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Manoharan Valerio M, Arana K, Guan J, Chan SW, Yang X, Kurd N, Lee A, Shastri N, Coscoy L, Robey EA. The promiscuous development of an unconventional Qa1b-restricted T cell population. Front Immunol 2023; 14:1250316. [PMID: 38022509 PMCID: PMC10644506 DOI: 10.3389/fimmu.2023.1250316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
MHC-E restricted CD8 T cells show promise in vaccine settings, but their development and specificity remain poorly understood. Here we focus on a CD8 T cell population reactive to a self-peptide (FL9) bound to mouse MHC-E (Qa-1b) that is presented in response to loss of the MHC I processing enzyme ERAAP, termed QFL T cells. We find that mature QFL thymocytes are predominantly CD8αβ+CD4-, show signs of agonist selection, and give rise to both CD8αα and CD8αβ intraepithelial lymphocytes (IEL), as well as memory phenotype CD8αβ T cells. QFL T cells require the MHC I subunit β-2 microglobulin (β2m), but do not require Qa1b or classical MHC I for positive selection. However, QFL thymocytes do require Qa1b for agonist selection and full functionality. Our data highlight the relaxed requirements for positive selection of an MHC-E restricted T cell population and suggest a CD8αβ+CD4- pathway for development of CD8αα IELs.
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Affiliation(s)
- Michael Manoharan Valerio
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Kathya Arana
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Jian Guan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Shiao Wei Chan
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Xiaokun Yang
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Nadia Kurd
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Angus Lee
- Gene Targeting Facility Cancer Research Laboratory, University of California Berkeley, Berkeley, CA, United States
| | - Nilabh Shastri
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Laurent Coscoy
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
| | - Ellen A. Robey
- Division of Immunology and Molecular Medicine, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, United States
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2
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El Bissati K, Krishack PA, Zhou Y, Weber CR, Lykins J, Jankovic D, Edelblum KL, Fraczek L, Grover H, Chentoufi AA, Singh G, Reardon C, Dubey JP, Reed S, Alexander J, Sidney J, Sette A, Shastri N, McLeod R. CD4 + T Cell Responses to Toxoplasma gondii Are a Double-Edged Sword. Vaccines (Basel) 2023; 11:1485. [PMID: 37766162 PMCID: PMC10535856 DOI: 10.3390/vaccines11091485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/26/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
CD4+ T cells have been found to play critical roles in the control of both acute and chronic Toxoplasma infection. Previous studies identified a protective role for the Toxoplasma CD4+ T cell-eliciting peptide AS15 (AVEIHRPVPGTAPPS) in C57BL/6J mice. Herein, we found that immunizing mice with AS15 combined with GLA-SE, a TLR-4 agonist in emulsion adjuvant, can be either helpful in protecting male and female mice at early stages against Type I and Type II Toxoplasma parasites or harmful (lethal with intestinal, hepatic, and spleen pathology associated with a storm of IL6). Introducing the universal CD4+ T cell epitope PADRE abrogates the harmful phenotype of AS15. Our findings demonstrate quantitative and qualitative features of an effective Toxoplasma-specific CD4+ T cell response that should be considered in testing next-generation vaccines against toxoplasmosis. Our results also are cautionary that individual vaccine constituents can cause severe harm depending on the company they keep.
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Affiliation(s)
- Kamal El Bissati
- Institute of Molecular Engineering, University of Chicago Medical Center, Chicago, IL 60637, USA
| | - Paulette A. Krishack
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; (P.A.K.); (C.R.W.); (G.S.); (C.R.)
| | - Ying Zhou
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL 60637, USA; (Y.Z.); (J.L.); (L.F.); (R.M.)
| | - Christopher R. Weber
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; (P.A.K.); (C.R.W.); (G.S.); (C.R.)
| | - Joseph Lykins
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL 60637, USA; (Y.Z.); (J.L.); (L.F.); (R.M.)
- Department of Emergency Medicine, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02215, USA
| | - Dragana Jankovic
- Immunoparasitology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Karen L. Edelblum
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Center for Immunity and Inflammation, Laboratory Medicine, Department of Pathology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Laura Fraczek
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL 60637, USA; (Y.Z.); (J.L.); (L.F.); (R.M.)
| | - Harshita Grover
- Division of Immunology and Pathogenesis, Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA; (H.G.); (N.S.)
| | - Aziz A. Chentoufi
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria 0028, South Africa;
| | - Gurminder Singh
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; (P.A.K.); (C.R.W.); (G.S.); (C.R.)
| | - Catherine Reardon
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; (P.A.K.); (C.R.W.); (G.S.); (C.R.)
| | - J. P. Dubey
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Steve Reed
- Infectious Diseases Research Institute, 1616 Eastlake Ave E #400, Seattle, WA 98102, USA;
| | - Jeff Alexander
- PaxVax, 3985-A Sorrento Valley Blvd, San Diego, CA 92121, USA;
| | - John Sidney
- La Jolla Institute of Allergy and Immunology, 9420 Athena Cir, La Jolla, CA 92037, USA; (J.S.); (A.S.)
| | - Alessandro Sette
- La Jolla Institute of Allergy and Immunology, 9420 Athena Cir, La Jolla, CA 92037, USA; (J.S.); (A.S.)
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA; (H.G.); (N.S.)
| | - Rima McLeod
- Department of Ophthalmology and Visual Sciences, University of Chicago, Chicago, IL 60637, USA; (Y.Z.); (J.L.); (L.F.); (R.M.)
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3
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Geiger KM, Manoharan M, Coombs R, Arana K, Park CS, Lee AY, Shastri N, Robey EA, Coscoy L. Murine cytomegalovirus downregulates ERAAP and induces an unconventional T cell response to self. Cell Rep 2023; 42:112317. [PMID: 36995940 PMCID: PMC10539480 DOI: 10.1016/j.celrep.2023.112317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 01/02/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
The endoplasmic reticulum aminopeptidase associated with antigen processing (ERAAP) plays a crucial role in shaping the peptide-major histocompatibility complex (MHC) class I repertoire and maintaining immune surveillance. While murine cytomegalovirus (MCMV) has multiple strategies for manipulating the antigen processing pathway to evade immune responses, the host has also developed ways to counter viral immune evasion. In this study, we find that MCMV modulates ERAAP and induces an interferon γ (IFN-γ)-producing CD8+ T cell effector response that targets uninfected ERAAP-deficient cells. We observe that ERAAP downregulation during infection leads to the presentation of the self-peptide FL9 on non-classical Qa-1b, thereby eliciting Qa-1b-restricted QFL T cells to proliferate in the liver and spleen of infected mice. QFL T cells upregulate effector markers upon MCMV infection and are sufficient to reduce viral load after transfer to immunodeficient mice. Our study highlights the consequences of ERAAP dysfunction during viral infection and provides potential targets for anti-viral therapies.
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Affiliation(s)
- Kristina M Geiger
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Manoharan
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel Coombs
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kathya Arana
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chan-Su Park
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Angus Y Lee
- Cancer Research Lab, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nilabh Shastri
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ellen A Robey
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Laurent Coscoy
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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4
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Martín-Esteban A, Rodriguez JC, Peske D, Lopez de Castro JA, Shastri N, Sadegh-Nasseri S. The ER Aminopeptidases, ERAP1 and ERAP2, synergize to self-modulate their respective activities. Front Immunol 2022; 13:1066483. [PMID: 36569828 PMCID: PMC9774488 DOI: 10.3389/fimmu.2022.1066483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction Critical steps in Major Histocompatibility Complex Class I (MHC-I) antigen presentation occur in the endoplasmic reticulum (ER). In general, peptides that enter the ER are longer than the optimal length for MHC-I binding. The final trimming of MHC-I epitopes is performed by two related aminopeptidases, ERAP1 and ERAP2 in humans that possess unique and complementary substrate trimming specificities. While ERAP1 efficiently trims peptides longer than 9 residues, ERAP2 preferentially trims peptides shorter than 9 residues. Materials and Methods Using a combination of biochemical and proteomic studies followed by biological verification. Results We demonstrate that the optimal ligands for either enzyme act as inhibitors of the other enzyme. Specifically, the presence of octamers reduced the trimming of long peptides by ERAP1, while peptides longer than nonomers inhibit ERAP2 activity. Discussion We propose a mechanism for how ERAP1 and ERAP2 synergize to modulate their respective activities and shape the MHC-I peptidome by generating optimal peptides for presentation.
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Affiliation(s)
- Adrian Martín-Esteban
- Department of Pathology, Immunopathology Division, Johns Hopkins University, Baltimore, MD, United States,Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain,*Correspondence: Scheherazade Sadegh-Nasseri, ; Adrian Martín-Esteban,
| | - Jesus Contreras Rodriguez
- Department of Pathology, Immunopathology Division, Johns Hopkins University, Baltimore, MD, United States
| | - David Peske
- Department of Pathology, Immunopathology Division, Johns Hopkins University, Baltimore, MD, United States
| | | | - Nilabh Shastri
- Department of Pathology, Immunopathology Division, Johns Hopkins University, Baltimore, MD, United States
| | - Scheherazade Sadegh-Nasseri
- Department of Pathology, Immunopathology Division, Johns Hopkins University, Baltimore, MD, United States,*Correspondence: Scheherazade Sadegh-Nasseri, ; Adrian Martín-Esteban,
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5
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Park CS, Shastri N. The Role of T Cells in Obesity-Associated Inflammation and Metabolic Disease. Immune Netw 2022; 22:e13. [PMID: 35291655 PMCID: PMC8901709 DOI: 10.4110/in.2022.22.e13] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 12/01/2022] Open
Abstract
Chronic inflammation plays a critical role in the development of obesity-associated metabolic disorders such as insulin resistance. Obesity alters the microenvironment of adipose tissue and the intestines from anti-inflammatory to pro-inflammatory, which promotes low grade systemic inflammation and insulin resistance in obese mice. Various T cell subsets either help maintain metabolic homeostasis in healthy states or contribute to obesity-associated metabolic syndromes. In this review, we will discuss the T cell subsets that reside in adipose tissue and intestines and their role in the development of obesity-induced systemic inflammation.
