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Clements RL, Kennedy EA, Song D, Campbell A, An HH, Amses KR, Miller-Ensminger T, Addison MM, Eisenlohr LC, Chou ST, Jurado KA. Human erythroid progenitors express antigen presentation machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601047. [PMID: 39005276 PMCID: PMC11244935 DOI: 10.1101/2024.06.27.601047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Early-life immune exposures can profoundly impact lifelong health. However, functional mechanisms underlying fetal immune development remain incomplete. Erythrocytes are not typically considered active immune mediators, primarily because erythroid precursors discard their organelles as they mature, thus losing the ability to alter gene expression in response to stimuli. Erythroid progenitors and precursors circulate in human fetuses and neonates. Although there is limited evidence that erythroid precursors are immunomodulatory, our understanding of the underlying mechanisms remains inadequate. To define the immunobiological role of fetal and perinatal erythroid progenitors and precursors, we analyzed single cell RNA-sequencing data and found that transcriptomics support erythroid progenitors as putative immune mediators. Unexpectedly, we discovered that human erythroid progenitors constitutively express Major Histocompatibility Complex (MHC) class II antigen processing and presentation machinery, which are hallmarks of specialized antigen presenting immune cells. Furthermore, we demonstrate that erythroid progenitors internalize and cleave foreign proteins into peptide antigens. Unlike conventional antigen presenting cells, erythroid progenitors express atypical costimulatory molecules and immunoregulatory cytokines that direct the development of regulatory T cells, which are critical for establishing maternal-fetal tolerance. Expression of MHC II in definitive erythroid progenitors begins during the second trimester, coinciding with the appearance of mature T cells in the fetus, and is absent in primitive progenitors. Lastly, we demonstrate physical and molecular interaction potential of erythroid progenitors and T cells in the fetal liver. Our findings shed light on a unique orchestrator of fetal immunity and provide insight into the mechanisms by which erythroid cells contribute to host defense.
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Blander JM, Yee Mon KJ, Jha A, Roycroft D. The show and tell of cross-presentation. Adv Immunol 2023; 159:33-114. [PMID: 37996207 DOI: 10.1016/bs.ai.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Cross-presentation is the culmination of complex subcellular processes that allow the processing of exogenous proteins and the presentation of resultant peptides on major histocompatibility class I (MHC-I) molecules to CD8 T cells. Dendritic cells (DCs) are a cell type that uniquely specializes in cross-presentation, mainly in the context of viral or non-viral infection and cancer. DCs have an extensive network of endovesicular pathways that orchestrate the biogenesis of an ideal cross-presentation compartment where processed antigen, MHC-I molecules, and the MHC-I peptide loading machinery all meet. As a central conveyor of information to CD8 T cells, cross-presentation allows cross-priming of T cells which carry out robust adaptive immune responses for tumor and viral clearance. Cross-presentation can be canonical or noncanonical depending on the functional status of the transporter associated with antigen processing (TAP), which in turn influences the vesicular route of MHC-I delivery to internalized antigen and the cross-presented repertoire of peptides. Because TAP is a central node in MHC-I presentation, it is targeted by immune evasive viruses and cancers. Thus, understanding the differences between canonical and noncanonical cross-presentation may inform new therapeutic avenues against cancer and infectious disease. Defects in cross-presentation on a cellular and genetic level lead to immune-related disease progression, recurrent infection, and cancer progression. In this chapter, we review the process of cross-presentation beginning with the DC subsets that conduct cross-presentation, the signals that regulate cross-presentation, the vesicular trafficking pathways that orchestrate cross-presentation, the modes of cross-presentation, and ending with disease contexts where cross-presentation plays a role.
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Affiliation(s)
- J Magarian Blander
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States; Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, United States; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Cornell University, New York, NY, United States; Immunology and Microbial Pathogenesis Programs, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, United States.
| | - Kristel Joy Yee Mon
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Atimukta Jha
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - Dylan Roycroft
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, United States; Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, United States
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3
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Ciaston I, Dobosz E, Potempa J, Koziel J. The subversion of toll-like receptor signaling by bacterial and viral proteases during the development of infectious diseases. Mol Aspects Med 2022; 88:101143. [PMID: 36152458 PMCID: PMC9924004 DOI: 10.1016/j.mam.2022.101143] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/29/2022] [Accepted: 09/09/2022] [Indexed: 02/05/2023]
Abstract
Toll-like receptors (TLRs) are pattern recognition receptors (PRRs) that respond to pathogen-associated molecular patterns (PAMPs). The recognition of specific microbial ligands by TLRs triggers an innate immune response and also promotes adaptive immunity, which is necessary for the efficient elimination of invading pathogens. Successful pathogens have therefore evolved strategies to subvert and/or manipulate TLR signaling. Both the impairment and uncontrolled activation of TLR signaling can harm the host, causing tissue destruction and allowing pathogens to proliferate, thus favoring disease progression. In this context, microbial proteases are key virulence factors that modify components of the TLR signaling pathway. In this review, we discuss the role of bacterial and viral proteases in the manipulation of TLR signaling, highlighting the importance of these enzymes during the development of infectious diseases.
