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Zhang A, Piechocka-Trocha A, Li X, Walker BD. A Leucine Zipper Dimerization Strategy to Generate Soluble T Cell Receptors Using the Escherichia coli Expression System. Cells 2022; 11:cells11030312. [PMID: 35159122 PMCID: PMC8834513 DOI: 10.3390/cells11030312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 12/10/2022] Open
Abstract
T cell-mediated adaptive immunity plays a key role in immunological surveillance and host control of infectious diseases. A better understanding of T cell receptor (TCR) recognition of pathogen-derived epitopes or cancer-associated neoantigens is the basis for developing T cell-based vaccines and immunotherapies. Studies on the interaction between soluble TCR α:β heterodimers and peptide-bound major histocompatibility complexes (pMHCs) inform underlying mechanisms driving TCR recognition, but not every isolated TCR can be prepared in soluble form for structural and functional studies using conventional methods. Here, taking a challenging HIV-specific TCR as a model, we designed a general leucine zipper (LZ) dimerization strategy for soluble TCR preparation using the Escherichia coli expression system. We report details of TCR construction, inclusion body expression and purification, and protein refolding and purification. Measurements of binding affinity between the TCR and its specific pMHC using surface plasmon resonance (SPR) verify its activity. We conclude that this is a feasible approach to produce challenging TCRs in soluble form, needed for studies related to T cell recognition.
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Affiliation(s)
- Angela Zhang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Xiaolong Li
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Correspondence: (X.L.); (B.D.W.)
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Institute for Medical Engineering and Science (IMES) and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Correspondence: (X.L.); (B.D.W.)
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2
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Discovery of an ancient MHC category with both class I and class II features. Proc Natl Acad Sci U S A 2021; 118:2108104118. [PMID: 34903649 PMCID: PMC8713811 DOI: 10.1073/pnas.2108104118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 11/28/2022] Open
Abstract
Two classes of major histocompatibility complex (MHC) molecules, MHC class I and MHC class II, constitute the basis of our elaborate, adaptive immune system as antigen-presenting molecules. They perform distinct, critical functions: especially, MHC class I in case of antivirus and antitumor defenses, and MHC class II, in case of effective antibody responses. This important class diversification has long been enigmatic, as vestiges of the evolutionary molecular changes have not been found. The revealed ancient MHC category represents a plausible intermediate group between the two classes, and the data suggest that class II preceded class I in molecular evolution. Fundamental understanding of the molecular evolution of MHC molecules should contribute to understanding the basis of our complex biological defense system. Two classes of major histocompatibility complex (MHC) molecules, MHC class I and class II, play important roles in our immune system, presenting antigens to functionally distinct T lymphocyte populations. However, the origin of this essential MHC class divergence is poorly understood. Here, we discovered a category of MHC molecules (W-category) in the most primitive jawed vertebrates, cartilaginous fish, and also in bony fish and tetrapods. W-category, surprisingly, possesses class II–type α- and β-chain organization together with class I–specific sequence motifs for interdomain binding, and the W-category α2 domain shows unprecedented, phylogenetic similarity with β2-microglobulin of class I. Based on the results, we propose a model in which the ancestral MHC class I molecule evolved from class II–type W-category. The discovery of the ancient MHC group, W-category, sheds a light on the long-standing critical question of the MHC class divergence and suggests that class II type came first.