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Affiliation(s)
- Chan-Su Park
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nilabh Shastri
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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6
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Guan J, Sadegh-Nasseri S, Shastri N. Unusual distribution of a non-classical MHC I restricted CD8+ T population. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.104.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
A broad repertoire of peptides is constitutively presented through the MHC I molecules on the cell surface. ER aminopeptidase associated with Ag processing (ERAAP), a critical molecule in the antigen processing and presentation pathway, has profound effects on the generation of this peptide repertoire. Interestingly, the ERAAP deficient cells can be effectively detected by a unique population of the cytotoxic CD8+ T cell, named QFL-T cells which are specific for the ligand presented by the non-classical MHC Ib molecule, Qa-1b. The QFL-T cells showed similar characteristics with the other non-classical MHC Ib restricted unconventional T cells, such as the NKT or MAIT cells in their semi-invariant αβ TCRs, but their function(s) remains unknown. To study the potential function of the QFL-T cells, we assessed a variety of tissues for the ligand expression and the presence of the QFL-T cells. We observed high expression of this ERAAP dependent Qa-1b restricted ligand and relatively high frequency of the QFL-T cells in the small intestine. Remarkably, the number and the frequency of QFL-T cells among the intraepithelial lymphocytes (IELs) was tightly associated with the age and the gut microbiota of the mice. These findings suggest a role for gut microbiota in the homing/maintenance of the QFL-T cells in the small intestine.
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Affiliation(s)
- Jian Guan
- 1Johns Hopkins University School of Medicine
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7
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Park C, Guan J, Rhee P, Sadegh-Nasseri S, Shastri N. Fam49b, the source of antigenic peptide for ERAAP surveillance, controls thymocyte development. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.104.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
The aminopeptidase ERAAP, the ER aminopeptidase associated with antigen processing, is essential for trimming of peptides presented by classical and non-classical MHC class I molecules. The function of ERAAP is monitored by semi-invariant CD8+ T cells that recognize the QFL ligand. The QFL ligand consists of a 9-mer peptide encoded by the highly conserved Fam49a/b genes and is presented by non-classical Qa-1bmolecules expressed on surface of ERAAP-deficient cells only. Recently, Fam49b is identified as a novel negative regulator of TCR signaling, that functions by binding to active rac-1 and modulates reorganization of cytoskeleton. However, the function of Fam49b in T cells development has remained unclear. We show that Fam49b-deficient thymocytes receive higher TCR signaling and are defective in T cell development. Our studies reveal that Fam49b plays an important role in regulating thymocytes development and lineage commitment of conventional T cells as well as agonist selected T cells such as CD8αα αβ T cells. [This research was supported by NIH grants R01 AI130210 and R37 AI060040]
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Affiliation(s)
- Chansu Park
- 1Johns Hopkins University School of Medicine
| | - Jian Guan
- 1Johns Hopkins University School of Medicine
| | - Peter Rhee
- 1Johns Hopkins University School of Medicine
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8
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Park C, Guan J, Rhee P, Sadegh-Nasseri S, Shastri N. Fam49b-deficient lymphocytes modulate whole body energy metabolism. The Journal of Immunology 2021. [DOI: 10.4049/jimmunol.206.supp.93.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
TCR signal strength is determined by the balance of positively regulating, and negatively regulating proteins. Fam49b is identified as new negative regulator of TCR signaling that functions by binding to active rac-1 GTPase. In the absence of Fam49b, thymocytes receive higher TCR signaling and are defective in development of conventional T cell as well as agonist selected T cells such as CD8αα+ αβ T cells. Obesity is characterized by chronic inflammation and immune dysregulation, but the link between obesity and T cells has remains unclear. We show that Fam49b-deficient mice have a high level of energy expenditure and are resistant to high fat diet induced obesity. Furthermore, the higher energy expenditure characteristic was also observed in Fam49b-deficient chimera mice. The study reveals that Fam49b deficient lymphocytes play an important role in whole body energy metabolism. [This research was supported by NIH grants R01 AI130210 and R37 AI060040]
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Affiliation(s)
- Chansu Park
- 1Johns Hopkins University School of Medicine
| | - Jian Guan
- 1Johns Hopkins University School of Medicine
| | - Peter Rhee
- 1Johns Hopkins University School of Medicine
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9
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Guan J, Shastri N. Unusual distribution of a non-classical MHC I restricted CD8+ T population. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.140.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The normal peptide repertoire presented by MHC class I molecules on the cell surface is essential for immune surveillance of intracellular pathogens. The generation of this peptide repertoire is critically dependent upon the ER aminopeptidase associated with Ag processing (ERAAP). Interestingly, ERAAP-deficient cells are recognized by a unique population of cytotoxic T cells, called QFL-T cells, that are specific for the ligand presented by the non-classical MHC molecule, Qa-1b. The QFL-T cells are similar to other non-classical MHC restricted NKT or MAIT cells in their αβ TCRs, but their physiological function(s) are unknown. To identify the potential function of QFL-T cells, we assessed the expression of the Qa-1b restricted ligand as well as the distribution of QFL-T cells in various tissues. We found the ERAAP-dependent Qa-1b restricted ligand as well as the QFL-T cells were highly expressed in the intestine. Remarkably, relative to wild-type mice, the overall number and frequency of QFL-T cells among the intraepithelial lymphocytes(IELs) decreased significantly in the germ-free mice whereas the splenic QFL-T population remained unaffected. These findings suggest a role for gut-microbiota in the homing/maintenance of the QFL-T cells in the intestine.
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Affiliation(s)
- Jian Guan
- 1Department of Pathology and the Institute of Cell Engineering, Johns Hopkins University School of Medicine
| | - Nilabh Shastri
- 1Department of Pathology and the Institute of Cell Engineering, Johns Hopkins University School of Medicine
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10
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Abstract
Why does cancer develop in situations where the immune system is perfectly capable of eliminating it?
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Affiliation(s)
- Jian Guan
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, United States
| | - Nilabh Shastri
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, United States
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11
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Zhang J, Yang SJ, Gonzalez F, Yang J, Zhang Y, He M, Shastri N, Murthy N. A peptide-based fluorescent probe images ERAAP activity in cells and in high throughput assays. Chem Commun (Camb) 2018; 54:7215-7218. [PMID: 29897370 DOI: 10.1039/c7cc09598h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ERAAP is an intracellular amino-peptidase that plays a central role in determining the repertoire of peptides displayed by cells by MHC class I molecules, and dysfunctions in ERAAP are linked to a variety of diseases. There is therefore great interest in developing probes that can image ERAAP in cells. In this report we present a fluorescent probe, termed Ep, that can image ERAAP activity in live cells. Ep is composed of a 10 amino acid ERAAP substrate that has a donor quencher pair conjugated to it, composed of BODIPY and dinitro-toluene. Ep undergoes a 20-fold increase in fluorescence after ERAAP cleavage, and was able to image ERAAP activity in cell culture via fluorescence microscopy. In addition, we used Ep to develop a high throughput screen for ERAAP inhibitors, and screened an electrophile library containing 1460 compounds. From this Ep based screen we identified aromatic alkyne-ketone as a lead fragment that can irreversibly inhibit ERAAP activity. We anticipate numerous applications of Ep given its unique ability to image ERAAP within cells.
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Affiliation(s)
- Jingtuo Zhang
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720, USA.
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12
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Park C, Guan J, Ding T, Gonzalez F, Shastri N. Self-reactive T cells restricted by non-classical MHC Ib are associated with metabolic disease. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.99.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The normal peptide repertoire presented by classical and non-classical MHC class I molecules is regulated by ERAAP, the ER aminopeptidase associated with antigen processing. Loss of ERAAP’s peptide trimming function in cells causes dramatic changes in the peptide repertoire. The changes in the peptide repertoire enhance the immunogenicity of ERAAP-deficient cells and elicit potent immune responses in otherwise syngeneic wild-type mice. Normal ERAAP function is monitored by an unusual subset of semi-invariant CD8+ T cells that recognize the QFL ligand. The QFL ligand consists of a peptide encoded by the highly conserved FAM49a/b genes that is presented by Qa-1b, a non-classical MHC Ib molecule only on surface of ERAAP-deficient cells. We show that these QFL-specific CD8+ T cells (QFL-T cells) bear unique and semi-invariant αβ TCRs. Genetic manipulation of the expression of the self-QFL ligand and functional characteristics of QFL-T cells shows that in addition to monitoring ERAAP function, QFL-T cells may also regulate metabolic activity.
