategy for promoting the persistence of UCAR-T cells in clinical application. And it reveals the potential key factors of the poor persistence of UCAR-T along with new insights for future development.
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Affiliation(s)
- Wuling Li
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Center for Precision Medicine of Cancer, Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Xiuxiu Zhu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Center for Precision Medicine of Cancer, Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Yanmin Xu
- Chongqing Key Laboratory of Gene and Cell Therapy, Institute of Precision Medicine and Biotechnology, Chongqing Precision Biotech Co., Ltd., Chongqing, China
| | - Jun Chen
- Chongqing Key Laboratory of Gene and Cell Therapy, Institute of Precision Medicine and Biotechnology, Chongqing Precision Biotech Co., Ltd., Chongqing, China
| | - Hongtao Zhang
- Chongqing Key Laboratory of Gene and Cell Therapy, Institute of Precision Medicine and Biotechnology, Chongqing Precision Biotech Co., Ltd., Chongqing, China
| | - Zhi Yang
- Chongqing Key Laboratory of Gene and Cell Therapy, Institute of Precision Medicine and Biotechnology, Chongqing Precision Biotech Co., Ltd., Chongqing, China
| | - Yanan Qi
- Chongqing Key Laboratory of Gene and Cell Therapy, Institute of Precision Medicine and Biotechnology, Chongqing Precision Biotech Co., Ltd., Chongqing, China
| | - Juan Hong
- Chongqing Key Laboratory of Gene and Cell Therapy, Institute of Precision Medicine and Biotechnology, Chongqing Precision Biotech Co., Ltd., Chongqing, China
| | - Yunyan Li
- Chongqing Key Laboratory of Gene and Cell Therapy, Institute of Precision Medicine and Biotechnology, Chongqing Precision Biotech Co., Ltd., Chongqing, China
| | - Guixue Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, China
| | - Junjie Shen
- Chongqing Key Laboratory of Gene and Cell Therapy, Institute of Precision Medicine and Biotechnology, Chongqing Precision Biotech Co., Ltd., Chongqing, China
| | - Cheng Qian
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Center for Precision Medicine of Cancer, Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
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13
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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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14
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Cassioli C, Patrussi L, Valitutti S, Baldari CT. Learning from TCR Signaling and Immunological Synapse Assembly to Build New Chimeric Antigen Receptors (CARs). Int J Mol Sci 2022; 23:14255. [PMID: 36430728 PMCID: PMC9694822 DOI: 10.3390/ijms232214255] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Chimeric antigen receptor (CAR) T cell immunotherapy is a revolutionary pillar in cancer treatment. Clinical experience has shown remarkable successes in the treatment of certain hematological malignancies but only limited efficacy against B cell chronic lymphocytic leukemia (CLL) and other cancer types, especially solid tumors. A wide range of engineering strategies have been employed to overcome the limitations of CAR T cell therapy. However, it has become increasingly clear that CARs have unique, unexpected features; hence, a deep understanding of how CARs signal and trigger the formation of a non-conventional immunological synapse (IS), the signaling platform required for T cell activation and execution of effector functions, would lead a shift from empirical testing to the rational design of new CAR constructs. Here, we review current knowledge of CARs, focusing on their structure, signaling and role in CAR T cell IS assembly. We, moreover, discuss the molecular features accounting for poor responses in CLL patients treated with anti-CD19 CAR T cells and propose CLL as a paradigm for diseases connected to IS dysfunctions that could significantly benefit from the development of novel CARs to generate a productive anti-tumor response.
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Affiliation(s)
- Chiara Cassioli
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Laura Patrussi
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Salvatore Valitutti
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1037, Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse III-Paul Sabatier, 31037 Toulouse, France
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse, 31059 Toulouse, France
| | - Cosima T. Baldari
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
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15
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Pagliuca S, Gurnari C, Rubio MT, Visconte V, Lenz TL. Individual HLA heterogeneity and its implications for cellular immune evasion in cancer and beyond. Front Immunol 2022; 13:944872. [PMID: 36131910 PMCID: PMC9483928 DOI: 10.3389/fimmu.2022.944872] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/17/2022] [Indexed: 01/07/2023] Open
Abstract
Structural and functional variability of human leukocyte antigen (HLA) is the foundation for competent adaptive immune responses against pathogen and tumor antigens as it assures the breadth of the presented immune-peptidome, theoretically sustaining an efficient and diverse T cell response. This variability is presumably the result of the continuous selection by pathogens, which over the course of evolution shaped the adaptive immune system favoring the assortment of a hyper-polymorphic HLA system able to elaborate efficient immune responses. Any genetic alteration affecting this diversity may lead to pathological processes, perturbing antigen presentation capabilities, T-cell reactivity and, to some extent, natural killer cell functionality. A highly variable germline HLA genotype can convey immunogenetic protection against infections, be associated with tumor surveillance or influence response to anti-neoplastic treatments. In contrast, somatic aberrations of HLA loci, rearranging the original germline configuration, theoretically decreasing its variability, can facilitate mechanisms of immune escape that promote tumor growth and immune resistance. The purpose of the present review is to provide a unified and up-to-date overview of the pathophysiological consequences related to the perturbations of the genomic heterogeneity of HLA complexes and their impact on human diseases, with a special focus on cancer.
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Affiliation(s)
- Simona Pagliuca
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH, United States
- Service d’hématologie Clinique, Hôpital Brabois, CHRU Nancy and CNRS UMR 7365 IMoPa, Biopole de l’Université de Loarraine, Vandoeuvre les Nancy, France
| | - Carmelo Gurnari
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH, United States
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Marie Thérèse Rubio
- Service d’hématologie Clinique, Hôpital Brabois, CHRU Nancy and CNRS UMR 7365 IMoPa, Biopole de l’Université de Loarraine, Vandoeuvre les Nancy, France
| | - Valeria Visconte
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH, United States
| | - Tobias L. Lenz
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
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16
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T. RR, Smith JC. Structural patterns in class 1 major histocompatibility complex‐restricted nonamer peptide binding to T‐cell receptors. Proteins 2022; 90:1645-1654. [DOI: 10.1002/prot.26343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/12/2022] [Accepted: 03/27/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Rajitha Rajeshwar T.
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Jeremy C. Smith
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
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17
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Li W, Zhang Y, Li R, Wang Y, Chen L, Dai S. A Novel Tolerogenic Antibody Targeting Disulfide-Modified Autoantigen Effectively Prevents Type 1 Diabetes in NOD Mice. Front Immunol 2022; 13:877022. [PMID: 36032077 PMCID: PMC9406144 DOI: 10.3389/fimmu.2022.877022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/06/2022] [Indexed: 11/15/2022] Open
Abstract
Increasing evidence suggested that the islet amyloid polypeptide (IAPP) is an essential autoantigen in the pathogenesis of type 1 diabetes (T1D) in humans and non-obese diabetic (NOD) mice. A unique disulfide containing IAPP-derived peptide KS20 is one of the highly diabetogenic peptides in NOD mice. The KS20-reactive T cells, including prototypic pathogenic BDC5.2.9, accumulate in the pancreas of prediabetic and diabetic mice and contribute to disease development. We generated a monoclonal antibody (LD96.24) that interacts with IAg7-KS20 complexes with high affinity and specificity. LD96.24 recognized the IAg7-KS20 disulfide loop and blocked the interaction between IAg7-KS20 tetramers and cognate T cells but not other autoantigen-reactive T cells. The in vivo LD96.24 studies, at either early or late stages, drastically induced tolerance and delayed the onset of T1D disease in NOD mice by reducing the infiltration of not only IAPP-specific T cells but also chromogranin A and insulin-specific T cells in the pancreas, together with B cells and dendritic cells. LD96.24 can also significantly increase the ratio of Foxp3+ regulatory T cells with Interferon-gamma-secreting effector T cells. Our data suggested the important role of disulfide-modified peptides in the development of T1D. Targeting the complexes of Major histocompatibility complex (MHC)/disulfide modified antigens would influence the thiol redox balance and could be a novel immunotherapy for T1D.
