1
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Tenggara MK, Oh SH, Yang C, Nariya HK, Metz AM, Upadhyay AA, Gudipati DR, Guo L, McGhee EG, Gill K, Viox EG, Mason RD, Doria-Rose NA, Foulds KE, Mascola JR, Du Y, Fu H, Altman JD, Yan Q, Sheng Z, Bosinger SE, Kong R. Frequency-potency analysis of IgG+ memory B cells delineates neutralizing antibody responses at single-cell resolution. Cell Rep 2024; 43:113948. [PMID: 38483908 PMCID: PMC11003769 DOI: 10.1016/j.celrep.2024.113948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/06/2024] [Accepted: 02/26/2024] [Indexed: 04/02/2024] Open
Abstract
Identifying individual functional B cell receptors (BCRs) is common, but two-dimensional analysis of B cell frequency versus BCR potency would delineate both quantity and quality of antigen-specific memory B cells. We efficiently determine quantitative BCR neutralizing activities using a single-cell-derived antibody supernatant analysis (SCAN) workflow and develop a frequency-potency algorithm to estimate B cell frequencies at various neutralizing activity or binding affinity cutoffs. In an HIV-1 fusion peptide (FP) immunization study, frequency-potency curves elucidate the quantity and quality of FP-specific immunoglobulin G (IgG)+ memory B cells for different animals, time points, and antibody lineages at single-cell resolution. The BCR neutralizing activities are mainly determined by their affinities to soluble envelope trimer. Frequency analysis definitively demonstrates dominant neutralizing antibody lineages. These findings establish SCAN and frequency-potency analyses as promising approaches for general B cell analysis and monoclonal antibody (mAb) discovery. They also provide specific rationales for HIV-1 FP-directed vaccine optimization.
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Affiliation(s)
- Michelle K Tenggara
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Seo-Ho Oh
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Catherine Yang
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Hardik K Nariya
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Amanda M Metz
- Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Amit A Upadhyay
- Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Dedeepya R Gudipati
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Lizheng Guo
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Emily G McGhee
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Kiran Gill
- Emory National Primate Research Center, Atlanta, GA 30329, USA
| | - Elise G Viox
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rosemarie D Mason
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R Mascola
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Hematology and Medical Oncology and Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - John D Altman
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Qi Yan
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zizhang Sheng
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Steven E Bosinger
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rui Kong
- Emory Vaccine Center, Atlanta, GA 30329, USA; Emory National Primate Research Center, Atlanta, GA 30329, USA; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA.
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2
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Mopuri R, Welbourn S, Charles T, Ralli-Jain P, Rosales D, Burton S, Aftab A, Karunakaran K, Pellegrini K, Kilembe W, Karita E, Gnanakaran S, Upadhyay AA, Bosinger SE, Derdeyn CA. High throughput analysis of B cell dynamics and neutralizing antibody development during immunization with a novel clade C HIV-1 envelope. PLoS Pathog 2023; 19:e1011717. [PMID: 37878666 PMCID: PMC10627474 DOI: 10.1371/journal.ppat.1011717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/06/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023] Open
Abstract
A protective HIV-1 vaccine has been hampered by a limited understanding of how B cells acquire neutralizing activity. Our previous vaccines expressing two different HIV-1 envelopes elicited robust antigen specific serum IgG titers in 20 rhesus macaques; yet serum from only two animals neutralized the autologous virus. Here, we used high throughput immunoglobulin receptor and single cell RNA sequencing to characterize the overall expansion, recall, and maturation of antigen specific B cells longitudinally over 90 weeks. Diversification and expansion of many B cell clonotypes occurred broadly in the absence of serum neutralization. However, in one animal that developed neutralization, two neutralizing B cell clonotypes arose from the same immunoglobulin germline and were tracked longitudinally. Early antibody variants with high identity to germline neutralized the autologous virus while later variants acquired somatic hypermutation and increased neutralization potency. The early engagement of precursors capable of neutralization with little to no SHM followed by prolonged affinity maturation allowed the two neutralizing lineages to successfully persist despite many other antigen specific B cells. The findings provide new insight into B cells responding to HIV-1 envelope during heterologous prime and boost immunization in rhesus macaques and the development of selected autologous neutralizing antibody lineages.
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Affiliation(s)
- Rohini Mopuri
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Sarah Welbourn
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Tysheena Charles
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Pooja Ralli-Jain
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - David Rosales
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Samantha Burton
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Areeb Aftab
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Kirti Karunakaran
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Kathryn Pellegrini
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | | | | | - Sandrasegaram Gnanakaran
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Amit A. Upadhyay
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Steven E. Bosinger
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Cynthia A. Derdeyn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Infectious Diseases and Translational Medicine Unit, Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
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3
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Bollimpelli VS, Reddy PBJ, Gangadhara S, Charles TP, Burton SL, Tharp GK, Styles TM, Labranche CC, Smith JC, Upadhyay AA, Sahoo A, Legere T, Shiferaw A, Velu V, Yu T, Tomai M, Vasilakos J, Kasturi SP, Shaw GM, Montefiori D, Bosinger SE, Kozlowski PA, Pulendran B, Derdeyn CA, Hunter E, Amara RR. Intradermal but not intramuscular modified vaccinia Ankara immunizations protect against intravaginal tier2 simian-human immunodeficiency virus challenges in female macaques. Nat Commun 2023; 14:4789. [PMID: 37553348 PMCID: PMC10409804 DOI: 10.1038/s41467-023-40430-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
Route of immunization can markedly influence the quality of immune response. Here, we show that intradermal (ID) but not intramuscular (IM) modified vaccinia Ankara (MVA) vaccinations provide protection from acquisition of intravaginal tier2 simian-human immunodeficiency virus (SHIV) challenges in female macaques. Both routes of vaccination induce comparable levels of serum IgG with neutralizing and non-neutralizing activities. The protection in MVA-ID group correlates positively with serum neutralizing and antibody-dependent phagocytic activities, and envelope-specific vaginal IgA; while the limited protection in MVA-IM group correlates only with serum neutralizing activity. MVA-ID immunizations induce greater germinal center Tfh and B cell responses, reduced the ratio of Th1 to Tfh cells in blood and showed lower activation of intermediate monocytes and inflammasome compared to MVA-IM immunizations. This lower innate activation correlates negatively with induction of Tfh responses. These data demonstrate that the MVA-ID vaccinations protect against intravaginal SHIV challenges by modulating the innate and T helper responses.
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Affiliation(s)
- Venkata S Bollimpelli
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Pradeep B J Reddy
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Sailaja Gangadhara
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Tysheena P Charles
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Samantha L Burton
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Gregory K Tharp
- NHP Genomics Core Laboratory, Emory National Primate Research Center, Atlanta, GA, 30329, USA
| | - Tiffany M Styles
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Celia C Labranche
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Justin C Smith
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Amit A Upadhyay
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Anusmita Sahoo
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Traci Legere
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Ayalnesh Shiferaw
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Vijayakumar Velu
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory National Primate Research Center, Atlanta, GA, USA
| | - Tianwei Yu
- Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Mark Tomai
- 3M Corporate Research and Materials Lab, Saint Paul, MN, USA
| | | | - Sudhir P Kasturi
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory National Primate Research Center, Atlanta, GA, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Steven E Bosinger
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory National Primate Research Center, Atlanta, GA, USA
| | - Pamela A Kozlowski
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Bali Pulendran
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Cynthia A Derdeyn
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory National Primate Research Center, Atlanta, GA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Eric Hunter
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory National Primate Research Center, Atlanta, GA, USA
| | - Rama R Amara
- Emory Vaccine Center, Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA.
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, 30322, USA.
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4
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Viox EG, Hoang TN, Upadhyay AA, Nchioua R, Hirschenberger M, Strongin Z, Tharp GK, Pino M, Nguyen K, Harper JL, Gagne M, Marciano S, Boddapati AK, Pellegrini KL, Pradhan A, Tisoncik-Go J, Whitmore LS, Karunakaran KA, Roy M, Kirejczyk S, Curran EH, Wallace C, Wood JS, Connor-Stroud F, Voigt EA, Monaco CM, Gordon DE, Kasturi SP, Levit RD, Gale M, Vanderford TH, Silvestri G, Busman-Sahay K, Estes JD, Vaccari M, Douek DC, Sparrer KMJ, Johnson RP, Kirchhoff F, Schreiber G, Bosinger SE, Paiardini M. Modulation of type I interferon responses potently inhibits SARS-CoV-2 replication and inflammation in rhesus macaques. Sci Immunol 2023; 8:eadg0033. [PMID: 37506197 DOI: 10.1126/sciimmunol.adg0033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
Type I interferons (IFN-I) are critical mediators of innate control of viral infections but also drive the recruitment of inflammatory cells to sites of infection, a key feature of severe coronavirus disease 2019. Here, IFN-I signaling was modulated in rhesus macaques (RMs) before and during acute SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) infection using a mutated IFN-α2 (IFN-modulator; IFNmod), which has previously been shown to reduce the binding and signaling of endogenous IFN-I. IFNmod treatment in uninfected RMs was observed to induce a modest up-regulation of only antiviral IFN-stimulated genes (ISGs); however, in SARS-CoV-2-infected RMs, IFNmod reduced both antiviral and inflammatory ISGs. IFNmod treatment resulted in a potent reduction in SARS-CoV-2 viral loads both in vitro in Calu-3 cells and in vivo in bronchoalveolar lavage (BAL), upper airways, lung, and hilar lymph nodes of RMs. Furthermore, in SARS-CoV-2-infected RMs, IFNmod treatment potently reduced inflammatory cytokines, chemokines, and CD163+ MRC1- inflammatory macrophages in BAL and expression of Siglec-1 on circulating monocytes. In the lung, IFNmod also reduced pathogenesis and attenuated pathways of inflammasome activation and stress response during acute SARS-CoV-2 infection. Using an intervention targeting both IFN-α and IFN-β pathways, this study shows that, whereas early IFN-I restrains SARS-CoV-2 replication, uncontrolled IFN-I signaling critically contributes to SARS-CoV-2 inflammation and pathogenesis in the moderate disease model of RMs.