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3
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Wu Y, Zhang N, Hashimoto K, Xia C, Dijkstra JM. Structural Comparison Between MHC Classes I and II; in Evolution, a Class-II-Like Molecule Probably Came First. Front Immunol 2021; 12:621153. [PMID: 34194421 PMCID: PMC8236899 DOI: 10.3389/fimmu.2021.621153] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/04/2021] [Indexed: 01/03/2023] Open
Abstract
Structures of peptide-loaded major histocompatibility complex class I (pMHC-I) and class II (pMHC-II) complexes are similar. However, whereas pMHC-II complexes include similar-sized IIα and IIβ chains, pMHC-I complexes include a heavy chain (HC) and a single domain molecule β2-microglobulin (β2-m). Recently, we elucidated several pMHC-I and pMHC-II structures of primitive vertebrate species. In the present study, a comprehensive comparison of pMHC-I and pMHC-II structures helps to understand pMHC structural evolution and supports the earlier proposed—though debated—direction of MHC evolution from class II-type to class I. Extant pMHC-II structures share major functional characteristics with a deduced MHC-II-type homodimer ancestor. Evolutionary establishment of pMHC-I presumably involved important new functions such as (i) increased peptide selectivity by binding the peptides in a closed groove (ii), structural amplification of peptide ligand sequence differences by binding in a non-relaxed fashion, and (iii) increased peptide selectivity by syngeneic heterotrimer complex formation between peptide, HC, and β2-m. These new functions were associated with structures that since their establishment in early pMHC-I have been very well conserved, including a shifted and reorganized P1 pocket (aka A pocket), and insertion of a β2-m hydrophobic knob into the peptide binding domain β-sheet floor. A comparison between divergent species indicates better sequence conservation of peptide binding domains among MHC-I than among MHC-II, agreeing with more demanding interactions within pMHC-I complexes. In lungfishes, genes encoding fusions of all MHC-IIα and MHC-IIβ extracellular domains were identified, and although these lungfish genes presumably derived from classical MHC-II, they provide an alternative mechanistic hypothesis for how evolution from class II-type to class I may have occurred.
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Affiliation(s)
- Yanan Wu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Keiichiro Hashimoto
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Johannes M Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
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4
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Del Vecchio F, Martinez-Rodriguez V, Schukking M, Cocks A, Broseghini E, Fabbri M. Professional killers: The role of extracellular vesicles in the reciprocal interactions between natural killer, CD8+ cytotoxic T-cells and tumour cells. J Extracell Vesicles 2021; 10:e12075. [PMID: 33815694 PMCID: PMC8015281 DOI: 10.1002/jev2.12075] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/27/2021] [Accepted: 02/16/2021] [Indexed: 12/11/2022] Open
Abstract
Extracellular vesicles (EVs) mediate the cross‐talk between cancer cells and the cells of the surrounding Tumour Microenvironment (TME). Professional killer cells include Natural Killer (NK) cells and CD8+ Cytotoxic T‐lymphocytes (CTLs), which represent some of the most effective immune defense mechanisms against cancer cells. Recent evidence supports the role of EVs released by NK cells and CTLs in killing cancer cells, paving the road to a possible therapeutic role for such EVs. This review article provides the state‐of‐the‐art knowledge on the role of NK‐ and CTL‐derived EVs as anticancer agents, focusing on the different functions of different sub‐types of EVs. We also reviewed the current knowledge on the effects of cancer‐derived EVs on NK cells and CTLs, identifying areas for future investigation in the emerging new field of EV‐mediated immunotherapy of cancer.
