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Tiwari R, Singh VK, Rajneesh, Kumar A, Gautam V, Kumar R. MHC tetramer technology: Exploring T cell biology in health and disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 140:327-345. [PMID: 38762273 DOI: 10.1016/bs.apcsb.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Major histocompatibility complex (MHC) tetramers stand as formidable tools within T cell biology, facilitating the exploration and comprehension of immune responses. These artificial molecules, comprising four bound MHC molecules, typically with a specified peptide and a fluorescent label, play a pivotal role in characterizing T cell subsets, monitoring clonal expansion, and unraveling T cell dynamics during responses to infections or immunotherapies. Beyond their applications in T cell biology, MHC tetramers prove valuable in investigating a spectrum of diseases such as infectious diseases, autoimmune disorders, and cancers. Their instrumental role extends to vaccine research and development. Notably, when appropriately configured, tetramers transcend T cell biology research and find utility in exploring natural killer T cells and contributing to specific T cell clonal deletions.
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Affiliation(s)
- Rahul Tiwari
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Vishal Kumar Singh
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rajneesh
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Awnish Kumar
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Vibhav Gautam
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rajiv Kumar
- Centre of Experimental Medicine & Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India.
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2
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Kreissl FK, Banki MA, Droujinine IA. Molecular methods to study protein trafficking between organs. Proteomics 2023; 23:e2100331. [PMID: 36478633 DOI: 10.1002/pmic.202100331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022]
Abstract
Interorgan communication networks are key regulators of organismal homeostasis, and their dysregulation is associated with a variety of pathologies. While mass spectrometry proteomics identifies circulating proteins and can correlate their abundance with disease phenotypes, the tissues of origin and destinations of these secreted proteins remain largely unknown. In vitro approaches to study protein secretion are valuable, however, they may not mimic the complexity of in vivo environments. More recently, the development of engineered promiscuous BirA* biotin ligase derivatives has enabled tissue-specific tagging of cellular secreted proteomes in vivo. The use of biotin as a molecular tag provides information on the tissue of origin and destination, and enables the enrichment of low-abundance hormone proteins. Therefore, promiscuous protein biotinylation is a valuable tool to study protein secretion in vivo.
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Affiliation(s)
- Felix K Kreissl
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
| | - Michael A Banki
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Ilia A Droujinine
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
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3
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Sirithanakorn C, Cronan JE. Biotin, a universal and essential cofactor: Synthesis, ligation and regulation. FEMS Microbiol Rev 2021; 45:6081095. [PMID: 33428728 DOI: 10.1093/femsre/fuab003] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/08/2021] [Indexed: 12/22/2022] Open
Abstract
Biotin is a covalently attached enzyme cofactor required for intermediary metabolism in all three domains of life. Several important human pathogens (e.g. Mycobacterium tuberculosis) require biotin synthesis for pathogenesis. Humans lack a biotin synthetic pathway hence bacterial biotin synthesis is a prime target for new therapeutic agents. The biotin synthetic pathway is readily divided into early and late segments. Although pimelate, a seven carbon α,ω-dicarboxylic acid that contributes seven of the ten biotin carbons atoms, was long known to be a biotin precursor, its biosynthetic pathway was a mystery until the E. coli pathway was discovered in 2010. Since then, diverse bacteria encode evolutionarily distinct enzymes that replace enzymes in the E. coli pathway. Two new bacterial pimelate synthesis pathways have been elucidated. In contrast to the early pathway the late pathway, assembly of the fused rings of the cofactor, was long thought settled. However, a new enzyme that bypasses a canonical enzyme was recently discovered as well as homologs of another canonical enzyme that functions in synthesis of another protein-bound coenzyme, lipoic acid. Most bacteria tightly regulate transcription of the biotin synthetic genes in a biotin-responsive manner. The bifunctional biotin ligases which catalyze attachment of biotin to its cognate enzymes and repress biotin gene transcription are best understood regulatory system.
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Affiliation(s)
- Chaiyos Sirithanakorn
- Faculty of Medicine, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.,Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
| | - John E Cronan
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA.,Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
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4
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Wendorff M, Garcia Alvarez HM, Østerbye T, ElAbd H, Rosati E, Degenhardt F, Buus S, Franke A, Nielsen M. Unbiased Characterization of Peptide-HLA Class II Interactions Based on Large-Scale Peptide Microarrays; Assessment of the Impact on HLA Class II Ligand and Epitope Prediction. Front Immunol 2020; 11:1705. [PMID: 32903714 PMCID: PMC7438773 DOI: 10.3389/fimmu.2020.01705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/25/2020] [Indexed: 12/12/2022] Open
Abstract
Human Leukocyte Antigen class II (HLA-II) molecules present peptides to T lymphocytes and play an important role in adaptive immune responses. Characterizing the binding specificity of single HLA-II molecules has profound impacts for understanding cellular immunity, identifying the cause of autoimmune diseases, for immunotherapeutics, and vaccine development. Here, novel high-density peptide microarray technology combined with machine learning techniques were used to address this task at an unprecedented level of high-throughput. Microarrays with over 200,000 defined peptides were assayed with four exemplary HLA-II molecules. Machine learning was applied to mine the signals. The comparison of identified binding motifs, and power for predicting eluted ligands and CD4+ epitope datasets to that obtained using NetMHCIIpan-3.2, confirmed a high quality of the chip readout. These results suggest that the proposed microarray technology offers a novel and unique platform for large-scale unbiased interrogation of peptide binding preferences of HLA-II molecules.
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Affiliation(s)
- Mareike Wendorff
- Genetics & Bioinformatics, Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Thomas Østerbye
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Hesham ElAbd
- Genetics & Bioinformatics, Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Elisa Rosati
- Genetics & Bioinformatics, Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Frauke Degenhardt
- Genetics & Bioinformatics, Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Søren Buus
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Andre Franke
- Genetics & Bioinformatics, Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Morten Nielsen
- IIBIO, UNSAM-CONICET, Buenos Aires, Argentina.,Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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5
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Anastasakis D, Benhalevy D, Hafner M. Proximity-CLIP and Expedited Non-Radioactive Library Preparation of Small RNA Footprints for Next-Generation Sequencing. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2020; 131:e120. [PMID: 32438484 PMCID: PMC7316200 DOI: 10.1002/cpmb.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
During the course of their life cycle, most RNAs move between several cellular environments where they associate with different RNA binding proteins (RBPs). Reciprocally, a significant portion of RBPs reside in more than a single cellular compartment, where they can interact with discrete RNAs and even exert distinct biological roles. Proximity-CLIP combines proximity biotinylation of proteins with photoactivatable ribonucleoside-enhanced protein-RNA crosslinking to simultaneously profile the proteome, including RBPs and the RBP-bound transcriptome, in any given subcellular compartment. Here we provide a detailed experimental protocol for Proximity-CLIP along with a simplified non-radioactive, small-RNA cDNA library preparation protocol. Published 2020 U.S. Government. Basic Protocol 1: Cell culture, 4SU labeling, proximity biotinylation, and crosslinking Basic Protocol 2: Cell extraction, streptavidin affinity purification, and on-beads trypsinization Basic Protocol 3: RNA footprints cDNA library preparation Support Protocol: Preparation of RNA-seq libraries from intact RNA.
