1
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Zaman F, Smith ML, Balagopal A, Durand CM, Redd AD, Tobian AAR. Spatial technologies to evaluate the HIV-1 reservoir and its microenvironment in the lymph node. mBio 2024; 15:e0190924. [PMID: 39058091 PMCID: PMC11324018 DOI: 10.1128/mbio.01909-24] [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] [Indexed: 07/28/2024] Open
Abstract
The presence of the HIV-1 reservoir, a group of immune cells that contain intact, integrated, and replication-competent proviruses, is a major challenge to cure HIV-1. HIV-1 reservoir cells are largely unaffected by the cytopathic effects of viruses, antiviral immune responses, or antiretroviral therapy (ART). The HIV-1 reservoir is seeded early during HIV-1 infection and augmented during active viral replication. CD4+ T cells are the primary target for HIV-1 infection, and recent studies suggest that memory T follicular helper cells within the lymph node, more precisely in the B cell follicle, harbor integrated provirus, which contribute to viral rebound upon ART discontinuation. The B cell follicle, more specifically the germinal center, possesses a unique environment because of its distinct property of being partly immune privileged, potentially allowing HIV-1-infected cells within the lymph nodes to be protected from CD8+ T cells. This modified immune response in the germinal center of the follicle is potentially explained by the exclusion of CD8+ T cells and the presence of T regulatory cells at the junction of the follicle and extrafollicular region. The proviral makeup of HIV-1-infected cells is similar in lymph nodes and blood, suggesting trafficking between these compartments. Little is known about the cell-to-cell interactions, microenvironment of HIV-1-infected cells in the follicle, and trafficking between the lymph node follicle and other body compartments. Applying a spatiotemporal approach that integrates genomics, transcriptomics, and proteomics to investigate the HIV-1 reservoir and its neighboring cells in the lymph node has promising potential for informing HIV-1 cure efforts.
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Affiliation(s)
- Fatima Zaman
- Department of
Pathology, Johns Hopkins University School of
Medicine, Baltimore,
Maryland, USA
| | - Melissa L. Smith
- Department of
Biochemistry and Molecular Genetics, University of Louisville School of
Medicine, Louisville,
Kentucky, USA
| | - Ashwin Balagopal
- Division of Infectious
Diseases, Department of Medicine, Johns Hopkins
University, Baltimore,
Maryland, USA
| | - Christine M. Durand
- Division of Infectious
Diseases, Department of Medicine, Johns Hopkins
University, Baltimore,
Maryland, USA
| | - Andrew D. Redd
- Division of Infectious
Diseases, Department of Medicine, Johns Hopkins
University, Baltimore,
Maryland, USA
- Laboratory of
Immunoregulation, National Institute of Allergy and Infectious Diseases,
National Institutes of Health,
Bethesda, Maryland, USA
- Institute of
Infectious Disease and Molecular Medicine, University of Cape
Town, Cape Town,
South Africa
| | - Aaron A. R. Tobian
- Department of
Pathology, Johns Hopkins University School of
Medicine, Baltimore,
Maryland, USA
- Division of Infectious
Diseases, Department of Medicine, Johns Hopkins
University, Baltimore,
Maryland, USA
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2
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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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3
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A roadmap for translational cancer glycoimmunology at single cell resolution. J Exp Clin Cancer Res 2022; 41:143. [PMID: 35428302 PMCID: PMC9013178 DOI: 10.1186/s13046-022-02335-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/17/2022] [Indexed: 11/11/2022] Open
Abstract
Cancer cells can evade immune responses by exploiting inhibitory immune checkpoints. Immune checkpoint inhibitor (ICI) therapies based on anti-CTLA-4 and anti-PD-1/PD-L1 antibodies have been extensively explored over the recent years to unleash otherwise compromised anti-cancer immune responses. However, it is also well established that immune suppression is a multifactorial process involving an intricate crosstalk between cancer cells and the immune systems. The cancer glycome is emerging as a relevant source of immune checkpoints governing immunosuppressive behaviour in immune cells, paving an avenue for novel immunotherapeutic options. This review addresses the current state-of-the-art concerning the role played by glycans controlling innate and adaptive immune responses, while shedding light on available experimental models for glycoimmunology. We also emphasize the tremendous progress observed in the development of humanized models for immunology, the paramount contribution of advances in high-throughput single-cell analysis in this context, and the importance of including predictive machine learning algorithms in translational research. This may constitute an important roadmap for glycoimmunology, supporting careful adoption of models foreseeing clinical translation of fundamental glycobiology knowledge towards next generation immunotherapies.
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4
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Noto A, Suffiotti M, Joo V, Mancarella A, Procopio FA, Cavet G, Leung Y, Corpataux JM, Cavassini M, Riva A, Stamatatos L, Gottardo R, McDermott AB, Koup RA, Fenwick C, Perreau M, Pantaleo G. The deficiency in Th2-like Tfh cells affects the maturation and quality of HIV-specific B cell response in viremic infection. Front Immunol 2022; 13:960120. [PMID: 36091040 PMCID: PMC9450063 DOI: 10.3389/fimmu.2022.960120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
Optimal T follicular helper (Tfh) cells function is important to promote the development of germinal centers and maturation of high affinity antigen-specific B cells. We have found that the expression of CXCR3 defines distinct Tfh subsets: CXCR3+ Th1-like Tfh cells mainly producing single IFN-γ and dual IL-21/IFN-γ and CXCR3- Th2-like Tfh cells mainly producing single IL-4 and dual IL-21/IL-4 cytokines. CXCR3- Th2-like Tfhs are significantly reduced during ongoing HIV replication. While the percentage of Th2-like Tfh cells correlates with that of total and cycling HIV-specific B cells, the percentage of CXCR3+ Th1-like Tfhs correlates with HIV-specific B cells expressing T-bet and CXCR3. Of note, only IL-4 and IL-21 cytokines boosted efficient maturation of HIV-specific B cells while IFN-γ induced expression of T-bet and CXCR3 in B cells. Interestingly, total and HIV-specific CXCR3+ B cells showed lower rate of somatic hypermutation, as compared to CXCR3- B cells. Therefore, the imbalance in Th2/Th1-like Tfhs affects B cell responses in viremic HIV infection.
