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Sharma M, Niu L, Zhang X, Huang S. Comparative transcriptomes reveal pro-survival and cytotoxic programs of mucosal-associated invariant T cells upon Bacillus Calmette-Guérin stimulation. Front Cell Infect Microbiol 2023; 13:1134119. [PMID: 37091679 PMCID: PMC10116416 DOI: 10.3389/fcimb.2023.1134119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/15/2023] [Indexed: 04/08/2023] Open
Abstract
Mucosal-associated invariant T (MAIT) cells are protective against tuberculous and non-tuberculous mycobacterial infections with poorly understood mechanisms. Despite an innate-like nature, MAIT cell responses remain heterogeneous in bacterial infections. To comprehensively characterize MAIT activation programs responding to different bacteria, we stimulated MAIT cells with E. coli to compare with Bacillus Calmette-Guérin (BCG), which remains the only licensed vaccine and a feasible tool for investigating anti-mycobacterial immunity in humans. Upon sequencing mRNA from the activated and inactivated CD8+ MAIT cells, results demonstrated the altered MAIT cell gene profiles by each bacterium with upregulated expression of activation markers, transcription factors, cytokines, and cytolytic mediators crucial in anti-mycobacterial responses. Compared with E. coli, BCG altered more MAIT cell genes to enhance cell survival and cytolysis. Flow cytometry analyses similarly displayed a more upregulated protein expression of B-cell lymphoma 2 and T-box transcription factor Eomesodermin in BCG compared to E.coli stimulations. Thus, the transcriptomic program and protein expression of MAIT cells together displayed enhanced pro-survival and cytotoxic programs in response to BCG stimulation, supporting BCG induces cell-mediated effector responses of MAIT cells to fight mycobacterial infections.
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Affiliation(s)
| | | | | | - Shouxiong Huang
- Department of Environmental and Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
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2
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Wang L, Li X, Yang S, Chen X, Li J, Wang S, Zhang M, Zheng Z, Zhou J, Wang L, Wu Y. Proteomic identification of MHC class I-associated peptidome derived from non-obese diabetic mouse thymus and pancreas. J Proteomics 2023; 270:104746. [PMID: 36210013 DOI: 10.1016/j.jprot.2022.104746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/17/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
The peptides repertoire presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC I-associated peptidome (MIP), which regulates thymus development, peripheral survival and function during lifetime of CD8+ T cells. Type 1 diabetes (T1D) is an organ-specific autoimmune disease caused by pancreatic β cells destruction mediated primarily by autoreactive CD8+ T cells. Non-obese diabetic (NOD) mouse is an important animal model of T1D. Here, we deeply analyzed the MIP derived from NOD mice thymus and pancreas, and demonstrated that the thymus MIP source proteins partially shared with the MIP source proteins derived from NOD mice pancreas and β cell line. One H-2Kd restricted peptide SLC35B126-34 which was shared by MIP derived from both NOD mice pancreatic tissues and islet β-cell line, but absent in MIP from NOD thymus tissues, showed ability to stimulate IFN-γ secretion and proliferation of NOD mice splenic CD8+ T cells. The global view of the MHC I-associated self-peptides repertoire in the thymus and pancreas of NOD mice may serve as a biological reference to identify potential autoantigens targeted by autoreactive CD8+ T cells in T1D. Data are available via ProteomeXchange with identifier PXD031966. SIGNIFICANCE: The peptides repertoire presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC I-associated peptidome (MIP). The MIP presented by thymic antigen presenting cells (APCs) is crucial for shaping CD8+ T cell repertoire and self-tolerance, while the MIP presented by peripheral tissues and organs is not only involved in maintaining periphery CD8+ T cell survival and homeostasis, but also mediates immune surveillance and autoimmune responses of CD8+ T cells under pathological conditions. Type 1 diabetes (T1D) is an organ-specific autoimmune disease caused by the destruction of pancreatic β cells, mediated primarily by autoreactive CD8+ T cells. Non-obese diabetic (NOD) mouse is one of important animal models of spontaneous autoimmune diabetes that shares several key features with human T1D. The global view of the MHC I-associated self-peptides repertoire in the thymus and pancreas of NOD mice may serve as a good biological reference to identify potential autoantigens targeted by autoreactive CD8+ T cells in T1D. It has great significance for further clarifying the immune recognition and effect mechanism of autoreactive CD8+ T cells in the pathogenesis of T1D, and then developing antigen-specific immune intervention strategies.
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Affiliation(s)
- Lina Wang
- Department of Immunology, Medical College of Qingdao University, Qingdao, Shandong 266071, China; Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China; Department of Immunology, College of Basic Medicine, Weifang Medical University, Weifang 261053, China
| | - Xiangqian Li
- Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Shushu Yang
- Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Xiaoling Chen
- Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Jie Li
- Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Shufeng Wang
- Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Mengjun Zhang
- Department of Pharmaceutical Analysis, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Zhengni Zheng
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Jie Zhou
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Li Wang
- Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China.
| | - Yuzhang Wu
- Department of Immunology, Medical College of Qingdao University, Qingdao, Shandong 266071, China; Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China.
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3
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Hensen L, Illing PT, Rowntree LC, Davies J, Miller A, Tong SYC, Habel JR, van de Sandt CE, Flanagan K, Purcell AW, Kedzierska K, Clemens EB. T Cell Epitope Discovery in the Context of Distinct and Unique Indigenous HLA Profiles. Front Immunol 2022; 13:812393. [PMID: 35603215 PMCID: PMC9121770 DOI: 10.3389/fimmu.2022.812393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
CD8+ T cells are a pivotal part of the immune response to viruses, playing a key role in disease outcome and providing long-lasting immunity to conserved pathogen epitopes. Understanding CD8+ T cell immunity in humans is complex due to CD8+ T cell restriction by highly polymorphic Human Leukocyte Antigen (HLA) proteins, requiring T cell epitopes to be defined for different HLA allotypes across different ethnicities. Here we evaluate strategies that have been developed to facilitate epitope identification and study immunogenic T cell responses. We describe an immunopeptidomics approach to sequence HLA-bound peptides presented on virus-infected cells by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Using antigen presenting cell lines that stably express the HLA alleles characteristic of Indigenous Australians, this approach has been successfully used to comprehensively identify influenza-specific CD8+ T cell epitopes restricted by HLA allotypes predominant in Indigenous Australians, including HLA-A*24:02 and HLA-A*11:01. This is an essential step in ensuring high vaccine coverage and efficacy in Indigenous populations globally, known to be at high risk from influenza disease and other respiratory infections.