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Affiliation(s)
| | | | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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6
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Benhalevy D, Hafner M. Proximity-CLIP Provides a Snapshot of Protein-Occupied RNA Elements at Subcellular Resolution and Transcriptome-Wide Scale. Methods Mol Biol 2020; 2166:283-305. [PMID: 32710416 DOI: 10.1007/978-1-0716-0712-1_17] [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: 06/11/2023]
Abstract
The distribution of messenger RNAs (mRNAs) to specific subcellular locations has been studied for the past two decades. Technically, studies of RNA localization are lagging those related to protein localization. Here we provide a detailed protocol for Proximity-CLIP, a method recently developed by our group, that combines proximity biotinylation of proteins with photoactivatable ribonucleoside-enhanced protein-RNA cross-linking to simultaneously profile the proteome including RNA-binding proteins (RBPs) and the RBP-bound transcriptome in any given subcellular compartment. The approach is fractionation independent and also enables studying localized RNA-processing intermediates, as well as the identification of regulatory cis-acting elements on RNAs occupied by proteins in a cellular compartment-specific manner.
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Affiliation(s)
- Daniel Benhalevy
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
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7
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Increased yields and biological potency of knob-into-hole-based soluble MHC class II molecules. Nat Commun 2019; 10:4917. [PMID: 31664029 PMCID: PMC6820532 DOI: 10.1038/s41467-019-12902-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/04/2019] [Indexed: 12/19/2022] Open
Abstract
Assembly of soluble peptide-major histocompatibility complex class II (pMHCII) monomers into multimeric structures enables the detection of antigen-specific CD4+ T cells in biological samples and, in some configurations, their reprogramming in vivo. Unfortunately, current MHCII-αβ chain heterodimerization strategies are typically associated with low production yields and require the use of foreign affinity tags for purification, precluding therapeutic applications in humans. Here, we show that fusion of peptide-tethered or empty MHCII-αβ chains to the IgG1-Fc mutated to form knob-into-hole structures results in the assembly of highly stable pMHCII monomers. This design enables the expression and rapid purification of challenging pMHCII types at high yields without the need for leucine zippers and purification affinity tags. Importantly, this design increases the antigen-receptor signaling potency of multimerized derivatives useful for therapeutic applications and facilitates the detection and amplification of low-avidity T cell specificities in biological samples using flow cytometry.
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8
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Abelin JG, Harjanto D, Malloy M, Suri P, Colson T, Goulding SP, Creech AL, Serrano LR, Nasir G, Nasrullah Y, McGann CD, Velez D, Ting YS, Poran A, Rothenberg DA, Chhangawala S, Rubinsteyn A, Hammerbacher J, Gaynor RB, Fritsch EF, Greshock J, Oslund RC, Barthelme D, Addona TA, Arieta CM, Rooney MS. Defining HLA-II Ligand Processing and Binding Rules with Mass Spectrometry Enhances Cancer Epitope Prediction. Immunity 2019; 51:766-779.e17. [PMID: 31495665 DOI: 10.1016/j.immuni.2019.08.012] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/19/2019] [Accepted: 08/15/2019] [Indexed: 12/30/2022]
Abstract
Increasing evidence indicates CD4+ T cells can recognize cancer-specific antigens and control tumor growth. However, it remains difficult to predict the antigens that will be presented by human leukocyte antigen class II molecules (HLA-II), hindering efforts to optimally target them therapeutically. Obstacles include inaccurate peptide-binding prediction and unsolved complexities of the HLA-II pathway. To address these challenges, we developed an improved technology for discovering HLA-II binding motifs and conducted a comprehensive analysis of tumor ligandomes to learn processing rules relevant in the tumor microenvironment. We profiled >40 HLA-II alleles and showed that binding motifs were highly sensitive to HLA-DM, a peptide-loading chaperone. We also revealed that intratumoral HLA-II presentation was dominated by professional antigen-presenting cells (APCs) rather than cancer cells. Integrating these observations, we developed algorithms that accurately predicted APC ligandomes, including peptides from phagocytosed cancer cells. These tools and biological insights will enable improved HLA-II-directed cancer therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Asaf Poran
- Neon Therapeutics, Cambridge, MA 02139, USA
| | | | | | - Alex Rubinsteyn
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeff Hammerbacher
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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9
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Generation of Allergen-Specific Tetramers for a Murine Model of Airway Inflammation. Methods Mol Biol 2019. [PMID: 29956152 DOI: 10.1007/978-1-4939-7896-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The identification and analysis of allergen-specific CD4+ T cells is critical for understanding how these cells contribute to atopic disease and how to subvert their behavior through immune therapy. The advent of fluorescently labeled soluble tetramers of peptide:MHCII complexes (pMHCII tetramers) has provided investigators with an invaluable means to achieve this goal. Although pMHCII tetramers were first developed over two decades ago, their widespread use has been limited by the technical difficulty of generating these reagents. However, the adoption of various technical innovations from several labs over time has contributed greatly to the increased success in tetramer generation today. Here, we describe a comprehensive protocol for generating pMHCII tetramers using as an example a Derp1:I-Ab tetramer used to study allergen-specific CD4+ T cell responses in murine models of airway inflammation and allergic disease.
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10
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Goldberg MF, Roeske EK, Ward LN, Pengo T, Dileepan T, Kotov DI, Jenkins MK. Salmonella Persist in Activated Macrophages in T Cell-Sparse Granulomas but Are Contained by Surrounding CXCR3 Ligand-Positioned Th1 Cells. Immunity 2018; 49:1090-1102.e7. [PMID: 30552021 DOI: 10.1016/j.immuni.2018.10.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/16/2018] [Accepted: 10/10/2018] [Indexed: 12/11/2022]
Abstract
Salmonella enterica (Se) bacteria cause persistent intracellular infections while stimulating a robust interferon-γ-producing CD4+ T (Th1) cell response. We addressed this paradox of concomitant infection and immunity by tracking fluorescent Se organisms in mice. Se bacteria persisted in nitric oxide synthase (iNOS)-producing resident and recruited macrophages while inducing genes related to protection from nitric oxide. Se-infected cells occupied iNOS+ splenic granulomas that excluded T cells but were surrounded by mononuclear phagocytes producing the chemokines CXCL9 and CXCL10, and Se epitope-specific Th1 cells expressing CXCR3, the receptor for these chemokines. Blockade of CXCR3 inhibited Th1 occupancy of CXCL9/10-dense regions, reduced activation of the Th1 cells, and led to increased Se growth. Thus, intracellular Se bacteria survive in their hosts by counteracting toxic products of the innate immune response and by residing in T cell-sparse granulomas, away from abundant Th1 cells positioned via CXCR3 in a bordering region that act to limit infection.
