1
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Viox EG, Bosinger SE, Douek DC, Schreiber G, Paiardini M. Harnessing the power of IFN for therapeutic approaches to COVID-19. J Virol 2024:e0120423. [PMID: 38651899 DOI: 10.1128/jvi.01204-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
Interferons (IFNs) are essential for defense against viral infections but also drive recruitment of inflammatory cells to sites of infection, a key feature of severe COVID-19. Here, we explore the complexity of the IFN response in COVID-19, examine the effects of manipulating IFN on SARS-CoV-2 viral replication and pathogenesis, and highlight pre-clinical and clinical studies evaluating the therapeutic efficacy of IFN in limiting COVID-19 severity.
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Affiliation(s)
- Elise G Viox
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Steven E Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Emory NPRC Genomics Core Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory 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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2
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Moore KM, Pelletier AN, Lapp S, Metz A, Tharp GK, Lee M, Bhasin SS, Bhasin M, Sékaly RP, Bosinger SE, Suthar MS. Single-cell analysis reveals an antiviral network that controls Zika virus infection in human dendritic cells. J Virol 2024:e0019424. [PMID: 38567950 DOI: 10.1128/jvi.00194-24] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/12/2024] [Indexed: 04/16/2024] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus that caused an epidemic in the Americas in 2016 and is linked to severe neonatal birth defects, including microcephaly and spontaneous abortion. To better understand the host response to ZIKV infection, we adapted the 10× Genomics Chromium single-cell RNA sequencing (scRNA-seq) assay to simultaneously capture viral RNA and host mRNA. Using this assay, we profiled the antiviral landscape in a population of human monocyte-derived dendritic cells infected with ZIKV at the single-cell level. The bystander cells, which lacked detectable viral RNA, expressed an antiviral state that was enriched for genes coinciding predominantly with a type I interferon (IFN) response. Within the infected cells, viral RNA negatively correlated with type I IFN-dependent and -independent genes (the antiviral module). We modeled the ZIKV-specific antiviral state at the protein level, leveraging experimentally derived protein interaction data. We identified a highly interconnected network between the antiviral module and other host proteins. In this work, we propose a new paradigm for evaluating the antiviral response to a specific virus, combining an unbiased list of genes that highly correlate with viral RNA on a per-cell basis with experimental protein interaction data. IMPORTANCE Zika virus (ZIKV) remains a public health threat given its potential for re-emergence and the detrimental fetal outcomes associated with infection during pregnancy. Understanding the dynamics between ZIKV and its host is critical to understanding ZIKV pathogenesis. Through ZIKV-inclusive single-cell RNA sequencing (scRNA-seq), we demonstrate on the single-cell level the dynamic interplay between ZIKV and the host: the transcriptional program that restricts viral infection and ZIKV-mediated inhibition of that response. Our ZIKV-inclusive scRNA-seq assay will serve as a useful tool for gaining greater insight into the host response to ZIKV and can be applied more broadly to the flavivirus field.
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Affiliation(s)
- Kathryn M Moore
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Vaccine Center, Atlanta, Georgia, USA
- Emory National Primate Research Center, Atlanta, Georgia, USA
| | | | - Stacey Lapp
- Emory Vaccine Center, Atlanta, Georgia, USA
- Emory National Primate Research Center, Atlanta, Georgia, USA
| | - Amanda Metz
- Emory Vaccine Center, Atlanta, Georgia, USA
- Emory National Primate Research Center, Atlanta, Georgia, USA
| | - Gregory K Tharp
- Emory National Primate Research Center, Atlanta, Georgia, USA
- Emory NPRC Genomics Core Laboratory, Atlanta, Georgia, USA
| | - Michelle Lee
- Emory Vaccine Center, Atlanta, Georgia, USA
- Emory National Primate Research Center, Atlanta, Georgia, USA
| | - Swati Sharma Bhasin
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Manoj Bhasin
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Rafick-Pierre Sékaly
- Emory Vaccine Center, Atlanta, Georgia, USA
- Pathology Advanced Translational Research Unit, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Steven E Bosinger
- Emory Vaccine Center, Atlanta, Georgia, USA
- Emory National Primate Research Center, Atlanta, Georgia, USA
- Emory NPRC Genomics Core Laboratory, Atlanta, Georgia, USA
| | - Mehul S Suthar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Vaccine Center, Atlanta, Georgia, USA
- Emory National Primate Research Center, Atlanta, Georgia, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, USA
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3
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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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4
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Wang Q, Clark KM, Tiwari R, Raju N, Tharp GK, Rogers J, Harris RA, Raveendran M, Bosinger SE, Burdo TH, Silvestri G, Shan L. The CARD8 inflammasome dictates HIV/SIV pathogenesis and disease progression. Cell 2024; 187:1223-1237.e16. [PMID: 38428396 PMCID: PMC10919936 DOI: 10.1016/j.cell.2024.01.048] [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: 07/07/2023] [Revised: 11/16/2023] [Accepted: 01/29/2024] [Indexed: 03/03/2024]
Abstract
While CD4+ T cell depletion is key to disease progression in people living with HIV and SIV-infected macaques, the mechanisms underlying this depletion remain incompletely understood, with most cell death involving uninfected cells. In contrast, SIV infection of "natural" hosts such as sooty mangabeys does not cause CD4+ depletion and AIDS despite high-level viremia. Here, we report that the CARD8 inflammasome is activated immediately after HIV entry by the viral protease encapsulated in incoming virions. Sensing of HIV protease activity by CARD8 leads to rapid pyroptosis of quiescent cells without productive infection, while T cell activation abolishes CARD8 function and increases permissiveness to infection. In humanized mice reconstituted with CARD8-deficient cells, CD4+ depletion is delayed despite high viremia. Finally, we discovered loss-of-function mutations in CARD8 from "natural hosts," which may explain the peculiarly non-pathogenic nature of these infections. Our study suggests that CARD8 drives CD4+ T cell depletion during pathogenic HIV/SIV infections.
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Affiliation(s)
- Qiankun Wang
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Kolin M Clark
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ritudhwaj Tiwari
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Nagarajan Raju
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Gregory K Tharp
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Steven E Bosinger
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA; Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Tricia H Burdo
- Department of Microbiology, Immunology, and Inflammation, Center for Neurovirology and Gene Editing, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Guido Silvestri
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA; Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Liang Shan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA.
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5
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Moore KM, Pelletier AN, Lapp S, Metz A, Tharp GK, Lee M, Bhasin SS, Bhasin M, Sékaly RP, Bosinger SE, Suthar MS. Single cell analysis reveals an antiviral network that controls Zika virus infection in human dendritic cells. bioRxiv 2024:2024.01.19.576293. [PMID: 38293140 PMCID: PMC10827181 DOI: 10.1101/2024.01.19.576293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Zika virus (ZIKV) is a mosquito-borne flavivirus that caused an epidemic in the Americas in 2016 and is linked to severe neonatal birth defects, including microcephaly and spontaneous abortion. To better understand the host response to ZIKV infection, we adapted the 10x Genomics Chromium single cell RNA sequencing (scRNA-seq) assay to simultaneously capture viral RNA and host mRNA. Using this assay, we profiled the antiviral landscape in a population of human moDCs infected with ZIKV at the single cell level. The bystander cells, which lacked detectable viral RNA, expressed an antiviral state that was enriched for genes coinciding predominantly with a type I interferon (IFN) response. Within the infected cells, viral RNA negatively correlated with type I IFN dependent and independent genes (antiviral module). We modeled the ZIKV specific antiviral state at the protein level leveraging experimentally derived protein-interaction data. We identified a highly interconnected network between the antiviral module and other host proteins. In this work, we propose a new paradigm for evaluating the antiviral response to a specific virus, combining an unbiased list of genes that highly correlate with viral RNA on a per cell basis with experimental protein interaction data. Our ZIKV-inclusive scRNA-seq assay will serve as a useful tool to gaining greater insight into the host response to ZIKV and can be applied more broadly to the flavivirus field.
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6
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Ozonoff A, Jayavelu ND, Liu S, Melamed E, Milliren CE, Qi J, Geng LN, McComsey GA, Cairns CB, Baden LR, Schaenman J, Shaw AC, Samaha H, Seyfert-Margolis V, Krammer F, Rosen LB, Steen H, Syphurs C, Dandekar R, Shannon CP, Sekaly RP, Ehrlich LIR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Sesma AF, Simon V, van Bakel H, Kim-Schulze S, Hafler DA, Levy O, Kraft M, Bime C, Haddad EK, Calfee CS, Erle DJ, Langelier CR, Eckalbar W, Bosinger SE, Peters B, Kleinstein SH, Reed EF, Augustine AD, Diray-Arce J, Maecker HT, Altman MC, Montgomery RR, Becker PM, Rouphael N. Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study. Nat Commun 2024; 15:216. [PMID: 38172101 PMCID: PMC10764789 DOI: 10.1038/s41467-023-44090-5] [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: 03/17/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Post-acute sequelae of SARS-CoV-2 (PASC) is a significant public health concern. We describe Patient Reported Outcomes (PROs) on 590 participants prospectively assessed from hospital admission for COVID-19 through one year after discharge. Modeling identified 4 PRO clusters based on reported deficits (minimal, physical, mental/cognitive, and multidomain), supporting heterogenous clinical presentations in PASC, with sub-phenotypes associated with female sex and distinctive comorbidities. During the acute phase of disease, a higher respiratory SARS-CoV-2 viral burden and lower Receptor Binding Domain and Spike antibody titers were associated with both the physical predominant and the multidomain deficit clusters. A lower frequency of circulating B lymphocytes by mass cytometry (CyTOF) was observed in the multidomain deficit cluster. Circulating fibroblast growth factor 21 (FGF21) was significantly elevated in the mental/cognitive predominant and the multidomain clusters. Future efforts to link PASC to acute anti-viral host responses may help to better target treatment and prevention of PASC.
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Affiliation(s)
- Al Ozonoff
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | | | - Shanshan Liu
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | | | - Carly E Milliren
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | - Jingjing Qi
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Grace A McComsey
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, USA
| | | | - Lindsey R Baden
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Joanna Schaenman
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, USA
| | - Albert C Shaw
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, USA
| | | | | | | | - Lindsey B Rosen
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, USA
| | - Hanno Steen
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Caitlin Syphurs
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | - Ravi Dandekar
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Casey P Shannon
- Centre for Heart Lung Innovation, Providence Research, St. Paul's Hospital, and the PROOF Centre of Excellence, Vancouver, BC, Canada
| | - Rafick P Sekaly
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, USA
| | | | - David B Corry
- Baylor College of Medicine, and the Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey VA Medical Center, Houston, TX, USA
| | - Farrah Kheradmand
- Baylor College of Medicine, and the Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey VA Medical Center, Houston, TX, USA
| | - Mark A Atkinson
- University of Florida/University of South Florida, Tampa, FL, USA
| | | | | | - Jordan P Metcalf
- Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
| | | | | | | | | | | | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - David A Hafler
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, USA
| | - Ofer Levy
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | | | | | - Elias K Haddad
- Drexel University/Tower Health Hospital, Philadelphia, PA, USA
| | - Carolyn S Calfee
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - David J Erle
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Charles R Langelier
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Walter Eckalbar
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | | | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Steven H Kleinstein
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, USA
| | - Elaine F Reed
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, USA
| | - Alison D Augustine
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, USA
| | - Joann Diray-Arce
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | | | | | - Ruth R Montgomery
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, USA
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, USA
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7
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Laliberté A, Prelli Bozzo C, Stahl-Hennig C, Hunszinger V, Joas S, Sauermann U, Roshani B, Klippert A, Daskalaki M, Mätz-Rensing K, Stolte-Leeb N, Tharp GK, Fuchs D, Gupta PM, Silvestri G, Nelson SA, Parodi L, Giavedoni L, Bosinger SE, Sparrer KM, Kirchhoff F. Vpr attenuates antiviral immune responses and is critical for full pathogenicity of SIV mac239 in rhesus macaques. iScience 2023; 26:108351. [PMID: 38025783 PMCID: PMC10679897 DOI: 10.1016/j.isci.2023.108351] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/05/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
The accessory viral protein R (Vpr) is encoded by all primate lentiviruses. Vpr counteracts DNA repair pathways, modulates viral immune sensing, and induces cell-cycle arrest in cell culture. However, its impact in vivo is controversial. Here, we show that deletion of vpr is associated with delayed viral replication kinetics, rapid innate immune activation, development and maintenance of strong B and T cell responses, and increased neutralizing activity against SIVmac239 in rhesus macaques. All wild-type SIVmac239-infected animals maintained high viral loads, and five of six developed fatal immunodeficiency during ∼80 weeks of follow-up. Lack of Vpr was associated with better preservation of CD4+ T cells, lower viral loads, and an attenuated clinical course of infection in most animals. Our results show that Vpr contributes to efficient viral immune evasion and the full pathogenic potential of SIVmacin vivo. Inhibition of Vpr may improve humoral immune control of viral replication.
