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Sun Y, Pumroy RA, Mallik L, Chaudhuri A, Wang C, Hwang D, Danon JN, Goli KD, Moiseenkova-Bell V, Sgourakis NG. CryoEM structure of an MHC-I/TAPBPR peptide bound intermediate reveals the mechanism of antigen proofreading. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606663. [PMID: 39211162 PMCID: PMC11361172 DOI: 10.1101/2024.08.05.606663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Class I major histocompatibility complex (MHC-I) proteins play a pivotal role in adaptive immunity by displaying epitopic peptides to CD8+ T cells. The chaperones tapasin and TAPBPR promote the selection of immunogenic antigens from a large pool of intracellular peptides. Interactions of chaperoned MHC-I molecules with incoming peptides are transient in nature, and as a result, the precise antigen proofreading mechanism remains elusive. Here, we leverage a high-fidelity TAPBPR variant and conformationally stabilized MHC-I, to determine the solution structure of the human antigen editing complex bound to a peptide decoy by cryogenic electron microscopy (cryo-EM) at an average resolution of 3.0 Å. Antigen proofreading is mediated by transient interactions formed between the nascent peptide binding groove with the P2/P3 peptide anchors, where conserved MHC-I residues stabilize incoming peptides through backbone-focused contacts. Finally, using our high-fidelity chaperone, we demonstrate robust peptide exchange on the cell surface across multiple clinically relevant human MHC-I allomorphs. Our work has important ramifications for understanding the selection of immunogenic epitopes for T cell screening and vaccine design applications.
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2
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Papadaki GF, Woodward CH, Young MC, Winters TJ, Burslem GM, Sgourakis NG. A Chicken Tapasin ortholog can chaperone empty HLA-B∗37:01 molecules independent of other peptide-loading components. J Biol Chem 2023; 299:105136. [PMID: 37543367 PMCID: PMC10534222 DOI: 10.1016/j.jbc.2023.105136] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/07/2023] Open
Abstract
Human Tapasin (hTapasin) is the main chaperone of MHC-I molecules, enabling peptide loading and antigen repertoire optimization across HLA allotypes. However, it is restricted to the endoplasmic reticulum (ER) lumen as part of the protein loading complex (PLC), and therefore is highly unstable when expressed in recombinant form. Additional stabilizing co-factors such as ERp57 are required to catalyze peptide exchange in vitro, limiting uses for the generation of pMHC-I molecules of desired antigen specificities. Here, we show that the chicken Tapasin (chTapasin) ortholog can be expressed recombinantly at high yields in a stable form, independent of co-chaperones. chTapasin can bind the human HLA-B∗37:01 with low micromolar-range affinity to form a stable tertiary complex. Biophysical characterization by methyl-based NMR methods reveals that chTapasin recognizes a conserved β2m epitope on HLA-B∗37:01, consistent with previously solved X-ray structures of hTapasin. Finally, we provide evidence that the B∗37:01/chTapasin complex is peptide-receptive and can be dissociated upon binding of high-affinity peptides. Our results highlight the use of chTapasin as a stable scaffold for protein engineering applications aiming to expand the ligand exchange function on human MHC-I and MHC-like molecules.
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Affiliation(s)
- Georgia F Papadaki
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Claire H Woodward
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael C Young
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Trenton J Winters
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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3
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Li L, Peng X, Batliwala M, Bouvier M. Crystal structures of MHC class I complexes reveal the elusive intermediate conformations explored during peptide editing. Nat Commun 2023; 14:5020. [PMID: 37596268 PMCID: PMC10439229 DOI: 10.1038/s41467-023-40736-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
Studies have suggested that MHC class I (MHC I) molecules fluctuate rapidly between numerous conformational states and these motions support peptide sampling. To date, MHC I intermediates are largely uncharacterized experimentally and remain elusive. Here, we present x-ray crystal structures of HLA-B8 loaded with 20mer peptides that show pronounced distortions at the N-terminus of the groove. Long stretches of N-terminal amino acid residues are missing in the electron density maps creating an open-ended groove. Our structures also reveal highly unusual features in MHC I-peptide interaction at the N-terminus of the groove. Molecular dynamics simulations indicate that the complexes have varying degrees of conformational flexibility in a manner consistent with the structures. We suggest that our structures have captured the remarkable molecular dynamics of MHC I-peptide interaction. The visualization of peptide-dependent conformational motions in MHC I is a major step forward in our conceptual understanding of dynamics in high-affinity peptide selection.
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Affiliation(s)
- Lenong Li
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| | - Xubiao Peng
- Center for Quantum Technology Research and Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements, School of Physics, Beijing Institute of Technology, Beijing, 100081, China
| | - Mansoor Batliwala
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA.
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4
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Papadaki GF, Woodward CH, Young MC, Winters TJ, Burslem GM, Sgourakis NG. A Chicken Tapasin ortholog can chaperone empty HLA molecules independently of other peptide-loading components. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.23.546255. [PMID: 37425753 PMCID: PMC10326978 DOI: 10.1101/2023.06.23.546255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Human Tapasin (hTapasin) is the main chaperone of MHC-I molecules, enabling peptide loading and antigen repertoire optimization across HLA allotypes. However, it is restricted to the endoplasmic reticulum (ER) lumen as part of the protein loading complex (PLC) and therefore is highly unstable when expressed in recombinant form. Additional stabilizing co-factors such as ERp57 are required to catalyze peptide exchange in vitro , limiting uses for the generation of pMHC-I molecules of desired antigen specificities. Here, we show that the chicken Tapasin (chTapasin) ortholog can be expressed recombinantly at high yields in stable form, independently of co-chaperones. chTapasin can bind the human HLA-B * 37:01 with low micromolar-range affinity to form a stable tertiary complex. Biophysical characterization by methyl-based NMR methods reveals that chTapasin recognizes a conserved β 2 m epitope on HLA-B * 37:01, consistent with previously solved X-ray structures of hTapasin. Finally, we provide evidence that the B * 37:01/chTapasin complex is peptide-receptive and can be dissociated upon binding of high-affinity peptides. Our results highlight the use of chTapasin as a stable scaffold for future protein engineering applications aiming to expand the ligand exchange function on human MHC-I and MHC-like molecules.
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5
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Massa C, Wang Y, Marr N, Seliger B. Interferons and Resistance Mechanisms in Tumors and Pathogen-Driven Diseases—Focus on the Major Histocompatibility Complex (MHC) Antigen Processing Pathway. Int J Mol Sci 2023; 24:ijms24076736. [PMID: 37047709 PMCID: PMC10095295 DOI: 10.3390/ijms24076736] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/22/2023] [Accepted: 02/25/2023] [Indexed: 04/08/2023] Open
Abstract
Interferons (IFNs), divided into type I, type II, and type III IFNs represent proteins that are secreted from cells in response to various stimuli and provide important information for understanding the evolution, structure, and function of the immune system, as well as the signaling pathways of other cytokines and their receptors. They exert comparable, but also distinct physiologic and pathophysiologic activities accompanied by pleiotropic effects, such as the modulation of host responses against bacterial and viral infections, tumor surveillance, innate and adaptive immune responses. IFNs were the first cytokines used for the treatment of tumor patients including hairy leukemia, renal cell carcinoma, and melanoma. However, tumor cells often develop a transient or permanent resistance to IFNs, which has been linked to the escape of tumor cells and unresponsiveness to immunotherapies. In addition, loss-of-function mutations in IFN signaling components have been associated with susceptibility to infectious diseases, such as COVID-19 and mycobacterial infections. In this review, we summarize general features of the three IFN families and their function, the expression and activity of the different IFN signal transduction pathways, and their role in tumor immune evasion and pathogen clearance, with links to alterations in the major histocompatibility complex (MHC) class I and II antigen processing machinery (APM). In addition, we discuss insights regarding the clinical applications of IFNs alone or in combination with other therapeutic options including immunotherapies as well as strategies reversing the deficient IFN signaling. Therefore, this review provides an overview on the function and clinical relevance of the different IFN family members, with a specific focus on the MHC pathways in cancers and infections and their contribution to immune escape of tumors.
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Affiliation(s)
- Chiara Massa
- Medical Faculty, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany
- Institute for Translational Immunology, Brandenburg Medical School Theodor Fontane, Hochstr. 29, 14770 Brandenburg an der Havel, Germany
| | - Yuan Wang
- Medical Faculty, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany
| | - Nico Marr
- Institute for Translational Immunology, Brandenburg Medical School Theodor Fontane, Hochstr. 29, 14770 Brandenburg an der Havel, Germany
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar
| | - Barbara Seliger
- Medical Faculty, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany
- Institute for Translational Immunology, Brandenburg Medical School Theodor Fontane, Hochstr. 29, 14770 Brandenburg an der Havel, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany
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6
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Cruz FM, Chan A, Rock KL. Pathways of MHC I cross-presentation of exogenous antigens. Semin Immunol 2023; 66:101729. [PMID: 36804685 PMCID: PMC10023513 DOI: 10.1016/j.smim.2023.101729] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/18/2023]
Abstract
Phagocytes, particularly dendritic cells (DCs), generate peptide-major histocompatibility complex (MHC) I complexes from antigens they have collected from cells in tissues and report this information to CD8 T cells in a process called cross-presentation. This process allows CD8 T cells to detect, respond and eliminate abnormal cells, such as cancers or cells infected with viruses or intracellular microbes. In some settings, cross-presentation can help tolerize CD8 T cells to self-antigens. One of the principal ways that DCs acquire tissue antigens is by ingesting this material through phagocytosis. The resulting phagosomes are key hubs in the cross-presentation (XPT) process and in fact experimentally conferring the ability to phagocytize antigens can be sufficient to allow non-professional antigen presenting cells (APCs) to cross-present. Once in phagosomes, exogenous antigens can be cross-presented (XPTed) through three distinct pathways. There is a vacuolar pathway in which peptides are generated and then bind to MHC I molecules within the confines of the vacuole. Ingested exogenous antigens can also be exported from phagosomes to the cytosol upon vesicular rupture and/or possibly transport. Once in the cytosol, the antigen is degraded by the proteasome and the resulting oligopeptides can be transported to MHC I molecule in the endoplasmic reticulum (ER) (a phagosome-to-cytosol (P2C) pathway) or in phagosomes (a phagosome-to-cytosol-to-phagosome (P2C2P) pathway). Here we review how phagosomes acquire the necessary molecular components that support these three mechanisms and the contribution of these pathways. We describe what is known as well as the gaps in our understanding of these processes.