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Affiliation(s)
- Izabela Ciaston
- Department of Microbiology Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Ewelina Dobosz
- Department of Microbiology Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jan Potempa
- Department of Microbiology Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Department of Oral Health and Systemic Disease, University of Louisville School of Dentistry, University of Louisville, Louisville, KY, USA.
| | - Joanna Koziel
- Department of Microbiology Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
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4
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Structure determinants defining the specificity of papain-like cysteine proteases. Comput Struct Biotechnol J 2022; 20:6552-6569. [DOI: 10.1016/j.csbj.2022.11.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
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5
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The Key Role of Lysosomal Protease Cathepsins in Viral Infections. Int J Mol Sci 2022; 23:ijms23169089. [PMID: 36012353 PMCID: PMC9409221 DOI: 10.3390/ijms23169089] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Cathepsins encompass a family of lysosomal proteases that mediate protein degradation and turnover. Although mainly localized in the endolysosomal compartment, cathepsins are also found in the cytoplasm, nucleus, and extracellular space, where they are involved in cell signaling, extracellular matrix assembly/disassembly, and protein processing and trafficking through the plasma and nuclear membrane and between intracellular organelles. Ubiquitously expressed in the body, cathepsins play regulatory roles in a wide range of physiological processes including coagulation, hormone secretion, immune responses, and others. A dysregulation of cathepsin expression and/or activity has been associated with many human diseases, including cancer, diabetes, obesity, cardiovascular and inflammatory diseases, kidney dysfunctions, and neurodegenerative disorders, as well as infectious diseases. In viral infections, cathepsins may promote (1) activation of the viral attachment glycoproteins and entry of the virus into target cells; (2) antigen processing and presentation, enabling the virus to replicate in infected cells; (3) up-regulation and processing of heparanase that facilitates the release of viral progeny and the spread of infection; and (4) activation of cell death that may either favor viral clearance or assist viral propagation. In this review, we report the most relevant findings on the molecular mechanisms underlying cathepsin involvement in viral infection physiopathology, and we discuss the potential of cathepsin inhibitors for therapeutical applications in viral infectious diseases.
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6
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Hsu YW, Wong HSC, Huang WC, Yeh YH, Hsiao CD, Chang WC, Hsieh SL. Human rs75776403 polymorphism links differential phenotypic and clinical outcomes to a CLEC18A p.T151M-driven multiomics. J Biomed Sci 2022; 29:43. [PMID: 35717171 PMCID: PMC9206359 DOI: 10.1186/s12929-022-00822-1] [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: 03/10/2022] [Accepted: 06/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human traits, diseases susceptibility, and clinical outcomes vary hugely among individuals. Despite a fundamental understanding of genetic (or environmental) contributions, the detailed mechanisms of how genetic variation impacts molecular or cellular behaviours of a gene, and subsequently leads to such variability remain poorly understood. METHODS Here, in addition to phenome-wide correlations, we leveraged multiomics to exploit mechanistic links, from genetic polymorphism to protein structural or functional changes and a cross-omics perturbation landscape of a germline variant. RESULTS We identified a missense cis-acting expression quantitative trait locus in CLEC18A (rs75776403) in which the altered residue (T151→M151) disrupts the lipid-binding ability of the protein domain. The altered allele carriage led to a metabolic and proliferative shift, as well as immune deactivation, therefore determines human anthropometrics (body height), kidney, and hematological traits. CONCLUSIONS Collectively, we uncovered genetic pleiotropy in human complex traits and diseases via CLEC18A rs75776403-regulated pathways.
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Affiliation(s)
- Yu-Wen Hsu
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
| | - Henry Sung-Ching Wong
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Wan-Chen Huang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.,Institute of Medical Device and Imaging, National Taiwan University, Taipei, Taiwan
| | - Yi-Hung Yeh
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan. .,Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan. .,Integrative Research Center in Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
| | - Shie-Liang Hsieh
- Genomics Research Center, Academia Sinica, Taipei, Taiwan. .,Institute of Clinical Medicine, National Yang Ming Chiao Tung University School of Medicine, Taipei, Taiwan. .,Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei, Taiwan. .,Graduate of Institute of Cancer Biology and Drug Discovery, Taipei Medical University, Taipei, Taiwan.
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7
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Ng L, Wang X, Yang C, Su C, Li M, Cheung AKL. Celastrol Downmodulates Alpha-Synuclein-Specific T Cell Responses by Mediating Antigen Trafficking in Dendritic Cells. Front Immunol 2022; 13:833515. [PMID: 35309340 PMCID: PMC8926036 DOI: 10.3389/fimmu.2022.833515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Parkinson’s Disease (PD) is a neurodegenerative disease that affects the elderly. It is associated with motor dysfunction due to the accumulation of misfolded or aggregated fibrillar alpha-synuclein (α-syn) in the mid-brain. Current treatments are mainly focused on relieving the symptoms but are accompanied by side effects and are limited in halting disease progression. Increasing evidence points to peripheral immune cells underlying disease development, especially T cells contributing to α-syn-related neuroinflammation in PD. The onset of these cells is likely mediated by dendritic cells (DCs), whose role in α-syn-specific responses remain less studied. Moreover, Traditional Chinese medicine (TCM)-derived compounds that are candidates to treat PD may alleviate DC-T cell-mediated immune responses. Therefore, our study focused on the role of DC in response to fibrillar α-syn and subsequent induction of antigen-specific T cell responses, and the effect of TCM Curcumin-analog C1 and Tripterygium wilfordii Hook F-derived Celastrol. We found that although fibrillar α-syn did not induce significant inflammatory or T cell-mediating cytokines, robust pro-inflammatory T cell responses were found by co-culturing fibrillar α-syn-pulsed DCs with α-syn-specific CD4+ T cells. Celastrol, but not C1, reduced the onset of pro-inflammatory T cell differentiation, through promoting interaction of endosomal, amphisomal, and autophagic vesicles with fibrillar α-syn, which likely lead to its degradation and less antigen peptides available for presentation and T cell recognition. In conclusion, regulating the intracellular trafficking/processing of α-syn by DCs can be a potential approach to control the progression of PD, in which Celastrol is a potential candidate to accomplish this.
