1
|
Lanfermeijer J, van de Ven K, van Dijken H, Hendriks M, Talavera Ormeño CMP, de Heij F, Roholl P, Borghans JAM, van Baarle D, de Jonge J. Modified influenza M1 58-66 peptide vaccination induces non-relevant T-cells and may enhance pathology after challenge. NPJ Vaccines 2023; 8:116. [PMID: 37573454 PMCID: PMC10423225 DOI: 10.1038/s41541-023-00705-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 02/19/2022] [Accepted: 07/11/2023] [Indexed: 08/14/2023] Open
Abstract
CD8 + T cells are promising targets for vaccination against influenza A virus (IAV) infection. Their induction via peptide vaccination is not trivial, because peptides are weakly immunogenic. One strategy to overcome this is by vaccination with chemically enhanced altered peptide ligands (CPLs), which have improved MHC-binding and immunogenicity. It remains unknown how peptide-modification affects the resulting immune response. We studied the effect of CPLs derived from the influenza M158-66 epitope (GILGFVFTL) on the T-cell response. In HLA-A2*0201 transgenic mice, CPL-vaccination led to higher T-cell frequencies, but only a small percentage of the induced T cells recognized the GILG-wildtype (WT) peptide. CPL-vaccination resulted in a lower richness of the GILG-WT-specific T-cell repertoire and no improved protection against IAV-infection compared to GILG-WT peptide-vaccination. One CPL even appeared to enhance pathology after IAV-challenge. CPL-vaccination thus induces T cells not targeting the original peptide, which may lead to potential unwanted side effects.
Collapse
Affiliation(s)
- Josien Lanfermeijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Koen van de Ven
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Harry van Dijken
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Marion Hendriks
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Cami M P Talavera Ormeño
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Femke de Heij
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | - José A M Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
- Virology & Immunology Research. Dept Medical Microbiology and Infection prevention, University Medical Center Groningen, Groningen, the Netherlands
| | - Jørgen de Jonge
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
| |
Collapse
|
2
|
Massey J, Jackson K, Singh M, Hughes B, Withers B, Ford C, Khoo M, Hendrawan K, Zaunders J, Charmeteau-De Muylder B, Cheynier R, Luciani F, Ma D, Moore J, Sutton I. Haematopoietic Stem Cell Transplantation Results in Extensive Remodelling of the Clonal T Cell Repertoire in Multiple Sclerosis. Front Immunol 2022; 13:798300. [PMID: 35197974 PMCID: PMC8859174 DOI: 10.3389/fimmu.2022.798300] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 10/20/2021] [Accepted: 01/13/2022] [Indexed: 12/29/2022] Open
Abstract
Autologous haematopoietic stem cell transplantation (AHSCT) is a vital therapeutic option for patients with highly active multiple sclerosis (MS). Rates of remission suggest AHSCT is the most effective form of immunotherapy in controlling the disease. Despite an evolving understanding of the biology of immune reconstitution following AHSCT, the mechanism by which AHSCT enables sustained disease remission beyond the period of lymphopenia remains to be elucidated. Auto-reactive T cells are considered central to MS pathogenesis. Here, we analyse T cell reconstitution for 36 months following AHSCT in a cohort of highly active MS patients. Through longitudinal analysis of sorted naïve and memory T cell clones, we establish that AHSCT induces profound changes in the dominant T cell landscape of both CD4+ and CD8+ memory T cell clones. Lymphopenia induced homeostatic proliferation is followed by clonal attrition; with only 19% of dominant CD4 (p <0.025) and 13% of dominant CD8 (p <0.005) clones from the pre-transplant repertoire detected at 36 months. Recovery of a thymically-derived CD4 naïve T cell repertoire occurs at 12 months and is ongoing at 36 months, however diversity of the naïve populations is not increased from baseline suggesting the principal mechanism of durable remission from MS after AHSCT relates to depletion of putative auto-reactive clones. In a cohort of MS patients expressing the MS risk allele HLA DRB1*15:01, public clones are probed as potential biomarkers of disease. AHSCT appears to induce sustained periods of disease remission with dynamic changes in the clonal T cell repertoire out to 36 months post-transplant.
Collapse
Affiliation(s)
- Jennifer Massey
- Department of Haematology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Department of Neurology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
- *Correspondence: Jennifer Massey,
| | - Katherine Jackson
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Mandeep Singh
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Brendan Hughes
- School of Medical Sciences and Kirby Institute for Infection and Immunity, University of New South Wales (UNSW), Kensington, NSW, Australia
| | - Barbara Withers
- Department of Haematology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
| | - Carole Ford
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - Melissa Khoo
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - Kevin Hendrawan
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - John Zaunders
- Immunology Laboratory, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | | | - Rémi Cheynier
- Université de Paris, INSERM, CNRS, Institut Cochin, Paris, France
| | - Fabio Luciani
- School of Medical Sciences and Kirby Institute for Infection and Immunity, University of New South Wales (UNSW), Kensington, NSW, Australia
| | - David Ma
- Department of Haematology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
| | - John Moore
- Department of Haematology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
| | - Ian Sutton
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
- Department of Neurology, St Vincent’s Clinic, Darlinghurst, NSW, Australia
| |
Collapse
|
3
|
Tfh Cells in Health and Immunity: Potential Targets for Systems Biology Approaches to Vaccination. Int J Mol Sci 2020; 21:ijms21228524. [PMID: 33198297 PMCID: PMC7696930 DOI: 10.3390/ijms21228524] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022] Open
Abstract
T follicular helper (Tfh) cells are a specialised subset of CD4+ T cells that play a significant role in the adaptive immune response, providing critical help to B cells within the germinal centres (GC) of secondary lymphoid organs. The B cell receptors of GC B cells undergo multiple rounds of somatic hypermutation and affinity maturation within the GC response, a process dependent on cognate interactions with Tfh cells. B cells that receive sufficient help from Tfh cells form antibody-producing long-lived plasma and memory B cells that provide the basis of decades of effective and efficient protection and are considered the gold standard in correlates of protection post-vaccination. However, the T cell response to vaccination has been understudied, and over the last 10 years, exponential improvements in the technological underpinnings of sampling techniques, experimental and analytical tools have allowed multidisciplinary characterisation of the role of T cells and the immune system as a whole. Of particular interest to the field of vaccinology are GCs and Tfh cells, representing a unique target for improving immunisation strategies. Here, we discuss recent insights into the unique journey of Tfh cells from thymus to lymph node during differentiation and their role in the production of high-quality antibody responses as well as their journey back to the periphery as a population of memory cells. Further, we explore their function in health and disease and the power of next-generation sequencing techniques to uncover their potential as modulators of vaccine-induced immunity.
Collapse
|
4
|
D’Ippolito E, Wagner KI, Busch DH. Needle in a Haystack: The Naïve Repertoire as a Source of T Cell Receptors for Adoptive Therapy with Engineered T Cells. Int J Mol Sci 2020; 21:E8324. [PMID: 33171940 PMCID: PMC7664211 DOI: 10.3390/ijms21218324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 09/29/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/11/2022] Open
Abstract
T cell engineering with antigen-specific T cell receptors (TCRs) has allowed the generation of increasingly specific, reliable, and versatile T cell products with near-physiological features. However, a broad applicability of TCR-based therapies in cancer is still limited by the restricted number of TCRs, often also of suboptimal potency, available for clinical use. In addition, targeting of tumor neoantigens with TCR-engineered T cell therapy moves the field towards a highly personalized treatment, as tumor neoantigens derive from somatic mutations and are extremely patient-specific. Therefore, relevant TCRs have to be de novo identified for each patient and within a narrow time window. The naïve repertoire of healthy donors would represent a reliable source due to its huge diverse TCR repertoire, which theoretically entails T cells for any antigen specificity, including tumor neoantigens. As a challenge, antigen-specific naïve T cells are of extremely low frequency and mostly of low functionality, making the identification of highly functional TCRs finding a "needle in a haystack." In this review, we present the technological advancements achieved in high-throughput mapping of patient-specific neoantigens and corresponding cognate TCRs and how these platforms can be used to interrogate the naïve repertoire for a fast and efficient identification of rare but therapeutically valuable TCRs for personalized adoptive T cell therapy.
Collapse
MESH Headings
- Antigens, Neoplasm/genetics
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/immunology
- Humans
- Immunotherapy, Adoptive/methods
- Immunotherapy, Adoptive/trends
- Neoplasms/genetics
- Precision Medicine/methods
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/physiology
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/immunology
Collapse
Affiliation(s)
- Elvira D’Ippolito
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
| | - Karolin I. Wagner
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
- Focus Group ‘‘Clinical Cell Processing and Purification”, Institute for Advanced Study, Technische Universität München (TUM), 81675 Munich, Germany
| |
Collapse
|
5
|
Rowntree LC, Nguyen THO, Farenc C, Halim H, Hensen L, Rossjohn J, Kotsimbos TC, Purcell AW, Kedzierska K, Gras S, Mifsud NA. A Shared TCR Bias toward an Immunogenic EBV Epitope Dominates in HLA-B*07:02–Expressing Individuals. THE JOURNAL OF IMMUNOLOGY 2020; 205:1524-1534. [DOI: 10.4049/jimmunol.2000249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Academic Contribution Register] [Received: 03/11/2020] [Accepted: 07/19/2020] [Indexed: 11/19/2022]
|
6
|
The Identity Card of T Cells-Clinical Utility of T-cell Receptor Repertoire Analysis in Transplantation. Transplantation 2020; 103:1544-1555. [PMID: 31033649 DOI: 10.1097/tp.0000000000002776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/18/2022]
Abstract
There is a clear medical need to change the current strategy of "one-size-fits-all" immunosuppression for controlling transplant rejection to precision medicine and targeted immune intervention. As T cells play a key role in both undesired graft rejection and protection, a better understanding of the fate and function of both alloreactive graft-deteriorating T cells and those protecting to infections is required. The T-cell receptor (TCR) is the individual identity card of each T cell clone and can help to follow single specificities. In this context, tracking of lymphocytes with certain specificity in blood and tissue in clinical follow up is of especial importance. After overcoming technical limitations of the past, novel molecular technologies opened new avenues of diagnostics. Using advantages of next generation sequencing, a method was established for T-cell tracing by detection of variable TCR region as identifiers of individual lymphocyte clones. The current review describes principles of laboratory and computational methods of TCR repertoire analysis, and gives an overview on applications for the basic understanding of transplant biology and immune monitoring. The review also delineates methodological pitfalls and challenges. With the outlook on prediction of antigens in immune-mediated processes including those of unknown causative pathogens, monitoring the fate and function of individual T cell clones, and the adoptive transfer of protective effector or regulatory T cells, this review highlights the current and future capability of TCR repertoire analysis.