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Affiliation(s)
- Freidrich M Cruz
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Amanda Chan
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kenneth L Rock
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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7
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Shapiro IE, Bassani-Sternberg M. The impact of immunopeptidomics: From basic research to clinical implementation. Semin Immunol 2023; 66:101727. [PMID: 36764021 DOI: 10.1016/j.smim.2023.101727] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023]
Abstract
The immunopeptidome is the set of peptides presented by the major histocompatibility complex (MHC) molecules, in humans also known as the human leukocyte antigen (HLA), on the surface of cells that mediate T-cell immunosurveillance. The immunopeptidome is a sampling of the cellular proteome and hence it contains information about the health state of cells. The peptide repertoire is influenced by intra- and extra-cellular perturbations - such as in the case of drug exposure, infection, or oncogenic transformation. Immunopeptidomics is the bioanalytical method by which the presented peptides are extracted from biological samples and analyzed by high-performance liquid chromatography coupled to tandem mass spectrometry (MS), resulting in a deep qualitative and quantitative snapshot of the immunopeptidome. In this review, we discuss published immunopeptidomics studies from recent years, grouped into three main domains: i) basic, ii) pre-clinical and iii) clinical research and applications. We review selected fundamental immunopeptidomics studies on the antigen processing and presentation machinery, on HLA restriction and studies that advanced our understanding of various diseases, and how exploration of the antigenic landscape allowed immune targeting at the pre-clinical stage, paving the way to pioneering exploratory clinical trials where immunopeptidomics is directly implemented in the conception of innovative treatments for cancer patients.
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Affiliation(s)
- Ilja E Shapiro
- Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland; Agora Cancer Research Centre, 1011 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, 1005 Lausanne, Switzerland; Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland; Agora Cancer Research Centre, 1011 Lausanne, Switzerland; Center of Experimental Therapeutics, Department of Oncology, Centre hospitalier universitaire vaudois (CHUV), 1005 Lausanne, Switzerland.
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8
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Lan BH, Becker M, Freund C. The mode of action of tapasin on major histocompatibility class I (MHC-I) molecules. J Biol Chem 2023; 299:102987. [PMID: 36758805 PMCID: PMC10040737 DOI: 10.1016/j.jbc.2023.102987] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
Tapasin (Tsn) plays a critical role in antigen processing and presentation by major histocompatibility complex class I (MHC-I) molecules. The mechanism of Tsn-mediated peptide loading and exchange hinges on the conformational dynamics governing the interaction of Tsn and MHC-I with recent structural and functional studies pinpointing the critical sites of direct or allosteric regulation. In this review, we highlight these recent findings and relate them to the extensive molecular and cellular data that are available for these evolutionary interdependent proteins. Furthermore, allotypic differences of MHC-I with regard to the editing and chaperoning function of Tsn are reviewed and related to the mechanistic observations. Finally, evolutionary aspects of the mode of action of Tsn will be discussed, a short comparison with the Tsn-related molecule TAPBPR (Tsn-related protein) will be given, and the impact of Tsn on noncanonical MHC-I molecules will be described.
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Affiliation(s)
- By Huan Lan
- Institute of Chemistry & Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Moritz Becker
- Institute of Chemistry & Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Institute of Chemistry & Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Berlin, Germany.
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9
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Arman I, Haus-Cohen M, Reiter Y. The Intracellular Proteome as a Source for Novel Targets in CAR-T and T-Cell Engagers-Based Immunotherapy. Cells 2022; 12:cells12010027. [PMID: 36611821 PMCID: PMC9818436 DOI: 10.3390/cells12010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
The impressive clinical success of cancer immunotherapy has motivated the continued search for new targets that may serve to guide potent effector functions in an attempt to efficiently kill malignant cells. The intracellular proteome is an interesting source for such new targets, such as neo-antigens and others, with growing interest in their application for cell-based immunotherapies. These intracellular-derived targets are peptides presented by MHC class I molecules on the cell surface of malignant cells. These disease-specific class I HLA-peptide complexes can be targeted by specific TCRs or by antibodies that mimic TCR-specificity, termed TCR-like (TCRL) antibodies. Adoptive cell transfer of TCR engineered T cells and T-cell-receptor-like based CAR-T cells, targeted against a peptide-MHC of interest, are currently tested as cancer therapeutic agents in pre-clinical and clinical trials, along with soluble TCR- and TCRL-based agents, such as immunotoxins and bi-specific T cell engagers. Targeting the intracellular proteome using TCRL- and TCR-based molecules shows promising results in cancer immunotherapy, as exemplified by the success of the anti-gp100/HLA-A2 TCR-based T cell engager, recently approved by the FDA for the treatment of unresectable or metastatic uveal melanoma. This review is focused on the selection and isolation processes of TCR- and TCRL-based targeting moieties, with a spotlight on pre-clinical and clinical studies, examining peptide-MHC targeting agents in cancer immunotherapy.
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Meissner TB, Schulze HS, Dale SM. Immune Editing: Overcoming Immune Barriers in Stem Cell Transplantation. CURRENT STEM CELL REPORTS 2022; 8:206-218. [PMID: 36406259 PMCID: PMC9643905 DOI: 10.1007/s40778-022-00221-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 11/10/2022]
Abstract
Purpose of Review Human pluripotent stem cells have the potential to revolutionize the treatment of inborn and degenerative diseases, including aging and autoimmunity. A major barrier to their wider adoption in cell therapies is immune rejection. Genome editing allows for tinkering of the human genome in stem and progenitor cells and raises the prospect for overcoming the immune barriers to transplantation. Recent Findings Initial attempts have focused primarily on the major histocompatibility barrier that is formed by the human leukocyte antigens (HLA). More recently, immune checkpoint inhibitors, such as PD-L1, CD47, or HLA-G, are being explored both, in the presence or absence of HLA, to mitigate immune rejection by the various cellular components of the immune system. Summary In this review, we discuss progress in surmounting immune barriers to cell transplantation, with a particular focus on genetic engineering of human pluripotent stem and progenitor cells and the therapeutic cell types derived from them.
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Affiliation(s)
- Torsten B. Meissner
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA USA
- Department of Surgery, Harvard Medical School, Boston, MA USA
| | - Henrike S. Schulze
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA USA
| | - Stanley M. Dale
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA USA
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11
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Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation. Nat Commun 2022; 13:5470. [PMID: 36115831 PMCID: PMC9482634 DOI: 10.1038/s41467-022-33153-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/26/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractLoading of MHC-I molecules with peptide by the catalytic chaperone tapasin in the peptide loading complex plays a critical role in antigen presentation and immune recognition. Mechanistic insight has been hampered by the lack of detailed structural information concerning tapasin–MHC-I. We present here crystal structures of human tapasin complexed with the MHC-I molecule HLA-B*44:05, and with each of two anti-tapasin antibodies. The tapasin-stabilized peptide-receptive state of HLA-B*44:05 is characterized by distortion of the peptide binding groove and destabilization of the β2-microglobulin interaction, leading to release of peptide. Movements of the membrane proximal Ig-like domains of tapasin, HLA-B*44:05, and β2-microglobulin accompany the transition to a peptide-receptive state. Together this ensemble of crystal structures provides insights into a distinct mechanism of tapasin-mediated peptide exchange.
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12
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Hong KU, Gardner JQ, Doll MA, Stepp MW, Wilkey DW, Benz FW, Cai J, Merchant ML, Hein DW. Proteomic analysis of arylamine N-acetyltransferase 1 knockout breast cancer cells: Implications in immune evasion and mitochondrial biogenesis. Toxicol Rep 2022; 9:1566-1573. [PMID: 36158865 PMCID: PMC9500399 DOI: 10.1016/j.toxrep.2022.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/13/2022] [Accepted: 07/16/2022] [Indexed: 02/08/2023] Open
Abstract
Previous studies have shown that inhibition or depletion of N-acetyltransferase 1 (NAT1) in breast cancer cell lines leads to growth retardation both in vitro and in vivo, suggesting that NAT1 contributes to rapid growth of breast cancer cells. To understand molecular and cellular processes that NAT1 contributes to and generate novel hypotheses in regard to NAT1's role in breast cancer, we performed an unbiased analysis of proteomes of parental MDA-MB-231 breast cancer cells and two separate NAT1 knockout (KO) cell lines. Among 4890 proteins identified, 737 proteins were found significantly (p < 0.01) upregulated, and 651 proteins were significantly (p < 0.01) downregulated in both NAT1 KO cell lines. We performed enrichment analyses to identify Gene Ontology biological processes, molecular functions, and cellular components that were enriched in each data set. Among the proteins upregulated in NAT1 KO cells, pathways associated with MHC (major histocompatibility complex) I-mediated antigen presentation were significantly enriched. This raises an interesting and new hypothesis that upregulation of NAT1 in breast cancer cells may aid them evade immune detection. Multiple pathways involved in mitochondrial functions were collectively downregulated in NAT1 KO cells, including multiple subunits of mitochondrial ATP synthase (Complex V of the electron transport chain). This was accompanied by a reduction in cell cycle-associated proteins and an increase in pro-apoptotic pathways in NAT1 KO cells, consistent with reported observations that NAT1 KO cells exhibit a slower growth rate both in vitro and in vivo. Thus, mitochondrial dysfunction in NAT1 KO cells likely contributes to growth retardation.
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Affiliation(s)
- Kyung U. Hong
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Jonathan Q. Gardner
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Mark A. Doll
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Marcus W. Stepp
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Daniel W. Wilkey
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Frederick W. Benz
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Jian Cai
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, USA
| | - Michael L. Merchant
- Department of Medicine, School of Medicine, University of Louisville, Louisville, KY, USA
| | - David W. Hein
- Department of Pharmacology & Toxicology, School of Medicine, University of Louisville, Louisville, KY, USA,Correspondence to: Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, 505 S. Hancock Street, CTR Rm 303, Louisville, KY 40202, USA.