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Affiliation(s)
- Luca Hensen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Patricia T. Illing
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Louise C. Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jane Davies
- Menzies School of Health Research, Darwin, NT, Australia
| | - Adrian Miller
- Indigenous Engagement, CQUniversity, Townsville, QLD, Australia
| | - Steven Y. C. Tong
- Menzies School of Health Research, Darwin, NT, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jennifer R. Habel
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Carolien E. van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Katie L. Flanagan
- Department of Infectious Diseases and Tasmanian Vaccine Trial Centre, Launceston General Hospital, Launceston, TAS, Australia
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS, Australia
- Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- *Correspondence: Katherine Kedzierska,
| | - E. Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
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Pothast CR, Dijkland RC, Thaler M, Hagedoorn RS, Kester MGD, Wouters AK, Hiemstra PS, van Hemert MJ, Gras S, Falkenburg JHF, Heemskerk MHM. SARS-CoV-2-specific CD4 + and CD8 + T cell responses can originate from cross-reactive CMV-specific T cells. eLife 2022; 11:82050. [PMID: 36408799 PMCID: PMC9822249 DOI: 10.7554/elife.82050] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/13/2022] [Indexed: 11/22/2022] Open
Abstract
Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) specific CD4+ and CD8+ T cells in SARS-CoV-2-unexposed donors has been explained by the presence of T cells primed by other coronaviruses. However, based on the relatively high frequency and prevalence of cross-reactive T cells, we hypothesized cytomegalovirus (CMV) may induce these cross-reactive T cells. Stimulation of pre-pandemic cryo-preserved peripheral blood mononuclear cells (PBMCs) with SARS-CoV-2 peptides revealed that frequencies of SARS-CoV-2-specific T cells were higher in CMV-seropositive donors. Characterization of these T cells demonstrated that membrane-specific CD4+ and spike-specific CD8+ T cells originate from cross-reactive CMV-specific T cells. Spike-specific CD8+ T cells recognize SARS-CoV-2 spike peptide FVSNGTHWF (FVS) and dissimilar CMV pp65 peptide IPSINVHHY (IPS) presented by HLA-B*35:01. These dual IPS/FVS-reactive CD8+ T cells were found in multiple donors as well as severe COVID-19 patients and shared a common T cell receptor (TCR), illustrating that IPS/FVS-cross-reactivity is caused by a public TCR. In conclusion, CMV-specific T cells cross-react with SARS-CoV-2, despite low sequence homology between the two viruses, and may contribute to the pre-existing immunity against SARS-CoV-2.
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Affiliation(s)
- Cilia R Pothast
- Department of Hematology, Leiden University Medical CenterLeidenNetherlands
| | - Romy C Dijkland
- Department of Hematology, Leiden University Medical CenterLeidenNetherlands
| | - Melissa Thaler
- Department of Medical Microbiology, Leiden University Medical CenterLeidenNetherlands
| | - Renate S Hagedoorn
- Department of Hematology, Leiden University Medical CenterLeidenNetherlands
| | - Michel GD Kester
- Department of Hematology, Leiden University Medical CenterLeidenNetherlands
| | - Anne K Wouters
- Department of Hematology, Leiden University Medical CenterLeidenNetherlands
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical CenterLeidenNetherlands
| | - Martijn J van Hemert
- Department of Medical Microbiology, Leiden University Medical CenterLeidenNetherlands
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe UniversityVictoriaAustralia,Department of Biochemistry and Molecular Biology, Monash UniversityClaytonAustralia
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Critical Review of Existing MHC I Immunopeptidome Isolation Methods. Molecules 2020; 25:molecules25225409. [PMID: 33228004 PMCID: PMC7699222 DOI: 10.3390/molecules25225409] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/06/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022] Open
Abstract
Major histocompatibility complex class I (MHC I) plays a crucial role in the development of adaptive immune response in vertebrates. MHC molecules are cell surface protein complexes loaded with short peptides and recognized by the T-cell receptors (TCR). Peptides associated with MHC are named immunopeptidome. The MHC I immunopeptidome is produced by the proteasome degradation of intracellular proteins. The knowledge of the immunopeptidome repertoire facilitates the creation of personalized antitumor or antiviral vaccines. A huge number of publications on the immunopeptidome diversity of different human and mouse biological samples-plasma, peripheral blood mononuclear cells (PBMCs), and solid tissues, including tumors-appeared in the scientific journals in the last decade. Significant immunopeptidome identification efficiency was achieved by advances in technology: the immunoprecipitation of MHC and mass spectrometry-based approaches. Researchers optimized common strategies to isolate MHC-associated peptides for individual tasks. They published many protocols with differences in the amount and type of biological sample, amount of antibodies, type and amount of insoluble support, methods of post-fractionation and purification, and approaches to LC-MS/MS identification of immunopeptidome. These parameters have a large impact on the final repertoire of isolated immunopeptidome. In this review, we summarize and compare immunopeptidome isolation techniques with an emphasis on the results obtained.
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6
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Dragon AC, Zimmermann K, Nerreter T, Sandfort D, Lahrberg J, Klöß S, Kloth C, Mangare C, Bonifacius A, Tischer-Zimmermann S, Blasczyk R, Maecker-Kolhoff B, Uchanska-Ziegler B, Abken H, Schambach A, Hudecek M, Eiz-Vesper B. CAR-T cells and TRUCKs that recognize an EBNA-3C-derived epitope presented on HLA-B*35 control Epstein-Barr virus-associated lymphoproliferation. J Immunother Cancer 2020; 8:jitc-2020-000736. [PMID: 33127653 PMCID: PMC7604878 DOI: 10.1136/jitc-2020-000736] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
Background Immunosuppressive therapy or T-cell depletion in transplant patients can cause uncontrolled growth of Epstein-Barr virus (EBV)-infected B cells resulting in post-transplant lymphoproliferative disease (PTLD). Current treatment options do not distinguish between healthy and malignant B cells and are thereby often limited by severe side effects in the already immunocompromised patients. To specifically target EBV-infected B cells, we developed a novel peptide-selective chimeric antigen receptor (CAR) based on the monoclonal antibody TÜ165 which recognizes an Epstein-Barr nuclear antigen (EBNA)−3C-derived peptide in HLA-B*35 context in a T-cell receptor (TCR)-like manner. In order to attract additional immune cells to proximity of PTLD cells, based on the TÜ165 CAR, we moreover generated T cells redirected for universal cytokine-mediated killing (TRUCKs), which induce interleukin (IL)-12 release on target contact. Methods TÜ165-based CAR-T cells (CAR-Ts) and TRUCKs with inducible IL-12 expression in an all-in-one construct were generated. Functionality of the engineered cells was assessed in co-cultures with EBNA-3C-peptide-loaded, HLA-B*35-expressing K562 cells and EBV-infected B cells as PTLD model. IL-12, secreted by TRUCKs on target contact, was further tested for its chemoattractive and activating potential towards monocytes and natural killer (NK) cells. Results After co-cultivation with EBV target cells, TÜ165 CAR-Ts and TRUCKs showed an increased activation marker expression (CD137, CD25) and release of proinflammatory cytokines (interferon-γ and tumor necrosis factor-α). Moreover, TÜ165 CAR-Ts and TRUCKs released apoptosis-inducing mediators (granzyme B and perforin) and were capable to specifically lyse EBV-positive target cells. Live cell imaging revealed a specific attraction of TÜ165 CAR-Ts around EBNA-3C-peptide-loaded target cells. Of note, TÜ165 TRUCKs with inducible IL-12 showed highly improved effector functions and additionally led to recruitment of monocyte and NK cell lines. Conclusions Our results demonstrate that TÜ165 CAR-Ts recognize EBV peptide/HLA complexes in a TCR-like manner and thereby allow for recognizing an intracellular EBV target. TÜ165 TRUCKs equipped with inducible IL-12 expression responded even more effectively and released IL-12 recruited additional immune cells which are generally missing in proximity of lymphoproliferation in immunocompromised PTLD patients. This suggests a new and promising strategy to specifically target EBV-infected cells while sparing and mobilizing healthy immune cells and thereby enable control of EBV-associated lymphoproliferation.