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Affiliation(s)
- Michael F Goldberg
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Elizabeth K Roeske
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Lauren N Ward
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Thomas Pengo
- University of Minnesota Informatics Institute, Office of the Vice President for Research, Minneapolis, MN 55455, USA
| | - Thamotharampillai Dileepan
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Dmitri I Kotov
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Marc K Jenkins
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN 55455, USA.
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11
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Gan Y, Wang C, Fang Y, Yao Y, Tu X, Wang J, Huang X, Tan Y, Chen T, Zhang K, Shen Y, Zhou L, Liu J, Lai X. Mycobacterium tuberculosis peptide E7/HLA-DRB1 tetramers with different HLA-DR alleles bound CD4 + T cells might share identical CDR3 region. Sci Rep 2018; 8:9903. [PMID: 29967390 PMCID: PMC6028479 DOI: 10.1038/s41598-018-28344-7] [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: 04/10/2017] [Accepted: 06/21/2018] [Indexed: 12/02/2022] Open
Abstract
Human CD4+ T cells play an important role in the immune response to Mycobacterium tuberculosis (MTB). However, little is known about the spectratyping characteristics of the CD4+ T-cell receptor (TCR) α- and β-chains CDR3 region in tuberculosis (TB) patients. We sorted MTB peptide E7-bound CD4+ T cells by using E7/HLA-DR tetramers constructed with different HLA-DRB1 alleles and extracted the CDR3 amino-acid sequences of TCR α- and β-chains. The results showed that the CDR3 sequences of E7-bound CD4+ T cells were completely or partially identical in a single patient. The sequences of MTB peptide C5-bound CD4+ T cells shared another, and non-peptide bound CD4+ T cells, as well as unbound CD4+ T cells with tetramers were different from each other. Specifically, diverse CDR3 sequences of E7-bound CD4+ T cells displayed similar protein tertiary structure in one TB patient. In summary, the TCR α- and β-chains of CDR3 lineage of CD4+ T cells in TB patients apparently drifted, and the predominant CDR3 sequences of TCR α- and β-chains that recognized the MTB antigen exhibited peptide specificity, and certain HLA-DR restriction was also established. This study elucidates the possible causes and mechanisms of peptide-specific CD4+ T-cell-related presentation against MTB.
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Affiliation(s)
- Yichuan Gan
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Cong Wang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Yimin Fang
- State Key Laboratory of Respiratory Disease of China, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou, 510095, China
| | - Yanan Yao
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Xiaoxin Tu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Jiao Wang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Xi Huang
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease of China, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou, 510095, China
| | - Tao Chen
- Tuberculosis Control Center of Guangdong Province, 485 West Huangpu Avenue, Guangzhou, 510630, China
| | - Kouxing Zhang
- Third Affiliated Hospital of Sun Yat-sen University, 600 Tianhe Road, Guangzhou, 510630, China
| | - Yanming Shen
- State Key Laboratory of Respiratory Disease of China, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou, 510095, China
| | - Lin Zhou
- Tuberculosis Control Center of Guangdong Province, 485 West Huangpu Avenue, Guangzhou, 510630, China.
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease of China, Guangzhou Chest Hospital, 62 Hengzhigang Road, Guangzhou, 510095, China.
| | - Xiaomin Lai
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China.
- China Ministry of Education Key Laboratory of Tropical Diseases Control, Tuberculosis Research Institute, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China.
- Gangdong Provincial Department of Education Key Laboratory of Functional Molecules from Marine Microorganisms, Gangdong Provincial Research Center for Severe Infectious Disease Prevention and Control Technology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan Road II, Guangzhou, 510080, China.
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12
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Liu W, Vigdorovich V, Zhan C, Patskovsky Y, Bonanno JB, Nathenson SG, Almo SC. Increased Heterologous Protein Expression in Drosophila S2 Cells for Massive Production of Immune Ligands/Receptors and Structural Analysis of Human HVEM. Mol Biotechnol 2015. [DOI: 10.1007/s12033-015-9881-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Abstract
The binding between biotin and streptavidin or avidin is one of the strongest known non-covalent biological interactions. The (strept)avidin-biotin interaction has been widely used for decades in biological research and biotechnology. Therefore labeling of purified proteins by biotin is a powerful way to achieve protein capture, immobilization, and functionalization, as well as multimerizing or bridging molecules. Chemical biotinylation often generates heterogeneous products, which may have impaired function. Enzymatic biotinylation with E. coli biotin ligase (BirA) is highly specific in covalently attaching biotin to the 15 amino acid AviTag peptide, giving a homogeneous product with high yield. AviTag can conveniently be added genetically at the N-terminus, C-terminus, or in exposed loops of a target protein. We describe here procedures for AviTag insertion by inverse PCR, purification of BirA fused to glutathione-S-transferase (GST-BirA) from E. coli, BirA biotinylation of purified protein, and gel-shift analysis by SDS-PAGE to quantify the extent of biotinylation.
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Affiliation(s)
- Michael Fairhead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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14
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Assessment of CD4+ T cell responses to glutamic acid decarboxylase 65 using DQ8 tetramers reveals a pathogenic role of GAD65 121-140 and GAD65 250-266 in T1D development. PLoS One 2014; 9:e112882. [PMID: 25405480 PMCID: PMC4236121 DOI: 10.1371/journal.pone.0112882] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 10/19/2014] [Indexed: 11/19/2022] Open
Abstract
Susceptibility to type 1 diabetes (T1D) is strongly associated with MHC class II molecules, particularly HLA-DQ8 (DQ8: DQA1*03:01/DQB1*03:02). Monitoring T1D-specific T cell responses to DQ8-restricted epitopes may be key to understanding the immunopathology of the disease. In this study, we examined DQ8-restricted T cell responses to glutamic acid decarboxylase 65 (GAD65) using DQ8 tetramers. We demonstrated that GAD65 121-140 and GAD65 250-266 elicited responses from DQ8+ subjects. Circulating CD4+ T cells specific for these epitopes were detected significantly more often in T1D patients than in healthy individuals after in vitro expansion. T cell clones specific for GAD65 121-140 and GAD65 250-266 carried a Th1-dominant phenotype, with some of the GAD65 121-140-specific T cell clones producing IL-17. GAD65 250-266-specific CD4+ T cells could also be detected by direct ex vivo staining. Analysis of unmanipulated peripheral blood mononuclear cells (PBMCs) revealed that GAD65 250-266-specific T cells could be found in both healthy and diabetic individuals but the frequencies of specific T cells were higher in subjects with type 1 diabetes. Taken together, our results suggest a proinflammatory role for T cells specific for DQ8-restricted GAD65 121-140 and GAD65 250-266 epitopes and implicate their possible contribution to the progression of T1D.