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13
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Burassakarn A, Phusingha P, Yugawa T, Noguchi K, Ekalaksananan T, Vatanasapt P, Kiyono T, Pientong C. Human Papillomavirus 16 E6 Suppresses Transporter Associated with Antigen-Processing Complex in Human Tongue Keratinocyte Cells by Activating Lymphotoxin Pathway. Cancers (Basel) 2022; 14:cancers14081944. [PMID: 35454851 PMCID: PMC9028769 DOI: 10.3390/cancers14081944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/10/2022] [Accepted: 04/10/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary There is still limited knowledge of the critical pathogenic processes by which HPV16 induces oral carcinogenesis. Therefore, we aimed to illuminate the oncogenic role of HPV16 in the context of oral squamous cell carcinomas (OSCCs). Using human tongue keratinocyte cells, we demonstrated that HPV16 E6 promotes LTα1β2 and LTβR expression, thus promoting the lymphotoxin signaling pathway and leading to suppression of the transporter associated with the antigen-processing complex (TAPs; TAP1 and TAP2). Additionally, in vitro, we also demonstrated regulation of the antigenic peptide-loaded machinery in HPV-infected OSCC tissues through analysis of the transcriptomic profiles of the head and neck squamous cell carcinoma (HNSCC) cohort from the TCGA database, which was validated using fresh biopsied specimens. Thus, our study enhances the proposed functional role of HPV16 E6-associated immune-evasive properties in oral epithelial cells, revealing a possible mechanism underlying the development of HPV-mediated OSCCs. Abstract Infection by high-risk human papillomaviruses (hrHPVs), including HPV type 16 (HPV16), is a major risk factor for oral squamous cell carcinomas (OSCCs). However, the pathogenic mechanism by which hrHPVs promote oral carcinogenesis remains to be elucidated. Here, we demonstrated that the suppression of a transporter associated with the antigen-processing complex (TAPs; TAP1 and TAP2), which is a key molecule in the transportation of viral antigenic peptides into MHC class-I cells, is affected by the E6 protein of HPV16. Mechanistically, HPV-mediated immune evasion is principally mediated via the signal-transduction network of a lymphotoxin (LT) pathway, in particular LTα1β2 and LTβR. Our analysis of transcriptomic data from an HNSCC cohort from the Cancer Genome Atlas (TCGA) indicated that expression of TAP genes, particularly TAP2, was downregulated in HPV-infected cases. We further demonstrated that LTα1β2 and LTβR were upregulated, which was negatively correlated with TAP1 and TAP2 expression in HPV-positive clinical OSCC samples. Taken together, our findings imply that HPV16 E6 regulates the machinery of the antigenic peptide-loading system and helps to clarify the role of oncogenic viruses in the context of oral carcinoma.
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Affiliation(s)
- Ati Burassakarn
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (A.B.); (T.E.)
- HPV & EBV and Carcinogenesis Research Group, Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Pensiri Phusingha
- Center of Excellence for Antibody Research (CEAR), Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Takashi Yugawa
- Division of Carcinogenesis and Cancer Prevention, National Cancer Center Research Institute, Tokyo 104-0045, Japan;
| | - Kazuma Noguchi
- Department of Oral and Maxillofacial Surgery, Hyogo Medical University, Mukogawa-Cho 1-1, Nishinomiya 663-8501, Japan;
| | - Tipaya Ekalaksananan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (A.B.); (T.E.)
- HPV & EBV and Carcinogenesis Research Group, Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
| | - Patravoot Vatanasapt
- HPV & EBV and Carcinogenesis Research Group, Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
- Department of Otorhinolaryngology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Tohru Kiyono
- Project for Prevention of HPV-Related Cancer, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, 6-5-1 Kashiwanoha, Kashiwa 277-8577, Japan
- Correspondence: (T.K.); (C.P.); Tel./Fax: +66-4334-8385 (C.P.)
| | - Chamsai Pientong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand; (A.B.); (T.E.)
- HPV & EBV and Carcinogenesis Research Group, Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand;
- Correspondence: (T.K.); (C.P.); Tel./Fax: +66-4334-8385 (C.P.)
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14
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Dickinson Q, Meyer JG. Positional SHAP (PoSHAP) for Interpretation of machine learning models trained from biological sequences. PLoS Comput Biol 2022; 18:e1009736. [PMID: 35089914 PMCID: PMC8797255 DOI: 10.1371/journal.pcbi.1009736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022] Open
Abstract
Machine learning with multi-layered artificial neural networks, also known as "deep learning," is effective for making biological predictions. However, model interpretation is challenging, especially for sequential input data used with recurrent neural network architectures. Here, we introduce a framework called "Positional SHAP" (PoSHAP) to interpret models trained from biological sequences by utilizing SHapely Additive exPlanations (SHAP) to generate positional model interpretations. We demonstrate this using three long short-term memory (LSTM) regression models that predict peptide properties, including binding affinity to major histocompatibility complexes (MHC), and collisional cross section (CCS) measured by ion mobility spectrometry. Interpretation of these models with PoSHAP reproduced MHC class I (rhesus macaque Mamu-A1*001 and human A*11:01) peptide binding motifs, reflected known properties of peptide CCS, and provided new insights into interpositional dependencies of amino acid interactions. PoSHAP should have widespread utility for interpreting a variety of models trained from biological sequences.
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Affiliation(s)
- Quinn Dickinson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jesse G. Meyer
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
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15
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Vollmers S, Lobermeyer A, Körner C. The New Kid on the Block: HLA-C, a Key Regulator of Natural Killer Cells in Viral Immunity. Cells 2021; 10:cells10113108. [PMID: 34831331 PMCID: PMC8620871 DOI: 10.3390/cells10113108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 11/01/2022] Open
Abstract
The human leukocyte antigen system (HLA) is a cluster of highly polymorphic genes essential for the proper function of the immune system, and it has been associated with a wide range of diseases. HLA class I molecules present intracellular host- and pathogen-derived peptides to effector cells of the immune system, inducing immune tolerance in healthy conditions or triggering effective immune responses in pathological situations. HLA-C is the most recently evolved HLA class I molecule, only present in humans and great apes. Differentiating from its older siblings, HLA-A and HLA-B, HLA-C exhibits distinctive features in its expression and interaction partners. HLA-C serves as a natural ligand for multiple members of the killer-cell immunoglobulin-like receptor (KIR) family, which are predominately expressed by natural killer (NK) cells. NK cells are crucial for the early control of viral infections and accumulating evidence indicates that interactions between HLA-C and its respective KIR receptors determine the outcome and progression of viral infections. In this review, we focus on the unique role of HLA-C in regulating NK cell functions and its consequences in the setting of viral infections.
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16
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Mathematical modeling and stochastic simulations suggest that low-affinity peptides can bisect MHC1-mediated export of high-affinity peptides into "early"- and "late"-phases. Heliyon 2021; 7:e07466. [PMID: 34286133 PMCID: PMC8278427 DOI: 10.1016/j.heliyon.2021.e07466] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/23/2021] [Accepted: 06/29/2021] [Indexed: 02/01/2023] Open
Abstract
The peptide loading complex (PLC) is a multi-protein complex of the endoplasmic reticulum (ER) which optimizes major histocompatibility I (MHC1)-mediated export of intracellular high-affinity peptides. Whilst, the molecular biology of MHC1-mediated export is well supported by empirical data, the stoichiometry, kinetics and spatio-temporal profile of the participating molecular entities are a matter of considerable debate. Here, a low-affinity peptide-driven (LAPD)-model of MHC1-mediated high-affinity peptide export is formulated, implemented, analyzed and simulated. The model is parameterized in terms of the contribution of the shunt reaction to the concentration of exportable MHC1. Theoretical analyses and simulation studies of the model suggest that low-affinity peptides can bisect MHC1-mediated export of high-affinity peptides into time-dependent distinct “early”- and “late”-phases. The net exportable MHC1 (eM1β(t)) is a function of the retrograde (rM1β(t))- and anterograde (aM1β(t))-derived fractions. The “early”-phase is dominated by the contribution of the retrograde/recyclable (rM1β≈61%,aM1β≈39%) pathway to exportable MHC1, is characterized by Tapasin-mediated peptide-editing and is ATP-independent. The “late”-phase on the other hand, is characterized by de novo PLC-assembly, rapid disassembly and a significant contribution of the anterograde pathway to exportable MHC1 (rM1β≈21%,aM1β≈79%). The shunt reaction is rate limiting and may integrate peptide translocation with PLC-assembly/disassembly thereby, regulating peptide export under physiological and pathological (viral infections, dysplastic alterations) conditions.
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17
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Jongsma MLM, Neefjes J, Spaapen RM. Playing hide and seek: Tumor cells in control of MHC class I antigen presentation. Mol Immunol 2021; 136:36-44. [PMID: 34082257 DOI: 10.1016/j.molimm.2021.05.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/07/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022]
Abstract
MHC class I (MHC-I) molecules present a blueprint of the intracellular proteome to T cells allowing them to control infection or malignant transformation. As a response, pathogens and tumor cells often downmodulate MHC-I mediated antigen presentation to escape from immune surveillance. Although the fundamental rules of antigen presentation are known in detail, the players in this system are not saturated and new modules of regulation have recently been uncovered. Here, we update the understanding of antigen presentation by MHC-I molecules and how this can be exploited by tumors to prevent exposure of the intracellular proteome. This knowledge can provide new ways to improve immune responses against tumors and pathogens.
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Affiliation(s)
- M L M Jongsma
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - J Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - R M Spaapen
- Department of Immunopathology, Sanquin Research, Amsterdam, the Netherlands; Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Amsterdam, the Netherlands.
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18
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Demmers LC, Wu W, Heck AJR. HLA Class II Presentation Is Specifically Altered at Elevated Temperatures in the B-Lymphoblastic Cell Line JY. Mol Cell Proteomics 2021; 20:100089. [PMID: 33933681 PMCID: PMC8724904 DOI: 10.1016/j.mcpro.2021.100089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/25/2021] [Accepted: 04/13/2021] [Indexed: 12/22/2022] Open
Abstract
Human leukocyte antigen (HLA) molecules play critical roles in our adaptive immune system by signaling a cell's health status to the immune system, through presentation of small peptides. Understanding HLA biology is important because of its prominent role in autoimmune diseases and cancer immunotherapy. Although both the HLA class I and class II antigen processing and presentation pathways have been studied extensively, the fundamental rules in HLA class II antigen presentation still remain less understood. To clarify the mechanistic and adaptive differences between the HLA systems, we challenged a B lymphoblastic cell line (JY), widely used as model system in studying antigen presentation, with a high temperature treatment to mimic a "fever-like state", representing one of the most common physiological responses to infection. In the absence of real invading pathogenic peptides to present, we could focus on delineating the intrinsic HLA pathway adaptations in response to high temperature in this particular cell line. Following a three-pronged approach, we performed quantitative analyses of the proteome, the HLA class I ligandome, as well as the HLA class II ligandome. The data reveals that elevated temperature may already prepare these cells for an immune-like response through increased HLA class II presentation capacity and specific release of, from the invariant chain originating, CLIP peptides. Interestingly, at high temperature, prominent changes in the composition of the CLIP repertoire were observed, with enrichment of peptides containing C-terminal extensions beyond the CLIP-core region. Collectively, these illustrate intriguing temperature sensitive adaptations in this B cell line.