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Affiliation(s)
- Alessandra Noto
- Service Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Madeleine Suffiotti
- Service Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Victor Joo
- Service Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Antonio Mancarella
- Service Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Francesco A. Procopio
- Service Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Guy Cavet
- Atreca, Redwood City, CA, United States
| | | | - Jean-Marc Corpataux
- Service of Vascular Surgery, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Matthias Cavassini
- Service of Infectious Diseases, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Agostino Riva
- Division of Infectious Diseases, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Leonidas Stamatatos
- Department of Global Health, Seattle University of Washington, Seattle, WA, United States
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Richard A. Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Craig Fenwick
- Service Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Matthieu Perreau
- Service Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Giuseppe Pantaleo
- Service Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland,Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland,*Correspondence: Giuseppe Pantaleo,
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5
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Al-kolla R, Grifoni A, Crotty S, Sette A, Gianella S, Dan J. Design and validation of HIV peptide pools for detection of HIV-specific CD4+ and CD8+ T cells. PLoS One 2022; 17:e0268370. [PMID: 35972938 PMCID: PMC9380920 DOI: 10.1371/journal.pone.0268370] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/01/2022] [Indexed: 11/18/2022] Open
Abstract
Reagents to monitor T cell responses to the entire HIV genome, based on well characterized epitopes, are missing. Evaluation of HIV-specific T cell responses is of importance to study natural infection, and therapeutic and vaccine interventions. Experimentally derived CD4+ and CD8+ HIV epitopes from the HIV molecular immunology database were developed into Class I and Class II HIV megapools (MPs). We assessed HIV responses in persons with HIV pre antiretroviral therapy (ART) (n = 17) and post-ART (n = 18) and compared these responses to 15 controls without HIV (matched by sex at birth, age, and ethnicity). Using the Activation Induced Marker (AIM) assay, we quantified HIV-specific total CD4+, memory CD4+, circulating T follicular helper, total CD8+ and memory CD8+ T cells. We also compared the Class I and Class II HIV MPs to commercially available HIV gag peptide pools. Overall, HIV Class II MP detected HIV-specific CD4+ T cells in 21/35 (60%) HIV positive samples and 0/15 HIV negative samples. HIV Class I MP detected an HIV-specific CD8+ T cells in 17/35 (48.6%) HIV positive samples and 0/15 HIV negative samples. Our innovative HIV MPs are reflective of the entire HIV genome, and its performance is comparable to other commercially available peptide pools. Here, we detected HIV-specific CD4+ and CD8+ T cell responses in people on and off ART, but not in people without HIV.
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Affiliation(s)
- Rita Al-kolla
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, United States of America
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, United States of America
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, United States of America
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, United States of America
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, United States of America
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Sara Gianella
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Jennifer Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, United States of America
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
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6
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He C, Malone MJ, Wendel BS, Ma KY, Del Alcazar D, Weiner DB, De Jager PL, Del Río-Estrada PM, Ablanedo-Terrazas Y, Reyes-Terán G, Su LF, Jiang N. Transcriptome and TCR Repertoire Measurements of CXCR3 + T Follicular Helper Cells Within HIV-Infected Human Lymph Nodes. Front Immunol 2022; 13:859070. [PMID: 35619703 PMCID: PMC9128546 DOI: 10.3389/fimmu.2022.859070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/06/2022] [Indexed: 12/15/2022] Open
Abstract
Follicular-helper T cells (TFH) are an essential arm of the adaptive immune system. Although TFH were first discovered through their ability to contribute to antibody affinity maturation through co-stimulatory interactions with B cells, new light has been shed on their ability to remain a complex and functionally plastic cell type. Due to a lack sample availability, however, many studies have been limited to characterizing TFH in mice or non-canonical tissue types, such as peripheral blood. Such constraints have resulted in a limited, and sometimes contradictory, understanding of this fundamental cell type. One subset of TFH receiving attention in chronic infection are CXCR3-expressing TFH cells (CXCR3+TFH) due to their abnormal accumulation in secondary lymphoid tissues. Their function and clonal relationship with other TFH subsets in lymphoid tissues during infection, however, remains largely unclear. We thus systematically investigated this and other subsets of TFH within untreated HIV-infected human lymph nodes using Mass CyTOF and a combination of RNA and TCR repertoire sequencing. We show an inflation of the CXCR3+TFH compartment during HIV infection that correlates with a lower HIV burden. Deeper analysis into this population revealed a functional shift of CXCR3+TFH away from germinal center TFH (GC-TFH), including the altered expression of several important transcription factors and cytokines. CXCR3+TFH also upregulated cell migration transcriptional programs and were clonally related to peripheral TFH populations. In combination, these data suggest that CXCR3+TFH have a greater tendency to enter circulation than their CXCR3- counterparts, potentially functioning through distinct modalities that may lead to enhanced defense.
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Affiliation(s)
- Chenfeng He
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States
| | - Michael J. Malone
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States,Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, United States
| | - Ben S. Wendel
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States,McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Ke-Yue Ma
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, United States
| | - Daniel Del Alcazar
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA, United States,Corporal Michael J Crescenz Veterans Affairs Medical Center, Philadelphia, PA, United States
| | - David B. Weiner
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA, United States
| | - Philip L. De Jager
- Columbia University Medical Center, Center for Translational and Computational Neuroimmunology, New York, NY, United States
| | - Perla M. Del Río-Estrada
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México, Mexico
| | - Yuria Ablanedo-Terrazas
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México, Mexico
| | - Gustavo Reyes-Terán
- Comisión Coordinadora de Institutos Nacional de Salud y Hospitales de Alta Especialidad, Secretaría de Salud, Ciudad de México, Mexico
| | - Laura F. Su
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA, United States,Corporal Michael J Crescenz Veterans Affairs Medical Center, Philadelphia, PA, United States,*Correspondence: Ning Jiang, ; Laura F. Su,
| | - Ning Jiang
- Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States,Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, United States,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States,*Correspondence: Ning Jiang, ; Laura F. Su,
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7
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Li Y, Hu J, Wang Y, Liu D, Shi Y, Zhang J, Liu Y, Lin D, Lin J, Hu W, He H, Wang W, Fan W, Li L, Wang D, Wang K, Xu J. T-Cell Repertoire Characteristics of Asymptomatic and Re-Detectable Positive COVID-19 Patients. Front Immunol 2022; 12:769442. [PMID: 35154070 PMCID: PMC8828559 DOI: 10.3389/fimmu.2021.769442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/24/2021] [Indexed: 01/01/2023] Open
Abstract
The prevention of the COVID-19 pandemic is highly complicated by the prevalence of asymptomatic and recurrent infection. Many previous immunological studies have focused on symptomatic and convalescent patients, while the immune responses in asymptomatic patients and re-detectable positive cases remain unclear. Here we comprehensively analyzed the peripheral T-cell receptor (TCR) repertoire of 54 COVID-19 patients in different courses, including asymptomatic, symptomatic, convalescent, and re-detectable positive cases. We identified a set of V-J gene combinations characterizing the upward immune responses through asymptomatic and symptomatic courses. Furthermore, some of these V-J combinations could be awakened in the re-detectable positive cases, which may help predict the risk of recurrent infection. Therefore, TCR repertoire examination has the potential to strengthen the clinical surveillance and the immunotherapy development for COVID-19.
