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Altfeld M, Müller-Trutwin M. Allogeneic Natural Killer Cells: An Additional Player in Human Immunodeficiency Virus Cure Approaches? J Infect Dis 2024; 229:1249-1251. [PMID: 38206191 DOI: 10.1093/infdis/jiae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/07/2024] [Indexed: 01/12/2024] Open
Affiliation(s)
- Marcus Altfeld
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Leibniz Institute of Virology, Virus Immunology Department, Hamburg, Germany
- German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Michaela Müller-Trutwin
- Institut Pasteur, Université Paris Cité, HIV Inflammation and Persistence Unit, Paris, France
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2
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Peng Y, Yang H, Chen Q, Jin H, Xue YH, Du MQ, Liu S, Yao SY. An angel or a devil? Current view on the role of CD8 + T cells in the pathogenesis of myasthenia gravis. J Transl Med 2024; 22:183. [PMID: 38378668 PMCID: PMC10877804 DOI: 10.1186/s12967-024-04965-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/07/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Myasthenia gravis (MG) and the experimental autoimmune MG (EAMG) animal model are characterized by T-cell-induced and B-cell-dominated autoimmune diseases that affect the neuromuscular junction. Several subtypes of CD4+ T cells, including T helper (Th) 17 cells, follicular Th cells, and regulatory T cells (Tregs), contribute to the pathogenesis of MG. However, increasing evidence suggests that CD8+ T cells also play a critical role in the pathogenesis and treatment of MG. MAIN BODY Herein, we review the literature on CD8+ T cells in MG, focusing on their potential effector and regulatory roles, as well as on relevant evidence (peripheral, in situ, cerebrospinal fluid, and under different treatments), T-cell receptor usage, cytokine and chemokine expression, cell marker expression, and Treg, Tc17, CD3+CD8+CD20+ T, and CXCR5+ CD8+ T cells. CONCLUSIONS Further studies on CD8+ T cells in MG are necessary to determine, among others, the real pattern of the Vβ gene usage of autoantigen-specific CD8+ cells in patients with MG, real images of the physiology and function of autoantigen-specific CD8+ cells from MG/EAMG, and the subset of autoantigen-specific CD8+ cells (Tc1, Tc17, and IL-17+IFN-γ+CD8+ T cells). There are many reports of CD20-expressing T (or CD20 + T) and CXCR5+ CD8 T cells on autoimmune diseases, especially on multiple sclerosis and rheumatoid arthritis. Unfortunately, up to now, there has been no report on these T cells on MG, which might be a good direction for future studies.
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Affiliation(s)
- Yong Peng
- Department of Neurology, Affiliated First Hospital of Hunan Traditional Chinese Medical College, Zhuzhou, 412000, Hunan, China.
- Department of Neurology, The Third Affiliated Hospital of Hunan University of Chinese Medicine, Zhuzhou, 412000, Hunan, China.