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Affiliation(s)
- Filippo Del Vecchio
- University of Hawai'i Cancer Center Cancer Biology Program University of Hawai'i at Manoa Honolulu Hawaii USA
| | - Verena Martinez-Rodriguez
- University of Hawai'i Cancer Center Cancer Biology Program University of Hawai'i at Manoa Honolulu Hawaii USA.,Department of Cell and Molecular Biology John A. Burns School of Medicine University of Hawai'i at Manoa Honolulu Hawaii USA
| | - Monique Schukking
- University of Hawai'i Cancer Center Cancer Biology Program University of Hawai'i at Manoa Honolulu Hawaii USA.,Department of Molecular Biosciences & Bioengineering University of Hawai'i at Manoa Honolulu Hawaii USA
| | - Alexander Cocks
- University of Hawai'i Cancer Center Cancer Biology Program University of Hawai'i at Manoa Honolulu Hawaii USA
| | - Elisabetta Broseghini
- University of Hawai'i Cancer Center Cancer Biology Program University of Hawai'i at Manoa Honolulu Hawaii USA.,Department of Experimental, Diagnostic and Specialty Medicine (DIMES) University of Bologna Bologna Italy
| | - Muller Fabbri
- University of Hawai'i Cancer Center Cancer Biology Program University of Hawai'i at Manoa Honolulu Hawaii USA
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5
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Burley SK, Berman HM, Christie C, Duarte JM, Feng Z, Westbrook J, Young J, Zardecki C. RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education. Protein Sci 2018; 27:316-330. [PMID: 29067736 PMCID: PMC5734314 DOI: 10.1002/pro.3331] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/20/2017] [Accepted: 10/23/2017] [Indexed: 01/27/2023]
Abstract
The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open-access, digital-data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with ∼40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy.
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Affiliation(s)
- Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data BankInstitute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey08854
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical SchoolNew BrunswickNew Jersey08903
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of California, San DiegoLa JollaCalifornia92093
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data BankInstitute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey08854
| | - Cole Christie
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of California, San DiegoLa JollaCalifornia92093
| | - Jose M. Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data BankSan Diego Supercomputer Center, University of California, San DiegoLa JollaCalifornia92093
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data BankInstitute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey08854
| | - John Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data BankInstitute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey08854
| | - Jasmine Young
- Research Collaboratory for Structural Bioinformatics Protein Data BankInstitute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey08854
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data BankInstitute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew Jersey08854
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Vacchio MS, Bosselut R. What Happens in the Thymus Does Not Stay in the Thymus: How T Cells Recycle the CD4+-CD8+ Lineage Commitment Transcriptional Circuitry To Control Their Function. THE JOURNAL OF IMMUNOLOGY 2017; 196:4848-56. [PMID: 27260768 DOI: 10.4049/jimmunol.1600415] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/06/2016] [Indexed: 12/24/2022]
Abstract
MHC-restricted CD4(+) and CD8(+) T cells are at the core of most adaptive immune responses. Although these cells carry distinct functions, they arise from a common precursor during thymic differentiation, in a developmental sequence that matches CD4 and CD8 expression and functional potential with MHC restriction. Although the transcriptional control of CD4(+)-CD8(+) lineage choice in the thymus is now better understood, less was known about what maintains the CD4(+) and CD8(+) lineage integrity of mature T cells. In this review, we discuss the mechanisms that establish in the thymus, and maintain in postthymic cells, the separation of these lineages. We focus on recent studies that address the mechanisms of epigenetic control of Cd4 expression and emphasize how maintaining a transcriptional circuitry nucleated around Thpok and Runx proteins, the key architects of CD4(+)-CD8(+) lineage commitment in the thymus, is critical for CD4(+) T cell helper functions.
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Affiliation(s)
- Melanie S Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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7
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Arosa FA, Esgalhado AJ, Padrão CA, Cardoso EM. Divide, Conquer, and Sense: CD8 +CD28 - T Cells in Perspective. Front Immunol 2017; 7:665. [PMID: 28096804 PMCID: PMC5206803 DOI: 10.3389/fimmu.2016.00665] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/16/2016] [Indexed: 12/18/2022] Open
Abstract
Understanding the rationale for the generation of a pool of highly differentiated effector memory CD8+ T cells displaying a weakened capacity to scrutinize for peptides complexed with major histocompatibility class I molecules via their T cell receptor, lacking the “signal 2” CD28 receptor, and yet expressing a highly diverse array of innate receptors, from natural killer receptors, interleukin receptors, and damage-associated molecular pattern receptors, among others, is one of the most challenging issues in contemporary human immunology. The prevalence of these differentiated CD8+ T cells, also known as CD8+CD28−, CD8+KIR+, NK-like CD8+ T cells, or innate CD8+ T cells, in non-lymphoid organs and tissues, in peripheral blood of healthy elderly, namely centenarians, but also in stressful and chronic inflammatory conditions suggests that they are not merely end-of-the-line dysfunctional cells. These experienced CD8+ T cells are highly diverse and capable of sensing a variety of TCR-independent signals, which enables them to respond and fine-tune tissue homeostasis.