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Affiliation(s)
- Wei Li
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- National Health Commission (NHC) Key Laboratory of Pulmonary Immune-Related Diseases, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Yan Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ronghui Li
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- National Health Commission (NHC) Key Laboratory of Pulmonary Immune-Related Diseases, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Yang Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Lan Chen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Shaodong Dai
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
- *Correspondence: Shaodong Dai,
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18
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Wang Y, Tsitsiklis A, Devoe S, Gao W, Chu HH, Zhang Y, Li W, Wong WK, Deane CM, Neau D, Slansky JE, Thomas PG, Robey EA, Dai S. Peptide Centric Vβ Specific Germline Contacts Shape a Specialist T Cell Response. Front Immunol 2022; 13:847092. [PMID: 35967379 PMCID: PMC9372435 DOI: 10.3389/fimmu.2022.847092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 05/31/2022] [Indexed: 11/15/2022] Open
Abstract
Certain CD8 T cell responses are particularly effective at controlling infection, as exemplified by elite control of HIV in individuals harboring HLA-B57. To understand the structural features that contribute to CD8 T cell elite control, we focused on a strongly protective CD8 T cell response directed against a parasite-derived peptide (HF10) presented by an atypical MHC-I molecule, H-2Ld. This response exhibits a focused TCR repertoire dominated by Vβ2, and a representative TCR (TG6) in complex with Ld-HF10 reveals an unusual structure in which both MHC and TCR contribute extensively to peptide specificity, along with a parallel footprint of TCR on its pMHC ligand. The parallel footprint is a common feature of Vβ2-containing TCRs and correlates with an unusual Vα-Vβ interface, CDR loop conformations, and Vβ2-specific germline contacts with peptides. Vβ2 and Ld may represent "specialist" components for antigen recognition that allows for particularly strong and focused T cell responses.
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Affiliation(s)
- Yang Wang
- Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Alexandra Tsitsiklis
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Stephanie Devoe
- Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Wei Gao
- Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States
- Biological Physics Laboratory, College of Science, Beijing Forestry University, Beijing, China
| | - H. Hamlet Chu
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Yan Zhang
- Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States
| | - Wei Li
- Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States
| | - Wing Ki Wong
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | | | - David Neau
- Department of Chemistry and Chemical Biology, Northeastern Collaborative Access Team (NE-CAT), Advanced Photon Source, Argonne National Laboratory, Cornell University, Argonne, IL, United States
| | - Jill E. Slansky
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Ellen A. Robey
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Shaodong Dai
- Department of Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, CO, United States
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
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19
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Van Laethem F, Bhattacharya A, Craveiro M, Lu J, Sun PD, Singer A. MHC-independent αβT cells: Lessons learned about thymic selection and MHC-restriction. Front Immunol 2022; 13:953160. [PMID: 35911724 PMCID: PMC9331304 DOI: 10.3389/fimmu.2022.953160] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Understanding the generation of an MHC-restricted T cell repertoire is the cornerstone of modern T cell immunology. The unique ability of αβT cells to only recognize peptide antigens presented by MHC molecules but not conformational antigens is referred to as MHC restriction. How MHC restriction is imposed on a very large T cell receptor (TCR) repertoire is still heavily debated. We recently proposed the selection model, which posits that newly re-arranged TCRs can structurally recognize a wide variety of antigens, ranging from peptides presented by MHC molecules to native proteins like cell surface markers. However, on a molecular level, the sequestration of the essential tyrosine kinase Lck by the coreceptors CD4 and CD8 allows only MHC-restricted TCRs to signal. In the absence of Lck sequestration, MHC-independent TCRs can signal and instruct the generation of mature αβT cells that can recognize native protein ligands. The selection model thus explains how only MHC-restricted TCRs can signal and survive thymic selection. In this review, we will discuss the genetic evidence that led to our selection model. We will summarize the selection mechanism and structural properties of MHC-independent TCRs and further discuss the various non-MHC ligands we have identified.
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Affiliation(s)
- François Van Laethem
- Lymphocyte Development Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- Department of Biological Hematology, Centre Hospitalier Universitaire (CHU) Montpellier, Montpellier, France
- *Correspondence: François Van Laethem, ,
| | - Abhisek Bhattacharya
- Lymphocyte Development Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Marco Craveiro
- Lymphocyte Development Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jinghua Lu
- Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Peter D. Sun
- Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Alfred Singer
- Lymphocyte Development Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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20
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Glazer N, Akerman O, Louzoun Y. Naive and memory T cells TCR-HLA-binding prediction. OXFORD OPEN IMMUNOLOGY 2022; 3:iqac001. [PMID: 36846560 PMCID: PMC9914496 DOI: 10.1093/oxfimm/iqac001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/01/2022] [Accepted: 05/17/2022] [Indexed: 11/12/2022] Open
Abstract
T cells recognize antigens through the interaction of their T cell receptor (TCR) with a peptide-major histocompatibility complex (pMHC) molecule. Following thymic-positive selection, TCRs in peripheral naive T cells are expected to bind MHC alleles of the host. Peripheral clonal selection is expected to further increase the frequency of antigen-specific TCRs that bind to the host MHC alleles. To check for a systematic preference for MHC-binding T cells in TCR repertoires, we developed Natural Language Processing-based methods to predict TCR-MHC binding independently of the peptide presented for Class I MHC alleles. We trained a classifier on published TCR-pMHC binding pairs and obtained a high area under curve (AUC) of over 0.90 on the test set. However, when applied to TCR repertoires, the accuracy of the classifier dropped. We thus developed a two-stage prediction model, based on large-scale naive and memory TCR repertoires, denoted TCR HLA-binding predictor (CLAIRE). Since each host carries multiple human leukocyte antigen (HLA) alleles, we first computed whether a TCR on a CD8 T cell binds an MHC from any of the host Class-I HLA alleles. We then performed an iteration, where we predict the binding with the most probable allele from the first round. We show that this classifier is more precise for memory than for naïve cells. Moreover, it can be transferred between datasets. Finally, we developed a CD4-CD8 T cell classifier to apply CLAIRE to unsorted bulk sequencing datasets and showed a high AUC of 0.96 and 0.90 on large datasets. CLAIRE is available through a GitHub at: https://github.com/louzounlab/CLAIRE, and as a server at: https://claire.math.biu.ac.il/Home.