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Affiliation(s)
- Lam Ng
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Xiaohui Wang
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Chuanbin Yang
- Mr. & Mrs. Ko Chi Ming Center for Parkinson Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- Department of Geriatrics, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Chengfu Su
- Mr. & Mrs. Ko Chi Ming Center for Parkinson Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Min Li
- Mr. & Mrs. Ko Chi Ming Center for Parkinson Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- *Correspondence: Allen Ka Loon Cheung, ; Min Li,
| | - Allen Ka Loon Cheung
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- *Correspondence: Allen Ka Loon Cheung, ; Min Li,
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8
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Toulmin SA, Bhadiadra C, Paris AJ, Lin JH, Katzen J, Basil MC, Morrisey EE, Worthen GS, Eisenlohr LC. Type II alveolar cell MHCII improves respiratory viral disease outcomes while exhibiting limited antigen presentation. Nat Commun 2021; 12:3993. [PMID: 34183650 PMCID: PMC8239023 DOI: 10.1038/s41467-021-23619-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 05/05/2021] [Indexed: 02/06/2023] Open
Abstract
Type II alveolar cells (AT2s) are critical for basic respiratory homeostasis and tissue repair after lung injury. Prior studies indicate that AT2s also express major histocompatibility complex class II (MHCII) molecules, but how MHCII expression by AT2s is regulated and how it contributes to host defense remain unclear. Here we show that AT2s express high levels of MHCII independent of conventional inflammatory stimuli, and that selective loss of MHCII from AT2s in mice results in modest worsening of respiratory virus disease following influenza and Sendai virus infections. We also find that AT2s exhibit MHCII presentation capacity that is substantially limited compared to professional antigen presenting cells. The combination of constitutive MHCII expression and restrained antigen presentation may position AT2s to contribute to lung adaptive immune responses in a measured fashion, without over-amplifying damaging inflammation.
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Affiliation(s)
- Sushila A. Toulmin
- grid.239552.a0000 0001 0680 8770Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Chaitali Bhadiadra
- grid.239552.a0000 0001 0680 8770Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Andrew J. Paris
- grid.25879.310000 0004 1936 8972Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Jeffrey H. Lin
- grid.25879.310000 0004 1936 8972Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Jeremy Katzen
- grid.25879.310000 0004 1936 8972Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Maria C. Basil
- grid.25879.310000 0004 1936 8972Department of Medicine, Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA USA
| | - Edward E. Morrisey
- grid.25879.310000 0004 1936 8972Department of Medicine, Penn-CHOP Lung Biology Institute, University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Penn Institute for Regenerative Medicine, Perelman School of Medicine, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - G. Scott Worthen
- grid.25879.310000 0004 1936 8972Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA ,grid.239552.a0000 0001 0680 8770Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Laurence C. Eisenlohr
- grid.239552.a0000 0001 0680 8770Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
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9
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Partnering for the major histocompatibility complex class II and antigenic determinant requires flexibility and chaperons. Curr Opin Immunol 2021; 70:112-121. [PMID: 34146954 DOI: 10.1016/j.coi.2021.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
Cytotoxic, or helper T cells recognize antigen via T cell receptors (TCRs) that can see their target antigen as short sequences of peptides bound to the groove of proteins of major histocompatibility complex (MHC) class I, and class II respectively. For MHC class II epitope selection from exogenous pathogens or self-antigens, participation of several accessory proteins, molecular chaperons, processing enzymes within multiple vesicular compartments is necessary. A major contributing factor is the MHC class II structure itself that uniquely offers a dynamic and flexible groove essential for epitope selection. In this review, I have taken a historical perspective focusing on the flexibility of the MHC II molecules as the driving force in determinant selection and interactions with the accessory molecules in antigen processing, HLA-DM and HLA-DO.
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10
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Mayer RL, Impens F. Immunopeptidomics for next-generation bacterial vaccine development. Trends Microbiol 2021; 29:1034-1045. [PMID: 34030969 DOI: 10.1016/j.tim.2021.04.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance is an increasing global threat and alternative treatments substituting failing antibiotics are urgently needed. Vaccines are recognized as highly effective tools to mitigate antimicrobial resistance; however, the selection of bacterial antigens as vaccine candidates remains challenging. In recent years, advances in mass spectrometry-based proteomics have led to the development of so-called immunopeptidomics approaches that allow the untargeted discovery of bacterial epitopes that are presented on the surface of infected cells. Especially for intracellular bacterial pathogens, immunopeptidomics holds great promise to uncover antigens that can be encoded in viral vector- or nucleic acid-based vaccines. This review provides an overview of immunopeptidomics studies on intracellular bacterial pathogens and considers future directions and challenges in advancing towards next-generation vaccines.
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Affiliation(s)
- Rupert L Mayer
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Proteomics Core, VIB, Ghent, Belgium
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Proteomics Core, VIB, Ghent, Belgium.