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Affiliation(s)
- Yizhe Li
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Jian Hu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yongsi Wang
- Department of Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, China
| | - Dongdong Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yaling Shi
- Department of Laboratory Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiaqi Zhang
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuntao Liu
- Emergency Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dongzi Lin
- Department of Laboratory Medicine, The Fourth People’s Hospital of Foshan, Foshan, China
| | - Jing Lin
- Department of Clinical Laboratory, The First People’s Hospital of Foshan, Foshan, China
| | - Wei Hu
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Haolan He
- Department of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Wei Wang
- Department of Laboratory Medicine, The Fourth People’s Hospital of Foshan, Foshan, China
| | - Wentao Fan
- Department of Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, China
| | - Linlin Li
- Department of Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, China
| | - Dawei Wang
- Department of Pulmonary and Critical Care Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Kejian Wang
- The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, China
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jianhua Xu
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
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8
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Simonetti FR, Zhang H, Soroosh GP, Duan J, Rhodehouse K, Hill AL, Beg SA, McCormick K, Raymond HE, Nobles CL, Everett JK, Kwon KJ, White JA, Lai J, Margolick JB, Hoh R, Deeks SG, Bushman FD, Siliciano JD, Siliciano RF. Antigen-driven clonal selection shapes the persistence of HIV-1-infected CD4+ T cells in vivo. J Clin Invest 2021; 131:145254. [PMID: 33301425 DOI: 10.1172/jci145254] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/01/2020] [Indexed: 12/23/2022] Open
Abstract
Clonal expansion of infected CD4+ T cells is a major mechanism of HIV-1 persistence and a barrier to achieving a cure. Potential causes are homeostatic proliferation, effects of HIV-1 integration, and interaction with antigens. Here, we show that it is possible to link antigen responsiveness, the full proviral sequence, the integration site, and the T cell receptor β-chain (TCRβ) sequence to examine the role of recurrent antigenic exposure in maintaining the HIV-1 reservoir. We isolated CMV- and Gag-responding CD4+ T cells from 10 treated individuals. Proviral populations in CMV-responding cells were dominated by large clones, including clones harboring replication-competent proviruses. TCRβ repertoires showed high clonality driven by converging adaptive responses. Although some proviruses were in genes linked to HIV-1 persistence (BACH2, STAT5B, MKL1), the proliferation of infected cells under antigenic stimulation occurred regardless of the site of integration. Paired TCRβ and integration site analysis showed that infection could occur early or late in the course of a clone's response to antigen and could generate infected cell populations too large to be explained solely by homeostatic proliferation. Together, these findings implicate antigen-driven clonal selection as a major factor in HIV-1 persistence, a finding that will be a difficult challenge to eradication efforts.
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Affiliation(s)
- Francesco R Simonetti
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Garshasb P Soroosh
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jiayi Duan
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kyle Rhodehouse
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alison L Hill
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Subul A Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kevin McCormick
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Hayley E Raymond
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Christopher L Nobles
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - John K Everett
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kyungyoon J Kwon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jennifer A White
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph B Margolick
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases, and Global Medicine, UCSF, San Francisco, California, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, UCSF, San Francisco, California, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Howard Hughes Medical Institute, Baltimore, Maryland, USA
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9
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Pan YG, Aiamkitsumrit B, Bartolo L, Wang Y, Lavery C, Marc A, Holec PV, Rappazzo CG, Eilola T, Gimotty PA, Hensley SE, Antia R, Zarnitsyna VI, Birnbaum ME, Su LF. Vaccination reshapes the virus-specific T cell repertoire in unexposed adults. Immunity 2021; 54:1245-1256.e5. [PMID: 34004140 PMCID: PMC8192456 DOI: 10.1016/j.immuni.2021.04.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/01/2021] [Accepted: 04/21/2021] [Indexed: 11/30/2022]
Abstract
We examined how baseline CD4+ T cell repertoire and precursor states impact responses to pathogen infection in humans using primary immunization with yellow fever virus (YFV) vaccine. YFV-specific T cells in unexposed individuals were identified by peptide-MHC tetramer staining and tracked pre- and post-vaccination by tetramers and TCR sequencing. A substantial number of YFV-reactive T cells expressed memory phenotype markers and contained expanded clones in the absence of exposure to YFV. After vaccination, pre-existing YFV-specific T cell populations with low clonal diversity underwent limited expansion, but rare populations with a reservoir of unexpanded TCRs generated robust responses. These altered dynamics reorganized the immunodominance hierarchy and resulted in an overall increase in higher avidity T cells. Thus, instead of further increasing the representation of dominant clones, YFV vaccination recruits rare and more responsive T cells. Our findings illustrate the impact of vaccines in prioritizing T cell responses and reveal repertoire reorganization as a key component of effective vaccination.
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Affiliation(s)
- Yi-Gen Pan
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamas Aiamkitsumrit
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laurent Bartolo
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yifeng Wang
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Criswell Lavery
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA 19104, USA
| | - Adam Marc
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA 19104, USA
| | - Patrick V Holec
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Garrett Rappazzo
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Theresa Eilola
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Phyllis A Gimotty
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA, USA
| | | | - Michael E Birnbaum
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Laura F Su
- Department of Medicine, Division of Rheumatology, Perelman School of Medicine, Institute for Immunology, University of Pennsylvania, Philadelphia, PA 19104, USA; Corporal Michael J Crescenz VA Medical Center, Philadelphia, PA 19104, USA.
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10
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Kaw S, Ananth S, Tsopoulidis N, Morath K, Coban BM, Hohenberger R, Bulut OC, Klein F, Stolp B, Fackler OT. HIV-1 infection of CD4 T cells impairs antigen-specific B cell function. EMBO J 2020; 39:e105594. [PMID: 33146906 PMCID: PMC7737609 DOI: 10.15252/embj.2020105594] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/28/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022] Open
Abstract
Failures to produce neutralizing antibodies upon HIV‐1 infection result in part from B‐cell dysfunction due to unspecific B‐cell activation. How HIV‐1 affects antigen‐specific B‐cell functions remains elusive. Using an adoptive transfer mouse model and ex vivo HIV infection of human tonsil tissue, we found that expression of the HIV‐1 pathogenesis factor NEF in CD4 T cells undermines their helper function and impairs cognate B‐cell functions including mounting of efficient specific IgG responses. NEF interfered with T cell help via a specific protein interaction motif that prevents polarized cytokine secretion at the T‐cell–B‐cell immune synapse. This interference reduced B‐cell activation and proliferation and thus disrupted germinal center formation and affinity maturation. These results identify NEF as a key component for HIV‐mediated dysfunction of antigen‐specific B cells. Therapeutic targeting of the identified molecular surface in NEF will facilitate host control of HIV infection.