| | - Huan Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Quan Chen
- Department of Neurology, Affiliated First Hospital of Hunan Traditional Chinese Medical College, Zhuzhou, 412000, Hunan, China
- Department of Neurology, The Third Affiliated Hospital of Hunan University of Chinese Medicine, Zhuzhou, 412000, Hunan, China
| | - Hong Jin
- Department of Neurology, Affiliated First Hospital of Hunan Traditional Chinese Medical College, Zhuzhou, 412000, Hunan, China
- Department of Neurology, The Third Affiliated Hospital of Hunan University of Chinese Medicine, Zhuzhou, 412000, Hunan, China
| | - Ya-Hui Xue
- Department of Neurology, Affiliated First Hospital of Hunan Traditional Chinese Medical College, Zhuzhou, 412000, Hunan, China
- Department of Neurology, The Third Affiliated Hospital of Hunan University of Chinese Medicine, Zhuzhou, 412000, Hunan, China
| | - Miao-Qiao Du
- Department of Neurology, Affiliated First Hospital of Hunan Traditional Chinese Medical College, Zhuzhou, 412000, Hunan, China
- Department of Neurology, The Third Affiliated Hospital of Hunan University of Chinese Medicine, Zhuzhou, 412000, Hunan, China
| | - Shu Liu
- Department of Neurology, Affiliated First Hospital of Hunan Traditional Chinese Medical College, Zhuzhou, 412000, Hunan, China
- Department of Neurology, The Third Affiliated Hospital of Hunan University of Chinese Medicine, Zhuzhou, 412000, Hunan, China
| | - Shun-Yu Yao
- Department of Neurology, Affiliated First Hospital of Hunan Traditional Chinese Medical College, Zhuzhou, 412000, Hunan, China
- Department of Neurology, The Third Affiliated Hospital of Hunan University of Chinese Medicine, Zhuzhou, 412000, Hunan, China
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3
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Yin K, Peluso MJ, Luo X, Thomas R, Shin MG, Neidleman J, Andrew A, Young KC, Ma T, Hoh R, Anglin K, Huang B, Argueta U, Lopez M, Valdivieso D, Asare K, Deveau TM, Munter SE, Ibrahim R, Ständker L, Lu S, Goldberg SA, Lee SA, Lynch KL, Kelly JD, Martin JN, Münch J, Deeks SG, Henrich TJ, Roan NR. Long COVID manifests with T cell dysregulation, inflammation and an uncoordinated adaptive immune response to SARS-CoV-2. Nat Immunol 2024; 25:218-225. [PMID: 38212464 PMCID: PMC10834368 DOI: 10.1038/s41590-023-01724-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024]
Abstract
Long COVID (LC) occurs after at least 10% of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, yet its etiology remains poorly understood. We used 'omic" assays and serology to deeply characterize the global and SARS-CoV-2-specific immunity in the blood of individuals with clear LC and non-LC clinical trajectories, 8 months postinfection. We found that LC individuals exhibited systemic inflammation and immune dysregulation. This was evidenced by global differences in T cell subset distribution implying ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. LC individuals displayed increased frequencies of CD4+ T cells poised to migrate to inflamed tissues and exhausted SARS-CoV-2-specific CD8+ T cells, higher levels of SARS-CoV-2 antibodies and a mis-coordination between their SARS-CoV-2-specific T and B cell responses. Our analysis suggested an improper crosstalk between the cellular and humoral adaptive immunity in LC, which can lead to immune dysregulation, inflammation and clinical symptoms associated with this debilitating condition.
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Affiliation(s)
- Kailin Yin
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Xiaoyu Luo
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Reuben Thomas
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
| | - Min-Gyoung Shin
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
| | - Jason Neidleman
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Alicer Andrew
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Kyrlia C Young
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Tongcui Ma
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Khamal Anglin
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Beatrice Huang
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Urania Argueta
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Monica Lopez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Daisy Valdivieso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kofi Asare
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Tyler-Marie Deveau
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sadie E Munter
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rania Ibrahim
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Sulggi A Lee
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco, San Francisco, CA, USA
| | - Kara L Lynch
- Division of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Jan Münch
- Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm, Germany
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, CA, USA.