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Affiliation(s)
- Fernando A Arosa
- Health Sciences Research Centre (CICS-UBI), Universidade da Beira Interior, Covilhã, Portugal; Faculty of Health Sciences (FCS-UBI), Universidade da Beira Interior, Covilhã, Portugal
| | - André J Esgalhado
- Health Sciences Research Centre (CICS-UBI), Universidade da Beira Interior , Covilhã , Portugal
| | - Carolina A Padrão
- Health Sciences Research Centre (CICS-UBI), Universidade da Beira Interior , Covilhã , Portugal
| | - Elsa M Cardoso
- Health Sciences Research Centre (CICS-UBI), Universidade da Beira Interior, Covilhã, Portugal; Faculty of Health Sciences (FCS-UBI), Universidade da Beira Interior, Covilhã, Portugal
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8
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Attaf M, Holland SJ, Bartok I, Dyson J. αβ T cell receptor germline CDR regions moderate contact with MHC ligands and regulate peptide cross-reactivity. Sci Rep 2016; 6:35006. [PMID: 27775030 PMCID: PMC5075794 DOI: 10.1038/srep35006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 09/22/2016] [Indexed: 12/18/2022] Open
Abstract
αβ T cells respond to peptide epitopes presented by major histocompatibility complex (MHC) molecules. The role of T cell receptor (TCR) germline complementarity determining regions (CDR1 and 2) in MHC restriction is not well understood. Here, we examine T cell development, MHC restriction and antigen recognition where germline CDR loop structure has been modified by multiple glycine/alanine substitutions. Surprisingly, loss of germline structure increases TCR engagement with MHC ligands leading to excessive loss of immature thymocytes. MHC restriction is, however, strictly maintained. The peripheral T cell repertoire is affected similarly, exhibiting elevated cross-reactivity to foreign peptides. Our findings are consistent with germline TCR structure optimising T cell cross-reactivity and immunity by moderating engagement with MHC ligands. This strategy may operate alongside co-receptor imposed MHC restriction, freeing germline TCR structure to adopt this novel role in the TCR-MHC interface.
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Affiliation(s)
- Meriem Attaf
- Section of Molecular Immunology, Department of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Stephan J Holland
- Section of Molecular Immunology, Department of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Istvan Bartok
- Section of Molecular Immunology, Department of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Julian Dyson
- Section of Molecular Immunology, Department of Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
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9
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Reinherz EL, Wang JH. Codification of bidentate pMHC interaction with TCR and its co-receptor. Trends Immunol 2015; 36:300-6. [PMID: 25818864 PMCID: PMC4420642 DOI: 10.1016/j.it.2015.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 02/03/2023]
Abstract
A 1983 Immunology Today rostrum hypothesized that each T cell has two recognition units: a T cell receptor (TCR) complex, which binds antigen associated with a polymorphic region of a MHC molecule (pMHC), and a CD4 or CD8 molecule that binds to a conserved region of that same MHC gene product (class II or I, respectively). Structural biology has since precisely revealed those bidentate pMHC interactions. TCRαβ ligates the membrane-distal antigen-binding MHC platform, whereas CD8 clamps a membrane-proximal MHCI α3 domain loop and CD4 docks to a hydrophobic crevice between MHCII α2 and β2 domains. Here, we review how MHC class-restricted binding impacts signaling and lineage commitment, discussing TCR force-driven conformational transitions that may optimally expose the co-receptor docking site on MHC.
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Affiliation(s)
- Ellis L Reinherz
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Jia-huai Wang
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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