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Affiliation(s)
- Neta Glazer
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Ofek Akerman
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
| | - Yoram Louzoun
- Correspondence address. Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel. E-mail:
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21
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Krovi SH, Kuchroo VK. Activation pathways that drive CD4 + T cells to break tolerance in autoimmune diseases . Immunol Rev 2022; 307:161-190. [PMID: 35142369 PMCID: PMC9255211 DOI: 10.1111/imr.13071] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/11/2022]
Abstract
Autoimmune diseases are characterized by dysfunctional immune systems that misrecognize self as non-self and cause tissue destruction. Several cell types have been implicated in triggering and sustaining disease. Due to a strong association of major histocompatibility complex II (MHC-II) proteins with various autoimmune diseases, CD4+ T lymphocytes have been thoroughly investigated for their roles in dictating disease course. CD4+ T cell activation is a coordinated process that requires three distinct signals: Signal 1, which is mediated by antigen recognition on MHC-II molecules; Signal 2, which boosts signal 1 in a costimulatory manner; and Signal 3, which helps to differentiate the activated cells into functionally relevant subsets. These signals are disrupted during autoimmunity and prompt CD4+ T cells to break tolerance. Herein, we review our current understanding of how each of the three signals plays a role in three different autoimmune diseases and highlight the genetic polymorphisms that predispose individuals to autoimmunity. We also discuss the drawbacks of existing therapies and how they can be addressed to achieve lasting tolerance in patients.
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Affiliation(s)
- Sai Harsha Krovi
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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22
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Dembic Z. Defending and Integrating an Organism by the Immune System. Scand J Immunol 2022; 95:e13172. [PMID: 35416326 PMCID: PMC9285719 DOI: 10.1111/sji.13172] [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: 02/28/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022]
Abstract
The Integrity model proposes that the adaptive immune response defends, protects and keeps vigilance over the unity of an organism. These functions conceptually rely on three signals that can explain them. All signals have a dual character. The signal‐1 is the recognition of antigen or peptide/MHC ligand. The signal‐2 comprises either help and costimulation or suppression and coinhibition. Lastly, the signal‐3 signals tissues' condition, state or integrity. A part overlaps with the Danger‐associated molecular patterns, and the other part should be detected by putative cell‐surface molecules, intracellular factors or epigenetic events. They are called the Integrity‐associated molecular patterns (IAMPs). The IAMPs originate from damaged (positive signal‐3) or undamaged (negative signal‐3) tissues. The positive signal‐3 would induce costimulatory signal‐2, whereas the negative signal‐3 would induce coinhibitory signal‐2 in APCs. However, in analogue reality, we might more likely encounter a range of signals supposedly sensed by a group of responder cells and integrated overtime (quorum sensing). The predominant option would sway the decision of the immune system to perform either defence or protection (active tolerance). Thus, the quorum sensing supposedly delivers two qualitative thresholds for T (and B) cells' decisions to defend or suppress. If these were not attained, the vigilance (anergy) of adaptive immunocytes for T‐dependent antigens would ensue. These functions provide defence against pathogens and preservation of unity/integrity of an organism, which in turn permits protection of commensals.
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Affiliation(s)
- Zlatko Dembic
- Department of Oral Biology, University of Oslo, Norway
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23
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Huisman W, Hageman L, Leboux DAT, Khmelevskaya A, Efimov GA, Roex MCJ, Amsen D, Falkenburg JHF, Jedema I. Public T-Cell Receptors (TCRs) Revisited by Analysis of the Magnitude of Identical and Highly-Similar TCRs in Virus-Specific T-Cell Repertoires of Healthy Individuals. Front Immunol 2022; 13:851868. [PMID: 35401538 PMCID: PMC8987591 DOI: 10.3389/fimmu.2022.851868] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/04/2022] [Indexed: 01/11/2023] Open
Abstract
Since multiple different T-cell receptor (TCR) sequences can bind to the same peptide-MHC combination and the number of TCR-sequences that can theoretically be generated even exceeds the number of T cells in a human body, the likelihood that many public identical (PUB-I) TCR-sequences frequently contribute to immune responses has been estimated to be low. Here, we quantitatively analyzed the TCR-repertoires of 190 purified virus-specific memory T-cell populations, directed against 21 epitopes of Cytomegalovirus, Epstein-Barr virus and Adenovirus isolated from 29 healthy individuals, and determined the magnitude, defined as prevalence within the population and frequencies within individuals, of PUB-I TCR and of TCR-sequences that are highly-similar (PUB-HS) to these PUB-I TCR-sequences. We found that almost one third of all TCR nucleotide-sequences represented PUB-I TCR amino-acid (AA) sequences and found an additional 12% of PUB-HS TCRs differing by maximally 3 AAs. We illustrate that these PUB-I and PUB-HS TCRs were structurally related and contained shared core-sequences in their TCR-sequences. We found a prevalence of PUB-I and PUB-HS TCRs of up to 50% among individuals and showed frequencies of virus-specific PUB-I and PUB-HS TCRs making up more than 10% of each virus-specific T-cell population. These findings were confirmed by using an independent TCR-database of virus-specific TCRs. We therefore conclude that the magnitude of the contribution of PUB-I and PUB-HS TCRs to these virus-specific T-cell responses is high. Because the T cells from these virus-specific memory TCR-repertoires were the result of successful control of the virus in these healthy individuals, these PUB-HS TCRs and PUB-I TCRs may be attractive candidates for immunotherapy in immunocompromised patients that lack virus-specific T cells to control viral reactivation.
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Affiliation(s)
- Wesley Huisman
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands.,Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory for Blood Cell Research, Amsterdam, Netherlands
| | - Lois Hageman
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Didier A T Leboux
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Alexandra Khmelevskaya
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russia
| | - Grigory A Efimov
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russia
| | - Marthe C J Roex
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Derk Amsen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory for Blood Cell Research, Amsterdam, Netherlands
| | | | - Inge Jedema
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
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24
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Nakayama M, Michels AW. Using the T Cell Receptor as a Biomarker in Type 1 Diabetes. Front Immunol 2021; 12:777788. [PMID: 34868047 PMCID: PMC8635517 DOI: 10.3389/fimmu.2021.777788] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/26/2021] [Indexed: 12/20/2022] Open
Abstract
T cell receptors (TCRs) are unique markers that define antigen specificity for a given T cell. With the evolution of sequencing and computational analysis technologies, TCRs are now prime candidates for the development of next-generation non-cell based T cell biomarkers, which provide a surrogate measure to assess the presence of antigen-specific T cells. Type 1 diabetes (T1D), the immune-mediated form of diabetes, is a prototypical organ specific autoimmune disease in which T cells play a pivotal role in targeting pancreatic insulin-producing beta cells. While the disease is now predictable by measuring autoantibodies in the peripheral blood directed to beta cell proteins, there is an urgent need to develop T cell markers that recapitulate T cell activity in the pancreas and can be a measure of disease activity. This review focuses on the potential and challenges of developing TCR biomarkers for T1D. We summarize current knowledge about TCR repertoires and clonotypes specific for T1D and discuss challenges that are unique for autoimmune diabetes. Ultimately, the integration of large TCR datasets produced from individuals with and without T1D along with computational 'big data' analysis will facilitate the development of TCRs as potentially powerful biomarkers in the development of T1D.
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Affiliation(s)
- Maki Nakayama
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Aaron W Michels
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
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25
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Krueger PD, Osum KC, Jenkins MK. CD4 + Memory T-Cell Formation during Type 1 Immune Responses. Cold Spring Harb Perspect Biol 2021; 13:a038141. [PMID: 33903156 PMCID: PMC8635001 DOI: 10.1101/cshperspect.a038141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Naive CD4+ T cells become memory cells after proliferating in response to their cognate major histocompatibility complex class II (MHCII)-bound peptide and passing through an effector cell stage. The process by which CD4+ memory T cells emerge from the effector cell pool, however, is less well understood than in the case of CD8+ T cells. During certain acute infections, naive CD4+ T cells proliferate and differentiate into various forms of type 1 (Th1) and follicular helper (Tfh) effector cells. We review the evidence that about 10% of the cells in each of these subsets survive to become memory cells that resemble their effector cell precursors. The roles that asymmetric cell division, the TCF-1 transcription factor, metabolic activity, reactive oxygen species, and the IL-7 receptor play in the effector to memory cell transition are discussed. We propose a speculative model in which the metabolic activity needed for rapid clonal expansion also generates toxic products that induce apoptosis in most effector cells. Memory cells then arise from the effector cells in each subset that are at the low end of the metabolic activity spectrum.