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Affiliation(s)
- Sheetal Kaw
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Swetha Ananth
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Nikolaos Tsopoulidis
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Katharina Morath
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Bahar M Coban
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Ralph Hohenberger
- Department of Otorhinolaryngology, University Hospital Heidelberg, Heidelberg, Germany
| | - Olcay C Bulut
- German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, SLK Klinikum Am Gesundbrunnen, Heilbronn, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, University Hospital of Cologne, Cologne, Germany.,German Centre for Infection Research (DZIF), Partner Site Köln, Köln, Germany
| | - Bettina Stolp
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Oliver T Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Centre for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
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11
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Zhang T, Warden AR, Li Y, Ding X. Progress and applications of mass cytometry in sketching immune landscapes. Clin Transl Med 2020; 10:e206. [PMID: 33135337 PMCID: PMC7556381 DOI: 10.1002/ctm2.206] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022] Open
Abstract
Recently emerged mass cytometry (cytometry by time-of-flight [CyTOF]) technology permits the identification and quantification of inherently diverse cellular systems, and the simultaneous measurement of functional attributes at the single-cell resolution. By virtue of its multiplex ability with limited need for compensation, CyTOF has led a critical role in immunological research fields. Here, we present an overview of CyTOF, including the introduction of CyTOF principle and advantages that make it a standalone tool in deciphering immune mysteries. We then discuss the functional assays, introduce the bioinformatics to interpret the data yield via CyTOF, and depict the emerging clinical and research applications of CyTOF technology in sketching immune landscape in a wide variety of diseases.
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Affiliation(s)
- Ting Zhang
- State Key laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
| | - Antony R. Warden
- State Key laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
| | - Yiyang Li
- State Key laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
| | - Xianting Ding
- State Key laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
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12
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Niu X, Li S, Li P, Pan W, Wang Q, Feng Y, Mo X, Yan Q, Ye X, Luo J, Qu L, Weber D, Byrne-Steele ML, Wang Z, Yu F, Li F, Myers RM, Lotze MT, Zhong N, Han J, Chen L. Longitudinal Analysis of T and B Cell Receptor Repertoire Transcripts Reveal Dynamic Immune Response in COVID-19 Patients. Front Immunol 2020; 11:582010. [PMID: 33117392 PMCID: PMC7561365 DOI: 10.3389/fimmu.2020.582010] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/15/2020] [Indexed: 01/08/2023] Open
Abstract
Severe COVID-19 is associated with profound lymphopenia and an elevated neutrophil to lymphocyte ratio. We applied a novel dimer avoidance multiplexed polymerase chain reaction next-generation sequencing assay to analyze T (TCR) and B cell receptor (BCR) repertoires. Surprisingly, TCR repertoires were markedly diminished during the early onset of severe disease but recovered during the convalescent stage. Monitoring TCR repertoires could serve as an indicative biomarker to predict disease progression and recovery. Panoramic concurrent assessment of BCR repertoires demonstrated isotype switching and a transient but dramatic early IgA expansion. Dominant B cell clonal expansion with decreased diversity occurred following recovery from infection. Profound changes in T cell homeostasis raise critical questions about the early events in COVID-19 infection and demonstrate that immune repertoire analysis is a promising method for evaluating emergent host immunity to SARS-CoV-2 viral infection, with great implications for assessing vaccination and other immunological therapies.
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Affiliation(s)
- Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Song Li
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, China.,iRepertoire Inc., Huntsville, AL, United States
| | - Pingchao Li
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Wenjing Pan
- iRepertoire Inc., Huntsville, AL, United States.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Qian Wang
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ying Feng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaoneng Mo
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qihong Yan
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xianmiao Ye
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jia Luo
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Linbing Qu
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | | | | | - Zhe Wang
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, China
| | - Fengjia Yu
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, China
| | - Fang Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Michael T Lotze
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian Han
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, China.,iRepertoire Inc., Huntsville, AL, United States.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
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13
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Del Alcazar D, Wang Y, He C, Wendel BS, Del Río-Estrada PM, Lin J, Ablanedo-Terrazas Y, Malone MJ, Hernandez SM, Frank I, Naji A, Reyes-Terán G, Jiang N, Su LF. Mapping the Lineage Relationship between CXCR5 + and CXCR5 - CD4 + T Cells in HIV-Infected Human Lymph Nodes. Cell Rep 2020; 28:3047-3060.e7. [PMID: 31533030 PMCID: PMC6878759 DOI: 10.1016/j.celrep.2019.08.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/27/2019] [Accepted: 08/09/2019] [Indexed: 12/29/2022] Open
Abstract
CXCR5 is a key marker of follicular helper T (TFH) cells. Using primary lymph nodes (LNs) from HIV-infected patients, we identified a population of CXCR5− CD4+ T cells with TFH-cell-like features. This CXCR5− subset becomes expanded in severe HIV infection and is characterized by the upregulation of activation markers and high PD-1 and ICOS surface expression. Integrated analyses on the phenotypic heterogeneity, functional capacity, T cell receptor (TCR) repertoire, transcriptional profile, and epigenetic state of CXCR5−PD-1+ICOS+ T cells revealed a shared clonal relationship with TFH cells. CXCR5−PD-1+ICOS+ T cells retained a poised state for CXCR5 expression and exhibited a migratory transcriptional program. TCR sequence overlap revealed a contribution of LN-derived CXCR5−PD-1+ICOS+ T cells to circulating CXCR5− CD4+ T cells with B cell help function. These data link LN pathology to circulating T cells and expand the current understanding on the diversity of T cells that regulate B cell responses during chronic inflammation. Follicular helper T (TFH) cells are critical for antibody production. Del Alcazar et al. showed that TFH cells can lose their characteristic chemokine receptor, giving rise to migratory populations of CXCR5− T cells that retain B cell help function and are poised for CXCR5 expression.
