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Balasco N, Tagliamonte M, Buonaguro L, Vitagliano L, Paladino A. Structural and Dynamic-Based Characterization of the Recognition Patterns of E7 and TRP-2 Epitopes by MHC Class I Receptors through Computational Approaches. Int J Mol Sci 2024; 25:1384. [PMID: 38338663 PMCID: PMC10855917 DOI: 10.3390/ijms25031384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
A detailed comprehension of MHC-epitope recognition is essential for the design and development of new antigens that could be effectively used in immunotherapy. Yet, the high variability of the peptide together with the large abundance of MHC variants binding makes the process highly specific and large-scale characterizations extremely challenging by standard experimental techniques. Taking advantage of the striking predictive accuracy of AlphaFold, we report a structural and dynamic-based strategy to gain insights into the molecular basis that drives the recognition and interaction of MHC class I in the immune response triggered by pathogens and/or tumor-derived peptides. Here, we investigated at the atomic level the recognition of E7 and TRP-2 epitopes to their known receptors, thus offering a structural explanation for the different binding preferences of the studied receptors for specific residues in certain positions of the antigen sequences. Moreover, our analysis provides clues on the determinants that dictate the affinity of the same epitope with different receptors. Collectively, the data here presented indicate the reliability of the approach that can be straightforwardly extended to a large number of related systems.
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Affiliation(s)
- Nicole Balasco
- Institute of Molecular Biology and Pathology IBPM-CNR c/o Department Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy;
| | - Maria Tagliamonte
- Immunological Models Lab, Istituto Nazionale Tumori—Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)—“Fond. G. Pascale”, Via Mariano Semmola 53, 80131 Napoli, Italy; (M.T.); (L.B.)
| | - Luigi Buonaguro
- Immunological Models Lab, Istituto Nazionale Tumori—Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)—“Fond. G. Pascale”, Via Mariano Semmola 53, 80131 Napoli, Italy; (M.T.); (L.B.)
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging IBB-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy;
| | - Antonella Paladino
- Institute of Biostructures and Bioimaging IBB-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy;
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2
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Lin F, Dong X, Zhang Y, Cheng Y, Han T, Mo X, Fu H, Han W, Wang F, Tang F, Yan C, Sun Y, Xu Z, Wang Y, Zhang X, Huang X, Xu L. Time-dependent analysis of the impact on early cytomegalovirus reactivation of HLA mismatch and acute graft-versus-host disease after allogeneic hematopoietic cell transplantation from related donors in acquired aplastic anemia. Ann Hematol 2023; 102:2589-2598. [PMID: 37438489 DOI: 10.1007/s00277-023-05332-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/20/2023] [Indexed: 07/14/2023]
Abstract
Cytomegalovirus (CMV) reactivation is an important issue in allogeneic hematopoietic cell transplantation (HCT). The incidence of early CMV reactivation is notably high in HLA-mismatched HCT. However, the interactions between HLA mismatch and acute graft-versus-host disease (aGvHD), a time-dependent event, make it methodologically challenging to evaluate the independent impact on CMV reactivation of the two variables. We retrospectively analyzed 355 patients with acquired aplastic anemia who received related donor transplants using a unified antithymocyte globulin-based platform. Patients were divided into group 1 (6/6 HLA match), group 2 (1-2/6 HLA allelic mismatch), and group 3 (3/6 HLA allelic mismatch). The impact of covariates was analyzed through two models: (1) time-dependent Cox and (2) dynamic landmarking analysis. The time-dependent Cox model showed that the HLA mismatch of 3/6 alleles (hazard ratio (HR) =1.852, P = .004) and aGvHD (HR = 1.009, P = .019) were independent risk factors for CMV reactivation. With the dynamic landmarking analysis, a higher HLA disparity correlated to increased early CMV reactivation (HR = 1.606, P = .001) at all time points. Developing aGvHD following HCT was generally associated with a higher incidence of CMV reactivation (HR = 1.623, P = .013), though its impact decreased with successive later landmark time points. In conclusion, our data suggest that the higher HLA disparity and aGvHD increases susceptibility to early CMV reactivation. In particular, the dynamic landmarking analysis demonstrated the time-varying effect of aGvHD on CMV reactivation, and HLA mismatch showed a profound impact over time following HCT.
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Affiliation(s)
- Fan Lin
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Xinyu Dong
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Yuanyuan Zhang
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Yifei Cheng
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Tingting Han
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Xiaodong Mo
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Haixia Fu
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Wei Han
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Fengrong Wang
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Feifei Tang
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Chenhua Yan
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Yuqian Sun
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Zhengli Xu
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Yu Wang
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Xiaohui Zhang
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
| | - Xiaojun Huang
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China
- Peking-Tsinghua Centre for Life Sciences, Beijing, China
| | - Lanping Xu
- National Clinical Research Center for Hematologic Disease, Collaborative Innovation Center of Hematology, Beijing Key Laboratory of Hematopoietic Stem Cell Transplant, Peking University People's Hospital, Peking University Institute of Hematology, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, China.
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3
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Xia X, Cheng A, Wang M, Ou X, Sun D, Mao S, Huang J, Yang Q, Wu Y, Chen S, Zhang S, Zhu D, Jia R, Liu M, Zhao XX, Gao Q, Tian B. Functions of Viroporins in the Viral Life Cycle and Their Regulation of Host Cell Responses. Front Immunol 2022; 13:890549. [PMID: 35720341 PMCID: PMC9202500 DOI: 10.3389/fimmu.2022.890549] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Viroporins are virally encoded transmembrane proteins that are essential for viral pathogenicity and can participate in various stages of the viral life cycle, thereby promoting viral proliferation. Viroporins have multifaceted effects on host cell biological functions, including altering cell membrane permeability, triggering inflammasome formation, inducing apoptosis and autophagy, and evading immune responses, thereby ensuring that the virus completes its life cycle. Viroporins are also virulence factors, and their complete or partial deletion often reduces virion release and reduces viral pathogenicity, highlighting the important role of these proteins in the viral life cycle. Thus, viroporins represent a common drug-protein target for inhibiting drugs and the development of antiviral therapies. This article reviews current studies on the functions of viroporins in the viral life cycle and their regulation of host cell responses, with the aim of improving the understanding of this growing family of viral proteins.
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Affiliation(s)
- Xiaoyan Xia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Xin-Xin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China.,Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
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4
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T-cell receptor repertoire of cytomegalovirus-specific cytotoxic T-cells after allogeneic stem cell transplantation. Sci Rep 2020; 10:22218. [PMID: 33335252 PMCID: PMC7747720 DOI: 10.1038/s41598-020-79363-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023] Open
Abstract
Cytomegalovirus (CMV) infection is a major complication during allogeneic stem cell transplantation (allo-SCT). However, mechanisms of adaptive immunity that drive this remain unclear. To define early immunological responses to CMV after transplantation, we using next-generation sequencing to examine the repertoire of T-cell receptors in CD8+/CMV pp65 tetramer+ cells (CMV-CTLs) in peripheral blood samples obtained from 16 allo-SCT recipients with HLA-A*24:02 at the time of CMV reactivation. In most patients, TCR beta repertoire of CMV-CTLs was highly skewed (median Inverse Simpson's index: 1.595) and, 15 of 16 patients shared at least one TCR-beta clonotype with ≥ 2 patients. The shared TCRs were dominant in 12 patients and, two clonotypes were shared by about half of the patients. Similarity analysis showed that CDR3 sequences of shared TCRs were more similar than unshared TCRs. TCR beta repertoires of CMV-CTLs in 12 patients were also analyzed after 2-4 weeks to characterize the short-term dynamics of TCR repertoires. In ten patients, we observed persistence of prevailing clones. In the other two patients, TCR repertoires became more diverse, major clones declined, and new private clones subsequently emerged. These results provided the substantive clue to understand the immunological behavior against CMV reactivation after allo-SCT.
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5
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Li X, Zhang L, Liu Y, Ma L, Zhang N, Xia C. Structures of the MHC-I molecule BF2*1501 disclose the preferred presentation of an H5N1 virus-derived epitope. J Biol Chem 2020; 295:5292-5306. [PMID: 32152225 PMCID: PMC7170506 DOI: 10.1074/jbc.ra120.012713] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/06/2020] [Indexed: 01/05/2023] Open
Abstract
Lethal infections by strains of the highly-pathogenic avian influenza virus (HPAIV) H5N1 pose serious threats to both the poultry industry and public health worldwide. A lack of confirmed HPAIV epitopes recognized by cytotoxic T lymphocytes (CTLs) has hindered the utilization of CD8+ T-cell-mediated immunity and has precluded the development of effectively diversified epitope-based vaccination approaches. In particular, an HPAIV H5N1 CTL-recognized epitope based on the peptide MHC-I-β2m (pMHC-I) complex has not yet been designed. Here, screening a collection of selected peptides of several HPAIV strains against a specific pathogen-free pMHC-I (pBF2*1501), we identified a highly-conserved HPAIV H5N1 CTL epitope, named HPAIV-PA123-130 We determined the structure of the BF2*1501-PA123-130 complex at 2.1 Å resolution to elucidate the molecular mechanisms of a preferential presentation of the highly-conserved PA123-130 epitope in the chicken B15 lineage. Conformational characteristics of the PA123-130 epitope with a protruding Tyr-7 residue indicated that this epitope has great potential to be recognized by specific TCRs. Moreover, significantly increased numbers of CD8+ T cells specific for the HPAIV-PA123-130 epitope in peptide-immunized chickens indicated that a repertoire of CD8+ T cells can specifically respond to this epitope. We anticipate that the identification and structural characterization of the PA123-130 epitope reported here could enable further studies of CTL immunity against HPAIV H5N1. Such studies may aid in the development of vaccine development strategies using well-conserved internal viral antigens in chickens.
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Affiliation(s)
- Xiaoying Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China; School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, People's Republic of China
| | - Lijie Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China
| | - Yanjie Liu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China; Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apiculture, Chinese Academy of Agricultural Sciences, Beijing 100093, People's Republic of China
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing 100094, People's Republic of China; Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, China Agricultural University, Beijing 100094, People's Republic of China.