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Zhang X, Wang XX, Shusta EV. Creation and Evaluation of a Single-chain Antibody Tetramer that Targets Brain Endothelial Cells. AIChE J 2014; 60:1245-1252. [PMID: 24659822 DOI: 10.1002/aic.14348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Antibodies that target and internalize into blood-brain barrier (BBB) endothelial cells offer promise as drug delivery agents. Previously, we identified a single-chain antibody (scFvA) capable of binding to the BBB. In an attempt to improve the binding and internalization properties of the single chain antibody (scFvA), a biotinylation tag (Avitag) was fused to scFvA and the protein secreted by yeast. The scFvA-Avitag could be biotinylated by yeast-displayed BirA enzyme and biotinylated scFvA-Avitag could be used to create scFv tetramers. Tetramerization of scFvA improved the internalization of scFvA into BBB endothelial cells, and biotinylated scFvA-Avitag could also be used to target streptavidin-coated quantum dots for BBB endothelial cell internalization. Perfusing the rat brain with scFvA-tetramer confirmed that the antigen targeted by scFvA is distributed on blood side of the BBB, suggesting the potential for downstream application of scFvA in brain-targeted drug delivery.
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Affiliation(s)
- Xiaobin Zhang
- Dept. of Chemical and Biological Engineering; University of Wisconsin-Madison; Madison WI 53706
| | - Xin Xiang Wang
- Dept. of Chemical and Biological Engineering; University of Wisconsin-Madison; Madison WI 53706
| | - Eric V. Shusta
- Dept. of Chemical and Biological Engineering; University of Wisconsin-Madison; Madison WI 53706
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16
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Vigdorovich V, Ramagopal UA, Lázár-Molnár E, Sylvestre E, Lee JS, Hofmeyer KA, Zang X, Nathenson SG, Almo SC. Structure and T cell inhibition properties of B7 family member, B7-H3. Structure 2013; 21:707-17. [PMID: 23583036 DOI: 10.1016/j.str.2013.03.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/18/2013] [Accepted: 03/01/2013] [Indexed: 01/25/2023]
Abstract
T cell activity is controlled by a combination of antigen-dependent signaling through the T cell receptor and a set of auxiliary signals delivered through antigen-independent interactions, including the recognition of the B7 family of ligands. B7-H3 is a recently identified B7 family member that is strongly overexpressed in a range of cancers and correlates with poor prognosis. We report the crystal structure of murine B7-H3 at a 3 Å resolution, which provides a model for the organization of the IgV and IgC domains within the ectodomain. We demonstrate that B7-H3 inhibits T cell proliferation and show that the FG loop of the IgV domain plays a critical role in this function. B7-H3 crystallized as an unusual dimer arising from the exchange of the G strands in the IgV domains of partner molecules. This arrangement, in combination with previous reports, highlights the dynamic nature and plasticity of the immunoglobulin fold.
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Affiliation(s)
- Vladimir Vigdorovich
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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17
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Chong MK, Parthasarathy K, Yeo HY, Ng ML. Optimized sequential purification protocol for in vivo site-specific biotinylated full-length dengue virus capsid protein. Protein Eng Des Sel 2013; 26:377-87. [PMID: 23479673 DOI: 10.1093/protein/gzs107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dengue virus (DENV) capsid (C) protein is one of the three structural proteins that form a mature virus. The main challenge impeding the study of this protein is to generate pure non-truncated, full-length C proteins for structural and functional studies. This is mainly due to its small molecular weight, highly positively charged, stability and solubility properties. Here, we report a strategy to construct, express, biotinylate and purify non-truncated, full-length DENV C protein. A 6× His tag and a biotin acceptor peptide (BAP) were cloned at the N-terminus of C protein using overlapping extension-polymerase chain reaction method for site-specific biotinylation. The final construct was inserted into pET28a plasmid and BL-21 (CodonPlus) expression competent cell strain was selected as there are 12% rare codons in the C protein sequence. Strikingly, we found that our recombinant proteins with BAP were biotinylated endogenously with high efficiency in Escherichia coli BL-21 strains. To purify this His-tagged C protein, nickel-nitriloacetic acid affinity chromatography was first carried out under denaturing condition. After stepwise dialysis and concurrent refolding, ion exchange-fast protein liquid chromatography was performed to further separate the residual contaminants. To obtain C protein with high purity, a final round of purification with size exclusion chromatography was carried out and a single peak corresponding to C protein was attained. With this optimized sequential purification protocol, we successfully generated pure biotinylated full-length DENV C protein. The functionality of this purified non-truncated DENV C protein was examined and it was suitable for structural and molecular studies.
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Affiliation(s)
- Mun Keat Chong
- Flavivirology Laboratory, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
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18
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Liu DS, Phipps WS, Loh KH, Howarth M, Ting AY. Quantum dot targeting with lipoic acid ligase and HaloTag for single-molecule imaging on living cells. ACS NANO 2012; 6:11080-11087. [PMID: 23181687 PMCID: PMC3528850 DOI: 10.1021/nn304793z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We present a methodology for targeting quantum dots to specific proteins on living cells in two steps. In the first step, Escherichia coli lipoic acid ligase (LplA) site-specifically attaches 10-bromodecanoic acid onto a 13 amino acid recognition sequence that is genetically fused to a protein of interest. In the second step, quantum dots derivatized with HaloTag, a modified haloalkane dehalogenase, react with the ligated bromodecanoic acid to form a covalent adduct. We found this targeting method to be specific, fast, and fully orthogonal to a previously reported and analogous quantum dot targeting method using E. coli biotin ligase and streptavidin. We used these two methods in combination for two-color quantum dot visualization of different proteins expressed on the same cell or on neighboring cells. Both methods were also used to track single molecules of neurexin, a synaptic adhesion protein, to measure its lateral diffusion in the presence of neuroligin, its trans-synaptic adhesion partner.