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Affiliation(s)
- Daniel Del Alcazar
- Department of Medicine, Division of Rheumatology, Philadelphia VA Medical Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yifeng Wang
- Department of Medicine, Division of Rheumatology, Philadelphia VA Medical Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Chenfeng He
- Laboratory of Systems Immunology, Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Ben S Wendel
- Laboratory of Systems Immunology, Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA; McKetta Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Perla M Del Río-Estrada
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México, México
| | - Jerome Lin
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuria Ablanedo-Terrazas
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México, México
| | - Michael J Malone
- Laboratory of Systems Immunology, Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Stefany M Hernandez
- Laboratory of Systems Immunology, Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA; McKetta Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - Ian Frank
- Department of Medicine, Division of Infectious Disease, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ali Naji
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Gustavo Reyes-Terán
- Departamento de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias, Ciudad de México, México
| | - Ning Jiang
- Laboratory of Systems Immunology, Department of Biomedical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Laura F Su
- Department of Medicine, Division of Rheumatology, Philadelphia VA Medical Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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14
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Wendel BS, Fu Y, He C, Hernandez SM, Qu M, Zhang Z, Jiang Y, Han X, Xu J, Ding H, Jiang N, Shang H. Rapid HIV Progression Is Associated with Extensive Ongoing Somatic Hypermutation. THE JOURNAL OF IMMUNOLOGY 2020; 205:587-594. [PMID: 32591400 DOI: 10.4049/jimmunol.1901161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 05/15/2020] [Indexed: 12/24/2022]
Abstract
The Ab response to HIV is of great interest, particularly in the context of a protective vaccine and broadly neutralizing Abs, but research is typically geared toward elite controllers because of their ability to successfully control the virus. In this study, we studied the evolution of the Ab repertoire over the first year of HIV infection in people classified as rapid progressors (RP) compared with typical progressors. HIV RPs are an important yet understudied group of HIV patients classified by a rapid decline in CD4 counts and accelerated development of AIDS. We found that the global IgG somatic hypermutation load negatively correlated with disease progression, possibly because of exaggerated isotype switching of unmutated sequences in patients with low CD4 counts. We measured Ab sequence evolution over time using longitudinal samples taken during the early stages of infection and 1 year postinfection. Within clonal lineages spanning both timepoints, visit 2-derived sequences harbored considerably more mutations than their visit 1 relatives. Despite extensive ongoing somatic hypermutation, the initially strong signs of Ag selection pressure observed in visit 1-derived sequences decayed by visit 2. These data suggest that excessive immune activation in RPs leads to a hyperactive B cell response that fails to confer protection.
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Affiliation(s)
- Ben S Wendel
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Yajing Fu
- Key Laboratory of AIDS Immunology of National Health Commission (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Chenfeng He
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712; and
| | - Stefany M Hernandez
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Mingjuan Qu
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712; and
| | - Zining Zhang
- Key Laboratory of AIDS Immunology of National Health Commission (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Yongjun Jiang
- Key Laboratory of AIDS Immunology of National Health Commission (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Xiaoxu Han
- Key Laboratory of AIDS Immunology of National Health Commission (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Junjie Xu
- Key Laboratory of AIDS Immunology of National Health Commission (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Haibo Ding
- Key Laboratory of AIDS Immunology of National Health Commission (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China.,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Ning Jiang
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712; and .,Institute for Cellular and Molecular Biology, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712
| | - Hong Shang
- Key Laboratory of AIDS Immunology of National Health Commission (China Medical University), Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China; .,National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
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15
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Germinal centers B-cell reaction and T follicular helper cells in response to HIV-1 infection. Curr Opin HIV AIDS 2020; 14:246-252. [PMID: 30994502 DOI: 10.1097/coh.0000000000000557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW This review aims to summarize the recent findings on germinal center B-cell reaction and Tfh cells in HIV-1 infection, with particular emphasis on the spatial organization of the germinal center, follicular cell regulation, and cellular alterations resulting from HIV infection. RECENT FINDINGS HIV-specific bNAbs are generated by iterative cycles of B-cell maturation supported by GC environment. Recent observations underline that germinal center structural alterations at the earliest stages of HIV infection could impact Tfh cell and germinal center B-cell homeostasis, thus preventing the rise of efficient humoral immunity. Moreover, despite ART treatment, HIV-derived antigens persist, particularly in follicular CD4+ T cells. Antigenic persistence and variability lead to unregulated chronic stimulation. In this context, regulation of the germinal center appears of special interest. In addition to follicular T-regulatory cells (Tfr), new potent regulators of germinal center reaction, such as follicular CD8 T and NK cells have been recently identified. SUMMARY Altogether these new data provide a better understanding on how HIV infection severely impacts germinal center reaction. Here we propose several therapeutic approaches to promote the bNAb development in HIV-infected patients by improving the preservation of germinal center architecture and its regulation.
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16
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Niessl J, Baxter AE, Morou A, Brunet-Ratnasingham E, Sannier G, Gendron-Lepage G, Richard J, Delgado GG, Brassard N, Turcotte I, Fromentin R, Bernard NF, Chomont N, Routy JP, Dubé M, Finzi A, Kaufmann DE. Persistent expansion and Th1-like skewing of HIV-specific circulating T follicular helper cells during antiretroviral therapy. EBioMedicine 2020; 54:102727. [PMID: 32268275 PMCID: PMC7136607 DOI: 10.1016/j.ebiom.2020.102727] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/17/2020] [Accepted: 03/04/2020] [Indexed: 12/13/2022] Open
Abstract
Background Untreated HIV infection leads to alterations in HIV-specific CD4+ T cells including increased expression of co-inhibitory receptors (IRs) and skewing toward a T follicular helper cell (Tfh) signature. However, which changes are maintained after suppression of viral replication with antiretroviral therapy (ART) is poorly known. Methods We analyzed blood CD4+ T cells specific to HIV and comparative viral antigens in ART-treated people using a cytokine-independent activation-induced marker assay alone or in combination with functional readouts. Findings In intra-individual comparisons, HIV-specific CD4+ T cells were characterized by a larger fraction of circulating Tfh (cTfh) cells than CMV- and HBV-specific cells and preferentially expressed multiple IRs and showed elevated production of the Tfh cytokines CXCL13 and IL-21. In addition, HIV-specific cTfh exhibited a predominant Th1-like phenotype and function when compared to cTfh of other specificities, contrasting with a reduction in Th1-functions in HIV-specific non-cTfh. Using longitudinal samples, we demonstrate that this distinct HIV-specific cTfh profile was induced during chronic untreated HIV infection, persisted on ART and correlated with the translation-competent HIV reservoir but not with the total HIV DNA reservoir. Interpretation Expansion and altered features of HIV-specific cTfh cells are maintained during ART and may be driven by persistent HIV antigen expression. Funding This work was supported by the National Institutes of Health (NIH), the Canadian Institutes of Health Research (CIHR) and the FRQS AIDS and Infectious Diseases Network.