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6
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Marcinko TM, Liang C, Savinov S, Chen J, Vachet RW. Structural Heterogeneity in the Preamyloid Oligomers of β-2-Microglobulin. J Mol Biol 2019; 432:396-409. [PMID: 31711963 DOI: 10.1016/j.jmb.2019.10.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 11/29/2022]
Abstract
In dialysis patients, the protein β2-microglobulin (β2m) forms amyloid fibrils in a condition known as dialysis-related amyloidosis. To understand the early stages of the amyloid assembly process, we have used native electrospray ionization (ESI) together with ion mobility mass spectrometry (IM-MS) to study soluble preamyloid oligomers. ESI-IM-MS reveals the presence of multiple conformers for the dimer, tetramer, and hexamer that precede the Cu(II)-induced amyloid assembly process, results which are distinct from β2m oligomers formed at low pH. Experimental and computational results indicate that the predominant dimer is a Cu(II)-bound structure with an antiparallel side-by-side configuration. In contrast, tetramers exist in solution in both Cu(II)-bound and Cu(II)-free forms. Selective depletion of Cu(II)-bound species results in two primary conformers-one that is compact and another that is more expanded. Molecular modeling and molecular dynamics simulations identify models for these two tetrameric conformers with unique interactions and interfaces that enthalpically compensate for the loss of Cu(II). Unlike with other amyloid systems in which conformational heterogeneity is often associated with different amyloid morphologies or off-pathway events, conformational heterogeneity in the tetramer seems to be a necessary aspect of Cu(II)-induced amyloid formation by β2m. Moreover, the Cu(II)-free models represent a new advance in our understanding of Cu(II) release in Cu(II)-induced amyloid formation, laying a foundation for further mechanistic studies as well as development of new inhibition strategies.
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Affiliation(s)
- Tyler M Marcinko
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States
| | - Chungwen Liang
- Computational and Modeling Core Facility, Institute for Applied Life Sciences, Amherst, MA 01003, United States
| | - Sergey Savinov
- Computational and Modeling Core Facility, Institute for Applied Life Sciences, Amherst, MA 01003, United States; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, United States
| | - Jianhen Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States.
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7
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Stervbo U, Nienen M, Weist BJD, Kuchenbecker L, Hecht J, Wehler P, Westhoff TH, Reinke P, Babel N. BKV Clearance Time Correlates With Exhaustion State and T-Cell Receptor Repertoire Shape of BKV-Specific T-Cells in Renal Transplant Patients. Front Immunol 2019; 10:767. [PMID: 31024575 PMCID: PMC6468491 DOI: 10.3389/fimmu.2019.00767] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 03/22/2019] [Indexed: 01/08/2023] Open
Abstract
Reactivation of the BK polyomavirus is known to lead to severe complications in kidney transplant patients. The current treatment strategy relies on decreasing the immunosuppression to allow the immune system to clear the virus. Recently, we demonstrated a clear association between the resolution of BKV reactivation and reconstitution of BKV-specific CD4+ T-cells. However, which factors determine the duration of viral infection clearance remains so far unclear. Here we apply a combination of in-depth multi-parametric flow cytometry and NGS-based CDR3 beta chain receptor repertoire analysis of BKV-specific T-cells to a cohort of 7 kidney transplant patients during the clinical course of BKV reactivation. This way we followed TCR repertoires at single clone levels and functional activity of BKV-specific T-cells during the resolution of BKV infection. The duration of BKV clearance did not depend on the number of peripheral blood BKV-specific T-cells nor on a few immunodominant BKV-specific T-cell clones. Rather, the T-cell receptor repertoire diversity and exhaustion status of BKV-specific T-cells affected the duration of viral clearance: high clonotype diversity and lack of PD1 and TIM3 exhaustion markers on BKV-specific T-cells was associated with short clearance time. Our data thus demonstrate how the diversity and the exhaustion state of the T-cells can determine the clinical course of BKV infection.
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Affiliation(s)
- Ulrik Stervbo
- Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.,Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mikalai Nienen
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Institute for Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Labor Berlin-Charité Vivantes GmbH, Berlin, Germany
| | - Benjamin J D Weist
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Leon Kuchenbecker
- Applied Bioinformatics, Center for Bioinformatics Tübingen, University of Tübingen, Tübingen, Germany
| | - Jochen Hecht
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Patrizia Wehler
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Timm H Westhoff
- Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Petra Reinke
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Center for Advanced Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nina Babel
- Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.,Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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8
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Bradley P, Thomas PG. Using T Cell Receptor Repertoires to Understand the Principles of Adaptive Immune Recognition. Annu Rev Immunol 2019; 37:547-570. [PMID: 30699000 DOI: 10.1146/annurev-immunol-042718-041757] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Adaptive immune recognition is mediated by antigen receptors on B and T cells generated by somatic recombination during lineage development. The high level of diversity resulting from this process posed technical limitations that previously limited the comprehensive analysis of adaptive immune recognition. Advances over the last ten years have produced data and approaches allowing insights into how T cells develop, evolutionary signatures of recombination and selection, and the features of T cell receptors that mediate epitope-specific binding and T cell activation. The size and complexity of these data have necessitated the generation of novel computational and analytical approaches, which are transforming how T cell immunology is conducted. Here we review the development and application of novel biological, theoretical, and computational methods for understanding T cell recognition and discuss the potential for improved models of receptor:antigen interactions.
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Affiliation(s)
- Philip Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; .,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA;
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9
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Abstract
PURPOSE OF REVIEW The genetic susceptibility and dominant protection for type 1 diabetes (T1D) associated with human leukocyte antigen (HLA) haplotypes, along with minor risk variants, have long been thought to shape the T cell receptor (TCR) repertoire and eventual phenotype of autoreactive T cells that mediate β-cell destruction. While autoantibodies provide robust markers of disease progression, early studies tracking autoreactive T cells largely failed to achieve clinical utility. RECENT FINDINGS Advances in acquisition of pancreata and islets from T1D organ donors have facilitated studies of T cells isolated from the target tissues. Immunosequencing of TCR α/β-chain complementarity determining regions, along with transcriptional profiling, offers the potential to transform biomarker discovery. Herein, we review recent studies characterizing the autoreactive TCR signature in T1D, emerging technologies, and the challenges and opportunities associated with tracking TCR molecular profiles during the natural history of T1D.
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Affiliation(s)
- Laura M Jacobsen
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Amanda Posgai
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Howard R Seay
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Michael J Haller
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA.
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10
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Dash P, Fiore-Gartland AJ, Hertz T, Wang GC, Sharma S, Souquette A, Crawford JC, Clemens EB, Nguyen THO, Kedzierska K, La Gruta NL, Bradley P, Thomas PG. Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature 2017. [PMID: 28636592 DOI: 10.1038/nature22383] [Citation(s) in RCA: 500] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
T cells are defined by a heterodimeric surface receptor, the T cell receptor (TCR), that mediates recognition of pathogen-associated epitopes through interactions with peptide and major histocompatibility complexes (pMHCs). TCRs are generated by genomic rearrangement of the germline TCR locus, a process termed V(D)J recombination, that has the potential to generate marked diversity of TCRs (estimated to range from 1015 (ref. 1) to as high as 1061 (ref. 2) possible receptors). Despite this potential diversity, TCRs from T cells that recognize the same pMHC epitope often share conserved sequence features, suggesting that it may be possible to predictively model epitope specificity. Here we report the in-depth characterization of ten epitope-specific TCR repertoires of CD8+ T cells from mice and humans, representing over 4,600 in-frame single-cell-derived TCRαβ sequence pairs from 110 subjects. We developed analytical tools to characterize these epitope-specific repertoires: a distance measure on the space of TCRs that permits clustering and visualization, a robust repertoire diversity metric that accommodates the low number of paired public receptors observed when compared to single-chain analyses, and a distance-based classifier that can assign previously unobserved TCRs to characterized repertoires with robust sensitivity and specificity. Our analyses demonstrate that each epitope-specific repertoire contains a clustered group of receptors that share core sequence similarities, together with a dispersed set of diverse 'outlier' sequences. By identifying shared motifs in core sequences, we were able to highlight key conserved residues driving essential elements of TCR recognition. These analyses provide insights into the generalizable, underlying features of epitope-specific repertoires and adaptive immune recognition.
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Affiliation(s)
- Pradyot Dash
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Andrew J Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Tomer Hertz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - George C Wang
- Division of Geriatric Medicine and Gerontology, Biology of Healthy Aging Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, USA
| | - Shalini Sharma
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India
| | - Aisha Souquette
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Nicole L La Gruta
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Philip Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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11
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Hou D, Ying T, Wang L, Chen C, Lu S, Wang Q, Seeley E, Xu J, Xi X, Li T, Liu J, Tang X, Zhang Z, Zhou J, Bai C, Wang C, Byrne-Steele M, Qu J, Han J, Song Y. Immune Repertoire Diversity Correlated with Mortality in Avian Influenza A (H7N9) Virus Infected Patients. Sci Rep 2016; 6:33843. [PMID: 27669665 PMCID: PMC5037391 DOI: 10.1038/srep33843] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/02/2016] [Indexed: 01/09/2023] Open
Abstract
Specific changes in immune repertoires at genetic level responding to the lethal H7N9 virus are still poorly understood. We performed deep sequencing on the T and B cells from patients recently infected with H7N9 to explore the correlation between clinical outcomes and immune repertoire alterations. T and B cell repertoires display highly dynamic yet distinct clonotype alterations. During infection, T cell beta chain repertoire continues to contract while the diversity of immunoglobulin heavy chain repertoire recovers. Patient recovery is correlated to the diversity of T cell and B cell repertoires in different ways – higher B cell diversity and lower T cell diversity are found in survivors. The sequences clonally related to known antibodies with binding affinity to H7 hemagglutinin could be identified from survivors. These findings suggest that utilizing deep sequencing may improve prognostication during influenza infection and could help in development of antibody discovery methodologies for the treatment of virus infection.