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19
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Novel system for in vivo biotinylation and its application to crab antimicrobial protein scygonadin. Biotechnol Lett 2012; 34:1629-35. [PMID: 22566209 DOI: 10.1007/s10529-012-0942-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 04/18/2012] [Indexed: 10/28/2022]
Abstract
BirA is a biotin ligase from Escherichia coli that specifically biotinylates a lysine side-chain within a 15-amino acid acceptor peptide (also known as Avi-tag). We developed a protocol for producing recombinant BirA ligase in E. coli for in vitro biotinylation (Li and Sousa, Prot Expr Purif, 82:162-167, 2012) in which the target protein was expressed as both thioredoxin and MBP fusions, and was released by TEV protease-mediated cleavage. The liberated ligase and the fusion proteins were enzymatically active. Based on that observation, we have now developed a novel system for in vivo biotinylation by co-expressing the Avi-tagged target protein with the MBP-BirA fusion. The effectiveness of this system was demonstrated by the successful in vivo labeling of antimicrobial protein, scygonadin. This new system shows improved efficiency compared with pre-existing one and this is likely attributed to the high expression level and solubility of the co-expressed MBP-BirA.
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20
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Abstract
MHC class II tetramers have emerged as an important tool for characterization of the specificity and phenotype of CD4 T cell immune responses, useful in a large variety of disease and vaccine studies. Issues of specific T cell frequency, biodistribution, and avidity, coupled with the large genetic diversity of potential class II restriction elements, require targeted experimental design. Translational opportunities for immune disease monitoring are driving the rapid development of HLA class II tetramer use in clinical applications, together with innovations in tetramer production and epitope discovery.
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21
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Tykvart J, Šácha P, Bařinka C, Knedlík T, Starková J, Lubkowski J, Konvalinka J. Efficient and versatile one-step affinity purification of in vivo biotinylated proteins: expression, characterization and structure analysis of recombinant human glutamate carboxypeptidase II. Protein Expr Purif 2012; 82:106-15. [PMID: 22178733 PMCID: PMC3443621 DOI: 10.1016/j.pep.2011.11.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 11/28/2011] [Accepted: 11/29/2011] [Indexed: 10/14/2022]
Abstract
Affinity purification is a useful approach for purification of recombinant proteins. Eukaryotic expression systems have become more frequently used at the expense of prokaryotic systems since they afford recombinant eukaryotic proteins with post-translational modifications similar or identical to the native ones. Here, we present a one-step affinity purification set-up suitable for the purification of secreted proteins. The set-up is based on the interaction between biotin and mutated streptavidin. Drosophila Schneider 2 cells are chosen as the expression host, and a biotin acceptor peptide is used as an affinity tag. This tag is biotinylated by Escherichia coli biotin-protein ligase in vivo. We determined that localization of the ligase within the ER led to the most effective in vivo biotinylation of the secreted proteins. We optimized a protocol for large-scale expression and purification of AviTEV-tagged recombinant human glutamate carboxypeptidase II (Avi-GCPII) with milligram yields per liter of culture. We also determined the 3D structure of Avi-GCPII by X-ray crystallography and compared the enzymatic characteristics of the protein to those of its non-tagged variant. These experiments confirmed that AviTEV tag does not affect the biophysical properties of its fused partner. Purification approach, developed here, provides not only a sufficient amount of highly homogenous protein but also specifically and effectively biotinylates a target protein and thus enables its subsequent visualization or immobilization.
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Affiliation(s)
- J Tykvart
- Gilead Sciences and IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 6, Czech Republic
- Department of Biochemistry, Faculty of Natural Science, Charles University, Albertov 6, Prague 2, Czech Republic
| | - P Šácha
- Gilead Sciences and IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 6, Czech Republic
- Department of Biochemistry, Faculty of Natural Science, Charles University, Albertov 6, Prague 2, Czech Republic
| | - C Bařinka
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, Czech Republic
| | - T Knedlík
- Gilead Sciences and IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 6, Czech Republic
- Department of Biochemistry, Faculty of Natural Science, Charles University, Albertov 6, Prague 2, Czech Republic
| | - J Starková
- Gilead Sciences and IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 6, Czech Republic
| | - J Lubkowski
- Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA
| | - J Konvalinka
- Gilead Sciences and IOCB Research Centre, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 6, Czech Republic
- Department of Biochemistry, Faculty of Natural Science, Charles University, Albertov 6, Prague 2, Czech Republic
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22
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Han H, Liu Q, He W, Ong K, Liu X, Gao B. An efficient vector system to modify cells genetically. PLoS One 2011; 6:e26380. [PMID: 22096482 PMCID: PMC3214020 DOI: 10.1371/journal.pone.0026380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 09/26/2011] [Indexed: 11/18/2022] Open
Abstract
The transfer of foreign genes into mammalian cells has been essential for understanding the functions of genes and mechanisms of genetic diseases, for the production of coding proteins and for gene therapy applications. Currently, the identification and selection of cells that have received transferred genetic material can be accomplished by methods, including drug selection, reporter enzyme detection and GFP imaging. These methods may confer antibiotic resistance, or be disruptive, or require special equipment. In this study, we labeled genetically modified cells with a cell surface biotinylation tag by co-transfecting cells with BirA, a biotin ligase. The modified cells can be quickly isolated for downstream applications using a simple streptavidin bead method. This system can also be used to screen cells expressing two sets of genes from separate vectors.
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Affiliation(s)
- Huamin Han
- CAS Key Laboratory of Pathogenic Microbiology and Immunology (CASPMI), Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Qingjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology (CASPMI), Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Wen He
- CAS Key Laboratory of Pathogenic Microbiology and Immunology (CASPMI), Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Kristy Ong
- UCL Institute of Child Health, London, United Kingdom
| | - Xiaoli Liu
- Epigen Biotec Ltd, Beijing, People's Republic of China
| | - Bin Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology (CASPMI), Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
- China-Japan Joint Laboratory of Molecular Immunology and Microbiology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
- * E-mail:
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23
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Detection of protein-protein interactions using nonimmune IgG and BirA-mediated biotinylation. Biotechniques 2011; 49:881-6. [PMID: 21143209 DOI: 10.2144/000113550] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Detection of protein-protein interactions in cells is crucial for understanding the biological functions of proteins, including their roles in signal transduction. However, current methods require specific antibodies both for immunoprecipitation and detection, making them expensive and sometimes unreliable. Here we describe protocols for protein-protein interaction assays that use nonimmune IgG-conjugated Sepharose to precipitate the IgG binding domain (ZZ) fused to the bait protein; the interaction partner is fused to Avitag and biotinylated by BirA so that it can be detected by a one-step blot with Dylight 680 streptavidin to detect the Avitag fusion protein. Since this method does not require specific antibodies and is inexpensive, sensitive, and reliable, it should be useful for detecting protein-protein interactions in cells.