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Affiliation(s)
- Peter D Krueger
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Kevin C Osum
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Marc K Jenkins
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
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26
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Higdon LE, Schaffert S, Huang H, Montez-Rath ME, Lucia M, Jha A, Saligrama N, Margulies KB, Martinez OM, Davis MM, Khatri P, Maltzman JS. Evolution of Cytomegalovirus-Responsive T Cell Clonality following Solid Organ Transplantation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:2077-2085. [PMID: 34551964 PMCID: PMC8492537 DOI: 10.4049/jimmunol.2100404] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/04/2021] [Indexed: 12/30/2022]
Abstract
CMV infection is a significant complication after solid organ transplantation. We used single cell TCR αβ sequencing to determine how memory inflation impacts clonality and diversity of the CMV-responsive CD8 and CD4 T cell repertoire in the first year after transplantation in human subjects. We observed CD8 T cell inflation but no changes in clonal diversity, indicating homeostatic stability in clones. In contrast, the CD4 repertoire was diverse and stable over time, with no evidence of CMV-responsive CD4 T cell expansion. We identified shared CDR3 TCR motifs among patients but no public CMV-specific TCRs. Temporal changes in clonality in response to transplantation and in the absence of detectable viral reactivation suggest changes in the repertoire immediately after transplantation followed by an expansion with stable clonal competition that may mediate protection.
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Affiliation(s)
- Lauren E Higdon
- Nephrology Division, Department of Medicine, Stanford University, Palo Alto, CA
| | - Steven Schaffert
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA
- Biomedical Informatics Division, Department of Medicine, Stanford University, Stanford, CA
| | - Huang Huang
- Department of Microbiology and Immunology, Stanford University, Stanford CA
| | - Maria E Montez-Rath
- Nephrology Division, Department of Medicine, Stanford University, Palo Alto, CA
| | - Marc Lucia
- Department of Surgery, Stanford University, Stanford, CA
| | - Alokkumar Jha
- Cardiovascular Institute, Stanford University, Stanford, CA
| | - Naresha Saligrama
- Department of Microbiology and Immunology, Stanford University, Stanford CA
| | - Kenneth B Margulies
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford University, Stanford, CA; and
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA
- Biomedical Informatics Division, Department of Medicine, Stanford University, Stanford, CA
| | - Jonathan S Maltzman
- Nephrology Division, Department of Medicine, Stanford University, Palo Alto, CA;
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA
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27
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Joyce S, Ternette N. Know thy immune self and non-self: Proteomics informs on the expanse of self and non-self, and how and where they arise. Proteomics 2021; 21:e2000143. [PMID: 34310018 PMCID: PMC8865197 DOI: 10.1002/pmic.202000143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/30/2021] [Accepted: 07/19/2021] [Indexed: 12/30/2022]
Abstract
T cells play an important role in the adaptive immune response to a variety of infections and cancers. Initiation of a T cell mediated immune response requires antigen recognition in a process termed MHC (major histocompatibility complex) restri ction. A T cell antigen is a composite structure made up of a peptide fragment bound within the antigen‐binding groove of an MHC‐encoded class I or class II molecule. Insight into the precise composition and biology of self and non‐self immunopeptidomes is essential to harness T cell mediated immunity to prevent, treat, or cure infectious diseases and cancers. T cell antigen discovery is an arduous task! The pioneering work in the early 1990s has made large‐scale T cell antigen discovery possible. Thus, advancements in mass spectrometry coupled with proteomics and genomics technologies make possible T cell antigen discovery with ease, accuracy, and sensitivity. Yet we have only begun to understand the breadth and the depth of self and non‐self immunopeptidomes because the molecular biology of the cell continues to surprise us with new secrets directly related to the source, and the processing and presentation of MHC ligands. Focused on MHC class I molecules, this review, therefore, provides a brief historic account of T cell antigen discovery and, against a backdrop of key advances in molecular cell biologic processes, elaborates on how proteogenomics approaches have revolutionised the field.
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Affiliation(s)
- Sebastian Joyce
- Department of Veterans Affairs, Tennessee Valley Healthcare System and the Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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28
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Lanz AL, Masi G, Porciello N, Cohnen A, Cipria D, Prakaash D, Bálint Š, Raggiaschi R, Galgano D, Cole DK, Lepore M, Dushek O, Dustin ML, Sansom MSP, Kalli AC, Acuto O. Allosteric activation of T cell antigen receptor signaling by quaternary structure relaxation. Cell Rep 2021; 36:109375. [PMID: 34260912 PMCID: PMC8293630 DOI: 10.1016/j.celrep.2021.109375] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/05/2021] [Accepted: 06/18/2021] [Indexed: 01/05/2023] Open
Abstract
The mechanism of T cell antigen receptor (TCR-CD3) signaling remains elusive. Here, we identify mutations in the transmembrane region of TCRβ or CD3ζ that augment peptide T cell antigen receptor (pMHC)-induced signaling not explicable by enhanced ligand binding, lateral diffusion, clustering, or co-receptor function. Using a biochemical assay and molecular dynamics simulation, we demonstrate that the gain-of-function mutations loosen the interaction between TCRαβ and CD3ζ. Similar to the activating mutations, pMHC binding reduces TCRαβ cohesion with CD3ζ. This event occurs prior to CD3ζ phosphorylation and at 0°C. Moreover, we demonstrate that soluble monovalent pMHC alone induces signaling and reduces TCRαβ cohesion with CD3ζ in membrane-bound or solubilised TCR-CD3. Our data provide compelling evidence that pMHC binding suffices to activate allosteric changes propagating from TCRαβ to the CD3 subunits, reconfiguring interchain transmembrane region interactions. These dynamic modifications could change the arrangement of TCR-CD3 boundary lipids to license CD3ζ phosphorylation and initiate signal propagation. Mutations in TCRβ and CD3ζ TMRs that reduce their interaction augment signaling pMHC and anti-CD3 binding to TCR-CD3 induce similar quaternary structure relaxation Soluble monovalent pMHC alone signals and reduces TCRαβ cohesion with CD3ζ Allosteric changes in TCR-CD3 dynamics instigate T cell activation
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Affiliation(s)
- Anna-Lisa Lanz
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Giulia Masi
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Nicla Porciello
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - André Cohnen
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Deborah Cipria
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Dheeraj Prakaash
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Štefan Bálint
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Roberto Raggiaschi
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Donatella Galgano
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - David K Cole
- Division Infection & Immunity, Cardiff University, Cardiff CF14 4XN, UK; Immunocore Ltd., Abingdon OX14 4RY, UK
| | | | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Antreas C Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Oreste Acuto
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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29
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Structures suggest an approach for converting weak self-peptide tumor antigens into superagonists for CD8 T cells in cancer. Proc Natl Acad Sci U S A 2021; 118:2100588118. [PMID: 34074778 PMCID: PMC8201969 DOI: 10.1073/pnas.2100588118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Tumor vaccines using modified self-antigens that structurally enhance T cell receptor–peptide–major histocompatibility complex interactions greatly improve a T cell protective response against the tumor’s unmodified self-antigen. X-ray crystal structures of these interactions explain how the native and modified peptides can interact with the same T cell receptor, but with different affinities and abilities to drive T cell proliferation and differentiation. Tumors frequently express unmutated self-tumor–associated antigens (self-TAAs). However, trial results using self-TAAs as vaccine targets against cancer are mixed, often attributed to deletion of T cells with high-affinity receptors (TCRs) for self-TAAs during T cell development. Mutating these weak self-TAAs to produce higher affinity, effective vaccines is challenging, since the mutations may not benefit all members of the broad self-TAA–specific T cell repertoire. We previously identified a common weak murine self-TAA that we converted to a highly effective antitumor vaccine by a single amino acid substitution. In this case the modified and natural self-TAAs still raised very similar sets of CD8 T cells. Our structural studies herein show that the modification of the self-TAA resulted in a subtle change in the major histocompatibility complex I–TAA structure. This amino acid substitution allowed a dramatic conformational change in the peptide during subsequent TCR engagement, creating a large increase in TCR affinity and accounting for the efficacy of the modified self-TAA as a vaccine. These results show that carefully selected, well-characterized modifications to a poorly immunogenic self-TAA can rescue the immune response of the large repertoire of weakly responding natural self-TAA–specific CD8 T cells, driving them to proliferate and differentiate into functional effectors. Subsequently, the unmodified self-TAA on the tumor cells, while unable to drive this response, is nevertheless a sufficient target for the CD8 cytotoxic effectors. Our results suggest a pathway for more efficiently identifying variants of common self-TAAs, which could be useful in vaccine development, complementing other current nonantigen-specific immunotherapies.