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Affiliation(s)
- Julia Niessl
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada; Consortium for HIV/AIDS Vaccine Development (CHAVD), La Jolla, CA, United States
| | - Amy E Baxter
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada; Consortium for HIV/AIDS Vaccine Development (CHAVD), La Jolla, CA, United States
| | - Antigoni Morou
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada
| | - Elsa Brunet-Ratnasingham
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada
| | - Gérémy Sannier
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada
| | - Gabrielle Gendron-Lepage
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada
| | - Jonathan Richard
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada
| | - Gloria-Gabrielle Delgado
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada
| | - Nathalie Brassard
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada
| | - Isabelle Turcotte
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada
| | - Rémi Fromentin
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada
| | - Nicole F Bernard
- Chronic Viral Illnesses Service and Division of Hematology, McGill University Health Centre, Montreal, QC, Canada
| | - Nicolas Chomont
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illnesses Service and Division of Hematology, McGill University Health Centre, Montreal, QC, Canada; Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Mathieu Dubé
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada
| | - Andrés Finzi
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM) and Université de Montréal, Montreal, QC, Canada; Consortium for HIV/AIDS Vaccine Development (CHAVD), La Jolla, CA, United States.
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17
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Follicular T-cell subsets in HIV infection: recent advances in pathogenesis research. Curr Opin HIV AIDS 2020; 14:71-76. [PMID: 30585797 DOI: 10.1097/coh.0000000000000525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW T cells within B-cell follicles of secondary lymphoid tissues play key roles in HIV immunopathogenesis. This review highlights recent findings and identifies gaps in current knowledge. RECENT FINDINGS B-cell follicles are major sites of virus replication and demonstrate significant impairments in the generation of humoral immunity in HIV infection. Follicular T helper cells (Tfh), follicular T regulatory cells (Tfr) and follicular CD8 T cells (fCD8) play key roles in HIV immunopathogenesis. Tfh and more recently Tfr are highly permissive to HIV, and may serve as reservoirs of HIV in treated infection. Virus-specific CD8 T cells are less abundant in B-cell follicles than extrafollicular regions, but their effector mechanisms remain an area of significant controversy. Impairments in Tfh likely contribute to impaired humoral immunity and potential mechanisms include B-cell counter-regulatory mechanisms, Tfr suppression and diminished repertoire breadth. A better understanding of the roles of Tfh, Tfr and fCD8 in HIV immunopathogenesis is critical to the development of effective HIV vaccines and cure strategies. SUMMARY Tfh, Tfr and fCD8 contribute to HIV persistence and impaired humoral immunity. A better understanding of their roles could facilitate vaccine development and HIV cure strategies.
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18
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Sannier G, Dubé M, Kaufmann DE. Single-Cell Technologies Applied to HIV-1 Research: Reaching Maturity. Front Microbiol 2020; 11:297. [PMID: 32194526 PMCID: PMC7064469 DOI: 10.3389/fmicb.2020.00297] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/10/2020] [Indexed: 12/11/2022] Open
Abstract
The need for definitive answers probably explains our natural tendency to seek simplicity. The reductionist “bulk” approach, in which a mean behavior is attributed to a heterogeneous cell population, fulfills this need by considerably helping the conceptualization of complex biological processes. However, the limits of this methodology are becoming increasingly clear as models seek to explain biological events occurring in vivo, where heterogeneity is the rule. Research in the HIV-1 field is no exception: the challenges encountered in the development of preventive and curative anti-HIV-1 strategies may well originate in part from inadequate assumptions built on bulk technologies, highlighting the need for new perspectives. The emergence of diverse single-cell technologies set the stage for potential breakthrough discoveries, as heterogeneous processes can now be investigated with an unprecedented depth in topics as diverse as HIV-1 tropism, dynamics of the replication cycle, latency, viral reservoirs and immune control. In this review, we summarize recent advances in the HIV-1 field made possible by single-cell technologies, and contextualize their importance.
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Affiliation(s)
- Gérémy Sannier
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, QC, Canada
| | - Mathieu Dubé
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Daniel E Kaufmann
- Research Centre of the Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada.,Department of Medicine, Université de Montréal, Montreal, QC, Canada.,Consortium for HIV/AIDS Vaccine Development (Scripps CHAVD), La Jolla, CA, United States
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19
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Amodio D, Santilli V, Zangari P, Cotugno N, Manno EC, Rocca S, Rossi P, Cancrini C, Finocchi A, Chassiakos A, Petrovas C, Palma P. How to dissect the plasticity of antigen-specific immune response: a tissue perspective. Clin Exp Immunol 2020; 199:119-130. [PMID: 31626717 PMCID: PMC6954674 DOI: 10.1111/cei.13386] [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] [Accepted: 10/14/2019] [Indexed: 12/01/2022] Open
Abstract
Generation of antigen-specific humoral responses following vaccination or infection requires the maturation and function of highly specialized immune cells in secondary lymphoid organs (SLO), such as lymph nodes or tonsils. Factors that orchestrate the dynamics of these cells are still poorly understood. Currently, experimental approaches that enable a detailed description of the function of the immune system in SLO have been mainly developed and optimized in animal models. Conversely, methodological approaches in humans are mainly based on the use of blood-associated material because of the challenging access to tissues. Indeed, only few studies in humans were able to provide a discrete description of the complex network of cytokines, chemokines and lymphocytes acting in tissues after antigenic challenge. Furthermore, even fewer data are currently available on the interaction occurring within the complex micro-architecture of the SLO. This information is crucial in order to design particular vaccination strategies, especially for patients affected by chronic and immune compromising medical conditions who are under-vaccinated or who respond poorly to immunizations. Analysis of immune cells in different human tissues by high-throughput technologies, able to obtain data ranging from gene signature to protein expression and cell phenotypes, is needed to dissect the peculiarity of each immune cell in a definite human tissue. The main aim of this review is to provide an in-depth description of the current available methodologies, proven evidence and future perspectives in the analysis of immune mechanisms following immunization or infections in SLO.