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Affiliation(s)
- Dongni Hou
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Tianlei Ying
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Lili Wang
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Cuicui Chen
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Shuihua Lu
- Department of Respiratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Qin Wang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Eric Seeley
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Jianqing Xu
- Department of Respiratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Xiuhong Xi
- Department of Respiratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Tao Li
- Department of Respiratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Jie Liu
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xinjun Tang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhiyong Zhang
- Department of Respiratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Jian Zhou
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Chunxue Bai
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Chunlin Wang
- HudsonAlpha Institute for Biotechnology, Alabama, AL35806, USA
| | | | - Jieming Qu
- Department of Pulmonary Medicine, Ruijin Hospital, Shanghai Jiaotong University, Shanghai, 200025, China
| | - Jian Han
- HudsonAlpha Institute for Biotechnology, Alabama, AL35806, USA
| | - Yuanlin Song
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Department of Respiratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,Department of Pulmonary Medicine, Zhongshan Hospital, Qingpu Branch, Shanghai, 200032, China
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12
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Self-Amplifying mRNA Vaccines Expressing Multiple Conserved Influenza Antigens Confer Protection against Homologous and Heterosubtypic Viral Challenge. PLoS One 2016; 11:e0161193. [PMID: 27525409 PMCID: PMC4985159 DOI: 10.1371/journal.pone.0161193] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 08/01/2016] [Indexed: 11/19/2022] Open
Abstract
Current hemagglutinin (HA)-based seasonal influenza vaccines induce vaccine strain-specific neutralizing antibodies that usually fail to provide protection against mismatched circulating viruses. Inclusion in the vaccine of highly conserved internal proteins such as the nucleoprotein (NP) and the matrix protein 1 (M1) was shown previously to increase vaccine efficacy by eliciting cross-reactive T-cells. However, appropriate delivery systems are required for efficient priming of T-cell responses. In this study, we demonstrated that administration of novel self-amplifying mRNA (SAM®) vectors expressing influenza NP (SAM(NP)), M1 (SAM(M1)), and NP and M1 (SAM(M1-NP)) delivered with lipid nanoparticles (LNP) induced robust polyfunctional CD4 T helper 1 cells, while NP-containing SAM also induced cytotoxic CD8 T cells. Robust expansions of central memory (TCM) and effector memory (TEM) CD4 and CD8 T cells were also measured. An enhanced recruitment of NP-specific cytotoxic CD8 T cells was observed in the lungs of SAM(NP)-immunized mice after influenza infection that paralleled with reduced lung viral titers and pathology, and increased survival after homologous and heterosubtypic influenza challenge. Finally, we demonstrated for the first time that the co-administration of RNA (SAM(M1-NP)) and protein (monovalent inactivated influenza vaccine (MIIV)) was feasible, induced simultaneously NP-, M1- and HA-specific T cells and HA-specific neutralizing antibodies, and enhanced MIIV efficacy against a heterologous challenge. In conclusion, systemic administration of SAM vectors expressing conserved internal influenza antigens induced protective immune responses in mice, supporting the SAM® platform as another promising strategy for the development of broad-spectrum universal influenza vaccines.
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13
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Link CS, Eugster A, Heidenreich F, Rücker-Braun E, Schmiedgen M, Oelschlägel U, Kühn D, Dietz S, Fuchs Y, Dahl A, Domingues AMJ, Klesse C, Schmitz M, Ehninger G, Bornhäuser M, Schetelig J, Bonifacio E. Abundant cytomegalovirus (CMV) reactive clonotypes in the CD8(+) T cell receptor alpha repertoire following allogeneic transplantation. Clin Exp Immunol 2016; 184:389-402. [PMID: 26800118 DOI: 10.1111/cei.12770] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Indexed: 12/15/2022] Open
Abstract
Allogeneic stem cell transplantation is potentially curative, but associated with post-transplantation complications, including cytomegalovirus (CMV) infections. An effective immune response requires T cells recognizing CMV epitopes via their T cell receptors (TCRs). Little is known about the TCR repertoire, in particular the TCR-α repertoire and its clinical relevance in patients following stem cell transplantation. Using next-generation sequencing we examined the TCR-α repertoire of CD8(+) T cells and CMV-specific CD8(+) T cells in four patients. Additionally, we performed single-cell TCR-αβ sequencing of CMV-specific CD8(+) T cells. The TCR-α composition of human leucocyte antigen (HLA)-A*0201 CMVpp65- and CMVIE -specific T cells was oligoclonal and defined by few dominant clonotypes. Frequencies of single clonotypes reached up to 11% of all CD8(+) T cells and half of the total CD8(+) T cell repertoire was dominated by few CMV-reactive clonotypes. Some TCR-α clonotypes were shared between patients. Gene expression of the circulating CMV-specific CD8(+) T cells was consistent with chronically activated effector memory T cells. The CD8(+) T cell response to CMV reactivation resulted in an expansion of a few TCR-α clonotypes to dominate the CD8(+) repertoires. These results warrant further larger studies to define the ability of oligoclonally expanded T cell clones to achieve an effective anti-viral T cell response in this setting.
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Affiliation(s)
- C S Link
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus.,DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - A Eugster
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - F Heidenreich
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus
| | - E Rücker-Braun
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus
| | - M Schmiedgen
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus
| | - U Oelschlägel
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus
| | - D Kühn
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - S Dietz
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Y Fuchs
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - A Dahl
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany.,BIOTEChnology Center, TU Dresden, Dresden, Germany
| | - A M J Domingues
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - C Klesse
- DKMS Clinical Trials Unit, Dresden, Germany
| | - M Schmitz
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany.,Institut Für Immunologie, Medizinische Fakultät, TU Dresden, Dresden, Germany
| | - G Ehninger
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus.,DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - M Bornhäuser
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus.,DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
| | - J Schetelig
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus.,DKMS Clinical Trials Unit, Dresden, Germany
| | - E Bonifacio
- DFG Research Center for Regenerative Therapies Dresden, Dresden, Germany
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14
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Heightened self-reactivity associated with selective survival, but not expansion, of naïve virus-specific CD8+ T cells in aged mice. Proc Natl Acad Sci U S A 2016; 113:1333-8. [PMID: 26787864 DOI: 10.1073/pnas.1525167113] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In advanced age, decreased CD8(+) cytotoxic T-lymphocyte (CTL) responses to novel pathogens and cancer is paralleled by a decline in the number and function of naïve CTL precursors (CTLp). Although the age-related fall in CD8(+) T-cell numbers is well established, neither the underlying mechanisms nor the extent of variation for different epitope specificities have been defined. Furthermore, naïve CD8(+) T cells expressing high levels of CD44 accumulate with age, but it is unknown whether this accumulation reflects their preferential survival or an age-dependent driver of CD8(+) T-cell proliferation. Here, we track the number and phenotype of four influenza A virus (IAV)-specific CTLp populations in naïve C57BL/6 (B6) mice during aging, and compare T-cell receptor (TCR) clonal diversity for the CD44hi and CD44lo subsets of one such population. We show differential onset of decline for several IAV-specific CD8(+) T-cell populations with advanced age that parallel age-associated changes in the B6 immunodominance hierarchy, suggestive of distinct impacts of aging on different epitope-specific populations. Despite finding no evidence of clonal expansions in an aged, epitope-specific TCR repertoire, nonrandom alterations in TCR usage were observed, along with elevated CD5 and CD8 coreceptor expression. Collectively, these data demonstrate that naïve CD8(+) T cells expressing markers of heightened self-recognition are selectively retained, but not clonally expanded, during aging.
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15
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Cukalac T, Kan WT, Dash P, Guan J, Quinn KM, Gras S, Thomas PG, La Gruta NL. Paired TCRαβ analysis of virus-specific CD8(+) T cells exposes diversity in a previously defined 'narrow' repertoire. Immunol Cell Biol 2015; 93:804-14. [PMID: 25804828 DOI: 10.1038/icb.2015.44] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 02/07/2023]
Abstract
T-cell receptor (TCR) usage has an important role in determining the outcome of CD8(+) cytotoxic T-lymphocyte responses to viruses and other pathogens. However, the characterization of TCR usage from which such conclusions are drawn is based on exclusive analysis of either the TCRα chain or, more commonly, the TCRβ chain. Here, we have used a multiplexed reverse transcription-PCR protocol to analyse the CDR3 regions of both TCRα and β chains from single naive or immune epitope-specific cells to provide a comprehensive picture of epitope-specific TCR usage and selection into the immune response. Analysis of TCR repertoires specific for three influenza-derived epitopes (D(b)NP(366), D(b)PA(224) and D(b)PB1-F2(62)) showed preferential usage of particular TCRαβ proteins in the immune repertoire relative to the naive repertoire, in some cases, resulting in a complete shift in TRBV preference or CDR3 length, and restricted repertoire diversity. The NP(366)-specific TCRαβ repertoire, previously defined as clonally restricted based on TCRβ analysis, was similarly diverse as the PA(224)- and PB1-F2(62)-specific repertoires. Intriguingly, preferred TCR characteristics (variable gene usage, CDR3 length and junctional gene usage) appeared to be able to confer specificity either independently or in concert with one another, depending on the epitope specificity. These data have implications for established correlations between the nature of the TCR repertoire and response outcomes after infection, and suggest that analysis of a subset of cells or a single TCR chain does not accurately depict the nature of the antigen-specific TCRαβ repertoire.