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Affiliation(s)
- Alexandre Laliberté
- Institute of Molecular Virology – Ulm University Medical Center, Meyerhofstraße 1, 89081 Ulm, Germany
| | - Caterina Prelli Bozzo
- Institute of Molecular Virology – Ulm University Medical Center, Meyerhofstraße 1, 89081 Ulm, Germany
| | | | - Victoria Hunszinger
- Institute of Molecular Virology – Ulm University Medical Center, Meyerhofstraße 1, 89081 Ulm, Germany
| | - Simone Joas
- Institute of Molecular Virology – Ulm University Medical Center, Meyerhofstraße 1, 89081 Ulm, Germany
| | | | - Berit Roshani
- German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | | | - Maria Daskalaki
- German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | | | | | - Gregory K. Tharp
- Emory National Primate Research Center, Emory Vaccine Center and Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Dietmar Fuchs
- German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Prachi Mehrotra Gupta
- Emory National Primate Research Center, Emory Vaccine Center and Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Guido Silvestri
- Emory National Primate Research Center, Emory Vaccine Center and Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Sydney A. Nelson
- Emory National Primate Research Center, Emory Vaccine Center and Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Laura Parodi
- Host-Pathogen Interactions Program, Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Luis Giavedoni
- Host-Pathogen Interactions Program, Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Steven E. Bosinger
- Emory National Primate Research Center, Emory Vaccine Center and Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Konstantin M.J. Sparrer
- Institute of Molecular Virology – Ulm University Medical Center, Meyerhofstraße 1, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology – Ulm University Medical Center, Meyerhofstraße 1, 89081 Ulm, Germany
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8
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Gygi JP, Maguire C, Patel RK, Shinde P, Konstorum A, Shannon CP, Xu L, Hoch A, Jayavelu ND, Network I, Haddad EK, Reed EF, Kraft M, McComsey GA, Metcalf J, Ozonoff A, Esserman D, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen LB, van Bakel H, Wilson M, Eckalbar W, Maecker H, Langelier CR, Steen H, Altman MC, Montgomery RR, Levy O, Melamed E, Pulendran B, Diray-Arce J, Smolen KK, Fragiadakis GK, Becker PM, Augustine AD, Sekaly RP, Ehrlich LIR, Fourati S, Peters B, Kleinstein SH, Guan L. Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants. bioRxiv 2023:2023.11.03.565292. [PMID: 37986828 PMCID: PMC10659275 DOI: 10.1101/2023.11.03.565292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Hospitalized COVID-19 patients exhibit diverse clinical outcomes, with some individuals diverging over time even though their initial disease severity appears similar. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity. In this study, we carried out deep immunophenotyping and conducted longitudinal multi-omics modeling integrating ten distinct assays on a total of 1,152 IMPACC participants and identified several immune cascades that were significant drivers of differential clinical outcomes. Increasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, NETosis, and T-cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma immunoglobulins and B cells, as well as dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to the failure of viral clearance in patients with fatal illness. Our longitudinal multi-omics profiling study revealed novel temporal coordination across diverse omics that potentially explain disease progression, providing insights that inform the targeted development of therapies for hospitalized COVID-19 patients, especially those critically ill.
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9
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Wimmers F, Burrell AR, Feng Y, Zheng H, Arunachalam PS, Hu M, Spranger S, Nyhoff LE, Joshi D, Trisal M, Awasthi M, Bellusci L, Ashraf U, Kowli S, Konvinse KC, Yang E, Blanco M, Pellegrini K, Tharp G, Hagan T, Chinthrajah RS, Nguyen TT, Grifoni A, Sette A, Nadeau KC, Haslam DB, Bosinger SE, Wrammert J, Maecker HT, Utz PJ, Wang TT, Khurana S, Khatri P, Staat MA, Pulendran B. Multi-omics analysis of mucosal and systemic immunity to SARS-CoV-2 after birth. Cell 2023; 186:4632-4651.e23. [PMID: 37776858 PMCID: PMC10724861 DOI: 10.1016/j.cell.2023.08.044] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/18/2023] [Accepted: 08/31/2023] [Indexed: 10/02/2023]
Abstract
The dynamics of immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in infants and young children by analyzing blood samples and weekly nasal swabs collected before, during, and after infection with Omicron and non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, showed no sign of decay for up to 300 days. Infants mounted a robust mucosal immune response characterized by inflammatory cytokines, interferon (IFN) α, and T helper (Th) 17 and neutrophil markers (interleukin [IL]-17, IL-8, and CXCL1). The immune response in blood was characterized by upregulation of activation markers on innate cells, no inflammatory cytokines, but several chemokines and IFNα. The latter correlated with viral load and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single-cell multi-omics. Together, these data provide a snapshot of immunity to infection during the initial weeks and months of life.
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Affiliation(s)
- Florian Wimmers
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany; DFG Cluster of Excellence 2180 "Image-guided and Functional Instructed Tumor Therapy" (iFIT), University of Tuebingen, 72076 Tuebingen, Baden-Wuerttemberg, Germany; German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Baden-Wuerttemberg, Germany
| | - Allison R Burrell
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Environmental and Public Health Sciences, Division of Epidemiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Sara Spranger
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lindsay E Nyhoff
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Devyani Joshi
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Meera Trisal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Mayanka Awasthi
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Usama Ashraf
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
| | - Sangeeta Kowli
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Katherine C Konvinse
- Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Emily Yang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Blanco
- Stanford Genomics Service Center, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Gregory Tharp
- Yerkes National Primate Research Center, Atlanta, GA 30024, USA
| | - Thomas Hagan
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - R Sharon Chinthrajah
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - Tran T Nguyen
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kari C Nadeau
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - David B Haslam
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Steven E Bosinger
- Yerkes National Primate Research Center, Atlanta, GA 30024, USA; Department of Pathology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Taia T Wang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mary A Staat
- Department of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
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10
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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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11
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Gupta PM, Balle C, Tharp GK, Nelson SA, Gasper MA, Brown B, Alisoltani A, Onono M, Palanee-Phillips T, Nair G, Ayele H, Noel-Romas L, Passmore JAS, Burgener AD, Heffron R, Jaspan HB, Bosinger SE. Systems analysis reveals differential expression of endocervical genes in African women randomized to DMPA-IM, LNG implant or cu-IUD. Clin Immunol 2023; 255:109750. [PMID: 37660744 PMCID: PMC10570927 DOI: 10.1016/j.clim.2023.109750] [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: 07/18/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023]
Abstract
Although effective contraceptives are crucial for preventing unintended pregnancies, evidence suggests that their use may perturb the female genital tract (FGT). A comparative analysis of the effects of the most common contraceptives on the FGT have not been evaluated in a randomized clinical trial setting. Here, we evaluated the effect of three long-acting contraceptive methods: depot medroxyprogesterone acetate(DMPA-IM), levonorgestrel(LNG) implant, and a copper intrauterine device (Cu-IUD), on the endocervical host transcriptome in 188 women from the Evidence for Contraceptive Options and HIV Outcomes Trial (ECHO) trial. Cu-IUD usage showed the most extensive transcriptomic changes, and was associated with inflammatory and anti-viral host responses. DMPA-IM usage was enriched for pathways associated with T cell responses. LNG implant had the mildest effect on endocervical gene expression, and was associated with growth factor signaling. These data provide a mechanistic basis for the diverse influence that varying contraceptives have on the FGT.
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Affiliation(s)
- Prachi Mehrotra Gupta
- Emory National Primate Research Center (ENPRC) Genomics Core Laboratory, Division of Microbiology & Immunology, Emory University, Atlanta, GA, USA
| | - Christina Balle
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Gregory K Tharp
- Emory National Primate Research Center (ENPRC) Genomics Core Laboratory, Division of Microbiology & Immunology, Emory University, Atlanta, GA, USA
| | - Sydney A Nelson
- Emory National Primate Research Center (ENPRC) Genomics Core Laboratory, Division of Microbiology & Immunology, Emory University, Atlanta, GA, USA
| | | | - Bryan Brown
- Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Arghavan Alisoltani
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Thesla Palanee-Phillips
- Wits RHI, University of the Witwatersrand, Faculty of Health Sciences, School of Public Health, Johannesburg, South Africa; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | | | - Hosseana Ayele
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Laura Noel-Romas
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jo-Ann S Passmore
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; National Health Laboratory Service, Cape Town, South Africa; CAPRISA DSI-NRF Centre of Excellence in HIV Prevention, University of Cape Town, South Africa
| | - Adam D Burgener
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Renee Heffron
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Heather B Jaspan
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa; Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Steven E Bosinger
- Emory University School of Medicine, Department of Pathology & Laboratory Medicine, GA, USA; Emory Vaccine Center, Emory University, GA, USA.
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12
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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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13
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Dabee S, Balle C, Onono M, Innes S, Nair G, Palanee-Phillips T, Burgener AD, Bosinger SE, Passmore JAS, Heffron R, Jaspan H, Happel AU. Update on the Impact of Depot Medroxyprogesterone Acetate on Vaginal Mucosal Endpoints and Relevance to Sexually Transmitted Infections. Curr HIV/AIDS Rep 2023; 20:251-260. [PMID: 37341916 PMCID: PMC10403392 DOI: 10.1007/s11904-023-00662-0] [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] [Accepted: 05/29/2023] [Indexed: 06/22/2023]
Abstract
PURPOSE OF REVIEW The long-acting reversible intramuscularly-injected contraceptive depot medroxyprogesterone acetate (DMPA-IM) is widely used by cisgender women in Africa. Although DMPA-IM provides reliable contraception, potential effects on the female genital tract (FGT) mucosa have raised concern, including risk of HIV infection. This review summarises and compares evidence from observational cohort studies and the randomised Evidence for Contraceptive Options in HIV Outcomes (ECHO) Trial. RECENT FINDINGS Although previous observational studies found women using DMPA-IM had higher abundance of bacterial vaginosis (BV)-associated bacteria, increased inflammation, increased cervicovaginal HIV target cell density, and epithelial barrier damage, sub-studies of the ECHO Trial found no adverse changes in vaginal microbiome, inflammation, proteome, transcriptome, and risk of viral and bacterial STIs, other than an increase in Th17-like cells. Randomised data suggest that DMPA-IM use does not adversely change mucosal endpoints associated with acquisition of infections. These findings support the safe use of DMPA-IM in women at high risk of acquiring STIs, including HIV.