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30
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Removal of CD276 + cells from haploidentical memory T-cell grafts significantly lowers the risk of GVHD. Bone Marrow Transplant 2021; 56:2336-2354. [PMID: 33976380 PMCID: PMC8486669 DOI: 10.1038/s41409-021-01307-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/27/2021] [Accepted: 04/12/2021] [Indexed: 01/08/2023]
Abstract
Detrimental graft-versus-host disease (GVHD) still remains a major cause of death in hematopoietic stem cell transplantation (HSCT). The recently explored depletion of naive cells from mobilized grafts (CD45RA depletion) has shown considerable promise, yet is unable to eliminate the incidence of GVHD. Analysis of CD45RA-depleted haploidentical mixed lymphocytes culture (haplo-MLC) revealed insufficient suppression of alloresponses in the CD4+ compartment and identified CD276 as a marker for alloreactive memory Th1 T cells. Conclusively, depleting CD276+ cells from CD45RA-depleted haplo-MLC significantly attenuated alloreactivity to recipient cells while increasing antiviral reactivity and maintaining anti-third party reactivity in vitro. To evaluate these findings in vivo, bulk, CD45RA-depleted, or CD45RA/CD276-depleted CD4+ T cells from HLA-DR4negative healthy humans were transplanted into NSG-Ab°DR4 mice, a sensitive human allo-GVHD model. Compellingly, CD45RA/CD276-depleted grafts from HLA-DR4negative donors or in vivo depletion of CD276+ cells after transplant of HLA-DR4negative memory CD4 T cells significantly delay the onset of GVHD symptoms and significantly alleviate its severity in NSG-Ab°DR4 mice. The clinical courses correlated with diminished Th1-cytokine secretion and downregulated CXCR6 expression of engrafted peripheral T cells. Collectively, mismatched HLA-mediated GVHD can be controlled by depleting recipient-specific CD276+ alloreacting T cells from the graft, highlighting its application in haplo-HSCT.
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31
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Jain R, Jain A, Verma SK. Prediction of Epitope based Peptides for Vaccine Development from Complete Proteome of Novel Corona Virus (SARS-COV-2) Using Immunoinformatics. Int J Pept Res Ther 2021; 27:1729-1740. [PMID: 33897313 PMCID: PMC8051835 DOI: 10.1007/s10989-021-10205-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2021] [Indexed: 12/19/2022]
Abstract
COVID-19 is an infectious disease caused by a newly discovered corona virus SARS-COV-2. It is the most dangerous epidemic existing currently all over the world. To date, there is no licensed vaccine and not any particular efficient therapeutic agent available to prevent or cure the disease. So development of an effective vaccine is the urgent need of the time. The proposed study aims to identify potential vaccine candidates by screening the complete proteome of SARS-COV-2 using the computational approach. From 14 protein entries in UniProtKB, 4 proteins were screened for epitope prediction based on consensus antigenicity predictions and various physico-chemical criteria like transmembrane domain, allergenicity, GRAVY value, toxicity, stability index. Comprehensive analysis of these 4 antigens revealed that spike protein (P0DTC2) and nucleoprotein (P0DTC9) show the greatest potential for experimental immunogenicity analysis. These 2 proteins have several potential CD4+ and CD8+ T-cell epitopes, as well as high probability of B-cell epitope regions as compared to well-characterized antigen the matrix protein 1 [Influenza A virus (H5N1)]. In addition, the epitope SIIAYTMSL predicted from spike protein (P0DTC2) and epitope SPRWYFYYL predicted from nucleoprotein (P0DTC9) exhibited more than 60% population coverage in the target populations Europe, North America, South Asia, Northeast Asia taken in this study. These epitopes have also been found to exhibit highly significant TCR–pMHC interactions having a joint Z value of 4.51 and 4.37 respectively. Therefore, this analysis suggests that the predicted epitopes might be suitable vaccine candidates and should be subjected to further in-vivo and in-vitro studies.
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Affiliation(s)
- Richa Jain
- Institute of Engineering and Technology, Lucknow, Uttar Pradesh India
| | - Ankit Jain
- Indian Meteorological Department, Lucknow, India
| | - Santosh Kumar Verma
- Department of Civil Engineering, National Institute of Technology, Hamirpur, India
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32
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Padariya M, Kalathiya U, Mikac S, Dziubek K, Tovar Fernandez MC, Sroka E, Fahraeus R, Sznarkowska A. Viruses, cancer and non-self recognition. Open Biol 2021; 11:200348. [PMID: 33784856 PMCID: PMC8061760 DOI: 10.1098/rsob.200348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 03/04/2021] [Indexed: 12/11/2022] Open
Abstract
Virus-host interactions form an essential part of every aspect of life, and this review is aimed at looking at the balance between the host and persistent viruses with a focus on the immune system. The virus-host interaction is like a cat-and-mouse game and viruses have developed ingenious mechanisms to manipulate cellular pathways, most notably the major histocompatibility (MHC) class I pathway, to reside within infected cell while evading detection and destruction by the immune system. However, some of the signals sensing and responding to viral infection are derived from viruses and the fact that certain viruses can prevent the infection of others, highlights a more complex coexistence between the host and the viral microbiota. Viral immune evasion strategies also illustrate that processes whereby cells detect and present non-self genetic material to the immune system are interlinked with other cellular pathways. Immune evasion is a target also for cancer cells and a more detailed look at the interfaces between viral factors and components of the MHC class I peptide-loading complex indicates that these interfaces are also targets for cancer mutations. In terms of the immune checkpoint, however, viral and cancer strategies appear different.