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11
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Pertseva M, Gao B, Neumeier D, Yermanos A, Reddy ST. Applications of Machine and Deep Learning in Adaptive Immunity. Annu Rev Chem Biomol Eng 2021; 12:39-62. [PMID: 33852352 DOI: 10.1146/annurev-chembioeng-101420-125021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Adaptive immunity is mediated by lymphocyte B and T cells, which respectively express a vast and diverse repertoire of B cell and T cell receptors and, in conjunction with peptide antigen presentation through major histocompatibility complexes (MHCs), can recognize and respond to pathogens and diseased cells. In recent years, advances in deep sequencing have led to a massive increase in the amount of adaptive immune receptor repertoire data; additionally, proteomics techniques have led to a wealth of data on peptide-MHC presentation. These large-scale data sets are now making it possible to train machine and deep learning models, which can be used to identify complex and high-dimensional patterns in immune repertoires. This article introduces adaptive immune repertoires and machine and deep learning related to biological sequence data and then summarizes the many applications in this field, which span from predicting the immunological status of a host to the antigen specificity of individual receptors and the engineering of immunotherapeutics.
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Affiliation(s)
- Margarita Pertseva
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; .,Life Science Zurich Graduate School, ETH Zurich and University of Zurich, 8006 Zurich, Switzerland
| | - Beichen Gao
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland;
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland;
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; .,Department of Pathology and Immunology, University of Geneva, 1205 Geneva, Switzerland.,Department of Biology, Institute of Microbiology and Immunology, ETH Zurich, 8093 Zurich, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland;
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12
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Soloviova K, Fox EC, Dalton JP, Caffrey CR, Davies SJ. A secreted schistosome cathepsin B1 cysteine protease and acute schistosome infection induce a transient T helper 17 response. PLoS Negl Trop Dis 2019; 13:e0007070. [PMID: 30653492 PMCID: PMC6353221 DOI: 10.1371/journal.pntd.0007070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 01/30/2019] [Accepted: 12/11/2018] [Indexed: 12/11/2022] Open
Abstract
The natural history of schistosome infection in the mammalian host is determined by CD4+ T helper responses mounted against different parasite life cycle stages. A T helper 2 (TH2) response to schistosome eggs is required for host survival and establishment of chronic infection. However, a TH2 cell-derived cytokine also contributes to an immune milieu that is conducive to schistosome growth and development. Thus, the same responses that allow for host survival have been co-opted by schistosomes to facilitate parasite development and transmission, underscoring the significance of CD4+ T cell responses to both worms and eggs in the natural history of schistosome infection. Here we show that a cathepsin B1 cysteine protease secreted by schistosome worms not only induces TH2 responses, but also TH1 and TH17 responses, by a mechanism that is dependent on the proteolytic activity of the enzyme. Further investigation revealed that, in addition to the expected TH1 and TH2 responses, acute schistosome infection also induces a transient TH17 response that is rapidly down-regulated at the onset of oviposition. TH17 responses are implicated in the development of severe egg-induced pathology. The regulation of worm-induced TH17 responses during acute infection could therefore influence the expression of high and low pathology states as infection progresses. Schistosomiasis, a neglected tropical disease caused by parasites of the genus Schistosoma, is prevalent throughout the developing world, with more than 230 million people infected. Left untreated, schistosome infection may cause relatively mild disease with some morbidity, or, in a minority of cases, result in severe pathology and death. These variable outcomes are recapitulated in animal models, where the natural history of schistosome infection is profoundly influenced by the responses of host CD4+ T helper cells. Type 2 CD4+ T cell (TH2) responses, which allow for host survival by limiting pathology, have ironically also been co-opted by schistosomes to promote parasite development. On the other hand, TH17 responses have been implicated in the development of severe pathology, in both experimentally infected animals and naturally infected humans. Here we show that a schistosome proteolytic enzyme (SmCB1), produced in the parasite gut and released into the bloodstream, induces both TH2 and TH17 responses by a mechanism that requires the enzyme’s inherent proteolytic activity. Further investigation revealed that acute schistosome infection also induces a transient TH17 response that is rapidly down-regulated once parasite egg-laying commences. Regulation of TH17 responses during early infection may help determine whether mild or severe pathology develops as the infection progresses.
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Affiliation(s)
- Kateryna Soloviova
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Ellen C. Fox
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - John P. Dalton
- School of Biological Sciences, Medical Biology Centre, Queen’s University Belfast, Northern Ireland, United Kingdom
| | - Conor R. Caffrey
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Stephen J. Davies
- Department of Microbiology and Immunology, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- * E-mail:
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13
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Čaval T, Zhu J, Tian W, Remmelzwaal S, Yang Z, Clausen H, Heck AJR. Targeted Analysis of Lysosomal Directed Proteins and Their Sites of Mannose-6-phosphate Modification. Mol Cell Proteomics 2019; 18:16-27. [PMID: 30237200 PMCID: PMC6317476 DOI: 10.1074/mcp.ra118.000967] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/20/2018] [Indexed: 12/25/2022] Open
Abstract
Mannose-6-phosphate (M6P) is a distinctive post-translational modification critical for trafficking of lysosomal acid hydrolases into the lysosome. Improper trafficking into the lysosome, and/or lack of certain hydrolases, results in a toxic accumulation of their substrates within the lysosomes. To gain insight into the enzymes destined to the lysosome these glycoproteins can be distinctively enriched and studied using their unique M6P tag. Here we demonstrate, by adapting a protocol optimized for the enrichment of phosphopeptides using Fe3+-IMAC chromatography, that proteome-wide M6P glycopeptides can be selectively enriched and subsequently analyzed by mass spectrometry, taking advantage of exclusive phosphomannose oxonium fragment marker ions. As proof-of-concept of this protocol, applying it to HeLa cells, we identified hundreds of M6P-modified glycopeptides on 35 M6P-modified glycoproteins. We next targeted CHO cells, either wild-type or cells deficient in Acp2 and Acp5, which are acid phosphatases targeting M6P. In the KO CHO cells we observed a 20-fold increase of the abundance of the M6P-modification on endogenous CHO glycoproteins but also on the recombinantly over-expressed lysosomal human alpha-galactosidase. We conclude that our approach could thus be of general interest for characterization of M6P glycoproteomes as well as characterization of lysosomal enzymes used as treatment in enzyme replacement therapies targeting lysosomal storage diseases.