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24
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Use of HLA-DR*08032/E7 and HLA-DR*0818/E7 tetramers in tracking of epitope-specific CD4+ T cells in active and convalescent tuberculosis patients compared with control donors. Immunobiology 2011; 216:947-60. [PMID: 21281984 DOI: 10.1016/j.imbio.2011.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Revised: 01/02/2011] [Accepted: 01/04/2011] [Indexed: 11/22/2022]
Abstract
Comparative tracking of tetramer-positive and epitope-specific CD4(+) T cells in blood and other tissues from tuberculosis (TB) patients during TB development and treatment using control donor samples is not well characterized. In this study, a novel HLA-DR-restricted peptide E7 from the ESAT-6 protein of Mycobacterium tuberculosis (MTB) was used to prepare modified HLA-DR*08032/E7 tetramer (tetramer 1) and HLA-DR*0818/E7 tetramer (tetramer 2) to monitor a series of samples from TB patients and control donors. Tetramer staining showed that (1) by direct staining of single sample and flow cytometric analyses, detection of tetramer-positive CD4(+) T cells ranged from 0.1% to 8.8% (median 0.67% in tetramer 1 and 0.5% in tetramer 2), 0.1 to 10.7% (0.74% and 0.71%), 0.02 to 2.2% (0.25% and 0.25%), 0.02 to 0.48% (0.2% and 0.2%) and most at under 0-0.2% (0.2% and 0.16%) in the initial pulmonary TB (PTB) patients' blood, pleural fluid (PLF) of initial tuberculous pleuritis patients, non-TB patients' blood, healthy donors' blood and umbilical cord blood, respectively; significantly higher levels of CD4(+) T cells were detected in samples of TB patients than in three control donor groups; (2) by direct staining of time point TB samples and flow cytometric analyses, along with TB symptom amendment at day 60, tetramer-positive CD4(+) T cells began to decrease, until after 90-120 days, reached and kept at a relatively low even normal level about at 0.03-0.3%; (3) by enrichment approach, at least 10-fold increased memory tetramer-positive CD4(+) T cells were seen; (4) by in situ staining, tetramer-positive, IFN-γ-producing and/or TNF-α-producing CD4(+) T cells in the lymph node and lung granuloma and cavernous tissues of TB patients could be determined. Therefore, by further increasing the sample size tested to confirm the specificity and sensitivity of tetrameric molecules, it should be possible to develop them for use as research and diagnostic reagents.
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25
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Postel A, Letzel T, Müller F, Ehricht R, Pourquier P, Dauber M, Grund C, Beer M, Harder TC. In vivo biotinylated recombinant influenza A virus hemagglutinin for use in subtype-specific serodiagnostic assays. Anal Biochem 2010; 411:22-31. [PMID: 21172299 DOI: 10.1016/j.ab.2010.12.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 12/02/2010] [Accepted: 12/14/2010] [Indexed: 10/18/2022]
Abstract
There is an urgent need for robust subtype-specific serological tests to diagnose influenza A virus infections in poultry and mammals, including humans. Such assays require reliable subtype-specific sources of soluble and authentically folded seroreactive hemagglutinin (HA), one of the integral membrane proteins that determine the serological subtype of influenza viruses. To this purpose, a bigenic pFastBacDual baculovirus transfer vector allowing efficient invivo biotinylation of soluble HA homo-oligomers expressed via the secretory pathway was developed. An Avi-Tag allowed site-specific biotinylation by a coexpressed genetically modified BirA biotin ligase retained in the endoplasmic reticulum (ER). Highly seroreactive mono-biotinylated HA of recent H5 and H7 influenza A subtypes was secreted from recombinant baculovirus infected High-Five insect cells at levels sufficient to directly load streptavidin-coated enzyme-linked immunosorbent assay (ELISA) matrices, thereby avoiding any purification steps. The recombinant antigens retained authentic antigenicity, including conformation-dependent epitopes involved in hemagglutination inhibition as detected by monoclonal antibodies. This is the first bigenic invivo biotinylation system established for use in insect cells with secretable recombinant membrane proteins biotinylated by an ER-retained variant of BirA biotin ligase. The proposed technique is expected to significantly increase flexibility in the design of subtype-specific assays, thereby expanding the power of influenzaA virus serodiagnosis.
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Affiliation(s)
- Alexander Postel
- National Reference Laboratory for Avian Influenza Virus, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, D-17493 Greifswald, Germany
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26
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The Immune Tolerance Network at 10 years: tolerance research at the bedside. Nat Rev Immunol 2010; 10:797-803. [PMID: 20972473 DOI: 10.1038/nri2869] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Immune tolerance-inducing therapies reprogramme immune cells to eliminate pathogenic immune responses while preserving protective immunity. The Immune Tolerance Network (ITN), sponsored by the US National Institutes of Health, was established in 1999 to evaluate new tolerance-inducing therapies and carry out mechanistic studies using a unique interactive approach in partnership with industry, academia and foundations. Ten years later, the ITN has carried out approximately 36 clinical trials and tolerance studies examining innovative tolerogenic approaches in the settings of allergy, autoimmune diseases and organ transplantation. ITN investigators have published more than 80 original research papers based on this work. This Timeline article summarizes the progress and challenges of clinical research in the ITN.
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27
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Sims S, Willberg C, Klenerman P. MHC-peptide tetramers for the analysis of antigen-specific T cells. Expert Rev Vaccines 2010; 9:765-74. [PMID: 20624049 DOI: 10.1586/erv.10.66] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The development of the fluorescently labeled tetrameric MHC-peptide complex has enabled the direct visualization, quantification and phenotypic characterization of antigen-specific T cells using flow cytometry and has transformed our understanding of cellular immune responses. The combination of this technology with functional assays provides many new insights into these cells, allowing investigation into their lifecycle, manner of death and effector function. In this article, we hope to provide an overview of the techniques used in the construction of these tetramers, the problems and solutions associated with them, and the methods used in the study of antigen-specific T cells. Understanding how the antigen-specific cells develop and function in different circumstances and with different pathogens will be key to understanding natural host defense, as well as vaccine design and assessment.
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Affiliation(s)
- Stuart Sims
- Nuffield Department of Medicine and NIHR Biomedical Research Centre, University of Oxford, Oxford, UK.