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Affiliation(s)
- Laura C Demmers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands; Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands; Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands; Netherlands Proteomics Centre, Utrecht, Netherlands.
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19
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Dhatchinamoorthy K, Colbert JD, Rock KL. Cancer Immune Evasion Through Loss of MHC Class I Antigen Presentation. Front Immunol 2021; 12:636568. [PMID: 33767702 PMCID: PMC7986854 DOI: 10.3389/fimmu.2021.636568] [Citation(s) in RCA: 422] [Impact Index Per Article: 140.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 02/03/2023] Open
Abstract
Major histocompatibility class I (MHC I) molecules bind peptides derived from a cell's expressed genes and then transport and display this antigenic information on the cell surface. This allows CD8 T cells to identify pathological cells that are synthesizing abnormal proteins, such as cancers that are expressing mutated proteins. In order for many cancers to arise and progress, they need to evolve mechanisms to avoid elimination by CD8 T cells. MHC I molecules are not essential for cell survival and therefore one mechanism by which cancers can evade immune control is by losing MHC I antigen presentation machinery (APM). Not only will this impair the ability of natural immune responses to control cancers, but also frustrate immunotherapies that work by re-invigorating anti-tumor CD8 T cells, such as checkpoint blockade. Here we review the evidence that loss of MHC I antigen presentation is a frequent occurrence in many cancers. We discuss new insights into some common underlying mechanisms through which some cancers inactivate the MHC I pathway and consider some possible strategies to overcome this limitation in ways that could restore immune control of tumors and improve immunotherapy.
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20
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Lazaridou MF, Massa C, Handke D, Mueller A, Friedrich M, Subbarayan K, Tretbar S, Dummer R, Koelblinger P, Seliger B. Identification of microRNAs Targeting the Transporter Associated with Antigen Processing TAP1 in Melanoma. J Clin Med 2020; 9:jcm9092690. [PMID: 32825219 PMCID: PMC7563967 DOI: 10.3390/jcm9092690] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/15/2022] Open
Abstract
The underlying molecular mechanisms of the aberrant expression of components of the HLA class I antigen processing and presentation machinery (APM) in tumors leading to evasion from T cell-mediated immune surveillance could be due to posttranscriptional regulation mediated by microRNAs (miRs). So far, some miRs controlling the expression of different APM components have been identified. Using in silico analysis and an miR enrichment protocol in combination with small RNA sequencing, miR-26b-5p and miR-21-3p were postulated to target the 3′ untranslated region (UTR) of the peptide transporter TAP1, which was confirmed by high free binding energy and dual luciferase reporter assays. Overexpression of miR-26b-5p and miR-21-3p in melanoma cells downregulated the TAP1 protein and reduced expression of HLA class I cell surface antigens, which could be reverted by miR inhibitors. Moreover, miR-26b-5p overexpression induced a decreased T cell recognition. Furthermore, an inverse expression of miR-26b-5p and miR-21-3p with TAP1 was found in primary melanoma lesions, which was linked with the frequency of CD8+ T cell infiltration. Thus, miR-26-5p and miR-21-3p are involved in the HLA class I-mediated immune escape and might be used as biomarkers or therapeutic targets for HLA class Ilow melanoma cells.
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Affiliation(s)
- Maria-Filothei Lazaridou
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Chiara Massa
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Diana Handke
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Anja Mueller
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Michael Friedrich
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Karthikeyan Subbarayan
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Sandy Tretbar
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Reinhard Dummer
- Institute of Dermatology, University Hospital Zürich, 8091 Zürich, Switzerland;
| | - Peter Koelblinger
- Department of Dermatology and Allergology, University Hospital Salzburg, 5020 Salzburg, Austria;
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
- Correspondence: ; Tel.: +49-(0)-345-557-4054
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21
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Castagnoli L, De Santis F, Volpari T, Vernieri C, Tagliabue E, Di Nicola M, Pupa SM. Cancer Stem Cells: Devil or Savior-Looking behind the Scenes of Immunotherapy Failure. Cells 2020; 9:E555. [PMID: 32120774 PMCID: PMC7140486 DOI: 10.3390/cells9030555] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
Although the introduction of immunotherapy has tremendously improved the prognosis of patients with metastatic cancers of different histological origins, some tumors fail to respond or develop resistance. Broadening the clinical efficacy of currently available immunotherapy strategies requires an improved understanding of the biological mechanisms underlying cancer immune escape. Globally, tumor cells evade immune attack using two main strategies: avoiding recognition by immune cells and instigating an immunosuppressive tumor microenvironment. Emerging data suggest that the clinical efficacy of chemotherapy or molecularly targeted therapy is related to the ability of these therapies to target cancer stem cells (CSCs). However, little is known about the role of CSCs in mediating tumor resistance to immunotherapy. Due to their immunomodulating features and plasticity, CSCs can be especially proficient at evading immune surveillance, thus potentially representing the most prominent malignant cell component implicated in primary or acquired resistance to immunotherapy. The identification of immunomodulatory properties of CSCs that include mechanisms that regulate their interactions with immune cells, such as bidirectional release of particular cytokines/chemokines, fusion of CSCs with fusogenic stromal cells, and cell-to-cell communication exerted by extracellular vesicles, may significantly improve the efficacy of current immunotherapy strategies. The purpose of this review is to discuss the current scientific evidence linking CSC biological, immunological, and epigenetic features to tumor resistance to immunotherapy.
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Affiliation(s)
- Lorenzo Castagnoli
- Department of Research, Molecular Targeting Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Amadeo 42, 20133 Milan, Italy; (L.C.); (E.T.)
| | - Francesca De Santis
- Department of Medical Oncology and Hematology, Unit of Immunotherapy and Anticancer Innovative Therapeutics, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Venezian 1, 20133 Milan, Italy; (F.D.S.); (T.V.); (M.D.N.)
| | - Tatiana Volpari
- Department of Medical Oncology and Hematology, Unit of Immunotherapy and Anticancer Innovative Therapeutics, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Venezian 1, 20133 Milan, Italy; (F.D.S.); (T.V.); (M.D.N.)
| | - Claudio Vernieri
- Department of Medical Oncology and Hematology, FIRC Institute of Molecular Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133 Milan, Italy;
- IFOM, FIRC Institute of Molecular Oncology, via Adamello 16, 20139 Milan, Italy
| | - Elda Tagliabue
- Department of Research, Molecular Targeting Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Amadeo 42, 20133 Milan, Italy; (L.C.); (E.T.)
| | - Massimo Di Nicola
- Department of Medical Oncology and Hematology, Unit of Immunotherapy and Anticancer Innovative Therapeutics, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Venezian 1, 20133 Milan, Italy; (F.D.S.); (T.V.); (M.D.N.)
| | - Serenella M. Pupa
- Department of Research, Molecular Targeting Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Via Amadeo 42, 20133 Milan, Italy; (L.C.); (E.T.)
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22
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O’Rourke SM, Morozov GI, Roberts JT, Barb AW, Sgourakis NG. Production of soluble pMHC-I molecules in mammalian cells using the molecular chaperone TAPBPR. Protein Eng Des Sel 2019; 32:525-532. [PMID: 32725167 PMCID: PMC7451022 DOI: 10.1093/protein/gzaa015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/23/2020] [Accepted: 06/29/2020] [Indexed: 12/20/2022] Open
Abstract
Current approaches for generating major histocompatibility complex (MHC) Class-I proteins with desired bound peptides (pMHC-I) for research, diagnostic and therapeutic applications are limited by the inherent instability of empty MHC-I molecules. Using the properties of the chaperone TAP-binding protein related (TAPBPR), we have developed a robust method to produce soluble, peptide-receptive MHC-I molecules in Chinese Hamster Ovary cells at high yield, completely bypassing the requirement for laborious refolding from inclusion bodies expressed in E.coli. Purified MHC-I/TAPBPR complexes can be prepared for multiple human allotypes, and exhibit complex glycan modifications at the conserved Asn 86 residue. As a proof of concept, we demonstrate both HLA allele-specific peptide binding and MHC-restricted antigen recognition by T cells for two relevant tumor-associated antigens. Our system provides a facile, high-throughput approach for generating pMHC-I antigens to probe and expand TCR specificities present in polyclonal T cell repertoires.
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Affiliation(s)
- Sara M O’Rourke
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Giora I Morozov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jacob T Roberts
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Adam W Barb
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center University of Georgia, Athens, GA 30602, USA
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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23
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Manandhar T, Hò GGT, Pump WC, Blasczyk R, Bade-Doeding C. Battle between Host Immune Cellular Responses and HCMV Immune Evasion. Int J Mol Sci 2019; 20:E3626. [PMID: 31344940 PMCID: PMC6695940 DOI: 10.3390/ijms20153626] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 12/16/2022] Open
Abstract
Human cytomegalovirus (HCMV) is ubiquitously prevalent. HCMV infection is typically asymptomatic and controlled by the immune system in healthy individuals, yet HCMV can be severely pathogenic for the fetus during pregnancy and in immunocompromised persons, such as transplant recipients or HIV infected patients. HCMV has co-evolved with the hosts, developed strategies to hide from immune effector cells and to successfully survive in the human organism. One strategy for evading or delaying the immune response is maintenance of the viral genome to establish the phase of latency. Furthermore, HCMV immune evasion involves the downregulation of human leukocyte antigens (HLA)-Ia molecules to hide infected cells from T-cell recognition. HCMV expresses several proteins that are described for downregulation of the HLA class I pathway via various mechanisms. Here, we review the wide range of immune evasion mechanisms of HCMV. Understanding the mechanisms of HCMV immune evasion will contribute to the development of new customized therapeutic strategies against the virus.
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Affiliation(s)
- Trishna Manandhar
- Institute for Transfusion Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Gia-Gia T Hò
- Institute for Transfusion Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Wiebke C Pump
- Institute for Transfusion Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Rainer Blasczyk
- Institute for Transfusion Medicine, Hannover Medical School, 30625 Hannover, Germany
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24
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Woon AP, Purcell AW. The use of proteomics to understand antiviral immunity. Semin Cell Dev Biol 2018; 84:22-29. [PMID: 30449533 DOI: 10.1016/j.semcdb.2017.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/27/2017] [Accepted: 12/06/2017] [Indexed: 01/01/2023]
Abstract
Viruses are intracellular pathogens that cause a vast array of diseases, which are often severe and typified by high morbidity and mortality rates. Viral infections continue to be a global health burden and effective vaccines and therapeutics are constantly sought to prevent and treat these infections. The development of such treatments generally relies on understanding the mechanisms that underpin efficient host antiviral immune responses. This review summarises recent developments in our understanding of antiviral adaptive immunity and in particular, highlights the use of mass spectrometry to elucidate viral antigens and their processing and presentation to T cells and other immune effectors. These processed peptides serve as potential vaccine candidates or may facilitate clinical monitoring, diagnosis and immunotherapy of infectious diseases.