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Affiliation(s)
- Tomislav Čaval
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands;; §Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jing Zhu
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands;; §Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Weihua Tian
- ¶Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Faculty of Health Sciences, Nørre Alle 20, DK-2200 Copenhagen N, Denmark
| | - Sanne Remmelzwaal
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands;; §Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Zhang Yang
- ¶Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Faculty of Health Sciences, Nørre Alle 20, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- ¶Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Faculty of Health Sciences, Nørre Alle 20, DK-2200 Copenhagen N, Denmark
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands;; §Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands;.
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14
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Maschalidi S, Nunes-Hasler P, Nascimento CR, Sallent I, Lannoy V, Garfa-Traore M, Cagnard N, Sepulveda FE, Vargas P, Lennon-Duménil AM, van Endert P, Capiod T, Demaurex N, Darrasse-Jèze G, Manoury B. UNC93B1 interacts with the calcium sensor STIM1 for efficient antigen cross-presentation in dendritic cells. Nat Commun 2017; 8:1640. [PMID: 29158474 PMCID: PMC5696382 DOI: 10.1038/s41467-017-01601-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 10/02/2017] [Indexed: 11/25/2022] Open
Abstract
Dendritic cells (DC) have the unique ability to present exogenous antigens via the major histocompatibility complex class I pathway to stimulate naive CD8+ T cells. In DCs with a non-functional mutation in Unc93b1 (3d mutation), endosomal acidification, phagosomal maturation, antigen degradation, antigen export to the cytosol and the function of the store-operated-Ca2+-entry regulator STIM1 are impaired. These defects result in compromised antigen cross-presentation and anti-tumor responses in 3d-mutated mice. Here, we show that UNC93B1 interacts with the calcium sensor STIM1 in the endoplasmic reticulum, a critical step for STIM1 oligomerization and activation. Expression of a constitutively active STIM1 mutant, which no longer binds UNC93B1, restores antigen degradation and cross-presentation in 3d-mutated DCs. Furthermore, ablation of STIM1 in mouse and human cells leads to a decrease in cross-presentation. Our data indicate that the UNC93B1 and STIM1 cooperation is important for calcium flux and antigen cross-presentation in DCs. STIM proteins sense Ca2+ depletion in the ER and activate store-operated Ca2+ entry in response, a process associated with dendritic cell (DC) functions. Here, the authors show that optimal antigen cross-presentation in DCs requires the association of the chaperone molecule UNC93B1 with STIM1.
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Affiliation(s)
- Sophia Maschalidi
- INSERM UMR1163, Laboratory of Normal and Pathological Homeostasis of the Immune System, Imagine Institute, 75015, Paris, France.,Faculté de médecine Paris Descartes, Université Paris Descartes, 75015, Paris, France
| | - Paula Nunes-Hasler
- Department of Cell Physiology and Metabolism, University of Geneva, CH-1211, Geneva, Switzerland
| | - Clarissa R Nascimento
- Faculté de médecine Paris Descartes, Université Paris Descartes, 75015, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Unité 1151, 75015, Paris, France.,Centre National de la Recherche Scientifique, UMR 8253, 75015, Paris, France
| | - Ignacio Sallent
- Faculté de médecine Paris Descartes, Université Paris Descartes, 75015, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Unité 1151, 75015, Paris, France.,Centre National de la Recherche Scientifique, UMR 8253, 75015, Paris, France
| | - Valérie Lannoy
- Faculté de médecine Paris Descartes, Université Paris Descartes, 75015, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Unité 1151, 75015, Paris, France.,Centre National de la Recherche Scientifique, UMR 8253, 75015, Paris, France
| | - Meriem Garfa-Traore
- Faculté de médecine Paris Descartes, Université Paris Descartes, 75015, Paris, France.,Cell Imaging and Bioinformatic Platform, INSERM US24 Structure Federative de Recherche Necker, 75015, Paris, France
| | - Nicolas Cagnard
- Faculté de médecine Paris Descartes, Université Paris Descartes, 75015, Paris, France.,Cell Imaging and Bioinformatic Platform, INSERM US24 Structure Federative de Recherche Necker, 75015, Paris, France
| | - Fernando E Sepulveda
- INSERM UMR1163, Laboratory of Normal and Pathological Homeostasis of the Immune System, Imagine Institute, 75015, Paris, France.,Faculté de médecine Paris Descartes, Université Paris Descartes, 75015, Paris, France
| | - Pablo Vargas
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, UMR 144, 75005, Paris, France.,Institut Pierre-Gilles de Genes, PSL Research University, 75005, Paris, France
| | - Ana-Maria Lennon-Duménil
- Institut National de la Santé et de la Recherché Médicale, Unité 932, Institut Curie, PSL Research University, 75005, Paris, France
| | - Peter van Endert
- Faculté de médecine Paris Descartes, Université Paris Descartes, 75015, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Unité 1151, 75015, Paris, France.,Centre National de la Recherche Scientifique, UMR 8253, 75015, Paris, France
| | - Thierry Capiod
- Faculté de médecine Paris Descartes, Université Paris Descartes, 75015, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Unité 1151, 75015, Paris, France.,Centre National de la Recherche Scientifique, UMR 8253, 75015, Paris, France
| | - Nicolas Demaurex
- Department of Cell Physiology and Metabolism, University of Geneva, CH-1211, Geneva, Switzerland