| | - Nadia R Roan
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
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4
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Guo XY, Qu MM, Wang X, Wang ZR, Song JW, Yang BP, Guo YT, Zhang Y, Zhang C, Fan X, Xu W, Xu R, Zhang JY, Chen SY, Jiao YM, Sun LJ, Wang FS. Characteristics of blood immune cell profile and their correlation with disease progression in patients infected with HIV-1. BMC Infect Dis 2023; 23:893. [PMID: 38124099 PMCID: PMC10731693 DOI: 10.1186/s12879-023-08847-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Antiretroviral therapy (ART) can reduce viral load in individuals infected with human immunodeficiency virus (HIV); however, some HIV-infected individuals still cannot achieve optimal immune recovery even after ART. Hence, we described the profile of peripheral immune cells and explored the association with disease progression in patients infected with HIV-1. METHODS Mass cytometry analysis was used to characterize the circulating immune cells of 20 treatment-naïve (TNs), 20 immunological non-responders (INRs), 20 immunological responders (IRs), and 10 healthy controls (HCs). Correlation analysis was conducted between cell subpopulation percentages and indicators including HIV-1 cell-associated (CA)-RNA, DNA, CD4+ T cell count, and CD4/CD8 ratio. RESULTS Global activation, immunosenescence, and exhaustion phenotypes were observed in myeloid cells and T cells from individuals with HIV-1 infection. We also found that specific subsets or clusters of myeloid, CD4+ T, and CD8+ T cells were significantly lost or increased in TN individuals, which could be partially restored after receiving ART. The percentages of several subpopulations correlated with HIV-1 CA-RNA, DNA, CD4+ T cell count, and CD4/CD8 ratio, suggesting that changes in immune cell composition were associated with therapeutic efficacy. CONCLUSION These data provide a complete profile of immune cell subpopulations or clusters that are associated with disease progression during chronic HIV-1 infection, which will improve understanding regarding the mechanism of incomplete immune recovery in INRs.
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Affiliation(s)
- Xiao-Yan Guo
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China
| | - Meng-Meng Qu
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China
| | - Xi Wang
- Clinic of Center for Infection, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Ze-Rui Wang
- Department of Gastroenterology, First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Jin-Wen Song
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China
| | - Bao-Peng Yang
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China
| | - Yun-Tian Guo
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China
| | - Yang Zhang
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China
| | - Chao Zhang
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China
| | - Xing Fan
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China
| | - Wen Xu
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China
| | - Ruonan Xu
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China
| | - Ji-Yuan Zhang
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China
| | - Si-Yuan Chen
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China
| | - Yan-Mei Jiao
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China.
| | - Li-Jun Sun
- Clinic of Center for Infection, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
| | - Fu-Sheng Wang
- Senior Department of Infectious Diseases, The Fifth Medical Centre of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, 100039, China.
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5
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Bjorgen JC, Dick JK, Cromarty R, Hart GT, Rhein J. NK cell subsets and dysfunction during viral infection: a new avenue for therapeutics? Front Immunol 2023; 14:1267774. [PMID: 37928543 PMCID: PMC10620977 DOI: 10.3389/fimmu.2023.1267774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023] Open
Abstract
In the setting of viral challenge, natural killer (NK) cells play an important role as an early immune responder against infection. During this response, significant changes in the NK cell population occur, particularly in terms of their frequency, location, and subtype prevalence. In this review, changes in the NK cell repertoire associated with several pathogenic viral infections are summarized, with a particular focus placed on changes that contribute to NK cell dysregulation in these settings. This dysregulation, in turn, can contribute to host pathology either by causing NK cells to be hyperresponsive or hyporesponsive. Hyperresponsive NK cells mediate significant host cell death and contribute to generating a hyperinflammatory environment. Hyporesponsive NK cell populations shift toward exhaustion and often fail to limit viral pathogenesis, possibly enabling viral persistence. Several emerging therapeutic approaches aimed at addressing NK cell dysregulation have arisen in the last three decades in the setting of cancer and may prove to hold promise in treating viral diseases. However, the application of such therapeutics to treat viral infections remains critically underexplored. This review briefly explores several therapeutic approaches, including the administration of TGF-β inhibitors, immune checkpoint inhibitors, adoptive NK cell therapies, CAR NK cells, and NK cell engagers among other therapeutics.