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Affiliation(s)
- Amanda P Woon
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Anthony W Purcell
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
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25
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Van Chanh Le Q, Le TM, Cho HS, Kim WI, Hong K, Song H, Kim JH, Park C. Analysis of peptide-SLA binding by establishing immortalized porcine alveolar macrophage cells with different SLA class II haplotypes. Vet Res 2018; 49:96. [PMID: 30241566 PMCID: PMC6151021 DOI: 10.1186/s13567-018-0590-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/29/2018] [Indexed: 02/01/2023] Open
Abstract
Primary porcine alveolar macrophages (PAM) are useful for studying viral infections and immune response in pigs; however, long-term use of these cells is limited by the cells’ short lifespan. We immortalized primary PAMs by transfecting them with both hTERT and SV40LT and established two immortalized cell lines (iPAMs) actively proliferating even after 35 passages. These cells possessed the characteristics of primary PAMs, including strong expression of swine leukocyte antigen (SLA) class II genes and the inability to grow anchorage-independently. We characterized their SLA genes and subsequently performed peptide-SLA binding assays using a peptide from porcine circovirus type 2 open reading frame 2 to experimentally measure the binding affinity of the peptide to SLA class II. The number of peptides bound to cells measured by fluorescence was very low for PK15 cells (7.0% ± 1.5), which are not antigen-presenting cells, unlike iPAM61 (33.7% ± 3.4; SLA-DQA*0201/0303, DQB1*0201/0901, DRB1*0201/1301) and iPAM303 (73.3% ± 5.4; SLA DQA*0106/0201, DQB1*0202/0701, DRB1*0402/0602). The difference in peptide binding between the two iPAMs was likely due to the allelic differences between the SLA class II molecules that were expressed. The development of an immortal PAM cell panel harboring diverse SLA haplotypes and the use of an established method in this study can become a valuable tool for evaluating the interaction between antigenic peptides and SLA molecules and is important for many applications in veterinary medicine including vaccine development.
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Affiliation(s)
- Quy Van Chanh Le
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Thong Minh Le
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Hye-Sun Cho
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Won-Il Kim
- College of Veterinary Medicine, Chonbuk National University, Iksan, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Hyuk Song
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, Gwangjin-gu, Seoul, South Korea.
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Mpakali A, Maben Z, Stern LJ, Stratikos E. Molecular pathways for antigenic peptide generation by ER aminopeptidase 1. Mol Immunol 2018; 113:50-57. [PMID: 29678301 DOI: 10.1016/j.molimm.2018.03.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/11/2018] [Accepted: 03/29/2018] [Indexed: 10/17/2022]
Abstract
Endoplasmic Reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that can generate or destroy potential peptide ligands for MHC class I molecules. ERAP1 activity influences the cell-surface immunopeptidome and epitope immunodominance patterns but in complex and poorly understood manners. Two main distinct pathways have been proposed to account for ERAP1's effects on the nature and quantity of MHCI-bound peptides: i) ERAP1 trims peptides in solution, generating the correct length for binding to MHCI or overtrimming peptides so that they are too short to bind, and ii) ERAP1 trims peptides while they are partially bound onto MHCI in manner that leaves the peptide amino terminus accessible. For both pathways, once an appropriate length peptide is generated it could bind conventionally to MHCI, competing with further trimming by ERAP1. The two pathways, although not necessarily mutually exclusive, provide distinct vantage points for understanding of the rules behind the generation of the immunopeptidome. Resolution of the mechanistic details of ERAP1-mediated antigenic peptide generation can have important consequences for pharmacological efforts to regulate the immunopeptidome for therapeutic applications, and for understanding association of ERAP1 alleles with susceptibility to autoimmune disease and cancer. We review current evidence in support of these two pathways and discuss their relative importance and potential complementarity.
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Affiliation(s)
| | - Zachary Maben
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.
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HLA-G peptide preferences change in transformed cells: impact on the binding motif. Immunogenetics 2018; 70:485-494. [PMID: 29602958 PMCID: PMC6061458 DOI: 10.1007/s00251-018-1058-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 03/23/2018] [Indexed: 12/23/2022]
Abstract
HLA-G is known for its strictly restricted tissue distribution. HLA-G expression could be detected in immune privileged organs and many tumor entities such as leukemia, multiple myeloma, and non-Hodgkin and Hodgkin’s lymphoma. This functional variability from mediation of immune tolerance to facilitation of tumor immune evasion strategies might translate to a differential NK cell inhibition between immune-privileged organs and tumor cells. The biophysical invariability of the HLA-G heavy chain and its contrary diversity in immunity implicates a strong influence of the bound peptides on the pHLA-G structure. The aim was to determine if HLA-G displays a tissue-specific peptide repertoire. Therefore, using soluble sHLA-G technology, we analyzed the K562 and HDLM-2 peptide repertoires. Although both cell lines possess a comparable proteome and recruit HLA-G-restricted peptides through the same peptide-loading pathway, the peptide features appear to be cell specific. HDLM-2 derived HLA-G peptides are anchored by an Arg at p1 and K562-derived peptides are anchored by a Lys. At p2, no anchor motif could be determined while peptides were anchored at pΩ with a Leu and showed an auxiliary anchor motif Pro at p3. To appreciate if the peptide anchor alterations are due to a cell-specific differential peptidome, we performed analysis of peptide availability within the different cell types. Yet, the comparison of the cell-specific proteome and HLA-G-restricted ligandome clearly demonstrates a tissue-specific peptide selection by HLA-G molecules. This exclusive and unexpected observation suggests an exquisite immune function of HLA-G.
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Whole genome duplications have provided teleosts with many roads to peptide loaded MHC class I molecules. BMC Evol Biol 2018; 18:25. [PMID: 29471808 PMCID: PMC5824609 DOI: 10.1186/s12862-018-1138-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/15/2018] [Indexed: 12/31/2022] Open
Abstract
Background In sharks, chickens, rats, frogs, medaka and zebrafish there is haplotypic variation in MHC class I and closely linked genes involved in antigen processing, peptide translocation and peptide loading. At least in chicken, such MHCIa haplotypes of MHCIa, TAP2 and Tapasin are shown to influence the repertoire of pathogen epitopes being presented to CD8+ T-cells with subsequent effect on cell-mediated immune responses. Results Examining MHCI haplotype variation in Atlantic salmon using transcriptome and genome resources we found little evidence for polymorphism in antigen processing genes closely linked to the classical MHCIa genes. Looking at other genes involved in MHCI assembly and antigen processing we found retention of functional gene duplicates originating from the second vertebrate genome duplication event providing cyprinids, salmonids, and neoteleosts with the potential of several different peptide-loading complexes. One of these gene duplications has also been retained in the tetrapod lineage with orthologs in frogs, birds and opossum. Conclusion We postulate that the unique salmonid whole genome duplication (SGD) is responsible for eliminating haplotypic content in the paralog MHCIa regions possibly due to frequent recombination and reorganization events at early stages after the SGD. In return, multiple rounds of whole genome duplications has provided Atlantic salmon, other teleosts and even lower vertebrates with alternative peptide loading complexes. How this affects antigen presentation remains to be established. Electronic supplementary material The online version of this article (10.1186/s12862-018-1138-9) contains supplementary material, which is available to authorized users.
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Bauer J, Bakke O, Morth JP. Overview of the membrane-associated RING-CH (MARCH) E3 ligase family. N Biotechnol 2017; 38:7-15. [DOI: 10.1016/j.nbt.2016.12.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/05/2016] [Accepted: 12/13/2016] [Indexed: 12/17/2022]
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Abstract
Cross-presentation of internalized antigens by dendritic cells requires efficient delivery of Major Histocompatibility Complex (MHC) class I molecules to peptide-loading compartments. Strong evidence suggests that such loading can occur outside of the endoplasmic reticulum; however, the trafficking pathways and sources of class I molecules involved are poorly understood. Examination of non-professional, non-phagocytic cells has revealed a clathrin-independent, Arf6-dependent recycling pathway likely traveled by internalized optimally loaded (closed) class I molecules. Some closed and all open MHC class I molecules travel to late endosomes to be degraded but might also partly be re-loaded with peptides and recycled. Studies of viral interference revealed pathways in which class I molecules are directed to degradation in lysosomes upon ubiquitination at the surface, or upon AP-1 and HIV-nef-dependent misrouting from the Golgi network to lysosomes. While many observations made in non-professional cells remain to be re-examined in dendritic cells, available evidence suggests that both recycling and neo-synthesized class I molecules can be loaded with cross-presented peptides. Recycling molecules can be recruited to phagosomes triggered by innate signals such as TLR4 ligands, and may therefore specialize in loading with phagocytosed antigens. In contrast, AP-1-dependent accumulation at, or trafficking through, a Golgi compartment of newly synthesized molecules appears to be important for cross-presentation of soluble proteins and possibly of long peptides that are processed in the so-called vacuolar pathway. However, significant cell biological work will be required to confirm this or any other model and to integrate knowledge on MHC class I biochemistry and trafficking in models of CD8(+) T-cell priming by dendritic cells.
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Affiliation(s)
- Peter van Endert
- Institut National de la Santé et de la Recherche Médicale, Unité 1151, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Centre National de la Recherche Scientifique, Unité 8253, Paris, France
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Guiliano DB, North H, Panayoitou E, Campbell EC, McHugh K, Cooke FGM, Silvestre M, Bowness P, Powis SJ, Antoniou AN. Polymorphisms in the F Pocket of HLA-B27 Subtypes Strongly Affect Assembly, Chaperone Interactions, and Heavy-Chain Misfolding. Arthritis Rheumatol 2017; 69:610-621. [PMID: 27723268 DOI: 10.1002/art.39948] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 09/29/2016] [Indexed: 01/06/2023]
Abstract
OBJECTIVE HLA-B27 is associated with the inflammatory spondyloarthritides (SpA), although subtypes HLA-B*27:06 and HLA-B*27:09 are not. These subtypes differ from the HLA-B*27:05 disease-associated allele primarily at residues 114 and 116 of the heavy chain, part of the F pocket of the antigen-binding groove. Dimerization of HLA-B27 during assembly has been implicated in disease onset. The purpose of this study was to investigate the factors that influence differences in dimerization between disease-associated and non-disease-associated HLA-B27 alleles. METHODS HLA-B*27:05 and mutants resembling the HLA-B*27:06 and 09 subtypes were expressed in the rat C58 T cell line, the human CEM T cell line and its calnexin-deficient variant CEM.NKR. Immunoprecipitation, pulse-chase experiments, flow cytometry, and immunoblotting were performed to study the assembly kinetics, heavy-chain dimerization, and chaperone associations. RESULTS By expressing HLA-B*27:05, 06-like, and 09 alleles on a restrictive rat transporter associated with antigen processing background, we demonstrate that a tyrosine expressed at p116, either alone or together with an aspartic acid residue at p114, inhibited HLA-B27 dimerization and increased the assembly rate. F-pocket residues altered the associations with chaperones of the early major histocompatibility complex class I folding pathway. Calnexin was demonstrated to participate in endoplasmic reticulum (ER) stress-mediated degradation of dimers, whereas the oxidoreductase ERp57 does not appear to influence dimerization. CONCLUSION Residues within the F pocket of the peptide-binding groove, which differ between disease-associated and non-disease-associated HLA-B27 subtypes, can influence the assembly process and heavy-chain dimerization, events which have been linked to the initiation of disease pathogenesis.