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Affiliation(s)
| | - Jian Guan
- 2Peking University Health Science Center, China
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13
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Kanwar N, Hassan F, Barclay L, Langley C, Vinjé J, Bryant PW, George KS, Mosher L, Matthews-Greer JM, Rocha MA, Beenhouwer DO, Harrison CJ, Moffatt M, Shastri N, Selvarangan R. Evaluation of RIDA ®GENE norovirus GI/GII real time RT-PCR using stool specimens collected from children and adults with acute gastroenteritis. J Clin Virol 2018; 104:1-4. [PMID: 29702350 DOI: 10.1016/j.jcv.2018.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/06/2018] [Accepted: 04/07/2018] [Indexed: 11/24/2022]
Abstract
BACKGROUND Norovirus is the leading cause of epidemic and sporadic acute gastroenteritis (AGE) in the United States. Widespread prevalence necessitates implementation of accurate norovirus detection assays in clinical diagnostic laboratories. OBJECTIVE To evaluate RIDA®GENE norovirus GI/GII real-time RT-PCR assay (RGN RT-PCR) using stool samples from patients with sporadic AGE. STUDY DESIGN Patients between 14 days to 101 years of age with symptoms of AGE were enrolled prospectively at four sites across the United States during 2014-2015. Stool specimens were screened for the presence of norovirus RNA by the RGN RT-PCR assay. Results were compared with a reference method that included conventional RT-PCR and sequencing of a partial region of the 5'end of the norovirus ORF2 gene. RESULTS A total of 259 (36.0%) of 719 specimens tested positive for norovirus by the reference method. The RGN RT-PCR assay detected norovirus in 244 (94%) of these 259 norovirus positive specimens. The sensitivity and specificity (95% confidence interval) of the RGN RT-PCR assay for detecting norovirus genogroup (G) I was 82.8% (63.5-93.5) and 99.1% (98.0-99.6) and for GII was 94.8% (90.8-97.2) and 98.6% (96.9-99.4), respectively. Seven specimens tested positive by the RGN-RT PCR that were negative by the reference method. The fifteen false negative samples were typed as GII.4 Sydney, GII.13, GI.3, GI.5, GI.2, GII.1, and GII.3 in the reference method. CONCLUSIONS The RGN RT-PCR assay had a high sensitivity and specificity for the detection of norovirus in stool specimens from patients with sporadic AGE.
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Affiliation(s)
- N Kanwar
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital and Clinics, Kansas City, MO, USA
| | - F Hassan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital and Clinics, Kansas City, MO, USA
| | - L Barclay
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - C Langley
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - J Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - P W Bryant
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - K St George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - L Mosher
- Michigan Department of Human and Health Services, MI, USA
| | | | - M A Rocha
- Division of Infectious Diseases, VA Greater Los Angeles Healthcare System, CA, USA
| | - D O Beenhouwer
- Division of Infectious Diseases, VA Greater Los Angeles Healthcare System, CA, USA; Department of Medicine, University of California Los Angeles, CA, USA
| | - C J Harrison
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital and Clinics, Kansas City, MO, USA; Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - M Moffatt
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital and Clinics, Kansas City, MO, USA; Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - N Shastri
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital and Clinics, Kansas City, MO, USA; Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - R Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital and Clinics, Kansas City, MO, USA; Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA.
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14
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Abstract
Effective immune surveillance by CD8(+) cytotoxic T cells of intracellular microbes and cancer depends on the antigen presentation pathway. This pathway produces an optimal peptide repertoire for presentation by major histocompatibility (MHC) class I molecules (pMHCs I) on the cell surface. We have known for years that the pMHC I repertoire is a reflection of the intracellular protein pool. However, many studies have revealed that pMHCs I present peptides not only from precursors encoded in open-reading frames of mRNA transcripts but also cryptic peptides encoded in apparently 'untranslated' regions. These sources vastly increase the availability of peptides for presentation and immune evasion. Here, we review studies on the composition of the cryptic pMHC I repertoire, the immunological significance of these pMHC I, and the novel translational mechanisms that generate cryptic peptides from unusual sources.
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Affiliation(s)
- Shelley R Starck
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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15
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Sa Q, Ochiai E, Tiwari A, Mullins J, Shastri N, Mercier C, Cesbron-Delauw MF, Suzuki Y. Determination of a Key Antigen for Immunological Intervention To Target the Latent Stage of Toxoplasma gondii. J Immunol 2017; 198:4425-4434. [PMID: 28446567 DOI: 10.4049/jimmunol.1700062] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/30/2017] [Indexed: 01/23/2023]
Abstract
Toxoplasma gondii, an obligate intracellular protozoan parasite, establishes a chronic infection by forming cysts preferentially in the brain. Up to one third of the human population worldwide is estimated to be chronically infected with this parasite. However, there is currently no drug effective against the cyst form of the parasite. In addition, the protective immunity against the cysts remains largely unknown. We analyzed the molecular mechanisms by which the immune system detects host cells harboring the cysts to eliminate the latent stage of the parasite using mice with the H-2d haplotype, which are genetically resistant to the infection. Our study revealed that CD8+ immune T cells bearing TCR Vβ8.1, 8.2 chain have a potent activity to remove T. gondii cysts from the brain. Our studies also uncovered that H-2Ld is the major Ag-presenting molecule to CD8+ T cells for initiating cyst elimination, and that CD8+Vβ8.1, 8.2+ immune T cells recognize the N-terminal region (aa 41-152) of dense granule protein 6 (GRA6Nt) of the parasite presented by the H-2Ld molecule. Furthermore, CD8+ immune T cells induced by immunization with recombinant GRA6Nt were eventually capable of removing the cysts from the brain when transferred to infected immunodeficient mice lacking T cells. Thus, GRA6Nt is a novel and potent Ag to activate CD8+ T cells capable of removing T. gondii cysts. These observations offer a basis for immunological intervention to combat chronic infection with T. gondii by targeting the persistent cysts of the parasite.
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Affiliation(s)
- Qila Sa
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY 40536
| | - Eri Ochiai
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY 40536
| | - Ashish Tiwari
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY 40536
| | - Jeremi Mullins
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY 40536
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720; and
| | - Corinne Mercier
- Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble, CNRS-UMR5525, Université Grenoble Alpes, La Tronche 38700, France
| | - Marie-France Cesbron-Delauw
- Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble, CNRS-UMR5525, Université Grenoble Alpes, La Tronche 38700, France
| | - Yasuhiro Suzuki
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY 40536;
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16
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Guan J, Yang SJ, Gonzalez F, Yin Y, Shastri N. Antigen Processing in the Endoplasmic Reticulum Is Monitored by Semi-Invariant αβ TCRs Specific for a Conserved Peptide-Qa-1 b MHC Class Ib Ligand. J Immunol 2017; 198:2017-2027. [PMID: 28108559 DOI: 10.4049/jimmunol.1600764] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 12/19/2016] [Indexed: 12/11/2022]
Abstract
Ag processing in the endoplasmic reticulum (ER) by the ER aminopeptidase associated with Ag processing (ERAAP) is central to presentation of a normal peptide-MHC class I (MHC I) repertoire. Alternations in ERAAP function cause dramatic changes in the MHC I-presented peptides, which elicit potent immune responses. An unusual subset of CD8+ T cells monitor normal Ag processing by responding to a highly conserved FL9 peptide that is presented by Qa-1b, a nonclassical MHC Ib molecule (QFL) in ERAAP-deficient cells. To understand the structural basis for recognition of the conserved ligand, we analyzed the αβ TCRs of QFL-specific T cells. Individual cells in normal wild-type and TCRβ-transgenic mice were assessed for QFL-specific TCR α- and β-chains. The QFL-specific cells expressed a predominant semi-invariant TCR generated by DNA rearrangement of TRAV9d-3-TRAJ21 α-chain and TRBV5-TRBD1-TRBJ2-7 β-chain gene segments. Furthermore, the CDR3 regions of the α- as well as β-chains were required for QFL ligand recognition. Thus, the αβ TCRs used to recognize the peptide-Qa-1 ligand presented by ERAAP-deficient cells are semi-invariant and likely reflect a conserved mechanism for monitoring the fidelity of Ag processing in the ER.
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Affiliation(s)
- Jian Guan
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, People's Republic of China; and.,Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Soo Jung Yang
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Federico Gonzalez
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, People's Republic of China; and
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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17
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Prasad S, Starck SR, Shastri N. Presentation of Cryptic Peptides by MHC Class I Is Enhanced by Inflammatory Stimuli. J Immunol 2016; 197:2981-2991. [PMID: 27647836 DOI: 10.4049/jimmunol.1502045] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 08/16/2016] [Indexed: 12/14/2022]
Abstract
Cytolytic T cells eliminate infected or cancer cells by recognizing peptides presented by MHC class I molecules on the cell surface. The antigenic peptides are derived primarily from newly synthesized proteins including those produced by cryptic translation mechanisms. Previous studies have shown that cryptic translation can be initiated by distinct mechanisms at non-AUG codons in addition to conventional translation initiated at the canonical AUG start codon. In this study, we show that presentation of endogenously translated cryptic peptides is enhanced by TLR signaling pathways involved in pathogen recognition as well as by infection with different viruses. This enhancement of cryptic peptides was caused by proinflammatory cytokines, secreted in response to microbial infection. Furthermore, blocking these cytokines abrogated the enhancement of cryptic peptide presentation in response to infection. Thus, presentation of cryptic peptides is selectively enhanced during inflammation and infection, which could allow the immune system to detect intracellular pathogens that might otherwise escape detection because of inhibition of conventional host translation mechanisms.
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Affiliation(s)
- Sharanya Prasad
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Shelley R Starck
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720
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18
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Sanecka A, Yoshida N, Dougan SK, Jackson J, Shastri N, Ploegh H, Blanchard N, Frickel EM. Transnuclear CD8 T cells specific for the immunodominant epitope Gra6 lower acute-phase Toxoplasma gondii burden. Immunology 2016; 149:270-279. [PMID: 27377596 PMCID: PMC5046057 DOI: 10.1111/imm.12643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/26/2016] [Accepted: 06/29/2016] [Indexed: 11/27/2022] Open
Abstract
We generated a CD8 T‐cell receptor (TCR) transnuclear (TN) mouse specific to the Ld‐restricted immunodominant epitope of GRA6 from Toxoplasma gondii as a source of cells to facilitate further investigation into the CD8 T‐cell‐mediated response against this pathogen. The TN T cells bound Ld‐Gra6 tetramer and proliferated upon unspecific and peptide‐specific stimulation. The TCR beta sequence of the Gra6‐specific TN CD8 T cells is identical in its V‐ and J‐region to the TCR‐β harboured by a hybridoma line generated in response to Gra6 peptide. Adoptively transferred Gra6 TN CD8 T cells proliferated upon Toxoplasma infection in vivo and exhibited an activated phenotype similar to host CD8 T cells specific to Gra6. The brain of Toxoplasma‐infected mice carried Gra6 TN cells already at day 8 post‐infection. Both Gra6 TN mice as well as adoptively transferred Gra6 TN cells were able to significantly reduce the parasite burden in the acute phase of Toxoplasma infection. Overall, the Gra6 TN mouse represents a functional tool to study the protective and immunodominant specific CD8 T‐cell response to Toxoplasma in both the acute and the chronic phases of infection.