Collapse
|
7
|
MHC-II alleles shape the CDR3 repertoires of conventional and regulatory naïve CD4 + T cells. Proc Natl Acad Sci U S A 2020; 117:13659-13669. [PMID: 32482872 DOI: 10.1073/pnas.2003170117] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/12/2022] Open
Abstract
T cell maturation and activation depend upon T cell receptor (TCR) interactions with a wide variety of antigenic peptides displayed in a given major histocompatibility complex (MHC) context. Complementarity-determining region 3 (CDR3) is the most variable part of the TCRα and -β chains, which govern interactions with peptide-MHC complexes. However, it remains unclear how the CDR3 landscape is shaped by individual MHC context during thymic selection of naïve T cells. We established two mouse strains carrying distinct allelic variants of H2-A and analyzed thymic and peripheral production and TCR repertoires of naïve conventional CD4+ T (Tconv) and naïve regulatory CD4+ T (Treg) cells. Compared with tuberculosis-resistant C57BL/6 (H2-Ab) mice, the tuberculosis-susceptible H2-Aj mice had fewer CD4+ T cells of both subsets in the thymus. In the periphery, this deficiency was only apparent for Tconv and was compensated for by peripheral reconstitution for Treg We show that H2-Aj favors selection of a narrower and more convergent repertoire with more hydrophobic and strongly interacting amino acid residues in the middle of CDR3α and CDR3β, suggesting more stringent selection against a narrower peptide-MHC-II context. H2-Aj and H2-Ab mice have prominent reciprocal differences in CDR3α and CDR3β features, probably reflecting distinct modes of TCR fitting to MHC-II variants. These data reveal the mechanics and extent of how MHC-II shapes the naïve CD4+ T cell CDR3 landscape, which essentially defines adaptive response to infections and self-antigens.
Collapse
|
8
|
Speranza E, Ruibal P, Port JR, Feng F, Burkhardt L, Grundhoff A, Günther S, Oestereich L, Hiscox JA, Connor JH, Muñoz-Fontela C. T-Cell Receptor Diversity and the Control of T-Cell Homeostasis Mark Ebola Virus Disease Survival in Humans. J Infect Dis 2019; 218:S508-S518. [PMID: 29986035 DOI: 10.1093/infdis/jiy352] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/24/2022] Open
Abstract
Differences in T-cell phenotype, particularly the expression of markers of T-cell homeostasis, have been observed in fatal and nonfatal Ebola virus disease (EVD). However, the relationship between these markers with T-cell function and virus clearance during EVD is poorly understood. To gain biological insight into the role of T cells during EVD, combined transcriptomics and T-cell receptor sequencing was used to profile blood samples from fatal and nonfatal EVD patients from the recent West African EVD epidemic. Fatal EVD was characterized by strong T-cell activation and increased abundance of T-cell inhibitory molecules. However, the early T-cell response was oligoclonal and did not result in viral clearance. In contrast, survivors mounted highly diverse T-cell responses, maintained low levels of T-cell inhibitors, and cleared Ebola virus. Our findings highlight the importance of T-cell immunity in surviving EVD and strengthen the foundation for further research on targeting of the dendritic cell-T cell interface for postexposure immunotherapy.
Collapse
Affiliation(s)
- Emily Speranza
- Department of Microbiology, Boston University School of Medicine, Boston MA.,Department of Bioinformatics Program, Boston University, Boston MA.,Department of National Emerging Infectious Diseases Laboratories, Boston University, Boston MA.,Department of Mathematics and Statistics, Boston University, Boston MA
| | - Paula Ruibal
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Julia R Port
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| | - Feng Feng
- Department of Microbiology, Boston University School of Medicine, Boston MA.,Department of Mathematics and Statistics, Boston University, Boston MA
| | - Lia Burkhardt
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Stephan Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| | - Lisa Oestereich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| | - Julian A Hiscox
- Institute for Infection and Global Health, University of Liverpool, United Kingdom.,Singapore Immunology Network, A*STAR, Singapore
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston MA.,Department of Bioinformatics Program, Boston University, Boston MA.,Department of National Emerging Infectious Diseases Laboratories, Boston University, Boston MA.,Department of Mathematics and Statistics, Boston University, Boston MA
| | - César Muñoz-Fontela
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), Partner SiteHamburg, Germany
| |
Collapse
|
9
|
Brazão V, Santello FH, Colato RP, Mazotti TT, Tazinafo LF, Toldo MPA, do Vale GT, Tirapelli CR, do Prado JC. Melatonin: Antioxidant and modulatory properties in age-related changes during Trypanosoma cruzi infection. J Pineal Res 2017; 63. [PMID: 28370218 DOI: 10.1111/jpi.12409] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Academic Contribution Register] [Received: 12/21/2016] [Accepted: 03/24/2017] [Indexed: 01/02/2023]
Abstract
The purpose of this study was to investigate the effects of melatonin on selected biomarkers of innate and humoral immune response as well as the antioxidant/oxidant status (superoxide dismutase-SOD and reduced glutathione levels (GSH) to understand whether age-related changes would influence the development of acute Trypanosoma cruzi (T. cruzi) infection. Young- (5 weeks) and middle-aged (18 months) Wistar rats were orally treated with melatonin (gavage) (05 mg/kg/day), 9 days after infection. A significant increase in both SOD activity and GSH levels was found in plasma from all middle-aged melatonin-treated animals. Melatonin triggered enhanced expression of major histocompatibility class II (MHC-II) antigens on antigen-presenting cell (APC) and peritoneal macrophages in all treated animals. High levels of CD4+ CD28-negative T cells (*P<.05) were detected in middle-aged control animals. Melatonin induced a significant reduction (***P<.001) in CD28-negative in CD4+ and CD8+ T cells in middle-aged control animals. Contrarily, the same group displayed upregulated CD4+ CD28+ T and CD8+ CD28+ T cells. Melatonin also triggered an upregulation of CD80 and CD86 expression in all young-treated groups. Significant percentages of B and spleen dendritic cells in middle-aged infected and treated animals were observed. Our data reveal new features of melatonin action in inhibiting membrane lipid peroxidation, through the reduction in 8-isoprostane, upregulating the antioxidant defenses and triggering an effective balance in the antioxidant/oxidant status during acute infection. The ability of melatonin to counteract the immune alterations induced by aging added further support to its use as a potential therapeutic target not only for T. cruzi infection but also for other immunocompromised states.
Collapse
Affiliation(s)
- Vânia Brazão
- College of Pharmaceutical Sciences of Ribeirão Preto (FCFRP), University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Fabricia H Santello
- College of Pharmaceutical Sciences of Ribeirão Preto (FCFRP), University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Rafaela P Colato
- College of Pharmaceutical Sciences of Ribeirão Preto (FCFRP), University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Tamires T Mazotti
- College of Pharmaceutical Sciences of Ribeirão Preto (FCFRP), University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Lucas F Tazinafo
- College of Pharmaceutical Sciences of Ribeirão Preto (FCFRP), University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Míriam Paula A Toldo
- College of Pharmaceutical Sciences of Ribeirão Preto (FCFRP), University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Gabriel T do Vale
- Department of Psychiatric Nursing and Human Sciences, Laboratory of Pharmacology, College of Nursing of Ribeirão Preto, USP, Ribeirão Preto, SP, Brazil
| | - Carlos R Tirapelli
- Department of Psychiatric Nursing and Human Sciences, Laboratory of Pharmacology, College of Nursing of Ribeirão Preto, USP, Ribeirão Preto, SP, Brazil
| | - José C do Prado
- College of Pharmaceutical Sciences of Ribeirão Preto (FCFRP), University of São Paulo, Ribeirão Preto, SP, Brazil
| |
Collapse
|
10
|
Rojas JM, Rodríguez-Calvo T, Sevilla N. Recall T cell responses to bluetongue virus produce a narrowing of the T cell repertoire. Vet Res 2017; 48:38. [PMID: 28662714 PMCID: PMC5492282 DOI: 10.1186/s13567-017-0444-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 03/18/2017] [Accepted: 06/26/2017] [Indexed: 11/12/2022] Open
Abstract
In most viral infections, recall T cell responses are critical for protection. The magnitude of these secondary responses can also affect the CD8 and CD4 epitope repertoire diversity. Bluetongue virus (BTV) infection in sheep elicits a T cell response that contributes to viremia control and could be relevant for cross-protection between BTV serotypes. Here, we characterized CD4+ and CD8+ T cell responses during primary and recall responses. During primary immune responses, both CD4+ and CD8+ T cell populations expanded by 14 days post-infection (dpi). CD4+ T cell populations showed a lower peak of expansion and prolonged contraction phase compared to CD8+ T cell populations. Recall responses to BTV challenge led to BTV-specific expansion and activation of CD8+ but not of CD4+ T cells. The evolution of the BTV-specific TCR repertoire was also characterized in response to VP7 peptide stimulation. Striking differences in repertoire development were noted over the time-course of infection. During primary responses, a broader repertoire was induced for MHC-I and MHC-II epitopes. However, during memory responses, a narrowed repertoire was activated towards a dominant motif in VP7 comprising amino acids 139–291. Monocytes were also examined, and expanded during acute infection resolution. In addition, pro-inflammatory cytokine levels increased after BTV inoculation and persisted throughout the experiment, indicative of a prolonged inflammatory state during BTV infections. These findings could have implications for vaccine design as the narrowing memory T cell repertoire induced after BTV re-infection could lead to the development of protective immunodominant TCR repertoires that differs between individual sheep.
Collapse
Affiliation(s)
- José-Manuel Rojas
- Centro de Investigación en Sanidad Animal (CISA-INIA), Instituto Nacional de Investigación Agraria y Alimentaria, Ctra Algete a El Casar km 8, Valdeolmos, 28130, Madrid, Spain
| | - Teresa Rodríguez-Calvo
- Centro de Investigación en Sanidad Animal (CISA-INIA), Instituto Nacional de Investigación Agraria y Alimentaria, Ctra Algete a El Casar km 8, Valdeolmos, 28130, Madrid, Spain.,Institute of Diabetes Research, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Noemí Sevilla
- Centro de Investigación en Sanidad Animal (CISA-INIA), Instituto Nacional de Investigación Agraria y Alimentaria, Ctra Algete a El Casar km 8, Valdeolmos, 28130, Madrid, Spain.
| |
Collapse
|
11
|
Gnjatic S, Bronte V, Brunet LR, Butler MO, Disis ML, Galon J, Hakansson LG, Hanks BA, Karanikas V, Khleif SN, Kirkwood JM, Miller LD, Schendel DJ, Tanneau I, Wigginton JM, Butterfield LH. Identifying baseline immune-related biomarkers to predict clinical outcome of immunotherapy. J Immunother Cancer 2017; 5:44. [PMID: 28515944 PMCID: PMC5432988 DOI: 10.1186/s40425-017-0243-4] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 11/17/2016] [Accepted: 04/26/2017] [Indexed: 12/31/2022] Open
Abstract
As cancer strikes, individuals vary not only in terms of factors that contribute to its occurrence and development, but as importantly, in their capacity to respond to treatment. While exciting new therapeutic options that mobilize the immune system against cancer have led to breakthroughs for a variety of malignancies, success is limited to a subset of patients. Pre-existing immunological features of both the host and the tumor may contribute to how patients will eventually fare with immunotherapy. A broad understanding of baseline immunity, both in the periphery and in the tumor microenvironment, is needed in order to fully realize the potential of cancer immunotherapy. Such interrogation of the tumor, blood, and host immune parameters prior to treatment is expected to identify biomarkers predictive of clinical outcome as well as to elucidate why some patients fail to respond to immunotherapy. To approach these opportunities for progress, the Society for Immunotherapy of Cancer (SITC) reconvened the Immune Biomarkers Task Force. Comprised of an international multidisciplinary panel of experts, Working Group 4 sought to make recommendations that focus on the complexity of the tumor microenvironment, with its diversity of immune genes, proteins, cells, and pathways naturally present at baseline and in circulation, and novel tools to aid in such broad analyses.