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28
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Faner R, James E, Huston L, Pujol-Borrel R, Kwok WW, Juan M. Reassessing the role of HLA-DRB3 T-cell responses: evidence for significant expression and complementary antigen presentation. Eur J Immunol 2010; 40:91-102. [PMID: 19830726 DOI: 10.1002/eji.200939225] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In humans, several HLA-DRB loci (DRB1/3/4/5) encode diverse beta-chains that pair with alpha-chains to form DR molecules on the surface of APC. While DRB1 and DRB5 have been extensively studied, the role of DRB3/4 products of DR52/DR53 haplotypes has been largely neglected. To clarify the relative expression of DRB3, we quantified DRB3 mRNA levels in comparison with DRB1 mRNA from the same haplotype in both B cells and monocytes, observing quantitatively significant DRB3 synthesis. In CD19+ cells, DRB1*03/11/13 was 3.5-fold more abundant than DRB3, but in CD14+ this difference was only two-fold. Monocytes also had lower overall levels of DR mRNA compared with B cells, which was confirmed by cell surface staining of DRB1 and DRB3. To evaluate the functional role of DRB3, tetramer-guided epitope mapping was used to detect T cells against tetanus toxin and several influenza antigens presented by DRB3*0101/0202 or DRB1*03/11/13. None of the epitopes discovered were shared among any of the DR molecules. Quantitative assessment of DRB3-tetanus toxin specific T cells revealed that they are present at similar frequencies as those observed for DRB1. These results suggest that DRB3 plays a significant role in antigen presentation with different epitopic preferences to DRB1. Therefore, DRB3, like DRB5, serves to extend and complement the peptide repertoire of DRB1 in antigen presentation.
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Affiliation(s)
- Rosa Faner
- Laboratory of Immunobiology Research and Applications to Diagnosis (LIRAD). Banc de Sang i Teixits, Badalona, Spain
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29
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Justesen S, Harndahl M, Lamberth K, Nielsen LLB, Buus S. Functional recombinant MHC class II molecules and high-throughput peptide-binding assays. Immunome Res 2009; 5:2. [PMID: 19416502 PMCID: PMC2690590 DOI: 10.1186/1745-7580-5-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 05/05/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecules of the class II major histocompability complex (MHC-II) specifically bind and present exogenously derived peptide epitopes to CD4+ T helper cells. The extreme polymorphism of the MHC-II hampers the complete analysis of peptide binding. It is also a significant hurdle in the generation of MHC-II molecules as reagents to study and manipulate specific T helper cell responses. Methods to generate functional MHC-II molecules recombinantly, and measure their interaction with peptides, would be highly desirable; however, no consensus methodology has yet emerged. RESULTS We generated alpha and beta MHC-II chain constructs, where the membrane-spanning regions were replaced by dimerization motifs, and the C-terminal of the beta chains was fused to a biotinylation signal peptide (BSP) allowing for in vivo biotinylation. These chains were produced separately as inclusion bodies in E. coli , extracted into urea, and purified under denaturing and non-reducing conditions using conventional column chromatography. Subsequently, diluting the two chains into a folding reaction with appropriate peptide resulted in efficient peptide-MHC-II complex formation. Several different formats of peptide-binding assay were developed including a homogeneous, non-radioactive, high-throughput (HTS) binding assay. Binding isotherms were generated allowing the affinities of interaction to be determined. The affinities of the best binders were found to be in the low nanomolar range. Recombinant MHC-II molecules and accompanying HTS peptide-binding assay were successfully developed for nine different MHC-II molecules including the DPA1*0103/DPB1*0401 (DP401) and DQA1*0501/DQB1*0201, where both alpha and beta chains are polymorphic, illustrating the advantages of producing the two chains separately. CONCLUSION We have successfully developed versatile MHC-II resources, which may assist in the generation of MHC class II -wide reagents, data, and tools.
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Affiliation(s)
- Sune Justesen
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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30
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Howarth M, Ting AY. Imaging proteins in live mammalian cells with biotin ligase and monovalent streptavidin. Nat Protoc 2008; 3:534-45. [PMID: 18323822 DOI: 10.1038/nprot.2008.20] [Citation(s) in RCA: 196] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This protocol describes a simple and efficient way to label specific cell surface proteins with biophysical probes on mammalian cells. Cell surface proteins tagged with a 15-amino acid peptide are biotinylated by Escherichia coli biotin ligase (BirA), whereas endogenous proteins are not modified. The biotin group then allows sensitive and stable binding by streptavidin conjugates. This protocol describes the optimal use of BirA and streptavidin for site-specific labeling and also how to produce BirA and monovalent streptavidin. Streptavidin is tetravalent and the cross-linking of biotinylated targets disrupts many of streptavidin's applications. Monovalent streptavidin has only a single functional biotin-binding site, but retains the femtomolar affinity, low off-rate and high thermostability of wild-type streptavidin. Site-specific biotinylation and streptavidin staining take only a few minutes, while expression of BirA takes 4 d and expression of monovalent streptavidin takes 8 d.
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Affiliation(s)
- Mark Howarth
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
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31
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Vollers SS, Stern LJ. Class II major histocompatibility complex tetramer staining: progress, problems, and prospects. Immunology 2008; 123:305-13. [PMID: 18251991 DOI: 10.1111/j.1365-2567.2007.02801.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The use of major histocompatibility complex (MHC) tetramers in the detection and analysis of antigen-specific T cells has become more widespread since its introduction 11 years ago. Early challenges in the application of tetramer staining to CD4+ T cells centred around difficulties in the expression of various class II MHC allelic variants and the detection of low-frequency T cells in mixed populations. As many of the technical obstacles to class II MHC tetramer staining have been overcome, the focus has returned to uncertainties concerning how oligomer valency and T-cell receptor/MHC affinity affect tetramer binding. Such issues have become more important with an increase in the number of studies relying on direct ex vivo analysis of antigen-specific CD4+ T cells. In this review we discuss which problems in class II MHC tetramer staining have been solved to date, and which matters remain to be considered.