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Affiliation(s)
- Tania Cukalac
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Wan-Ting Kan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Pradyot Dash
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Guan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Kylie M Quinn
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Nicole L La Gruta
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
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16
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Clemens EB, Doherty PC, La Gruta NL, Turner SJ. Fixed expression of single influenza virus-specific TCR chains demonstrates the capacity for TCR α- and β-chain diversity in the face of peptide-MHC class I specificity. THE JOURNAL OF IMMUNOLOGY 2014; 194:898-910. [PMID: 25535284 DOI: 10.4049/jimmunol.1401792] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The characteristics of the TCR repertoire expressed by epitope-specific CD8(+) T cells can be an important determinant of the quality of immune protection against virus infection. Most studies of epitope-specific TCR repertoires focus solely on an analysis of TCR β-chains, rather than the combined TCRαβ heterodimers that confer specificity. Hence, the importance of complementary α- and β-chain pairing in determining TCR specificity and T cell function is not well understood. Our earlier study of influenza-specific TCR repertoires in a C57BL/6J mouse model described a structural basis for preferred TCRαβ pairing that determined exquisite specificity for the D(b)PA224 epitope from influenza A virus. We have now extended this analysis using retrogenic mice engineered to express single TCR α- or β-chains specific for the D(b)NP366 or D(b)PA224 epitopes derived from influenza A virus. We found that particular TCRαβ combinations were selected for recognition of these epitopes following infection, indicating that pairing of certain α- and β-chain sequences is key for determining TCR specificity. Furthermore, we demonstrated that some TCRαβ heterodimers were preferentially expanded from the naive repertoire in response to virus infection, suggesting that appropriate αβ pairing confers optimal T cell responsiveness to Ag.
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Affiliation(s)
- E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia; and
| | - Peter C Doherty
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia; and Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Nicole L La Gruta
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia; and
| | - Stephen J Turner
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia; and
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17
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Terasako-Saito K, Nakasone H, Tanaka Y, Yamazaki R, Sato M, Sakamoto K, Ishihara Y, Kawamura K, Akahoshi Y, Hayakawa J, Wada H, Harada N, Nakano H, Kameda K, Ugai T, Yamasaki R, Ashizawa M, Kimura SI, Kikuchi M, Tanihara A, Kanda J, Kako S, Nishida J, Kanda Y. Persistence of recipient-derived as well as donor-derived clones of cytomegalovirus pp65-specific cytotoxic T cells long after allogeneic hematopoietic stem cell transplantation. Transpl Infect Dis 2014; 16:930-40. [DOI: 10.1111/tid.12318] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/14/2014] [Indexed: 11/27/2022]
Affiliation(s)
- K. Terasako-Saito
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - H. Nakasone
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - Y. Tanaka
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - R. Yamazaki
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - M. Sato
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - K. Sakamoto
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - Y. Ishihara
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - K. Kawamura
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - Y. Akahoshi
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - J. Hayakawa
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - H. Wada
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - N. Harada
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - H. Nakano
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - K. Kameda
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - T. Ugai
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - R. Yamasaki
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - M. Ashizawa
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - S.-I. Kimura
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - M. Kikuchi
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - A. Tanihara
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - J. Kanda
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - S. Kako
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - J. Nishida
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
| | - Y. Kanda
- Division of Hematology; Saitama Medical Center; Jichi Medical University; Saitama Japan
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18
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Nivarthi UK, Gras S, Kjer-Nielsen L, Berry R, Lucet IS, Miles JJ, Tracy SL, Purcell AW, Bowden DS, Hellard M, Rossjohn J, McCluskey J, Bharadwaj M. An extensive antigenic footprint underpins immunodominant TCR adaptability against a hypervariable viral determinant. THE JOURNAL OF IMMUNOLOGY 2014; 193:5402-13. [PMID: 25355921 DOI: 10.4049/jimmunol.1401357] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mutations in T cell epitopes are implicated in hepatitis C virus (HCV) persistence and can impinge on vaccine development. We recently demonstrated a narrow bias in the human TCR repertoire targeted at an immunodominant, but highly mutable, HLA-B*0801-restricted epitope ((1395)HSKKKCDEL(1403) [HSK]). To investigate if the narrow TCR repertoire facilitates CTL escape, structural and biophysical studies were undertaken, alongside comprehensive functional analysis of T cells targeted at the natural variants of HLA-B*0801-HSK in different HCV genotypes and quasispecies. Interestingly, within the TCR-HLA-B*0801-HSK complex, the TCR contacts all available surface-exposed residues of the HSK determinant. This broad epitope coverage facilitates cross-genotypic reactivity and recognition of common mutations reported in HCV quasispecies, albeit to a varying degree. Certain mutations did abrogate T cell reactivity; however, natural variants comprising these mutations are reportedly rare and transient in nature, presumably due to fitness costs. Overall, despite a narrow bias, the TCR accommodated frequent mutations by acting like a blanket over the hypervariable epitope, thereby providing effective viral immunity. Our findings simultaneously advance the understanding of anti-HCV immunity and indicate the potential for cross-genotype HCV vaccines.
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Affiliation(s)
- Usha K Nivarthi
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3000, Australia
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3000, Australia
| | - Richard Berry
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Isabelle S Lucet
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - John J Miles
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom; Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia; School of Medicine, University of Queensland, Brisbane, Queensland 4006, Australia
| | - Samantha L Tracy
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - David S Bowden
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Margaret Hellard
- Centre for Population Health, Burnet Institute, Melbourne, Victoria 3004, Australia; Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria 3800, Australia; and Centre for Research Excellence into Injecting Drug Use, Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom;
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3000, Australia;
| | - Mandvi Bharadwaj
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3000, Australia;
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Hill BJ, Darrah PA, Ende Z, Ambrozak DR, Quinn KM, Darko S, Gostick E, Wooldridge L, van den Berg HA, Venturi V, Larsen M, Davenport MP, Seder RA, Price DA, Douek DC. Epitope specificity delimits the functional capabilities of vaccine-induced CD8 T cell populations. THE JOURNAL OF IMMUNOLOGY 2014; 193:5626-36. [PMID: 25348625 DOI: 10.4049/jimmunol.1401017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Despite progress toward understanding the correlates of protective T cell immunity in HIV infection, the optimal approach to Ag delivery by vaccination remains uncertain. We characterized two immunodominant CD8 T cell populations generated in response to immunization of BALB/c mice with a replication-deficient adenovirus serotype 5 vector expressing the HIV-derived Gag and Pol proteins at equivalent levels. The Gag-AI9/H-2K(d) epitope elicited high-avidity CD8 T cell populations with architecturally diverse clonotypic repertoires that displayed potent lytic activity in vivo. In contrast, the Pol-LI9/H-2D(d) epitope elicited motif-constrained CD8 T cell repertoires that displayed lower levels of physical avidity and lytic activity despite equivalent measures of overall clonality. Although low-dose vaccination enhanced the functional profiles of both epitope-specific CD8 T cell populations, greater polyfunctionality was apparent within the Pol-LI9/H-2D(d) specificity. Higher proportions of central memory-like cells were present after low-dose vaccination and at later time points. However, there were no noteworthy phenotypic differences between epitope-specific CD8 T cell populations across vaccine doses or time points. Collectively, these data indicate that the functional and phenotypic properties of vaccine-induced CD8 T cell populations are sensitive to dose manipulation, yet constrained by epitope specificity in a clonotype-dependent manner.
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Affiliation(s)
- Brenna J Hill
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Patricia A Darrah
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Zachary Ende
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - David R Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Kylie M Quinn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Sam Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Emma Gostick
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Linda Wooldridge
- Faculty of Medical and Veterinary Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Hugo A van den Berg
- Mathematics Institute, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vanessa Venturi
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Kensington 2052, New South Wales, Australia
| | - Martin Larsen
- INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, F-75013 Paris, France; and Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Universités, Université Pierre et Marie Curie (Université Paris 06), CR7, F-75013 Paris, France
| | - Miles P Davenport
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Kensington 2052, New South Wales, Australia
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - David A Price
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom;
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892;
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20
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Thorborn G, Ploquin MJ, Eksmond U, Pike R, Bayer W, Dittmer U, Hasenkrug KJ, Pepper M, Kassiotis G. Clonotypic composition of the CD4+ T cell response to a vectored retroviral antigen is determined by its speed. THE JOURNAL OF IMMUNOLOGY 2014; 193:1567-77. [PMID: 25000983 DOI: 10.4049/jimmunol.1400667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The mechanisms whereby different vaccines may expand distinct Ag-specific T cell clonotypes or induce disparate degrees of protection are incompletely understood. We found that several delivery modes of a model retroviral Ag, including natural infection, preferentially expanded initially rare high-avidity CD4(+) T cell clonotypes, known to mediate protection. In contrast, the same Ag vectored by human adenovirus serotype 5 induced clonotypic expansion irrespective of avidity, eliciting a predominantly low-avidity response. Nonselective clonotypic expansion was caused by relatively weak adenovirus serotype 5-vectored Ag presentation and was reproduced by replication-attenuated retroviral vaccines. Mechanistically, the potency of Ag presentation determined the speed and, consequently, completion of the CD4(+) T cell response. Whereas faster completion retained the initial advantage of high-avidity clonotypes, slower completion permitted uninhibited accumulation of low-avidity clonotypes. These results highlighted the importance of Ag presentation patterns in determining the clonotypic composition of vaccine-induced T cell responses and ultimately the efficacy of vaccination.
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Affiliation(s)
- Georgina Thorborn
- Division of Immunoregulation, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Mickaël J Ploquin
- Division of Immunoregulation, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Urszula Eksmond
- Division of Immunoregulation, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Rebecca Pike
- Division of Immunoregulation, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Wibke Bayer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen 45147, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen 45147, Germany
| | - Kim J Hasenkrug
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Marion Pepper
- Department of Immunology, University of Washington, Seattle, WA 98195; and
| | - George Kassiotis
- Division of Immunoregulation, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom; Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, United Kingdom
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21
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Thorborn G, Young GR, Kassiotis G. Effective T helper cell responses against retroviruses: are all clonotypes equal? J Leukoc Biol 2014; 96:27-37. [PMID: 24737804 DOI: 10.1189/jlb.2ri0613-347r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The critical importance of CD4(+) T cells in coordinating innate and adaptive immune responses is evidenced by the susceptibility to various pathogenic and opportunistic infections that arises from primary or acquired CD4(+) T cell immunodeficiency, such as following HIV-1 infection. However, despite the clearly defined roles of cytotoxic CD8(+) T cells and antibodies in host protection from retroviruses, the ability of CD4(+) T cells to exert a similar function remains unclear. Recent studies in various settings have drawn attention to the complexity of the T cell response within and between individuals. Distinct TCR clonotypes within an individual differ substantially in their response to the same epitope. Functionally similar, "public" TCR clonotypes can also dominate the response of different individuals. TCR affinity for antigen directly influences expansion and differentiation of responding T cells, also likely affecting their ultimate protective capacity. With this increasing understanding of the parameters that determine the magnitude and effector type of the T cell response, we are now better equipped to address the protective capacity against retroviruses of CD4(+) T cell clonotypes induced by natural infection or vaccination.