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Affiliation(s)
- Smritee Dabee
- Center for Global Infectious Disease, Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109 USA
| | - Christina Balle
- Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
| | | | - Steve Innes
- Desmond Tutu Health Foundation, 3 Woodlands Rd, Woodstock, Cape Town, 7915 South Africa
| | - Gonasagrie Nair
- Desmond Tutu Health Foundation, 3 Woodlands Rd, Woodstock, Cape Town, 7915 South Africa
| | - Thesla Palanee-Phillips
- Wits Reproductive Health and HIV Institute, University of the Witwatersrand, Klein St & Esselen St, Hillbrow, Johannesburg 2001 South Africa
| | - Adam D. Burgener
- Center for Global Health and Diseases, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106 USA
- Department of Obstetrics and Gynecology, University of Manitoba, 66 Chancellors Cir, Winnipeg, MB R3T 2N2 Canada
- Unit of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institute, Karolinska University Hospital, Visionsgatan 18, L8, 171 76 Solna, Sweden
| | - Steven E. Bosinger
- ENPRC Genomics Core Laboratory, Emory National Primate Research Center, 954 Gatewood Rd NE, Atlanta, GA 30329 USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 2015 Uppergate Dr, Atlanta, GA 30307 USA
- Emory Vaccine Center, Emory University, 7 1st Ave, Atlanta, GA 30317 USA
| | - Jo-Ann S. Passmore
- Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
- National Health Laboratory Service, Anzio Road, Observatory, Cape Town, 7925 South Africa
| | - Renee Heffron
- Department of Medicine, University of Alabama at Birmingham, 845 19th Street South, AL 35294-2170 Birmingham, USA
- Department of Global Health, University of Washington, 1510 San Juan Road NE, Seattle, WA 98195 USA
| | - Heather Jaspan
- Center for Global Infectious Disease, Seattle Children’s Research Institute, 307 Westlake Ave. N, Seattle, WA 98109 USA
- Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
- Department of Pediatrics, University of Washington, 1959 NE Pacific St., Seattle, WA 98195 USA
- Department of Global Health, University of Washington, 1510 San Juan Road NE, Seattle, WA 98195 USA
| | - Anna-Ursula Happel
- Department of Pathology, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925 South Africa
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14
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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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15
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Diray-Arce J, Fourati S, Doni Jayavelu N, Patel R, Maguire C, Chang AC, Dandekar R, Qi J, Lee BH, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi JP, Kho A, Chen J, Pawar S, Gonzalez-Reiche AS, Hoch A, Milliren CE, Overton JA, Westendorf K, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen L, Grubaugh ND, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier CR, Levy O, Altman MC, Maecker H, Montgomery RR, Haddad EK, Sekaly RP, Esserman D, Ozonoff A, Becker PM, Augustine AD, Guan L, Peters B, Kleinstein SH. Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. Cell Rep Med 2023; 4:101079. [PMID: 37327781 PMCID: PMC10203880 DOI: 10.1016/j.xcrm.2023.101079] [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: 08/30/2022] [Revised: 01/31/2023] [Accepted: 05/16/2023] [Indexed: 06/18/2023]
Abstract
The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1-3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling of >15,000 longitudinal blood and nasal samples from 540 participants of the IMPACC cohort, using 14 distinct assays. These unbiased analyses identify cellular and molecular signatures present within 72 h of hospital admission that distinguish moderate from severe and fatal COVID-19 disease. Importantly, cellular and molecular states also distinguish participants with more severe disease that recover or stabilize within 28 days from those that progress to fatal outcomes (TG4 vs. TG5). Furthermore, our longitudinal design reveals that these biologic states display distinct temporal patterns associated with clinical outcomes. Characterizing host immune responses in relation to heterogeneity in disease course may inform clinical prognosis and opportunities for intervention.
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Affiliation(s)
- Joann Diray-Arce
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Slim Fourati
- Emory School of Medicine, Atlanta, GA 30322, USA
| | | | - Ravi Patel
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Cole Maguire
- The University of Texas at Austin, Austin, TX 78712, USA
| | - Ana C Chang
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ravi Dandekar
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Jingjing Qi
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian H Lee
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick van Zalm
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew Schroeder
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Ernie Chen
- Yale School of Medicine, New Haven, CT 06510, USA
| | | | | | | | - Alvin Kho
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jing Chen
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Annmarie Hoch
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Carly E Milliren
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA
| | | | | | - Charles B Cairns
- Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA
| | | | | | | | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lindsey Rosen
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20814, USA
| | | | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Wilson
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Jayant Rajan
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Hanno Steen
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Walter Eckalbar
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Chris Cotsapas
- Yale School of Medicine, New Haven, CT 06510, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | | | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Matthew C Altman
- Benaroya Research Institute, University of Washington, Seattle, WA 98101, USA
| | - Holden Maecker
- Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | | | - Elias K Haddad
- Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA
| | | | | | - Al Ozonoff
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20814, USA
| | - Alison D Augustine
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20814, USA
| | - Leying Guan
- Yale School of Public Health, New Haven, CT 06510, USA
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
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16
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Arunachalam PS, Scott MKD, Hagan T, Li C, Feng Y, Wimmers F, Grigoryan L, Trisal M, Edara VV, Lai L, Chang SE, Feng A, Dhingra S, Shah M, Lee AS, Chinthrajah S, Sindher SB, Mallajosyula V, Gao F, Sigal N, Kowli S, Gupta S, Pellegrini K, Tharp G, Maysel-Auslender S, Hamilton S, Aoued H, Hrusovsky K, Roskey M, Bosinger SE, Maecker HT, Boyd SD, Davis MM, Utz PJ, Suthar MS, Khatri P, Nadeau KC, Pulendran B. Addendum: Systems vaccinology of the BNT162b2 mRNA vaccine in humans. Nature 2023:10.1038/s41586-023-05977-x. [PMID: 37225997 DOI: 10.1038/s41586-023-05977-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Madeleine K D Scott
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Thomas Hagan
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Lilit Grigoryan
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Meera Trisal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | | | - Lilin Lai
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Sarah Esther Chang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Allan Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Shaurya Dhingra
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mihir Shah
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Alexandra S Lee
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Sharon Chinthrajah
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Sayantani B Sindher
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Fei Gao
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Natalia Sigal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Sangeeta Kowli
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Sheena Gupta
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | | | - Gregory Tharp
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Sofia Maysel-Auslender
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | | | - Hadj Aoued
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | | | | | - Steven E Bosinger
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Scott D Boyd
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mehul S Suthar
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA.
- Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
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17
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Mutascio S, Mota T, Franchitti L, Sharma AA, Willemse A, Bergstresser SN, Wang H, Statzu M, Tharp GK, Weiler J, Sékaly RP, Bosinger SE, Paiardini M, Silvestri G, Jones RB, Kulpa DA. CD8 + T cells promote HIV latency by remodeling CD4 + T cell metabolism to enhance their survival, quiescence, and stemness. Immunity 2023; 56:1132-1147.e6. [PMID: 37030290 PMCID: PMC10880039 DOI: 10.1016/j.immuni.2023.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 06/24/2022] [Revised: 11/16/2022] [Accepted: 03/15/2023] [Indexed: 04/10/2023]
Abstract
HIV infection persists during antiretroviral therapy (ART) due to a reservoir of latently infected cells that harbor replication-competent virus and evade immunity. Previous ex vivo studies suggested that CD8+ T cells from people with HIV may suppress HIV expression via non-cytolytic mechanisms, but the mechanisms responsible for this effect remain unclear. Here, we used a primary cell-based in vitro latency model and demonstrated that co-culture of autologous activated CD8+ T cells with HIV-infected memory CD4+ T cells promoted specific changes in metabolic and/or signaling pathways resulting in increased CD4+ T cell survival, quiescence, and stemness. Collectively, these pathways negatively regulated HIV expression and ultimately promoted the establishment of latency. As shown previously, we observed that macrophages, but not B cells, promoted latency in CD4+ T cells. The identification of CD8-specific mechanisms of pro-latency activity may favor the development of approaches to eliminate the viral reservoir in people with HIV.
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Affiliation(s)
- Simona Mutascio
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Talia Mota
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Lavinia Franchitti
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Ashish A Sharma
- Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Abigail Willemse
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | | | - Hong Wang
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Maura Statzu
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Gregory K Tharp
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Jared Weiler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Rafick-Pierre Sékaly
- Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Steven E Bosinger
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Mirko Paiardini
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Guido Silvestri
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Deanna A Kulpa
- Emory National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Department of Pathology & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30322, USA.
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18
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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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19
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Byrnes SJ, Busman-Sahay K, Angelovich TA, Younger S, Taylor-Brill S, Nekorchuk M, Bondoc S, Dannay R, Terry M, Cochrane CR, Jenkins TA, Roche M, Deleage C, Bosinger SE, Paiardini M, Brew BJ, Estes JD, Churchill MJ. Chronic immune activation and gut barrier dysfunction is associated with neuroinflammation in ART-suppressed SIV+ rhesus macaques. PLoS Pathog 2023; 19:e1011290. [PMID: 36989320 PMCID: PMC10085024 DOI: 10.1371/journal.ppat.1011290] [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: 08/11/2022] [Revised: 04/10/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
HIV-associated neurocognitive disorders (HAND) affect ~40% of virally suppressed people with HIV (PWH), however, the precise viral dependent and independent changes to the brain are unclear. Here we characterized the CNS reservoir and immune environment of SIV-infected (SIV+) rhesus macaques during acute (n = 4), chronic (n = 12) or ART-suppressed SIV infection (n = 11). Multiplex immunofluorescence for markers of SIV infection (vRNA/vDNA) and immune activation was performed on frontal cortex and matched colon tissue. SIV+ animals contained detectable viral DNA+ cells that were not reduced in the frontal cortex or the gut by ART, supporting the presence of a stable viral reservoir in these compartments. SIV+ animals had impaired blood brain barrier (BBB) integrity and heightened levels of astrocytes or myeloid cells expressing antiviral, anti-inflammatory or oxidative stress markers which were not abrogated by ART. Neuroinflammation and BBB dysfunction correlated with measures of viremia and immune activation in the gut. Furthermore, SIV-uninfected animals with experimentally induced gut damage and colitis showed a similar immune activation profile in the frontal cortex to those of SIV-infected animals, supporting the role of chronic gut damage as an independent source of neuroinflammation. Together, these findings implicate gut-associated immune activation/damage as a significant contributor to neuroinflammation in ART-suppressed HIV/SIV infection which may drive HAND pathogenesis.
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Affiliation(s)
- Sarah J. Byrnes
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
| | - Kathleen Busman-Sahay
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Thomas A. Angelovich
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
- Life Science, Burnet Institute, Melbourne, Australia
- Department of Infectious Diseases, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Skyler Younger
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Sol Taylor-Brill
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Michael Nekorchuk
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Stephen Bondoc
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Rachel Dannay
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Margaret Terry
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | | | - Trisha A. Jenkins
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
| | - Michael Roche
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
- Department of Infectious Diseases, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Bruce J. Brew
- Peter Duncan Neurosciences Unit, Departments of Neurology and Immunology St Vincent’s Hospital, University of New South Wales and University of Notre Dame, Sydney, New South Wales, Australia
| | - Jacob D. Estes
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Melissa J. Churchill
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Australia
- Life Science, Burnet Institute, Melbourne, Australia
- Departments of Microbiology and Medicine, Monash University, Clayton, Australia
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20
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Statzu M, Jin W, Fray EJ, Wong AKH, Kumar MR, Ferrer E, Docken SS, Pinkevych M, McBrien JB, Fennessey CM, Keele BF, Liang S, Harper JL, Mutascio S, Franchitti L, Wang H, Cicetti D, Bosinger SE, Carnathan DG, Vanderford TH, Margolis DM, Garcia-Martinez JV, Chahroudi A, Paiardini M, Siliciano J, Davenport MP, Kulpa DA, Siliciano RS, Silvestri G. CD8 + lymphocytes do not impact SIV reservoir establishment under ART. Nat Microbiol 2023; 8:299-308. [PMID: 36690860 PMCID: PMC9894752 DOI: 10.1038/s41564-022-01311-9] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 12/15/2022] [Indexed: 01/24/2023]
Abstract
Persistence of the human immunodeficiency virus type-1 (HIV-1) latent reservoir in infected individuals remains a problem despite fully suppressive antiretroviral therapy (ART). While reservoir formation begins during acute infection, the mechanisms responsible for its establishment remain unclear. CD8+ T cells are important during the initial control of viral replication. Here we examined the effect of CD8+ T cells on formation of the latent reservoir in simian immunodeficiency virus (SIV)-infected macaques by performing experimental CD8+ depletion either before infection or before early (that is, day 14 post-infection) ART initiation. We found that CD8+ depletion resulted in slower decline of viremia, indicating that CD8+ lymphocytes reduce the average lifespan of productively infected cells during acute infection and early ART, presumably through SIV-specific cytotoxic T lymphocyte (CTL) activity. However, CD8+ depletion did not change the frequency of infected CD4+ T cells in the blood or lymph node as measured by the total cell-associated viral DNA or intact provirus DNA assay. In addition, the size of the persistent reservoir remained the same when measuring the kinetics of virus rebound after ART interruption. These data indicate that during early SIV infection, the viral reservoir that persists under ART is established largely independent of CTL control.
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Grants
- P30 AI050409 NIAID NIH HHS
- P51 OD011132 NIH HHS
- R01 AI143414 NIAID NIH HHS
- 75N91019D00024 NCI NIH HHS
- HHSN261201500003I NCI NIH HHS
- UM1 AI164562 NIAID NIH HHS
- UM1 AI164567 NIAID NIH HHS
- R01 AI125064 NIAID NIH HHS
- CU | National Cancer Institute, Cairo University (NCI)
- National Cancer Institute, National Institutes of Health, under Contract No. 75N91019D00024/HHSN261201500003I.
- This work was supported by UM1AI164562, co-funded by National Heart, Lung and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, National Institute on Drug Abuse and the National Institute of Allergy and Infectious Diseases (to G.S., D.A.K., M.P.1), and NIH NIAID R01-AI143414 (to G.S. and D.A.K), and R01-AI125064 (to G.S., A.C., D.A.K.).