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Affiliation(s)
- Anna Christina Dragon
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Katharina Zimmermann
- Institute for Experimental Hematology, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Thomas Nerreter
- Department of Internal Medicine II, Universitätsklinikum Würzburg, Wuerzburg, Bayern, Germany
| | - Deborah Sandfort
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Julia Lahrberg
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Stephan Klöß
- Institute of Cellular Therapeutics, Hannover Medical School, Hannover, Niedersachsen, Germany.,Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Sachsen, Germany
| | - Christina Kloth
- Institute for Experimental Hematology, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Caroline Mangare
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Agnes Bonifacius
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Sabine Tischer-Zimmermann
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Rainer Blasczyk
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Britta Maecker-Kolhoff
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Niedersachsen, Germany
| | | | - Hinrich Abken
- Regensburg Center for Interventional Immunology (RCI), Department of Genetic Immunotherapy, Universitätsklinikum Regensburg, Regensburg, Bayern, Germany
| | - Axel Schambach
- Institute for Experimental Hematology, Hannover Medical School, Hannover, Niedersachsen, Germany.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Michael Hudecek
- Department of Internal Medicine II, Universitätsklinikum Würzburg, Wuerzburg, Bayern, Germany
| | - Britta Eiz-Vesper
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hannover, Niedersachsen, Germany
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7
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Reyes-Vargas E, Barker AP, Zhou Z, He X, Jensen PE. HLA-DM catalytically enhances peptide dissociation by sensing peptide-MHC class II interactions throughout the peptide-binding cleft. J Biol Chem 2020; 295:2959-2973. [PMID: 31969393 PMCID: PMC7062162 DOI: 10.1074/jbc.ra119.010645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/13/2020] [Indexed: 11/06/2022] Open
Abstract
Human leukocyte antigen-DM (HLA-DM) is an integral component of the major histocompatibility complex class II (MHCII) antigen-processing and -presentation pathway. HLA-DM shapes the immune system by differentially catalyzing peptide exchange on MHCII molecules, thereby editing the peptide-MHCII (pMHCII) repertoire by imposing a bias on the foreign and self-derived peptide cargos that are presented on the cell surface for immune surveillance and tolerance induction by CD4+ T cells. To better understand DM selectivity, here we developed a real-time fluorescence anisotropy assay to delineate the pMHCII intrinsic stability, DM-binding affinity, and catalytic turnover, independent kinetic parameters of HLA-DM enzymatic activity. We analyzed prominent pMHCII contacts by differentiating the kinetic parameters in pMHCII homologs, observing that peptide interactions throughout the MHCII-binding cleft influence both the rate of peptide dissociation from the DM-pMHCII catalytic complex and the binding affinity of HLA-DM for a pMHCII. We show that the intrinsic stability of a pMHCII linearly correlates with DM catalytic turnover, but is nonlinearly correlated with its binding affinity. Surprisingly, interactions at the peptides N terminus up to and including MHCII position one (P1) anchor affected the catalytic turnover, suggesting that the active DM-pMHCII catalytic complex operates on pMHCII complexes with full peptide occupancy. Furthermore, interactions at the peptide C terminus modulated DM-binding affinity, suggesting distal communication between peptide interactions with the MHCII and the DM-pMHCII binding interface. Our results imply an intimate linkage between the DM-pMHCII interface and peptide-MHCII interactions throughout the peptide-binding cleft.
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Affiliation(s)
- Eduardo Reyes-Vargas
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Adam P Barker
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112; Department of Pathology, ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah 84108
| | - Zemin Zhou
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Xiao He
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112.
| | - Peter E Jensen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112; Department of Pathology, ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah 84108.
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8
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Li L, Batliwala M, Bouvier M. ERAP1 enzyme-mediated trimming and structural analyses of MHC I-bound precursor peptides yield novel insights into antigen processing and presentation. J Biol Chem 2019; 294:18534-18544. [PMID: 31601650 PMCID: PMC6901306 DOI: 10.1074/jbc.ra119.010102] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/20/2019] [Indexed: 01/07/2023] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) and ERAP2 critically shape the major histocompatibility complex I (MHC I) immunopeptidome. The ERAPs remove N-terminal residues from antigenic precursor peptides and generate optimal-length peptides (i.e. 8-10-mers) to fit into the MHC class I groove. It is therefore intriguing that MHC class I molecules can present N-terminally extended peptides on the cell surface that can elicit CD8+ T-cell responses. This observation likely reflects gaps in our understanding of how antigens are processed by the ERAP enzymes. To better understand ERAPs' function in antigen processing, here we generated a nested set of N-terminally extended 10-20-mer peptides (RA) n AAKKKYCL covalently bound to the human leukocyte antigen (HLA)-B*0801. We used X-ray crystallography, thermostability assessments, and an ERAP1-trimming assay to characterize these complexes. The X-ray structures determined at 1.40-1.65 Å resolutions revealed that the residue extensions (RA) n unexpectedly protrude out of the A pocket of HLA-B*0801, whereas the AAKKKYCL core of all peptides adopts similar, bound conformations. HLA-B*0801 residue 62 was critical to open the A pocket. We also show that HLA-B*0801 and antigenic precursor peptides form stable complexes. Finally, ERAP1-mediated trimming of the MHC I-bound peptides required a minimal length of 14 amino acids. We propose a mechanistic model explaining how ERAP1-mediated trimming of MHC I-bound peptides in cells can generate peptides of canonical as well as noncanonical lengths that still serve as stable MHC I ligands. Our results provide a framework to better understand how the ERAP enzymes influence the MHC I immunopeptidome.
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Affiliation(s)
- Lenong Li
- Department of Microbiology and Immunology, University of Illinois, Chicago, Illinois 60612
| | - Mansoor Batliwala
- Department of Microbiology and Immunology, University of Illinois, Chicago, Illinois 60612
| | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois, Chicago, Illinois 60612, To whom correspondence should be addressed:
Dept. of Microbiology and Immunology, University of Illinois at Chicago, 909 S. Wolcott Ave., Chicago, IL 60612. Tel.:
312-355-0664; E-mail:
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9
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Zhang X, Qi Y, Zhang Q, Liu W. Application of mass spectrometry-based MHC immunopeptidome profiling in neoantigen identification for tumor immunotherapy. Biomed Pharmacother 2019; 120:109542. [PMID: 31629254 DOI: 10.1016/j.biopha.2019.109542] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/04/2019] [Accepted: 10/04/2019] [Indexed: 12/15/2022] Open
Abstract
One of the challenges for cancer vaccine and adoptive T-cell-based immunotherapy is to identify the major histocompatibility complex (MHC)-associated non-self neoantigens recognized by T cells. T cell epitope in silico prediction algorithms have been widely used for neoantigen prediction; nonetheless, this platform lacks the experimental evidence of directly identification of the presented epitopes on cell surface. Currently, mass spectrometry (MS)-based proteomics is an advanced analytical technology for large-scale peptide sequencing, which has become a powerful tool for directly profiling the immunopeptidome presented by MHC molecules. Integrating with next-generation sequencing, proteogenomic analysis provides the "gold standard" for neoantigen identification at protein level. This method discovers the tumor-specific neoantigens derived from somatic mutations, proteasome splicing, noncoding RNA, and post-translational modified antigens. Herein, we review basis of antigen processing and presentation, tumor antigen classification, existing approaches for neoantigen discovery, quantitative proteomics, epitope prediction programs, and advantages and drawbacks of proteomics workflow for MHC immunopeptidome profiling. Furthermore, we summarize 40 recently published reports addressing the fundamental theory, breakthrough and most advanced updates for the mass spectrometry-based neoantigen discovery for cancer immunotherapy.