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Affiliation(s)
- Elise G Viox
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Timothy N Hoang
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Amit A Upadhyay
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | | | - Zachary Strongin
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Gregory K Tharp
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Maria Pino
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Kevin Nguyen
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Justin L Harper
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shir Marciano
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Arun K Boddapati
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Kathryn L Pellegrini
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Arpan Pradhan
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jennifer Tisoncik-Go
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Leanne S Whitmore
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Kirti A Karunakaran
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Melissa Roy
- Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | | | - Elizabeth H Curran
- Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Chelsea Wallace
- Division of Animal Resources, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jennifer S Wood
- Division of Animal Resources, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Fawn Connor-Stroud
- Division of Animal Resources, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Emily A Voigt
- RNA Vaccines Group, Access to Advanced Health Institute, Seattle, WA 98102, USA
| | - Christopher M Monaco
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - David E Gordon
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sudhir P Kasturi
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Rebecca D Levit
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Thomas H Vanderford
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- School of Health and Biomedical Sciences, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3000, Australia
| | - Monica Vaccari
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA
- Department of Microbiology and Immunology, Tulane School of Medicine, New Orleans, LA 70112, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - R Paul Johnson
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Infectious Disease Division, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
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5
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Upadhyay AA, Viox EG, Hoang TN, Boddapati AK, Pino M, Lee MYH, Corry J, Strongin Z, Cowan DA, Beagle EN, Horton TR, Hamilton S, Aoued H, Harper JL, Edwards CT, Nguyen K, Pellegrini KL, Tharp GK, Piantadosi A, Levit RD, Amara RR, Barratt-Boyes SM, Ribeiro SP, Sekaly RP, Vanderford TH, Schinazi RF, Paiardini M, Bosinger SE. TREM2 + and interstitial-like macrophages orchestrate airway inflammation in SARS-CoV-2 infection in rhesus macaques. Nat Commun 2023; 14:1914. [PMID: 37024448 PMCID: PMC10078029 DOI: 10.1038/s41467-023-37425-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 03/16/2023] [Indexed: 04/08/2023] Open
Abstract
The immunopathological mechanisms driving the development of severe COVID-19 remain poorly defined. Here, we utilize a rhesus macaque model of acute SARS-CoV-2 infection to delineate perturbations in the innate immune system. SARS-CoV-2 initiates a rapid infiltration of plasmacytoid dendritic cells into the lower airway, commensurate with IFNA production, natural killer cell activation, and a significant increase of blood CD14-CD16+ monocytes. To dissect the contribution of lung myeloid subsets to airway inflammation, we generate a longitudinal scRNA-Seq dataset of airway cells, and map these subsets to corresponding populations in the human lung. SARS-CoV-2 infection elicits a rapid recruitment of two macrophage subsets: CD163+MRC1-, and TREM2+ populations that are the predominant source of inflammatory cytokines. Treatment with baricitinib (Olumiant®), a JAK1/2 inhibitor is effective in eliminating the influx of non-alveolar macrophages, with a reduction of inflammatory cytokines. This study delineates the major lung macrophage subsets driving airway inflammation during SARS-CoV-2 infection.
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Affiliation(s)
- Amit A Upadhyay
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Elise G Viox
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Timothy N Hoang
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Arun K Boddapati
- Emory NPRC Genomics Core Laboratory, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Maria Pino
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Michelle Y-H Lee
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Jacqueline Corry
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zachary Strongin
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - David A Cowan
- Emory NPRC Genomics Core Laboratory, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Elizabeth N Beagle
- Emory NPRC Genomics Core Laboratory, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Tristan R Horton
- Emory NPRC Genomics Core Laboratory, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Sydney Hamilton
- Emory NPRC Genomics Core Laboratory, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Hadj Aoued
- Emory NPRC Genomics Core Laboratory, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Justin L Harper
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Christopher T Edwards
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Kevin Nguyen
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Kathryn L Pellegrini
- Emory NPRC Genomics Core Laboratory, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gregory K Tharp
- Emory NPRC Genomics Core Laboratory, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Rebecca D Levit
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Rama R Amara
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Simon M Barratt-Boyes
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Susan P Ribeiro
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Rafick P Sekaly
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Thomas H Vanderford
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, USA.
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, USA.
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6
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Hoang TN, Viox EG, Upadhyay AA, Strongin Z, Tharp GK, Pino M, Nchioua R, Hirschenberger M, Gagne M, Nguyen K, Harper JL, Marciano S, Boddapati AK, Pellegrini KL, Tisoncik-Go J, Whitmore LS, Karunakaran KA, Roy M, Kirejczyk S, Curran EH, Wallace C, Wood JS, Connor-Stroud F, Kasturi SP, Levit RD, Gale M, Vanderford TH, Silvestri G, Busman-Sahay K, Estes JD, Vaccari M, Douek DC, Sparrer KM, Kirchhoff F, Johnson RP, Schreiber G, Bosinger SE, Paiardini M. Modulation of type I interferon responses potently inhibits SARS-CoV-2 replication and inflammation in rhesus macaques. bioRxiv 2022:2022.10.21.512606. [PMID: 36324810 PMCID: PMC9628196 DOI: 10.1101/2022.10.21.512606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Type-I interferons (IFN-I) are critical mediators of innate control of viral infections, but also drive recruitment of inflammatory cells to sites of infection, a key feature of severe COVID-19. Here, and for the first time, IFN-I signaling was modulated in rhesus macaques (RMs) prior to and during acute SARS-CoV-2 infection using a mutated IFNα2 (IFN-modulator; IFNmod), which has previously been shown to reduce the binding and signaling of endogenous IFN-I. In SARS-CoV-2-infected RMs, IFNmod reduced both antiviral and inflammatory ISGs. Notably, IFNmod treatment resulted in a potent reduction in (i) SARS-CoV-2 viral load in Bronchoalveolar lavage (BAL), upper airways, lung, and hilar lymph nodes; (ii) inflammatory cytokines, chemokines, and CD163+MRC1-inflammatory macrophages in BAL; and (iii) expression of Siglec-1, which enhances SARS-CoV-2 infection and predicts disease severity, on circulating monocytes. In the lung, IFNmod also reduced pathogenesis and attenuated pathways of inflammasome activation and stress response during acute SARS-CoV-2 infection. This study, using an intervention targeting both IFN-α and IFN-β pathways, shows that excessive inflammation driven by type 1 IFN critically contributes to SARS-CoV-2 pathogenesis in RMs, and demonstrates the potential of IFNmod to limit viral replication, SARS-CoV-2 induced inflammation, and COVID-19 severity.
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Affiliation(s)
- Timothy N. Hoang
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,These authors contributed equally
| | - Elise G. Viox
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,These authors contributed equally
| | - Amit A. Upadhyay
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,These authors contributed equally
| | - Zachary Strongin
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Gregory K. Tharp
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Maria Pino
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | | | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Nguyen
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Justin L. Harper
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Shir Marciano
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Arun K. Boddapati
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Kathryn L. Pellegrini
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jennifer Tisoncik-Go
- Department of Immunology, University of Washington School of Medicine, and the Washington National Primate Research Center, Seattle, WA, 98109, USA
| | - Leanne S. Whitmore
- Department of Immunology, University of Washington School of Medicine, and the Washington National Primate Research Center, Seattle, WA, 98109, USA
| | - Kirti A. Karunakaran
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Melissa Roy
- Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Shannon Kirejczyk
- Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Elizabeth H. Curran
- Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Chelsea Wallace
- Division of Animal Resources, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jennifer S. Wood
- Division of Animal Resources, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Fawn Connor-Stroud
- Division of Animal Resources, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Sudhir P. Kasturi
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Rebecca D. Levit
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Michael Gale
- Department of Immunology, University of Washington School of Medicine, and the Washington National Primate Research Center, Seattle, WA, 98109, USA
| | - Thomas H. Vanderford
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Monica Vaccari
- Division of Immunology, Tulane National Primate Research Center, Covington, LA 70433, USA,Department of Microbiology and Immunology, Tulane School of Medicine, New Orleans, LA 70112, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - R. Paul Johnson
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Infectious Disease Division, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA,Correspondence to: (M.P; Lead Contact); (S.E.B.)