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Affiliation(s)
- Anna Sanecka
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, UK
| | - Nagisa Yoshida
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, UK
| | - Stephanie K Dougan
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John Jackson
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Hidde Ploegh
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicolas Blanchard
- INSERM UMR1043, CNRS UMR5282, Université de Toulouse-UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, France
| | - Eva-Maria Frickel
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, Mill Hill Laboratory, London, UK.
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19
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Chu HH, Chan SW, Gosling JP, Blanchard N, Tsitsiklis A, Lythe G, Shastri N, Molina-París C, Robey EA. Continuous Effector CD8(+) T Cell Production in a Controlled Persistent Infection Is Sustained by a Proliferative Intermediate Population. Immunity 2016; 45:159-71. [PMID: 27421704 DOI: 10.1016/j.immuni.2016.06.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 03/31/2016] [Accepted: 04/20/2016] [Indexed: 01/22/2023]
Abstract
Highly functional CD8(+) effector T (Teff) cells can persist in large numbers during controlled persistent infections, as exemplified by rare HIV-infected individuals who control the virus. Here we examined the cellular mechanisms that maintain ongoing T effector responses using a mouse model for persistent Toxoplasma gondii infection. In mice expressing the protective MHC-I molecule, H-2L(d), a dominant T effector response against a single parasite antigen was maintained without a contraction phase, correlating with ongoing presentation of the dominant antigen. Large numbers of short-lived Teff cells were continuously produced via a proliferative, antigen-dependent intermediate (Tint) population with a memory-effector hybrid phenotype. During an acute, resolved infection, decreasing antigen load correlated with a sharp drop in the Tint cell population and subsequent loss of the ongoing effector response. Vaccination approaches aimed at the development of Tint populations might prove effective against pathogens that lead to chronic infection.
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Affiliation(s)
- H Hamlet Chu
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Shiao-Wei Chan
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - John Paul Gosling
- Departments of Statistics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | - Nicolas Blanchard
- Center of Pathophysiology of Toulouse-Purpan, INSERM UMR1043-CNRS UMR5282, University of Toulouse, 31024 Toulouse Cedex 3, France
| | - Alexandra Tsitsiklis
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Grant Lythe
- Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Carmen Molina-París
- Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
| | - Ellen A Robey
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA.
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20
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Nagarajan NA, de Verteuil DA, Sriranganadane D, Yahyaoui W, Thibault P, Perreault C, Shastri N. ERAAP Shapes the Peptidome Associated with Classical and Nonclassical MHC Class I Molecules. J Immunol 2016; 197:1035-43. [PMID: 27371725 DOI: 10.4049/jimmunol.1500654] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 04/19/2016] [Indexed: 11/19/2022]
Abstract
The peptide repertoire presented by classical as well as nonclassical MHC class I (MHC I) molecules is altered in the absence of the endoplasmic reticulum aminopeptidase associated with Ag processing (ERAAP). To characterize the extent of these changes, peptides from cells lacking ERAAP were eluted from the cell surface and analyzed by high-throughput mass spectrometry. We found that most peptides found in wild-type (WT) cells were retained in the absence of ERAAP. In contrast, a subset of "ERAAP-edited" peptides was lost in WT cells, and ERAAP-deficient cells presented a unique "unedited" repertoire. A substantial fraction of MHC-associated peptides from ERAAP-deficient cells contained N-terminal extensions and had a different molecular composition than did those from WT cells. We found that the number and immunogenicity of peptides associated with nonclassical MHC I was increased in the absence of ERAAP. Conversely, only peptides presented by classical MHC I were immunogenic in ERAAP-sufficient cells. Finally, MHC I peptides were also derived from different intracellular sources in ERAAP-deficient cells.
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Affiliation(s)
- Niranjana A Nagarajan
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720; and
| | - Danielle A de Verteuil
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Dev Sriranganadane
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Wafaa Yahyaoui
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720; and
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21
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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: 251] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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Affiliation(s)
- Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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23
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Yang SJ, Shastri N. The ER-resident protease ERAAP generates CD4+ T cell epitopes (APP5P.104). The Journal of Immunology 2015. [DOI: 10.4049/jimmunol.194.supp.183.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
ERAAP, the ER aminopeptidase associated with antigen processing is well established as a critical player in shaping the peptide repertoire presented by MHC class I molecules to CD8+ T cells. Remarkably, we found that ERAAP also influences the repertoire of endogenous peptides presented by MHC class II molecules to CD4+ T cells. ERAAP-knock out mice elicited CD4+ T cells in response to ERAAP-dependent peptides presented by Ab MHC class II molecules. The generation of these peptides was TAP-independent but required endosomal proteolysis. Further supporting its role in MHC class II processing pathway, ERAAP was found in Lamp1+ vesicles in addition to its normal ER location in mature dendritic cells. Thus, a novel ERAAP-dependent endosomal pathway influences the peptide repertoire presented by MHC II molecules and CD4+ T cells responses.
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24
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Grover HS, Chu HH, Kelly FD, Yang SJ, Reese ML, Blanchard N, Gonzalez F, Chan SW, Boothroyd JC, Shastri N, Robey EA. Impact of regulated secretion on antiparasitic CD8 T cell responses. Cell Rep 2014; 7:1716-1728. [PMID: 24857659 DOI: 10.1016/j.celrep.2014.04.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 02/21/2014] [Accepted: 04/16/2014] [Indexed: 10/25/2022] Open
Abstract
CD8 T cells play a key role in defense against the intracellular parasite Toxoplasma, but why certain CD8 responses are more potent than others is not well understood. Here, we describe a parasite antigen, ROP5, that elicits a CD8 T cell response in genetically susceptible mice. ROP5 is secreted via parasite organelles termed rhoptries that are injected directly into host cells during invasion, whereas the protective, dense-granule antigen GRA6 is constitutively secreted into the parasitophorous vacuole. Transgenic parasites in which the ROP5 antigenic epitope was targeted for secretion through dense granules led to enhanced CD8 T cell responses, whereas targeting the GRA6 epitope to rhoptries led to reduced CD8 responses. CD8 T cell responses to the dense-granule-targeted ROP5 epitope resulted in reduced parasite load in the brain. These data suggest that the mode of secretion affects the efficacy of parasite-specific CD8 T cell responses.
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Affiliation(s)
- Harshita Satija Grover
- Division of Immunology and Pathogenesis, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - H Hamlet Chu
- Division of Immunology and Pathogenesis, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Felice D Kelly
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
| | - Soo Jung Yang
- Division of Immunology and Pathogenesis, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Michael L Reese
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
| | - Nicolas Blanchard
- Center of Pathophysiology of Toulouse-Purpan, INSERM UMR1043-CNRS UMR5282, University of Toulouse, 31024 Toulouse Cedex 3, France
| | - Federico Gonzalez
- Division of Immunology and Pathogenesis, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - Shiao Wei Chan
- Division of Immunology and Pathogenesis, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
| | - John C Boothroyd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5124, USA
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA.
| | - Ellen A Robey
- Division of Immunology and Pathogenesis, Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA.
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25
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Yang SJ, Shastri N. ERAAP associates with MHC I molecules for generation of optimal MHC I peptide repertoire. (APP3P.100). The Journal of Immunology 2014. [DOI: 10.4049/jimmunol.192.supp.111.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Endoplasmic reticulum (ER) aminopeptidase associated with antigen processing (ERAAP) plays a critical role in the generation of the peptide repertoire presented by MHC I by trimming precursor peptides to optimal length. How ERAAP carries out this function and whether ERAAP activity is influenced by MHC I or other molecules in the ER is unknown. Here, we show that ERAAP physically associates with MHC I during peptide trimming events in the ER. ERAAP or its truncated domains II/III interacted with empty MHC I in the ER, but this interaction was independent of the peptide-loading complex. Most importantly, overexpression of domain II/III interrupted ERAAP function in wild-type cells resulting in altered-peptide presentation by MHC I. Thus, ERAAP function can be regulated by its association with MHC I and perhaps other key ER molecules.