| | - Guillaume Darrasse-Jèze
- Faculté de médecine Paris Descartes, Université Paris Descartes, 75015, Paris, France.,Institut National de la Santé et de la Recherche Médicale, Unité 1151, 75015, Paris, France.,Centre National de la Recherche Scientifique, UMR 8253, 75015, Paris, France
| | - Bénédicte Manoury
- Faculté de médecine Paris Descartes, Université Paris Descartes, 75015, Paris, France. .,Institut National de la Santé et de la Recherche Médicale, Unité 1151, 75015, Paris, France. .,Centre National de la Recherche Scientifique, UMR 8253, 75015, Paris, France.
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15
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Regulation of inflammation by microbiota interactions with the host. Nat Immunol 2017; 18:851-860. [PMID: 28722709 DOI: 10.1038/ni.3780] [Citation(s) in RCA: 411] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/30/2017] [Indexed: 12/13/2022]
Abstract
The study of the intestinal microbiota has begun to shift from cataloging individual members of the commensal community to understanding their contributions to the physiology of the host organism in health and disease. Here, we review the effects of the microbiome on innate and adaptive immunological players from epithelial cells and antigen-presenting cells to innate lymphoid cells and regulatory T cells. We discuss recent studies that have identified diverse microbiota-derived bioactive molecules and their effects on inflammation within the intestine and distally at sites as anatomically remote as the brain. Finally, we highlight new insights into how the microbiome influences the host response to infection, vaccination and cancer, as well as susceptibility to autoimmune and neurodegenerative disorders.
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16
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Pauwels AM, Trost M, Beyaert R, Hoffmann E. Patterns, Receptors, and Signals: Regulation of Phagosome Maturation. Trends Immunol 2017; 38:407-422. [PMID: 28416446 PMCID: PMC5455985 DOI: 10.1016/j.it.2017.03.006] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/18/2017] [Accepted: 03/21/2017] [Indexed: 12/13/2022]
Abstract
Recognition of microbial pathogens and dead cells and their phagocytic uptake by specialized immune cells are essential to maintain host homeostasis. Phagosomes undergo fusion and fission events with endosomal and lysosomal compartments, a process called ‘phagosome maturation’, which leads to the degradation of the phagosomal content. However, many phagocytic cells also act as antigen-presenting cells and must balance degradation and peptide preservation. Emerging evidence indicates that receptor engagement by phagosomal cargo, as well as inflammatory mediators and cellular activation affect many aspects of phagosome maturation. Unsurprisingly, pathogens have developed strategies to hijack this machinery, thereby interfering with host immunity. Here, we highlight progress in this field, summarize findings on the impact of immune signals, and discuss consequences for pathogen elimination. Self and non-self immune signals are able to delay or accelerate phagosome maturation, and their effects are dependent on the phagocytic cell type, duration of stimulation, and whether the stimulus is particle bound or present in the cellular environment. Acceleration of phagosome maturation enhances pathogen killing, while a delay in phagosome maturation preserves antigenic peptides for presentation to T cells and to initiate adaptive immune responses. Besides its functions in pathogen killing and antigen presentation, the phagosome also functions as a signaling platform and interacts with other cell organelles. Some pathogens are able to arrest phagosome maturation to enhance their intraphagosomal survival and replication or to promote phagosomal escape. The latex bead phagocytosis model system combined with mass spectrometry is a powerful technique to analyze changes in the phagosomal proteome.
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Affiliation(s)
- Anne-Marie Pauwels
- Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Matthias Trost
- MRC Protein Phosphorylation Unit, University of Dundee, Dundee, UK; Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Rudi Beyaert
- Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Eik Hoffmann
- Unit of Molecular Signal Transduction in Inflammation, VIB Center for Inflammation Research, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Current address: Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
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17
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Sadegh-Nasseri S. A step-by-step overview of the dynamic process of epitope selection by major histocompatibility complex class II for presentation to helper T cells. F1000Res 2016; 5. [PMID: 27347387 PMCID: PMC4902097 DOI: 10.12688/f1000research.7664.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/27/2016] [Indexed: 11/25/2022] Open
Abstract
T cell antigen receptors (TCRs) expressed on cytotoxic or helper T cells can only see their specific target antigen as short sequences of peptides bound to the groove of proteins of major histocompatibility complex (MHC) class I, and class II respectively. In addition to the many steps, several participating proteins, and multiple cellular compartments involved in the processing of antigens, the MHC structure, with its dynamic and flexible groove, has perfectly evolved as the underlying instrument for epitope selection. In this review, I have taken a step-by-step, and rather historical, view to describe antigen processing and determinant selection, as we understand it today, all based on decades of intense research by hundreds of laboratories.