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Division of Pathology, Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Correspondence to: (M.P; Lead Contact); (S.E.B.)
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7
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Welbourn S, Chakraborty S, Yang JE, Gleinich AS, Gangadhara S, Khan S, Ferrebee C, Yagnik B, Burton S, Charles T, Smith SA, Williams D, Mopuri R, Upadhyay AA, Thompson J, Price MA, Wang S, Qin Z, Shen X, Williams LD, Eisel N, Peters T, Zhang L, Kilembe W, Karita E, Tomaras GD, Bosinger SE, Amara RR, Azadi P, Wright ER, Gnanakaran S, Derdeyn CA. A neutralizing antibody target in early HIV-1 infection was recapitulated in rhesus macaques immunized with the transmitted/founder envelope sequence. PLoS Pathog 2022; 18:e1010488. [PMID: 35503780 PMCID: PMC9106183 DOI: 10.1371/journal.ppat.1010488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/13/2022] [Accepted: 04/01/2022] [Indexed: 11/21/2022] Open
Abstract
Transmitted/founder (T/F) HIV-1 envelope proteins (Envs) from infected individuals that developed neutralization breadth are likely to possess inherent features desirable for vaccine immunogen design. To explore this premise, we conducted an immunization study in rhesus macaques (RM) using T/F Env sequences from two human subjects, one of whom developed potent and broad neutralizing antibodies (Z1800M) while the other developed little to no neutralizing antibody responses (R66M) during HIV-1 infection. Using a DNA/MVA/protein immunization protocol, 10 RM were immunized with each T/F Env. Within each T/F Env group, the protein boosts were administered as either monomeric gp120 or stabilized trimeric gp140 protein. All vaccination regimens elicited high titers of antigen-specific IgG, and two animals that received monomeric Z1800M Env gp120 developed autologous neutralizing activity. Using early Env escape variants isolated from subject Z1800M as guides, the serum neutralizing activity of the two immunized RM was found to be dependent on the gp120 V5 region. Interestingly, the exact same residues of V5 were also targeted by a neutralizing monoclonal antibody (nmAb) isolated from the subject Z1800M early in infection. Glycan profiling and computational modeling of the Z1800M Env gp120 immunogen provided further evidence that the V5 loop is exposed in this T/F Env and was a dominant feature that drove neutralizing antibody targeting during infection and immunization. An expanded B cell clonotype was isolated from one of the neutralization-positive RM and nmAbs corresponding to this group demonstrated V5-dependent neutralization similar to both the RM serum and the human Z1800M nmAb. The results demonstrate that neutralizing antibody responses elicited by the Z1800M T/F Env in RM converged with those in the HIV-1 infected human subject, illustrating the potential of using immunogens based on this or other T/F Envs with well-defined immunogenicity as a starting point to drive breadth.
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Affiliation(s)
- Sarah Welbourn
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Srirupa Chakraborty
- Theoretical Biology and Biophysics Group, Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Anne S. Gleinich
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Sailaja Gangadhara
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Salar Khan
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Courtney Ferrebee
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Bhrugu Yagnik
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Samantha Burton
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Tysheena Charles
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - S. Abigail Smith
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Danielle Williams
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Rohini Mopuri
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Amit A. Upadhyay
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Justin Thompson
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Matt A. Price
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
- International AIDS Vaccine Initiative, New York city, New York, United States of America
| | - Shiyu Wang
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Zhaohui Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Xiaoying Shen
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - LaTonya D. Williams
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Nathan Eisel
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Tiffany Peters
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Lu Zhang
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - William Kilembe
- Center for Family Health Research in Zambia (CFHRZ), Lusaka, Zambia
| | | | - Georgia D. Tomaras
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Steven E. Bosinger
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Rama R. Amara
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics Group, Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Cynthia A. Derdeyn
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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8
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Corry J, Kettenburg G, Upadhyay AA, Wallace M, Marti MM, Wonderlich ER, Bissel SJ, Goss K, Sturgeon TJ, Watkins SC, Reed DS, Bosinger SE, Barratt-Boyes SM. Infiltration of inflammatory macrophages and neutrophils and widespread pyroptosis in lung drive influenza lethality in nonhuman primates. PLoS Pathog 2022; 18:e1010395. [PMID: 35271686 PMCID: PMC8939778 DOI: 10.1371/journal.ppat.1010395] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/22/2022] [Accepted: 02/24/2022] [Indexed: 01/04/2023] Open
Abstract
Severe influenza kills tens of thousands of individuals each year, yet the mechanisms driving lethality in humans are poorly understood. Here we used a unique translational model of lethal H5N1 influenza in cynomolgus macaques that utilizes inhalation of small-particle virus aerosols to define mechanisms driving lethal disease. RNA sequencing of lung tissue revealed an intense interferon response within two days of infection that resulted in widespread expression of interferon-stimulated genes, including inflammatory cytokines and chemokines. Macaques with lethal disease had rapid and profound loss of alveolar macrophages (AMs) and infiltration of activated CCR2+ CX3CR1+ interstitial macrophages (IMs) and neutrophils into lungs. Parallel changes of AMs and neutrophils in bronchoalveolar lavage (BAL) correlated with virus load when compared to macaques with mild influenza. Both AMs and IMs in lethal influenza were M1-type inflammatory macrophages which expressed neutrophil chemotactic factors, while neutrophils expressed genes associated with activation and generation of neutrophil extracellular traps (NETs). NETs were prominent in lung and were found in alveolar spaces as well as lung parenchyma. Genes associated with pyroptosis but not apoptosis were increased in lung, and activated inflammatory caspases, IL-1β and cleaved gasdermin D (GSDMD) were present in bronchoalveolar lavage fluid and lung homogenates. Cleaved GSDMD was expressed by lung macrophages and alveolar epithelial cells which were present in large numbers in alveolar spaces, consistent with loss of epithelial integrity. Cleaved GSDMD colocalized with viral NP-expressing cells in alveoli, reflecting pyroptosis of infected cells. These novel findings reveal that a potent interferon and inflammatory cascade in lung associated with infiltration of inflammatory macrophages and neutrophils, elaboration of NETs and cell death by pyroptosis mediates lethal H5N1 influenza in nonhuman primates, and by extension humans. These innate pathways represent promising therapeutic targets to prevent severe influenza and potentially other primary viral pneumonias in humans. Influenza can cause acute lung injury and death, but the mechanisms resulting in lethal influenza in humans are not well understood. We used a novel model of lethal influenza in nonhuman primates caused by aerosol infection with highly pathogenic avian influenza virus that closely resembles human disease to define how the virus causes severe pneumonia. We found that a potent innate immune response starting with high-level production of interferons and inflammatory factors in the lung drives severe disease. Inflammatory cells including macrophages and neutrophils were recruited into lung because of this early response, which in turn led to release of neutrophil extracellular traps that blocked lung alveoli. In addition, a particularly inflammatory form of cell death known as pyroptosis occurred in lungs during lethal influenza. These new findings show that an intense interferon response leading to an inflammatory cascade of macrophages and neutrophils, release of neutrophil extracellular traps, and cell death by pyroptosis is responsible for acute lung injury in lethal influenza. These innate pathways could be targeted by drugs to prevent lung injury in critically ill influenza patients.
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Affiliation(s)
- Jacqueline Corry
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (JC); (SMBB)
| | - Gwenddolen Kettenburg
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Amit A. Upadhyay
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Megan Wallace
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Michelle M. Marti
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Elizabeth R. Wonderlich
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Stephanie J. Bissel
- Division of Neuropathology, Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kyndal Goss
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Timothy J. Sturgeon
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Simon C. Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Douglas S. Reed
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Steven E. Bosinger
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Simon M. Barratt-Boyes
- Department of Infectious Diseases & Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (JC); (SMBB)
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9
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Antanasijevic A, Bowman CA, Kirchdoerfer RN, Cottrell CA, Ozorowski G, Upadhyay AA, Cirelli KM, Carnathan DG, Enemuo CA, Sewall LM, Nogal B, Zhao F, Groschel B, Schief WR, Sok D, Silvestri G, Crotty S, Bosinger SE, Ward AB. From structure to sequence: Antibody discovery using cryoEM. Sci Adv 2022; 8:eabk2039. [PMID: 35044813 PMCID: PMC8769551 DOI: 10.1126/sciadv.abk2039] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/23/2021] [Indexed: 06/02/2023]
Abstract
One of the rate-limiting steps in analyzing immune responses to vaccines or infections is the isolation and characterization of monoclonal antibodies. Here, we present a hybrid structural and bioinformatic approach to directly assign the heavy and light chains, identify complementarity-determining regions, and discover sequences from cryoEM density maps of serum-derived polyclonal antibodies bound to an antigen. When combined with next-generation sequencing of immune repertoires, we were able to specifically identify clonal family members, synthesize the monoclonal antibodies, and confirm that they interact with the antigen in a manner equivalent to the corresponding polyclonal antibodies. This structure-based approach for identification of monoclonal antibodies from polyclonal sera opens new avenues for analysis of immune responses and iterative vaccine design.