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26
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Chen L, Fischer R, Peng Y, Reeves E, McHugh K, Ternette N, Hanke T, Dong T, Elliott T, Shastri N, Kollnberger S, James E, Kessler B, Bowness P. Critical role of endoplasmic reticulum aminopeptidase 1 in determining the length and sequence of peptides bound and presented by HLA-B27. Arthritis Rheumatol 2014; 66:284-94. [PMID: 24504800 DOI: 10.1002/art.38249] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 10/22/2013] [Indexed: 12/16/2022]
Abstract
OBJECTIVE HLA-B27 and endoplasmic reticulum aminopeptidase 1 (ERAP1) are the two strongest genetic factors predisposing to ankylosing spondylitis (AS). A key aminopeptidase in class I major histocompatibility complex presentation, ERAP1 potentially contributes to the pathogenesis of AS by altering HLA-B27 peptide presentation. The aim of this study was to analyze the effects of ERAP1 on the HLA-B27 peptide repertoire and peptide presentation to cytotoxic T lymphocytes (CTLs). METHODS ERAP1-silenced and -competent HeLa.B27 and C1R.B27 cells were isotope-labeled, mixed, lysed, and then immunoprecipitated using W6/32 or ME1 antibodies. Peptides bound to HLA-B27 were eluted and analyzed by tandem mass spectrometry. Selected peptides were synthesized and tested for HLA-B27 binding ability. The effect of ERAP1 silencing/mutation on presentation of an immunodominant viral HLA-B27 epitope, KK10, to CTLs was also studied. RESULTS In both HeLa.B27 and C1R.B27 cells, the proportion of 9-mer HLA-B27-bound peptides was decreased by ERAP1 silencing, whereas the percentages of longer peptides (11-13 mer) were increased. Surprisingly, following ERAP1 silencing, C-terminally extended peptides were readily identified. These were better able to bind to HLA-B27 than were N-terminally extended peptides lacking an arginine at position 2. In both HeLa.B27 cells and mouse fibroblasts expressing HLA-B27, the absence of ERAP1 reduced peptide recognition by HLA-B27-restricted KK10-specific CTLs following infection with recombinant vaccinia virus or transfection with minigenes expressing KK10 precursors. Presence of an AS-protective variant of ERAP1, K528R, as compared to wild-type ERAP1, reduced the peptide recognition by KK10 CTLs following transfection with extended KK10 minigenes. CONCLUSION These results show that ERAP1 directly alters peptide binding and presentation by HLA-B27, thus demonstrating a potential pathogenic mechanism in AS. Inhibition of ERAP1 could potentially be used for treatment of AS and other ERAP1-associated diseases.
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Shastri N, Nagarajan N, Lind KC, Kanaseki T. Monitoring peptide processing for MHC class I molecules in the endoplasmic reticulum. Curr Opin Immunol 2013; 26:123-7. [PMID: 24556408 DOI: 10.1016/j.coi.2013.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 11/18/2013] [Indexed: 01/22/2023]
Abstract
Classical MHC class I molecules open a window into the cell by presenting intracellular peptides (pMHC I) on the surface. The peptides are used for immune surveillance by circulating CD8+ T and NK cells to detect and eliminate infected or tumor cells. Not surprisingly, viruses and tumor cells have evolved immune evasion mechanisms to keep the window shades down and the cytotoxic cells oblivious to their presence. Here, we review counter mechanisms that nevertheless allow the immune system to detect and eliminate cells unable to properly process antigenic peptides in the endoplasmic reticulum.
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Affiliation(s)
- Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
| | - Niranjana Nagarajan
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Kristin C Lind
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Takayuki Kanaseki
- Department of Pathology, School of Medicine, Sapporo Medical University, Sapporo, Japan
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Kanaseki T, Lind KC, Escobar H, Nagarajan N, Reyes-Vargas E, Rudd B, Rockwood AL, Van Kaer L, Sato N, Delgado JC, Shastri N. ERAAP and tapasin independently edit the amino and carboxyl termini of MHC class I peptides. J Immunol 2013; 191:1547-55. [PMID: 23863903 DOI: 10.4049/jimmunol.1301043] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Effective CD8(+) T cell responses depend on presentation of a stable peptide repertoire by MHC class I (MHC I) molecules on the cell surface. The overall quality of peptide-MHC I complexes (pMHC I) is determined by poorly understood mechanisms that generate and load peptides with appropriate consensus motifs onto MHC I. In this article, we show that both tapasin (Tpn), a key component of the peptide loading complex, and the endoplasmic reticulum aminopeptidase associated with Ag processing (ERAAP) are quintessential editors of distinct structural features of the peptide repertoire. We carried out reciprocal immunization of wild-type mice with cells from Tpn- or ERAAP-deficient mice. Specificity analysis of T cell responses showed that absence of Tpn or ERAAP independently altered the peptide repertoire by causing loss as well as gain of new pMHC I. Changes in amino acid sequences of MHC-bound peptides revealed that ERAAP and Tpn, respectively, defined the characteristic amino and carboxy termini of canonical MHC I peptides. Thus, the optimal pMHC I repertoire is produced by two distinct peptide editing steps in the endoplasmic reticulum.
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Affiliation(s)
- Takayuki Kanaseki
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Feliu V, Vasseur V, Grover HS, Chu HH, Brown MJ, Wang J, Boyle JP, Robey EA, Shastri N, Blanchard N. Location of the CD8 T cell epitope within the antigenic precursor determines immunogenicity and protection against the Toxoplasma gondii parasite. PLoS Pathog 2013; 9:e1003449. [PMID: 23818852 PMCID: PMC3688528 DOI: 10.1371/journal.ppat.1003449] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Accepted: 05/07/2013] [Indexed: 12/24/2022] Open
Abstract
CD8 T cells protect the host from disease caused by intracellular pathogens, such as the Toxoplasma gondii (T. gondii) protozoan parasite. Despite the complexity of the T. gondii proteome, CD8 T cell responses are restricted to only a small number of peptide epitopes derived from a limited set of antigenic precursors. This phenomenon is known as immunodominance and is key to effective vaccine design. However, the mechanisms that determine the immunogenicity and immunodominance hierarchy of parasite antigens are not well understood. Here, using genetically modified parasites, we show that parasite burden is controlled by the immunodominant GRA6-specific CD8 T cell response but not by responses to the subdominant GRA4- and ROP7-derived epitopes. Remarkably, optimal processing and immunodominance were determined by the location of the peptide epitope at the C-terminus of the GRA6 antigenic precursor. In contrast, immunodominance could not be explained by the peptide affinity for the MHC I molecule or the frequency of T cell precursors in the naive animals. Our results reveal the molecular requirements for optimal presentation of an intracellular parasite antigen and for eliciting protective CD8 T cells.
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Affiliation(s)
- Virginie Feliu
- INSERM, U1043, Toulouse, France
- CNRS, U5282, Toulouse, France
- Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, France
| | - Virginie Vasseur
- INSERM, U1043, Toulouse, France
- CNRS, U5282, Toulouse, France
- Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, France
| | - Harshita S. Grover
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - H. Hamlet Chu
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Mark J. Brown
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jeremy Wang
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Jon P. Boyle
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ellen A. Robey
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Nicolas Blanchard
- INSERM, U1043, Toulouse, France
- CNRS, U5282, Toulouse, France
- Université de Toulouse, UPS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, France
- * E-mail:
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Howland SW, Poh CM, Gun SY, Claser C, Malleret B, Shastri N, Ginhoux F, Grotenbreg GM, Rénia L. Brain microvessel cross-presentation is a hallmark of experimental cerebral malaria. EMBO Mol Med 2013; 5:984-99. [PMID: 23681698 PMCID: PMC3721469 DOI: 10.1002/emmm.201202273] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 04/04/2013] [Accepted: 04/05/2013] [Indexed: 01/02/2023] Open
Abstract
Cerebral malaria is a devastating complication of Plasmodium falciparum infection. Its pathogenesis is complex, involving both parasite- and immune-mediated events. CD8+ T cells play an effector role in murine experimental cerebral malaria (ECM) induced by Plasmodium berghei ANKA (PbA) infection. We have identified a highly immunogenic CD8 epitope in glideosome-associated protein 50 that is conserved across rodent malaria species. Epitope-specific CD8+ T cells are induced during PbA infection, migrating to the brain just before neurological signs manifest. They are functional, cytotoxic and can damage the blood–brain barrier in vivo. Such CD8+ T cells are also found in the brain during infection with parasite strains/species that do not induce neuropathology. We demonstrate here that PbA infection causes brain microvessels to cross-present parasite antigen, while non-ECM-causing parasites do not. Further, treatment with fast-acting anti-malarial drugs before the onset of ECM reduces parasite load and thus antigen presentation in the brain, preventing ECM death. Thus our data suggest that combined therapies targeting both the parasite and host antigen-presenting cells may improve the outcome of CM patients.
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Affiliation(s)
- Shanshan W Howland
- Singapore Immunology Network, Agency for Science, Technology and Research A*STAR, Singapore, Singapore
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Prasad S, Starck S, Shastri N. Presentation of cryptic peptides by MHC I molecules is enhanced by inflammatory stimuli. (P5003). The Journal of Immunology 2013. [DOI: 10.4049/jimmunol.190.supp.110.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Cytolytic T cells eliminate infected cells by recognizing intracellular peptides presented by MHC class I molecules. The antigenic peptides are derived primarily from newly synthesized proteins including those produced by cryptic translation. Previous studies have shown that in addition to the canonical AUG codon, translation can be initiated at non-AUG codons . Furthermore, translation initiation at non-AUG codons such as CUG is mechanistically distinct from canonical translation initiation as it is resistant to protein synthesis inhibitors that cause global translation shutdown. Here, we show that Toll-like receptor (TLR) signaling pathways involved in pathogen recognition enhance presentation of the cryptic peptides. Moreover, infection of bone-marrow derived macrophages with MCMV, influenza viruses or pro-inflammatory cytokines also enhances cryptic peptide presentation. Thus, translation and presentation of cryptic peptides may allow the immune system to detect intracellular pathogens that inhibit host translation and presentation of peptides from conventional sources.