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Affiliation(s)
- Xiaomei Zhang
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Yue Qi
- Thoracic & GI oncology branch, National Cancer Institute, CCR, NIH, Bethesda, MD 20814, USA
| | - Qi Zhang
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China; Cell-Gene Therapy Translational Medicine Research Center, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Wei Liu
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China; Thoracic & GI oncology branch, National Cancer Institute, CCR, NIH, Bethesda, MD 20814, USA.
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10
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Eggink LL, Roby KF, Cote R, Kenneth Hoober J. An innovative immunotherapeutic strategy for ovarian cancer: CLEC10A and glycomimetic peptides. J Immunother Cancer 2018; 6:28. [PMID: 29665849 PMCID: PMC5905120 DOI: 10.1186/s40425-018-0339-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/03/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Receptors specific for the sugar N-acetylgalactosamine (GalNAc) include the human type II, C-type lectin receptor macrophage galactose-type lectin/C-type lectin receptor family member 10A (MGL/CLEC10A/CD301) that is expressed prominently by human peripheral immature dendritic cells, dendritic cells in the skin, alternatively-activated (M2a) macrophages, and to lesser extents by several other types of tissues. CLEC10A is an endocytic receptor on antigen-presenting cells and has been proposed to play an important role in maturation of dendritic cells and initiation of an immune response. In this study, we asked whether a peptide that binds in the GalNAc-binding site of CLEC10A would serve as an effective tool to activate an immune response against ovarian cancer. METHODS A 12-mer sequence emerged from a screen of a phage display library with a GalNAc-specific lectin. The peptide, designated svL4, and a shorter peptide consisting of the C-terminal 6 amino acids, designated sv6D, were synthesized as tetravalent structures based on a tri-lysine core. In silico and in vitro binding assays were developed to evaluate binding of the peptides to GalNAc-specific receptors. Endotoxin-negative peptide solutions were administered by subcutaneous injection and biological activity of the peptides was determined by secretion of cytokines and the response of peritoneal immune cells in mice. Anti-cancer activity was studied in a murine model of ovarian cancer. RESULTS The peptides bound to recombinant human CLEC10A with high avidity, with half-maximal binding in the low nanomolar range. Binding to the receptor was Ca2+-dependent. Subcutaneous injection of low doses of peptides into mice on alternate days resulted in several-fold expansion of populations of mature immune cells within the peritoneal cavity. Peptide sv6D effectively suppressed development of ascites in a murine ovarian cancer model as a monotherapy and in combination with the chemotherapeutic drug paclitaxel or the immunotherapeutic antibody against the receptor PD-1. Toxicity, including antigenicity and release of cytotoxic levels of cytokines, was not observed. CONCLUSION sv6D is a functional ligand for CLEC10A and induces maturation of immune cells in the peritoneal cavity. The peptide caused a highly significant extension of survival of mice with implanted ovarian cancer cells with a favorable toxicity and non-antigenic profile.
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Affiliation(s)
- Laura L Eggink
- Susavion Biosciences, Inc., 1615 W. University Drive, Suite 132, Tempe, AZ, 85281, USA
| | | | - Robert Cote
- Susavion Biosciences, Inc., 1615 W. University Drive, Suite 132, Tempe, AZ, 85281, USA
| | - J Kenneth Hoober
- Susavion Biosciences, Inc., 1615 W. University Drive, Suite 132, Tempe, AZ, 85281, USA.
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11
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Chong C, Marino F, Pak H, Racle J, Daniel RT, Müller M, Gfeller D, Coukos G, Bassani-Sternberg M. High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome. Mol Cell Proteomics 2018; 17:533-548. [PMID: 29242379 PMCID: PMC5836376 DOI: 10.1074/mcp.tir117.000383] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/12/2017] [Indexed: 12/11/2022] Open
Abstract
Comprehensive knowledge of the human leukocyte antigen (HLA) class-I and class-II peptides presented to T-cells is crucial for designing innovative therapeutics against cancer and other diseases. However methodologies for their purification for mass-spectrometry analysis have been a major limitation. We designed a novel high-throughput, reproducible and sensitive method for sequential immuno-affinity purification of HLA-I and -II peptides from up to 96 samples in a plate format, suitable for both cell lines and tissues. Our methodology drastically reduces sample-handling and can be completed within five hours. We challenged our methodology by extracting HLA peptides from multiple replicates of tissues (n = 7) and cell lines (n = 21, 108 cells per replicate), which resulted in unprecedented depth, sensitivity and high reproducibility (Pearson correlations up to 0.98 and 0.97 for HLA-I and HLA-II). Because of the method's achieved sensitivity, even single measurements of peptides purified from 107 B-cells resulted in the identification of more than 1700 HLA-I and 2200 HLA-II peptides. We demonstrate the feasibility of performing drug-screening by using ovarian cancer cells treated with interferon gamma (IFNγ). Our analysis revealed an augmented presentation of chymotryptic-like and longer ligands associated with IFNγ induced changes of the antigen processing and presentation machinery. This straightforward method is applicable for basic and clinical applications.
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Affiliation(s)
- Chloe Chong
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Fabio Marino
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - HuiSong Pak
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Julien Racle
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
- **Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Roy T Daniel
- ¶Service of Neurosurgery, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Markus Müller
- ‖Vital IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David Gfeller
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
- **Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - George Coukos
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- From the ‡Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland;
- §Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
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12
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MHC-I peptides get out of the groove and enable a novel mechanism of HIV-1 escape. Nat Struct Mol Biol 2017; 24:387-394. [PMID: 28218747 DOI: 10.1038/nsmb.3381] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 01/20/2017] [Indexed: 12/18/2022]
Abstract
Major histocompatibility complex class I (MHC-I) molecules play a crucial role in immunity by capturing peptides for presentation to T cells and natural killer (NK) cells. The peptide termini are tethered within the MHC-I antigen-binding groove, but it is unknown whether other presentation modes occur. Here we show that 20% of the HLA-B*57:01 peptide repertoire comprises N-terminally extended sets characterized by a common motif at position 1 (P1) to P2. Structures of HLA-B*57:01 presenting N-terminally extended peptides, including the immunodominant HIV-1 Gag epitope TW10 (TSTLQEQIGW), showed that the N terminus protrudes from the peptide-binding groove. The common escape mutant TSNLQEQIGW bound HLA-B*57:01 canonically, adopting a dramatically different conformation than the TW10 peptide. This affected recognition by killer cell immunoglobulin-like receptor (KIR) 3DL1 expressed on NK cells. We thus define a previously uncharacterized feature of the human leukocyte antigen class I (HLA-I) immunopeptidome that has implications for viral immune escape. We further suggest that recognition of the HLA-B*57:01-TW10 epitope is governed by a 'molecular tension' between the adaptive and innate immune systems.