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Affiliation(s)
- Aleksandar Antanasijevic
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Charles A. Bowman
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert N. Kirchdoerfer
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Christopher A. Cottrell
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amit A. Upadhyay
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30329, USA
- Yerkes Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Yerkes Nonhuman Primate Genomics Core, Emory University, Atlanta, GA 30329, USA
| | - Kimberly M. Cirelli
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Diane G. Carnathan
- Yerkes Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Yerkes Nonhuman Primate Genomics Core, Emory University, Atlanta, GA 30329, USA
| | - Chiamaka A. Enemuo
- Yerkes Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Yerkes Nonhuman Primate Genomics Core, Emory University, Atlanta, GA 30329, USA
| | - Leigh M. Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bartek Nogal
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fangzhu Zhao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative–Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bettina Groschel
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R. Schief
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Devin Sok
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- International AIDS Vaccine Initiative–Neutralizing Antibody Center (IAVI-NAC), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Guido Silvestri
- Yerkes Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Yerkes Nonhuman Primate Genomics Core, Emory University, Atlanta, GA 30329, USA
| | - Shane Crotty
- Vaccine Discovery Division, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Steven E. Bosinger
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30329, USA
- Yerkes Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Yerkes Nonhuman Primate Genomics Core, Emory University, Atlanta, GA 30329, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
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10
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Upadhyay AA, Hoang TN, Pino M, Boddapati AK, Viox EG, Lee MYH, Corry J, Strongin Z, Cowan DA, Beagle EN, Horton TR, Hamilton S, Aoued H, Harper JL, Nguyen K, Pellegrini KL, Tharp GK, Piantadosi A, Levit RD, Amara RR, Barratt-Boyes SM, Ribeiro SP, Sekaly RP, Vanderford TH, Schinazi RF, Paiardini M, Bosinger SE. TREM2+ and interstitial macrophages orchestrate airway inflammation in SARS-CoV-2 infection in rhesus macaques. bioRxiv 2021. [PMID: 34642693 PMCID: PMC8509096 DOI: 10.1101/2021.10.05.463212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The COVID-19 pandemic remains a global health crisis, yet, the immunopathological mechanisms driving the development of severe disease remain poorly defined. Here, we utilize a rhesus macaque (RM) model of SARS-CoV-2 infection to delineate perturbations in the innate immune system during acute infection using an integrated systems analysis. We found that SARS-CoV-2 initiated a rapid infiltration (two days post infection) of plasmacytoid dendritic cells into the lower airway, commensurate with IFNA production, natural killer cell activation, and induction of interferon-stimulated genes. At this early interval, we also observed a significant increase of blood CD14-CD16+ monocytes. To dissect the contribution of lung myeloid subsets to airway inflammation, we generated a novel compendium of RM-specific lung macrophage gene expression using a combination of sc-RNA-Seq data and bulk RNA-Seq of purified populations under steady state conditions. Using these tools, we generated a longitudinal sc-RNA-seq dataset of airway cells in SARS-CoV-2-infected RMs. We identified that SARS-CoV-2 infection elicited a rapid recruitment of two subsets of macrophages into the airway: a C206+MRC1-population resembling murine interstitial macrophages, and a TREM2+ population consistent with CCR2+ infiltrating monocytes, into the alveolar space. These subsets were the predominant source of inflammatory cytokines, accounting for ~75% of IL6 and TNF production, and >90% of IL10 production, whereas the contribution of CD206+MRC+ alveolar macrophages was significantly lower. Treatment of SARS-CoV-2 infected RMs with baricitinib (Olumiant ® ), a novel JAK1/2 inhibitor that recently received Emergency Use Authorization for the treatment of hospitalized COVID-19 patients, was remarkably effective in eliminating the influx of infiltrating, non-alveolar macrophages in the alveolar space, with a concomitant reduction of inflammatory cytokines. This study has delineated the major subsets of lung macrophages driving inflammatory and anti-inflammatory cytokine production within the alveolar space during SARS-CoV-2 infection. One sentence summary Multi-omic analyses of hyperacute SARS-CoV-2 infection in rhesus macaques identified two population of infiltrating macrophages, as the primary orchestrators of inflammation in the lower airway that can be successfully treated with baricitinib.
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11
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Salinas E, Boisvert M, Upadhyay AA, Bédard N, Nelson SA, Bruneau J, Derdeyn CA, Marcotrigiano J, Evans MJ, Bosinger SE, Shoukry NH, Grakoui A. Early T follicular helper cell activity accelerates hepatitis C virus-specific B cell expansion. J Clin Invest 2021; 131:140590. [PMID: 33463551 DOI: 10.1172/jci140590] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022] Open
Abstract
Early appearance of neutralizing antibodies during acute hepatitis C virus (HCV) infection is associated with spontaneous viral clearance. However, the longitudinal changes in antigen-specific memory B cell (MBCs) associated with divergent HCV infection outcomes remain undefined. We characterized longitudinal changes in E2 glycoprotein-specific MBCs from subjects who either spontaneously resolved acute HCV infection or progressed to chronic infection, using single-cell RNA-seq and functional assays. HCV-specific antibodies in plasma from chronically infected subjects recognized multiple E2 genotypes, while those from spontaneous resolvers exhibited variable cross-reactivity to heterotypic E2. E2-specific MBCs from spontaneous resolvers peaked early after infection (4-6 months), following expansion of activated circulating T follicular helper cells (cTfh) expressing interleukin 21. In contrast, E2-specific MBCs from chronically infected subjects, enriched in VH1-69, expanded during persistent infection (> 1 year), in the absence of significantly activated cTfh expansion. Early E2-specific MBCs from spontaneous resolvers produced monoclonal antibodies (mAbs) with fewer somatic hypermutations and lower E2 binding but similar neutralization as mAbs from late E2-specific MBCs of chronically infected subjects. These findings indicate that early cTfh activity accelerates expansion of E2-specific MBCs during acute infection, which might contribute to spontaneous clearance of HCV.
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Affiliation(s)
- Eduardo Salinas
- Division of Infectious diseases, Emory Vaccine Center, Division of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.,Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
| | - Maude Boisvert
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Amit A Upadhyay
- Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
| | - Nathalie Bédard
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Sydney A Nelson
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, Georgia, USA
| | - Julie Bruneau
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Département de Médecine Familiale et de Médecine D'Urgence, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Cynthia A Derdeyn
- Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
| | - Joseph Marcotrigiano
- Structural Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Matthew J Evans
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Steven E Bosinger
- Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA.,Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, Georgia, USA
| | - Naglaa H Shoukry
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Arash Grakoui
- Division of Infectious diseases, Emory Vaccine Center, Division of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.,Yerkes National Primate Research Center, Emory Vaccine Center, Atlanta, Georgia, USA
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12
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Lee MYH, Upadhyay AA, Walum H, Chan CN, Dawoud RA, Grech C, Harper JL, Karunakaran KA, Nelson SA, Mahar EA, Goss KL, Carnathan DG, Cervasi B, Gill K, Tharp GK, Wonderlich ER, Velu V, Barratt-Boyes SM, Paiardini M, Silvestri G, Estes JD, Bosinger SE. Tissue-specific transcriptional profiling of plasmacytoid dendritic cells reveals a hyperactivated state in chronic SIV infection. PLoS Pathog 2021; 17:e1009674. [PMID: 34181694 PMCID: PMC8270445 DOI: 10.1371/journal.ppat.1009674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 07/09/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022] Open
Abstract
HIV associated immune activation (IA) is associated with increased morbidity in people living with HIV (PLWH) on antiretroviral therapy, and remains a barrier for strategies aimed at reducing the HIV reservoir. The underlying mechanisms of IA have not been definitively elucidated, however, persistent production of Type I IFNs and expression of ISGs is considered to be one of the primary factors. Plasmacytoid DCs (pDCs) are a major producer of Type I IFN during viral infections, and are highly immunomodulatory in acute HIV and SIV infection, however their role in chronic HIV/SIV infection has not been firmly established. Here, we performed a detailed transcriptomic characterization of pDCs in chronic SIV infection in rhesus macaques, and in sooty mangabeys, a natural host non-human primate (NHP) species that undergoes non-pathogenic SIV infection. We also investigated the immunostimulatory capacity of lymph node homing pDCs in chronic SIV infection by contrasting gene expression of pDCs isolated from lymph nodes with those from blood. We observed that pDCs in LNs, but not blood, produced high levels of IFNα transcripts, and upregulated gene expression programs consistent with T cell activation and exhaustion. We apply a novel strategy to catalogue uncharacterized surface molecules on pDCs, and identified the lymphoid exhaustion markers TIGIT and LAIR1 as highly expressed in SIV infection. pDCs from SIV-infected sooty mangabeys lacked the activation profile of ISG signatures observed in infected macaques. These data demonstrate that pDCs are a primary producer of Type I IFN in chronic SIV infection. Further, this study demonstrated that pDCs trafficking to LNs persist in a highly activated state well into chronic infection. Collectively, these data identify pDCs as a highly immunomodulatory cell population in chronic SIV infection, and a putative therapeutic target to reduce immune activation.