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Affiliation(s)
- Sharanya Prasad
- 1Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Shelley Starck
- 1Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Nilabh Shastri
- 1Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
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Abstract
The ER aminopeptidase associated with antigen processing, ERAAP (or ERAP1), is essential for trimming peptides that are presented by MHC class I molecules. ERAP1 is inhibited by human cytomegalovirus, and ERAP1 polymorphisms are associated with autoimmune diseases. How the immune system detects ERAAP dysfunction, however, is unknown. We have shown previously that ERAAP-deficient cells present an immunogenic pMHC I repertoire, that elicits CD8+ T cell response in WT mice. Additionally, we discovered that the WT CD8+ T cells recognized novel peptides presented by non-classical, or MHC class Ib, molecules on ERAAP-deficient cells. The MHC Ib restricted WT CD8 T cells eliminated ERAAP-deficient cells in vitro and in vivo. We identified the FL9 peptide, presented by Qa-1(b), a MHC class Ib molecule exclusively on ERAAP-deficient cells. Remarkably, T cells specific for the FL9-Qa-1(b) complex were frequent in naïve WT mice, and had an antigen-experienced phenotype. Thus, novel non-classical pQa-1(b) complexes direct cytotoxic T cells to target cells with defective peptide processing in the endoplasmic reticulum. Here, we discuss the implications of our findings, and the possible roles of pMHC Ib-specific T cells in immune surveillance for ERAAP dysfunction.
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Affiliation(s)
- Niranjana A Nagarajan
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3200, USA
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Abstract
Immune surveillance of infected or tumor cells by CD8(+) T cells requires that MHC class I molecules present a diverse repertoire of peptides on the cell surface. Even a few copies of individual peptides among this mixture are sufficient for recognition by the antigen receptors of appropriate CD8(+) T cells. Here we describe a method for biochemical analysis of the naturally processed peptides in living cells. The peptide mixture in cell extracts is fractionated using reverse phase high performance liquid chromatography and detected by the activation of CD8(+) T cell hybridomas. The results provide information on the structure and amount of the peptides and yield insights into the mechanisms that generate the naturally processed peptides.
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Affiliation(s)
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
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Starck SR, Jiang V, Pavon-Eternod M, Prasad S, McCarthy B, Pan T, Shastri N. Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I. Science 2012; 336:1719-23. [PMID: 22745432 DOI: 10.1126/science.1220270] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Effective immune surveillance by cytotoxic T cells requires newly synthesized polypeptides for presentation by major histocompatibility complex (MHC) class I molecules. These polypeptides are produced not only from conventional AUG-initiated, but also from cryptic non-AUG-initiated, reading frames by distinct translational mechanisms. Biochemical analysis of ribosomal initiation complexes at CUG versus AUG initiation codons revealed that cells use an elongator leucine-bound transfer RNA (Leu-tRNA) to initiate translation at cryptic CUG start codons. CUG/Leu-tRNA initiation was independent of the canonical initiator tRNA (AUG/Met-tRNA(i)(Met)) pathway but required expression of eukaryotic initiation factor 2A. Thus, a tRNA-based translation initiation mechanism allows non-AUG-initiated protein synthesis and supplies peptides for presentation by MHC class I molecules.
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Affiliation(s)
- Shelley R Starck
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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Heathfield S, Parker B, Zeef L, Bruce I, Alexander Y, Collins F, Stone M, Wang E, Williams AS, Wright HL, Thomas HB, Moots RJ, Edwards SW, Bullock C, Chapman V, Walsh DA, Mobasheri A, Kendall D, Kelly S, Bayley R, Buckley CD, Young SP, Rump-Goodrich L, Middleton J, Chen L, Fisher R, Kollnberger S, Shastri N, Kessler BM, Bowness P, Nazeer Moideen A, Evans L, Osgood L, Williams AS, Jones SA, Nowell MA, Mahadik Y, Young S, Morgan M, Gordon C, Harper L, Giles JL, Paul Morgan B, Harris CL, Rysnik OJ, McHugh K, Kollnberger S, Payeli S, Marroquin O, Shaw J, Renner C, Bowness P, Nayar S, Cloake T, Bombardieri M, Pitzalis C, Buckley C, Barone F, Barone F, Nayar S, Cloake T, Lane P, Coles M, Buckley C, Williams EL, Edwards CJ, Cooper C, Oreffo RO, Dunn S, Crawford A, Wilkinson M, Le Maitre C, Bunning R, Daniels J, Phillips KLE, Chiverton N, Le Maitre CL, Kollnberger S, Shaw J, Ridley A, Wong-Baeza I, McHugh K, Keidel S, Chan A, Bowness P, Gullick NJ, Abozaid HS, Jayaraj DM, Evans HG, Scott DL, Choy EH, Taams LS, Hickling M, Golor G, Jullion A, Shaw S, Kretsos K, Bari SF, Rhys-Dillon B, Amos N, Siebert S, Phillips KLE, Chiverton N, Bunning RD, Haddock G, Cross AK, Le Maitre CL, Kate I, Phillips E, Cross A, Chiverton N, Haddock G, Bunning RAD, Le Maitre CL, Ceeraz S, Spencer J, Choy E, Corrigall V, Crilly A, Palmer H, Lockhart J, Plevin R, Ferrell WR, McInnes I, Hutchinson D, Perry L, DiCicco M, Humby F, Kelly S, Hands R, Buckley C, McInnes I, Taylor P, Bombardieri M, Pitzalis C, Mehta P, Mitchell A, Tysoe C, Caswell R, Owens M, Vincent T, Hashmi TM, Price-Forbes A, Sharp CA, Murphy H, Wood EF, Doherty T, Sheldon J, Sofat N, Goff I, Platt PN, Abdulkader R, Clunie G, Ismajli M, Nikiphorou E, Young A, Tugnet N, Dixey J, Banik S, Alcorn D, Hunter J, Win Maw W, Patil P, Hayes F, Main Wong W, Borg FA, Dasgupta B, Malaviya AP, Ostor AJ, Chana JK, Ahmed AA, Edmonds S, Hayes F, Coward L, Borg F, Heaney J, Amft N, Simpson J, Dhillon V, Ayalew Y, Khattak F, Gayed M, Amarasena RI, McKenna F, Amarasena RI, McKenna F, Mc Laughlin M, Baburaj K, Fattah Z, Ng N, Wilson J, Colaco B, Williams MR, Adizie T, Dasgupta B, Casey M, Lip S, Tan S, Anderson D, Robertson C, Devanny I, Field M, Walker D, Robinson S, Ryan S, Hassell A, Bateman J, Allen M, Davies D, Crouch C, Walker-Bone K, Gainsborough N, Gullick NJ, Lutalo PM, Davies UM, Walker-Bone K, Mckew JR, Millar AM, Wright SA, Bell AL, Thapper M, Roussou T, Cumming J, Hull RG, Thapper M, Roussou T, McKeogh J, O'Connor MB, Hassan AI, Bond U, Swan J, Phelan MJ, Coady D, Kumar N, Farrow L, Bukhari M, Oldroyd AG, Greenbank C, McBeth J, Duncan R, Brown D, Horan M, Pendleton N, Littlewood A, Cordingley L, Mulvey M, Curtis EM, Cole ZA, Crozier SR, Georgia N, Robinson SM, Godfrey KM, Sayer AA, Inskip HM, Cooper C, Harvey NC, Davies R, Mercer L, Galloway J, Low A, Watson K, Lunt M, Symmons D, Hyrich K, Chitale S, Estrach C, Moots RJ, Goodson NJ, Rankin E, Jiang CQ, Cheng KK, Lam TH, Adab P, Ling S, Chitale S, Moots RJ, Estrach C, Goodson NJ, Humphreys J, Ellis C, Bunn D, Verstappen SM, Symmons D, Fluess E, Macfarlane GJ, Bond C, Jones GT, Scott IC, Steer S, Lewis CM, Cope A, Mulvey MR, Macfarlane GJ, Symmons D, Lovell K, Keeley P, Woby S, Beasley M, McBeth J, Viatte S, Plant D, Lunt M, Fu B, Parker B, Galloway J, Solymossy C, Worthington J, Symmons D, Dixey J, Young A, Barton A, Williams FM, Osei-Bordom DC, Popham M, MacGregor A, Spector T, Little J, Herrick A, Pushpakom S, Ennis H, McBurney H, Worthington J, Newman W, Ibrahim I, Plant D, Hyrich K, Morgan A, Wilson A, Isaacs J, Barton A, Sanderson T, Hewlett S, Calnan M, Morris M, Raza K, Kumar K, Cardy CM, Pauling JD, Jenkins J, Brown SJ, McHugh N, Nikiphorou E, Mugford M, Davies C, Cooper N, Brooksby A, Bunn D, Symmons D, MacGregor A, Dures E, Ambler N, Fletcher D, Pope D, Robinson F, Rooke R, Hewlett S, Gorman CL, Reynolds P, Hakim AJ, Bosworth A, Weaver D, Kiely PD, Skeoch S, Jani M, Amarasena R, Rao C, Macphie E, McLoughlin Y, Shah P, Else S, Semenova O, Thompson H, Ogunbambi O, Kallankara S, Patel Y, Baguley E, Jani M, Halsey J, Severn A, Bukhari M, Selvan S, Price E, Husain MJ, Brophy S, Phillips CJ, Cooksey R, Irvine E, Siebert S, Lendrem D, Mitchell S, Bowman S, Price E, Pease CT, Emery P, Andrews J, Bombardieri M, Sutcliffe N, Pitzalis C, Lanyon P, Hunter J, Gupta M, McLaren J, Regan M, Cooper A, Giles I, Isenberg D, Griffiths B, Foggo H, Edgar S, Vadivelu S, Coady D, McHugh N, Ng WF, Dasgupta B, Taylor P, Iqbal I, Heron L, Pilling C, Marks J, Hull R, Ledingham J, Han C, Gathany T, Tandon N, Hsia E, Taylor P, Strand V, Sensky T, Harta N, Fleming S, Kay L, Rutherford M, Nicholl K, Kay L, Rutherford M, Nicholl K, Eyre T, Wilson G, Johnson P, Russell M, Timoshanko J, Duncan G, Spandley A, Roskell S, Coady D, West L, Adshead R, Donnelly SP, Ashton S, Tahir H, Patel D, Darroch J, Goodson NJ, Boulton J, Ellis B, Finlay R, Lendrem D, Mitchell S, Bowman S, Price E, Pease CT, Emery P, Andrews J, Bombardieri M, Sutcliffe N, Pitzalis C, Lanyon P, Hunter J, Gupta M, McLaren J, Regan M, Cooper A, Giles I, Isenberg D, Vadivelu S, Coady D, McHugh N, Griffiths B, Foggo H, Edgar S, Ng WF, Murray-Brown W, Priori R, Tappuni T, Vartoukian S, Seoudi N, Picarelli G, Fortune F, Valesini G, Pitzalis C, Bombardieri M, Ball E, Rooney M, Bell A, Merida AA, Isenberg D, Tarelli E, Axford J, Giles I, Pericleous C, Pierangeli SS, Ioannou J, Rahman A, Alavi A, Hughes M, Evans B, Bukhari M, Parker B, Zaki A, Alexander Y, Bruce I, Hui M, Garner R, Rees F, Bavakunji R, Daniel P, Varughese S, Srikanth A, Andres M, Pearce F, Leung J, Lim K, Regan M, Lanyon P, Oomatia A, Petri M, Fang H, Birnbaum J, Amissah-Arthur M, Gayed M, Stewart K, Jennens H, Braude S, Gordon C, Sutton EJ, Watson KD, Gordon C, Yee CS, Lanyon P, Jayne D, Isenberg D, Rahman A, Akil M, McHugh N, Ahmad Y, Amft N, D'Cruz D, Edwards CJ, Griffiths B, Khamashta M, Teh LS, Zoma A, Bruce I, Dey ID, Kenu E, Isenberg D, Pericleous C, Garza-Garcia A, Murfitt L, Driscoll PC, Isenberg D, Pierangeli S, Giles I, Ioannou Y, Rahman A, Reynolds JA, Ray DW, O'Neill T, Alexander Y, Bruce I, Segeda I, Shevchuk S, Kuvikova I, Brown N, Bruce I, Venning M, Mehta P, Dhanjal M, Mason J, Nelson-Piercy C, Basu N, Paudyal P, Stockton M, Lawton S, Dent C, Kindness K, Meldrum G, John E, Arthur C, West L, Macfarlane MV, Reid DM, Jones GT, Macfarlane GJ, Yates M, Loke Y, Watts R, MacGregor A, Adizie T, Christidis D, Dasgupta B, Williams M, Sivakumar R, Misra R, Danda D, Mahendranath KM, Bacon PA, Mackie SL, Pease CT. Basic science * 232. Certolizumab pegol prevents pro-inflammatory alterations in endothelial cell function. Rheumatology (Oxford) 2012. [DOI: 10.1093/rheumatology/kes108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Nagarajan N, Gonzalez F, Shastri N. Cytotoxic T cells specific for the non-classical MHC class I molecule Qa-1 detect defects in ER antigen processing. Mol Immunol 2012. [DOI: 10.1016/j.molimm.2012.02.