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13
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Kochin V, Kanaseki T, Tokita S, Miyamoto S, Shionoya Y, Kikuchi Y, Morooka D, Hirohashi Y, Tsukahara T, Watanabe K, Toji S, Kokai Y, Sato N, Torigoe T. HLA-A24 ligandome analysis of colon and lung cancer cells identifies a novel cancer-testis antigen and a neoantigen that elicits specific and strong CTL responses. Oncoimmunology 2017; 6:e1293214. [PMID: 28533942 DOI: 10.1080/2162402x.2017.1293214] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/01/2017] [Accepted: 02/04/2017] [Indexed: 01/05/2023] Open
Abstract
This study focused on HLA-A24 and comprehensively analyzed the ligandome of colon and lung cancer cells without the use of MHC-binding in silico prediction algorithms. Affinity purification using the antibody specific to HLA-A24 followed by LC-MS/MS sequencing was used to detect peptides, which harbored the known characteristics of HLA-A24 peptides in terms of length and anchor motifs. Ligandome analysis demonstrated the natural presentation of two different types of novel tumor-associated antigens. The ligandome contained a peptide derived from SUV39H2, a gene found to be expressed in a variety of cancers but not in normal tissues (except for the testis). The SUV39H2 peptide is immunogenic and elicits cytotoxic CD8+ T-cell (CTL) responses against cancer cells and is thus a novel cancer-testis antigen. Moreover, we found that microsatellite instability (MSI)-colon cancer cells displayed a neoepitope with an amino-acid substitution, while microsatellite stable (MSS)-colon and lung cancer cells displayed its counterpart peptide without the substitution. Structure modeling of peptide-HLA-A24 complexes predicted that the mutated residue at P8 was accessible to T-cell receptors. The neoepitope readily elicited CTL responses, which discriminated it from its wild-type counterpart, and the CTLs exhibited considerably high cytotoxicity against MSS-colon cancer cells carrying the responsible gene mutation. The specific and strong CTL lysis observed in this study fosters our understanding of immune surveillance against neoantigens.
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Affiliation(s)
- Vitaly Kochin
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Serina Tokita
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Sho Miyamoto
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Yosuke Shionoya
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Yasuhiro Kikuchi
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Daichi Morooka
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | | | | | - Kazue Watanabe
- Department of Pathology, Sapporo Medical University, Sapporo, Japan.,Research and Development Division, Medical and Biological Laboratories Company, Limited, Ina, Japan
| | - Shingo Toji
- Research and Development Division, Medical and Biological Laboratories Company, Limited, Ina, Japan
| | - Yasuo Kokai
- Department of Biomedical Engineering, Sapporo Medical University, Sapporo, Japan
| | - Noriyuki Sato
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
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14
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Zhou Z, Reyes-Vargas E, Escobar H, Chang KY, Barker AP, Rockwood AL, Delgado JC, He X, Jensen PE. Peptidomic analysis of type 1 diabetes associated HLA-DQ molecules and the impact of HLA-DM on peptide repertoire editing. Eur J Immunol 2016; 47:314-326. [PMID: 27861808 DOI: 10.1002/eji.201646656] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/21/2016] [Accepted: 11/10/2016] [Indexed: 11/08/2022]
Abstract
HLA-DM and class II associated invariant chain (Ii) are key cofactors in the MHC class II (MHCII) antigen processing pathway. We used tandem mass spectrometry sequencing to directly interrogate the global impact of DM and Ii on the repertoire of MHCII-bound peptides in human embryonic kidney 293T cells expressing HLA-DQ molecules in the absence or presence of these cofactors. We found that Ii and DM have a major impact on the repertoire of peptides presented by DQ1 and DQ6, with the caveat that this technology is not quantitative. The peptide repertoires of type 1 diabetes (T1D) associated DQ8, DQ2, and DQ8/2 are altered to a lesser degree by DM expression, and these molecules share overlapping features in their peptide binding motifs that are distinct from control DQ1 and DQ6 molecules. Peptides were categorized into DM-resistant, DM-dependent, or DM-sensitive groups based on the mass spectrometry data, and representative peptides were tested in competitive binding assays and peptide dissociation rate experiments with soluble DQ6. Our data support the conclusion that high intrinsic stability of DQ-peptide complexes is necessary but not sufficient to confer resistance to DM editing, and provide candidate parameters that may be useful in predicting the sensitivity of T-cell epitopes to DM editing.
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Affiliation(s)
- Zemin Zhou
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | | | | | - Kuan Y Chang
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Adam P Barker
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Alan L Rockwood
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Julio C Delgado
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Xiao He
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Peter E Jensen
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
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15
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Analysis of Major Histocompatibility Complex-Bound HIV Peptides Identified from Various Cell Types Reveals Common Nested Peptides and Novel T Cell Responses. J Virol 2016; 90:8605-20. [PMID: 27440904 DOI: 10.1128/jvi.00599-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/13/2016] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED Despite the critical role of epitope presentation for immune recognition, we still lack a comprehensive definition of HIV peptides presented by HIV-infected cells. Here we identified 107 major histocompatibility complex (MHC)-bound HIV peptides directly from the surface of live HIV-transfected 293T cells, HIV-infected B cells, and primary CD4 T cells expressing a variety of HLAs. The majority of peptides were 8 to 12 amino acids (aa) long and mostly derived from Gag and Pol. The analysis of the total MHC-peptidome and of HLA-A02-bound peptides identified new noncanonical HIV peptides of up to 16 aa that could not be predicted by HLA anchor scanning and revealed an heterogeneous surface peptidome. Nested sets of surface HIV peptides included optimal and extended HIV epitopes and peptides partly overlapping or distinct from known epitopes, revealing new immune responses in HIV-infected persons. Surprisingly, in all three cell types, a majority of Gag peptides derived from p15 rather than from the most immunogenic p24. The cytosolic degradation of peptide precursors in corresponding cells confirmed the generation of identified surface-nested peptides. Cytosolic degradation revealed peptides commonly produced in all cell types and displayed by various HLAs, peptides commonly produced in all cell types and selectively displayed by specific HLAs, and peptides produced in only one cell type. Importantly, we identified areas of proteins leading to common presentations of noncanonical peptides by several cell types with distinct HLAs. These peptides may benefit the design of immunogens, focusing T cell responses on relevant markers of HIV infection in the context of HLA diversity. IMPORTANCE The recognition of HIV-infected cells by immune T cells relies on the presentation of HIV-derived peptides by diverse HLA molecules at the surface of cells. The landscape of HIV peptides displayed by HIV-infected cells is not well defined. Considering the diversity of HLA molecules in the human population, it is critical for vaccine design to identify HIV peptides that may be displayed despite the HLA diversity. We identified 107 HIV peptides directly from the surface of three cell types infected with HIV. They corresponded to nested sets of HIV peptides of canonical and novel noncanonical lengths not predictable by the presence of HLA anchors. Importantly, we identified areas of HIV proteins leading to presentation of noncanonical peptides by several cell types with distinct HLAs. Including such peptides in vaccine immunogen may help to focus immune responses on common markers of HIV infection in the context of HLA diversity.