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Affiliation(s)
- Michelle Y.-H. Lee
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Amit A. Upadhyay
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Hasse Walum
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Chi N. Chan
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Reem A. Dawoud
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Christine Grech
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Justin L. Harper
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Kirti A. Karunakaran
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Sydney A. Nelson
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Ernestine A. Mahar
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Kyndal L. Goss
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Diane G. Carnathan
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | - Barbara Cervasi
- Flow Cytometry Core, Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Kiran Gill
- Flow Cytometry Core, Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Gregory K. Tharp
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
| | | | - Vijayakumar Velu
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Simon M. Barratt-Boyes
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Mirko Paiardini
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Guido Silvestri
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, United States of America
| | - Steven E. Bosinger
- Division of Microbiology & Immunology, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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13
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Harper J, Huot N, Micci L, Tharp G, King C, Rascle P, Shenvi N, Wang H, Galardi C, Upadhyay AA, Villinger F, Lifson J, Silvestri G, Easley K, Jacquelin B, Bosinger S, Müller-Trutwin M, Paiardini M. IL-21 and IFNα therapy rescues terminally differentiated NK cells and limits SIV reservoir in ART-treated macaques. Nat Commun 2021; 12:2866. [PMID: 34001890 PMCID: PMC8129202 DOI: 10.1038/s41467-021-23189-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Unlike HIV infection, which progresses to AIDS absent suppressive anti-retroviral therapy, nonpathogenic infections in natural hosts, such African green monkeys, are characterized by a lack of gut microbial translocation and robust secondary lymphoid natural killer cell responses resulting in an absence of chronic inflammation and limited SIV dissemination in lymph node B-cell follicles. Here we report, using the pathogenic model of antiretroviral therapy-treated, SIV-infected rhesus macaques that sequential interleukin-21 and interferon alpha therapy generate terminally differentiated blood natural killer cells (NKG2a/clowCD16+) with potent human leukocyte antigen-E-restricted activity in response to SIV envelope peptides. This is in contrast to control macaques, where less differentiated, interferon gamma-producing natural killer cells predominate. The frequency and activity of terminally differentiated NKG2a/clowCD16+ natural killer cells correlates with a reduction of replication-competent SIV in lymph node during antiretroviral therapy and time to viral rebound following analytical treatment interruption. These data demonstrate that African green monkey-like natural killer cell differentiation profiles can be rescued in rhesus macaques to promote viral clearance in tissues.
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Affiliation(s)
- Justin Harper
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Nicolas Huot
- Institut Pasteur, Unité HIV, Inflammation et Persistance, Paris, France
| | - Luca Micci
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gregory Tharp
- Nonhuman Primate Genomics Core, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Colin King
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Philippe Rascle
- Institut Pasteur, Unité HIV, Inflammation et Persistance, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Neeta Shenvi
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Hong Wang
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Cristin Galardi
- UNC HIV Cure Center and Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,HIV Discovery, ViiV Healthcare, Research Triangle Park, NC, USA
| | - Amit A Upadhyay
- Nonhuman Primate Genomics Core, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Francois Villinger
- Department of Biology, New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, USA
| | - Jeffrey Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Kirk Easley
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Steven Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Nonhuman Primate Genomics Core, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA. .,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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14
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Routhu NK, Cheedarla N, Gangadhara S, Bollimpelli VS, Boddapati AK, Shiferaw A, Rahman SA, Sahoo A, Edara VV, Lai L, Floyd K, Wang S, Fischinger S, Atyeo C, Shin SA, Gumber S, Kirejczyk S, Cohen J, Jean SM, Wood JS, Connor-Stroud F, Stammen RL, Upadhyay AA, Pellegrini K, Montefiori D, Shi PY, Menachery VD, Alter G, Vanderford TH, Bosinger SE, Suthar MS, Amara RR. A modified vaccinia Ankara vector-based vaccine protects macaques from SARS-CoV-2 infection, immune pathology, and dysfunction in the lungs. Immunity 2021; 54:542-556.e9. [PMID: 33631118 PMCID: PMC7859620 DOI: 10.1016/j.immuni.2021.02.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/04/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023]
Abstract
A combination of vaccination approaches will likely be necessary to fully control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Here, we show that modified vaccinia Ankara (MVA) vectors expressing membrane-anchored pre-fusion stabilized spike (MVA/S) but not secreted S1 induced strong neutralizing antibody responses against SARS-CoV-2 in mice. In macaques, the MVA/S vaccination induced strong neutralizing antibodies and CD8+ T cell responses, and conferred protection from SARS-CoV-2 infection and virus replication in the lungs as early as day 2 following intranasal and intratracheal challenge. Single-cell RNA sequencing analysis of lung cells on day 4 after infection revealed that MVA/S vaccination also protected macaques from infection-induced inflammation and B cell abnormalities and lowered induction of interferon-stimulated genes. These results demonstrate that MVA/S vaccination induces neutralizing antibodies and CD8+ T cells in the blood and lungs and is a potential vaccine candidate for SARS-CoV-2.
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Affiliation(s)
- Nanda Kishore Routhu
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sailaja Gangadhara
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Venkata Satish Bollimpelli
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Arun K. Boddapati
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Ayalnesh Shiferaw
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sheikh Abdul Rahman
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Anusmita Sahoo
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Venkata Viswanadh Edara
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lilin Lai
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Katharine Floyd
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shelly Wang
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Sally A. Shin
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Sanjeev Gumber
- Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Shannon Kirejczyk
- Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Joyce Cohen
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Sherrie M. Jean
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Jennifer S. Wood
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Fawn Connor-Stroud
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Rachelle L. Stammen
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Amit A. Upadhyay
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Kathryn Pellegrini
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - David Montefiori
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Thomas H. Vanderford
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Steven E. Bosinger
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pathology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Mehul S. Suthar
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rama Rao Amara
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Microbiology and Immunology, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA,Corresponding author
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15
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Muttineni R, Kammili N, Bingi TC, Rao M. R, Putty K, Dholaniya PS, Puli RK, Pakalapati S, S. S, K. S, Doodipala MR, Upadhyay AA, Bosinger SE, Amara RR, Kondapi AK. Clinical and whole genome characterization of SARS-CoV-2 in India. PLoS One 2021; 16:e0246173. [PMID: 33529260 PMCID: PMC7853523 DOI: 10.1371/journal.pone.0246173] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
We report clinical profile of hundred and nine patients with SARS CoV-2 infection, and whole genome sequences (WGS) of seven virus isolates from the first reported cases in India, with various international travel histories. Comorbidities such as diabetes, hypertension, and cardiovascular disease were frequently associated with severity of the disease. WBC and neutrophil counts showed an increase, while lymphocyte counts decreased in patients with severe infection suggesting a possible neutrophil mediated organ damage, while immune activity may be diminished with decrease in lymphocytes leading to disease severity. Increase in SGOT, SGPT and blood urea suggests the functional deficiencies of liver, heart, and kidney in patients who succumbed to the disease when compared to the group of recovered patients. The WGS analysis showed that these isolates were classified into two clades: I/A3i, and A2a (four according to GISAID: O, L, GR, and GH). Further, WGS phylogeny and travel history together indicate possible transmission from Middle East and Europe. Three S protein variants: Wuhan reference, D614G, and Y28H were identified predicted to possess different binding affinities to host ACE2.
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Affiliation(s)
| | - Nagamani Kammili
- Department of Microbiology, Gandhi Medical College and Hospital, Secunderabad, India
| | - Thrilok Chander Bingi
- Department of General Medicine, Gandhi Medical College and Hospital, Secunderabad, India
| | - Raja Rao M.
- Department of General Medicine, Gandhi Medical College and Hospital, Secunderabad, India
| | - Kalyani Putty
- Department of Veterinary Biotechnology, College of Veterinary Science, Rajendranagar, PVNR Telangana Veterinary University, Hyderabad, India
| | - Pankaj Singh Dholaniya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Ravi Kumar Puli
- Telangana State Council for Science and Technology, Government of Telangana, Hyderabad, India
| | - Sunitha Pakalapati
- Department of Microbiology, Gandhi Medical College and Hospital, Secunderabad, India
| | - Saritha S.
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Shekar K.