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Grover H, Vasseur V, Féliu V, Wang J, Boyle J, Chu H, Chéneau C, Robey E, Shastri N, Blanchard N. Protein topology and epitope position play a critical role in shaping CD8 T cell immunodominance to the Toxoplasma gondii parasite. Mol Immunol 2012. [DOI: 10.1016/j.molimm.2012.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Shastri N, Chen K. Equal Immune Rights For All Polypeptides (106.38). The Journal of Immunology 2012. [DOI: 10.4049/jimmunol.188.supp.106.38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Effective immune surveillance requires that MHC class I molecules display a peptide repertoire on the surface representing all cellular proteins. How the peptide repertoire can be comprehensive despite large differences in abundance and stability of individual proteins is not known. We show here that peptide presentation by MHC I molecules is strongly influenced by the pioneer round of translation (PRT) associated with nonsense mediated decay (NMD) of mRNAs. The PRT allows cells to detect and eliminate aberrant mRNAs containing premature stop codons. Inhibition of PRT by knock-down of CBP80, a unique cap-binding protein reduced peptide presentation by MHC class I molecules on the cell surface without affecting global protein synthesis. On the other hand, introduction of premature stop codons changed mRNA stability without affecting peptide presentation by MHC I on the cell surface. Thus, the pioneer round of translation could be used to derive peptides presentation by MHC I molecules to generate a comprehensive display of virtually all endogenous proteins.
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Affiliation(s)
| | - Keling Chen
- 1Molecular and Cell Biology, UC Berkeley, Berkeley, CA
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Grover H, Reese M, Blanchard N, Gonzalez F, Chan S, Robey E, Shastri N. The mechanism of resistance to parasite infection. (100.14). The Journal of Immunology 2011. [DOI: 10.4049/jimmunol.186.supp.100.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The parasite, Toxoplasma gondii (T. gondii) can cause severe disease in immunocompromised humans. Susceptibility to T. gondii is also linked to the MHC haplotype: B10.D2 (H-2d) mice are relatively resistant to T. gondii infection than C57Bl/6 mice (B6, H-2b). CD8 T cells, activated by MHC molecules, are known to be that primary mediators of protection from T. gondii, and it is possible that differences in their responses might determine susceptibility to infection. Indeed, in H-2d mice, we recently identified the key immunodominant peptide, HF10, contained in the GRA6 protein that elicited protective CD8 T cell responses. In contrast, we show here that the CD8 T cell response to T. gondii in susceptible B6 mice is weaker and specific for a distinct peptide derived from the ROP5 protein. Furthermore, unlike the HF10 peptide that generated protective CD8 T cells in H-2d mice, immunization with the ROP5 peptide failed to diminish the parasite burden in chronically infected H-2b mice. Thus, susceptibility to T. gondii correlates with MHC-linked processing of specific parasite proteins that elicit differential CD8 T cell responses in mice.
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Affiliation(s)
| | | | - Nicolas Blanchard
- 3INSERM U563-Centre de Physiopathologie de Toulouse-Purpan, Toulouse, France
| | | | - Shiao Chan
- 1University of California, Berkeley, Berkeley, CA
| | - Ellen Robey
- 1University of California, Berkeley, Berkeley, CA
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40
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Bakker A, Shastri N. The role of ERAAP polymorphisms in the autoimmune disease Ankylosing Spondylitis (100.17). The Journal of Immunology 2011. [DOI: 10.4049/jimmunol.186.supp.100.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Ankylosing spondylitis (AS) is a chronic inflammatory joint disease of the axial skeleton, ultimately leading to fusion of the spine. For over three decades it has been known that the MHC class I molecule HLA-B27 is strongly associated with AS. In addition, the ER-resident aminopeptidase ERAAP (or ERAP1) was recently shown to be associated with as much as 26% of the risk for developing AS in HLA-B27 positive individuals. Multiple non-synonymous SNPs have been identified in the ERAAP gene that increase the risk of AS, but the functional significance of these polymorphisms is not known. The ERAAP protease is an essential component of the MHC class I pathway where it trims antigenic peptides in the ER. The significant association of both HLA-B27 and ERAAP with AS suggests that an altered MHC class I antigen processing pathway could play an important role in this partially T cell-mediated disease. To test this hypothesis we have analyzed the antigen processing capacity of several polymorphic forms of human ERAAP in ERAAP-deficient cells. All the polymorphic ERAAP constructs tested were enzymatically active and able to trim model antigenic peptides in different cell lines, with either no or minor differences in the quantity of total epitopes generated. We will discuss the implications of these findings.
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Affiliation(s)
- Arne Bakker
- 1University of California Berkeley, Berkeley, CA
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41
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Nagarajan N, Gonzalez F, Shastri N. A novel MHC class Ib-mediated immune surveillance mechanism detects the absence of ERAAP (100.16). The Journal of Immunology 2011. [DOI: 10.4049/jimmunol.186.supp.100.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Immune surveillance mechanisms detect failures in vital parts of the host immune system, such as in the antigen processing pathway. The ER aminopeptidase associated with antigen processing, ERAAP, is an essential component of the antigen processing pathway, and is required to generate the final peptides presented by MHC class I molecules. It has been unclear how the immune system detects deficiencies in ERAAP function, and here we describe a potential mechanism to do so. Non-classical MHC class I, or MHC class Ib, molecules present novel peptides in ERAAP-deficient cells, and elicit potent CD8 T cell responses in wild-type mice. Using these CD8 T cells as a probe, we identified a novel peptide presented by Qa-1b. FL9-Qa-1b-specific CD8 T cells can be readily detected in naïve mice and constitute a substantial fraction of the anti-ERAAP-/- immune response in wild-type mice. Additionally, WT CD8 T cells detect and eliminate MHC class Ib-expressing ERAAP-deficient cells. Therefore, we suggest that presentation of the FL9 peptide by Qa-1b molecules is a surveillance mechanism for detecting inhibition of ERAAP function.
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Lind K, Escobar H, Reyes-Vargas E, Delgado J, Shastri N. ERAAP-deficiency differentially affects peptide presentation across multiple MHC I (100.15). The Journal of Immunology 2011. [DOI: 10.4049/jimmunol.186.supp.100.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Genome-wide association studies in humans have linked polymorphisms in the ER aminopeptidase associated with antigen processing (ERAAP) as well as particular MHC class I molecules to autoimmune diseases. How ERAAP polymorphisms affect function of different MHC I molecules is not known. ERAAP normally trims antigenic precursor peptides to generate potential peptide-MHC I ligands that can be recognized by CD8 T cells. To detect changes in the peptide repertoires displayed by different MHC I molecules, we immunized wild-type B10.D2 (H-2d) mice with ERAAP-deficient (ERAAP-KO) cells and analyzed the specificity of the CD8 T cell response. In wild-type mice, anti-ERAAP KO T cells responded primarily to peptides presented by Kd, and not the other two MHC I molecules, Dd and Ld of the H-2d haplotype. We also assessed the MHC I bound peptide repertoire by mass spectrometry. This analysis revealed that Dd and Kd molecules were bound to large number of shared as well as unique peptides, some with N-terminal extensions. Remarkably, Ld bound peptides were not detected in ERAAP-deficient mice. Thus, changes in ERAAP expression can have a major influence on the peptide repertoire presented by different MHC I molecules as well as on CD8 T cell responses.