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Affiliation(s)
- Maura Statzu
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Wang Jin
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Emily J Fray
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew Kam Ho Wong
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Mithra R Kumar
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Ferrer
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steffen S Docken
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Mykola Pinkevych
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Julia B McBrien
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, 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
| | - Shan Liang
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Justin L Harper
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Simona Mutascio
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Lavinia Franchitti
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Hong Wang
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Davide Cicetti
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Steven E Bosinger
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Diane G Carnathan
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Thomas H Vanderford
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - David M Margolis
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, USA
| | - J Victor Garcia-Martinez
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, USA
| | - Ann Chahroudi
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Mirko Paiardini
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Janet Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Deanna A Kulpa
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Robert S Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Guido Silvestri
- Emory National Primate Research Center, Department of Pathology and Laboratory Medicine, and Emory Vaccine Center, Emory University, Atlanta, GA, USA.
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21
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Wimmers F, Burrell AR, Feng Y, Zheng H, Arunachalam PS, Hu M, Spranger S, Nyhoff L, Joshi D, Trisal M, Awasthi M, Bellusci L, Ashraf U, Kowli S, Konvinse KC, Yang E, Blanco M, Pellegrini K, Tharp G, Hagan T, Chinthrajah RS, Grifoni A, Sette A, Nadeau KC, Haslam DB, Bosinger SE, Wrammert J, Maecker HT, Utz PJ, Wang TT, Khurana S, Khatri P, Staat MA, Pulendran B. Systems biological assessment of the temporal dynamics of immunity to a viral infection in the first weeks and months of life. medRxiv 2023:2023.01.28.23285133. [PMID: 36778389 PMCID: PMC9915811 DOI: 10.1101/2023.01.28.23285133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The dynamics of innate and adaptive immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to SARS-CoV-2 infection in infants and young children in the first weeks and months of life by analyzing blood samples collected before, during, and after infection with Omicron and Non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, were stably maintained for >300 days. Antigen-specific memory B cell (MCB) responses were durable for 150 days but waned thereafter. Somatic hypermutation of V-genes in MCB accumulated progressively over 9 months. The innate response was characterized by upregulation of activation markers on blood innate cells, and a plasma cytokine profile distinct from that seen in adults, with no inflammatory cytokines, but an early and transient accumulation of chemokines (CXCL10, IL8, IL-18R1, CSF-1, CX3CL1), and type I IFN. The latter was strongly correlated with viral load, and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single-cell transcriptomics. Consistent with this, single-cell ATAC-seq revealed enhanced accessibility of chromatic loci targeted by interferon regulatory factors (IRFs) and reduced accessibility of AP-1 targeted loci, as well as traces of epigenetic imprinting in monocytes, during convalescence. Together, these data provide the first snapshot of immunity to infection during the initial weeks and months of life.
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Affiliation(s)
- Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Molecular Medicine, Interfaculty Institute for Biochemistry, University of Tuebingen, Tuebingen, Germany
- DFG Cluster of Excellence 2180 ‘Image-guided and Functional Instructed Tumor Therapy’ (iFIT), University of Tuebingen, Tuebingen, Germany
- German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Allison R. Burrell
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Environmental and Public Health Sciences, Division of Epidemiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Hong Zheng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Prabhu S. Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Mengyun Hu
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Sara Spranger
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Lindsay Nyhoff
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine
| | - Devyani Joshi
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine
| | - Meera Trisal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Mayanka Awasthi
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Usama Ashraf
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
| | - Sangeeta Kowli
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Katherine C. Konvinse
- Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Emily Yang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Blanco
- Stanford Genomics Service Center, Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Gregory Tharp
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Thomas Hagan
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - R. Sharon Chinthrajah
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Kari C. Nadeau
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - David B. Haslam
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Steven E. Bosinger
- Yerkes National Primate Research Center, Atlanta, GA, USA
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jens Wrammert
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine
| | - Holden T. Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul J. Utz
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Taia T. Wang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, 20993, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Mary A. Staat
- Department of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
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22
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Brown BP, Feng C, Tanko RF, Jaumdally SZ, Bunjun R, Dabee S, Happel AU, Gasper M, Nyangahu DD, Onono M, Nair G, Palanee-Phillips T, Scoville CW, Heller K, Baeten JM, Bosinger SE, Burgener A, Passmore JAS, Heffron R, Jaspan HB. Copper intrauterine device increases vaginal concentrations of inflammatory anaerobes and depletes lactobacilli compared to hormonal options in a randomized trial. Nat Commun 2023; 14:499. [PMID: 36717556 PMCID: PMC9886933 DOI: 10.1038/s41467-023-36002-4] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 01/12/2023] [Indexed: 02/01/2023] Open
Abstract
Effective contraceptives are a global health imperative for reproductive-aged women. However, there remains a lack of rigorous data regarding the effects of contraceptive options on vaginal bacteria and inflammation. Among 218 women enrolled into a substudy of the ECHO Trial (NCT02550067), we evaluate the effect of injectable intramuscular depot medroxyprogesterone acetate (DMPA-IM), levonorgestrel implant (LNG), and a copper intrauterine device (Cu-IUD) on the vaginal environment after one and six consecutive months of use, using 16S rRNA gene sequencing and multiplex cytokine assays. Primary endpoints include incident BV occurrence, bacterial diversity, and bacterial and cytokine concentrations. Secondary endpoints are bacterial and cytokine concentrations associated with later HIV seroconversion. Participants randomized to Cu-IUD exhibit elevated bacterial diversity, increased cytokine concentrations, and decreased relative abundance of lactobacilli after one and six months of use, relative to enrollment and other contraceptive options. Total bacterial loads of women using Cu-IUD increase 5.5 fold after six months, predominantly driven by increases in the concentrations of several inflammatory anaerobes. Furthermore, growth of L. crispatus (MV-1A-US) is inhibited by Cu2+ ions below biologically relevant concentrations, in vitro. Our work illustrates deleterious effects on the vaginal environment induced by Cu-IUD initiation, which may adversely impact sexual and reproductive health.
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Affiliation(s)
- Bryan P Brown
- Seattle Children's Research Institute, Seattle, USA.
- University of Washington, Seattle, USA.
| | - Colin Feng
- Seattle Children's Research Institute, Seattle, USA
| | - Ramla F Tanko
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- The Medical Research Centre, Institute of Medical Research and Medicinal Plant Studies (IMPM), Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | - Shameem Z Jaumdally
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Rubina Bunjun
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Smritee Dabee
- Seattle Children's Research Institute, Seattle, USA
- University of Washington, Seattle, USA
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anna-Ursula Happel
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Melanie Gasper
- Seattle Children's Research Institute, Seattle, USA
- University of Washington, Seattle, USA
| | - Donald D Nyangahu
- Seattle Children's Research Institute, Seattle, USA
- University of Washington, Seattle, USA
| | | | | | | | | | | | - Jared M Baeten
- University of Washington, Seattle, USA
- Gilead Sciences, Inc, Seattle, USA
| | - Steven E Bosinger
- Yerkes National Primate Research Center, Atlanta, USA
- Emory University, Atlanta, USA
| | - Adam Burgener
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, USA
- University of Manitoba, Winnipeg, Canada
- Karolinska Institute, Stockholm, Sweden
| | - Jo-Ann S Passmore
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
| | - Renee Heffron
- University of Washington, Seattle, USA
- University of Alabama, Birmingham, USA
| | - Heather B Jaspan
- Seattle Children's Research Institute, Seattle, USA.
- University of Washington, Seattle, USA.
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
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23
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Goll JB, Bosinger SE, Jensen TL, Walum H, Grimes T, Tharp GK, Natrajan MS, Blazevic A, Head RD, Gelber CE, Steenbergen KJ, Patel NB, Sanz P, Rouphael NG, Anderson EJ, Mulligan MJ, Hoft DF. Corrigendum: The Vacc-SeqQC project: Benchmarking RNA-Seq for clinical vaccine studies. Front Immunol 2023; 14:1163550. [PMID: 36911714 PMCID: PMC9996330 DOI: 10.3389/fimmu.2023.1163550] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fimmu.2022.1093242.].
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Affiliation(s)
- Johannes B Goll
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Steven E Bosinger
- Division of Microbiology & Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, United States.,Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States.,Emory NPRC Genomics Core, Emory National Primate Research Center, Emory University, Atlanta, GA, United States.,Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States
| | - Travis L Jensen
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Hasse Walum
- Division of Microbiology & Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Tyler Grimes
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Gregory K Tharp
- Emory NPRC Genomics Core, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Muktha S Natrajan
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States.,Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Azra Blazevic
- Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Richard D Head
- McDonnell Genome Institute, Washington University, St. Louis, MO, United States
| | - Casey E Gelber
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Kristen J Steenbergen
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Nirav B Patel
- Emory NPRC Genomics Core, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Patrick Sanz
- Office of Biodefense, Research Resources and Translational Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Nadine G Rouphael
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States.,Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States.,Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA, United States
| | - Evan J Anderson
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA, United States.,Center for Childhood Infections and Vaccines (CCIV) of Children's Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Mark J Mulligan
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States.,Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States.,Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA, United States.,New York University Vaccine Center, New York, NY, United States
| | - Daniel F Hoft
- Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO, United States.,Department of Molecular Microbiology & Immunology, Saint Louis University, St. Louis, MO, United States
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24
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Smith SA, Murray PM, Amancha PK, Ackerley CG, Tharp GK, Bosinger SE, Amara RR, Kelley CF. T-cell activation and B-cell interaction signatures in rectal tissues are associated with HIV replication in ex-vivo model of infection. AIDS 2022; 36:2101-2106. [PMID: 35969202 PMCID: PMC10228710 DOI: 10.1097/qad.0000000000003356] [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] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The rectal mucosa is a critical site of HIV vulnerability. We sought to identify transcriptomic features of rectal mucosal tissue prior to exposure associated with support or restriction of HIV replication. DESIGN Rectal tissue from HIV-negative cis gender men ( n = 57) underwent concurrent RNAseq transcriptomic analyses (two biopsies/participant) and challenge with HIV in the ex-vivo explant model of infection (three biopsies challenged/participant) as part of a larger cohort study to understand the rectal mucosal immune environment among MSM. METHODS P24 was quantified in the explant supernatants over a culture period of 18 days via ELISA. Participant median p24 log area under the curve was correlated with bulk transcriptomic data (Illumina HiSeq3000) to identify associations between gene expression and p24 production. Significant differentially expressed genes (DEGs) were identified via DESeq2 analysis and analyzed with Reactome to identify pathways of interest. RESULTS In total, 183 DEG (181 upregulated, two downregulated) were associated with higher p24 accumulation in the ex-vivo challenge model, including T-cell activation, B-cell function, and chemokine DEG. Reactome analysis of the upregulated genes identified 'Adaptive Immune System', 'Cytokine Signaling in Immune System', and 'Innate Immune System' as significantly upregulated pathways. CONCLUSION For the first time, we identified rectal tissue transcriptomic signatures associated with increased p24 production utilizing an ex-vivo model. Our findings are highly relevant to HIV transmission and the early establishment of HIV reservoirs in humans, and future studies should examine the identified pathways as targets for new or improved biomedical prevention or treatment interventions.