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Affiliation(s)
- Sabrina S Vollers
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
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Leisner C, Loeth N, Lamberth K, Justesen S, Sylvester-Hvid C, Schmidt EG, Claesson M, Buus S, Stryhn A. One-pot, mix-and-read peptide-MHC tetramers. PLoS One 2008; 3:e1678. [PMID: 18301755 PMCID: PMC2244712 DOI: 10.1371/journal.pone.0001678] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 01/21/2008] [Indexed: 11/19/2022] Open
Abstract
Background Cytotoxic T Lymphocytes (CTL) recognize complexes of peptide ligands and Major Histocompatibility Complex (MHC) class I molecules presented at the surface of Antigen Presenting Cells (APC). Detection and isolation of CTL's are of importance for research on CTL immunity, and development of vaccines and adoptive immune therapy. Peptide-MHC tetramers have become important reagents for detection and enumeration of specific CTL's. Conventional peptide-MHC-tetramer production involves recombinant MHC production, in vitro refolding, biotinylation and tetramerization; each step followed by various biochemical steps such as chromatographic purification, concentration etc. Such cumbersome production protocols have limited dissemination and restricted availability of peptide-MHC tetramers effectively precluding large-scale screening strategies involving many different peptide-MHC tetramers. Methodology/Principal Findings We have developed an approach whereby any given tetramer specificity can be produced within 2 days with very limited effort and hands-on time. The strategy is based on the isolation of correctly oxidized, in vivo biotinylated recombinant MHC I heavy chain (HC). Such biotinylated MHC I HC molecules can be refolded in vitro, tetramerized with streptavidin, and used for specific T cell staining-all in a one-pot reaction without any intervening purification steps. Conclusions/Significance We have developed an efficient “one-pot, mix-and-read” strategy for peptide-MHC tetramer generation, and demonstrated specific T cell straining comparable to a commercially available MHC-tetramer. Here, seven peptide-MHC tetramers representing four different human MHC (HLA) class I proteins have been generated. The technique should be readily extendable to any binding peptide and pre-biotinylated MHC (at this time we have over 40 different pre-biotinylated HLA proteins). It is simple, robust, and versatile technique with a very broad application potential as it can be adapted both to small- and large-scale production of one or many different peptide-MHC tetramers for T cell isolation, or epitope screening.
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Affiliation(s)
- Christian Leisner
- Laboratories of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
| | - Nina Loeth
- Laboratories of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Lamberth
- Laboratories of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
| | - Sune Justesen
- Laboratories of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
| | | | - Esben G. Schmidt
- Laboratories of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
| | - Mogens Claesson
- Laboratories of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
| | - Soren Buus
- Laboratories of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
- *E-mail:
| | - Anette Stryhn
- Laboratories of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
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Basile G, Peticca M, Catello S. Site-specific biotinylation of human myeloid differentiation protein 88 in Drosophila melanogaster Schneider 2 cell cytoplasm. Mol Biotechnol 2007; 35:253-61. [PMID: 17652789 DOI: 10.1007/bf02686011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 10/22/2022]
Abstract
In this work we describe the production of site-specific biotinylated human myeloid differentiation factor 88 (MyD88). A vector containing a coding sequence for a peptide derived from the carboxyl terminus of the Klebsiella pneumoniae oxalacetate decarboxylase alpha subunit was used to allow expression and biotinylation of MyD88 in Drosophila melanogaster Schneider 2 cell cytoplasm. As estimated by a comparison of Schneider 2 lysate with standard protein, the maximum expression level was 1.3 mug 107 cells-1. About 4 mg of biotinylated protein was purified by affinity chromatography on monomeric avidin from a 1-L culture. Exogenous biotin added to the culture medium increased the biotinylation efficiency of the expressed protein. Biotinylated MyD88 produced in Drosophila cells was able to precipitate recombinant MyD88 expressed in human embryonic kidney cells. The stable expression of MyD88 in Drosophila Schneider 2 cells offers a convenient and attractive method for large-scale production, which may be required to clarify the role of MyD88 in the inflammatory response. Moreover, site-specific biotinylation of MyD88 provides a useful tag for interaction assays where high sensitivity is required.
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Affiliation(s)
- G Basile
- Tecnogen S.C.p.A. Molecular Biology Area, Piana di Monte Verna, Caserta, Italy.
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Barat B, Wu AM. Metabolic biotinylation of recombinant antibody by biotin ligase retained in the endoplasmic reticulum. BIOMOLECULAR ENGINEERING 2007; 24:283-91. [PMID: 17379573 PMCID: PMC2682619 DOI: 10.1016/j.bioeng.2007.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Accepted: 02/01/2007] [Indexed: 11/23/2022]
Abstract
Due to its strength and specificity, the interaction between avidin and biotin has been used in a variety of scientific and medical applications ranging from immunohistochemistry to drug targeting. The present study describes two methods for biotinylation of proteins secreted from eukaryotic cells using the Escherichia coli biotin protein ligase. In one system the biotin ligase was co-secreted from the cells along with substrate protein enabling extracellular biotinylation of the tagged protein. In the other system, biotin ligase was engineered to be retained in the endoplasmic reticulum (ER) and metabolically biotinylates the secretory protein as it passes through the ER. An engineered antibody fragment, a diabody with specificity for carcinoembryonic antigen (CEA) was fused to the biotin acceptor domain (123 amino acid) of Propionibacterium shermanii. Coexpression of the fusion protein with ER retained biotin ligase showed higher biotinylation efficiency than biotinylation by co-secreted ligase. Biotinylation of the anti-CEA diabody tagged with a short (15 amino acid, Biotin Avitag) biotin acceptor peptide was also successful. Utilization of ER retained biotin ligase for biotinylation of protein is an attractive alternative for efficiently producing uniformly biotinylated recombinant proteins for a variety of avidin-biotin technologies.
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Affiliation(s)
- Bhaswati Barat
- Crump Institute for Molecular Imaging, Department of Molecular & Medical Pharmacology, David Geffen School of Medicine at UCLA, 700 Westwood Plaza, Los Angeles, CA 90095
| | - Anna M. Wu
- Crump Institute for Molecular Imaging, Department of Molecular & Medical Pharmacology, David Geffen School of Medicine at UCLA, 700 Westwood Plaza, Los Angeles, CA 90095
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Scriba TJ, Purbhoo M, Day CL, Robinson N, Fidler S, Fox J, Weber JN, Klenerman P, Sewell AK, Phillips RE. Ultrasensitive Detection and Phenotyping of CD4+ T Cells with Optimized HLA Class II Tetramer Staining. THE JOURNAL OF IMMUNOLOGY 2005; 175:6334-43. [PMID: 16272285 DOI: 10.4049/jimmunol.175.10.6334] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
HLA class I tetramers have revolutionized the study of Ag-specific CD8+ T cell responses. Technical problems and the rarity of Ag-specific CD4+ Th cells have not allowed the potential of HLA class II tetramers to be fully realized. Here, we optimize HLA class II tetramer staining methods through the use of a comprehensive panel of HIV-, influenza-, CMV-, and tetanus toxoid-specific tetramers. We find rapid and efficient staining of DR1- and DR4-restricted CD4+ cell lines and clones and show that TCR internalization is not a requirement for immunological staining. We combine tetramer staining with magnetic bead enrichment to detect rare Ag-specific CD4+ T cells with frequencies as low as 1 in 250,000 (0.0004% of CD4+ cells) in human PBLs analyzed directly ex vivo. This ultrasensitive detection allowed phenotypic analysis of rare CD4+ T lymphocytes that had experienced diverse exposure to Ag during the course of viral infections. These cells would not be detectable with normal flow-cytometric techniques.
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Affiliation(s)
- Thomas J Scriba
- The Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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