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16
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Starck SR, Tsai JC, Chen K, Shodiya M, Wang L, Yahiro K, Martins-Green M, Shastri N, Walter P. Translation from the 5' untranslated region shapes the integrated stress response. Science 2016; 351:aad3867. [PMID: 26823435 DOI: 10.1126/science.aad3867] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translated regions distinct from annotated coding sequences have emerged as essential elements of the proteome. This includes upstream open reading frames (uORFs) present in mRNAs controlled by the integrated stress response (ISR) that show "privileged" translation despite inhibited eukaryotic initiation factor 2-guanosine triphosphate-initiator methionyl transfer RNA (eIF2·GTP·Met-tRNA(i )(Met)). We developed tracing translation by T cells to directly measure the translation products of uORFs during the ISR. We identified signature translation events from uORFs in the 5' untranslated region of binding immunoglobulin protein (BiP) mRNA (also called heat shock 70-kilodalton protein 5 mRNA) that were not initiated at the start codon AUG. BiP expression during the ISR required both the alternative initiation factor eIF2A and non-AUG-initiated uORFs. We propose that persistent uORF translation, for a variety of chaperones, shelters select mRNAs from the ISR, while simultaneously generating peptides that could serve as major histocompatibility complex class I ligands, marking cells for recognition by the adaptive immune system.
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Affiliation(s)
- Shelley R Starck
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA. Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
| | - Jordan C Tsai
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA
| | - Keling Chen
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Michael Shodiya
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Lei Wang
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA 92521, USA
| | - Kinnosuke Yahiro
- Departments of Molecular Infectiology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Manuela Martins-Green
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA 92521, USA
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
| | - Peter Walter
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.
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17
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Manandhar T, Kunze-Schumacher H, Huyton T, Celik AA, Blasczyk R, Bade-Doeding C. Understanding the obstacle of incompatibility at residue 156 within HLA-B*35 subtypes. Immunogenetics 2016; 68:247-60. [PMID: 26758079 PMCID: PMC4799800 DOI: 10.1007/s00251-015-0896-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 12/23/2015] [Indexed: 01/22/2023]
Abstract
Defining permissive and non-permissive mismatches for transplantation is a demanding challenge. Single mismatches at amino acid (AA) position 156 of human leucocyte antigen (HLA) class I have been described to alter the peptide motif, repertoire, or mode of peptide loading through differential interaction with the peptide-loading complex. Hence, a single mismatch can tip the balance and trigger an immunological reaction. HLA-B*35 subtypes have been described to evade the loading complex, 156 mismatch distinguishing B*35:01 and B*35:08 changes the binding groove sufficiently to alter the sequence features of the selected peptide repertoire. To understand the functional influences of residue 156 in B*35 variants, we analyzed the peptide binding profiles of HLA-B*35:01156Leu, B*35:08156Arg and B*35:62156Trp. The glycoprotein tapasin represents a target for immune evasions and functions within the multimeric peptide-loading complex to stabilize empty class I molecules and promote acquisition of high-affinity peptides. All three B*35 subtypes showed a tapasin-independent mode of peptide acquisition. HLA-B*35-restricted peptides of low- and high-binding affinities were recovered in the presence and absence of tapasin and subsequently sequenced utilizing mass spectrometry. The peptides derived from B*35 variants differ substantially in their features dependent on their mode of recruitment; all peptides were preferentially anchored by Pro at p2 and Tyr, Phe, Leu, or Lys at pΩ. However, the Trp at residue 156 altered the p2 motif to an Ala and restricted the pΩ to a Trp. Our results highlight the importance of understanding the impact of key micropolymorphism and how a single AA mismatch orchestrates the neighboring AAs.
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Affiliation(s)
- Trishna Manandhar
- Hannover Medical School, Institute for Transfusion Medicine, Feodor-Lynen-Str. 5, 30625, Hannover, Germany
| | - Heike Kunze-Schumacher
- Hannover Medical School, Institute for Transfusion Medicine, Feodor-Lynen-Str. 5, 30625, Hannover, Germany
| | - Trevor Huyton
- Hannover Medical School, Institute for Transfusion Medicine, Feodor-Lynen-Str. 5, 30625, Hannover, Germany
| | - Alexander A Celik
- Hannover Medical School, Institute for Transfusion Medicine, Feodor-Lynen-Str. 5, 30625, Hannover, Germany
| | - Rainer Blasczyk
- Hannover Medical School, Institute for Transfusion Medicine, Feodor-Lynen-Str. 5, 30625, Hannover, Germany
| | - Christina Bade-Doeding
- Hannover Medical School, Institute for Transfusion Medicine, Feodor-Lynen-Str. 5, 30625, Hannover, Germany.
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18
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Schellens IMM, Hoof I, Meiring HD, Spijkers SNM, Poelen MCM, van Gaans-van den Brink JAM, van der Poel K, Costa AI, van Els CACM, van Baarle D, Kesmir C. Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome. PLoS One 2015; 10:e0136417. [PMID: 26375851 PMCID: PMC4574158 DOI: 10.1371/journal.pone.0136417] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 08/04/2015] [Indexed: 01/23/2023] Open
Abstract
The cytotoxic T cell (CTL) response is determined by the peptide repertoire presented by the HLA class I molecules of an individual. We performed an in-depth analysis of the peptide repertoire presented by a broad panel of common HLA class I molecules on four B lymphoblastoid cell-lines (BLCL). Peptide elution and mass spectrometry analysis were utilised to investigate the number and abundance of self-peptides. Altogether, 7897 unique self-peptides, derived of 4344 proteins, were eluted. After viral infection, the number of unique self-peptides eluted significantly decreased compared to uninfected cells, paralleled by a decrease in the number of source proteins. In the overall dataset, the total number of unique self-peptides eluted from HLA-B molecules was larger than from HLA-A molecules, and they were derived from a larger number of source proteins. These results in B cells suggest that HLA-B molecules possibly present a more diverse repertoire compared to their HLA-A counterparts, which may contribute to their immunodominance. This study provides a unique data set giving new insights into the complex system of antigen presentation for a broad panel of HLA molecules, many of which were never studied this extensively before.