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Affiliation(s)
- S. Abigail Smith
- Division of Infectious Disease, The Hope Clinic of the Emory Vaccine Center, Decatur, GA, USA
| | - Phillip M. Murray
- Division of Infectious Disease, The Hope Clinic of the Emory Vaccine Center, Decatur, GA, USA
| | - Praveen K. Amancha
- Division of Infectious Disease, The Hope Clinic of the Emory Vaccine Center, Decatur, GA, USA
| | - Cassie G. Ackerley
- Division of Infectious Disease, The Hope Clinic of the Emory Vaccine Center, Decatur, GA, USA
| | - Gregory K. Tharp
- Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Steven E. Bosinger
- Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Rama R. Amara
- Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Colleen F. Kelley
- Division of Infectious Disease, The Hope Clinic of the Emory Vaccine Center, Decatur, GA, USA
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25
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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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26
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Bunjun R, Ramla TF, Jaumdally SZ, Noël-Romas L, Ayele H, Brown BP, Gamieldien H, Harryparsad R, Dabee S, Nair G, Onono M, Palanee-Phillips T, Scoville CW, Heller KB, Baeten JM, Bosinger SE, Burgener A, Passmore JAS, Jaspan H, Heffron R. Initiating Intramuscular Depot Medroxyprogesterone Acetate Increases Frequencies of Th17-like Human Immunodeficiency Virus Target Cells in the Genital Tract of Women in South Africa: A Randomized Trial. Clin Infect Dis 2022; 75:2000-2011. [PMID: 35941737 PMCID: PMC9710690 DOI: 10.1093/cid/ciac284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/15/2022] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Cervicovaginal CD4+ T cells are preferential targets for human immunodeficiency virus (HIV) infection and have consequently been used as a proxy measure for HIV susceptibility. The ECHO randomized trial offered a unique opportunity to consider the association between contraceptives and Th17-like cells within a trial designed to evaluate HIV risk. In a mucosal substudy of the ECHO trial, we compared the impact of initiating intramuscular depot medroxyprogesterone acetate (DMPA-IM), copper-IUD, and the levonorgestrel (LNG) implant on cervical T cells. METHODS Cervical cytobrushes from 58 women enrolled in the ECHO trial were collected at baseline and 1 month after contraceptive initiation. We phenotyped cervical T cells using multiparameter flow cytometry, characterized the vaginal microbiome using 16s sequencing, and determined proteomic signatures associated with Th17-like cells using mass spectrometry. RESULTS Unlike the LNG implant or copper-IUD, DMPA-IM was associated with higher frequencies of cervical Th17-like cells within 1 month of initiation (P = .012), including a highly susceptible, activated population co-expressing CD38, CCR5, and α4β7 (P = .003). After 1 month, women using DMPA-IM also had more Th17-like cells than women using the Cu-IUD (P = .0002) or LNG implant (P = .04). Importantly, in women using DMPA-IM, proteomic signatures signifying enhanced mucosal barrier function were associated with the increased abundance of Th17-like cells. We also found that a non-Lactobacillus-dominant microbiome at baseline was associated with more Th17-like cells post-DMPA-IM (P = .03), although this did not influence barrier function. CONCLUSIONS Our data suggest that DMPA-IM-driven accumulation of HIV-susceptible Th17-like cells might be counteracted by their role in maintaining mucosal barrier integrity. CLINICAL TRIALS REGISTRATION NCT02550067.
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Affiliation(s)
- Rubina Bunjun
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Tanko F Ramla
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa,The Medical Research Centre, Institute of Medical Research and Medicinal Plant Studies (IMPM), Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | - Shameem Z Jaumdally
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Laura Noël-Romas
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA,Department of Obstetrics and Gynecology, University of Manitoba, Winnipeg, Canada
| | - Hossaena Ayele
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA
| | - Bryan P Brown
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Hoyam Gamieldien
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Rushil Harryparsad
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Smritee Dabee
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | | | | | - Thesla Palanee-Phillips
- Wits Reproductive Health and HIV Institute (WHRI), Johannesburg, South Africa,University of Washington, Seattle, Washington, USA
| | | | | | | | - Steven E Bosinger
- Emory University, Atlanta, Georgia, USA,Yerkes National Primate Research Center, Atlanta, Georgia, USA
| | - Adam Burgener
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA,Department of Obstetrics and Gynecology, University of Manitoba, Winnipeg, Canada,Unit of Infectious Diseases, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
| | - Jo-Ann S Passmore
- Correspondence: J.-A. S. Passmore, Institute of Infectious Disease and Molecular Medicine, Division of Virology, Faculty of Health Sciences, University of Cape Town, Observatory 7925, South Africa ()
| | - Heather Jaspan
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa,Seattle Children’s Research Institute, Seattle, Washington, USA,University of Washington, Seattle, Washington, USA
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27
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Strongin Z, Hoang TN, Tharp GK, Rahmberg AR, Harper JL, Nguyen K, Franchitti L, Cervasi B, Lee M, Zhang Z, Boritz EA, Silvestri G, Marconi VC, Bosinger SE, Brenchley JM, Kulpa DA, Paiardini M. The role of CD101-expressing CD4 T cells in HIV/SIV pathogenesis and persistence. PLoS Pathog 2022; 18:e1010723. [PMID: 35867722 PMCID: PMC9348691 DOI: 10.1371/journal.ppat.1010723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/23/2022] [Revised: 08/03/2022] [Accepted: 07/01/2022] [Indexed: 11/18/2022] Open
Abstract
Despite the advent of effective antiretroviral therapy (ART), human immunodeficiency virus (HIV) continues to pose major challenges, with extensive pathogenesis during acute and chronic infection prior to ART initiation and continued persistence in a reservoir of infected CD4 T cells during long-term ART. CD101 has recently been characterized to play an important role in CD4 Treg potency. Using the simian immunodeficiency virus (SIV) model of HIV infection in rhesus macaques, we characterized the role and kinetics of CD101+ CD4 T cells in longitudinal SIV infection. Phenotypic analyses and single-cell RNAseq profiling revealed that CD101 marked CD4 Tregs with high immunosuppressive potential, distinct from CD101- Tregs, and these cells also were ideal target cells for HIV/SIV infection, with higher expression of CCR5 and α4β7 in the gut mucosa. Notably, during acute SIV infection, CD101+ CD4 T cells were preferentially depleted across all CD4 subsets when compared with their CD101- counterpart, with a pronounced reduction within the Treg compartment, as well as significant depletion in mucosal tissue. Depletion of CD101+ CD4 was associated with increased viral burden in plasma and gut and elevated levels of inflammatory cytokines. While restored during long-term ART, the reconstituted CD101+ CD4 T cells display a phenotypic profile with high expression of inhibitory receptors (including PD-1 and CTLA-4), immunsuppressive cytokine production, and high levels of Ki-67, consistent with potential for homeostatic proliferation. Both the depletion of CD101+ cells and phenotypic profile of these cells found in the SIV model were confirmed in people with HIV on ART. Overall, these data suggest an important role for CD101-expressing CD4 T cells at all stages of HIV/SIV infection and a potential rationale for targeting CD101 to limit HIV pathogenesis and persistence, particularly at mucosal sites.
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Affiliation(s)
- Zachary Strongin
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Timothy N. Hoang
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Gregory K. Tharp
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Andrew R. Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH; Bethesda, Maryland, United States of America
| | - Justin L. Harper
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Kevin Nguyen
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Lavinia Franchitti
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Barbara Cervasi
- Flow Cytometry Core, Emory Vaccine Center, Emory University; Atlanta, Georgia, United States of America
| | - Max Lee
- Vaccine Research Center, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Zhan Zhang
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Eli A. Boritz
- Vaccine Research Center, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, United States of America
- Division of Infectious Diseases, Emory University School of Medicine; Atlanta, Georgia, United States of America
| | - Vincent C. Marconi
- Division of Infectious Diseases, Emory University School of Medicine; Atlanta, Georgia, United States of America
- Division of Infectious Diseases Research, Atlanta Veterans Affairs Medical Center; Atlanta, Georgia, United States of America
- Rollins School of Public Health, Emory University; Atlanta, Georgia, United States of America
- Emory Vaccine Center, Atlanta, Georgia, United States of America
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, United States of America
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH; Bethesda, Maryland, United States of America
| | - Deanna A. Kulpa
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, United States of America
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, United States of America
- * E-mail:
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28
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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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Harper J, Ribeiro SP, Chan CN, Aid M, Deleage C, Micci L, Pino M, Cervasi B, Raghunathan G, Rimmer E, Ayanoglu G, Wu G, Shenvi N, Barnard RJ, Del Prete GQ, Busman-Sahay K, Silvestri G, Kulpa DA, Bosinger SE, Easley KA, Howell BJ, Gorman D, Hazuda DJ, Estes JD, Sekaly RP, Paiardini M. Interleukin-10 contributes to reservoir establishment and persistence in SIV-infected macaques treated with antiretroviral therapy. J Clin Invest 2022; 132:155251. [PMID: 35230978 PMCID: PMC9012284 DOI: 10.1172/jci155251] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 09/22/2021] [Accepted: 02/23/2022] [Indexed: 11/24/2022] Open
Abstract
Interleukin-10 (IL-10) is an immunosuppressive cytokine that signals through STAT3 to regulate T follicular helper (Tfh) cell differentiation and germinal center formation. In SIV-infected macaques, levels of IL-10 in plasma and lymph nodes (LNs) were induced by infection and not normalized with antiretroviral therapy (ART). During chronic infection, plasma IL-10 and transcriptomic signatures of IL-10 signaling were correlated with the cell-associated SIV-DNA content within LN CD4+ memory subsets, including Tfh cells, and predicted the frequency of CD4+ Tfh cells and their cell-associated SIV-DNA content during ART, respectively. In ART-treated rhesus macaques, cells harboring SIV-DNA by DNAscope were preferentially found in the LN B cell follicle in proximity to IL-10. Finally, we demonstrated that the in vivo neutralization of soluble IL-10 in ART-treated, SIV-infected macaques reduced B cell follicle maintenance and, by extension, LN memory CD4+ T cells, including Tfh cells and those expressing PD-1 and CTLA-4. Thus, these data support a role for IL-10 in maintaining a pool of target cells in lymphoid tissue that serve as a niche for viral persistence. Targeting IL-10 signaling to impair CD4+ T cell survival and improve antiviral immune responses may represent a novel approach to limit viral persistence in ART-suppressed people living with HIV.
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Affiliation(s)
- Justin Harper
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Susan P. Ribeiro
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Chi Ngai Chan
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Malika Aid
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, NIH, Frederick, Maryland, USA
| | - Luca Micci
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Discovery Oncology, Merck & Co., Inc., Boston, Massachusetts, USA
| | - Maria Pino
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Barbara Cervasi
- Flow Cytometry Core, Emory Vaccine Center, Emory University, Atlanta, Georgia, USA
| | | | - Eric Rimmer
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., South San Francisco, California, USA
| | - Gulesi Ayanoglu
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., South San Francisco, California, USA
| | - Guoxin Wu
- Department of Infectious Disease, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - Neeta Shenvi
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Richard J.O. Barnard
- Department of Infectious Disease, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, National Cancer Institute, NIH, Frederick, Maryland, USA
| | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Deanna A. Kulpa
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kirk A. Easley
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Bonnie J. Howell
- Department of Infectious Disease, Merck & Co., Inc., West Point, Pennsylvania, USA
| | | | - Daria J. Hazuda
- Department of Infectious Disease, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - Jacob D. Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
- Division of Pathobiology and Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, Oregon, USA
| | | | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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30
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Tanko RF, Bunjun R, Dabee S, Jaumdally SZ, Onono M, Nair G, Palanee-Phillips T, Harryparsad R, Happel AU, Gamieldien H, Qumbelo Y, Sinkala M, Scoville CW, Heller K, Baeten JM, Bosinger SE, Burgener A, Heffron R, Jaspan HB, Passmore JAS. The Effect Of Contraception On Genital Cytokines In Women Randomized To Copper Intrauterine Device, Intramuscular Depot Medroxyprogesterone Acetate Or Levonorgestrel Implant. J Infect Dis 2022; 226:907-919. [PMID: 35263421 PMCID: PMC9470113 DOI: 10.1093/infdis/jiac084] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/08/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The ECHO Trial randomized women to intramuscular depot medroxyprogesterone acetate (DMPA-IM), levonorgestrel implant (LNG-implant), or copper intrauterine device (Cu-IUD). In a sub-study of the ECHO Trial, we tested the hypothesis that contraceptives influence genital inflammation by comparing cervicovaginal cytokine changes following contraception initiation. In addition, we compared cytokine profiles in women who acquired HIV (cases) versus those remaining HIV-negative (controls). METHODS Women (n=251) from South Africa and Kenya were included. Twenty-seven cervicovaginal cytokines were measured by Luminex at baseline, 1- and 6-month post-contraceptive initiation. In addition, cytokines were measured pre-seroconversion in HIV cases (n=25) and controls (n=100). RESULTS At 6-months post-contraceptive initiation, women using Cu-IUD had increased concentrations of 25/27 cytokines compared to their respective baseline concentrations. In contrast, women initiating DMPA-IM and LNG-implant did not experience changes in cervicovaginal cytokines. Pre-seroconversion concentrations of IL-1β, IL-6, and TNF-α, previously associated with HIV risk, correlated with increased HIV risk in a logistic regression analysis, although not significantly after correcting for multiple comparisons. Adjusting for contraceptive arm did not alter these results. CONCLUSION Although Cu-IUD use broadly increased cervicovaginal cytokine concentrations at 6-months post-insertion, these inflammatory changes were found not to be a significant driver of HIV risk.