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18
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Vasanth G, Kiron V, Kulkarni A, Dahle D, Lokesh J, Kitani Y. A Microbial Feed Additive Abates Intestinal Inflammation in Atlantic Salmon. Front Immunol 2015; 6:409. [PMID: 26347738 PMCID: PMC4541333 DOI: 10.3389/fimmu.2015.00409] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 07/27/2015] [Indexed: 01/01/2023] Open
Abstract
The efficacy of a microbial feed additive (Bactocell®) in countering intestinal inflammation in Atlantic salmon was examined in this study. Fish were fed either the additive-coated feed (probiotic) or feed without it (control). After an initial 3-week feeding, an inflammatory condition was induced by anally intubating all the fish with oxazolone. The fish were offered the feeds for 3 more weeks. Distal intestine from the groups was obtained at 4 h, 24 h, and 3 weeks, after oxazolone treatment. Inflammatory responses were prominent in both groups at 24 h, documented by changes in intestinal micromorphology, expression of inflammation-related genes, and intestinal proteome. The control group was characterized by edema, widening of intestinal villi and lamina propria, infiltration of granulocytes and lymphocytes, and higher expression of genes related to inflammatory responses, mul1b, il1b, tnfa, ifng, compared to the probiotic group or other time points of the control group. Further, the protein expression in the probiotic group at 24 h after inducing inflammation revealed five differentially regulated proteins – Calr, Psma5, Trp1, Ctsb, and Naga. At 3 weeks after intubation, the inflammatory responses subsided in the probiotic group. The findings provide evidence that the microbial additive contributes to intestinal homeostasis in Atlantic salmon.
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Affiliation(s)
- Ghana Vasanth
- Faculty of Biosciences and Aquaculture, University of Nordland , Bodø , Norway
| | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, University of Nordland , Bodø , Norway
| | - Amod Kulkarni
- Faculty of Biosciences and Aquaculture, University of Nordland , Bodø , Norway
| | - Dalia Dahle
- Faculty of Biosciences and Aquaculture, University of Nordland , Bodø , Norway
| | - Jep Lokesh
- Faculty of Biosciences and Aquaculture, University of Nordland , Bodø , Norway
| | - Yoichiro Kitani
- Faculty of Biosciences and Aquaculture, University of Nordland , Bodø , Norway
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19
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Merkenschlager J, Kassiotis G. Narrowing the Gap: Preserving Repertoire Diversity Despite Clonal Selection during the CD4 T Cell Response. Front Immunol 2015; 6:413. [PMID: 26322045 PMCID: PMC4531291 DOI: 10.3389/fimmu.2015.00413] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/28/2015] [Indexed: 01/14/2023] Open
Abstract
T cell immunity relies on the generation and maintenance of a diverse repertoire of T cell antigen receptors (TCRs). The strength of signaling emanating from the TCR dictates the fate of T cells during development, as well as during the immune response. Whereas development of new T cells in the thymus increases the available TCR repertoire, clonal selection during the immune response narrows TCR diversity through the outgrowth of clonotypes with the fittest TCR. To ensure maintenance of TCR diversity in the antigen-selected repertoire, specific mechanisms can be envisaged that facilitate the participation of T cell clonotypes with less than best fit TCRs. Here, we summarize the evidence for the existence of such mechanisms that can prevent the loss of diversity. A number of T cell-autonomous or extrinsic factors can reverse clonotypic hierarchies set by TCR affinity for given antigen. Although not yet complete, understanding of these factors and their mechanism of action will be critical in interventional attempts to mold the antigen-selected TCR repertoire.
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Affiliation(s)
| | - George Kassiotis
- Mill Hill Laboratory, The Francis Crick Institute , London , UK ; Department of Medicine, Faculty of Medicine, Imperial College London , London , UK
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20
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Sadegh-Nasseri S, Kim A. MHC Class II Auto-Antigen Presentation is Unconventional. Front Immunol 2015; 6:372. [PMID: 26257739 PMCID: PMC4510428 DOI: 10.3389/fimmu.2015.00372] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/06/2015] [Indexed: 01/09/2023] Open
Abstract
Antigen presentation is highly critical in adoptive immunity. Only by interacting with antigens presented by major histocompatibility complex class II molecules, helper T cells can be stimulated to fight infections or diseases. The degradation of a full protein into small peptide fragments bound to class II molecules is a dynamic, lengthy process consisting of many steps and chaperons. Deregulation in any step of antigen processing could lead to the development of self-reactive T cells or defective immune response to pathogens. Indeed, human leukocyte antigens class II genes are the predominant contributors to susceptibility to autoimmune diseases. Conventional antigen-processing calls for internalization of extracellular antigens followed by processing and epitope selection within antigen-processing subcellular compartments, enriched with all necessary accessory molecules, processing enzymes, and proper pH and denaturing conditions. However, recent data examining the temporal relationship between antigen uptakes, processing, and epitope selection revealed unexpected characteristics for auto-antigenic epitopes, which were not shared with antigenic epitopes from pathogens. This review provides a discussion of the relevance of these findings to the mechanisms of autoimmunity.