- Virus Research Laboratory, Department of Zoology, Osmania University, Hyderabad, India
| | | | - Amit A. Upadhyay
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America
| | - Steven E. Bosinger
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America
| | - Rama R. Amara
- Department of Microbiology and Immunology, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States of America
| | - Anand K. Kondapi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
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16
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Hoang TN, Pino M, Boddapati AK, Viox EG, Starke CE, Upadhyay AA, Gumber S, Nekorchuk M, Busman-Sahay K, Strongin Z, Harper JL, Tharp GK, Pellegrini KL, Kirejczyk S, Zandi K, Tao S, Horton TR, Beagle EN, Mahar EA, Lee MY, Cohen J, Jean SM, Wood JS, Connor-Stroud F, Stammen RL, Delmas OM, Wang S, Cooney KA, Sayegh MN, Wang L, Filev PD, Weiskopf D, Silvestri G, Waggoner J, Piantadosi A, Kasturi SP, Al-Shakhshir H, Ribeiro SP, Sekaly RP, Levit RD, Estes JD, Vanderford TH, Schinazi RF, Bosinger SE, Paiardini M. Baricitinib treatment resolves lower-airway macrophage inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques. Cell 2021; 184:460-475.e21. [PMID: 33278358 PMCID: PMC7654323 DOI: 10.1016/j.cell.2020.11.007] [Citation(s) in RCA: 139] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/08/2020] [Accepted: 11/04/2020] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2-induced hypercytokinemia and inflammation are critically associated with COVID-19 severity. Baricitinib, a clinically approved JAK1/JAK2 inhibitor, is currently being investigated in COVID-19 clinical trials. Here, we investigated the immunologic and virologic efficacy of baricitinib in a rhesus macaque model of SARS-CoV-2 infection. Viral shedding measured from nasal and throat swabs, bronchoalveolar lavages, and tissues was not reduced with baricitinib. Type I interferon (IFN) antiviral responses and SARS-CoV-2-specific T cell responses remained similar between the two groups. Animals treated with baricitinib showed reduced inflammation, decreased lung infiltration of inflammatory cells, reduced NETosis activity, and more limited lung pathology. Importantly, baricitinib-treated animals had a rapid and remarkably potent suppression of lung macrophage production of cytokines and chemokines responsible for inflammation and neutrophil recruitment. These data support a beneficial role for, and elucidate the immunological mechanisms underlying, the use of baricitinib as a frontline treatment for inflammation induced by SARS-CoV-2 infection.
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Affiliation(s)
- Timothy N. Hoang
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Maria Pino
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Arun K. Boddapati
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Elise G. Viox
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Carly E. Starke
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Amit A. Upadhyay
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Sanjeev Gumber
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA,Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Michael Nekorchuk
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Zachary Strongin
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Justin L. Harper
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Gregory K. Tharp
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Kathryn L. Pellegrini
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Shannon Kirejczyk
- Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Keivan Zandi
- Center for AIDS Research, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sijia Tao
- Center for AIDS Research, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Tristan R. Horton
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Elizabeth N. Beagle
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Ernestine A. Mahar
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Michelle Y.H. Lee
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Joyce Cohen
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Sherrie M. Jean
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jennifer S. Wood
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Fawn Connor-Stroud
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Rachelle L. Stammen
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Olivia M. Delmas
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Shelly Wang
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Kimberly A. Cooney
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Michael N. Sayegh
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Lanfang Wang
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Peter D. Filev
- Department of Radiology and Imaging Sciences, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jesse Waggoner
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA,Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Sudhir P. Kasturi
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Hilmi Al-Shakhshir
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Susan P. Ribeiro
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Rafick P. Sekaly
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Rebecca D. Levit
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA,Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Thomas H. Vanderford
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Raymond F. Schinazi
- Center for AIDS Research, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30322, USA,Corresponding author
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA,Corresponding author
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA,Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA,Corresponding author
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17
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Havenar-Daughton C, Carnathan DG, Boopathy AV, Upadhyay AA, Murrell B, Reiss SM, Enemuo CA, Gebru EH, Choe Y, Dhadvai P, Viviano F, Kaushik K, Bhiman JN, Briney B, Burton DR, Bosinger SE, Schief WR, Irvine DJ, Silvestri G, Crotty S. Rapid Germinal Center and Antibody Responses in Non-human Primates after a Single Nanoparticle Vaccine Immunization. Cell Rep 2020; 29:1756-1766.e8. [PMID: 31722194 PMCID: PMC6905039 DOI: 10.1016/j.celrep.2019.10.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/06/2019] [Accepted: 10/02/2019] [Indexed: 11/25/2022] Open
Abstract
The first immunization in a protein prime-boost vaccination is likely to
be critical for how the immune response unfolds. Using fine needle aspirates
(FNAs) of draining lymph nodes (LNs), we tracked the kinetics of the primary
immune response in rhesus monkeys immunized intramuscularly (IM) or
subcutaneously (s.c.) with an eOD-GT8 60-mer nanoparticle immunogen to
facilitate clinical trial design. Significant numbers of germinal center B
(BGC) cells and antigen-specific CD4 T cells were detectable in
the draining LN as early as 7 days post-immunization and peaked near day 21.
Strikingly, s.c. immunization results in 10-fold larger antigen-specific
BGC cell responses compared to IM immunization. Lymphatic
drainage studies revealed that s.c. immunization resulted in faster and more
consistent axillary LN drainage than IM immunization. These data indicate robust
antigen-specific germinal center responses can occur rapidly to a single
immunization with a nanoparticle immunogen and vaccine drainage substantially
impacts immune responses in local LNs. The first immunization of protein prime-boost vaccination is likely
critical but has been understudied in large animals and humans. Havenar-Daughton
et al. use lymph node fine needle aspirates to determine primary germinal center
response kinetics in rhesus monkeys immunized intramuscularly or subcutaneously
with a clinical trial candidate nanoparticle immunogen.
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Affiliation(s)
- Colin Havenar-Daughton
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Diane G Carnathan
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Archana V Boopathy
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amit A Upadhyay
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Samantha M Reiss
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chiamaka A Enemuo
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Etse H Gebru
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Yury Choe
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Pallavi Dhadvai
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Federico Viviano
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Kirti Kaushik
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jinal N Bhiman
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - Bryan Briney
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - Steven E Bosinger
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - William R Schief
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - Darrell J Irvine
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - Guido Silvestri
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA.
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA 92037, USA; Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA.
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18
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Hoang TN, Pino M, Boddapati AK, Viox EG, Starke CE, Upadhyay AA, Gumber S, Busman-Sahay K, Strongin Z, Harper JL, Tharp GK, Pellegrini KL, Kirejczyk S, Zandi K, Tao S, Horton TR, Beagle EN, Mahar EA, Lee MY, Cohen J, Jean SM, Wood JS, Connor-Stroud F, Stammen RL, Delmas OM, Wang S, Cooney KA, Sayegh MN, Wang L, Weiskopf D, Filev PD, Waggoner J, Piantadosi A, Kasturi SP, Al-Shakhshir H, Ribeiro SP, Sekaly RP, Levit RD, Estes JD, Vanderford TH, Schinazi RF, Bosinger SE, Paiardini M. Baricitinib treatment resolves lower airway inflammation and neutrophil recruitment in SARS-CoV-2-infected rhesus macaques. bioRxiv 2020:2020.09.16.300277. [PMID: 32995780 PMCID: PMC7523106 DOI: 10.1101/2020.09.16.300277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Effective therapeutics aimed at mitigating COVID-19 symptoms are urgently needed. SARS-CoV-2 induced hypercytokinemia and systemic inflammation are associated with disease severity. Baricitinib, a clinically approved JAK1/2 inhibitor with potent anti-inflammatory properties is currently being investigated in COVID-19 human clinical trials. Recent reports suggest that baricitinib may also have antiviral activity in limiting viral endocytosis. Here, we investigated the immunologic and virologic efficacy of baricitinib in a rhesus macaque model of SARS-CoV-2 infection. Viral shedding measured from nasal and throat swabs, bronchoalveolar lavages and tissues was not reduced with baricitinib. Type I IFN antiviral responses and SARS-CoV-2 specific T cell responses remained similar between the two groups. Importantly, however, animals treated with baricitinib showed reduced immune activation, decreased infiltration of neutrophils into the lung, reduced NETosis activity, and more limited lung pathology. Moreover, baricitinib treated animals had a rapid and remarkably potent suppression of alveolar macrophage derived production of cytokines and chemokines responsible for inflammation and neutrophil recruitment. These data support a beneficial role for, and elucidate the immunological mechanisms underlying, the use of baricitinib as a frontline treatment for severe inflammation induced by SARS-CoV-2 infection.