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Affiliation(s)
- Jacob C. Bjorgen
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Jenna K. Dick
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
- Center for Immunology, University of Minnesota, Minneapolis, MN, United States
| | - Ross Cromarty
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - Geoffrey T. Hart
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
- Center for Immunology, University of Minnesota, Minneapolis, MN, United States
| | - Joshua Rhein
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
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6
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Ma T, Suryawanshi RK, Miller SR, Ly KK, Thomas R, Elphick N, Yin K, Luo X, Kaliss N, Chen IP, Montano M, Sreekumar B, Standker L, Münch J, Heath Damron F, Palop JJ, Ott M, Roan NR. Post-acute immunological and behavioral sequelae in mice after Omicron infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543758. [PMID: 37333294 PMCID: PMC10274741 DOI: 10.1101/2023.06.05.543758] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Progress in understanding long COVID and developing effective therapeutics is hampered in part by the lack of suitable animal models. Here we used ACE2-transgenic mice recovered from Omicron (BA.1) infection to test for pulmonary and behavioral post-acute sequelae. Through in-depth phenotyping by CyTOF, we demonstrate that naïve mice experiencing a first Omicron infection exhibit profound immune perturbations in the lung after resolving acute infection. This is not observed if mice were first vaccinated with spike-encoding mRNA. The protective effects of vaccination against post-acute sequelae were associated with a highly polyfunctional SARS-CoV-2-specific T cell response that was recalled upon BA.1 breakthrough infection but not seen with BA.1 infection alone. Without vaccination, the chemokine receptor CXCR4 was uniquely upregulated on multiple pulmonary immune subsets in the BA.1 convalescent mice, a process previously connected to severe COVID-19. Taking advantage of recent developments in machine learning and computer vision, we demonstrate that BA.1 convalescent mice exhibited spontaneous behavioral changes, emotional alterations, and cognitive-related deficits in context habituation. Collectively, our data identify immunological and behavioral post-acute sequelae after Omicron infection and uncover a protective effect of vaccination against post-acute pulmonary immune perturbations.
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Affiliation(s)
- Tongcui Ma
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | | | - Stephanie R. Miller
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Katie K. Ly
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Reuben Thomas
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Natalie Elphick
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
| | - Kailin Yin
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Xiaoyu Luo
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, United States
| | - Nick Kaliss
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Irene P Chen
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California San Francisco; San Francisco, CA, USA
- Department of Medicine, University of California San Francisco; San Francisco, CA, USA
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | | | | | - Ludger Standker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - Jan Münch
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - F. Heath Damron
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown WV, USA
| | - Jorge J. Palop
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Melanie Ott
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco; San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Nadia R. Roan
- Gladstone Institutes of Virology, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, United States
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7
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Yin K, Peluso MJ, Luo X, Thomas R, Shin MG, Neidleman J, Andrew A, Young K, Ma T, Hoh R, Anglin K, Huang B, Argueta U, Lopez M, Valdivieso D, Asare K, Deveau TM, Munter SE, Ibrahim R, Ständker L, Lu S, Goldberg SA, Lee SA, Lynch KL, Kelly JD, Martin JN, Münch J, Deeks SG, Henrich TJ, Roan NR. Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527892. [PMID: 36798286 PMCID: PMC9934605 DOI: 10.1101/2023.02.09.527892] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Long COVID (LC), a type of post-acute sequelae of SARS-CoV-2 infection (PASC), occurs after at least 10% of SARS-CoV-2 infections, yet its etiology remains poorly understood. Here, we used multiple "omics" assays (CyTOF, RNAseq/scRNAseq, Olink) and serology to deeply characterize both global and SARS-CoV-2-specific immunity from blood of individuals with clear LC and non-LC clinical trajectories, 8 months following infection and prior to receipt of any SARS-CoV-2 vaccine. Our analysis focused on deep phenotyping of T cells, which play important roles in immunity against SARS-CoV-2 yet may also contribute to COVID-19 pathogenesis. Our findings demonstrate that individuals with LC exhibit systemic inflammation and immune dysregulation. This is evidenced by global differences in T cell subset distribution in ways that imply ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. Individuals with LC harbored increased frequencies of CD4+ T cells poised to migrate to inflamed tissues, and exhausted SARS-CoV-2-specific CD8+ T cells. They also harbored significantly higher levels of SARS-CoV-2 antibodies, and in contrast to non-LC individuals, exhibited a mis-coordination between their SARS-CoV-2-specific T and B cell responses. RNAseq/scRNAseq and Olink analyses similarly revealed immune dysregulatory mechanisms, along with non-immune associated perturbations, in individuals with LC. Collectively, our data suggest that proper crosstalk between the humoral and cellular arms of adaptive immunity has broken down in LC, and that this, perhaps in the context of persistent virus, leads to the immune dysregulation, inflammation, and clinical symptoms associated with this debilitating condition.