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Affiliation(s)
| | - Helen North
- NHS Blood and Transplant, Colindale Blood Centre, London, UK
| | - Eleni Panayoitou
- NHS North West Surrey Clinical Commissioning Group, Weybridge, UK
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Kelly A, Trowsdale J. Introduction: MHC/KIR and governance of specificity. Immunogenetics 2017; 69:481-488. [PMID: 28695288 PMCID: PMC5537316 DOI: 10.1007/s00251-017-0986-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 04/12/2017] [Indexed: 12/02/2022]
Abstract
The MHC controls specificity, to ensure that appropriate immune responses are mounted to invading pathogens whilst maintaining tolerance to the host. It encodes molecules that act as sentinels, providing a snapshot of the health of the interior and exterior of the cell for immune surveillance. To maintain the ability to respond appropriately to any disease requires a delicate balance of expression and function, and many subtleties of the system have been described at the gene, individual and population level. The main players are the highly polymorphic classical MHC class I and class II molecules, as well as some non-classical loci of both types. Transporter associated with antigen processing (TAP) peptide transporters, proteasome components and Tapasin, encoded within the MHC, are also involved in selection of peptide for presentation. The plethora of mechanisms microorganisms use to subvert immune recognition, through blocking these antigen processing and presentation pathways, attests to the importance of HLA in resistance to infection. There is continued interest in MHC genetics in its own right, as well as in relation to KIR, to transplantation, infection, autoimmunity and reproduction. Also of topical interest, cancer immunotherapy through checkpoint inhibition depends on highly specific recognition of cancer peptide antigen and continued expression of HLA molecules. Here, we briefly introduce some background to the MHC/KIR axis in man. This special issue of immunogenetics expands on these topics, in humans and other model species.
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Affiliation(s)
- Adrian Kelly
- Department of Pathology, University of Cambridge, Cambridge, CB21QP, UK
| | - John Trowsdale
- Department of Pathology, University of Cambridge, Cambridge, CB21QP, UK.
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Scheiblhofer S, Laimer J, Machado Y, Weiss R, Thalhamer J. Influence of protein fold stability on immunogenicity and its implications for vaccine design. Expert Rev Vaccines 2017; 16:479-489. [PMID: 28290225 PMCID: PMC5490637 DOI: 10.1080/14760584.2017.1306441] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION In modern vaccinology and immunotherapy, recombinant proteins more and more replace whole organisms to induce protective or curative immune responses. Structural stability of proteins is of crucial importance for efficient presentation of antigenic peptides on MHC, which plays a decisive role for triggering strong immune reactions. Areas covered: In this review, we discuss structural stability as a key factor for modulating the potency of recombinant vaccines and its importance for antigen proteolysis, presentation, and stimulation of B and T cells. Moreover, the impact of fold stability on downstream events determining the differentiation of T cells into effector cells is reviewed. We summarize studies investigating the impact of protein fold stability on the outcome of the immune response and provide an overview on computational methods to estimate the effects of point mutations on protein stability. Expert commentary: Based on this information, the rational design of up-to-date vaccines is discussed. A model for predicting immunogenicity of proteins based on their conformational stability at different pH values is proposed.
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Affiliation(s)
- Sandra Scheiblhofer
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
| | - Josef Laimer
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
| | - Yoan Machado
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
| | - Richard Weiss
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
| | - Josef Thalhamer
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
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The Pathophysiological Impact of HLA Class Ia and HLA-G Expression and Regulatory T Cells in Malignant Melanoma: A Review. J Immunol Res 2016; 2016:6829283. [PMID: 27999823 PMCID: PMC5141560 DOI: 10.1155/2016/6829283] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/16/2016] [Accepted: 10/12/2016] [Indexed: 12/21/2022] Open
Abstract
Malignant melanoma, a very common type of cancer, is a rapidly growing cancer of the skin with an increase in incidence among the Caucasian population. The disease is seen through all age groups and is very common in the younger age groups. Several studies have examined the risk factors and pathophysiological mechanisms of malignant melanoma, which have enlightened our understanding of the development of the disease, but we have still to fully understand the complex immunological interactions. The examination of the interaction between the human leucocyte antigen (HLA) system and prognostic outcome has shown interesting results, and a correlation between the down- or upregulation of these antigens and prognosis has been seen through many different types of cancer. In malignant melanoma, HLA class Ia has been seen to influence the effects of pharmaceutical drug treatment as well as the overall prognosis, and the HLA class Ib and regulatory T cells have been correlated with tumor progression. Although there is still no standardized immunological treatment worldwide, the interaction between the human leucocyte antigen (HLA) system and tumor progression seems to be a promising focus in the way of optimizing the treatment of malignant melanoma.
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Rock KL, Reits E, Neefjes J. Present Yourself! By MHC Class I and MHC Class II Molecules. Trends Immunol 2016; 37:724-737. [PMID: 27614798 DOI: 10.1016/j.it.2016.08.010] [Citation(s) in RCA: 480] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/09/2016] [Accepted: 08/15/2016] [Indexed: 12/01/2022]
Abstract
Since the discovery of MHC molecules, it has taken 40 years to arrive at a coherent picture of how MHC class I and MHC class II molecules really work. This is a story of the proteases and MHC-like chaperones that support the MHC class I and II molecules in presenting peptides to the immune system. We now understand that the MHC system shapes both the repertoire of presented peptides and the subsequent T cell response, with important implications ranging from transplant rejection to tumor immunotherapies. Here we present an illustrated review of the ins and outs of MHC class I and MHC class II antigen presentation.
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Affiliation(s)
- Kenneth L Rock
- Department of Pathology, UMass Medical School, Worcester, MA, USA
| | - Eric Reits
- Department of Cell Biology and Histology, Amsterdam Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jacques Neefjes
- Department of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Leiden, The Netherlands.
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Wynne JW, Woon AP, Dudek NL, Croft NP, Ng JHJ, Baker ML, Wang LF, Purcell AW. Characterization of the Antigen Processing Machinery and Endogenous Peptide Presentation of a Bat MHC Class I Molecule. THE JOURNAL OF IMMUNOLOGY 2016; 196:4468-76. [PMID: 27183594 DOI: 10.4049/jimmunol.1502062] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 03/23/2016] [Indexed: 11/19/2022]
Abstract
Bats are a major reservoir of emerging and re-emerging infectious diseases, including severe acute respiratory syndrome-like coronaviruses, henipaviruses, and Ebola virus. Although highly pathogenic to their spillover hosts, bats harbor these viruses, and a large number of other viruses, with little or no clinical signs of disease. How bats asymptomatically coexist with these viruses is unknown. In particular, little is known about bat adaptive immunity, and the presence of functional MHC molecules is mostly inferred from recently described genomes. In this study, we used an affinity purification/mass spectrometry approach to demonstrate that a bat MHC class I molecule, Ptal-N*01:01, binds antigenic peptides and associates with peptide-loading complex components. We identified several bat MHC class I-binding partners, including calnexin, calreticulin, protein disulfide isomerase A3, tapasin, TAP1, and TAP2. Additionally, endogenous peptide ligands isolated from Ptal-N*01:01 displayed a relatively broad length distribution and an unusual preference for a C-terminal proline residue. Finally, we demonstrate that this preference for C-terminal proline residues was observed in Hendra virus-derived peptides presented by Ptal-N*01:01 on the surface of infected cells. To our knowledge, this is the first study to identify endogenous and viral MHC class I ligands for any bat species and, as such, provides an important avenue for monitoring and development of vaccines against major bat-borne viruses both in the reservoir and spillover hosts. Additionally, it will provide a foundation to understand the role of adaptive immunity in bat antiviral responses.
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Affiliation(s)
- James W Wynne
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria 3220, Australia
| | - Amanda P Woon
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; and
| | - Nadine L Dudek
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; and
| | - Nathan P Croft
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; and
| | - Justin H J Ng
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Graduate Medical School, Singapore 169857, Republic of Singapore
| | - Michelle L Baker
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, Victoria 3220, Australia
| | - Lin-Fa Wang
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Graduate Medical School, Singapore 169857, Republic of Singapore
| | - Anthony W Purcell
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; and
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Ghanem E, Al-Balushi M. Adopting the rapamycin trapping assay to track the trafficking of murine MHC class I alleles, H-2K(b). BMC Cell Biol 2015; 16:30. [PMID: 26714929 PMCID: PMC4696223 DOI: 10.1186/s12860-015-0077-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/14/2015] [Indexed: 11/22/2022] Open
Abstract
Background In mammalian cells, the quality control (QC) of properly folded proteins is monitored in the early secretory pathway, particularly in the endoplasmic reticulum (ER). Several proteins, including our protein of interest, major histocompatibility complex class I (MHC class I), can bypass the first line of ER-QC and reside in post-ER compartments in an unfolded form. Such forms entail both monomeric and dimeric structures that are devoid of peptides and thus cannot fulfill the immunological function of antigen presentation at the cell surface. MHC class I structures become mature and properly folded once loaded with the appropriate peptides in the framework of the peptide loading complex (PLC). Despite the flood of information on the diverse trafficking behavior of different MHC class I alleles, there is still controversy on the actual trajectory followed by improperly folded murine MHC class I alleles, namely H-2Kb. In this study, we employ an in vitro rapamycin trapping assay, live cell imaging, and a biochemical COPII budding approach to further investigate the trafficking of H-2Kb beyond the level of the ER. Results We confirm the egress of H-2Kb in an unfolded form to a post-ER compartment from where they can cycle back to the ER. Deciphering the exact identity of the post-ER compartment by laser scanning microscopy did not only point to the existence of the ERGIC and cis-Golgi compartments as residency areas for unfolded proteins, but also to the involvement of an addional compartment, that lies in close proximity and possesses high resemblance to the aforementioned compartments. Interestingly, we were capable of showing using the same rapamycin trapping assay that H-2Kb can undergo a potential maturation event during their cycling; this is attained upon addition of peptides and trapping of accumulated post-ER molecules at the cell surface. Conclusions Our findings deepen the understanding of H-2Kb trafficking outside the ER and pave the way to decipher the role and the trafficking of certain PLC chaperones, such as tapasin, throughout H-2Kb post-ER QC. Finally, we demonstrate the plausible usage of the rapamycin assay to assess the trafficking of defected proteins especially in diseases and under therapeutic studies.