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Affiliation(s)
- Timothy N Hoang
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Maria Pino
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Arun K Boddapati
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Elise G Viox
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Carly E Starke
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Amit A Upadhyay
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Sanjeev Gumber
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
- Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Zachary Strongin
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Justin L Harper
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Gregory K Tharp
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Kathryn L Pellegrini
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Shannon Kirejczyk
- Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Keivan Zandi
- Center for AIDS Research, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Sijia Tao
- Center for AIDS Research, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Tristan R Horton
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Elizabeth N Beagle
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Ernestine A Mahar
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Michelle Yh Lee
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Joyce Cohen
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Sherrie M Jean
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Jennifer S Wood
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Fawn Connor-Stroud
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Rachelle L Stammen
- Division of Animal Resources, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Olivia M Delmas
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Shelly Wang
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Kimberly A Cooney
- Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Michael N Sayegh
- Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Lanfang Wang
- Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Peter D Filev
- Department of Radiology and Imaging Sciences, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Jesse Waggoner
- Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Anne Piantadosi
- Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Sudhir P Kasturi
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Hilmi Al-Shakhshir
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Susan P Ribeiro
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Rafick P Sekaly
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Rebecca D Levit
- Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
- Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Thomas H Vanderford
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Raymond F Schinazi
- Center for AIDS Research, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
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19
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Arunachalam PS, Wimmers F, Mok CKP, Perera RAPM, Scott M, Hagan T, Sigal N, Feng Y, Bristow L, Tak-Yin Tsang O, Wagh D, Coller J, Pellegrini KL, Kazmin D, Alaaeddine G, Leung WS, Chan JMC, Chik TSH, Choi CYC, Huerta C, Paine McCullough M, Lv H, Anderson E, Edupuganti S, Upadhyay AA, Bosinger SE, Maecker HT, Khatri P, Rouphael N, Peiris M, Pulendran B. Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans. Science 2020; 369:1210-1220. [PMID: 32788292 DOI: 10.1126/science.abc6261] [Citation(s) in RCA: 761] [Impact Index Per Article: 190.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/10/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023]
Abstract
Coronavirus disease 2019 (COVID-19) represents a global crisis, yet major knowledge gaps remain about human immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We analyzed immune responses in 76 COVID-19 patients and 69 healthy individuals from Hong Kong and Atlanta, Georgia, United States. In the peripheral blood mononuclear cells (PBMCs) of COVID-19 patients, we observed reduced expression of human leukocyte antigen class DR (HLA-DR) and proinflammatory cytokines by myeloid cells as well as impaired mammalian target of rapamycin (mTOR) signaling and interferon-α (IFN-α) production by plasmacytoid dendritic cells. By contrast, we detected enhanced plasma levels of inflammatory mediators-including EN-RAGE, TNFSF14, and oncostatin M-which correlated with disease severity and increased bacterial products in plasma. Single-cell transcriptomics revealed a lack of type I IFNs, reduced HLA-DR in the myeloid cells of patients with severe COVID-19, and transient expression of IFN-stimulated genes. This was consistent with bulk PBMC transcriptomics and transient, low IFN-α levels in plasma during infection. These results reveal mechanisms and potential therapeutic targets for COVID-19.
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Affiliation(s)
- Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chris Ka Pun Mok
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong
| | - Ranawaka A P M Perera
- Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, HKU, Hong Kong
| | - Madeleine Scott
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.,Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas Hagan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Natalia Sigal
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurel Bristow
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Owen Tak-Yin Tsang
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Dhananjay Wagh
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John Coller
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kathryn L Pellegrini
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Dmitri Kazmin
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ghina Alaaeddine
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Wai Shing Leung
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Jacky Man Chun Chan
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Thomas Shiu Hong Chik
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Chris Yau Chung Choi
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Christopher Huerta
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Michele Paine McCullough
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong
| | - Evan Anderson
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Srilatha Edupuganti
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Amit A Upadhyay
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Steve E Bosinger
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30329, USA
| | - Holden Terry Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.,Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nadine Rouphael
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong.,Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, HKU, Hong Kong
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA. .,Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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20
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Nixon CC, Mavigner M, Sampey GC, Brooks AD, Spagnuolo RA, Irlbeck DM, Mattingly C, Ho PT, Schoof N, Cammon CG, Tharp GK, Kanke M, Wang Z, Cleary RA, Upadhyay AA, De C, Wills SR, Falcinelli SD, Galardi C, Walum H, Schramm NJ, Deutsch J, Lifson JD, Fennessey CM, Keele BF, Jean S, Maguire S, Liao B, Browne EP, Ferris RG, Brehm JH, Favre D, Vanderford TH, Bosinger SE, Jones CD, Routy JP, Archin NM, Margolis DM, Wahl A, Dunham RM, Silvestri G, Chahroudi A, Garcia JV. Systemic HIV and SIV latency reversal via non-canonical NF-κB signalling in vivo. Nature 2020; 578:160-165. [PMID: 31969707 PMCID: PMC7111210 DOI: 10.1038/s41586-020-1951-3] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 12/16/2019] [Indexed: 01/27/2023]
Abstract
Long-lasting, latently infected resting CD4+ T cells are the greatest obstacle to obtaining a cure for HIV infection, as these cells can persist despite decades of treatment with antiretroviral therapy (ART). Estimates indicate that more than 70 years of continuous, fully suppressive ART are needed to eliminate the HIV reservoir1. Alternatively, induction of HIV from its latent state could accelerate the decrease in the reservoir, thus reducing the time to eradication. Previous attempts to reactivate latent HIV in preclinical animal models and in clinical trials have measured HIV induction in the peripheral blood with minimal focus on tissue reservoirs and have had limited effect2-9. Here we show that activation of the non-canonical NF-κB signalling pathway by AZD5582 results in the induction of HIV and SIV RNA expression in the blood and tissues of ART-suppressed bone-marrow-liver-thymus (BLT) humanized mice and rhesus macaques infected with HIV and SIV, respectively. Analysis of resting CD4+ T cells from tissues after AZD5582 treatment revealed increased SIV RNA expression in the lymph nodes of macaques and robust induction of HIV in almost all tissues analysed in humanized mice, including the lymph nodes, thymus, bone marrow, liver and lung. This promising approach to latency reversal-in combination with appropriate tools for systemic clearance of persistent HIV infection-greatly increases opportunities for HIV eradication.
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Affiliation(s)
- Christopher C Nixon
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maud Mavigner
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Gavin C Sampey
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Qura Therapeutics, Chapel Hill, NC, USA
| | - Alyssa D Brooks
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Rae Ann Spagnuolo
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David M Irlbeck
- Qura Therapeutics, Chapel Hill, NC, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, NC, USA
| | - Cameron Mattingly
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Phong T Ho
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nils Schoof
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Corinne G Cammon
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Greg K Tharp
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Matthew Kanke
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhang Wang
- GlaxoSmithKline Research and Development, Collegeville, PA, USA
| | - Rachel A Cleary
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amit A Upadhyay
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Chandrav De
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Saintedym R Wills
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Qura Therapeutics, Chapel Hill, NC, USA
| | - Shane D Falcinelli
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cristin Galardi
- Qura Therapeutics, Chapel Hill, NC, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, NC, USA
| | - Hasse Walum
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Nathaniel J Schramm
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Christine M Fennessey
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sherrie Jean
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Sean Maguire
- GlaxoSmithKline Research and Development, Collegeville, PA, USA
| | - Baolin Liao
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Edward P Browne
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Robert G Ferris
- Qura Therapeutics, Chapel Hill, NC, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, NC, USA
| | - Jessica H Brehm
- Qura Therapeutics, Chapel Hill, NC, USA
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, NC, USA
| | - David Favre
- Qura Therapeutics, Chapel Hill, NC, USA
- GlaxoSmithKline Research and Development, Collegeville, PA, USA
| | | | - Steven E Bosinger
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jean-Pierre Routy
- Chronic Viral Infection Service, McGill University Health Centre, Montreal, Quebec, Canada
- Division of Hematology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Nancie M Archin
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David M Margolis
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Qura Therapeutics, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Angela Wahl
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richard M Dunham
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Qura Therapeutics, Chapel Hill, NC, USA.
- HIV Drug Discovery, ViiV Healthcare, Research Triangle Park, NC, USA.
| | - Guido Silvestri
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA.
- Emory + Children's Center for Childhood Infections and Vaccines, Atlanta, GA, USA.