Collapse
Affiliation(s)
- Sacha Gnjatic
- Department of Hematology/Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, S5-105, 1470 Madison Avenue, Box 1128, New York, NY 10029 USA
| | - Vincenzo Bronte
- Head of Immunology Section, University of Verona, Piazzale Le L. A. Scuro, 10, Verona, Italy
| | - Laura Rosa Brunet
- Immodulon Therapeutics Ltd, Stockley Park, 6-9 The Square, Uxbridge, UK
| | - Marcus O Butler
- Princess Margaret Hospital/Ontario Cancer Institute, RM 9-622, 610 University Ave, Toronto, ON Canada
| | - Mary L Disis
- University of Washington, Tumor Vaccine Group, 850 Mercer Street, Box 358050, Seattle, WA 98109 USA
| | - Jérôme Galon
- INSERM - Cordeliers Research Center, Integrative Cancer Immunology Laboratory, 15 rue de l'Ecole de Médecine, Paris, France
| | - Leif G Hakansson
- CanImGuide Therapeutics AB, Domkyrkovägen 23, Hoellviken, Sweden
| | - Brent A Hanks
- Duke University Medical Center, 308 Research Drive, LSRC, Room C203, Box 3819, Durham, NC 27708 USA
| | - Vaios Karanikas
- Roche Innovation Center Zurich, Wagistrasse 18, Schlieren, Switzerland
| | - Samir N Khleif
- Georgia Cancer Center, Augusta University, 1120 15th Street, CN-2101A, Augusta, GA 30912 USA
| | - John M Kirkwood
- University of Pittsburgh, Hillman Cancer Center-Research Pavilion, 5117 Centre Avenue, Suite 1.32, Pittsburg, PA 15213 USA
| | - Lance D Miller
- Wake Forest School of Medicine, 1 Medical Center Blvd, Winston Salem, NC 27157 USA
| | - Dolores J Schendel
- Medigene Immunotherapies GmbH, Lochhamer Strasse 11, Planegg-Martinsried, Germany
| | | | - Jon M Wigginton
- MacroGenics, Inc., 9704 Medical Center Drive, Rockville, MD 20850 USA
| | - Lisa H Butterfield
- Department of Medicine, Surgery and Immunology, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Pittsburgh, PA 15213 USA
| |
Collapse
|
12
|
Du VY, Bansal A, Carlson J, Salazar-Gonzalez JF, Salazar MG, Ladell K, Gras S, Josephs TM, Heath SL, Price DA, Rossjohn J, Hunter E, Goepfert PA. HIV-1-Specific CD8 T Cells Exhibit Limited Cross-Reactivity during Acute Infection. THE JOURNAL OF IMMUNOLOGY 2016; 196:3276-86. [PMID: 26983786 DOI: 10.4049/jimmunol.1502411] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Academic Contribution Register] [Received: 11/13/2015] [Accepted: 02/11/2016] [Indexed: 01/03/2023]
Abstract
Prior work has demonstrated that HIV-1-specific CD8 T cells can cross-recognize variant epitopes. However, most of these studies were performed in the context of chronic infection, where the presence of viral quasispecies makes it difficult to ascertain the true nature of the original antigenic stimulus. To overcome this limitation, we evaluated the extent of CD8 T cell cross-reactivity in patients with acute HIV-1 clade B infection. In each case, we determined the transmitted founder virus sequence to identify the autologous epitopes restricted by individual HLA class I molecules. Our data show that cross-reactive CD8 T cells are infrequent during the acute phase of HIV-1 infection. Moreover, in the uncommon instances where cross-reactive responses were detected, the variant epitopes were poorly recognized in cytotoxicity assays. Molecular analysis revealed that similar antigenic structures could be cross-recognized by identical CD8 T cell clonotypes mobilized in vivo, yet even subtle differences in a single TCR-accessible peptide residue were sufficient to disrupt variant-specific reactivity. These findings demonstrate that CD8 T cells are highly specific for autologous epitopes during acute HIV-1 infection. Polyvalent vaccines may therefore be required to provide optimal immune cover against this genetically labile pathogen.
Collapse
Affiliation(s)
- Victor Y Du
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Anju Bansal
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | | | | | - Maria G Salazar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Kristin Ladell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Stephanie Gras
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Tracy M Josephs
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Sonya L Heath
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294
| | - David A Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom; Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Jamie Rossjohn
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom; Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Eric Hunter
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30329
| | - Paul A Goepfert
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294;
| |
Collapse
|
13
|
Stipp SR, Iniguez A, Wan F, Wodarz D. Timing of CD8 T cell effector responses in viral infections. ROYAL SOCIETY OPEN SCIENCE 2016; 3:150661. [PMID: 26998338 PMCID: PMC4785989 DOI: 10.1098/rsos.150661] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Academic Contribution Register] [Received: 12/03/2015] [Accepted: 01/22/2016] [Indexed: 06/05/2023]
Abstract
CD8 T cell or cytotoxic T lymphocyte (CTL) responses are an important branch of the immune system in the fight against viral infections. The dynamics of anti-viral CTL responses have been characterized in some detail, both experimentally and with mathematical models. An interesting experimental observation concerns the timing of CTL responses. A recent study reported that in pneumonia virus of mice the effector CTL tended to arrive in the lung only after maximal virus loads had been achieved, an observation that seems at first counterintuitive because prevention of pathology would require earlier CTL-mediated activity. A delay in CTL-mediated effector activity has also been quoted as a possible explanation for the difficulties associated with CTL-based vaccines. This paper uses mathematical models to show that in specific parameter regimes, delayed CTL effector activity can be advantageous for the host in the sense that it can increase the chances of virus clearance. The increased ability of the CTL to clear the infection, however, is predicted to come at the cost of acute pathology, giving rise to a trade-off, which is discussed in the light of evolutionary processes. This work provides a theoretical basis for understanding the described experimental observations.
Collapse
Affiliation(s)
- Shaun R. Stipp
- Institute for Mathematical Behavioral Sciences, University of California, Irvine, CA, USA
| | - Abdon Iniguez
- Mathematical and Computational Systems Biology, University of California, Irvine, CA, USA
| | - Frederic Wan
- Department of Mathematics, University of California, Irvine, CA, USA
| | - Dominik Wodarz
- Department of Mathematics, University of California, Irvine, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| |
Collapse
|
14
|
Laydon DJ, Bangham CRM, Asquith B. Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140291. [PMID: 26150657 PMCID: PMC4528489 DOI: 10.1098/rstb.2014.0291] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Accepted: 05/03/2015] [Indexed: 12/26/2022] Open
Abstract
A highly diverse T-cell receptor (TCR) repertoire is a fundamental property of an effective immune system, and is associated with efficient control of viral infections and other pathogens. However, direct measurement of total TCR diversity is impossible. The diversity is high and the frequency distribution of individual TCRs is heavily skewed; the diversity therefore cannot be captured in a blood sample. Consequently, estimators of the total number of TCR clonotypes that are present in the individual, in addition to those observed, are essential. This is analogous to the 'unseen species problem' in ecology. We review the diversity (species richness) estimators that have been applied to T-cell repertoires and the methods used to validate these estimators. We show that existing approaches have significant shortcomings, and frequently underestimate true TCR diversity. We highlight our recently developed estimator, DivE, which can accurately estimate diversity across a range of immunological and biological systems.
Collapse
MESH Headings
- Animals
- Gene Rearrangement, T-Lymphocyte
- Genetic Variation
- Host-Pathogen Interactions/genetics
- Host-Pathogen Interactions/immunology
- Humans
- Lymphocyte Count
- Models, Genetic
- Models, Immunological
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Statistics, Nonparametric
- T-Lymphocytes/immunology
Collapse
Affiliation(s)
- Daniel J Laydon
- Section of Immunology, Wright-Fleming Institute, Imperial College School of Medicine, London W2 1PG, UK
| | - Charles R M Bangham
- Section of Immunology, Wright-Fleming Institute, Imperial College School of Medicine, London W2 1PG, UK
| | - Becca Asquith
- Section of Immunology, Wright-Fleming Institute, Imperial College School of Medicine, London W2 1PG, UK
| |
Collapse
|
15
|
Martyushev AP, Petravic J, Grimm AJ, Alinejad-Rokny H, Gooneratne SL, Reece JC, Cromer D, Kent SJ, Davenport MP. Epitope-specific CD8+ T cell kinetics rather than viral variability determine the timing of immune escape in simian immunodeficiency virus infection. THE JOURNAL OF IMMUNOLOGY 2015; 194:4112-21. [PMID: 25825438 DOI: 10.4049/jimmunol.1400793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Academic Contribution Register] [Received: 03/27/2014] [Accepted: 03/01/2015] [Indexed: 11/19/2022]
Abstract
CD8(+) T cells are important for the control of chronic HIV infection. However, the virus rapidly acquires "escape mutations" that reduce CD8(+) T cell recognition and viral control. The timing of when immune escape occurs at a given epitope varies widely among patients and also among different epitopes within a patient. The strength of the CD8(+) T cell response, as well as mutation rates, patterns of particular amino acids undergoing escape, and growth rates of escape mutants, may affect when escape occurs. In this study, we analyze the epitope-specific CD8(+) T cells in 25 SIV-infected pigtail macaques responding to three SIV epitopes. Two epitopes showed a variable escape pattern and one had a highly monomorphic escape pattern. Despite very different patterns, immune escape occurs with a similar delay of on average 18 d after the epitope-specific CD8(+) T cells reach 0.5% of total CD8(+) T cells. We find that the most delayed escape occurs in one of the highly variable epitopes, and that this is associated with a delay in the epitope-specific CD8(+) T cells responding to this epitope. When we analyzed the kinetics of immune escape, we found that multiple escape mutants emerge simultaneously during the escape, implying that a diverse population of potential escape mutants is present during immune selection. Our results suggest that the conservation or variability of an epitope does not appear to affect the timing of immune escape in SIV. Instead, timing of escape is largely determined by the kinetics of epitope-specific CD8(+) T cells.