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Affiliation(s)
- Ramla F Tanko
- Institute of Infectious Disease and Molecular Medicine (IDM), Department of Pathology, University of Cape Town, South Africa.,The Medical Research Centre, Institute of Medical Research and Medicinal Plant Studies (IMPM), Ministry of Scientific Research and Innovation, Yaoundé, Cameroon
| | - Rubina Bunjun
- Institute of Infectious Disease and Molecular Medicine (IDM), Department of Pathology, University of Cape Town, South Africa
| | | | - Shameem Z Jaumdally
- Institute of Infectious Disease and Molecular Medicine (IDM), Department of Pathology, University of Cape Town, South Africa
| | | | | | - Thesla Palanee-Phillips
- Wits Reproductive Health and HIV Institute, University of the Witwatersrand, Johannesburg, South Africa
| | - Rushil Harryparsad
- Institute of Infectious Disease and Molecular Medicine (IDM), Department of Pathology, University of Cape Town, South Africa
| | - Anna-Ursula Happel
- Institute of Infectious Disease and Molecular Medicine (IDM), Department of Pathology, University of Cape Town, South Africa
| | - Hoyam Gamieldien
- Institute of Infectious Disease and Molecular Medicine (IDM), Department of Pathology, University of Cape Town, South Africa
| | - Yamkela Qumbelo
- Institute of Infectious Disease and Molecular Medicine (IDM), Department of Pathology, University of Cape Town, South Africa
| | - Musalula Sinkala
- Institute of Infectious Disease and Molecular Medicine (IDM), Department of Pathology, University of Cape Town, South Africa
| | | | | | - Jared M Baeten
- University of Washington, Seattle, USA.,Gilead Sciences, Foster City, USA
| | - Steven E Bosinger
- Emory University, Atlanta, USA.,Yerkes National Primate Research Center, Atlanta, USA
| | - Adam Burgener
- Center for Global Health and Diseases, Case Western Reserve University, Ohio, USA.,Department of Obstetrics & Gynecology and Medical Microbiology, University of Manitoba, Canada.,Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | | | - Heather B Jaspan
- Institute of Infectious Disease and Molecular Medicine (IDM), Department of Pathology, University of Cape Town, South Africa.,Seattle Children's Research Institute, Seattle, USA
| | - Jo-Ann S Passmore
- Institute of Infectious Disease and Molecular Medicine (IDM), Department of Pathology, University of Cape Town, South Africa.,NRF-DST CAPRISA Centre of Excellence in HIV Prevention, Durban, South Africa.,National Health Laboratory Service, Cape Town, South Africa
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31
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Balle C, Gupta PM, Tharp GK, Nelson SA, Konstantinus IN, Lennard K, Jaumdally SZ, Happel AU, Barnabas SL, Gill K, Bekker LG, Passmore JAS, Jaspan HB, Bosinger SE. Systems Analysis Reveals Contraceptive-Induced Alteration of Cervicovaginal Gene Expression in a Randomized Trial. Front Reprod Health 2022; 4:781687. [PMID: 36303659 PMCID: PMC9580795 DOI: 10.3389/frph.2022.781687] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/31/2022] [Indexed: 12/15/2022] Open
Abstract
Hormonal contraceptives (HCs) are vital in managing the reproductive health of women. However, HC usage has been linked to perturbations in cervicovaginal immunity and increased risk of sexually transmitted infections. Here, we evaluated the impact of three HCs on the cervicovaginal environment using high-throughput transcriptomics. From 2015 to 2017, 130 adolescent females aged 15-19 years were enrolled into a substudy of UChoose, a single-site, open-label randomized, crossover trial (NCT02404038) and randomized to injectable norethisterone-enanthate (Net-En), combined oral contraceptives (COC), or etonorgesterol/ethinyl-estradiol-combined contraceptive vaginal ring (CCVR). Cervicovaginal samples were collected after 16 weeks of randomized HC use and analyzed by RNA-Seq, 16S rRNA gene sequencing, and Luminex analysis. Participants in the CCVR arm had a significant elevation of transcriptional networks driven by IL-6, IL-1, and NFKB, and lower expression of genes supporting epithelial barrier integrity. An integrated multivariate analysis demonstrated that networks of microbial dysbiosis and inflammation best discriminated the CCVR arm from the other contraceptive groups, while genes involved in epithelial cell differentiation were predictive of the Net-En and COC arms. Collectively, these data from a randomized trial represent the most comprehensive "omics" analyses of the cervicovaginal response to HCs and provide important mechanistic guidelines for the provision of HCs in sub-Saharan Africa.
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Affiliation(s)
- Christina Balle
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Prachi M. Gupta
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Gregory K. Tharp
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Sydney A. Nelson
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA, United States
| | - Iyaloo N. Konstantinus
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa,Namibia Institute of Pathology, Windhoek, Namibia
| | - Katie Lennard
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Shameem Z. Jaumdally
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Shaun L. Barnabas
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa,Desmond Tutu Health Centre, University of Cape Town, Cape Town, South Africa,Family Clinical Research Center, Stellenbosch University, Tygerberg, South Africa
| | - Katherine Gill
- Desmond Tutu Health Centre, University of Cape Town, Cape Town, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu Health Centre, University of Cape Town, Cape Town, South Africa
| | - Jo-Ann S. Passmore
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa,National Health Laboratory Service, Cape Town, South Africa
| | - Heather B. Jaspan
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States,Department of Pediatrics and Global Health, University of Washington, Seattle, WA, United States
| | - Steven E. Bosinger
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA, United States,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States,Emory Vaccine Center, Emory University, Atlanta, GA, United States,*Correspondence: Steven E. Bosinger
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32
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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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33
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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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34
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Goll JB, Bosinger SE, Jensen TL, Walum H, Grimes T, Tharp GK, Natrajan MS, Blazevic A, Head RD, Gelber CE, Steenbergen KJ, Patel NB, Sanz P, Rouphael NG, Anderson EJ, Mulligan MJ, Hoft DF. The Vacc-SeqQC project: Benchmarking RNA-Seq for clinical vaccine studies. Front Immunol 2022; 13:1093242. [PMID: 36741404 PMCID: PMC9893923 DOI: 10.3389/fimmu.2022.1093242] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/30/2022] [Indexed: 01/20/2023] Open
Abstract
Introduction Over the last decade, the field of systems vaccinology has emerged, in which high throughput transcriptomics and other omics assays are used to probe changes of the innate and adaptive immune system in response to vaccination. The goal of this study was to benchmark key technical and analytical parameters of RNA sequencing (RNA-seq) in the context of a multi-site, double-blind randomized vaccine clinical trial. Methods We collected longitudinal peripheral blood mononuclear cell (PBMC) samples from 10 subjects before and after vaccination with a live attenuated Francisella tularensis vaccine and performed RNA-Seq at two different sites using aliquots from the same sample to generate two replicate datasets (5 time points for 50 samples each). We evaluated the impact of (i) filtering lowly-expressed genes, (ii) using external RNA controls, (iii) fold change and false discovery rate (FDR) filtering, (iv) read length, and (v) sequencing depth on differential expressed genes (DEGs) concordance between replicate datasets. Using synthetic mRNA spike-ins, we developed a method for empirically establishing minimal read-count thresholds for maintaining fold change accuracy on a per-experiment basis. We defined a reference PBMC transcriptome by pooling sequence data and established the impact of sequencing depth and gene filtering on transcriptome representation. Lastly, we modeled statistical power to detect DEGs for a range of sample sizes, effect sizes, and sequencing depths. Results and Discussion Our results showed that (i) filtering lowly-expressed genes is recommended to improve fold-change accuracy and inter-site agreement, if possible guided by mRNA spike-ins (ii) read length did not have a major impact on DEG detection, (iii) applying fold-change cutoffs for DEG detection reduced inter-set agreement and should be used with caution, if at all, (iv) reduction in sequencing depth had a minimal impact on statistical power but reduced the identifiable fraction of the PBMC transcriptome, (v) after sample size, effect size (i.e. the magnitude of fold change) was the most important driver of statistical power to detect DEG. The results from this study provide RNA sequencing benchmarks and guidelines for planning future similar vaccine studies.
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Affiliation(s)
- Johannes B Goll
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Steven E Bosinger
- Division of Microbiology & Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, United States.,Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA, United States.,Emory NPRC Genomics Core, Emory National Primate Research Center, Emory University, Atlanta, GA, United States.,Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States
| | - Travis L Jensen
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Hasse Walum
- Division of Microbiology & Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Tyler Grimes
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Gregory K Tharp
- Emory NPRC Genomics Core, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Muktha S Natrajan
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States.,Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States
| | - Azra Blazevic
- Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Richard D Head
- McDonnell Genome Institute, Washington University, St. Louis, MO, United States
| | - Casey E Gelber
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Kristen J Steenbergen
- Department of Biomedical Data Science and Bioinformatics, The Emmes Company, LLC, Rockville, MD, United States
| | - Nirav B Patel
- Emory NPRC Genomics Core, Emory National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Patrick Sanz
- Office of Biodefense, Research Resources and Translational Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Nadine G Rouphael
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States.,Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States.,Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA, United States
| | - Evan J Anderson
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA, United States.,Center for Childhood Infections and Vaccines (CCIV) of Children's Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
| | - Mark J Mulligan
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States.,Hope Clinic of the Emory Vaccine Center, Emory University, Atlanta, GA, United States.,Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA, United States.,New York University Vaccine Center, New York, NY, United States
| | - Daniel F Hoft
- Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO, United States.,Department of Molecular Microbiology & Immunology, Saint Louis University, St. Louis, MO, United States
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35
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Gopalakrishnan RM, Aid M, Mercado NB, Davis C, Malik S, Geiger E, Varner V, Jones R, Bosinger SE, Piedra-Mora C, Martinot AJ, Barouch DH, Reeves RK, Tan CS. Increased IL-6 expression precedes reliable viral detection in the rhesus macaque brain during acute SIV infection. JCI Insight 2021; 6:e152013. [PMID: 34676832 PMCID: PMC8564899 DOI: 10.1172/jci.insight.152013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 06/02/2021] [Accepted: 09/15/2021] [Indexed: 12/02/2022] Open
Abstract
Knowledge of immune activation in the brain during acute HIV infection is crucial for the prevention and treatment of HIV-associated neurological disorders. We determined regional brain (basal ganglia, thalamus, and frontal cortex) immune and virological profiles at 7 and 14 days post infection (dpi) with SIVmac239 in rhesus macaques. The basal ganglia and thalamus had detectable viruses earlier (7 dpi) than the frontal cortex (14 dpi) and contained higher quantities of viruses than the latter. Increased immune activation of astrocytes and significant infiltration of macrophages in the thalamus at 14 dpi coincided with elevated plasma viral load, and SIV colocalized only within macrophages. RNA signatures of proinflammatory responses, including IL-6, were detected at 7 dpi in microglia and interestingly, preceded reliable detection of virus in tissues and were maintained in the chronically infected macaques. Countering the proinflammatory response, the antiinflammatory response was not detected until increased TGF-β expression was found in perivascular macrophages at 14 dpi. But this response was not detected in chronic infection. Our data provide evidence that the interplay of acute proinflammatory and antiinflammatory responses in the brain likely contributed to the overt neuroinflammation, where the immune activation preceded reliable viral detection.