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Affiliation(s)
- Monikaben Padariya
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Umesh Kalathiya
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Sara Mikac
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Katarzyna Dziubek
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Maria C. Tovar Fernandez
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Ewa Sroka
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
| | - Robin Fahraeus
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, F-75010 Paris, France
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653 Brno, Czech Republic
- Department of Medical Biosciences, Umeå University, Building 6M, 901 85 Umeå, Sweden
| | - Alicja Sznarkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822 Gdansk, Poland
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33
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Yuan H, Ma L, Zhang L, Li X, Xia C. Crystal structure of the giant panda MHC class I complex: First insights into the viral peptide presentation profile in the bear family. Protein Sci 2020; 29:2468-2481. [PMID: 33078460 DOI: 10.1002/pro.3980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 01/03/2023]
Abstract
The viral cytotoxic T lymphocyte (CTL) epitope peptides presented by classical MHC-I molecules require the assembly of a peptide-MHC-I-β2m (pMHC-I) trimolecular complex for T cell receptor (TCR) recognition, which is the critical activation link for triggering antiviral T cell immunity. Research on T cell immunology in the Ursidae family, especially structural immunology, is still lacking. In this study, the structure of the key trimolecular complex pMHC-I, which binds a peptide from canine distemper virus, was solved for the first time using giant panda as a representative species of Ursidae. The structural characteristics of the giant panda pMHC-I complex (pAime-128), including the unique pockets in the peptide-binding groove (PBG), were analyzed in detail. Comparing the pAime-128 to others in the bear family and extending the comparison to other mammals revealed distinct features. The interaction between MHC-I and β2m, the features of pAime-128 involved in TCR docking and cluster of differentiation 8 (CD8) binding, the anchor sites in the PBG, and the CTL epitopes of potential viruses that infect pandas were clarified. Unique features of pMHC-I viral antigen presentation in the panda were revealed by solving the three-dimensional (3D) structure of pAime-128. The distinct characteristics of pAime-128 indicate an unusual event that emerged during the evolution of the MHC system in the bear family. These results provide a new platform for research on panda CTL immunity and the design of vaccines for application in the bear family.
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Affiliation(s)
- Hongyu Yuan
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lijie Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaoying Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.,College of Veterinary Medicine, Henan Agricultural University, No. 15 Longzihu University Area, Zhengzhou New District, Zhengzhou, Henan, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
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34
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Wu D, Gallagher DT, Gowthaman R, Pierce BG, Mariuzza RA. Structural basis for oligoclonal T cell recognition of a shared p53 cancer neoantigen. Nat Commun 2020; 11:2908. [PMID: 32518267 PMCID: PMC7283474 DOI: 10.1038/s41467-020-16755-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/19/2020] [Indexed: 01/21/2023] Open
Abstract
Adoptive cell therapy (ACT) with tumor-specific T cells can mediate cancer regression. The main target of tumor-specific T cells are neoantigens arising from mutations in self-proteins. Although the majority of cancer neoantigens are unique to each patient, and therefore not broadly useful for ACT, some are shared. We studied oligoclonal T-cell receptors (TCRs) that recognize a shared neoepitope arising from a driver mutation in the p53 oncogene (p53R175H) presented by HLA-A2. Here we report structures of wild-type and mutant p53-HLA-A2 ligands, as well as structures of three tumor-specific TCRs bound to p53R175H-HLA-A2. These structures reveal how a driver mutation in p53 rendered a self-peptide visible to T cells. The TCRs employ structurally distinct strategies that are highly focused on the mutation to discriminate between mutant and wild-type p53. The TCR-p53R175H-HLA-A2 complexes provide a framework for designing TCRs to improve potency for ACT without sacrificing specificity.
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Affiliation(s)
- Daichao Wu
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Histology and Embryology, Hengyang Medical College, University of South China, Hengyang, Hunan, 421001, China
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - D Travis Gallagher
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- National Institute of Standards and Technology, Gaitherburg, MD, 20899, USA
| | - Ragul Gowthaman
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Brian G Pierce
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Roy A Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA.
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
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MHC-II alleles shape the CDR3 repertoires of conventional and regulatory naïve CD4 + T cells. Proc Natl Acad Sci U S A 2020; 117:13659-13669. [PMID: 32482872 DOI: 10.1073/pnas.2003170117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
T cell maturation and activation depend upon T cell receptor (TCR) interactions with a wide variety of antigenic peptides displayed in a given major histocompatibility complex (MHC) context. Complementarity-determining region 3 (CDR3) is the most variable part of the TCRα and -β chains, which govern interactions with peptide-MHC complexes. However, it remains unclear how the CDR3 landscape is shaped by individual MHC context during thymic selection of naïve T cells. We established two mouse strains carrying distinct allelic variants of H2-A and analyzed thymic and peripheral production and TCR repertoires of naïve conventional CD4+ T (Tconv) and naïve regulatory CD4+ T (Treg) cells. Compared with tuberculosis-resistant C57BL/6 (H2-Ab) mice, the tuberculosis-susceptible H2-Aj mice had fewer CD4+ T cells of both subsets in the thymus. In the periphery, this deficiency was only apparent for Tconv and was compensated for by peripheral reconstitution for Treg We show that H2-Aj favors selection of a narrower and more convergent repertoire with more hydrophobic and strongly interacting amino acid residues in the middle of CDR3α and CDR3β, suggesting more stringent selection against a narrower peptide-MHC-II context. H2-Aj and H2-Ab mice have prominent reciprocal differences in CDR3α and CDR3β features, probably reflecting distinct modes of TCR fitting to MHC-II variants. These data reveal the mechanics and extent of how MHC-II shapes the naïve CD4+ T cell CDR3 landscape, which essentially defines adaptive response to infections and self-antigens.
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Serçinoğlu O, Ozbek P. Sequence-structure-function relationships in class I MHC: A local frustration perspective. PLoS One 2020; 15:e0232849. [PMID: 32421728 PMCID: PMC7233585 DOI: 10.1371/journal.pone.0232849] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/22/2020] [Indexed: 12/22/2022] Open
Abstract
Class I Major Histocompatibility Complex (MHC) binds short antigenic peptides with the help of Peptide Loading Complex (PLC), and presents them to T-cell Receptors (TCRs) of cytotoxic T-cells and Killer-cell Immunglobulin-like Receptors (KIRs) of Natural Killer (NK) cells. With more than 10000 alleles, human MHC (Human Leukocyte Antigen, HLA) is the most polymorphic protein in humans. This allelic diversity provides a wide coverage of peptide sequence space, yet does not affect the three-dimensional structure of the complex. Moreover, TCRs mostly interact with HLA in a common diagonal binding mode, and KIR-HLA interaction is allele-dependent. With the aim of establishing a framework for understanding the relationships between polymorphism (sequence), structure (conserved fold) and function (protein interactions) of the human MHC, we performed here a local frustration analysis on pMHC homology models covering 1436 HLA I alleles. An analysis of local frustration profiles indicated that (1) variations in MHC fold are unlikely due to minimally-frustrated and relatively conserved residues within the HLA peptide-binding groove, (2) high frustration patches on HLA helices are either involved in or near interaction sites of MHC with the TCR, KIR, or tapasin of the PLC, and (3) peptide ligands mainly stabilize the F-pocket of HLA binding groove.