Collapse
Affiliation(s)
- Alexey P Martyushev
- Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia; and
| | - Janka Petravic
- Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia; and
| | - Andrew J Grimm
- Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia; and
| | - Hamid Alinejad-Rokny
- Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia; and
| | - Shayarana L Gooneratne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jeanette C Reece
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Deborah Cromer
- Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia; and
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Miles P Davenport
- Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia; and
| |
Collapse
|
16
|
Libbey JE, Fujinami RS. Adaptive immune response to viral infections in the central nervous system. HANDBOOK OF CLINICAL NEUROLOGY 2014. [PMID: 25015488 DOI: 10.1016/b978-0-444-0.00010-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Subscribe] [Academic Contribution Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jane E Libbey
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Robert S Fujinami
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
17
|
Libbey JE, Fujinami RS. Adaptive immune response to viral infections in the central nervous system. HANDBOOK OF CLINICAL NEUROLOGY 2014; 123:225-47. [PMID: 25015488 DOI: 10.1016/b978-0-444-53488-0.00010-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jane E Libbey
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Robert S Fujinami
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
18
|
Abstract
UNLABELLED Although CD8(+) T cells are important for the control of HIV-1 in vivo, the precise correlates of immune efficacy remain unclear. In this study, we conducted a comprehensive analysis of viral sequence variation and T-cell receptor (TCR) repertoire composition across multiple epitope specificities in a group of antiretroviral treatment-naive individuals chronically infected with HIV-1. A negative correlation was detected between changes in antigen-specific TCR repertoire diversity and CD8(+) T-cell response magnitude, reflecting clonotypic expansions and contractions related to alterations in cognate viral epitope sequences. These patterns were independent of the individual, as evidenced by discordant clonotype-specific transitions directed against different epitopes in single subjects. Moreover, long-term asymptomatic HIV-1 infection was characterized by evolution of the TCR repertoire in parallel with viral replication. Collectively, these data suggest a continuous bidirectional process of adaptation between HIV-1 and virus-specific CD8(+) T-cell clonotypes orchestrated at the TCR-antigen interface. IMPORTANCE We describe a relation between viral epitope mutation, antigen-specific T-cell expansion, and the repertoire of responding clonotypes in chronic HIV-1 infection. This work provides insights into the process of coadaptation between the human immune system and a rapidly evolving lentivirus.
Collapse
|
19
|
Abstract
PURPOSE OF REVIEW Renal transplantation in childhood is a well established procedure with excellent short-term outcomes. However, waiting times for transplantation are still relatively long if living donation cannot be performed, and long-term outcomes after transplantation have not significantly improved during the last decade. RECENT FINDINGS This review describes alternative modalities to improve donation rates such as en bloc kidney transplantation from young donors, ABO-incompatible transplantation and kidney paired donation. This review also deals with long-term post-transplant morbidities, such as follows: first, medication side-effects (metabolic syndrome, cardiovascular disease) and with the benefits of steroid and calcineurin inhibitor drug minimization; second, the deleterious impact of viral infections and their management and third, chronic antibody-mediated rejection, its therapeutic and prevention possibilities. SUMMARY Donor shortage and long-term morbidities, after transplantation, are still relevant issues in paediatric renal transplantation medicine. Significant research and efforts have been made to advance the field and create novel approaches for improvement of transplantation rates and post-transplant graft or patient survival. These modalities are to be established in the routine setting.
Collapse
|
20
|
Quantification of HTLV-1 clonality and TCR diversity. PLoS Comput Biol 2014; 10:e1003646. [PMID: 24945836 PMCID: PMC4063693 DOI: 10.1371/journal.pcbi.1003646] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 11/18/2013] [Accepted: 03/14/2014] [Indexed: 01/01/2023] Open
Abstract
Estimation of immunological and microbiological diversity is vital to our understanding of infection and the immune response. For instance, what is the diversity of the T cell repertoire? These questions are partially addressed by high-throughput sequencing techniques that enable identification of immunological and microbiological "species" in a sample. Estimators of the number of unseen species are needed to estimate population diversity from sample diversity. Here we test five widely used non-parametric estimators, and develop and validate a novel method, DivE, to estimate species richness and distribution. We used three independent datasets: (i) viral populations from subjects infected with human T-lymphotropic virus type 1; (ii) T cell antigen receptor clonotype repertoires; and (iii) microbial data from infant faecal samples. When applied to datasets with rarefaction curves that did not plateau, existing estimators systematically increased with sample size. In contrast, DivE consistently and accurately estimated diversity for all datasets. We identify conditions that limit the application of DivE. We also show that DivE can be used to accurately estimate the underlying population frequency distribution. We have developed a novel method that is significantly more accurate than commonly used biodiversity estimators in microbiological and immunological populations.
Collapse
|
21
|
The impact of viral evolution and frequency of variant epitopes on primary and memory human immunodeficiency virus type 1-specific CD8⁺ T cell responses. Virology 2013; 450-451:34-48. [PMID: 24503065 DOI: 10.1016/j.virol.2013.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 07/13/2013] [Revised: 09/11/2013] [Accepted: 10/08/2013] [Indexed: 12/18/2022]
Abstract
It is unclear if HIV-1 variants lose the ability to prime naïve CD8(+) cytotoxic T lymphocytes (CTL) during progressive, untreated infection. We conducted a comprehensive longitudinal analysis of viral evolution and its impact on primary and memory CD8(+) T cell responses pre-seroconversion (SC), post-SC, and during combination antiretroviral therapy (cART). Memory T cell responses targeting autologous virus variants reached a nadir by 8 years post-SC with development of AIDS, followed by a transient enhancement of anti-HIV-1 CTL responses upon initiation of cART. We show broad and high magnitude primary T cell responses to late variants in pre-SC T cells, comparable to primary anti-HIV-1 responses induced in T cells from uninfected persons. Despite evolutionary changes, CD8(+) T cells could still be primed to HIV-1 variants. Hence, vaccination against late, mutated epitopes could be successful in enhancing primary reactivity of T cells for control of the residual reservoir of HIV-1 during cART.
Collapse
|
22
|
Zehn D, Roepke S, Weakly K, Bevan MJ, Prlic M. Inflammation and TCR signal strength determine the breadth of the T cell response in a bim-dependent manner. THE JOURNAL OF IMMUNOLOGY 2013; 192:200-5. [PMID: 24273000 DOI: 10.4049/jimmunol.1302289] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 11/19/2022]
Abstract
Generating a diverse T cell memory population through vaccination is a promising strategy to overcome pathogen epitope variability and tolerance to tumor Ags. The effector and memory pool becomes broad in TCR diversity by recruiting high- and low-affinity T cells. We wanted to determine which factors dictate whether a memory T cell pool has a broad versus focused repertoire. We find that inflammation increases the magnitude of low- and high-affinity T cell responses equally well, arguing against a synergistic effect of TCR and inflammatory signals on T cell expansion. We dissect the differential effects of TCR signal strength and inflammation and demonstrate that they control effector T cell survival in a bim-dependent manner. Importantly, bim-dependent cell death is overcome with a high Ag dose in the context of an inflammatory environment. Our data define the framework for the generation of a broad T cell memory pool to inform future vaccine design.
Collapse
Affiliation(s)
- Dietmar Zehn
- Swiss Vaccine Research Institute, 1066 Epalinges, Switzerland
| | | | | | | | | |
Collapse
|
23
|
Iglesias MC, Briceno O, Gostick E, Moris A, Meaudre C, Price DA, Ungeheuer MN, Saez-Cirion A, Mallone R, Appay V. Immunodominance of HLA-B27-restricted HIV KK10-specific CD8+ T-cells is not related to naïve precursor frequency. Immunol Lett 2013; 149:119-22. [DOI: 10.1016/j.imlet.2012.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 06/28/2012] [Revised: 09/26/2012] [Accepted: 10/01/2012] [Indexed: 02/05/2023]
|
24
|
Viral antigen density and confinement time regulate the reactivity pattern of CD4 T-cell responses to vaccinia virus infection. Proc Natl Acad Sci U S A 2012; 110:288-93. [PMID: 23248307 DOI: 10.1073/pnas.1208328110] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/26/2023] Open
Abstract
T-cell recognition of ligands is polyspecific. This translates into antiviral T-cell responses having a range of potency and specificity for viral ligands. How these ligand recognition patterns are established is not fully understood. Here, we show that an activation threshold regulates whether robust CD4 T-cell activation occurs following viral infection. The activation threshold was variable because of its dependence on the density of the viral peptide (p)MHC displayed on infected cells. Furthermore, the activation threshold was not observed to be a specific equilibrium affinity (K(D)) or half-life (t(1/2)) of the TCR-viral pMHC interaction, rather it correlated with the confinement time of TCR-pMHC interactions, i.e., the half-life (t(1/2)) of the interaction accounting for the effects of TCR-pMHC rebinding. One effect of a variable activation threshold is to allow high-density viral pMHC ligands to expand CD4 T cells with a variety of potency and peptide cross-reactivity patterns for the viral pMHC ligand, some of which are only poorly activated by infections that produce a lower density of the viral pMHC ligand. These results argue that antigen concentration is a key component in determining the pattern of K(D), t(1/2) and peptide cross-reactivity of the TCRs expressed on CD4 T cells responding to infection.
Collapse
|
25
|
Costa C, Saldan A, Cavallo R. Evaluation of virus-specific cellular immune response in transplant patients. World J Virol 2012; 1:150-3. [PMID: 24175220 PMCID: PMC3782278 DOI: 10.5501/wjv.v1.i6.150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Academic Contribution Register] [Received: 08/08/2011] [Revised: 08/23/2012] [Accepted: 11/07/2012] [Indexed: 02/05/2023] Open
Abstract
Virus-specific immune responses have a major impact on the outcome of the infection. Viral agents that are characterized by latency, such as herpesviruses and polyomaviruses, require a continuous immune control to reduce the extent of viral reactivation, as viral clearance cannot be accomplished, independently from the anti-viral treatment. In transplant patients, morbidity and mortality related to viral infections are significantly increased. In fact, the key steps of activation of T-cells are major target for anti-rejection immunosuppressive therapy and anti-viral immune response may be altered when infected cells and cellular effectors of immune response coexist in a transplanted organ. The role of cellular immune response in controlling viral replication and the main methods employed for its evaluation will be discussed. In particular, the main features, including both advantages and limitations, of available assays, including intracellular cytokine staining, major histocompatibility complex - multimer-based assays, Elispot assay, and QuantiFERON test, will be described. The potential applications of these assays in the transplant context will be discussed, particularly in relation to cytomegalovirus and polyomavirus BK infection. The relevance of introducing viro-immunological monitoring, beside virological monitoring, in order to identify the risk profile for viral infections in the transplant patients will allows for define a patient-tailored clinical management, particular in terms of modulation of immunosuppressive therapy and anti-viral administration.