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Affiliation(s)
- Kailin Yin
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Xiaoyu Luo
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Reuben Thomas
- Gladstone Institutes, University of California, San Francisco, USA
| | - Min-Gyoung Shin
- Gladstone Institutes, University of California, San Francisco, USA
| | - Jason Neidleman
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Alicer Andrew
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Kyrlia Young
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Tongcui Ma
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Khamal Anglin
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Beatrice Huang
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Urania Argueta
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Monica Lopez
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Daisy Valdivieso
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Kofi Asare
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Tyler-Marie Deveau
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Sadie E Munter
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Rania Ibrahim
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Sulggi A Lee
- Zuckerberg San Francisco General Hospital and the University of California, San Francisco, USA
| | - Kara L Lynch
- Division of Laboratory Medicine, University of California, San Francisco, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, USA
| | - Jan Münch
- Core Facility Functional Peptidomics, Ulm University Medical Center, Meyerhofstrasse 1, Ulm, Germany
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, University of California, San Francisco, USA
| | - Nadia R Roan
- Gladstone Institutes, University of California, San Francisco, USA
- Department of Urology, University of California, San Francisco, USA
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8
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Inamo J, Keegan J, Griffith A, Ghosh T, Horisberger A, Howard K, Pulford J, Murzin E, Hancock B, Jonsson AH, Seifert J, Feser ML, Norris JM, Cao Y, Apruzzese W, Louis Bridges S, Bykerk V, Goodman S, Donlin L, Firestein GS, Perlman H, Bathon JM, Hughes LB, Tabechian D, Filer A, Pitzalis C, Anolik JH, Moreland L, Guthridge JM, James JA, Brenner MB, Raychaudhuri S, Sparks JA, Michael Holers V, Deane KD, Lederer JA, Rao DA, Zhang F. Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547507. [PMID: 37461737 PMCID: PMC10349983 DOI: 10.1101/2023.07.03.547507] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease with currently no universally highly effective prevention strategies. Identifying pathogenic immune phenotypes in 'At-Risk' populations prior to clinical disease onset is crucial to establishing effective prevention strategies. Here, we applied mass cytometry to deeply characterize the immunophenotypes in blood from At-Risk individuals identified through the presence of serum antibodies to citrullinated protein antigens (ACPA) and/or first-degree relative (FDR) status (n=52), as compared to established RA (n=67), and healthy controls (n=48). We identified significant cell expansions in At-Risk individuals compared with controls, including CCR2+CD4+ T cells, T peripheral helper (Tph) cells, type 1 T helper cells, and CXCR5+CD8+ T cells. We also found that CD15+ classical monocytes were specifically expanded in ACPA-negative FDRs, and an activated PAX5 low naïve B cell population was expanded in ACPA-positive FDRs. Further, we developed an "RA immunophenotype score" classification method based on the degree of enrichment of cell states relevant to established RA patients. This score significantly distinguished At-Risk individuals from controls. In all, we systematically identified activated lymphocyte phenotypes in At-Risk individuals, along with immunophenotypic differences among both ACPA+ and ACPA-FDR At-Risk subpopulations. Our classification model provides a promising approach for understanding RA pathogenesis with the goal to further improve prevention strategies and identify novel therapeutic targets.