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Affiliation(s)
- Onur Serçinoğlu
- Department of Bioengineering, Recep Tayyip Erdogan University, Faculty of Engineering, Fener, Rize, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Marmara University, Faculty of Engineering, Goztepe, Istanbul, Turkey
- * E-mail:
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37
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Abstract
Throughout the body, T cells monitor MHC-bound ligands expressed on the surface of essentially all cell types. MHC ligands that trigger a T cell immune response are referred to as T cell epitopes. Identifying such epitopes enables tracking, phenotyping, and stimulating T cells involved in immune responses in infectious disease, allergy, autoimmunity, transplantation, and cancer. The specific T cell epitopes recognized in an individual are determined by genetic factors such as the MHC molecules the individual expresses, in parallel to the individual's environmental exposure history. The complexity and importance of T cell epitope mapping have motivated the development of computational approaches that predict what T cell epitopes are likely to be recognized in a given individual or in a broader population. Such predictions guide experimental epitope mapping studies and enable computational analysis of the immunogenic potential of a given protein sequence region.
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Affiliation(s)
- Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, USA; ,
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark;
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, B1650 Buenos Aires, Argentina
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, USA; ,
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
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38
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Affiliation(s)
- Pirooz Zareie
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Carine Farenc
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Nicole L. La Gruta
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia
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39
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Morath A, Schamel WW. αβ and γδ T cell receptors: Similar but different. J Leukoc Biol 2020; 107:1045-1055. [DOI: 10.1002/jlb.2mr1219-233r] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 12/15/2019] [Accepted: 01/13/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Anna Morath
- Signalling Research Centres BIOSS and CIBSS University of Freiburg Freiburg Germany
- Institute of Biology III Faculty of Biology University of Freiburg Freiburg Germany
- Spemann Graduate School of Biology and Medicine (SGBM) University of Freiburg Freiburg Germany
| | - Wolfgang W. Schamel
- Signalling Research Centres BIOSS and CIBSS University of Freiburg Freiburg Germany
- Institute of Biology III Faculty of Biology University of Freiburg Freiburg Germany
- Center for Chronic Immunodeficiency (CCI) Medical Center Freiburg and Faculty of Medicine University of Freiburg Freiburg Germany
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40
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Ma L, Zhang N, Qu Z, Liang R, Zhang L, Zhang B, Meng G, Dijkstra JM, Li S, Xia MC. A Glimpse of the Peptide Profile Presentation by Xenopus laevis MHC Class I: Crystal Structure of p Xela-UAA Reveals a Distinct Peptide-Binding Groove. THE JOURNAL OF IMMUNOLOGY 2019; 204:147-158. [PMID: 31776204 DOI: 10.4049/jimmunol.1900865] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/27/2019] [Indexed: 12/15/2022]
Abstract
The African clawed frog, Xenopus laevis, is a model species for amphibians. Before metamorphosis, tadpoles do not efficiently express the single classical MHC class I (MHC-I) molecule Xela-UAA, but after metamorphosis, adults express this molecule in abundance. To elucidate the Ag-presenting mechanism of Xela-UAA, in this study, the Xela-UAA structure complex (pXela-UAAg) bound with a peptide from a synthetic random peptide library was determined. The amino acid homology between the Xela-UAA and MHC-I sequences of different species is <45%, and these differences are fully reflected in the three-dimensional structure of pXela-UAAg. Because of polymorphisms and interspecific differences in amino acid sequences, pXela-UAAg forms a distinct peptide-binding groove and presents a unique peptide profile. The most important feature of pXela-UAAg is the two-amino acid insertion in the α2-helical region, which forms a protrusion of ∼3.8 Å that is involved in TCR docking. Comparison of peptide-MHC-I complex (pMHC-I) structures showed that only four amino acids in β2-microglobulin that were bound to MHC-I are conserved in almost all jawed vertebrates, and the most unique feature in nonmammalian pMHC-I molecules is that the AB loop bound β2-microglobulin. Additionally, the binding distance between pMHC-I and CD8 molecules in nonmammals is different from that in mammals. These unique features of pXela-UAAg provide enhanced knowledge of T cell immunity and bridge the knowledge gap regarding the coevolutionary progression of the MHC-I complex from aquatic to terrestrial species.
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Affiliation(s)
- Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zehui Qu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Ruiying Liang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Lijie Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Bing Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Geng Meng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100094, China; and
| | - Johannes M Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Shen Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Max Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China;
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41
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Dembic Z. On integrity in immunity during ontogeny or how thymic regulatory T cells work. Scand J Immunol 2019; 90:e12806. [PMID: 31276223 DOI: 10.1111/sji.12806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 12/14/2022]
Abstract
The Standard model of T cell recognition asserts that T cell receptor (TCR) specificities are positively and negatively selected during ontogeny in the thymus and that peripheral T cell repertoire has mild self-major histocompatibility complex (MHC) reactivity, known as MHC restriction of foreign antigen. Thus, the TCR must bind both a restrictive molecule (MHC allele) and a peptide reclining in its groove (pMHC ligand) in order to transmit signal into a T cell. The Standard and Cohn's Tritope models suggest contradictory roles for complementarity-determining regions (CDRs) of the TCRs. Here, I discuss both concepts and propose a different solution to ontogenetic mechanism for TCR-MHC-conserved interaction. I suggest that double (CD4+ CD8+ )-positive (DP) developing thymocytes compete with their αβTCRs for binding to self-pMHC on cortical thymic epithelial cells (cTECs) that present a selected set of tissue-restricted antigens. The competition between DPs involves TCR editing and secondary rearrangements, similar to germinal-centre B cell somatic hypermutation. These processes would generate cells with higher TCR affinity for self-pMHC, facilitating sufficiently long binding to cTECs to become thymic T regulatory cells (tTregs). Furthermore, CD4+ Foxp3+ tTregs can be generated by mTECs via Aire-dependent and Aire-independent pathways, and additionally on thymic bone marrow-derived APCs including thymic Aire-expressing B cells. Thymic Tregs differ from the induced peripheral Tregs, which comprise the negative feedback loop to restrain immune responses. The implication of thymocytes' competition for the highest binding to self-pMHC is the co-evolution of species-specific αβTCR V regions with MHC alleles.
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Affiliation(s)
- Zlatko Dembic
- Department of Oral Biology, University of Oslo, Oslo, Norway
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42
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43
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Abstract
The repertoire of αβ T cell antigen receptors (TCRs) on mature T cells is selected in the thymus where it is rendered both self-tolerant and restricted to the recognition of major histocompatibility complex molecules presenting peptide antigens (pMHC). It remains unclear whether germline TCR sequences exhibit an inherent bias to interact with pMHC prior to selection. Here, we isolated TCR libraries from unselected thymocytes and upon reexpression of these random TCR repertoires in recipient T cell hybridomas, interrogated their reactivities to antigen-presenting cell lines. While these random TCR combinations could potentially have reacted with any surface molecule on the cell lines, the hybridomas were stimulated most frequently by pMHC ligands. The nature and CDR3 loop composition of the TCRβ chain played a dominant role in determining pMHC-reactivity. Replacing the germline regions of mouse TCRβ chains with those of other jawed vertebrates preserved reactivity to mouse pMHC. Finally, introducing the CD4 coreceptor into the hybridomas increased the proportion of cells that could respond to pMHC ligands. Thus, αβ TCRs display an intrinsic and evolutionary conserved bias for pMHC molecules in the absence of any selective pressure, which is further strengthened in the presence of coreceptors.