Collapse
Affiliation(s)
- Cristina Costa
- Cristina Costa, Alda Saldan, Rossana Cavallo, Virology Unit, University Hospital San Giovanni Battista di Torino, 10126 Turin, Italy
| | | | | |
Collapse
|
26
|
Baumgartner CK, Yagita H, Malherbe LP. A TCR affinity threshold regulates memory CD4 T cell differentiation following vaccination. THE JOURNAL OF IMMUNOLOGY 2012; 189:2309-17. [PMID: 22844120 DOI: 10.4049/jimmunol.1200453] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 12/16/2022]
Abstract
Diverse Ag-specific memory TCR repertoires are essential for protection against pathogens. Subunit vaccines that combine peptide or protein Ags with TLR agonists are very potent at inducing T cell immune responses, but their capacity to elicit stable and diverse memory CD4 T cell repertoires has not been evaluated. In this study, we examined the evolution of a complex Ag-specific population during the transition from primary effectors to memory T cells after peptide or protein vaccination. Both vaccination regimens induced equally diverse effector CD4 TCR repertoires, but peptide vaccines skewed the memory CD4 TCR repertoire toward high-affinity clonotypes whereas protein vaccines maintained low-affinity clonotypes in the memory compartment. CD27-mediated signaling was essential for the maintenance of low-affinity clonotypes after protein vaccination but was not sufficient to promote their survival following peptide vaccination. The rapid culling of the TCR repertoire in peptide-immunized mice coincided with a prolonged proliferation phase during which low-affinity clonotypes disappeared despite exhibiting no sign of enhanced apoptosis. Our study reveals a novel affinity threshold for memory CD4 T cell differentiation following vaccination and suggests a role for nonapoptotic cell death in the regulation of CD4 T cell clonal selection.
Collapse
|
27
|
Sainz-Perez A, Lim A, Lemercier B, Leclerc C. The T-cell receptor repertoire of tumor-infiltrating regulatory T lymphocytes is skewed toward public sequences. Cancer Res 2012; 72:3557-69. [PMID: 22573714 DOI: 10.1158/0008-5472.can-12-0277] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/08/2023]
Abstract
The accumulation of CD4(+) T regulatory cells (Treg) in tumor tissue is a widely described phenomenon in mouse models and in human cancer patients. Understanding the mechanisms by which Treg migrate and accumulate in tumors is important because they strongly influence the potential efficacy of many immunotherapies. In this study, we used immunoscope technology to analyze the T-cell receptor (TCR) repertoire of tumor-infiltrating T cells in non-TCR transgenic mice. Both tumor-infiltrating Tregs and T effector cells (Teff) displayed sequence profiles in the CDR3 region that were characteristic of biased repertoires seen during clonal cell expansions, implying that strong T-cell responses have occurred within the tumor tissue. By comparing the TCR sequences of tumor-infiltrating Tregs, we obtained evidence of the presence of so-called public TCR sequences that are common to many individuals yet were tumor-specific in nature. Such comparisons also suggested that the Treg-Teff conversion process is not an active process at the tumor site or tumor-draining lymph nodes. Our findings strongly suggest that Treg infiltration of tumor tissue is followed by marked proliferation of a few dominant T-cell clones in the tumor.
Collapse
Affiliation(s)
- Alexander Sainz-Perez
- Institut Pasteur, Immune Regulation and Vaccinology Unit, Department of Immunology, Paris, France
| | | | | | | |
Collapse
|
28
|
Young GR, Ploquin MJY, Eksmond U, Wadwa M, Stoye JP, Kassiotis G. Negative selection by an endogenous retrovirus promotes a higher-avidity CD4+ T cell response to retroviral infection. PLoS Pathog 2012; 8:e1002709. [PMID: 22589728 PMCID: PMC3349761 DOI: 10.1371/journal.ppat.1002709] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 01/03/2012] [Accepted: 04/04/2012] [Indexed: 11/18/2022] Open
Abstract
Effective T cell responses can decisively influence the outcome of retroviral infection. However, what constitutes protective T cell responses or determines the ability of the host to mount such responses is incompletely understood. Here we studied the requirements for development and induction of CD4+ T cells that were essential for immunity to Friend virus (FV) infection of mice, according to their TCR avidity for an FV-derived epitope. We showed that a self peptide, encoded by an endogenous retrovirus, negatively selected a significant fraction of polyclonal FV-specific CD4+ T cells and diminished the response to FV infection. Surprisingly, however, CD4+ T cell-mediated antiviral activity was fully preserved. Detailed repertoire analysis revealed that clones with low avidity for FV-derived peptides were more cross-reactive with self peptides and were consequently preferentially deleted. Negative selection of low-avidity FV-reactive CD4+ T cells was responsible for the dominance of high-avidity clones in the response to FV infection, suggesting that protection against the primary infecting virus was mediated exclusively by high-avidity CD4+ T cells. Thus, although negative selection reduced the size and cross-reactivity of the available FV-reactive naïve CD4+ T cell repertoire, it increased the overall avidity of the repertoire that responded to infection. These findings demonstrate that self proteins expressed by replication-defective endogenous retroviruses can heavily influence the formation of the TCR repertoire reactive with exogenous retroviruses and determine the avidity of the response to retroviral infection. Given the overabundance of endogenous retroviruses in the human genome, these findings also suggest that endogenous retroviral proteins, presented by products of highly polymorphic HLA alleles, may shape the human TCR repertoire that reacts with exogenous retroviruses or other infecting pathogens, leading to interindividual heterogeneity.
Collapse
Affiliation(s)
- George R. Young
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
| | - Mickaël J.-Y. Ploquin
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
| | - Urszula Eksmond
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
| | - Munisch Wadwa
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
| | - Jonathan P. Stoye
- Division of Virology, MRC National Institute for Medical Research, London, United Kingdom
| | - George Kassiotis
- Division of Immunoregulation, MRC National Institute for Medical Research, London, United Kingdom
| |
Collapse
|
29
|
Moon HJ, Lee JS, Choi YK, Park JY, Talactac MR, Chowdhury MY, Poo H, Sung MH, Lee JH, Jung JU, Kim CJ. Induction of type I interferon by high-molecular poly-γ-glutamate protects B6.A2G-Mx1 mice against influenza A virus. Antiviral Res 2012; 94:98-102. [DOI: 10.1016/j.antiviral.2012.02.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 10/29/2011] [Revised: 02/17/2012] [Accepted: 02/21/2012] [Indexed: 11/27/2022]
|
30
|
Cole DK, Gallagher K, Lemercier B, Holland CJ, Junaid S, Hindley JP, Wynn KK, Gostick E, Sewell AK, Gallimore AM, Ladell K, Price DA, Gougeon ML, Godkin A. Modification of the carboxy-terminal flanking region of a universal influenza epitope alters CD4⁺ T-cell repertoire selection. Nat Commun 2012; 3:665. [PMID: 22314361 PMCID: PMC3293629 DOI: 10.1038/ncomms1665] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 10/19/2011] [Accepted: 01/05/2012] [Indexed: 02/01/2023] Open
Abstract
Human CD4(+) αβ T cells are activated via T-cell receptor recognition of peptide epitopes presented by major histocompatibility complex (MHC) class II (MHC-II). The open ends of the MHC-II binding groove allow peptide epitopes to extend beyond a central nonamer core region at both the amino- and carboxy-terminus. We have previously found that these non-bound C-terminal residues can alter T cell activation in an MHC allele-transcending fashion, although the mechanism for this effect remained unclear. Here we show that modification of the C-terminal peptide-flanking region of an influenza hemagglutinin (HA(305-320)) epitope can alter T-cell receptor binding affinity, T-cell activation and repertoire selection of influenza-specific CD4(+) T cells expanded from peripheral blood. These data provide the first demonstration that changes in the C-terminus of the peptide-flanking region can substantially alter T-cell receptor binding affinity, and indicate a mechanism through which peptide flanking residues could influence repertoire selection.
Collapse
Affiliation(s)
- David K. Cole
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
- These authors contributed equally to this work
| | - Kathleen Gallagher
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
- These authors contributed equally to this work
| | - Brigitte Lemercier
- Institut Pasteur, Antiviral Immunity, Biotherapy and Vaccine Unit, Department of Infection and Epidemiology, rue du Dr. Roux, 75015 Paris, France
- These authors contributed equally to this work
| | - Christopher J. Holland
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Sayed Junaid
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - James P. Hindley
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Katherine K. Wynn
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Emma Gostick
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Andrew K. Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Awen M. Gallimore
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Kristin Ladell
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - David A. Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
| | - Marie-Lise Gougeon
- Institut Pasteur, Antiviral Immunity, Biotherapy and Vaccine Unit, Department of Infection and Epidemiology, rue du Dr. Roux, 75015 Paris, France
| | - Andrew Godkin
- Institute of Infection and Immunity, Cardiff University School of Medicine, The Henry Wellcome Building, Cardiff CF14 4XN, Wales, UK
- Department of Medicine, University Hospital of Wales, Cardiff CF14 4XW, Wales, UK
| |
Collapse
|
31
|
Janbazian L, Price DA, Canderan G, Filali-Mouhim A, Asher TE, Ambrozak DR, Scheinberg P, Boulassel MR, Routy JP, Koup RA, Douek DC, Sekaly RP, Trautmann L. Clonotype and repertoire changes drive the functional improvement of HIV-specific CD8 T cell populations under conditions of limited antigenic stimulation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2012; 188:1156-67. [PMID: 22210916 PMCID: PMC3262882 DOI: 10.4049/jimmunol.1102610] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 12/23/2022]
Abstract
Persistent exposure to cognate Ag leads to the functional impairment and exhaustion of HIV-specific CD8 T cells. Ag withdrawal, attributable either to antiretroviral treatment or the emergence of epitope escape mutations, causes HIV-specific CD8 T cell responses to wane over time. However, this process does not continue to extinction, and residual CD8 T cells likely play an important role in the control of HIV replication. In this study, we conducted a longitudinal analysis of clonality, phenotype, and function to define the characteristics of HIV-specific CD8 T cell populations that persist under conditions of limited antigenic stimulation. Ag decay was associated with dynamic changes in the TCR repertoire, increased expression of CD45RA and CD127, decreased expression of programmed death-1, and the emergence of polyfunctional HIV-specific CD8 T cells. High-definition analysis of individual clonotypes revealed that the Ag loss-induced gain of function within HIV-specific CD8 T cell populations could be attributed to two nonexclusive mechanisms: 1) functional improvement of persisting clonotypes; and 2) recruitment of particular clonotypes endowed with superior functional capabilities.