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Affiliation(s)
| | - George R Young
- Divisions of Immunoregulation and Virology, Medical Research Council National Institute for Medical Research, The Ridgeway, London, United Kingdom; and
| | - George Kassiotis
- Divisions of Immunoregulation and Department of Medicine, Faculty of Medicine, Imperial College London, United Kingdom
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22
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Cukalac T, Chadderton J, Zeng W, Cullen JG, Kan WT, Doherty PC, Jackson DC, Turner SJ, La Gruta NL. The Influenza Virus–Specific CTL Immunodominance Hierarchy in Mice Is Determined by the Relative Frequency of High-Avidity T Cells. THE JOURNAL OF IMMUNOLOGY 2014; 192:4061-8. [DOI: 10.4049/jimmunol.1301403] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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23
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Reproducible selection of high avidity CD8+ T-cell clones following secondary acute virus infection. Proc Natl Acad Sci U S A 2014; 111:1485-90. [PMID: 24474775 DOI: 10.1073/pnas.1323736111] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recall of memory CD8(+) cytotoxic T lymphocytes (CTLs), elicited by prior virus infection or vaccination, is critical for immune protection. The extent to which this arises as a consequence of stochastic clonal expansion vs. active selection of particular clones remains unclear. Using a parallel adoptive transfer protocol in combination with single cell analysis to define the complementarity determining region (CDR) 3α and CDR3β regions of individual T-cell receptor (TCR) heterodimers, we characterized the antigen-driven recall of the same memory CTL population in three individual recipients. This high-resolution analysis showed reproducible enrichment (or diminution) of particular TCR clonotypes across all challenged animals. These changes in clonal composition were TCRα- and β chain-dependent and were directly related to the avidity of the TCR for the virus-derived peptide (p) + major histocompatibility complex class I molecule. Despite this shift in clonotype representation indicative of differential selection, there was no evidence of overall repertoire narrowing, suggesting a strategy to optimize CTL responses while safeguarding TCR diversity.
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24
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Košík I, Krejnusová I, Práznovská M, Russ G. The multifaceted effect of PB1-F2 specific antibodies on influenza A virus infection. Virology 2013; 447:1-8. [PMID: 24210094 DOI: 10.1016/j.virol.2013.08.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 06/15/2013] [Accepted: 08/20/2013] [Indexed: 11/24/2022]
Abstract
PB1-F2 is a small influenza A virus (IAV) protein encoded by an alternative reading frame of the PB1 gene. During IAV infection, antibodies to PB1-F2 proteins are induced. To determine their function and contribution to virus infection, three distinct approaches were employed: passive transfer of anti-PB1-F2 MAbs and polyclonal antibodies, active immunization with PB1-F2 peptides and DNA vaccination with plasmids expressing various parts of PB1-F2. Mostly N-terminal specific antibodies were detected in polyclonal sera raised to complete PB1-F2. Passive and active immunization revealed that antibodies recognizing the N-terminal part of the PB1-F2 molecule have no remarkable effect on the course of IAV infection. Interestingly antibodies against the C-terminal region of PB1-F2, obtained by immunization with KLH-PB1-F2 C-terminal peptide or DNA immunization with pC-ter.PB1-F2 plasmid, partially protected mice against virus infection. To our knowledge, this is the first report demonstrating the biological relevance of humoral immunity against PB1-F2 protein in vivo.
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Affiliation(s)
- I Košík
- Institute of Virology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovak Republic
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25
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Nakasone H, Tanaka Y, Yamazaki R, Terasako K, Sato M, Sakamoto K, Yamasaki R, Wada H, Ishihara Y, Kawamura K, Machishima T, Ashizawa M, Kimura SI, Kikuchi M, Tanihara A, Kanda J, Kako S, Nishida J, Kanda Y. Single-cell T-cell receptor-β analysis of HLA-A*2402-restricted CMV- pp65-specific cytotoxic T-cells in allogeneic hematopoietic SCT. Bone Marrow Transplant 2013; 49:87-94. [DOI: 10.1038/bmt.2013.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/19/2013] [Accepted: 05/23/2013] [Indexed: 11/09/2022]
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26
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An insight into the PB1F2 protein and its multifunctional role in enhancing the pathogenicity of the influenza A viruses. Virology 2013; 440:97-104. [DOI: 10.1016/j.virol.2013.02.025] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 01/18/2013] [Accepted: 02/27/2013] [Indexed: 02/01/2023]
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27
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Park MS, Park SY, Miller KR, Collins EJ, Lee HY. Accurate structure prediction of peptide-MHC complexes for identifying highly immunogenic antigens. Mol Immunol 2013; 56:81-90. [PMID: 23688437 DOI: 10.1016/j.molimm.2013.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/09/2013] [Accepted: 04/15/2013] [Indexed: 12/26/2022]
Abstract
Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide-MHC complex. Here, we present an in silico protocol for predicting peptide-MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide-MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.
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Affiliation(s)
- Min-Sun Park
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, NY 14642, USA
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28
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Ecological analysis of antigen-specific CTL repertoires defines the relationship between naive and immune T-cell populations. Proc Natl Acad Sci U S A 2013; 110:1839-44. [PMID: 23319654 DOI: 10.1073/pnas.1222149110] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ecology is typically thought of as the study of interactions organisms have with each other and their environment and is focused on the distribution and abundance of organisms both within and between environments. On a molecular level, the capacity to probe analogous questions in the field of T-cell immunology is imperative as we acquire substantial datasets both on epitope-specific T-cell populations through high-resolution analyses of T-cell receptor (TCR) use and on global T-cell populations analyzed via high-throughput DNA sequencing. Here, we present the innovative application of existing statistical measures (used typically in the field of ecology), together with unique statistical analyses, to comprehensively assess how the naïve epitope-specific CD8(+) cytotoxic T lymphocyte (CTL) repertoire translates to that found following an influenza-virus-specific immune response. Such interrogation of our extensive, cumulated TCR CDR3β sequence datasets, derived from both naïve and immune CD8(+) T-cell populations specific for four different influenza-derived epitopes (D(b)NP(366), influenza nucleoprotein amino acid residues 366-374; D(b)PA(224), influenza acid polymerase amino acid residues 224-233; D(b)PB1-F2(62), influenza polymerase B 1 reading frame 2 amino acid residues 62-70; K(b)NS2(114), and influenza nonstructural protein 2 amino acid residues 114-121), demonstrates that epitope-specific TCR use in an antiviral immune response is the consequence of a complex interplay between the intrinsic characteristics of the naïve cytotoxic T lymphocyte precursor pool and extrinsic (likely antigen driven) influences, the contribution of which varies in an epitope-specific fashion.
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29
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Luciani F, Sanders MT, Oveissi S, Pang KC, Chen W. Increasing viral dose causes a reversal in CD8+ T cell immunodominance during primary influenza infection due to differences in antigen presentation, T cell avidity, and precursor numbers. THE JOURNAL OF IMMUNOLOGY 2012; 190:36-47. [PMID: 23233728 DOI: 10.4049/jimmunol.1200089] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
T cell responses are characterized by the phenomenon of immunodominance (ID), whereby peptide-specific T cells are elicited in a reproducible hierarchy of dominant and subdominant responses. However, the mechanisms that give rise to ID are not well understood. We investigated the effect of viral dose on primary CD8(+) T cell (T(CD8+)) ID by injecting mice i.p. with various doses of influenza A virus and assessing the primary T(CD8+) response to five dominant and subdominant peptides. Increasing viral dose enhanced the overall strength of the T(CD8+) response, and it altered the ID hierarchy: specifically, NP(366-374) T(CD8+) were dominant at low viral doses but were supplanted by PA(224-233) T(CD8+) at high doses. To understand the basis for this reversal, we mathematically modeled these T(CD8+) responses and used Bayesian statistics to obtain estimates for Ag presentation, T(CD8+) precursor numbers, and avidity. Interestingly, at low viral doses, Ag presentation most critically shaped ID hierarchy, enabling T(CD8+) specific to the more abundantly presented NP(366-374) to dominate. By comparison, at high viral doses, T(CD8+) avidity and precursor numbers appeared to be the major influences on ID hierarchy, resulting in PA(224-233) T(CD8+) usurping NP(366-374) cells as the result of higher avidity and precursor numbers. These results demonstrate that the nature of primary T(CD8+) responses to influenza A virus is highly influenced by Ag dose, which, in turn, determines the relative importance of Ag presentation, T(CD8+) avidity, and precursor numbers in shaping the ID hierarchy. These findings provide valuable insights for future T(CD8+)-based vaccination strategies.
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Affiliation(s)
- Fabio Luciani
- Infection and Inflammation Research Centre, School of Medical Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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30
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Gras S, Burrows SR, Turner SJ, Sewell AK, McCluskey J, Rossjohn J. A structural voyage toward an understanding of the MHC-I-restricted immune response: lessons learned and much to be learned. Immunol Rev 2012; 250:61-81. [DOI: 10.1111/j.1600-065x.2012.01159.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stephanie Gras
- Department of Biochemistry and Molecular Biology; School of Biomedical Sciences; Monash University; Clayton; Australia
| | - Scott R. Burrows
- Queensland Institute of Medical Research and Australian Centre for Vaccine Development; Brisbane; Australia
| | - Stephen J. Turner
- Department of Microbiology and Immunology; University of Melbourne; Parkville; Australia
| | - Andrew K. Sewell
- Institute of Infection and Immunity; Cardiff University School of Medicine; Cardiff; UK
| | - James McCluskey
- Department of Microbiology and Immunology; University of Melbourne; Parkville; Australia
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31
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La Gruta N, Kelso A, Brown LE, Chen W, Jackson DC, Turner SJ. Role of CD8(+) T-cell immunity in influenza infection: potential use in future vaccine development. Expert Rev Respir Med 2012; 3:523-37. [PMID: 20477341 DOI: 10.1586/ers.09.44] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Continued circulation of the highly pathogenic avian H5N1 influenza A virus has many people worried that an influenza pandemic is imminent. Compounding this is the realization that H5N1 vaccines based on current influenza vaccine technology (designed to generate protective antibody responses) may be suboptimal at providing protection. As a consequence, there is recent interest in vaccine strategies that elicit cellular immunity, particularly the cytotoxic T lymphocyte response, in an effort to provide protection against a potential pandemic. A major issue is the lack of information about the precise role that these 'hitmen' of the immune system have in protecting against both pandemic and seasonal influenza. We need to know more about how the induction and maintenance of cytotoxic T lymphocytes after influenza infection can impact protection from further infection. The challenge is then to use this information in the design of vaccines that will protect against pandemic influenza and will help optimize CD8(+) killer T-cell responses in other infections.