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44
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Gao K, Chen L, Zhang Y, Zhao Y, Wan Z, Wu J, Lin L, Kuang Y, Lu J, Zhang X, Tian L, Liu X, Qiu X. Germline-Encoded TCR-MHC Contacts Promote TCR V Gene Bias in Umbilical Cord Blood T Cell Repertoire. Front Immunol 2019; 10:2064. [PMID: 31543879 PMCID: PMC6730489 DOI: 10.3389/fimmu.2019.02064] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/15/2019] [Indexed: 12/17/2022] Open
Abstract
T cells recognize antigens as peptides bound to major histocompatibility complex (MHC) proteins through T cell receptors (TCRs) on their surface. To recognize a wide range of pathogens, each individual possesses a substantial number of TCRs with an extremely high degree of variability. It remains controversial whether germline-encoded TCR repertoire is shaped by MHC polymorphism and, if so, what is the preference between MHC genetic variants and TCR V gene compatibility. To investigate the "net" genetic association between MHC variations and TRBV genes, we applied quantitative trait locus (QTL) mapping to test the associations between MHC polymorphism and TCR β chain V (TRBV) genes usage using umbilical cord blood (UCB) samples of 201 Chinese newborns. We found TRBV gene and MHC loci that are predisposed to interact with one another differ from previous conclusions. The majority of MHC amino acid residues associated with the TRBV gene usage show spatial proximities in known structures of TCR-pMHC complexes. These results show for the first time that MHC variants bias TRBV gene usage in UCB of Chinese ancestry and indicate that germline-encoded contacts influence TCR-MHC interactions in intact T cell repertoires.
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Affiliation(s)
- Kai Gao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | | | | | - Yi Zhao
- BGI-Shenzhen, Shenzhen, China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | | | | | | | - Yashu Kuang
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jinhua Lu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Women and Children's Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiuqing Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | | | - Xiao Liu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Xiu Qiu
- Division of Birth Cohort Study, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Women and Children's Health Care, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.,Department of Obstetrics and Gynecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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45
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Carter JA, Preall JB, Grigaityte K, Goldfless SJ, Jeffery E, Briggs AW, Vigneault F, Atwal GS. Single T Cell Sequencing Demonstrates the Functional Role of αβ TCR Pairing in Cell Lineage and Antigen Specificity. Front Immunol 2019; 10:1516. [PMID: 31417541 PMCID: PMC6684766 DOI: 10.3389/fimmu.2019.01516] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/18/2019] [Indexed: 12/13/2022] Open
Abstract
Although structural studies of individual T cell receptors (TCRs) have revealed important roles for both the α and β chain in directing MHC and antigen recognition, repertoire-level immunogenomic analyses have historically examined the β chain alone. To determine the amount of useful information about TCR repertoire function encoded within αβ pairings, we analyzed paired TCR sequences from nearly 100,000 unique CD4+ and CD8+ T cells captured using two different high-throughput, single-cell sequencing approaches. Our results demonstrate little overlap in the healthy CD4+ and CD8+ repertoires, with shared TCR sequences possessing significantly shorter CDR3 sequences corresponding to higher generation probabilities. We further utilized tools from information theory and machine learning to show that while α and β chains are only weakly associated with lineage, αβ pairings appear to synergistically drive TCR-MHC interactions. Vαβ gene pairings were found to be the TCR feature most informative of T cell lineage, supporting the existence of germline-encoded paired αβ TCR-MHC interaction motifs. Finally, annotating our TCR pairs using a database of sequences with known antigen specificities, we demonstrate that approximately a third of the T cells possess α and β chains that each recognize different known antigens, suggesting that αβ pairing is critical for the accurate inference of repertoire functionality. Together, these findings provide biological insight into the functional implications of αβ pairing and highlight the utility of single-cell sequencing in immunogenomics.
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Affiliation(s)
- Jason A. Carter
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | | | - Kristina Grigaityte
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | | | | | | | | | - Gurinder S. Atwal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
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46
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Molecular constraints on CDR3 for thymic selection of MHC-restricted TCRs from a random pre-selection repertoire. Nat Commun 2019; 10:1019. [PMID: 30833553 PMCID: PMC6399321 DOI: 10.1038/s41467-019-08906-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/07/2019] [Indexed: 12/19/2022] Open
Abstract
The αβ T cell receptor (TCR) repertoire on mature T cells is selected in the thymus, but the basis for thymic selection of MHC-restricted TCRs from a randomly generated pre-selection repertoire is not known. Here we perform comparative repertoire sequence analyses of pre-selection and post-selection TCR from multiple MHC-sufficient and MHC-deficient mouse strains, and find that MHC-restricted and MHC-independent TCRs are primarily distinguished by features in their non-germline CDR3 regions, with many pre-selection CDR3 sequences not compatible with MHC-binding. Thymic selection of MHC-independent TCR is largely unconstrained, but the selection of MHC-specific TCR is restricted by both CDR3 length and specific amino acid usage. MHC-restriction disfavors TCR with CDR3 longer than 13 amino acids, limits positively charged and hydrophobic amino acids in CDR3β, and clonally deletes TCRs with cysteines in their CDR3 peptide-binding regions. Together, these MHC-imposed structural constraints form the basis to shape VDJ recombination sequences into MHC-restricted repertoires. For T cells, functional antigen receptors are selected in the thymus from a pre-selection repertoire by interaction with self MHCs. Here the authors show that specific, non-germline coded features located in the complementarity determining region 3 of the pre-selection antigen receptors are essential for the selection of MHC-restricted repertoire.
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47
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Breaking tolerance with engineered class I antigen-presenting molecules. Proc Natl Acad Sci U S A 2019; 116:3136-3145. [PMID: 30728302 DOI: 10.1073/pnas.1807465116] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Successful efforts to activate T cells capable of recognizing weak cancer-associated self-antigens have employed altered peptide antigens to activate T cell responses capable of cross-reacting on native tumor-associated self. A limitation of this approach is the requirement for detailed knowledge about the altered self-peptide ligands used in these vaccines. In the current study we considered allorecognition as an approach for activating CTL capable of recognizing weak or self-antigens in the context of self-MHC. Nonself antigen-presenting molecules typically contain polymorphisms that influence interactions with the bound peptide and TCR interface. Recognition of these nonself structures results in peptide-dependent alloimmunity. Alloreactive T cells target their inducing alloantigens as well as third-party alloantigens but generally fail to target self-antigens. Certain residues located on the alpha-1/2 domains of class I antigen-presenting molecules primarily interface with TCR. These residues are more conserved within and across species than are residues that determine peptide antigen binding properties. Class I variants designed with amino acid substitutions at key positions within the conserved helical structures are shown to provide strong activating signals to alloreactive CD8 T cells while avoiding changes in naturally bound peptide ligands. Importantly, CTL activated in this manner can break self-tolerance by reacting to self-peptides presented by native MHC. The ability to activate self-tolerant T cells capable of cross-reacting on self-peptide-MHC in vivo represents an approach for inducing autoimmunity, with possible application in cancer vaccines.
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48
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Abstract
Major histocompatibility class I (MHC-I) molecules bind peptides derived from cellular synthesis and display them at the cell surface for recognition by receptors on T lymphocytes (TCR) or natural killer (NK) cells. Such recognition provides a crucial step in autoimmunity, identification of bacterial and viral pathogens, and anti-tumor responses. Understanding the mechanism by which such antigenic peptides in the ER are loaded and exchanged for higher affinity peptides onto MHC molecules has recently been clarified by cryo-EM and X-ray studies of the multimolecular peptide loading complex (PLC) and a unimolecular tapasin-like chaperone designated TAPBPR. Insights from these structural studies and complementary solution NMR experiments provide a basis for understanding mechanisms related to immune antigen presentation.
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49
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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] [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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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] [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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