Collapse
Affiliation(s)
- Loury Janbazian
- Laboratory of Immunology, Department of Microbiology and Immunology, Université de Montréal, Montreal, H2X 1P1, Canada
| | - David A. Price
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Institute of InfectionandImmunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, Wales, UK
| | - Glenda Canderan
- Vaccine and Gene Therapy Institute - Florida (VGTI-FL), Port Saint Lucie, FL 34987, USA
| | - Abdelali Filali-Mouhim
- Laboratory of Immunology, Department of Microbiology and Immunology, Université de Montréal, Montreal, H2X 1P1, Canada
| | - Tedi E. Asher
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David R. Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phillip Scheinberg
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mohamad Rachid Boulassel
- Division of Hematology, Royal Victoria Hospital, McGill University Health Centre, Montreal, H3A 1A1, Canada
| | - Jean-Pierre Routy
- Division of Hematology, Royal Victoria Hospital, McGill University Health Centre, Montreal, H3A 1A1, Canada
| | - Richard A. Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rafick-Pierre Sekaly
- Laboratory of Immunology, Department of Microbiology and Immunology, Université de Montréal, Montreal, H2X 1P1, Canada
- Vaccine and Gene Therapy Institute - Florida (VGTI-FL), Port Saint Lucie, FL 34987, USA
- Faculty of Medicine, Department of Microbiology and Immunology, McGill University, Montreal, H3A 2B4, Canada
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Lydie Trautmann
- Vaccine and Gene Therapy Institute - Florida (VGTI-FL), Port Saint Lucie, FL 34987, USA
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| |
Collapse
|
32
|
HLA B*5701-positive long-term nonprogressors/elite controllers are not distinguished from progressors by the clonal composition of HIV-specific CD8+ T cells. J Virol 2012; 86:4014-8. [PMID: 22278241 DOI: 10.1128/jvi.06982-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/17/2022] Open
Abstract
To better understand the qualitative features of effective human immunodeficiency virus (HIV)-specific immunity, we examined the TCR clonal composition of CD8(+) T cells recognizing conserved HIV p24-derived epitopes in HLA-B*5701-positive long-term nonprogressors/elite controllers (LTNP/EC) and HLA-matched progressors. Both groups displayed oligoclonal HLA-B5701-restricted p24-specific CD8(+) T-cell responses with similar levels of diversity and few public clonotypes. Thus, HIV-specific CD8(+) T-cell responses in LTNP/EC are not differentiated from those of progressors on the basis of clonal diversity or TCR sharing.
Collapse
|
33
|
Quigley MF, Almeida JR, Price DA, Douek DC. Unbiased molecular analysis of T cell receptor expression using template-switch anchored RT-PCR. ACTA ACUST UNITED AC 2011; Chapter 10:Unit10.33. [PMID: 21809317 DOI: 10.1002/0471142735.im1033s94] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 02/05/2023]
Abstract
A detailed knowledge of the principles that guide clonal selection within the memory and effector T cell pools is essential to further our understanding of the factors that influence effective T cell-mediated immunity and has direct implications for the rational design of vaccines and immunotherapies. This unit provides methods for the unbiased quantification and characterization of all expressed T cell receptor (TCR) gene products within any defined T cell population. The approach is based on a template-switch anchored reverse transcription-polymerase chain reaction (RT-PCR) and is optimized for the analysis of antigen-specific T cells isolated directly ex vivo.
Collapse
Affiliation(s)
- Máire F Quigley
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | | |
Collapse
|
34
|
Wu Y, Gao F, Liu J, Qi J, Gostick E, Price DA, Gao GF. Structural Basis of Diverse Peptide Accommodation by the Rhesus Macaque MHC Class I Molecule Mamu-B*17: Insights into Immune Protection from Simian Immunodeficiency Virus. THE JOURNAL OF IMMUNOLOGY 2011; 187:6382-92. [DOI: 10.4049/jimmunol.1101726] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 01/12/2023]
|
35
|
Berger CT, Frahm N, Price DA, Mothe B, Ghebremichael M, Hartman KL, Henry LM, Brenchley JM, Ruff LE, Venturi V, Pereyra F, Sidney J, Sette A, Douek DC, Walker BD, Kaufmann DE, Brander C. High-functional-avidity cytotoxic T lymphocyte responses to HLA-B-restricted Gag-derived epitopes associated with relative HIV control. J Virol 2011; 85:9334-45. [PMID: 21752903 PMCID: PMC3165743 DOI: 10.1128/jvi.00460-11] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 03/07/2011] [Accepted: 06/30/2011] [Indexed: 12/20/2022] Open
Abstract
Virus-specific cytotoxic T lymphocytes (CTL) with high levels of functional avidity have been associated with viral clearance in hepatitis C virus infection and with enhanced antiviral protective immunity in animal models. However, the role of functional avidity as a determinant of HIV-specific CTL efficacy remains to be assessed. Here we measured the functional avidities of HIV-specific CTL responses targeting 20 different, optimally defined CTL epitopes restricted by 13 different HLA class I alleles in a cohort comprising 44 HIV controllers and 68 HIV noncontrollers. Responses restricted by HLA-B alleles and responses targeting epitopes located in HIV Gag exhibited significantly higher functional avidities than responses restricted by HLA-A or HLA-C molecules (P = 0.0003) or responses targeting epitopes outside Gag (P < 0.0001). The functional avidities of Gag-specific and HLA-B-restricted responses were higher in HIV controllers than in noncontrollers (P = 0.014 and P = 0.018) and were not restored in HIV noncontrollers initiating antiretroviral therapy. T-cell receptor (TCR) analyses revealed narrower TCR repertoires in higher-avidity CTL populations, which were dominated by public TCR sequences in HIV controllers. Together, these data link the presence of high-avidity Gag-specific and HLA-B-restricted CTL responses with viral suppression in vivo and provide new insights into the immune parameters that mediate spontaneous control of HIV infection.
Collapse
Affiliation(s)
- Christoph T. Berger
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Nicole Frahm
- Fred Hutchinson Cancer Research Center/NIAID HIV Vaccine Trials Network (HVTN), Seattle, Washington
| | - David A. Price
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
- Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff, Wales, United Kingdom
| | - Beatriz Mothe
- Lluita contra la Sida Foundation, Hospital Germans Trias i Pujol, Universitat Autònoma de Badalona, Barcelona, Spain
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Musie Ghebremichael
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kari L. Hartman
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Leah M. Henry
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Jason M. Brenchley
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
| | - Laura E. Ruff
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
| | - Vanessa Venturi
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Kensington, New South Wales, Australia
| | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Daniel E. Kaufmann
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
| | - Christian Brander
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard, Boston, Massachusetts
- IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
| |
Collapse
|
36
|
Iglesias MC, Almeida JR, Fastenackels S, van Bockel DJ, Hashimoto M, Venturi V, Gostick E, Urrutia A, Wooldridge L, Clement M, Gras S, Wilmann PG, Autran B, Moris A, Rossjohn J, Davenport MP, Takiguchi M, Brander C, Douek DC, Kelleher AD, Price DA, Appay V. Escape from highly effective public CD8+ T-cell clonotypes by HIV. Blood 2011; 118:2138-49. [PMID: 21734237 PMCID: PMC3162351 DOI: 10.1182/blood-2011-01-328781] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 01/04/2011] [Accepted: 06/20/2011] [Indexed: 11/20/2022] Open
Abstract
Mapping the precise determinants of T-cell efficacy against viruses in humans is a public health priority with crucial implications for vaccine design. To inform this effort, we performed a comprehensive analysis of the effective CD8(+) T-cell clonotypes that constitute responses specific for the HIV p24 Gag-derived KK10 epitope (KRWIILGLNK; residues 263-272) restricted by HLA-B*2705, which are known to confer superior control of viral replication in HIV-infected individuals. Particular KK10-specific CD8(+) T-cell clonotypes, characterized by TRBV4-3/TRBJ1-3 gene rearrangements, were found to be preferentially selected in vivo and shared between individuals. These "public" clonotypes exhibit high levels of TCR avidity and Ag sensitivity, which impart functional advantages and enable effective suppression of HIV replication. The early L(268)M mutation at position 6 of the KK10 epitope enables the virus to avoid recognition by these highly effective CD8(+) T-cell clonotypes. However, alternative clonotypes with variant reactivity provide flexibility within the overall KK10-specific response. These findings provide refined mechanistic insights into the workings of an effective CD8(+) T-cell response against HIV.
Collapse
Affiliation(s)
- Maria Candela Iglesias
- Inserm UMR S 945, Infections and Immunity, Université Pierre et Marie Curie-Paris 6, Hôpital Pitié-Salpêtrière, Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Abstract
Abstract The immune system of an organism is an essential component of the defense mechanism aimed at combating pathogenic stress. Age-associated immune dysfunction, also dubbed "immune senescence," manifests as increased susceptibility to infections, increased onset and progression of autoimmune diseases, and onset of neoplasia. Over the years, extensive research has generated consensus in terms of the phenotypic and functional defects within the immune system in various organisms, including humans. Indeed, age-associated alterations such as thymic involution, T cell repertoire skewing, decreased ability to activate naïve T cells and to generate robust memory responses, have been shown to have a causative role in immune decline. Further, understanding the molecular mechanisms underlying the generation of proteotoxic stress, DNA damage response, modulation of ubiquitin proteasome pathway, and regulation of transcription factor NFκB activation, in immune decline, have paved the way to delineating signaling pathways that cross-talk and impact immune senescence. Given the role of the immune system in combating infections, its effectiveness with age may well be a marker of health and a predictor of longevity. It is therefore believed that a better understanding of the mechanisms underlying immune senescence will lead to an effective interventional strategy aimed at improving the health span of individuals. Antioxid. Redox Signal. 14, 1551-1585.
Collapse
Affiliation(s)
- Subramaniam Ponnappan
- Department of Geriatrics, University of Arkansas for Medical Sciences, 4301 W. Markham, Little Rock, AR 72205, USA
| | | |
Collapse
|
38
|
Venturi V, Quigley MF, Greenaway HY, Ng PC, Ende ZS, McIntosh T, Asher TE, Almeida JR, Levy S, Price DA, Davenport MP, Douek DC. A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2011; 186:4285-94. [PMID: 21383244 DOI: 10.4049/jimmunol.1003898] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 01/19/2023]
Abstract
The human naive T cell repertoire is the repository of a vast array of TCRs. However, the factors that shape their hierarchical distribution and relationship with the memory repertoire remain poorly understood. In this study, we used polychromatic flow cytometry to isolate highly pure memory and naive CD8(+) T cells, stringently defined with multiple phenotypic markers, and used deep sequencing to characterize corresponding portions of their respective TCR repertoires from four individuals. The extent of interindividual TCR sharing and the overlap between the memory and naive compartments within individuals were determined by TCR clonotype frequencies, such that higher-frequency clonotypes were more commonly shared between compartments and individuals. TCR clonotype frequencies were, in turn, predicted by the efficiency of their production during V(D)J recombination. Thus, convergent recombination shapes the TCR repertoire of the memory and naive T cell pools, as well as their interrelationship within and between individuals.