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9
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Collins DR, Hitschfel J, Urbach JM, Mylvaganam GH, Ly NL, Arshad U, Racenet ZJ, Yanez AG, Diefenbach TJ, Walker BD. Cytolytic CD8 + T cells infiltrate germinal centers to limit ongoing HIV replication in spontaneous controller lymph nodes. Sci Immunol 2023; 8:eade5872. [PMID: 37205767 DOI: 10.1126/sciimmunol.ade5872] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/26/2023] [Indexed: 05/21/2023]
Abstract
Follicular CD8+ T cells (fCD8) mediate surveillance in lymph node (LN) germinal centers against lymphotropic infections and cancers, but the precise mechanisms by which these cells mediate immune control remain incompletely resolved. To address this, we investigated functionality, clonotypic compartmentalization, spatial localization, phenotypic characteristics, and transcriptional profiles of LN-resident virus-specific CD8+ T cells in persons who control HIV without medications. Antigen-induced proliferative and cytolytic potential consistently distinguished spontaneous controllers from noncontrollers. T cell receptor analysis revealed complete clonotypic overlap between peripheral and LN-resident HIV-specific CD8+ T cells. Transcriptional analysis of LN CD8+ T cells revealed gene signatures of inflammatory chemotaxis and antigen-induced effector function. In HIV controllers, the cytotoxic effectors perforin and granzyme B were elevated among virus-specific CXCR5+ fCD8s proximate to foci of HIV RNA within germinal centers. These results provide evidence consistent with cytolytic control of lymphotropic infection supported by inflammatory recruitment, antigen-specific proliferation, and cytotoxicity of fCD8s.
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Affiliation(s)
- David R Collins
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Julia Hitschfel
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Institute of Clinical and Molecular Virology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Geetha H Mylvaganam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ngoc L Ly
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Umar Arshad
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Adrienne G Yanez
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Medical Engineering and Sciences and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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10
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Cocker ATH, Guethlein LA, Parham P. The CD56-CD16+ NK cell subset in chronic infections. Biochem Soc Trans 2023:233017. [PMID: 37140380 DOI: 10.1042/bst20221374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/05/2023]
Abstract
Long-term human diseases can shape the immune system, and natural killer (NK) cells have been documented to differentiate into distinct subsets specifically associated with chronic virus infections. One of these subsets found in large frequencies in HIV-1 are the CD56-CD16+ NK cells, and this population's association with chronic virus infections is the subject of this review. Human NK cells are classically defined by CD56 expression, yet increasing evidence supports the NK cell status of the CD56-CD16+ subset which we discuss herein. We then discuss the evidence linking CD56-CD16+ NK cells to chronic virus infections, and the potential immunological pathways that are altered by long-term infection that could be inducing the population's differentiation. An important aspect of NK cell regulation is their interaction with human leukocyte antigen (HLA) class-I molecules, and we highlight work that indicates both virus and genetic-mediated variations in HLA expression that have been linked to CD56-CD16+ NK cell frequencies. Finally, we offer a perspective on CD56-CD16+ NK cell function, taking into account recent work that implies the subset is comparable to CD56+CD16+ NK cell functionality in antibody-dependent cell cytotoxicity response, and the definition of CD56-CD16+ NK cell subpopulations with varying degranulation capacity against target cells.
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Affiliation(s)
- Alexander T H Cocker
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, U.S.A
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, U.S.A
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, U.S.A
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, U.S.A
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, U.S.A
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, U.S.A
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11
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George AF, Roan NR. Advances in HIV Research Using Mass Cytometry. Curr HIV/AIDS Rep 2023; 20:76-85. [PMID: 36689119 PMCID: PMC9869313 DOI: 10.1007/s11904-023-00649-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 01/24/2023]
Abstract
PURPOSE OF REVIEW This review describes how advances in CyTOF and high-dimensional analysis methods have furthered our understanding of HIV transmission, pathogenesis, persistence, and immunity. RECENT FINDINGS CyTOF has generated important insight on several aspects of HIV biology: (1) the differences between cells permissive to productive vs. latent HIV infection, and the HIV-induced remodeling of infected cells; (2) factors that contribute to the persistence of the long-term HIV reservoir, in both blood and tissues; and (3) the impact of HIV on the immune system, in the context of both uncontrolled and controlled infection. CyTOF and high-dimensional analysis tools have enabled in-depth assessment of specific host antigens remodeled by HIV, and have revealed insights into the features of HIV-infected cells enabling them to survive and persist, and of the immune cells that can respond to and potentially control HIV replication. CyTOF and other related high-dimensional phenotyping approaches remain powerful tools for translational research, and applied HIV to cohort studies can inform on mechanisms of HIV pathogenesis and persistence, and potentially identify biomarkers for viral eradication or control.
