1
|
Kusnadi A, Ramírez-Suástegui C, Fajardo V, Chee SJ, Meckiff BJ, Simon H, Pelosi E, Seumois G, Ay F, Vijayanand P, Ottensmeier CH. Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8 + T cells. Sci Immunol 2021; 6:eabe4782. [PMID: 33478949 PMCID: PMC8101257 DOI: 10.1126/sciimmunol.abe4782] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/15/2021] [Indexed: 12/11/2022]
Abstract
The molecular properties of CD8+ T cells that respond to SARS-CoV-2 infection are not fully known. Here, we report on the single-cell transcriptomes of >80,000 virus-reactive CD8+ T cells, obtained using a modified Antigen-Reactive T cell Enrichment (ARTE) assay, from 39 COVID-19 patients and 10 healthy subjects. COVID-19 patients segregated into two groups based on whether the dominant CD8+ T cell response to SARS-CoV-2 was 'exhausted' or not. SARS-CoV-2-reactive cells in the exhausted subset were increased in frequency and displayed lesser cytotoxicity and inflammatory features in COVID-19 patients with mild compared to severe illness. In contrast, SARS-CoV-2-reactive cells in the dominant non-exhausted subset from patients with severe disease showed enrichment of transcripts linked to co-stimulation, pro-survival NF-κB signaling, and anti-apoptotic pathways, suggesting the generation of robust CD8+ T cell memory responses in patients with severe COVID-19 illness. CD8+ T cells reactive to influenza and respiratory syncytial virus from healthy subjects displayed polyfunctional features and enhanced glycolysis. Cells with such features were largely absent in SARS-CoV-2-reactive cells from both COVID-19 patients and healthy controls non-exposed to SARS-CoV-2. Overall, our single-cell analysis revealed substantial diversity in the nature of CD8+ T cells responding to SARS-CoV-2.
Collapse
Affiliation(s)
| | | | | | - Serena J Chee
- NIHR and CRUK Southampton Experimental Cancer Medicine Center, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Hayley Simon
- La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Emanuela Pelosi
- Southampton Specialist Virology Centre, Department of Infection, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | - Ferhat Ay
- La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Pandurangan Vijayanand
- La Jolla Institute for Immunology, La Jolla, CA 92037.
- Liverpool Head and Neck Center, Institute of Translational Medicine, University of Liverpool & Clatterbridge Cancer Center NHS Foundation Trust, Liverpool, UK
- Department of Medicine, University of California San Diego, La Jolla, CA 92037
| | - Christian H Ottensmeier
- La Jolla Institute for Immunology, La Jolla, CA 92037.
- Liverpool Head and Neck Center, Institute of Translational Medicine, University of Liverpool & Clatterbridge Cancer Center NHS Foundation Trust, Liverpool, UK
| |
Collapse
|
2
|
van den Berg SPH, Pardieck IN, Lanfermeijer J, Sauce D, Klenerman P, van Baarle D, Arens R. The hallmarks of CMV-specific CD8 T-cell differentiation. Med Microbiol Immunol 2019; 208:365-373. [PMID: 30989333 PMCID: PMC6647465 DOI: 10.1007/s00430-019-00608-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/02/2019] [Indexed: 12/13/2022]
Abstract
Upon cytomegalovirus (CMV) infection, large T-cell responses are elicited that remain high or even increase over time, a phenomenon named memory T-cell inflation. Besides, the maintained robust T-cell response, CMV-specific T cells seem to have a distinctive phenotype, characterized by an advanced differentiation state. Here, we will review this "special" differentiation status by discussing the cellular phenotype based on the expression of CD45 isoforms, costimulatory, inhibitory and natural killer receptors, adhesion and lymphocyte homing molecules, transcription factors, cytokines and cytotoxic molecules. In addition, we focus on whether the differentiation state of CMV-specific CD8 T cells is unique in comparison with other chronic viruses and we will discuss the possible impact of factors such as antigen exposure and aging on the advanced differentiation status of CMV-specific CD8 T cells.
Collapse
Affiliation(s)
- Sara P H van den Berg
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Iris N Pardieck
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Josien Lanfermeijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Delphine Sauce
- Sorbonne Université, INSERM, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Paul Klenerman
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Debbie van Baarle
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
| |
Collapse
|
3
|
Enhanced PD-1 expression by T cells in cerebrospinal fluid does not reflect functional exhaustion during chronic human immunodeficiency virus type 1 infection. J Virol 2010; 84:131-40. [PMID: 19828602 DOI: 10.1128/jvi.01181-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
During chronic viral infections, T cells are exhausted due to constant antigen exposure and are associated with enhanced programmed death 1 (PD-1) expression. Deficiencies in the PD-1/programmed death-ligand 1 (PD-L1) pathway are associated with autoimmune diseases, including those of the central nervous system (CNS). To understand the role of PD-1 expression in regulating T-cell immunity in the CNS during chronic infection, we characterized PD-1 expression in cerebrospinal fluid (CSF) and blood of individuals with chronic human immunodeficiency virus type 1 (HIV-1) infection. PD-1 expression was higher on HIV-specific CD8(+) T cells than on total CD8(+) T cells in both CSF and blood. PD-1 expression on CSF T cells correlated positively with CSF HIV-1 RNA and inversely with blood CD4(+) T-cell counts, suggesting that HIV-1 infection drives higher PD-1 expression on CSF T cells. However, in every HIV-positive individual, PD-1 expression was higher on T cells in CSF than on those in blood, despite HIV-1 RNA levels being lower. Among healthy HIV-negative controls, PD-1 expression was higher in CSF than in blood. Furthermore, frequencies of the senescence marker CD57 were lower on CSF T cells than on blood T cells, consistent with our prior observation of enhanced ex vivo functional capacity of CSF T cells. The higher PD-1 expression level on CSF T cells therefore does not reflect cellular exhaustion but may be a mechanism to downregulate immune-mediated tissue damage in the CNS. As inhibition of the PD-1/PD-L1 pathway is pursued as a therapeutic option for viral infections, potential effects of such a blockade on development of autoimmune responses in the CNS should be considered.