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Affiliation(s)
- Nicole La Gruta
- Department of Microbiology and Immunology, The University of Melbourne, Royal Parade, Parkville, Victoria 3010, Australia
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32
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Hou Y, Guo Y, Wu C, Shen N, Jiang Y, Wang J. Prediction and identification of T cell epitopes in the H5N1 influenza virus nucleoprotein in chicken. PLoS One 2012; 7:e39344. [PMID: 22745738 PMCID: PMC3379973 DOI: 10.1371/journal.pone.0039344] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 05/18/2012] [Indexed: 11/19/2022] Open
Abstract
T cell epitopes can be used for the accurate monitoring of avian influenza virus (AIV) immune responses and the rational design of vaccines. No T cell epitopes have been previously identified in the H5N1 AIV virus nucleoprotein (NP) in chickens. For the first time, this study used homology modelling techniques to construct three-dimensional structures of the peptide-binding domains of chicken MHC class Ι molecules for four commonly encountered unique haplotypes, i.e., B4, B12, B15, and B19. H5N1 AIV NP was computationally parsed into octapeptides or nonapeptides according to the peptide-binding motifs of MHC class I molecules of the B4, B12, B15 and B19 haplotypes. Seventy-five peptide sequences were modelled and their MHC class I molecule-binding abilities were analysed by molecular docking. Twenty-five peptides (Ten for B4, six for B12, two for B15, and seven for B19) were predicted to be potential T cell epitopes in chicken. Nine of these peptides and one unrelated peptide were manually synthesized and their T cell responses were tested in vitro. Spleen lymphocytes were collected from SPF chickens that had been immunised with a NP-expression plasmid, pCAGGS-NP, and they were stimulated using the synthesized peptides. The secretion of chicken IFN-γ and the proliferation of CD8(+) T cells were tested using an ELISA kit and flow cytometry, respectively. The significant secretion of chicken IFN-γ and proliferation of CD8(+) T lymphocytes increased by 13.7% and 11.9% were monitored in cells stimulated with peptides NP(89-97) and NP(198-206), respectively. The results indicate that peptides NP(89-97) (PKKTGGPIY) and NP(198-206) (KRGINDRNF) are NP T cell epitopes in chicken of certain haplotypes. The method used in this investigation is applicable to predicting T cell epitopes for other antigens in chicken, while this study also extends our understanding of the mechanisms of the immune response to AIV in chicken.
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Affiliation(s)
- Yanxia Hou
- Centre for Animal Infectious Disease Diagnosis and Technical Services and State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, People’s Republic of China
| | - Yingying Guo
- Centre for Animal Infectious Disease Diagnosis and Technical Services and State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, People’s Republic of China
| | - Chunyan Wu
- Centre for Animal Infectious Disease Diagnosis and Technical Services and State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, People’s Republic of China
| | - Nan Shen
- Centre for Animal Infectious Disease Diagnosis and Technical Services and State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, People’s Republic of China
| | - Yongping Jiang
- Centre for Animal Infectious Disease Diagnosis and Technical Services and State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, People’s Republic of China
- Animal Influenza Laboratory of the Ministry of Agriculture and State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, People’s Republic of China
- * E-mail: (YJ); (JW)
| | - Jingfei Wang
- Centre for Animal Infectious Disease Diagnosis and Technical Services and State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, People’s Republic of China
- * E-mail: (YJ); (JW)
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33
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Tan ACL, Eriksson EMY, Kedzierska K, Deliyannis G, Valkenburg SA, Zeng W, Jackson DC. Polyfunctional CD8(+) T cells are associated with the vaccination-induced control of a novel recombinant influenza virus expressing an HCV epitope. Antiviral Res 2012; 94:168-78. [PMID: 22504097 DOI: 10.1016/j.antiviral.2012.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 03/20/2012] [Accepted: 03/27/2012] [Indexed: 01/26/2023]
Abstract
In hepatitis C virus (HCV) infection, CD8(+) T cell responses have been shown to be important in viral clearance. Examining the efficacy of CD8(+) T cell vaccines against HCV has been limited by the lack of an HCV infectious model in mice and the differences between MHC restriction in humans and mice. Using HLA-A2 transgenic HHD mice, we demonstrate that intranasally delivered Pam2Cys-based lipopeptides containing HLA-A2-restricted HCV epitopes can induce polyfunctional CD8(+) T cell responses in several organs including the liver. To examine the activity of these responses in an infectious context, we developed a recombinant influenza virus that expresses the NS5B(2594-2602) epitope from non-structural protein 5B of hepatitis C virus (PR8-HCV(NS5B)). We showed that mice inoculated with a lipopeptide containing the NS5B epitope had reduced viral loads following challenge with the PR8-HCV(NS5B) virus. This reduction was associated with the induction of NS5B(2594-2602)-specific IFN-γ and TNF-α co-producing CD8(+) T cells. The T cell receptor usage in the NS5B(2594-2602) response was found to exhibit a Vβ8.1/8.2 bias that was characterized by a narrow repertoire and a common CDR3β motif. This work has identified CD8(+) T cell functions induced by lipopeptides that are associated with viral control and demonstrate the potential of lipopeptide-based vaccines as candidates for treatment of HCV infection.
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Affiliation(s)
- Amabel C L Tan
- Department of Microbiology & Immunology, The University of Melbourne, Parkville, Victoria, Australia
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34
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Wang GC, Dash P, McCullers JA, Doherty PC, Thomas PG. T cell receptor αβ diversity inversely correlates with pathogen-specific antibody levels in human cytomegalovirus infection. Sci Transl Med 2012; 4:128ra42. [PMID: 22491952 PMCID: PMC3593633 DOI: 10.1126/scitranslmed.3003647] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A diverse T cell receptor (TCR) repertoire capable of recognizing a broad range of antigenic peptides is thought to be central to effective pathogen-specific immunity by counteracting escape mutations, selecting high-avidity T cells, and providing T cell specificities with comprehensive functional characteristics. However, evidence that TCR diversity is important for the successful control of human infections is limited. A single-cell strategy for the clonotypic analysis of human CD8⁺ TCRαβ repertoires was used to probe the diversity and magnitude of individual human cytomegalovirus (CMV)-specific CD8⁺ T cells recovered directly ex vivo. We found that CD8⁺ TCRαβ repertoire diversity, but not the size of the CD8⁺ T cell response, was inversely related to circulating CMV-specific antibody levels, a measure that has been correlated epidemiologically with differential mortality risks and found here to be higher in persons with detectable (versus undetectable) CMV viral loads. Overall, our findings indicate that CD8⁺ T cell diversity may be more important than T cell abundance in limiting the negative consequences of CMV persistence, demonstrate high prevalence of both TCRα and TCRβ public motif usage, and suggest that a highly diverse TCRαβ repertoire may be an important benchmark and target in the success of immunotherapeutic strategies.
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Affiliation(s)
- George C Wang
- Division of Geriatric Medicine and Gerontology, Biology of Healthy Aging Program, Johns Hopkins University School of Medicine, 5505 Hopkins Bayview Circle, Baltimore, MD 21224, USA.
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35
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Differentiation-dependent functional and epigenetic landscapes for cytokine genes in virus-specific CD8+ T cells. Proc Natl Acad Sci U S A 2011; 108:15306-11. [PMID: 21876173 DOI: 10.1073/pnas.1112520108] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the simultaneous engagement of multiple effector mechanisms is thought to characterize optimal CD8(+) T-cell immunity and facilitate pathogen clearance, the differentiation pathways leading to the acquisition and maintenance of such polyfunctional activity are not well understood. Division-dependent profiles of effector molecule expression for virus-specific T cells are analyzed here by using a combination of carboxyfluorescein succinimidyl ester dilution and intracellular cytokine staining subsequent to T-cell receptor ligation. The experiments show that, although the majority of naive CD8(+) T-cell precursors are preprogrammed to produce TNF-α soon after stimulation and a proportion make both TNF-α and IL-2, the progressive acquisition of IFN-γ expression depends on continued lymphocyte proliferation. Furthermore, the extensive division characteristic of differentiation to peak effector activity is associated with the progressive dominance of IFN-γ and the concomitant loss of polyfunctional cytokine production, although this is not apparent for long-term CD8(+) T-cell memory. Such proliferation-dependent variation in cytokine production appears tied to the epigenetic signatures within the ifnG and tnfA proximal promoters. Specifically, those cytokine gene loci that are rapidly expressed following antigen stimulation at different stages of T-cell differentiation can be shown (by ChIP) to have permissive epigenetic and RNA polymerase II docking signatures. Thus, the dynamic changes in cytokine profiles for naive, effector, and memory T cells are underpinned by specific epigenetic landscapes that regulate responsiveness following T-cell receptor ligation.