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Affiliation(s)
- Esther Ghanem
- Department of Biology, Faculty of Natural and Applied Sciences, Notre Dame University, 72, Zouk Mosbeh, Keserwan district, Lebanon.
| | - Mohammed Al-Balushi
- Department of Microbiology and Immunology, Sultan Qaboos University, Muscat, Oman.
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Dong W, Yin X, Sun L, Wang J, Sun S, Zhu G, Wu S, Bao W. Age-associated methylation change of TAP1 promoter in piglet. Gene 2015; 573:70-4. [PMID: 26169022 DOI: 10.1016/j.gene.2015.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/29/2015] [Accepted: 07/09/2015] [Indexed: 01/01/2023]
Abstract
Diarrhea and edematous disease are two major causes of mortality in postweaning piglets. These conditions lead to huge economic losses in the swine industry. Escherichia coli F18 is the primary causative agent of these two diseases. Transported associated with antigen processing (TAP) plays an important role in the immune response and the TAP1 gene could be an effective anti-E. coli F18 molecular marker in pigs. The aim of this study was to determine the correlation between TAP1 gene promoter CpG island methylation status and mRNA expression in piglets. In this study, bisulfite sequencing PCR (BSP) was used to detect the methylation status of the TAP1 gene promoter CpG islands and fluorescence quantitative PCR was used to detect TAP1 expression in the jejunum of Sutai piglets from birth to weaning age. The fragment of the TAP1 gene promoter region under investigation has no mutation, has 13 putative transcription factor binding sites containing 19 CpG sites, and may be important for regulation of gene expression. With increasing age, the overall methylation levels decreased, while the TAP1 expression levels increased, indicating a negative correlation between TAP1 expression and promoter methylation levels. Variance analysis showed significant differences in the methylation status of CpG_4, CpG_13 and CpG_15 among the different age groups (P<0.05). Our data indicate that TAP1 expression is increased by demethylation of promoter CpG islands, with CpG_4, CpG_13 and CpG_15 implicated as the critical regulatory sites.
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Affiliation(s)
- Wenhua Dong
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Xuemei Yin
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Li Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Jing Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Shouyong Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China.
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Zachova K, Krupka M, Raska M. Antigen Cross-Presentation and Heat Shock Protein-Based Vaccines. Arch Immunol Ther Exp (Warsz) 2015; 64:1-18. [DOI: 10.1007/s00005-015-0370-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 08/31/2015] [Indexed: 12/15/2022]
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Zou N, Yang L, Chen L, Li T, Jin T, Peng H, Zhang S, Wang D, Li R, Liu C, Jiang J, Wang L, Liang W, Hu J, Li S, Wu C, Cui X, Chen Y, Li F. Heterozygote of TAP1 Codon637 decreases susceptibility to HPV infection but increases susceptibility to esophageal cancer among the Kazakh populations. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015. [PMID: 26205887 PMCID: PMC4514451 DOI: 10.1186/s13046-015-0185-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background The role of human papillomavirus (HPV) may be involved in the development of esophageal cancer (EC) and the polymorphic immune response gene transporter associated with antigen processing (TAP) may be involved in HPV persistence and subsequent cancer carcinogenesis. The current study aims to provide association evidence for HPV with EC, to investigate TAP1 polymorphisms in EC and assess its association with HPV statuses and EC in Kazakhs. Methods The HPV genotypes in 361 patients with EC and 66 controls selected from Kazakh population were evaluated using PCR. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to detect two SNPs of TAP1 in 150 cases comprised of 75 HPV+ and 75 HPV- patients and 283 pure ethnic population of Kazakh and evaluate their associations with susceptibility to EC. A case-to-case comparison based on the genotyping results was conducted to address the function of TAP1 variants in the involvement of HPV. Results The presence of four HPV genotypes in EC tissues ― including HPV 16, 18, 31, 45 ― was significantly higher at 64.6 % than those in controls at 18.2 % (P < 0.001). Such presence was strongly associated with increased risk of EC (OR 8.196; 95 % CI 4.280–15.964). The infection of HPV16, and multi-infection of 16 and 18 significantly increase the risk for developing EC (OR 4.616, 95 % CI 2.099–10.151; and OR 6.029, 95 % CI 1.395–26.057 respectively). Heterozygote of TAP1 D637G had a significantly higher risk for developing EC (OR 1.626; 95 % CI 1.080–2.449). The odds ratio for HPV infection was significantly lower among carriers of TAP1 D637G polymorphism (OR 0.281; 95 % CI 0.144–0.551). Conclusions HPV infection exhibits a strong positive association with the risk of EC in Kazakhs. Heterozygote of TAP1 D637G decreases susceptibility to HPV infection in patients with EC but increases susceptibility to EC among the Kazakh populations.
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Affiliation(s)
- Ningjing Zou
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Lan Yang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Ling Chen
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Tingting Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Tingting Jin
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Hao Peng
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Shumao Zhang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Dandan Wang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Ranran Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Chunxia Liu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Jinfang Jiang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Lianghai Wang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Weihua Liang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Jianming Hu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Shugang Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China.
| | - Chuanyue Wu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China. .,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Xiaobin Cui
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China. .,Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Yunzhao Chen
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China. .,Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Feng Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, North 4th Road, Shihezi, Xinjiang, 832002, China. .,Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Pickering AM, Lehr M, Miller RA. Lifespan of mice and primates correlates with immunoproteasome expression. J Clin Invest 2015; 125:2059-68. [PMID: 25866968 PMCID: PMC4463211 DOI: 10.1172/jci80514] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/05/2015] [Indexed: 12/24/2022] Open
Abstract
There is large variation in lifespan among different species, and there is evidence that modulation of proteasome function may contribute to longevity determination. Comparative biology provides a powerful tool for identifying genes and pathways that control the rate of aging. Here, we evaluated skin-derived fibroblasts and demonstrate that among primate species, longevity correlated with an elevation in proteasomal activity as well as immunoproteasome expression at both the mRNA and protein levels. Immunoproteasome enhancement occurred with a concurrent increase in other elements involved in MHC class I antigen presentation, including β-2 microglobulin, (TAP1), and TAP2. Fibroblasts from long-lived primates also appeared more responsive to IFN-γ than cells from short-lived primate species, and this increase in IFN-γ responsiveness correlated with elevated expression of the IFN-γ receptor protein IFNGR2. Elevation of immunoproteasome and proteasome activity was also observed in the livers of long-lived Snell dwarf mice and in mice exposed to drugs that have been shown to extend lifespan, including rapamycin, 17-α-estradiol, and nordihydroguaiaretic acid. This work suggests that augmented immunoproteasome function may contribute to lifespan differences in mice and among primate species.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 2
- ATP Binding Cassette Transporter, Subfamily B, Member 3
- ATP-Binding Cassette Transporters/biosynthesis
- ATP-Binding Cassette Transporters/genetics
- Animals
- Antigen Presentation
- Cells, Cultured
- Dwarfism/genetics
- Dwarfism/physiopathology
- Estradiol/pharmacology
- Female
- Fibroblasts/cytology
- Fibroblasts/drug effects
- Fibroblasts/metabolism
- Gene Expression Regulation
- Histocompatibility Antigens Class I/immunology
- Histocompatibility Antigens Class I/metabolism
- Interferon-gamma/pharmacology
- Janus Kinases/physiology
- Longevity/drug effects
- Longevity/immunology
- Longevity/physiology
- Male
- Masoprocol/pharmacology
- Mice/physiology
- Mice, Inbred C3H
- Mice, Mutant Strains
- Oxidative Stress
- Primates/physiology
- Proteasome Endopeptidase Complex/biosynthesis
- Proteasome Endopeptidase Complex/chemistry
- Proteasome Endopeptidase Complex/genetics
- Proteasome Endopeptidase Complex/metabolism
- Protein Subunits
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Receptors, Interferon/physiology
- STAT Transcription Factors/physiology
- Signal Transduction
- Sirolimus/pharmacology
- Species Specificity
- Up-Regulation
- beta 2-Microglobulin/biosynthesis
- beta 2-Microglobulin/genetics
- Interferon gamma Receptor
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Zhu SP, Yin XM, Sun L, Sun SY, Bao WB, Wu SL. Differential expression of porcine TAP1 gene in the populations of pigs. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415010147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Peptide-Based Vaccination and Induction of CD8+ T-Cell Responses Against Tumor Antigens in Breast Cancer. BioDrugs 2014; 29:15-30. [DOI: 10.1007/s40259-014-0114-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Murat P, Tellam J. Effects of messenger RNA structure and other translational control mechanisms on major histocompatibility complex-I mediated antigen presentation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:157-71. [PMID: 25264139 PMCID: PMC4359683 DOI: 10.1002/wrna.1262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/18/2014] [Accepted: 07/23/2014] [Indexed: 12/21/2022]
Abstract
Effective T‐cell surveillance of antigen‐presenting cells is dependent on the expression of an array of antigenic peptides bound to major histocompatibility complex (MHC) class I (MHC‐I) or class II (MHC‐II) molecules. Pathogens co‐evolving with their hosts exploit crucial translational regulatory mechanisms in order to evade host immune recognition and thereby sustain their infection. Evasion strategies that downregulate viral protein synthesis and thereby restrict antigen presentation to cytotoxic T‐cells through the endogenous MHC‐I pathway have been implicated in the pathogenesis of viral‐associated malignancies. An understanding of the mechanisms by which messenger RNA (mRNA) structure modulates both viral mRNA translation and the antigen processing machinery to escape immune surveillance, will stimulate the development of alternative therapeutic strategies focused on RNA‐directed drugs designed to enhance immune responses against infected cells. In this review, we discuss regulatory aspects of the MHC‐I pathway and summarize current knowledge of the role attributed by mRNA structure and other translational regulatory mechanisms in immune evasion. In particular we highlight the impact of recently identified G‐quadruplex structures within virally encoded transcripts as unique regulatory signals for translational control and antigen presentation. WIREs RNA 2015, 6:157–171. doi: 10.1002/wrna.1262 This article is categorized under:
RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems Translation > Translation Regulation
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Affiliation(s)
- Pierre Murat
- Department of Chemistry, University of Cambridge, Cambridge, UK
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Genetic variations of TAP1 gene exon 3 affects gene expression and Escherichia coli F18 resistance in piglets. Int J Mol Sci 2014; 15:11161-71. [PMID: 24955792 PMCID: PMC4100205 DOI: 10.3390/ijms150611161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 05/22/2014] [Accepted: 05/27/2014] [Indexed: 11/21/2022] Open
Abstract
Firstly, our research group identified Sutai pigs’ phenotypes that exhibited extreme resistance and susceptibility to the Escherichia coli F18 respectively, and then eight ETEC (Enterotoxigenic Escherichia coli) F18-resistant piglets and eight ETEC F18-sensitive piglets were selected. Then, the TAP1 (Transporter associated with antigen processing) mRNA relative expression levels were analyzed in 11 tissues of the resistant and susceptible phenotypes. Simultaneously, we detected the genetic variations in exon 3 of the TAP1 gene and evaluated the TAP1 mRNA expression levels among the different genotype pigs to study the effects of the genetic variation on gene expression, and the E. coli F18 resistance. The results revealed higher expression levels in the resistant genotypes than that in the susceptible genotypes in 11 tissues, with significant differences in the spleen, lymph node, lung, thymus, duodenum and jejunum. Furthermore, a G729A mutation was identified in the TAP1 gene exon 3, and this mutation deviates from Hardy-Weinberg equilibrium (p < 0.01). The TAP1 mRNA levels in GG genotype were significantly higher than that in the other two genotypes, with significant differences in the liver, lung, kidney, thymus, lymph node, duodenum and jejunum tissues. We speculated that high expression of the TAP1 gene might confer resistance against the E. coli F18, the G729A mutation had a significant effect on the mRNA expression, and individuals with the GG genotype possessed a stronger ability to resist the E. coli F18 infection.