Collapse
|
4
|
Burgers WA, Riou C, Mlotshwa M, Maenetje P, de Assis Rosa D, Brenchley J, Mlisana K, Douek DC, Koup R, Roederer M, de Bruyn G, Karim SA, Williamson C, Gray CM. Association of HIV-specific and total CD8+ T memory phenotypes in subtype C HIV-1 infection with viral set point. THE JOURNAL OF IMMUNOLOGY 2009; 182:4751-61. [PMID: 19342652 DOI: 10.4049/jimmunol.0803801] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Understanding early immunological events during HIV-1 infection that may set the course of disease progression is important for identifying correlates of viral control. This study explores the association of differentiation profiles of HIV-specific and total memory CD8(+) T cells with viral set point. A cohort of 47 HIV-1-infected individuals, with differing viral set points at 12 mo, were recruited during acute infection. We identified that the magnitude of IFN-gamma(+) T cell responses at 6 mo postinfection did not associate with viral set point at 12 mo. A subset of 16 individuals was further studied to characterize CD8(+) T cells for expression patterns of markers for memory differentiation, survival (CD127), senescence (CD57), and negative regulation (programmed death-1). We show that viral control and the predicted tempo of HIV disease progression in the first year of infection was associated with a synchronous differentiation of HIV-specific and total CD8(+) memory subpopulations. At 6-9 mo postinfection, those with low viral set points had a significantly higher proportion of early differentiated HIV-specific and total memory CD8(+) cells of a central memory (CD45RO(+)CD27(+)CCR7(+)) and intermediate memory (CD45RO(-)CD27(+)CCR7(-)) phenotype. Those with high viral set points possessed significantly larger frequencies of effector memory (CD45RO(+)CD27(-)CCR7(-)) cells. The proportions of memory subsets significantly correlated with CD38(+)CD8(+) T cells. Thus, it is likely that a high Ag burden resulting in generalized immune activation may drive differentiation of HIV-specific and total memory CD8(+) T cells.
Collapse
Affiliation(s)
- Wendy A Burgers
- Division of Medical Virology, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Palmer BE, Mack DG, Martin AK, Gillespie M, Mroz MM, Maier LA, Fontenot AP. Up-regulation of programmed death-1 expression on beryllium-specific CD4+ T cells in chronic beryllium disease. THE JOURNAL OF IMMUNOLOGY 2008; 180:2704-12. [PMID: 18250483 DOI: 10.4049/jimmunol.180.4.2704] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chronic beryllium disease (CBD) is caused by workplace exposure to beryllium and is characterized by the accumulation of memory CD4+ T cells in the lung. These cells respond vigorously to beryllium salts in culture by producing proinflammatory Th1-type cytokines. The presence of these inflammatory cytokines leads to the recruitment of alveolar macrophages, alveolitis, and subsequent granuloma development. It has been shown that chronic exposure to conventional Ags leads to up-regulation in the expression of negative regulators of T cells such as programmed death-1 (PD-1). Due to the persistence of beryllium in the lung after the cessation of exposure, aberrant regulation of the PD-1 pathway may play an important role in CBD development. In the present study, PD-1 expression was measured on blood and bronchoalveolar lavage (BAL) CD4+ T cells from beryllium-sensitized and CBD subjects. PD-1 expression was significantly higher on BAL CD4+ T cells compared with those cells in blood, with the highest expression on the beryllium-specific T cell subset. In addition, the expression of PD-1 on BAL CD4+ T cells directly correlated with the severity of the T cell alveolitis. Increased expression of the PD-1 ligands, PD-L1 and PD-L2, on BAL CD14+ cells compared with blood was also seen. The addition of anti-PD-1 ligand mAbs augmented beryllium-induced CD4+ T cell proliferation, and an inverse correlation was seen between PD-1 expression on beryllium-specific CD4+ T cells and beryllium-induced proliferation. Thus, the PD-1 pathway is active in beryllium-induced disease and plays a key role in controlling beryllium-induced T cell proliferation.
Collapse
Affiliation(s)
- Brent E Palmer
- Department of Medicine, University of Colorado at Denver and Health Sciences Center, 4200 East Ninth Avenue, Denver, CO 80202, USA
| | | | | | | | | | | | | |
Collapse
|