Collapse
MESH Headings
- Adult
- Clone Cells
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor/immunology
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Immunoglobulin Variable Region/biosynthesis
- Immunoglobulin Variable Region/genetics
- Immunoglobulin Variable Region/isolation & purification
- Immunologic Memory/genetics
- Male
- Middle Aged
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/isolation & purification
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Recombination, Genetic/immunology
- Resting Phase, Cell Cycle/genetics
- Resting Phase, Cell Cycle/immunology
- T-Lymphocyte Subsets/cytology
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- Young Adult
Collapse
Affiliation(s)
- Vanessa Venturi
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Burwitz BJ, Ende Z, Sudolcan B, Reynolds MR, Greene JM, Bimber BN, Almeida JR, Kurniawan M, Venturi V, Gostick E, Wiseman RW, Douek DC, Price DA, O'Connor DH. Simian immunodeficiency virus SIVmac239Deltanef vaccination elicits different Tat28-35SL8-specific CD8+ T-cell clonotypes compared to a DNA prime/adenovirus type 5 boost regimen in rhesus macaques. J Virol 2011; 85:3683-9. [PMID: 21270159 PMCID: PMC3067854 DOI: 10.1128/jvi.02112-10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 10/05/2010] [Accepted: 01/20/2011] [Indexed: 11/20/2022] Open
Abstract
Different human immunodeficiency virus (HIV)/simian immunodeficiency virus (SIV) vaccine vectors expressing the same viral antigens can elicit disparate T-cell responses. Within this spectrum, replicating variable vaccines, like SIVmac239Δnef, appear to generate particularly efficacious CD8(+) T-cell responses. Here, we sequenced T-cell receptor β-chain (TRB) gene rearrangements from immunodominant Mamu-A 01-restricted Tat(28-35)SL8-specific CD8(+) T-cell populations together with the corresponding viral epitope in four rhesus macaques during acute SIVmac239Δnef infection. Ultradeep pyrosequencing showed that viral variants arose with identical kinetics in SIVmac239Δnef and pathogenic SIVmac239 infection. Furthermore, distinct Tat(28-35)SL8-specific T-cell receptor (TCR) repertoires were elicited by SIVmac239Δnef compared to those observed following a DNA/Ad5 prime-boost regimen, likely reflecting differences in antigen sequence stability.
Collapse
MESH Headings
- Adenoviridae/genetics
- Adenoviruses, Human
- Animals
- CD8-Positive T-Lymphocytes/immunology
- Drug Carriers/administration & dosage
- Gene Products, nef/immunology
- Genetic Vectors
- High-Throughput Nucleotide Sequencing
- Immunization, Secondary/methods
- Macaca mulatta
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- SAIDS Vaccines/administration & dosage
- SAIDS Vaccines/immunology
- Simian Immunodeficiency Virus/immunology
- T-Lymphocyte Subsets/immunology
- Vaccination/methods
- Vaccines, DNA/administration & dosage
- Vaccines, DNA/immunology
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/immunology
Collapse
Affiliation(s)
- Benjamin J. Burwitz
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Zachary Ende
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Benjamin Sudolcan
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Matthew R. Reynolds
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Justin M. Greene
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Benjamin N. Bimber
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Jorge R. Almeida
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Monica Kurniawan
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Vanessa Venturi
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Emma Gostick
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Roger W. Wiseman
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Daniel C. Douek
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - David A. Price
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - David H. O'Connor
- Department of Pathology, University of Wisconsin—Madison, Madison, Wisconsin 53706, Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, Wisconsin National Primate Research Center, Madison, Wisconsin 53706, Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW 2052, Australia, Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| |
Collapse
|
40
|
van Bockel DJ, Price DA, Munier ML, Venturi V, Asher TE, Ladell K, Greenaway HY, Zaunders J, Douek DC, Cooper DA, Davenport MP, Kelleher AD. Persistent survival of prevalent clonotypes within an immunodominant HIV gag-specific CD8+ T cell response. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2011; 186:359-71. [PMID: 21135165 DOI: 10.4049/jimmunol.1001807] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 04/26/2024]
Abstract
CD8(+) T cells play a significant role in the control of HIV replication, yet the associated qualitative and quantitative factors that determine the outcome of infection remain obscure. In this study, we examined Ag-specific CD8(+) TCR repertoires longitudinally in a cohort of HLA-B*2705(+) long-term nonprogressors with chronic HIV-1 infection using a combination of molecular clonotype analysis and polychromatic flow cytometry. In each case, CD8(+) T cell populations specific for the immunodominant p24 Gag epitope KRWIILGLNK (KK10; residues 263-272) and naturally occurring variants thereof, restricted by HLA-B*2705, were studied at multiple time points; in addition, comparative data were collected for CD8(+) T cell populations specific for the CMV pp65 epitope NLVPMVATV (NV9; residues 495-503), restricted by HLA-A*0201. Dominant KK10-specific clonotypes persisted for several years and exhibited greater stability than their contemporaneous NV9-specific counterparts. Furthermore, these dominant KK10-specific clonotypes exhibited cross-reactivity with antigenic variants and expressed significantly higher levels of CD127 (IL-7Rα) and Bcl-2. Of note, we also found evidence that promiscuous TCR α-chain pairing associated with alterations in fine specificity for KK10 variants could contribute to TCR β-chain prevalence. Taken together, these data suggest that an antiapoptotic phenotype and the ability to cross-recognize variant epitopes contribute to clonotype longevity and selection within the peripheral memory T cell pool in the presence of persistent infection with a genetically unstable virus.
Collapse
Affiliation(s)
- David J van Bockel
- St. Vincent's Centre for Applied Medical Research, University of New South Wales, Sydney, New South Wales, Australia.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Abstract
Protective immunity against a variety of infections depends on the amplification and differentiation of rare naïve antigen-specific CD4 and CD8 T cells. Recent evidence indicates that the clonotypic composition of the responding T-cell compartment has a critical role in the immune defense against pathogens. The present review compares and contrasts how naive CD4 and CD8 T cells recognize their cognate antigen, and discusses the factors that regulate the genesis and maintenance of the CD4 and CD8 T-cell receptor repertoire diversity.
Collapse
|
42
|
Schaubert KL, Price DA, Salkowitz JR, Sewell AK, Sidney J, Asher TE, Blondelle SE, Adams S, Marincola FM, Joseph A, Sette A, Douek DC, Ayyavoo V, Storkus W, Leung MY, Ng HL, Yang OO, Goldstein H, Wilson DB, Kan-Mitchell J. Generation of robust CD8+ T-cell responses against subdominant epitopes in conserved regions of HIV-1 by repertoire mining with mimotopes. Eur J Immunol 2010; 40:1950-62. [PMID: 20432235 PMCID: PMC3086652 DOI: 10.1002/eji.200940079] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/06/2022]
Abstract
HLA-A 0201-restricted virus-specific CD8(+) CTL do not appear to control HIV effectively in vivo. To enhance the immunogenicity of a highly conserved subdominant epitope, TV9 (TLNAWVKVV, p24 Gag(19-27)), mimotopes were designed by screening a large combinatorial nonapeptide library with TV9-specific CTL primed in vitro from healthy donors. A mimic peptide with a low binding affinity to HLA-A 0201, TV9p6 (KINAWIKVV), was studied further. Parallel cultures of in vitro-primed CTL showed that TV9p6 consistently activated cross-reactive and equally functional CTL as measured by cytotoxicity, cytokine production and suppression of HIV replication in vitro. Comparison of TCRB gene usage between CTL primed from the same donors with TV9 or TV9p6 revealed a degree of clonal overlap in some cases and an example of a conserved TCRB sequence encoded distinctly at the nucleotide level between individuals (a "public" TCR); however, in the main, distinct clonotypes were recruited by each peptide antigen. These findings indicate that mimotopes can mobilize functional cross-reactive clonotypes that are less readily recruited from the naïve T-cell pool by the corresponding WT epitope. Mimotope-induced repertoire diversification could potentially override subdominance under certain circumstances and enhance vaccine-induced responses to conserved but poorly immunogenic determinants within the HIV proteome.
Collapse
Affiliation(s)
- Keri L. Schaubert
- Department of Biological Sciences and Border Biomedical Research Institute, University of Texas at El Paso, El Paso, TX 79968
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201
| | - David A. Price
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
- Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff, CF14 4XN, Wales, UK
| | - Janelle R. Salkowitz
- Department of Biological Sciences and Border Biomedical Research Institute, University of Texas at El Paso, El Paso, TX 79968
| | - Andrew K. Sewell
- Department of Infection, Immunity and Biochemistry, Cardiff University School of Medicine, Cardiff, CF14 4XN, Wales, UK
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Tedi E. Asher
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Sylvie E. Blondelle
- Torrey Pines Institute for Molecular Studies, San Diego, CA 92121
- Mixture Sciences Incorporated, San Diego, CA 92121
| | - Sharon Adams
- Immunogenetics Section, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892
| | - Francesco M. Marincola
- Immunogenetics Section, Department of Transfusion Medicine, National Institutes of Health, Bethesda, MD 20892
| | - Aviva Joseph
- Departments of Microbiology & Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Velpandi Ayyavoo
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261
| | - Walter Storkus
- Departments of Immunology and Dermatology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15261
| | - Ming-Ying Leung
- Department of Mathematical Sciences, University of Texas at El Paso, El Paso, TX 79968
| | - Hwee L. Ng
- Department of Medicine and AIDS Institute, Center for Health Sciences, University of California Los Angeles, CA 90095
| | - Otto O. Yang
- Department of Medicine and AIDS Institute, Center for Health Sciences, University of California Los Angeles, CA 90095
| | - Harris Goldstein
- Departments of Microbiology & Immunology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Darcy B. Wilson
- Torrey Pines Institute for Molecular Studies, San Diego, CA 92121
- Mixture Sciences Incorporated, San Diego, CA 92121
| | - June Kan-Mitchell
- Department of Biological Sciences and Border Biomedical Research Institute, University of Texas at El Paso, El Paso, TX 79968
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201
| |
Collapse
|
43
|
Rudd BD, Venturi V, Smithey MJ, Way SS, Davenport MP, Nikolich-Zugich J. Diversity of the CD8+ T cell repertoire elicited against an immunodominant epitope does not depend on the context of infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2010; 184:2958-2965. [PMID: 20164421 PMCID: PMC4161216 DOI: 10.4049/jimmunol.0903493] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 11/19/2022]
Abstract
The diversity of the pathogen-specific T cell repertoire is believed to be important in allowing recognition of different pathogen epitopes and their variants and thereby reducing the opportunities for mutation-driven pathogen escape. However, the extent to which the TCR repertoire can be manipulated by different vaccine strategies so as to obtain broad diversity and optimal protection is incompletely understood. We have investigated the influence of the infectious/inflammatory context on the TCR diversity of the CD8(+) T cell response specific for the immunodominant epitope in C57BL/6 mice, derived from glycoprotein B of HSV-1. To that effect, we compared TCR V segment utilization, CDR3 length, and sequence diversity of the response to natural HSV-1 infection with those elicited by either Listeria monocytogenes or vaccinia virus expressing the immunodominant epitope in C57BL/6 mice. We demonstrate that although the type of infection in which the epitope was encountered can influence the magnitude of the CD8(+) T cell responses, TCR beta-chain repertoires did not significantly differ among the three infections. These results suggest that widely different live vaccine vectors may have little impact upon the diversity of the induced CTL response, which has important implications for the design of live CTL vaccine strategies against acute and chronic infections.