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Affiliation(s)
- D. Amodio
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
- Department of Systems MedicineUniversity of Rome Tor VergataRomeItaly
| | - V. Santilli
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
| | - P. Zangari
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
| | - N. Cotugno
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
| | - E. C. Manno
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
| | - S. Rocca
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
| | - P. Rossi
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
- Department of Systems MedicineUniversity of Rome Tor VergataRomeItaly
| | - C. Cancrini
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
- Department of Systems MedicineUniversity of Rome Tor VergataRomeItaly
| | - A. Finocchi
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
- Department of Systems MedicineUniversity of Rome Tor VergataRomeItaly
| | - A. Chassiakos
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - C. Petrovas
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMDUSA
| | - P. Palma
- Research Unit in Congenital and Perinatal InfectionsImmune and Infectious Diseases DivisionAcademic Department of PediatricsOspedale Pediatrico Bambino Gesù, IRCCSRomeItaly
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20
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Yu J, Peng J, Chi H. Systems immunology: Integrating multi-omics data to infer regulatory networks and hidden drivers of immunity. ACTA ACUST UNITED AC 2019; 15:19-29. [PMID: 32789283 DOI: 10.1016/j.coisb.2019.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The immune system is a highly complex and dynamic biological system. It operates through intracellular molecular networks and intercellular (cell-cell) interaction networks. Systems immunology is an emerging discipline that applies systems biology approaches of integrating high-throughput multi-omics measurements with computational network modeling to better understand immunity at various scales. In this review, we summarize key omics technologies and computational approaches used for immunological studies at both population and single-cell levels. We highlight the hidden driver analysis based on data-driven networks and comment on the potential of translating systems immunology discoveries to immunotherapy of cancer and other human diseases.
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Affiliation(s)
- Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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21
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Wu SG, Pan W, Liu H, Byrne-Steele ML, Brown B, Depinet M, Hou X, Han J, Li S. High throughput sequencing of T-cell receptor repertoire using dry blood spots. J Transl Med 2019; 17:47. [PMID: 30777078 PMCID: PMC6379990 DOI: 10.1186/s12967-019-1796-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/09/2019] [Indexed: 11/12/2022] Open
Abstract
Background Immunology research, particularly next generation sequencing (NGS) of the immune T-cell receptor β (TCRβ) repertoire, has advanced progression in several fields, including treatment of various cancers and autoimmune diseases. This study aimed to identify the TCR repertoires from dry blood spots (DBS), a method that will help collecting real-world data for biomarker applications. Methods Finger-prick blood was collected onto a Whatman filter card. RNA was extracted from DBS of the filter card, and fully automated multiplex PCR was performed to generate a TCRβ chain library for next generation sequencing (NGS) analysis of unique CDR3s (uCDR3). Results We demonstrated that the dominant clonotypes from the DBS results recapitulated those found in whole blood. According to the statistical analysis and laboratory confirmation, 40 of 2-mm punch disks from the filter cards were enough to detect the shared top clones and have strong correlation in the uCDR3 discovery with whole blood. uCDR3 discovery was neither affected by storage temperatures (room temperature versus − 20 °C) nor storage durations (1, 14, and 28 days) when compared to whole blood. About 74–90% of top 50 uCDR3 clones of whole blood could also be detected from DBS. A low rate of clonotype sharing, 0.03–1.5%, was found among different individuals. Conclusions The DBS-based TCR repertoire profiling method is minimally invasive, provides convenient sampling, and incorporates fully automated library preparation. The system is sensitive to low RNA input, and the results are highly correlated with whole blood uCDR3 discovery allowing study scale-up to better understand the relationship and mutual influences between the immune and diseases. Electronic supplementary material The online version of this article (10.1186/s12967-019-1796-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shang-Gin Wu
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University, Taipei, 10002, Taiwan.,Department of Internal Medicine, National Taiwan University Cancer Center, National Taiwan University, Taipei, 10672, Taiwan
| | - Wenjing Pan
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.,iRepertoire Inc., 800 Hudson Way Suite 2319, Huntsville, AL, 35806, USA
| | - Hongna Liu
- iCubate Inc., Huntsville, AL, 35806, USA
| | | | - Brittany Brown
- iRepertoire Inc., 800 Hudson Way Suite 2319, Huntsville, AL, 35806, USA
| | - Mollye Depinet
- iRepertoire Inc., 800 Hudson Way Suite 2319, Huntsville, AL, 35806, USA
| | - Xiaohong Hou
- iRepertoire Inc., 800 Hudson Way Suite 2319, Huntsville, AL, 35806, USA
| | - Jian Han
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA. .,iRepertoire Inc., 800 Hudson Way Suite 2319, Huntsville, AL, 35806, USA.
| | - Song Li
- iRepertoire Inc., 800 Hudson Way Suite 2319, Huntsville, AL, 35806, USA.
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22
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Huang Q, Hu J, Tang J, Xu L, Ye L. Molecular Basis of the Differentiation and Function of Virus Specific Follicular Helper CD4 + T Cells. Front Immunol 2019; 10:249. [PMID: 30828337 PMCID: PMC6384271 DOI: 10.3389/fimmu.2019.00249] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/29/2019] [Indexed: 12/12/2022] Open
Abstract
During viral infection, virus-specific follicular helper T cells provide important help to cognate B cells for their survival, consecutive proliferation and mutation and eventual differentiation into memory B cells and antibody-secreting plasma cells. Similar to Tfh cells generated in other conditions, the differentiation of virus-specific Tfh cells can also be characterized as a process involved multiple factors and stages, however, which also exhibits distinct features. Here, we mainly focus on the current understanding of Tfh fate commitment, functional maturation, lineage maintenance and memory transition and formation in the context of viral infection.