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Affiliation(s)
- Ingrid M. M. Schellens
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Ilka Hoof
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Hugo D. Meiring
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Institute for Translational Vaccinology (Intravacc), Bilthoven, The Netherlands
| | - Sanne N. M. Spijkers
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Martien C. M. Poelen
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Kees van der Poel
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ana I. Costa
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Cecile A. C. M. van Els
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Debbie van Baarle
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- * E-mail:
| | - Can Kesmir
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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19
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Chen L, Reyes-Vargas E, Dai H, Escobar H, Rudd B, Fairbanks J, Ho A, Cusick MF, Kumánovics A, Delgado J, He X, Jensen PE. Expression of the mouse MHC class Ib H2-T11 gene product, a paralog of H2-T23 (Qa-1) with shared peptide-binding specificity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 193:1427-39. [PMID: 24958902 PMCID: PMC4211609 DOI: 10.4049/jimmunol.1302048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mouse MHC class Ib gene H2-T11 is 95% identical at the DNA level to H2-T23, which encodes Qa-1, one of the most studied MHC class Ib molecules. H2-T11 mRNA was observed to be expressed widely in tissues of C57BL/6 mice, with the highest levels in thymus. To circumvent the availability of a specific mAb, cells were transduced with cDNA encoding T11 with a substituted α3 domain. Hybrid T11D3 protein was expressed at high levels similar to control T23D3 molecules on the surface of both TAP(+) and TAP(-) cells. Soluble T11D3 was generated by folding in vitro with Qa-1 determinant modifier, the dominant peptide presented by Qa-1. The circular dichroism spectrum of this protein was similar to that of other MHC class I molecules, and it was observed to bind labeled Qa-1 determinant modifier peptide with rapid kinetics. By contrast to the Qa-1 control, T11 tetramers did not react with cells expressing CD94/NKG2A, supporting the conclusion that T11 cannot replace Qa-1 as a ligand for NK cell inhibitory receptors. T11 also failed to substitute for Qa-1 in the presentation of insulin to a Qa-1-restricted T cell hybridoma. Despite divergent function, T11 was observed to share peptide-loading specificity with Qa-1. Direct analysis by tandem mass spectrometry of peptides eluted from T11D3 and T23D3 isolated from Hela cells demonstrated a diversity of peptides with a clear motif that was shared between the two molecules. Thus, T11 is a paralog of T23 encoding an MHC class Ib molecule that shares peptide-binding specificity with Qa-1 but differs in function.
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Affiliation(s)
- Lili Chen
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | | | - Hu Dai
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | | | - Brant Rudd
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | - Jared Fairbanks
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | - Alexander Ho
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | - Mathew F Cusick
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | - Attila Kumánovics
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and ARUP Laboratories, Salt Lake City, UT 84112
| | - Julio Delgado
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and ARUP Laboratories, Salt Lake City, UT 84112
| | - Xiao He
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and
| | - Peter E Jensen
- Department of Pathology, University of Utah, Salt Lake City, UT 84112; and ARUP Laboratories, Salt Lake City, UT 84112
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20
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Yanaka S, Ueno T, Shi Y, Qi J, Gao GF, Tsumoto K, Sugase K. Peptide-dependent conformational fluctuation determines the stability of the human leukocyte antigen class I complex. J Biol Chem 2014; 289:24680-90. [PMID: 25028510 DOI: 10.1074/jbc.m114.566174] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In immune-mediated control of pathogens, human leukocyte antigen (HLA) class I presents various antigenic peptides to CD8(+) T-cells. Long-lived peptide presentation is important for efficient antigen-specific T-cell activation. Presentation time depends on the peptide sequence and the stability of the peptide-HLA complex (pHLA). However, the determinant of peptide-dependent pHLA stability remains elusive. Here, to reveal the pHLA stabilization mechanism, we examined the crystal structures of an HLA class I allomorph in complex with HIV-derived peptides and evaluated site-specific conformational fluctuations using NMR. Although the crystal structures of various pHLAs were almost identical independent of the peptides, fluctuation analyses identified a peptide-dependent minor state that would be more tightly packed toward the peptide. The minor population correlated well with the thermostability and cell surface presentation of pHLA, indicating that this newly identified minor state is important for stabilizing the pHLA and facilitating T-cell recognition.
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Affiliation(s)
- Saeko Yanaka
- From the Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 277-8562, Japan
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto 860-0811, Japan
| | - Yi Shi
- Research Network of Immunity and Health, Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing 100101, China, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- Research Network of Immunity and Health, Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing 100101, China, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - George F Gao
- Research Network of Immunity and Health, Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing 100101, China, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kouhei Tsumoto
- From the Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 277-8562, Japan, Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 108-8693, Japan, Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, Tokyo 108-8693, Japan, and
| | - Kenji Sugase
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Osaka 618-8503, Japan
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21
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Expanding the detectable HLA peptide repertoire using electron-transfer/higher-energy collision dissociation (EThcD). Proc Natl Acad Sci U S A 2014; 111:4507-12. [PMID: 24616531 DOI: 10.1073/pnas.1321458111] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The identification of peptides presented by human leukocyte antigen (HLA) class I is tremendously important for the understanding of antigen presentation mechanisms under healthy or diseased conditions. Currently, mass spectrometry-based methods represent the best methodology for the identification of HLA class I-associated peptides. However, the HLA class I peptide repertoire remains largely unexplored because the variable nature of endogenous peptides represents difficulties in conventional peptide fragmentation technology. Here, we substantially enhanced (about threefold) the identification success rate of peptides presented by HLA class I using combined electron-transfer/higher-energy collision dissociation (EThcD), reporting over 12,000 high-confident (false discovery rate <1%) peptides from a single human B-cell line. The direct importance of such an unprecedented large dataset is highlighted by the discovery of unique features in antigen presentation. The observation that a substantial part of proteins is sampled across different HLA alleles, and the common occurrence of HLA class I nested sets, suggest that the constraints of HLA class I to comprehensively present the health states of cells are not as tight as previously thought. Our dataset contains a substantial set of peptides bearing a variety of posttranslational modifications presented with marked allele-specific differences. We propose that EThcD should become the method of choice in analyzing HLA class I-presented peptides.
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22
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Schittenhelm RB, Dudek NL, Croft NP, Ramarathinam SH, Purcell AW. A comprehensive analysis of constitutive naturally processed and presented HLA-C*04:01 (Cw4)-specific peptides. ACTA ACUST UNITED AC 2014; 83:174-9. [PMID: 24397554 DOI: 10.1111/tan.12282] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 11/06/2013] [Accepted: 12/03/2013] [Indexed: 02/01/2023]
Abstract
The human B lymphoblastoid cell line C1R is widely regarded as human leukocyte antigen-A (HLA-A)/HLA-B negative and is therefore frequently exploited as a recipient cell line to study HLA class I functions. However, the normal levels of HLA-C*04:01 often hamper the investigation of introduced HLA class I allomorphs, which is particularly evident in sensitive applications such as mass spectrometry. Here we describe the comprehensive analysis of endogenous HLA-C*04:01 ligands expressed on the surface of C1R cells to (i) define a large sequence dataset of HLA-C*04:01 ligands, to (ii) refine the HLA-C*04:01 peptide-binding motif and (iii) to provide a resource that allows discrimination between peptides bound to introduced HLA class I subtypes and to the endogenous HLA-C*04:01 molecules.
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Affiliation(s)
- R B Schittenhelm
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800, Victoria, Australia
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23
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Dudek NL, Tan CT, Gorasia DG, Croft NP, Illing PT, Purcell AW. Constitutive and inflammatory immunopeptidome of pancreatic β-cells. Diabetes 2012; 61:3018-25. [PMID: 22872234 PMCID: PMC3478525 DOI: 10.2337/db11-1333] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Type 1 diabetes is characterized by the autoimmune destruction of pancreatic β-cells. Recognition of major histocompatibility complex (MHC)-bound peptides is critical for both the initiation and progression of disease. In this study, MHC peptide complexes were purified from NIT-1 β-cells, interferon-γ (IFN-γ)-treated NIT-1 cells, splenic and thymic tissue of 12-week-old NOD mice, and peptides identified by mass spectrometry. In addition to global liquid chromatography-tandem mass spectrometry analysis, the targeted approach of multiple-reaction monitoring was used to quantitate the immunodominant K(d)-restricted T-cell epitope islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP)₂₀₆₋₂₁₄. We identified >2,000 MHC-bound peptides; 1,100 of these presented by β-cells grown under normal conditions or after exposure to IFN-γ. These include sequences from a number of known autoantigens. Quantitation of IGRP₂₀₆₋₂₁₄ revealed low-level presentation by K(d) (~25 complexes/cell) on NIT-1 cells after IFN-γ treatment compared with the simultaneous presentation of the endogenously processed K(d)-restricted peptide Janus kinase-1₃₅₅₋₃₆₃ (~15,000 copies/cell). We have successfully sequenced peptides from NIT-1 β-cells under basal and inflammatory conditions. We have shown the feasibility of quantitating disease-associated peptides and provide the first direct demonstration of the disparity between presentation of a known autoantigenic epitope and a common endogenously presented peptide.