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Affiliation(s)
- Raja Mohan Gopalakrishnan
- Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Malika Aid
- Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Noe B. Mercado
- Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Caitlin Davis
- Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Shaily Malik
- Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Emma Geiger
- Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Valerie Varner
- Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Rhianna Jones
- Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven E. Bosinger
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Cesar Piedra-Mora
- Department of Comparative Pathobiology, Section of Pathology, and Departments of Infectious Diseases and Global Health and Biomedical Sciences, Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, USA
| | - Amanda J. Martinot
- Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Department of Comparative Pathobiology, Section of Pathology, and Departments of Infectious Diseases and Global Health and Biomedical Sciences, Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - R. Keith Reeves
- Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - C. Sabrina Tan
- Center for Virology and Vaccine Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
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36
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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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37
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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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38
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Arunachalam PS, Scott MKD, Hagan T, Li C, Feng Y, Wimmers F, Grigoryan L, Trisal M, Edara VV, Lai L, Chang SE, Feng A, Dhingra S, Shah M, Lee AS, Chinthrajah S, Sindher SB, Mallajosyula V, Gao F, Sigal N, Kowli S, Gupta S, Pellegrini K, Tharp G, Maysel-Auslender S, Hamilton S, Aoued H, Hrusovsky K, Roskey M, Bosinger SE, Maecker HT, Boyd SD, Davis MM, Utz PJ, Suthar MS, Khatri P, Nadeau KC, Pulendran B. Systems vaccinology of the BNT162b2 mRNA vaccine in humans. Nature 2021; 596:410-416. [PMID: 34252919 PMCID: PMC8761119 DOI: 10.1038/s41586-021-03791-x] [Citation(s) in RCA: 252] [Impact Index Per Article: 84.0] [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: 04/19/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023]
Abstract
The emergency use authorization of two mRNA vaccines in less than a year from the emergence of SARS-CoV-2 represents a landmark in vaccinology1,2. Yet, how mRNA vaccines stimulate the immune system to elicit protective immune responses is unknown. Here we used a systems vaccinology approach to comprehensively profile the innate and adaptive immune responses of 56 healthy volunteers who were vaccinated with the Pfizer-BioNTech mRNA vaccine (BNT162b2). Vaccination resulted in the robust production of neutralizing antibodies against the wild-type SARS-CoV-2 (derived from 2019-nCOV/USA_WA1/2020) and, to a lesser extent, the B.1.351 strain, as well as significant increases in antigen-specific polyfunctional CD4 and CD8 T cells after the second dose. Booster vaccination stimulated a notably enhanced innate immune response as compared to primary vaccination, evidenced by (1) a greater frequency of CD14+CD16+ inflammatory monocytes; (2) a higher concentration of plasma IFNγ; and (3) a transcriptional signature of innate antiviral immunity. Consistent with these observations, our single-cell transcriptomics analysis demonstrated an approximately 100-fold increase in the frequency of a myeloid cell cluster enriched in interferon-response transcription factors and reduced in AP-1 transcription factors, after secondary immunization. Finally, we identified distinct innate pathways associated with CD8 T cell and neutralizing antibody responses, and show that a monocyte-related signature correlates with the neutralizing antibody response against the B.1.351 variant. Collectively, these data provide insights into the immune responses induced by mRNA vaccination and demonstrate its capacity to prime the innate immune system to mount a more potent response after booster immunization.
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Affiliation(s)
- Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Madeleine K D Scott
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Thomas Hagan
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Lilit Grigoryan
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Meera Trisal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | | | - Lilin Lai
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Sarah Esther Chang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Allan Feng
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Shaurya Dhingra
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mihir Shah
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Alexandra S Lee
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Sharon Chinthrajah
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Sayantani B Sindher
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Fei Gao
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Natalia Sigal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Sangeeta Kowli
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Sheena Gupta
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | | | - Gregory Tharp
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Sofia Maysel-Auslender
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | | | - Hadj Aoued
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | | | | | - Steven E Bosinger
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Scott D Boyd
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Mehul S Suthar
- Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA.
- Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA, USA.
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39
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Wimmers F, Donato M, Kuo A, Ashuach T, Gupta S, Li C, Dvorak M, Foecke MH, Chang SE, Hagan T, De Jong SE, Maecker HT, van der Most R, Cheung P, Cortese M, Bosinger SE, Davis M, Rouphael N, Subramaniam S, Yosef N, Utz PJ, Khatri P, Pulendran B. The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination. Cell 2021; 184:3915-3935.e21. [PMID: 34174187 PMCID: PMC8316438 DOI: 10.1016/j.cell.2021.05.039] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [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: 01/21/2021] [Revised: 03/15/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022]
Abstract
Emerging evidence indicates a fundamental role for the epigenome in immunity. Here, we mapped the epigenomic and transcriptional landscape of immunity to influenza vaccination in humans at the single-cell level. Vaccination against seasonal influenza induced persistently diminished H3K27ac in monocytes and myeloid dendritic cells (mDCs), which was associated with impaired cytokine responses to Toll-like receptor stimulation. Single-cell ATAC-seq analysis revealed an epigenomically distinct subcluster of monocytes with reduced chromatin accessibility at AP-1-targeted loci after vaccination. Similar effects were observed in response to vaccination with the AS03-adjuvanted H5N1 pandemic influenza vaccine. However, this vaccine also stimulated persistently increased chromatin accessibility at interferon response factor (IRF) loci in monocytes and mDCs. This was associated with elevated expression of antiviral genes and heightened resistance to the unrelated Zika and Dengue viruses. These results demonstrate that vaccination stimulates persistent epigenomic remodeling of the innate immune system and reveal AS03's potential as an epigenetic adjuvant.
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Affiliation(s)
- Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alex Kuo
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shakti Gupta
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0412, La Jolla, CA 92093, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mariko Hinton Foecke
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, 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
| | - Sanne E De Jong
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Peggie Cheung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mario Cortese
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven E Bosinger
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mark Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, 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
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0412, La Jolla, CA 92093, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, 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; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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40
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Flynn JK, Langner CA, Karmele EP, Baker PJ, Pei L, Gorfu EG, Bochart RM, Santiana M, Smelkinson MG, Nutman TB, Altan-Bonnet N, Bosinger SE, Kelsall BL, Brenchley JM, Ortiz AM. Luminal microvesicles uniquely influence translocating bacteria after SIV infection. Mucosal Immunol 2021; 14:937-948. [PMID: 33731830 PMCID: PMC8225551 DOI: 10.1038/s41385-021-00393-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/10/2020] [Revised: 12/23/2020] [Accepted: 02/16/2021] [Indexed: 02/04/2023]
Abstract
Microbial translocation contributes to persistent inflammation in both treated and untreated HIV infection. Although translocation is due in part to a disintegration of the intestinal epithelial barrier, there is a bias towards the translocation of Proteobacteria. We hypothesized that intestinal epithelial microvesicle cargo differs after HIV infection and contributes to biased translocation. We isolated gastrointestinal luminal microvesicles before and after progressive simian immunodeficiency virus (SIV) infection in rhesus macaques and measured miRNA and antimicrobial peptide content. We demonstrate that these microvesicles display decreased miR-28-5p, -484, -584-3p, and -584-5p, and let-7b-3p, as well as increased beta-defensin 1 after SIV infection. We further observed dose-dependent growth sensitivity of commensal Lactobacillus salivarius upon co-culture with isolated microvesicles. Infection-associated microvesicle differences were not mirrored in non-progressively SIV-infected sooty mangabeys. Our findings describe novel alterations of antimicrobial control after progressive SIV infection that influence the growth of translocating bacterial taxa. These studies may lead to the development of novel therapeutics for treating chronic HIV infection, microbial translocation, and inflammation.
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Affiliation(s)
- Jacob K. Flynn
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892
| | - Charlotte A. Langner
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892
| | - Erik P. Karmele
- Mucosal Immunobiology Section, Laboratory of Molecular Immunology, NIAID, NIH, Bethesda, MD 20892
| | - Phillip J. Baker
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892
| | - Luxin Pei
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892
| | - Edlawit G. Gorfu
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892
| | - Rachele M. Bochart
- Division of Animal Resources, Yerkes National Primate Research Center (YNPRC), Atlanta, GA 30329
| | - Marianita Santiana
- Laboratory of Host-Pathogen Dynamics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | | | - Thomas B. Nutman
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Nihal Altan-Bonnet
- Laboratory of Host-Pathogen Dynamics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Steven E. Bosinger
- Yerkes Nonhuman Primate Genomics Core Laboratory, YNPRC, Atlanta, GA 30329,Division of Microbiology & Immunology, YNPRC, Atlanta, GA 30329,Department of Pathology & Laboratory Medicine, School of Medicine, Emory University, Atlanta, GA 30329
| | - Brian L. Kelsall
- Mucosal Immunobiology Section, Laboratory of Molecular Immunology, NIAID, NIH, Bethesda, MD 20892
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892,Corresponding author: Jason Brenchley, 4 Memorial Drive, 9000 Rockville Pike, Bethesda MD 20892, Phone: 301-496-1498, Fax: 301-480-1535,
| | - Alexandra M. Ortiz
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892
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41
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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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42
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Sultan JS, Wang T, Hunte R, Srinivasan S, McWalters J, Tharp GK, Bosinger SE, Fiedler TL, Atrio JM, Murphy K, Barnett R, Ray LR, Krows ML, Fredricks DN, Irungu E, Ngure K, Mugo N, Marrazzo J, Keller MJ, Herold BC. Differences in vaginal microbiota, host transcriptome and proteins in women with bacterial vaginosis are associated with metronidazole treatment response. J Infect Dis 2021; 224:2094-2104. [PMID: 34003290 DOI: 10.1093/infdis/jiab266] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 02/23/2021] [Accepted: 05/17/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Bacterial vaginosis (BV) treatment failures and recurrences are common. To identify features associated with treatment response, we compared vaginal microbiota and host ectocervical transcriptome before and after oral metronidazole therapy. METHODS Women with BV (Bronx, NY and Thika, Kenya) received 7 days of oral metronidazole at enrollment (Day 0) and underwent genital tract sampling of microbiome (16S rRNA gene sequencing), transcriptome (RNAseq), and immune mediator concentrations on Day 0, 15 and 35. RESULTS Bronx participants were more likely than Thika participants to clinically respond to metronidazole (19/20 vs 10/18, respectively, p=0.0067) and by changes in microbiota composition and diversity. After dichotomizing the cohort into responders and non-responders by change in alpha diversity between Day 35 and Day 0, we identified transcription differences associated with chemokine signaling (q=0.002) and immune system process (q=2.5e-8) that differentiated responders from non-responders were present at enrollment. Responders had significantly lower levels of CXCL9 in cervicovaginal lavage on Day 0 (p< 0.007) and concentrations of CXCL9, CXCL10 and MCP-1 increased significantly between Day 0 and Day 35 in responders versus non-responders. CONCLUSIONS Response to metronidazole is characterized by significant changes in chemokines and related transcripts suggesting that treatments that promote these pathways may prove beneficial.
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Affiliation(s)
- Joyce Serebrenik Sultan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Richard Hunte
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jessica McWalters
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gregory K Tharp
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Steven E Bosinger
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA, USA.,Emory University School of Medicine, Department of Pathology & Laboratory Medicine, Atlanta, GA, USA.,Emory Vaccine Center, Emory University, Atlanta,GA, USA
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jessica M Atrio
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kerry Murphy
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rebecca Barnett
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Laurie R Ray
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Meighan L Krows
- Department of Global Health, University of Washington, Seattle WA, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elizabeth Irungu
- Department of Medicine, Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Kenneth Ngure
- Department of Medicine, Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Nelly Mugo
- Department of Medicine, Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Jeanne Marrazzo
- University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Marla J Keller
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Betsy C Herold
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
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43
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Vanderheiden A, Thomas J, Soung AL, Davis-Gardner ME, Floyd K, Jin F, Cowan DA, Pellegrini K, Creanga A, Pegu A, Derrien-Colemyn A, Shi PY, Grakoui A, Klein RS, Bosinger SE, Kohlmeier JE, Menachery VD, Suthar MS. CCR2-dependent monocyte-derived cells restrict SARS-CoV-2 infection. bioRxiv 2021. [PMID: 33972938 DOI: 10.1101/2021.05.03.442538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
SARS-CoV-2 has caused a historic pandemic of respiratory disease (COVID-19) and current evidence suggests severe disease is associated with dysregulated immunity within the respiratory tract. However, the innate immune mechanisms that mediate protection during COVID-19 are not well defined. Here we characterize a mouse model of SARS-CoV-2 infection and find that early CCR2-dependent infiltration of monocytes restricts viral burden in the lung. We find that a recently developed mouse-adapted MA-SARS-CoV-2 strain, as well as the emerging B. 1.351 variant, trigger an inflammatory response in the lung characterized by expression of pro-inflammatory cytokines and interferon-stimulated genes. scRNA-seq analysis of lung homogenates identified a hyper-inflammatory monocyte profile. Using intravital antibody labeling, we demonstrate that MA-SARS-CoV-2 infection leads to increases in circulating monocytes and an influx of CD45+ cells into the lung parenchyma that is dominated by monocyte-derived cells. We utilize this model to demonstrate that mechanistically, CCR2 signaling promotes infiltration of classical monocytes into the lung and expansion of monocyte-derived cells. Parenchymal monocyte-derived cells appear to play a protective role against MA-SARS-CoV-2, as mice lacking CCR2 showed higher viral loads in the lungs, increased lung viral dissemination, and elevated inflammatory cytokine responses. These studies have identified a CCR2-monocyte axis that is critical for promoting viral control and restricting inflammation within the respiratory tract during SARS-CoV-2 infection.