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Affiliation(s)
- Ashley F George
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA, 94143, USA
| | - Nadia R Roan
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, 94158, USA.
- Department of Urology, University of California at San Francisco, San Francisco, CA, 94143, USA.
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12
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Etemad B, Sun X, Li Y, Melberg M, Moisi D, Gottlieb R, Ahmed H, Aga E, Bosch RJ, Acosta EP, Yuki Y, Martin MP, Carrington M, Gandhi RT, Jacobson JM, Volberding P, Connick E, Mitsuyasu R, Frank I, Saag M, Eron JJ, Skiest D, Margolis DM, Havlir D, Schooley RT, Lederman MM, Yu XG, Li JZ. HIV post-treatment controllers have distinct immunological and virological features. Proc Natl Acad Sci U S A 2023; 120:e2218960120. [PMID: 36877848 PMCID: PMC10089217 DOI: 10.1073/pnas.2218960120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/06/2023] [Indexed: 03/08/2023] Open
Abstract
HIV post-treatment controllers (PTCs) are rare individuals who maintain low levels of viremia after stopping antiretroviral therapy (ART). Understanding the mechanisms of HIV post-treatment control will inform development of strategies aiming at achieving HIV functional cure. In this study, we evaluated 22 PTCs from 8 AIDS Clinical Trials Group (ACTG) analytical treatment interruption (ATI) studies who maintained viral loads ≤400 copies/mL for ≥24 wk. There were no significant differences in demographics or frequency of protective and susceptible human leukocyte antigen (HLA) alleles between PTCs and post-treatment noncontrollers (NCs, n = 37). Unlike NCs, PTCs demonstrated a stable HIV reservoir measured by cell-associated RNA (CA-RNA) and intact proviral DNA assay (IPDA) during analytical treatment interruption (ATI). Immunologically, PTCs demonstrated significantly lower CD4+ and CD8+ T cell activation, lower CD4+ T cell exhaustion, and more robust Gag-specific CD4+ T cell responses and natural killer (NK) cell responses. Sparse partial least squares discriminant analysis (sPLS-DA) identified a set of features enriched in PTCs, including a higher CD4+ T cell% and CD4+/CD8+ ratio, more functional NK cells, and a lower CD4+ T cell exhaustion level. These results provide insights into the key viral reservoir features and immunological profiles for HIV PTCs and have implications for future studies evaluating interventions to achieve an HIV functional cure.
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Affiliation(s)
- Behzad Etemad
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02139
| | - Xiaoming Sun
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA02139
| | - Yijia Li
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02139
| | - Meghan Melberg
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02139
| | - Daniela Moisi
- School of Medicine, Case Western Reserve University, Cleveland, OH44106
| | - Rachel Gottlieb
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02139
| | - Hayat Ahmed
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02139
| | - Evgenia Aga
- Harvard T. H. Chan School of Public Health, Boston, MA02115
| | | | - Edward P. Acosta
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL35233
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD21702
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20814
| | - Maureen P. Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD21702
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20814
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA02139
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD21702
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20814
| | - Rajesh T. Gandhi
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA02114
| | | | - Paul Volberding
- School of Medicine, University of California San Francisco, San Francisco, CA94143
| | | | - Ronald Mitsuyasu
- School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Ian Frank
- School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Michael Saag
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL35233
| | - Joseph J. Eron
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Daniel Skiest
- Department of Medicine, University of Massachusetts Chan Medical School - Baystate, Springfield, MA01199
| | - David M. Margolis
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Diane Havlir
- School of Medicine, University of California San Francisco, San Francisco, CA94143
| | - Robert T. Schooley
- Department of Medicine, University of California San Diego, San Diego, CA92103
| | | | - Xu G. Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA02139
| | - Jonathan Z. Li
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02139
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