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Affiliation(s)
- Nadine L. Dudek
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
- Corresponding author: Anthony W. Purcell, , or Nadine L. Dudek,
| | - Chor Teck Tan
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Dhana G. Gorasia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Nathan P. Croft
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Patricia T. Illing
- Department of Immunology and Microbiology, The University of Melbourne, Victoria, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
- Corresponding author: Anthony W. Purcell, , or Nadine L. Dudek,
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24
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Origin and plasticity of MHC I-associated self peptides. Autoimmun Rev 2011; 11:627-35. [PMID: 22100331 DOI: 10.1016/j.autrev.2011.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 11/02/2011] [Indexed: 01/13/2023]
Abstract
Endogenous peptides presented by MHC I molecules represent the essence of self for CD8 T lymphocytes. These MHC I peptides (MIPs) regulate all key events that occur during the lifetime of CD8 T cells. CD8 T cells are selected on self-MIPs, sustained by self-MIPs, and activated in the presence of self-MIPs. Recently, large-scale mass spectrometry studies have revealed that the self-MIP repertoire is more complex and plastic than previously anticipated. The composition of the self-MIP repertoire varies from one cell type to another and can be perturbed by cell-intrinsic and -extrinsic factors including dysregulation of cellular metabolism and infection. The complexity and plasticity of the self-MIP repertoire represent a major challenge for the maintenance of self tolerance and can have pervasive effects on the global functioning of the immune system.
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25
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Machine learning competition in immunology - Prediction of HLA class I binding peptides. J Immunol Methods 2011; 374:1-4. [PMID: 21986107 DOI: 10.1016/j.jim.2011.09.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 09/22/2011] [Indexed: 11/23/2022]
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26
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Large-scale characterization of peptide-MHC binding landscapes with structural simulations. Proc Natl Acad Sci U S A 2011; 108:6981-6. [PMID: 21478437 DOI: 10.1073/pnas.1018165108] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Class I major histocompatibility complex proteins play a critical role in the adaptive immune system by binding to peptides derived from cytosolic proteins and presenting them on the cell surface for surveillance by T cells. The varied peptide binding specificity of these highly polymorphic molecules has important consequences for vaccine design, transplantation, autoimmunity, and cancer development. Here, we describe a molecular modeling study of MHC-peptide interactions that integrates sampling techniques from protein-protein docking, loop modeling, de novo structure prediction, and protein design in order to construct atomically detailed peptide binding landscapes for a diverse set of MHC proteins. Specificity profiles derived from these landscapes recover key features of experimental binding profiles and can be used to predict peptide binding with reasonable accuracy. Family wide comparison of the predicted binding landscapes recapitulates previously reported patterns of specificity divergence and peptide-repertoire diversity while providing a structural basis for observed specificity patterns. The size and sequence diversity of these structure-based binding landscapes enable us to identify subtle patterns of covariation between peptide sequence positions; analysis of the associated structural models suggests physical interactions that may mediate these sequence correlations.
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27
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Escobar H, Reyes-Vargas E, Jensen PE, Delgado JC, Crockett DK. Utility of characteristic QTOF MS/MS fragmentation for MHC class I peptides. J Proteome Res 2011; 10:2494-507. [PMID: 21413816 DOI: 10.1021/pr101272k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Systematic investigation of cellular process by mass spectrometric detection of peptides obtained from proteins digestion or directly from immuno-purification can be a powerful tool when used appropriately. The true sequence of these peptides is defined by the interpretation of spectral data using a variety of available algorithms. However peptide match algorithm scoring is typically based on some, but not all, of the mechanisms of peptide fragmentation. Although algorithm rules for soft ionization techniques generally fit very well to tryptic peptides, manual validation of spectra is often required for endogenous peptides such as MHC class I molecules where traditional trypsin digest techniques are not used. This study summarizes data mining and manual validation of hundreds of peptide sequences from MHC class I molecules in publically available data files. We herein describe several important features to improve and quantify manual validation for these endogenous peptides--post automated algorithm searching. Important fragmentation patterns are discussed for the studied MHC Class I peptides. These findings lead to practical rules that are helpful when performing manual validation. Furthermore, these observations may be useful to improve current peptide search algorithms or development of novel software tools.
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Affiliation(s)
- Hernando Escobar
- ARUP Institute for Clinical and Experimental Pathology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, United States
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28
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Blanchard N, Kanaseki T, Escobar H, Delebecque F, Nagarajan NA, Reyes-Vargas E, Crockett DK, Raulet DH, Delgado JC, Shastri N. Endoplasmic reticulum aminopeptidase associated with antigen processing defines the composition and structure of MHC class I peptide repertoire in normal and virus-infected cells. THE JOURNAL OF IMMUNOLOGY 2010; 184:3033-42. [PMID: 20173027 DOI: 10.4049/jimmunol.0903712] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The MHC class I (MHC-I) molecules ferry a cargo of peptides to the cell surface as potential ligands for CD8(+) cytotoxic T cells. For nearly 20 years, the cargo has been described as a collection of short 8-9 mer peptides, whose length and sequences were believed to be primarily determined by the peptide-binding groove of MHC-I molecules. Yet the mechanisms for producing peptides of such optimal length and composition have remained unclear. In this study, using mass spectrometry, we determined the amino acid sequences of a large number of naturally processed peptides in mice lacking the endoplasmic reticulum aminopeptidase associated with Ag processing (ERAAP). We find that ERAAP-deficiency changed the oeuvre and caused a marked increase in the length of peptides normally presented by MHC-I. Furthermore, we observed similar changes in the length of viral peptides recognized by CD8(+) T cells in mouse CMV-infected ERAAP-deficient mice. In these mice, a distinct CD8(+) T cell population was elicited with specificity for an N-terminally extended epitope. Thus, the characteristic length, as well as the composition of MHC-I peptide cargo, is determined not only by the MHC-I peptide-binding groove but also by ERAAP proteolysis in the endoplasmic reticulum.
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Affiliation(s)
- Nicolas Blanchard
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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29
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Perreault C. The Origin and Role of MHC Class I-Associated Self-Peptides. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2010; 92:41-60. [DOI: 10.1016/s1877-1173(10)92003-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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30
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Identification of naturally processed ligands in the C57BL/6 mouse using large-scale mass spectrometric peptide sequencing and bioinformatics prediction. Immunogenetics 2009; 61:241-6. [DOI: 10.1007/s00251-009-0360-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 01/30/2009] [Indexed: 10/21/2022]
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