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46
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The genotype of the transporter associated with antigen processing gene affects susceptibility to colorectal cancer in Japanese. Environ Health Prev Med 2014; 19:265-70. [PMID: 24803408 DOI: 10.1007/s12199-014-0388-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/04/2014] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE Although colorectal cancer (CRC) is one of the most frequent malignancies in Japan, the associated genetic factors remain to be elucidated. Functional loss of the transporter associated with antigen processing (TAP) 1 gene induces carcinogenesis. We investigated whether single nucleotide polymorphisms (SNPs) in the TAP1 gene (rs735883) are associated with susceptibility to CRC in a Japanese population. METHODS The study participants were 143 cases and 243 clinical controls. After extracting DNA from their peripheral blood cells, genotyping was conducted by the polymerase chain reaction-restriction fragment length polymorphism method. RESULTS Participants with a mutated allele had an increased risk for CRC. The adjusted odds ratios for the C/T, T/T, and the mutation type (C/T + T/T) compared to that of wild type (C/C) were 2.27 [95 % confidence interval (CI), 1.43-3.67], 1.95 (95 % CI, 0.88-4.30), and 2.22 (95 % CI, 1.42-3.55), respectively. Furthermore, a significant trend in the rate of cases was observed with an increasing number of mutated alleles (P for trend = 0.0068). CONCLUSIONS The genotype of the TAP1 gene is associated with susceptibility to CRC.
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Bailey A, van Hateren A, Elliott T, Werner JM. Two polymorphisms facilitate differences in plasticity between two chicken major histocompatibility complex class I proteins. PLoS One 2014; 9:e89657. [PMID: 24586943 PMCID: PMC3930747 DOI: 10.1371/journal.pone.0089657] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 01/21/2014] [Indexed: 11/18/2022] Open
Abstract
Major histocompatibility complex class I molecules (MHC I) present peptides to cytotoxic T-cells at the surface of almost all nucleated cells. The function of MHC I molecules is to select high affinity peptides from a large intracellular pool and they are assisted in this process by co-factor molecules, notably tapasin. In contrast to mammals, MHC homozygous chickens express a single MHC I gene locus, termed BF2, which is hypothesised to have co-evolved with the highly polymorphic tapasin within stable haplotypes. The BF2 molecules of the B15 and B19 haplotypes have recently been shown to differ in their interactions with tapasin and in their peptide selection properties. This study investigated whether these observations might be explained by differences in the protein plasticity that is encoded into the MHC I structure by primary sequence polymorphisms. Furthermore, we aimed to demonstrate the utility of a complimentary modelling approach to the understanding of complex experimental data. Combining mechanistic molecular dynamics simulations and the primary sequence based technique of statistical coupling analysis, we show how two of the eight polymorphisms between BF2*15∶01 and BF2*19∶01 facilitate differences in plasticity. We show that BF2*15∶01 is intrinsically more plastic than BF2*19∶01, exploring more conformations in the absence of peptide. We identify a protein sector of contiguous residues connecting the membrane bound α3 domain and the heavy chain peptide binding site. This sector contains two of the eight polymorphic residues. One is residue 22 in the peptide binding domain and the other 220 is in the α3 domain, a putative tapasin binding site. These observations are in correspondence with the experimentally observed functional differences of these molecules and suggest a mechanism for how modulation of MHC I plasticity by tapasin catalyses peptide selection allosterically.
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Affiliation(s)
- Alistair Bailey
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andy van Hateren
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Tim Elliott
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jörn M. Werner
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton, United Kingdom
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Association analysis of tapasin polymorphisms with aspirin-exacerbated respiratory disease in asthmatics. Pharmacogenet Genomics 2014; 23:341-8. [PMID: 23736108 DOI: 10.1097/fpc.0b013e328361d4bb] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Aspirin-exacerbated respiratory disease (AERD) is characterized by the development of airway obstruction in asthmatic individuals following the ingestion of aspirin or other nonsteroidal anti-inflammatory drugs. TAPBP (TAP-binding protein, tapasin) is upregulated by eicosanoids, which act as potent inflammatory molecules in aspirin-related reactions. Thus, functional alterations in the TAPBP gene may contribute toward AERD. OBJECTIVES We examined the relationship between the single nucleotide polymorphisms on the TAPBP gene and AERD. MATERIALS AND METHODS A group of asthmatic patients (n=1252) underwent the oral aspirin challenge. Oral aspirin challenge reactions were categorized into two groups as follows: 15% or greater decreases in forced expiratory volume in 1 s or naso-ocular and skin reactions (AERD), or 15% or less decreases in forced expiratory volume in 1 s without naso-ocular and skin reactions (aspirin-tolerant asthma). Five single nucleotide polymorphisms of the TAPBP gene were genotyped. RESULTS Logistic regression analysis showed that the minor allele frequencies of TAPBP rs2071888 C>G (Thr260Arg) on exon 4 (P>0.05), which was in absolute linkage disequilibrium with rs1059288 T>C on 3'UTR, were significantly higher in the AERD group than in the aspirin-tolerant asthma group, and the P values remained significant after multiple comparisons (Pcorr=0.006, odds ratio: 1.37, 95% confidence interval: 1.11-1.69, additive model; Pcorr=0.009, odds ratio: 1.52, 95% confidence interval: 1.14-2.03, dominant model). Alpha-helical wheel plotting showed that 260Arg had greater hydrophilic helical property than 260Thr. CONCLUSION TAPBP polymorphisms may play a role in the development of AERD.
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Abstract
The mammalian immune system has evolved to display peptides derived from microbial antigens to immune effector cells. Liberated from the intact antigens through distinct proteolytic mechanisms, these peptides are subsequently transported to the cell surface while bound to chaperone-like receptors known as major histocompatibility complex molecules. These complexes are then scrutinized by T-cells that express receptors with specificity for specific major histocompatibility complex-peptide complexes. In normal uninfected cells, this process of antigen processing and presentation occurs continuously, with the resultant array of self-antigen-derived peptides displayed on the surface of these cells. Changes in this cellular peptide array alert the immune system to changes in the intracellular environment that may be associated with infection, oncogenesis or other abnormal cellular processes, resulting in a cascade of events that result in the elimination of the abnormal cell. Since peptides play such an essential role in informing the immune system of infection with viral or microbial pathogens and the transformation of cells in malignancy, the tools of proteomics, in particular mass spectrometry, are ideally suited to study these immune responses at a molecular level. Recent advances in studies of immune responses that have utilized mass spectrometry and associated technologies are reviewed. The authors gaze into the future and look at current challenges and where proteomics will impact in immunology over the next 5 years.
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Affiliation(s)
- Nicholas A Williamson
- The University of Melbourne, Department of Biochemistry & Molecular Biology, The Bio21 Molecular Science & Biotechnology Institute, 3010, Victoria, Australia.
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50
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Association of TAP gene polymorphisms and risk of cervical intraepithelial neoplasia. DISEASE MARKERS 2013; 35:79-84. [PMID: 24288424 PMCID: PMC3774964 DOI: 10.1155/2013/368732] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 05/02/2013] [Indexed: 11/18/2022]
Abstract
BACKGROUND Transporter associated with antigen processing (TAP) is responsible for peptide loading onto class I major histocompatibility complex (MHC-I) molecules. TAP seems to facilitate the detection of HPV by MHC-I molecules and contributes to successful eradication of HPV. TAP polymorphisms could have an important impact on the course of HPV infection. OBJECTIVE The aim of this study is to evaluate the association between five TAP gene polymorphisms and the risk of CIN. Methods. This case-control study investigated five common TAP polymorphisms in TAP1 (1341 and 2254) and TAP2 (1135, 1693, and 1993) in 616 women with CIN and 206 controls. Associations between gene polymorphisms and risk of CIN were analysed by univariate and multivariable models. The combined effect of the five TAP gene polymorphisms on the risk for CIN was investigated by haplotype analysis. RESULTS No significant difference in genotype distribution of the five TAP polymorphisms was observed in women with CIN and controls. Haplotype analysis revealed that women with haplotype mut-wt-wt-wt-wt (TAP polymorphisms t1135-t1341-t1693-t1993-t2254) had a significantly lower risk for CIN, compared to women with the haplotype wt-wt-wt-wt-wt (P = 0.006; OR 0.5 [0.35-0.84]). CONCLUSION Identification of this haplotype combination could be used to identify women, less susceptible for development of CIN following HPV infection.
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