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Affiliation(s)
- Qizhao Huang
- Cancer Center, The General Hospital of Western Theater Command, Chengdu, China.,Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Jianjun Hu
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Jianfang Tang
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Lifan Xu
- Institute of Immunology, Third Military Medical University, Chongqing, China
| | - Lilin Ye
- Institute of Immunology, Third Military Medical University, Chongqing, China
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23
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Dan JM, Havenar-Daughton C, Kendric K, Al-Kolla R, Kaushik K, Rosales SL, Anderson EL, LaRock CN, Vijayanand P, Seumois G, Layfield D, Cutress RI, Ottensmeier CH, Lindestam Arlehamn CS, Sette A, Nizet V, Bothwell M, Brigger M, Crotty S. Recurrent group A Streptococcus tonsillitis is an immunosusceptibility disease involving antibody deficiency and aberrant T FH cells. Sci Transl Med 2019; 11:eaau3776. [PMID: 30728285 PMCID: PMC6561727 DOI: 10.1126/scitranslmed.aau3776] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/29/2018] [Accepted: 01/11/2019] [Indexed: 12/11/2022]
Abstract
"Strep throat" is highly prevalent among children, yet it is unknown why only some children develop recurrent tonsillitis (RT), a common indication for tonsillectomy. To gain insights into this classic childhood disease, we performed phenotypic, genotypic, and functional studies on pediatric group A Streptococcus (GAS) RT and non-RT tonsils from two independent cohorts. GAS RT tonsils had smaller germinal centers, with an underrepresentation of GAS-specific CD4+ germinal center T follicular helper (GC-TFH) cells. RT children exhibited reduced antibody responses to an important GAS virulence factor, streptococcal pyrogenic exotoxin A (SpeA). Risk and protective human leukocyte antigen (HLA) class II alleles for RT were identified. Lastly, SpeA induced granzyme B production in GC-TFH cells from RT tonsils with the capacity to kill B cells and the potential to hobble the germinal center response. These observations suggest that RT is a multifactorial disease and that contributors to RT susceptibility include HLA class II differences, aberrant SpeA-activated GC-TFH cells, and lower SpeA antibody titers.
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Affiliation(s)
- Jennifer M Dan
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Colin Havenar-Daughton
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA 92037, USA
| | - Kayla Kendric
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Rita Al-Kolla
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Kirti Kaushik
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Sandy L Rosales
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Ericka L Anderson
- Department of Pediatrics, School of Medicine, UCSD, La Jolla, CA 92037, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, La Jolla, CA 92037, USA
- Human Longevity Inc., San Diego, CA 92121, USA
| | - Christopher N LaRock
- Department of Pediatrics, School of Medicine, UCSD, La Jolla, CA 92037, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, La Jolla, CA 92037, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Pandurangan Vijayanand
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Grégory Seumois
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - David Layfield
- Cancer Sciences Division, Faculty of Medicine, University of Southampton, UK
| | - Ramsey I Cutress
- Cancer Sciences Division, Faculty of Medicine, University of Southampton, UK
| | | | | | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Victor Nizet
- Department of Pediatrics, School of Medicine, UCSD, La Jolla, CA 92037, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD, La Jolla, CA 92037, USA
| | - Marcella Bothwell
- Division of Pediatric Otolaryngology, Rady Children's Hospital, San Diego, CA 92123, USA
- Department of Surgery, UCSD, La Jolla, CA 92037, USA
- Department of Otolaryngology, Head and Neck Surgery, Naval Medical Center San Diego, San Diego, CA 92134, USA
| | - Matthew Brigger
- Division of Pediatric Otolaryngology, Rady Children's Hospital, San Diego, CA 92123, USA
- Department of Surgery, UCSD, La Jolla, CA 92037, USA
- Department of Otolaryngology, Head and Neck Surgery, Naval Medical Center San Diego, San Diego, CA 92134, USA
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
- Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA 92037, USA
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24
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Wagar LE, DiFazio RM, Davis MM. Advanced model systems and tools for basic and translational human immunology. Genome Med 2018; 10:73. [PMID: 30266097 PMCID: PMC6162943 DOI: 10.1186/s13073-018-0584-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/17/2018] [Indexed: 12/31/2022] Open
Abstract
There are fundamental differences between humans and the animals we typically use to study the immune system. We have learned much from genetically manipulated and inbred animal models, but instances in which these findings have been successfully translated to human immunity have been rare. Embracing the genetic and environmental diversity of humans can tell us about the fundamental biology of immune cell types and the elasticity of the immune system. Although people are much more immunologically diverse than conventionally housed animal models, tools and technologies are now available that permit high-throughput analysis of human samples, including both blood and tissues, which will give us deep insights into human immunity in health and disease. As we gain a more detailed picture of the human immune system, we can build more sophisticated models to better reflect this complexity, both enabling the discovery of new immunological mechanisms and facilitating translation into the clinic.
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Affiliation(s)
- Lisa E Wagar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Robert M DiFazio
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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25
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Moysi E, Petrovas C, Koup RA. The role of follicular helper CD4 T cells in the development of HIV-1 specific broadly neutralizing antibody responses. Retrovirology 2018; 15:54. [PMID: 30081906 PMCID: PMC6080353 DOI: 10.1186/s12977-018-0437-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/28/2018] [Indexed: 01/23/2023] Open
Abstract
The induction of HIV-1-specific antibodies that can neutralize a broad number of isolates is a major goal of HIV-1 vaccination strategies. However, to date no candidate HIV-1 vaccine has successfully elicited broadly neutralizing antibodies of sufficient quality and breadth for protection. In this review, we focus on the role of follicular helper CD4 T-cells (Tfh) in the development of such cross-reactive protective antibodies. We discuss germinal center (GC) formation and the dynamics of Tfh and GC B cells during HIV-1/SIV infection and vaccination. Finally, we consider future directions for the study of Tfh and offer perspective on factors that could be modulated to enhance Tfh function in the context of prophylactic vaccination.
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Affiliation(s)
- Eirini Moysi
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, USA
| | | | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, USA
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26
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Harnessing T Follicular Helper Cell Responses for HIV Vaccine Development. Viruses 2018; 10:v10060336. [PMID: 29921828 PMCID: PMC6024737 DOI: 10.3390/v10060336] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/15/2018] [Accepted: 06/16/2018] [Indexed: 12/12/2022] Open
Abstract
Passive administration of broadly neutralizing antibodies (bNAbs) capable of recognizing a broad range of viral strains to non-human primates has led to protection from infection with chimeric SIV/HIV virus (SHIV). This data suggests that generating protective antibody responses could be an effective strategy for an HIV vaccine. However, classic vaccine approaches have failed so far to induce such protective antibodies in HIV vaccine trials. HIV-specific bNAbs identified in natural infection show high levels of somatic hypermutations, demonstrating that they underwent extensive affinity maturation. It is likely that to gain ability to recognize diverse viral strains, vaccine-induced humoral responses will also require complex, iterative maturation. T follicular helper cells (Tfh) are a specialized CD4+ T cell subset that provides help to B cells in the germinal center for the generation of high-affinity and long-lasting humoral responses. It is therefore probable that the quality and quantity of Tfh responses upon vaccination will impact development of bNAbs. Here, we review studies that advanced our understanding of Tfh differentiation, function and regulation. We discuss correlates of Tfh responses and bNAb development in natural HIV infection. Finally, we highlight recent strategies to optimize Tfh responses upon vaccination and their impact on prophylactic HIV vaccine research.
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