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Affiliation(s)
| | - AeRyon Kim
- Department of Pathology, Johns Hopkins School of Medicine , Baltimore, MD , USA
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21
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Wang F, Muller S. Manipulating autophagic processes in autoimmune diseases: a special focus on modulating chaperone-mediated autophagy, an emerging therapeutic target. Front Immunol 2015; 6:252. [PMID: 26042127 PMCID: PMC4437184 DOI: 10.3389/fimmu.2015.00252] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 05/07/2015] [Indexed: 12/14/2022] Open
Abstract
Autophagy, a constitutive intracellular degradation pathway, displays essential role in the homeostasis of immune cells, antigen processing and presentation, and many other immune processes. Perturbation of autophagy has been shown to be related to several autoimmune syndromes, including systemic lupus erythematosus. Therefore, modulating autophagy processes appears most promising for therapy of such autoimmune diseases. Autophagy can be said non-selective or selective; it is classified into three main forms, namely macroautophagy, microautophagy, and chaperone-mediated autophagy (CMA), the former process being by far the most intensively investigated. The role of CMA remains largely underappreciated in autoimmune diseases, even though CMA has been claimed to play pivotal functions into major histocompatibility complex class II-mediated antigen processing and presentation. Therefore, hereby, we give a special focus on CMA as a therapeutic target in autoimmune diseases, based in particular on our most recent experimental results where a phosphopeptide modulates lupus disease by interacting with CMA regulators. We propose that specifically targeting lysosomes and lysosomal pathways, which are central in autophagy processes and seem to be altered in certain autoimmune diseases such as lupus, could be an innovative approach of efficient and personalized treatment.
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Affiliation(s)
- Fengjuan Wang
- Immunopathology and Therapeutic Chemistry/Laboratory of Excellence MEDALIS, CNRS, Institut de Biologie Moléculaire et Cellulaire , Strasbourg , France
| | - Sylviane Muller
- Immunopathology and Therapeutic Chemistry/Laboratory of Excellence MEDALIS, CNRS, Institut de Biologie Moléculaire et Cellulaire , Strasbourg , France ; University of Strasbourg Institute for Advanced Study , Strasbourg , France
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22
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Kim A, Sadegh-Nasseri S. Determinants of immunodominance for CD4 T cells. Curr Opin Immunol 2015; 34:9-15. [PMID: 25576665 DOI: 10.1016/j.coi.2014.12.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/17/2014] [Indexed: 10/24/2022]
Abstract
The term immunodominance was originally defined as a restricted T cell response to a short peptide sequence derived from a given protein. The question of what determines immunodominance has been a longstanding battle for the past two decades. Hundreds of papers have been written on different aspects of epitope selection during antigen processing documenting the complexity of the process. Antigen processing machinery involves several accessory molecules and chaperons coevolved with proteins of Major Histocompatibility Complex (MHC) molecules that each plays its part in epitope selection. These molecules are targeted to specialized vesicular compartments that also accommodate antigen processing enzymes called cathepsins. Within the antigen processing compartments, highly regulated pH gradient and reducing conditions and enzymes necessary for denaturation of the antigens are available and function to optimize processing of antigen and selection of the fittest for transport to the cell membrane and presentation to T cells. Despite the complexity, a cell free reductionist antigen processing system was recently reported that included only few purified proteins, but was shown to process and select physiologically relevant epitopes from full length protein antigens. Due to its minimalist nature the system has been quite helpful in dissecting the factors that contribute to epitope selection during antigen processing. In this review, we would summarize and highlight models that may explain how the dominant epitope may be selected for presentation to CD4(+) helper T cells.
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Affiliation(s)
- AeRyon Kim
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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23
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van Kasteren SI, Overkleeft HS. Endo-lysosomal proteases in antigen presentation. Curr Opin Chem Biol 2014; 23:8-15. [PMID: 25213682 DOI: 10.1016/j.cbpa.2014.08.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 02/04/2023]
Abstract
Endo-lysosomal proteases have long been attractive, yet elusive, targets for medicinal chemistry. They have found to play key roles in health and disease; with protease under- and over-activity having been implicated in cancer, osteoporosis and Alzheimer's disease. Here we will discuss their role in the adaptive immune response. The crucial roles of these enzymes multiple processes in antigen presentation will be discussed: from activating MHC-II receptors, to the production of epitopes from antigens and the activation of Toll-like receptors. The early efforts at pharmacological interventions in these pathways will also be discussed.
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Affiliation(s)
- Sander I van Kasteren
- Division of Chemical Biology, Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratory, The Netherlands.
| | - Herman S Overkleeft
- Division of Chemical Biology, Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratory, The Netherlands
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24
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Abstract
Macrophages are capable of assuming distinct, meta-stable, functional phenotypes in response to environmental cues-a process referred to as macrophage polarization. The identity and plasticity of polarized macrophage subsets as well as their functions in the maintenance of homeostasis and the progression of various pathologies have become areas of intense interest. Yet, the mechanisms by which they achieve subset-specific functions at the cellular level remain unclear. It is becoming apparent that phagocytosis and phagosome maturation differ depending on the polarization of macrophages. This minireview summarizes recent progress in this field, highlighting developing trends and discussing the molecular mechanisms that underlie subset-specific functions.
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Affiliation(s)
- Johnathan Canton
- Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
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