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Affiliation(s)
- Kristin Lind
- 1University of California, Berkeley, Berkeley, CA
| | - Hernando Escobar
- 2ARUP Institute for Clinical and Experimental Pathology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Eduardo Reyes-Vargas
- 2ARUP Institute for Clinical and Experimental Pathology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
| | - Julio Delgado
- 2ARUP Institute for Clinical and Experimental Pathology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT
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43
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Starck S, Jiang V, Pavon-Eternod M, Prasad S, Pan T, Shastri N. Cryptic tRNAi shapes the pMHC I repertoire (100.5). The Journal of Immunology 2011. [DOI: 10.4049/jimmunol.186.supp.100.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
MHC class I molecules present peptides on the cell surface for immune surveillance of viruses and cancer. Interestingly, the peptides are encoded not only in conventional AUG-initiated translational reading frames but also in non-AUG initiated cryptic reading frames. Whether the same or distinct translational machinery is used to produce cryptic peptides at non-AUG start codons, such as CUG, is not known. Here, we show that translational initiation of antigenic precursors at cryptic CUG codons is differentially regulated by ribosomal initiation complexes that contain novel initiator tRNAs. This tRNA is distinct from Met-initiator tRNA and enhances initiation at CUG start codons. Thus, a novel tRNA -based mechanism can supply peptides for presentation by MHC I.
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Affiliation(s)
| | - Vivian Jiang
- 1University of California Berkeley, Berkeley, CA
| | | | | | - Tao Pan
- 2University of Chicago, Chicago, IL
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44
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Abstract
Effectiveness of immune surveillance of intracellular viruses and bacteria depends upon a functioning antigen presentation pathway that allows infected cells to reveal the presence of an intracellular pathogen. The antigen presentation pathway uses virtually all endogenous polypeptides as a source to produce antigenic peptides that are eventually chaperoned to the cell surface by MHC class I molecules. Intriguingly, MHC I molecules present peptides encoded not only in the primary open reading frames but also those encoded in alternate reading frames. Here, we review recent studies on the generation of cryptic pMHC I. We focus on the immunological significance of cryptic pMHC I, and the novel translational mechanisms that allow production of these antigenic peptides from unconventional sources.
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Affiliation(s)
- Shelley R. Starck
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, LSA 421, Berkeley, CA 94720-3200 USA
| | - Nilabh Shastri
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, LSA 421, Berkeley, CA 94720-3200 USA
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45
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Blanchard N, Shastri N. Topological journey of parasite-derived antigens for presentation by MHC class I molecules. Trends Immunol 2010; 31:414-21. [PMID: 20869317 DOI: 10.1016/j.it.2010.08.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 08/12/2010] [Accepted: 08/13/2010] [Indexed: 12/21/2022]
Abstract
Within cells of their host, many bacteria and parasites inhabit specialized compartments, such as a modified phagosome for Mycobacterium tuberculosis or a parasitophorous vacuole for Toxoplasma gondii. These locations could exclude microbial material from entry into the MHC class I surveillance pathway. Remarkably, however, under these circumstances, cells can still signal the presence of invading pathogens to circulating CD8(+) T cells, which typically play a key role in protection against such intracellular organisms. Here, we review MHC I presentation pathways in various contexts, ranging from model antigens in non-infectious settings to pathogen-infected cells. We suggest that presentation of intracellular pathogens can be described as not just one, but several distinct pathways; perhaps because diverse pathogens have evolved different strategies to interact with host cells.
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Affiliation(s)
- Nicolas Blanchard
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3200, USA.
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46
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Kanaseki T, Camfiled Lind K, Shastri N. Editing the pMHCI repertoire in the ER by tapasin and ERAAP (130.24). The Journal of Immunology 2010. [DOI: 10.4049/jimmunol.184.supp.130.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The peptide/MHC class I complexes (pMHCI) displayed on the cell surface are essential for eliciting CD8+ T cell responses for adaptive immunity. How appropriate pMHCI are assembled within the peptide loading complex (PLC) in the endoplasmic reticulum (ER) is unclear. Here we show that tapasin, the core component of the PLC, edits the pMHCI repertoire in vivo. Compared to cells from wild-type mice, cells from tapasin-deficient mice express an immunologically distinct pMHCI repertoire. Tapasin-deficient cells lack many normal pMHCI and also express a set of novel pMHCI on the surface. Thus, CD8+ T cells responses are elicited in reciprocal immunizations between wild-type and tapasin-deficient mice. Interestingly, this set of pMHCI ligands is distinct from that found earlier in mice lacking ERAAP, the ER aminopeptidase associated with antigen processing. Taken together these findings suggest that the pMHC I repertore is edited independently by tapasin and ERAAP in the ER.
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Affiliation(s)
- Takayuki Kanaseki
- 1University of California, Berkeley, Berkeley, CA
- 2Pathology, Sapporo Medical University, Sapporo, Japan
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47
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Satija H, Blanchard N, Gonzalez F, Robey E, Shastri N. Identity of Toxoplasma gondii antigens that elicit CD4 T cells and their protective potential (130.13). The Journal of Immunology 2010. [DOI: 10.4049/jimmunol.184.supp.130.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Toxoplasma gondii (Toxo) can cause severe disease in immunocompromised individuals. Previous studies in various strains of mice have shown that genetic resistance to disease is linked to the MHC locus and protection is largely mediated by Toxo-specific CD8 T cells. In B10.D2 (H-2d) mice, CD8 T cells recognize an immunodominant peptide derived from the Toxo-protein, GRA6. However, a GRA6-specific response is not detected in C57BL/6 (B6, H-2b) mice. Instead, Toxo immunization of B6 mice elicits primarily a CD4 T cell response to unknown Toxo antigens. To identify the CD4 T cell stimulating antigens, we generated a Toxo-specific, lacZ inducible, CD4 T cell hybridoma and used it as a probe to screen a Toxo-cDNA library in bone marrow derived dendritic cells. The results reveal that CD4 T cells can be elicited by a hypothetical protein in the Toxo sequence database. We have defined the minimal peptide presented by MHC class II molecules and we will discuss the protective potential of this peptide-specific CD4 T cells in Toxo infected mice.
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Affiliation(s)
| | | | | | - Ellen Robey
- 1University of California, Berkeley, Berkeley, CA
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48
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Abstract
Many prokaryotic and eukaryotic parasites multiply in specialized subcellular niches in the host cell. The invading microbes hijack key cellular functions to establish the intracellular niches but, unlike viruses, do not need the protein synthesis machinery of host cells to replicate. Circulating CD8+ T cells provide protective immunity by recognizing pathogen-derived peptide major histocompatibility complex class I molecules (pMHC I) expressed by infected cells. Here, we review studies on the complex and varied pathways that produce the appropriate pMHC I as ligands for the CD8+ T cells. We also discuss possible explanations for the curious observations that CD8+ T cells are specific for fewer pMHC I ligands in parasite infections compared to the diversity of pMHC I ligands in viral infections.
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Affiliation(s)
- Nicolas Blanchard
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200, USA.
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49
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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. J Immunol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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50
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Labelle P, Hahn NE, Fraser JK, Kendall LV, Ziman M, James E, Shastri N, Griffey SM. Mousepox detected in a research facility: case report and failure of mouse antibody production testing to identify Ectromelia virus in contaminated mouse serum. Comp Med 2009; 59:180-186. [PMID: 19389311 PMCID: PMC2703149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 03/18/2008] [Accepted: 08/10/2008] [Indexed: 05/27/2023]
Abstract
An outbreak of mousepox in a research institution was caused by Ectromelia-contaminated mouse serum that had been used for bone marrow cell culture and the cells subsequently injected into the footpads of mice. The disease initially was diagnosed by identification of gross and microscopic lesions typical for Ectromelia infection, including foci of necrosis in the liver and spleen and eosinophilic intracytoplasmic inclusion bodies in the skin. The source of infection was determined by PCR analysis to be serum obtained from a commercial vendor. To determine whether viral growth in tissue culture was required to induce viral infection, 36 mice (BALB/cJ, C57BL/6J) were experimentally exposed intraperitoneally, intradermally (footpad), or intranasally to contaminated serum or bone marrow cell cultures using the contaminated serum in the culture medium. Mice were euthanized when clinical signs developed or after 12 wk. Necropsy, PCR of spleen, and serum ELISA were performed on all mice. Mice injected with cell cultures and their cage contacts developed mousepox, antibodies to Ectromelia, and lesions, whereas mice injected with serum without cells did not. Mouse antibody production, a tool commonly used to screen biologic materials for viral contamination, failed to detect active Ectromelia contamination in mouse serum.
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Affiliation(s)
| | - Nina E Hahn
- Office of Laboratory Animal Care, University of California, Berkeley, California
| | | | - Lonnie V Kendall
- Center for Laboratory Animal Sciences, University of California, Davis, California
| | - Melanie Ziman
- Center for Comparative Medicine, School of Veterinary Medicine, University of California, Davis, California
| | - Edward James
- Molecular and Cell Biology Department, University of California, Berkeley, California
| | - Nilabh Shastri
- Molecular and Cell Biology Department, University of California, Berkeley, California
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