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44
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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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45
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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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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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47
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Aid M, Busman-Sahay K, Vidal SJ, Maliga Z, Bondoc S, Starke C, Terry M, Jacobson CA, Wrijil L, Ducat S, Brook OR, Miller AD, Porto M, Pellegrini KL, Pino M, Hoang TN, Chandrashekar A, Patel S, Stephenson K, Bosinger SE, Andersen H, Lewis MG, Hecht JL, Sorger PK, Martinot AJ, Estes JD, Barouch DH. Vascular Disease and Thrombosis in SARS-CoV-2-Infected Rhesus Macaques. Cell 2020; 183:1354-1366.e13. [PMID: 33065030 PMCID: PMC7546181 DOI: 10.1016/j.cell.2020.10.005] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [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: 08/27/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022]
Abstract
The COVID-19 pandemic has led to extensive morbidity and mortality throughout the world. Clinical features that drive SARS-CoV-2 pathogenesis in humans include inflammation and thrombosis, but the mechanistic details underlying these processes remain to be determined. In this study, we demonstrate endothelial disruption and vascular thrombosis in histopathologic sections of lungs from both humans and rhesus macaques infected with SARS-CoV-2. To define key molecular pathways associated with SARS-CoV-2 pathogenesis in macaques, we performed transcriptomic analyses of bronchoalveolar lavage and peripheral blood and proteomic analyses of serum. We observed macrophage infiltrates in lung and upregulation of macrophage, complement, platelet activation, thrombosis, and proinflammatory markers, including C-reactive protein, MX1, IL-6, IL-1, IL-8, TNFα, and NF-κB. These results suggest a model in which critical interactions between inflammatory and thrombosis pathways lead to SARS-CoV-2-induced vascular disease. Our findings suggest potential therapeutic targets for COVID-19.
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Affiliation(s)
- Malika Aid
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | | | - Samuel J Vidal
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Zoltan Maliga
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen Bondoc
- Oregon Health & Sciences University, Beaverton, OR 97006, USA
| | - Carly Starke
- Oregon Health & Sciences University, Beaverton, OR 97006, USA
| | - Margaret Terry
- Oregon Health & Sciences University, Beaverton, OR 97006, USA
| | - Connor A Jacobson
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Linda Wrijil
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA
| | - Sarah Ducat
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA
| | - Olga R Brook
- Department of Radiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Andrew D Miller
- Department of Biomedical Sciences, Section of Anatomic Pathology, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA
| | | | - Kathryn L Pellegrini
- Yerkes Genomics Core Laboratory, 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
| | - Timothy N Hoang
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Shivani Patel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Kathryn Stephenson
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - 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 & Laboratory Medicine, Emory School of Medicine, Emory University, Atlanta, GA 30329, USA
| | | | | | - Jonathan L Hecht
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda J Martinot
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Tufts University Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA
| | - Jacob D Estes
- Oregon Health & Sciences University, Beaverton, OR 97006, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
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48
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Balle C, Konstantinus IN, Jaumdally SZ, Havyarimana E, Lennard K, Esra R, Barnabas SL, Happel AU, Moodie Z, Gill K, Pidwell T, Karaoz U, Brodie E, Maseko V, Gamieldien H, Bosinger SE, Myer L, Bekker LG, Passmore JAS, Jaspan HB. Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial. Nat Commun 2020; 11:5578. [PMID: 33149114 PMCID: PMC7643181 DOI: 10.1038/s41467-020-19382-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 09/08/2019] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
Young women in sub-Saharan Africa are disproportionally affected by HIV infection and unintended pregnancies. However, hormonal contraceptive (HC) use may influence HIV risk through changes in genital tract microbiota and inflammatory cytokines. To investigate this, 130 HIV negative adolescent females aged 15-19 years were enrolled into a substudy of UChoose, an open-label randomized crossover study (NCT02404038), comparing acceptability and contraceptive product preference as a proxy for HIV prevention delivery methods. Participants were randomized to injectable norethisterone enanthate (Net-En), combined oral contraceptives (COC) or etonorgesterol/ethinyl estradiol combined contraceptive vaginal ring (CCVR) for 16 weeks, then crossed over to another HC for 16 weeks. Cervicovaginal samples were collected at baseline, crossover and exit for characterization of the microbiota and measurement of cytokine levels; primary endpoints were cervical T cell activation, vaginal microbial diversity and cytokine concentrations. Adolescents randomized to COCs had lower vaginal microbial diversity and relative abundance of HIV risk-associated taxa compared to Net-En or CCVR. Cervicovaginal inflammatory cytokine concentrations were significantly higher in adolescents randomized to CCVR compared to COC and Net-En. This suggests that COC use may induce an optimal vaginal ecosystem by decreasing bacterial diversity and inflammatory taxa, while CCVR use is associated with genital inflammation.
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Affiliation(s)
- Christina Balle
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Iyaloo N Konstantinus
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Shameem Z Jaumdally
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Enock Havyarimana
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Katie Lennard
- Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Rachel Esra
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Shaun L Barnabas
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Katherine Gill
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Tanya Pidwell
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Ulas Karaoz
- Earth and Environmental Science, Lawrence Berkeley National Laboratories, Berkeley, CA, 94720, USA
| | - Eoin Brodie
- Earth and Environmental Science, Lawrence Berkeley National Laboratories, Berkeley, CA, 94720, USA.,University of California, Berkeley, CA, USA
| | - Venessa Maseko
- National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa
| | - Hoyam Gamieldien
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Steven E Bosinger
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine; Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Landon Myer
- Division of Epidemiology, Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Jo-Ann S Passmore
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,National Health Laboratory Service, Cape Town, South Africa
| | - Heather B Jaspan
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa. .,Seattle Children's Research Institute, Seattle, WA, USA. .,University of Washington Department of Pediatrics and Global Health, Seattle, WA, USA.
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49
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Konstantinus IN, Balle C, Jaumdally SZ, Galmieldien H, Pidwell T, Masson L, Tanko RF, Happel AU, Sinkala M, Myer L, Bosinger SE, Gill K, Bekker LG, Jaspan HB, Passmore JAS. Impact of Hormonal Contraceptives on Cervical T-helper 17 Phenotype and Function in Adolescents: Results from a Randomized, Crossover Study Comparing Long-acting Injectable Norethisterone Oenanthate (NET-EN), Combined Oral Contraceptive Pills, and Combined Contraceptive Vaginal Rings. Clin Infect Dis 2020; 71:e76-e87. [PMID: 31675420 PMCID: PMC7755094 DOI: 10.1093/cid/ciz1063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 06/11/2019] [Accepted: 10/25/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Adolescents in sub-Saharan Africa are at risk for human immunodeficiency virus (HIV) infection and unintended pregnancies. Observational studies suggest that injectable hormonal contraceptives (HCs) increase the HIV risk, although their effects on genital inflammation, particularly HIV-susceptible T-helper 17 (Th17) cells, are unknown. In a randomized crossover study, the effect of injectable norethisterone oenanthate (NET-EN), combined contraceptive vaginal rings (CCVR; NuvaRing), and combined oral contraceptive pills (COCPs) on cervical Th17 cells and cytokines were compared. METHODS Adolescents (n = 130; 15-19 years) were randomly assigned 1:1:1 to NET-EN, CCVR, or COCPs for 16 weeks, then subsequently crossed over to another HC for 16 weeks. Estrogen, follicular stimulating hormone (FSH), and luteinizing hormone (LH) levels were measured. Chemokine receptor 5 (CCR5), human leukocyte antigen (HLA) DR isotope, and cluster of differentiation 38 (CD38) expression by cervical cytobrush-derived CD4+ T cells was assessed by fluorescence-activated cell sorting. Th17 cells were defined as CCR6+ and CCR10-. Cervicovaginal Th17-related cytokines were measured by Luminex. RESULTS CCVR use for the first 16 weeks was associated with reduced Th17 frequencies and lower FSH and LH concentrations, as compared to NET-EN and COCPs, with FSH concentrations and Th17 frequencies correlating significantly. However, Th17-related cytokine concentrations (interleukin [IL]-21, IL-1β, tumor necrosis factor-α, interferon-γ) and CCR5, HLA-DR, CD38, and Th17 frequencies were significantly higher in CCVR than NET-EN and COCP. At crossover, CCVR users changing to COCPs or NET-EN did not resolve activation or cytokines, although switching from COCP to CCVRs increased cytokine concentrations. CONCLUSIONS CCVR use altered endogenous hormone levels and associated cervical Th17 cell frequencies to a greater extent than use of NET-EN or COCPs, although Th17 cells were more activated and Th17-related cytokine concentrations were elevated. While CCVRs may impact the HIV risk by regulating Th17 numbers, increased activation and inflammation may balance any risk gains.
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Affiliation(s)
- Iyaloo N Konstantinus
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Christina Balle
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Shameem Z Jaumdally
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Hoyam Galmieldien
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Tanya Pidwell
- Desmond Tutu Human Immunodeficiency Virus Centre, University of Cape Town, Cape Town, South Africa
| | - Lindi Masson
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ramla F Tanko
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anna-Ursula Happel
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Musalula Sinkala
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Landon Myer
- Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Steven E Bosinger
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, USA
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Atlanta, USA
| | - Katherine Gill
- Desmond Tutu Human Immunodeficiency Virus Centre, University of Cape Town, Cape Town, South Africa
| | - Linda-Gail Bekker
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Desmond Tutu Human Immunodeficiency Virus Centre, University of Cape Town, Cape Town, South Africa
| | - Heather B Jaspan
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Seattle Children’s Research Institute, Seattle, Washington, USA
- University of Washington Department of Pediatrics and Global Health, Seattle, Washington, USA
| | - Jo-Ann S Passmore
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
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50
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Zanoni M, Palesch D, Pinacchio C, Statzu M, Tharp GK, Paiardini M, Chahroudi A, Bosinger SE, Yoon J, Cox B, Silvestri G, Kulpa DA. Innate, non-cytolytic CD8+ T cell-mediated suppression of HIV replication by MHC-independent inhibition of virus transcription. PLoS Pathog 2020; 16:e1008821. [PMID: 32941545 PMCID: PMC7523993 DOI: 10.1371/journal.ppat.1008821] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 03/25/2020] [Revised: 09/29/2020] [Accepted: 07/18/2020] [Indexed: 12/31/2022] Open
Abstract
MHC-I-restricted, virus-specific cytotoxic CD8+ T cells (CTLs) may control human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) replication via the recognition and killing of productively infected CD4+ T cells. Several studies in SIV-infected macaques suggest that CD8+ T cells may also decrease virus production by suppressing viral transcription. Here, we show that non-HIV-specific, TCR-activated non-cytolytic CD8+ T cells suppress HIV transcription via a virus- and MHC-independent immunoregulatory mechanism that modulates CD4+ T cell proliferation and activation. We also demonstrate that this CD8+ T cell-mediated effect promotes the survival of infected CD4+ T cells harboring integrated, inducible virus. Finally, we used RNA sequencing and secretome analyses to identify candidate cellular pathways that are involved in the virus-silencing mediated by these CD8+ T cells. This study characterizes a previously undescribed mechanism of immune-mediated HIV silencing that may be involved in the establishment and maintenance of the reservoir under antiretroviral therapy and therefore represent a major obstacle to HIV eradication. Antiretroviral therapy (ART) has revolutionized the fight against the HIV pandemic, but this approach requires life-long treatment in order to maintain suppression of virus replication, as rapid viral rebound follows ART discontinuation. Our current inability to cure HIV infection despite ART is due to a persistent reservoir of latently infected CD4+ T cells harboring replication competent HIV integrated in their genome. Advancing our understanding of how the virus reservoir is established and maintained in the setting of ART-treated HIV-infection may reveal novel targets for immune-based interventions that can eradicate HIV. In this study, we developed an innovative co-culture experimental system to identify and characterize an important antiviral and immunoregulatory activity of non-cytolytic CD8+ T lymphocytes on activated CD4+ T cells. This activity drives CD4+ T cells into a more resting state that is less conducive to HIV transcription, thereby promoting the survival of infected CD4+ T cells harboring integrated, inducible virus. In addition, we identified cellular pathways that may mediate the CD8+ T cell-mediated transcriptional silencing of HIV in CD4+ T cells. The possibility that this non-cytolytic activity of CD8+ T cells may sustain the in vivo pool of latently infected CD4+ T cells under ART therefore represents a key, previously unrecognized obstacle to the elimination of the virus reservoir and the eradication of HIV infection.
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Affiliation(s)
- Michelle Zanoni
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - David Palesch
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Claudia Pinacchio
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Maura Statzu
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Gregory K. Tharp
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Ann Chahroudi
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
| | - Jack Yoon
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Bryan Cox
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
| | - Deanna A. Kulpa
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, and Emory Vaccine Center Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
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