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36
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Smith AM, Adler FR, McAuley JL, Gutenkunst RN, Ribeiro RM, McCullers JA, Perelson AS. Effect of 1918 PB1-F2 expression on influenza A virus infection kinetics. PLoS Comput Biol 2011; 7:e1001081. [PMID: 21379324 PMCID: PMC3040654 DOI: 10.1371/journal.pcbi.1001081] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 01/12/2011] [Indexed: 12/19/2022] Open
Abstract
Relatively little is known about the viral factors contributing to the lethality of the 1918 pandemic, although its unparalleled virulence was likely due in part to the newly discovered PB1-F2 protein. This protein, while unnecessary for replication, increases apoptosis in monocytes, alters viral polymerase activity in vitro, enhances inflammation and increases secondary pneumonia in vivo. However, the effects the PB1-F2 protein have in vivo remain unclear. To address the mechanisms involved, we intranasally infected groups of mice with either influenza A virus PR8 or a genetically engineered virus that expresses the 1918 PB1-F2 protein on a PR8 background, PR8-PB1-F2(1918). Mice inoculated with PR8 had viral concentrations peaking at 72 hours, while those infected with PR8-PB1-F2(1918) reached peak concentrations earlier, 48 hours. Mice given PR8-PB1-F2(1918) also showed a faster decline in viral loads. We fit a mathematical model to these data to estimate parameter values. The model supports a higher viral production rate per cell and a higher infected cell death rate with the PR8-PB1-F2(1918) virus. We discuss the implications these mechanisms have during an infection with a virus expressing a virulent PB1-F2 on the possibility of a pandemic and on the importance of antiviral treatments. Influenza A virus is a respiratory pathogen that causes significant morbidity and mortality in infected individuals, particularly during pandemics like the 1918–1919 Spanish Flu pandemic. Recent data suggests that the influenza virus PB1-F2 protein contributes to disease severity. Here, we use data from infected mice together with quantitative analyses to understand how the PB1-F2 protein from the 1918–1919 pandemic strain influences viral kinetics. We find that the rates of virus growth and decay are increased when the 1918 PB1-F2 is present. Our analyses suggest that infection with an influenza virus possessing the 1918 PB1-F2 protein results in a higher rate of viral production from infected cells and a higher rate of infected cell death. These results provide new insights into the mechanisms of PB1-F2 and the virulence and pathogenesis of pandemic strains of influenza.
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Affiliation(s)
- Amber M. Smith
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Frederick R. Adler
- Departments of Mathematics and Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Julie L. McAuley
- Department of Immunology and Microbiology, University of Melbourne, Victoria, Australia
| | - Ryan N. Gutenkunst
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Ruy M. Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jonathan A. McCullers
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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37
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Dash P, McClaren JL, Oguin TH, Rothwell W, Todd B, Morris MY, Becksfort J, Reynolds C, Brown SA, Doherty PC, Thomas PG. Paired analysis of TCRα and TCRβ chains at the single-cell level in mice. J Clin Invest 2011; 121:288-95. [PMID: 21135507 PMCID: PMC3007160 DOI: 10.1172/jci44752] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 10/20/2010] [Indexed: 11/17/2022] Open
Abstract
Characterizing the TCRα and TCRβ chains expressed by T cells responding to a given pathogen or underlying autoimmunity helps in the development of vaccines and immunotherapies, respectively. However, our understanding of complementary TCRα and TCRβ chain utilization is very limited for pathogen- and autoantigen-induced immunity. To address this problem, we have developed a multiplex nested RT-PCR method for the simultaneous amplification of transcripts encoding the TCRα and TCRβ chains from single cells. This multiplex method circumvented the lack of antibodies specific for variable regions of mouse TCRα chains and the need for prior knowledge of variable region usage in the TCRβ chain, resulting in a comprehensive, unbiased TCR repertoire analysis with paired coexpression of TCRα and TCRβ chains with single-cell resolution. Using CD8+ CTLs specific for an influenza epitope recovered directly from the pneumonic lungs of mice, this technique determined that 25% of such effectors expressed a dominant, nonproductively rearranged Tcra transcript. T cells with these out-of-frame Tcra mRNAs also expressed an alternate, in-frame Tcra, whereas approximately 10% of T cells had 2 productive Tcra transcripts. The proportion of cells with biallelic transcription increased over the course of a response, a finding that has implications for immune memory and autoimmunity. This technique may have broad applications in mouse models of human disease.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Animals
- Antigens, Viral/immunology
- Complementarity Determining Regions
- Epitopes/immunology
- Female
- Humans
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Molecular Sequence Data
- Orthomyxoviridae/immunology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Reverse Transcriptase Polymerase Chain Reaction/methods
- T-Lymphocytes, Cytotoxic/immunology
- Transcription, Genetic
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Affiliation(s)
- Pradyot Dash
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jennifer L. McClaren
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas H. Oguin
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - William Rothwell
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Brandon Todd
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa Y. Morris
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jared Becksfort
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Cory Reynolds
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Scott A. Brown
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Peter C. Doherty
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul G. Thomas
- St Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
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38
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Allen S, Turner SJ, Bourges D, Gleeson PA, Driel IR. Shaping the T‐cell repertoire in the periphery. Immunol Cell Biol 2010; 89:60-9. [DOI: 10.1038/icb.2010.133] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Stacey Allen
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne Parkville Victoria Australia
| | - Stephen J Turner
- Department of Microbiology and Immunology, The University of Melbourne Parkville Victoria Australia
| | - Dorothée Bourges
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne Parkville Victoria Australia
| | - Paul A Gleeson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne Parkville Victoria Australia
| | - Ian R Driel
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne Parkville Victoria Australia
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39
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Moffat JM, Handel A, Doherty PC, Turner SJ, Thomas PG, La Gruta NL. Influenza epitope-specific CD8+ T cell avidity, but not cytokine polyfunctionality, can be determined by TCRβ clonotype. THE JOURNAL OF IMMUNOLOGY 2010; 185:6850-6. [PMID: 21041725 DOI: 10.4049/jimmunol.1002025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cytokine polyfunctionality has recently emerged as a correlate of effective CTL immunity to viruses and tumors. Although the determinants of polyfunctionality remain unclear, there are published instances of a link between the production of multiple effector molecules and the peptide plus MHC class I molecule avidity of T cell populations. Influenza A virus infection of C57BL/6J mice induces CTL populations specific for multiple viral epitopes, each with varying proportions of monofunctional (IFN-γ(+) only) or polyfunctional (IFN-γ(+)TNF-α(+)IL-2(+)) CTLs. In this study, we probe the link between TCR avidity and polyfunctionality for two dominant influenza epitopes (D(b)NP(366) and D(b)PA(224)) by sequencing the TCR CDR3β regions of influenza-specific IFN-γ(+) versus IFN-γ(+)IL-2(+) cells, or total tetramer(+) versus high-avidity CTLs (as defined by the peptide plus MHC class I molecule-TCR dissociation rate). Preferential selection for particular clonotypes was evident for the high-avidity D(b)PA(224)-specific set but not for any of the other subsets examined. These data suggest that factors other than TCRβ sequence influence cytokine profiles and demonstrate no link between differential avidity and polyfunctionality.
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Affiliation(s)
- Jessica M Moffat
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
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40
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Le Goffic R, Bouguyon E, Chevalier C, Vidic J, Da Costa B, Leymarie O, Bourdieu C, Decamps L, Dhorne-Pollet S, Delmas B. Influenza A virus protein PB1-F2 exacerbates IFN-beta expression of human respiratory epithelial cells. THE JOURNAL OF IMMUNOLOGY 2010; 185:4812-23. [PMID: 20844191 DOI: 10.4049/jimmunol.0903952] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The PB1-F2 protein of the influenza A virus (IAV) contributes to viral pathogenesis by a mechanism that is not well understood. PB1-F2 was shown to modulate apoptosis and to be targeted by the CD8(+) T cell response. In this study, we examined the downstream effects of PB1-F2 protein during IAV infection by measuring expression of the cellular genes in response to infection with wild-type WSN/33 and PB1-F2 knockout viruses in human lung epithelial cells. Wild-type virus infection resulted in a significant induction of genes involved in innate immunity. Knocking out the PB1-F2 gene strongly decreased the magnitude of expression of cellular genes implicated in antiviral response and MHC class I Ag presentation, suggesting that PB1-F2 exacerbates innate immune response. Biological network analysis revealed the IFN pathway as a link between PB1-F2 and deregulated genes. Using quantitative RT-PCR and IFN-β gene reporter assay, we determined that PB1-F2 mediates an upregulation of IFN-β expression that is dependent on NF-κB but not on AP-1 and IFN regulatory factor-3 transcription factors. Recombinant viruses knocked out for the PB1-F2 and/or the nonstructural viral protein 1 (the viral antagonist of the IFN response) genes provide further evidence that PB1-F2 increases IFN-β expression and that nonstructural viral protein 1 strongly antagonizes the effect of PB1-F2 on the innate response. Finally, we compared the effect of PB1-F2 variants taken from several IAV strains on IFN-β expression and found that PB1-F2-mediated IFN-β induction is significantly influenced by its amino acid sequence, demonstrating its importance in the host cell response triggered by IAV infection.
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Affiliation(s)
- Ronan Le Goffic
- Unité de Virologie et Immunologie Moléculaires, Unité de Recherche 892 Institut National de la Recherche Agronomique, Domaine de Vilvert, Jouy-en-Josas, France.