| | - J Victor Garcia
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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21
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Cirelli KM, Carnathan DG, Nogal B, Martin JT, Rodriguez OL, Upadhyay AA, Enemuo CA, Gebru EH, Choe Y, Viviano F, Nakao C, Pauthner MG, Reiss S, Cottrell CA, Smith ML, Bastidas R, Gibson W, Wolabaugh AN, Melo MB, Cossette B, Kumar V, Patel NB, Tokatlian T, Menis S, Kulp DW, Burton DR, Murrell B, Schief WR, Bosinger SE, Ward AB, Watson CT, Silvestri G, Irvine DJ, Crotty S. Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance. Cell 2020; 180:206. [PMID: 31923396 PMCID: PMC7009795 DOI: 10.1016/j.cell.2019.12.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Havenar-Daughton C, Sarkar A, Kulp DW, Toy L, Hu X, Deresa I, Kalyuzhniy O, Kaushik K, Upadhyay AA, Menis S, Landais E, Cao L, Diedrich JK, Kumar S, Schiffner T, Reiss SM, Seumois G, Yates JR, Paulson JC, Bosinger SE, Wilson IA, Schief WR, Crotty S. The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen. Sci Transl Med 2019; 10:10/448/eaat0381. [PMID: 29973404 DOI: 10.1126/scitranslmed.aat0381] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/30/2018] [Indexed: 12/12/2022]
Abstract
Traditional vaccine development to prevent some of the worst current pandemic diseases has been unsuccessful so far. Germline-targeting immunogens have potential to prime protective antibodies (Abs) via more targeted immune responses. Success of germline-targeting vaccines in humans will depend on the composition of the human naive B cell repertoire, including the frequencies and affinities of epitope-specific B cells. However, the human naive B cell repertoire remains largely undefined. Assessment of antigen-specific human naive B cells among hundreds of millions of B cells from multiple donors may be used as pre-phase 1 ex vivo human testing to potentially forecast B cell and Ab responses to new vaccine designs. VRC01 is an HIV broadly neutralizing Ab (bnAb) against the envelope CD4-binding site (CD4bs). We characterized naive human B cells recognizing eOD-GT8, a germline-targeting HIV-1 vaccine candidate immunogen designed to prime VRC01-class Abs. Several distinct subclasses of VRC01-class naive B cells were identified, sharing sequence characteristics with inferred precursors of known bnAbs VRC01, VRC23, PCIN63, and N6. Multiple naive B cell clones exactly matched mature VRC01-class bnAb L-CDR3 sequences. Non-VRC01-class B cells were also characterized, revealing recurrent public light chain sequences. Unexpectedly, we also identified naive B cells related to the IOMA-class CD4bs bnAb. These different subclasses within the human repertoire had strong initial affinities (KD) to the immunogen, up to 13 nM, and represent encouraging indications that multiple independent pathways may exist for vaccine-elicited VRC01-class bnAb development in most individuals. The frequencies of these distinct eOD-GT8 B cell specificities give insights into antigen-specific compositional features of the human naive B cell repertoire and provide actionable information for vaccine design and advancement.
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Affiliation(s)
- Colin Havenar-Daughton
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. .,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Anita Sarkar
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.,Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Laura Toy
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhen Hu
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Isaiah Deresa
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kirti Kaushik
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amit A Upadhyay
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Sergey Menis
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elise Landais
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Liwei Cao
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sonu Kumar
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Torben Schiffner
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Samantha M Reiss
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Grégory Seumois
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James C Paulson
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven E Bosinger
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Ian A Wilson
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William R Schief
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. .,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA 92093, USA
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23
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Cirelli KM, Carnathan DG, Nogal B, Martin JT, Rodriguez OL, Upadhyay AA, Enemuo CA, Gebru EH, Choe Y, Viviano F, Nakao C, Pauthner MG, Reiss S, Cottrell CA, Smith ML, Bastidas R, Gibson W, Wolabaugh AN, Melo MB, Cossette B, Kumar V, Patel NB, Tokatlian T, Menis S, Kulp DW, Burton DR, Murrell B, Schief WR, Bosinger SE, Ward AB, Watson CT, Silvestri G, Irvine DJ, Crotty S. Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance. Cell 2019; 177:1153-1171.e28. [PMID: 31080066 PMCID: PMC6619430 DOI: 10.1016/j.cell.2019.04.012] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/26/2019] [Accepted: 04/05/2019] [Indexed: 12/14/2022]
Abstract
Conventional immunization strategies will likely be insufficient for the development of a broadly neutralizing antibody (bnAb) vaccine for HIV or other difficult pathogens because of the immunological hurdles posed, including B cell immunodominance and germinal center (GC) quantity and quality. We found that two independent methods of slow delivery immunization of rhesus monkeys (RMs) resulted in more robust T follicular helper (TFH) cell responses and GC B cells with improved Env-binding, tracked by longitudinal fine needle aspirates. Improved GCs correlated with the development of >20-fold higher titers of autologous nAbs. Using a new RM genomic immunoglobulin locus reference, we identified differential IgV gene use between immunization modalities. Ab mapping demonstrated targeting of immunodominant non-neutralizing epitopes by conventional bolus-immunized animals, whereas slow delivery-immunized animals targeted a more diverse set of epitopes. Thus, alternative immunization strategies can enhance nAb development by altering GCs and modulating the immunodominance of non-neutralizing epitopes.
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Affiliation(s)
- Kimberly M Cirelli
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Diane G Carnathan
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bartek Nogal
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jacob T Martin
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Oscar L Rodriguez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amit A Upadhyay
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA
| | - Chiamaka A Enemuo
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Etse H Gebru
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yury Choe
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Federico Viviano
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Catherine Nakao
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Matthias G Pauthner
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Samantha Reiss
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Christopher A Cottrell
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raiza Bastidas
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - William Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Amber N Wolabaugh
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA
| | - Mariane B Melo
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Benjamin Cossette
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Venkatesh Kumar
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Nirav B Patel
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Talar Tokatlian
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sergey Menis
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Dennis R Burton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - William R Schief
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Steven E Bosinger
- Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Andrew B Ward
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Guido Silvestri
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Darrell J Irvine
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA; Departments of Biological Engineering and Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (Scripps CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
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24
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Upadhyay AA, Kauffman RC, Wolabaugh AN, Cho A, Patel NB, Reiss SM, Havenar-Daughton C, Dawoud RA, Tharp GK, Sanz I, Pulendran B, Crotty S, Lee FEH, Wrammert J, Bosinger SE. BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data. Genome Med 2018; 10:20. [PMID: 29558968 PMCID: PMC5859752 DOI: 10.1186/s13073-018-0528-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/23/2018] [Indexed: 01/21/2023] Open
Abstract
B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for clonotype identification in human and rhesus macaque influenza vaccine and simian immunodeficiency virus vaccine induced vaccine-induced plasmablasts and naïve and antigen-specific memory B cells. BALDR enables matching of clonotype identity with single-cell transcriptional information in B cell lineages and will have broad application in the fields of vaccines, human immunodeficiency virus broadly neutralizing antibody development, and cancer. BALDR is available at https://github.com/BosingerLab/BALDR.
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Affiliation(s)
- Amit A Upadhyay
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Robert C Kauffman
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Amber N Wolabaugh
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Alice Cho
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Nirav B Patel
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, 954 Gatewood Rd, Atlanta, GA, 30329, USA
| | - Samantha M Reiss
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, USA
| | - Colin Havenar-Daughton
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, USA
| | - Reem A Dawoud
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Gregory K Tharp
- Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, 954 Gatewood Rd, Atlanta, GA, 30329, USA
| | - Iñaki Sanz
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.,Division of Rheumatology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, USA.,Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - F Eun-Hyung Lee
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.,Divisions of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, GA, USA
| | - Jens Wrammert
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA. .,Yerkes NHP Genomics Core Laboratory, Yerkes National Primate Research Center, 954 Gatewood Rd, Atlanta, GA, 30329, USA. .,Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, USA.
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25
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Upadhyay AA, Fleetwood AD, Adebali O, Finn RD, Zhulin IB. Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes. PLoS Comput Biol 2016; 12:e1004862. [PMID: 27049771 PMCID: PMC4822843 DOI: 10.1371/journal.pcbi.1004862] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/10/2016] [Indexed: 12/15/2022] Open
Abstract
Cellular receptors usually contain a designated sensory domain that recognizes the signal. Per/Arnt/Sim (PAS) domains are ubiquitous sensors in thousands of species ranging from bacteria to humans. Although PAS domains were described as intracellular sensors, recent structural studies revealed PAS-like domains in extracytoplasmic regions in several transmembrane receptors. However, these structurally defined extracellular PAS-like domains do not match sequence-derived PAS domain models, and thus their distribution across the genomic landscape remains largely unknown. Here we show that structurally defined extracellular PAS-like domains belong to the Cache superfamily, which is homologous to, but distinct from the PAS superfamily. Our newly built computational models enabled identification of Cache domains in tens of thousands of signal transduction proteins including those from important pathogens and model organisms. Furthermore, we show that Cache domains comprise the dominant mode of extracellular sensing in prokaryotes. Cell-surface receptors control multiple cellular functions and are attractive targets for drug design. These receptors often have dedicated extracellular domains that bind signaling molecules, such as hormones and nutrients. Computational identification of these ligand-binding domains in genomic sequences is a pre-requisite for their further experimental characterization. Using available three-dimensional structures of several bacterial cell-surface receptors, we built computational models that enabled identification of the Cache domain, as the most common extracellular sensor module in prokaryotes, including many important pathogens. We also demonstrated that the Cache domain is homologous to, but sufficiently different from the most common intracellular sensor module, the PAS domain. These findings provide a unified view on molecular principles of signal recognition by extra- and intracellular receptors.
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Affiliation(s)
- Amit A. Upadhyay
- Genome Science and Technology Graduate Program, University of Tennessee–Oak Ridge National Laboratory, Knoxville, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Aaron D. Fleetwood
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Ogun Adebali
- Genome Science and Technology Graduate Program, University of Tennessee–Oak Ridge National Laboratory, Knoxville, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Robert D. Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Igor B. Zhulin
- Genome Science and Technology Graduate Program, University of Tennessee–Oak Ridge National Laboratory, Knoxville, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
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