Collapse
Affiliation(s)
- Brian D. Rudd
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ 85724 and the BIO-5 Institute, University of Arizona, Tucson,AZ 85719
| | - Vanessa Venturi
- Centre for Vascular Research, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Megan J. Smithey
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ 85724 and the BIO-5 Institute, University of Arizona, Tucson,AZ 85719
| | - Sing Sing Way
- Department of Pediatrics, Center for Infectious Disease and Microbiology Translational Research, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
| | - Miles P. Davenport
- Centre for Vascular Research, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Janko Nikolich-Zugich
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ 85724 and the BIO-5 Institute, University of Arizona, Tucson,AZ 85719
| |
Collapse
|
44
|
Stirk ER, Lythe G, van den Berg HA, Hurst GAD, Molina-París C. The limiting conditional probability distribution in a stochastic model of T cell repertoire maintenance. Math Biosci 2010; 224:74-86. [PMID: 20060005 DOI: 10.1016/j.mbs.2009.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 07/03/2009] [Revised: 12/11/2009] [Accepted: 12/16/2009] [Indexed: 10/20/2022]
Abstract
The limiting conditional probability distribution (LCD) has been much studied in the field of mathematical biology, particularly in the context of epidemiology and the persistence of epidemics. However, it has not yet been applied to the immune system. One of the characteristic features of the T cell repertoire is its diversity. This diversity declines in old age, whence the concepts of extinction and persistence are also relevant to the immune system. In this paper we model T cell repertoire maintenance by means of a continuous-time birth and death process on the positive integers, where the origin is an absorbing state. We show that eventual extinction is guaranteed. The late-time behaviour of the process before extinction takes place is modelled by the LCD, which we prove always exists for the process studied here. In most cases, analytic expressions for the LCD cannot be computed but the probability distribution may be approximated by means of the stationary probability distributions of two related processes. We show how these approximations are related to the LCD of the original process and use them to study the LCD in two special cases. We also make use of the large N expansion to derive a further approximation to the LCD. The accuracy of the various approximations is then analysed.
Collapse
Affiliation(s)
- Emily R Stirk
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK.
| | | | | | | | | |
Collapse
|
45
|
Greenaway HY, Kurniawan M, Price DA, Douek DC, Davenport MP, Venturi V. Extraction and characterization of the rhesus macaque T-cell receptor beta-chain genes. Immunol Cell Biol 2009; 87:546-53. [PMID: 19506572 PMCID: PMC2756323 DOI: 10.1038/icb.2009.38] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/26/2022]
Abstract
Rhesus macaque models have been instrumental in the development and testing of vaccines before human studies and have provided fundamental insights into the determinants of immune efficacy in a variety of infectious diseases. However, the characterization of antigen-specific T-cell receptor (TCR) repertoires during adaptive immune responses in these models has earlier relied on human TCR gene assignments. Here, we extracted and characterized TCR beta-chain (TRB) genes from the recently sequenced rhesus macaque genome that are homologous to the human TRB genes. Comparison of the rhesus macaque TRB genes with the human TRB genes showed an average best match similarity of 92.9%. Furthermore, we confirmed the usage of most rhesus macaque TRB genes by expressed TCRbeta sequences within epitope-specific TCR repertoires. This primary description of the rhesus macaque TRB genes will provide a standardized nomenclature and enable better characterization of TCR usage in studies that use this species.
Collapse
Affiliation(s)
- Hui Yee Greenaway
- Complex Systems in Biology Group, Centre for Vascular Research, University of New South Wales, Kensington NSW 2052, Australia
| | - Monica Kurniawan
- Complex Systems in Biology Group, Centre for Vascular Research, University of New South Wales, Kensington NSW 2052, Australia
| | - David A Price
- Department of Medical Biochemistry and Immunology, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
- Human Immunology Section, Vaccine Research Center, NIAID/NIH, Bethesda MD 20892, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, NIAID/NIH, Bethesda MD 20892, USA
| | - Miles P Davenport
- Complex Systems in Biology Group, Centre for Vascular Research, University of New South Wales, Kensington NSW 2052, Australia
| | - Vanessa Venturi
- Complex Systems in Biology Group, Centre for Vascular Research, University of New South Wales, Kensington NSW 2052, Australia
| |
Collapse
|
46
|
Geldmacher C, Metzler IS, Tovanabutra S, Asher TE, Gostick E, Ambrozak DR, Petrovas C, Schuetz A, Ngwenyama N, Kijak G, Maboko L, Hoelscher M, McCutchan F, Price DA, Douek DC, Koup RA. Minor viral and host genetic polymorphisms can dramatically impact the biologic outcome of an epitope-specific CD8 T-cell response. Blood 2009; 114:1553-62. [PMID: 19542300 PMCID: PMC2731637 DOI: 10.1182/blood-2009-02-206193] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 02/19/2009] [Accepted: 03/31/2009] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus-1 subtypes A and C differ in the highly conserved Gag-TL9 epitope at a single amino acid position. Similarly, the TL9 presenting human leukocyte antigen (HLA) class I molecules B42 and B81 differ only at 6 amino acid positions. Here, we addressed the influence of such minor viral and host genetic variation on the TL9-specific CD8 T-cell response. The clonotypic characteristics of CD8 T-cell populations elicited by subtype A or subtype C were distinct, and these responses differed substantially with respect to the recognition and selection of TL9 variants. Irrespective of the presenting HLA class I molecule, CD8 T-cell responses elicited by subtype C exhibited largely comparable TL9 variant cross-recognition properties, expressed T-cell receptors that used almost exclusively the TRBV 12-3 gene, and selected for predictable patterns of viral variation within TL9. In contrast, subtype A elicited TL9-specific CD8 T-cell populations with completely different, more diverse TCRBV genes and did not select for viral variants. Moreover, TL9 variant cross-recognition properties were extensive in B81(+) subjects but limited in B42(+) subjects. Thus, minor viral and host genetic polymorphisms can dramatically alter the immunologic and virologic outcome of an epitope-specific CD8 T-cell response.
Collapse
Affiliation(s)
- Christof Geldmacher
- Immunology Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Almeida JR, Sauce D, Price DA, Papagno L, Shin SY, Moris A, Larsen M, Pancino G, Douek DC, Autran B, Sáez-Cirión A, Appay V. Antigen sensitivity is a major determinant of CD8+ T-cell polyfunctionality and HIV-suppressive activity. Blood 2009; 113:6351-60. [PMID: 19389882 PMCID: PMC2710928 DOI: 10.1182/blood-2009-02-206557] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 02/19/2009] [Accepted: 04/15/2009] [Indexed: 12/23/2022] Open
Abstract
CD8(+) T cells are major players in the immune response against HIV. However, recent failures in the development of T cell-based vaccines against HIV-1 have emphasized the need to reassess our basic knowledge of T cell-mediated efficacy. CD8(+) T cells from HIV-1-infected patients with slow disease progression exhibit potent polyfunctionality and HIV-suppressive activity, yet the factors that unify these properties are incompletely understood. We performed a detailed study of the interplay between T-cell functional attributes using a bank of HIV-specific CD8(+) T-cell clones isolated in vitro; this approach enabled us to overcome inherent difficulties related to the in vivo heterogeneity of T-cell populations and address the underlying determinants that synthesize the qualities required for antiviral efficacy. Conclusions were supported by ex vivo analysis of HIV-specific CD8(+) T cells from infected donors. We report that attributes of CD8(+) T-cell efficacy against HIV are linked at the level of antigen sensitivity. Highly sensitive CD8(+) T cells display polyfunctional profiles and potent HIV-suppressive activity. These data provide new insights into the mechanisms underlying CD8(+) T-cell efficacy against HIV, and indicate that vaccine strategies should focus on the induction of HIV-specific T cells with high levels of antigen sensitivity to elicit potent antiviral efficacy.
Collapse
Affiliation(s)
- Jorge R Almeida
- Institut National de la Santé et de la Recherche Médicale Unité, Hôpital Pitié-Salpêtrière, Université Pierre et Marie Curie, Paris, France
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
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: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution 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.
Collapse
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
| |
Collapse
|
49
|
Wooldridge L, Lissina A, Cole DK, van den Berg HA, Price DA, Sewell AK. Tricks with tetramers: how to get the most from multimeric peptide-MHC. Immunology 2009; 126:147-64. [PMID: 19125886 PMCID: PMC2632693 DOI: 10.1111/j.1365-2567.2008.02848.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 02/11/2008] [Revised: 03/18/2008] [Accepted: 03/18/2008] [Indexed: 01/16/2023] Open
Abstract
The development of fluorochrome-conjugated peptide-major histocompatibility complex (pMHC) multimers in conjunction with continuing advances in flow cytometry has transformed the study of antigen-specific T cells by enabling their visualization, enumeration, phenotypic characterization and isolation from ex vivo samples. Here, we bring together and discuss some of the 'tricks' that can be used to get the most out of pMHC multimers. These include: (1) simple procedures that can substantially enhance the staining intensity of cognate T cells with pMHC multimers; (2) the use of pMHC multimers to stain T cells with very-low-affinity T-cell receptor (TCR)/pMHC interactions, such as those that typically predominate in tumour-specific responses; and (3) the physical grading and clonotypic dissection of antigen-specific T cells based on the affinity of their cognate TCR using mutant pMHC multimers in conjunction with new approaches to the molecular analysis of TCR gene expression. We also examine how soluble pMHC can be used to examine T-cell activation, manipulate T-cell responses and study allogeneic and superantigen interactions with TCRs. Finally, we discuss the problems that arise with pMHC class II (pMHCII) multimers because of the low affinity of TCR/pMHCII interactions and lack of 'coreceptor help'.
Collapse
Affiliation(s)
- Linda Wooldridge
- Department of Medical Biochemistry and Immunology, Cardiff University School of Medicine, Henry Wellcome Building, Heath Park, Cardiff, UK
| | | | | | | | | | | |
Collapse
|
50
|
Venturi V, Chin HY, Asher TE, Ladell K, Scheinberg P, Bornstein E, van Bockel D, Kelleher AD, Douek DC, Price DA, Davenport MP. TCR beta-chain sharing in human CD8+ T cell responses to cytomegalovirus and EBV. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2008; 181:7853-62. [PMID: 19017975 DOI: 10.4049/jimmunol.181.11.7853] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Academic Contribution Register] [Indexed: 11/19/2022]
Abstract
The CD8(+) TCR repertoires specific for many immunogenic epitopes of CMV and EBV are dominated by a few TCR clonotypes and involve public TCRs that are shared between many MHC-matched individuals. In previous studies, we demonstrated that the observed sharing of epitope-specific TCRbeta chains between individuals is strongly associated with TCRbeta production frequency, and that a process of convergent recombination facilitates the more efficient production of some TCRbeta sequences. In this study, we analyzed a total of 2836 TCRbeta sequences from 23 CMV-infected and 10 EBV-infected individuals to investigate the factors that influence the sharing of TCRbeta sequences in the CD8(+) T cell responses to two immunodominant HLA-A*0201-restricted epitopes from these viruses. The most shared TCRbeta amino acid sequences were found to have two features that indicate efficient TCRbeta production, as follows: 1) they required fewer nucleotide additions, and 2) they were encoded by a greater variety of nucleotide sequences. We used simulations of random V(D)J recombination to demonstrate that the in silico TCRbeta production frequency was predictive of the extent to which both TCRbeta nucleotide and amino acid sequences were shared in vivo. These results suggest that TCRbeta production frequency plays an important role in the interindividual sharing of TCRbeta sequences within CD8(+) T cell responses specific for CMV and EBV.
Collapse
Affiliation(s)
- Vanessa Venturi
- Complex Systems in Biology Group, Centre for Vascular Research, University of New South Wales, Kensington, Australia
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|