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41
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McAuley JL, Chipuk JE, Boyd KL, Van De Velde N, Green DR, McCullers JA. PB1-F2 proteins from H5N1 and 20 century pandemic influenza viruses cause immunopathology. PLoS Pathog 2010; 6:e1001014. [PMID: 20661425 PMCID: PMC2908617 DOI: 10.1371/journal.ppat.1001014] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 06/23/2010] [Indexed: 01/21/2023] Open
Abstract
With the recent emergence of a novel pandemic strain, there is presently intense interest in understanding the molecular signatures of virulence of influenza viruses. PB1-F2 proteins from epidemiologically important influenza A virus strains were studied to determine their function and contribution to virulence. Using 27-mer peptides derived from the C-terminal sequence of PB1-F2 and chimeric viruses engineered on a common background, we demonstrated that induction of cell death through PB1-F2 is dependent upon BAK/BAX mediated cytochrome c release from mitochondria. This function was specific for the PB1-F2 protein of A/Puerto Rico/8/34 and was not seen using PB1-F2 peptides derived from past pandemic strains. However, PB1-F2 proteins from the three pandemic strains of the 20th century and a highly pathogenic strain of the H5N1 subtype were shown to enhance the lung inflammatory response resulting in increased pathology. Recently circulating seasonal influenza A strains were not capable of this pro-inflammatory function, having lost the PB1-F2 protein's immunostimulatory activity through truncation or mutation during adaptation in humans. These data suggest that the PB1-F2 protein contributes to the virulence of pandemic strains when the PB1 gene segment is recently derived from the avian reservoir. There is presently great interest in understanding how influenza viruses cause disease. In this paper, we explore the role of the influenza virus PB1-F2 protein in disease. We show that the ability of the protein to cause cell death is mediated through a mitochondrial death pathway controlled by proteins called BAX or BAK. However, this function of the protein only seems to be relevant to a restricted set of viruses and not past pandemic strains. Instead, the ability to generate inflammation in the lung proves to be a common trait of all past pandemic strains as well as the H5N1 highly pathogenic avian influenza strains which remain a significant pandemic threat. It appears likely that this pro-inflammatory phenotype is a characteristic of viruses emerging from the avian reservoir and is therefore important for new strains that cross the species barrier and establish themselves in humans. During circulation and adaptation in the mammalian lung, this function is typically lost. Of note, the novel 2009 H1N1 pandemic strain does not express a full-length PB1-F2. Were it to acquire a fully functional, inflammatory PB1-F2 through reassortment, this could herald greatly enhanced disease potential.
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Affiliation(s)
- Julie L. McAuley
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Jerry E. Chipuk
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Kelli L. Boyd
- Department of Pathology, Division of Comparative Medicine, Vanderbilt University, Nashville, Tennessee, United States of America.
| | - Nick Van De Velde
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Douglas R. Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Jonathan A. McCullers
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- * E-mail:
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42
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La Gruta NL, Rothwell WT, Cukalac T, Swan NG, Valkenburg SA, Kedzierska K, Thomas PG, Doherty PC, Turner SJ. Primary CTL response magnitude in mice is determined by the extent of naive T cell recruitment and subsequent clonal expansion. J Clin Invest 2010; 120:1885-94. [PMID: 20440073 DOI: 10.1172/jci41538] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 03/10/2010] [Indexed: 12/27/2022] Open
Abstract
CD8+ T cell responses to viral infection are characterized by the emergence of dominant and subdominant CTL populations. The immunodominance hierarchies of these populations are highly reproducible for any given spectrum of virus-induced peptide-MHCI complexes and are likely determined by multiple factors. Recent studies demonstrate a direct correlation between naive epitope-specific CD8+ T cell precursor (CTLp) frequency and the magnitude of the response after antigen challenge. Thus, the number of available precursors in the naive pool has emerged as a key predictor of immunodominance. In contrast to this, we report here no consistent relationship between CTLp frequency and the subsequent magnitude of the immune response for 4 influenza virus-derived epitopes following intranasal infection of mice with influenza A virus. Rather, the characteristic, antigen-driven T cell immunodominance hierarchy was determined by the extent of recruitment from the available pool of epitope-specific precursors and the duration of their continued expansion over the course of the infection. These findings suggest possibilities for enhancing protective immune memory by maximizing both the size and diversity of typically subdominant T cell responses through rational vaccine design.
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Affiliation(s)
- Nicole L La Gruta
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia.
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43
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Abstract
T cell receptor (TCR) nucleotide sequences are often generated during analyses of T cell responses to pathogens or autoantigens. The most important region of the TCR is the third complementarity-determining region (CDR3) whose nucleotide sequence is unique to each T cell clone. The CDR3 interacts with the peptide and thus is important for recognizing pathogen or autoantigen epitopes. While conventions exist for identifying the various TCR chains, there is a lack of a concise nomenclature that would identify both the amino acid translation and nucleotide sequence of the CDR3. This deficiency makes the comparison of published TCR genetic and proteomic information difficult. To enhance information sharing among different databases and to facilitate computational assessment of clonotypic T cell repertoires, we propose a clonotype nomenclature. The rules for generating a clonotype identifier are simple and easy to follow, and have a built-in error-checking system. The identifier includes the V and J region, the CDR3 length as well as its human or mouse origin. The framework of this naming system could also be expanded to the B cell receptor.
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44
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Turner SJ, La Gruta NL, Kedzierska K, Thomas PG, Doherty PC. Functional implications of T cell receptor diversity. Curr Opin Immunol 2009; 21:286-90. [PMID: 19524428 DOI: 10.1016/j.coi.2009.05.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 05/05/2009] [Indexed: 01/27/2023]
Abstract
Naive T cells are recruited into any given host response by recognizing a spectrum of possible antigens with 'sufficient' avidity. Does selecting a more functionally diverse array give better immune control? Perhaps low avidity 'killers' that 'kiss and run' operate optimally to eliminate virus-infected targets, while high avidity 'helpers' that stay faithfully in place produce more cytokine. Recent findings indeed suggest that the selection of a broad T cell receptor repertoire is characteristic of the initial phase following antigen contact, while continued exposure leads to further cycles of division and the progressive numerical dominance of 'best-fit' clonotypes. Here, we review recent advances demonstrating a link between T cell repertoire diversity and immunity to infection, and consider the potential mechanisms at play.
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Affiliation(s)
- Stephen J Turner
- Department of Microbiology and Immunology, The University of Melbourne, Victoria, Australia.
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45
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Price DA, Asher TE, Wilson NA, Nason MC, Brenchley JM, Metzler IS, Venturi V, Gostick E, Chattopadhyay PK, Roederer M, Davenport MP, Watkins DI, Douek DC. Public clonotype usage identifies protective Gag-specific CD8+ T cell responses in SIV infection. J Exp Med 2009; 206:923-36. [PMID: 19349463 PMCID: PMC2715115 DOI: 10.1084/jem.20081127] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 03/16/2009] [Indexed: 01/13/2023] Open
Abstract
Despite the pressing need for an AIDS vaccine, the determinants of protective immunity to HIV remain concealed within the complexity of adaptive immune responses. We dissected immunodominant virus-specific CD8(+) T cell populations in Mamu-A*01(+) rhesus macaques with primary SIV infection to elucidate the hallmarks of effective immunity at the level of individual constituent clonotypes, which were identified according to the expression of distinct T cell receptors (TCRs). The number of public clonotypes, defined as those that expressed identical TCR beta-chain amino acid sequences and recurred in multiple individuals, contained within the acute phase CD8(+) T cell population specific for the biologically constrained Gag CM9 (CTPYDINQM; residues 181-189) epitope correlated negatively with the virus load set point. This independent molecular signature of protection was confirmed in a prospective vaccine trial, in which clonotype engagement was governed by the nature of the antigen rather than the context of exposure and public clonotype usage was associated with enhanced recognition of epitope variants. Thus, the pattern of antigen-specific clonotype recruitment within a protective CD8(+) T cell population is a prognostic indicator of vaccine efficacy and biological outcome in an AIDS virus infection.
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Affiliation(s)
- David A. Price
- Vaccine Research Center, Biostatistics Research Branch, and Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
- Department of Medical Biochemistry and Immunology, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, UK
| | - Tedi E. Asher
- Vaccine Research Center, Biostatistics Research Branch, and Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Nancy A. Wilson
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53711
| | - Martha C. Nason
- Vaccine Research Center, Biostatistics Research Branch, and Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jason M. Brenchley
- Vaccine Research Center, Biostatistics Research Branch, and Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Ian S. Metzler
- Vaccine Research Center, Biostatistics Research Branch, and Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Vanessa Venturi
- Centre for Vascular Research, University of New South Wales, Kensington 2052, Sydney, Australia
| | - Emma Gostick
- Department of Medical Biochemistry and Immunology, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, UK
| | - Pratip K. Chattopadhyay
- Vaccine Research Center, Biostatistics Research Branch, and Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Mario Roederer
- Vaccine Research Center, Biostatistics Research Branch, and Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Miles P. Davenport
- Centre for Vascular Research, University of New South Wales, Kensington 2052, Sydney, Australia
| | - David I. Watkins
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53711
| | - Daniel C. Douek
- Vaccine Research Center, Biostatistics Research Branch, and Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
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Co MDT, Kilpatrick ED, Rothman AL. Dynamics of the CD8 T-cell response following yellow fever virus 17D immunization. Immunology 2009; 128:e718-27. [PMID: 19740333 DOI: 10.1111/j.1365-2567.2009.03070.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Management of yellow fever is focused on the prevention of illness by the use of the yellow fever virus (YFV) 17D vaccine. The role of neutralizing antibodies in protection is generally accepted with YFV-specific T cells likely contributing to the control of viral replication. We studied CD8(+) T-cell responses to four defined human leucocyte antigen-B35-restricted epitopes in YFV vaccine recipients as a model of the kinetics of cytotoxic T-lymphocyte responses to an acute human viral infection. Multiple features of these epitope-specific responses were analysed after vaccination including magnitude, cytokine production, phenotype and T-cell receptor repertoire. Peak peptide-specific interferon-gamma (IFN-gamma) responses of almost 1% of CD8(+) T cells were seen as early as 2 weeks post-vaccination; however, dominant responses varied between donors. Peptide-specific responses were still detectable at 54 months post-vaccination. Tetramer-positive cells, at high frequencies, were detected as early as 7-9 days, before detectable IFN-gamma-producing cells, suggesting a defect in the functional capacity of some antigen-specific cells early post-vaccination. The predominant memory phenotype of the tetramer-positive population was a differentiated effector (CD45RA(+) CCR7(-) CD62L(-)) phenotype. The T-cell receptor Vbeta analysis revealed a diverse oligoclonal repertoire in tetramer-positive T-cell populations in two individuals. These characteristics of the YFV-specific T-cell response could contribute to vaccine effectiveness.
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Affiliation(s)
- Mary Dawn T Co
- Center for Infectious Disease and Vaccine Research, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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