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Wu TTH, Travaglini KJ, Rustagi A, Xu D, Zhang Y, Andronov L, Jang S, Gillich A, Dehghannasiri R, Martínez-Colón GJ, Beck A, Liu DD, Wilk AJ, Morri M, Trope WL, Bierman R, Weissman IL, Shrager JB, Quake SR, Kuo CS, Salzman J, Moerner W, Kim PS, Blish CA, Krasnow MA. Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung. J Exp Med 2024; 221:e20232192. [PMID: 38597954 PMCID: PMC11009983 DOI: 10.1084/jem.20232192] [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: 11/28/2023] [Revised: 02/09/2024] [Accepted: 03/04/2024] [Indexed: 04/11/2024] Open
Abstract
Early stages of deadly respiratory diseases including COVID-19 are challenging to elucidate in humans. Here, we define cellular tropism and transcriptomic effects of SARS-CoV-2 virus by productively infecting healthy human lung tissue and using scRNA-seq to reconstruct the transcriptional program in "infection pseudotime" for individual lung cell types. SARS-CoV-2 predominantly infected activated interstitial macrophages (IMs), which can accumulate thousands of viral RNA molecules, taking over 60% of the cell transcriptome and forming dense viral RNA bodies while inducing host profibrotic (TGFB1, SPP1) and inflammatory (early interferon response, CCL2/7/8/13, CXCL10, and IL6/10) programs and destroying host cell architecture. Infected alveolar macrophages (AMs) showed none of these extreme responses. Spike-dependent viral entry into AMs used ACE2 and Sialoadhesin/CD169, whereas IM entry used DC-SIGN/CD209. These results identify activated IMs as a prominent site of viral takeover, the focus of inflammation and fibrosis, and suggest targeting CD209 to prevent early pathology in COVID-19 pneumonia. This approach can be generalized to any human lung infection and to evaluate therapeutics.
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Affiliation(s)
- Timothy Ting-Hsuan Wu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Kyle J. Travaglini
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Duo Xu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Yue Zhang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Leonid Andronov
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - SoRi Jang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Astrid Gillich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
| | - Roozbeh Dehghannasiri
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Giovanny J. Martínez-Colón
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Aimee Beck
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Dan Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Aaron J. Wilk
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Winston L. Trope
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Rob Bierman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joseph B. Shrager
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Stephen R. Quake
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Christin S. Kuo
- Department of Pediatrics, Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Salzman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - W.E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Peter S. Kim
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Catherine A. Blish
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mark A. Krasnow
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, San Francisco, CA, USA
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Lee MJ, de los Rios Kobara I, Barnard TR, Vales Torres X, Tobin NH, Ferbas KG, Rimoin AW, Yang OO, Aldrovandi GM, Wilk AJ, Fulcher JA, Blish CA. NK Cell-Monocyte Cross-talk Underlies NK Cell Activation in Severe COVID-19. J Immunol 2024; 212:1693-1705. [PMID: 38578283 PMCID: PMC11102029 DOI: 10.4049/jimmunol.2300731] [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] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
NK cells in the peripheral blood of severe COVID-19 patients exhibit a unique profile characterized by activation and dysfunction. Previous studies have identified soluble factors, including type I IFN and TGF-β, that underlie this dysregulation. However, the role of cell-cell interactions in modulating NK cell function during COVID-19 remains unclear. To address this question, we combined cell-cell communication analysis on existing single-cell RNA sequencing data with in vitro primary cell coculture experiments to dissect the mechanisms underlying NK cell dysfunction in COVID-19. We found that NK cells are predicted to interact most strongly with monocytes and that this occurs via both soluble factors and direct interactions. To validate these findings, we performed in vitro cocultures in which NK cells from healthy human donors were incubated with monocytes from COVID-19+ or healthy donors. Coculture of healthy NK cells with monocytes from COVID-19 patients recapitulated aspects of the NK cell phenotype observed in severe COVID-19, including decreased expression of NKG2D, increased expression of activation markers, and increased proliferation. When these experiments were performed in a Transwell setting, we found that only CD56bright CD16- NK cells were activated in the presence of severe COVID-19 patient monocytes. O-link analysis of supernatants from Transwell cocultures revealed that cultures containing severe COVID-19 patient monocytes had significantly elevated levels of proinflammatory cytokines and chemokines, as well as TGF-β. Collectively, these results demonstrate that interactions between NK cells and monocytes in the peripheral blood of COVID-19 patients contribute to NK cell activation and dysfunction in severe COVID-19.
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Affiliation(s)
- Madeline J. Lee
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
- Stanford Immunology Program, Stanford University School of Medicine, Palo Alto, CA
| | - Izumi de los Rios Kobara
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
- Stanford Immunology Program, Stanford University School of Medicine, Palo Alto, CA
| | - Trisha R. Barnard
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
| | - Xariana Vales Torres
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
- Stanford Immunology Program, Stanford University School of Medicine, Palo Alto, CA
| | - Nicole H. Tobin
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Kathie G. Ferbas
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Anne W. Rimoin
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA
| | - Otto O. Yang
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Grace M. Aldrovandi
- Division of Infectious Diseases, Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Aaron J. Wilk
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Palo Alto, CA
| | - Jennifer A. Fulcher
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Catherine A. Blish
- Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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Dzanibe S, Wilk AJ, Canny S, Ranganath T, Alinde B, Rubelt F, Huang H, Davis MM, Holmes SP, Jaspan HB, Blish CA, Gray CM. Premature skewing of T cell receptor clonality and delayed memory expansion in HIV-exposed infants. Nat Commun 2024; 15:4080. [PMID: 38744812 PMCID: PMC11093981 DOI: 10.1038/s41467-024-47955-5] [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: 05/25/2023] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
While preventing vertical HIV transmission has been very successful, HIV-exposed uninfected infants (iHEU) experience an elevated risk to infections compared to HIV-unexposed and uninfected infants (iHUU). Here we present a longitudinal multimodal analysis of infant immune ontogeny that highlights the impact of HIV/ARV exposure. Using mass cytometry, we show alterations in T cell memory differentiation between iHEU and iHUU being significant from week 15 of life. The altered memory T cell differentiation in iHEU was preceded by lower TCR Vβ clonotypic diversity and linked to TCR clonal depletion within the naïve T cell compartment. Compared to iHUU, iHEU had elevated CD56loCD16loPerforin+CD38+CD45RA+FcεRIγ+ NK cells at 1 month postpartum and whose abundance pre-vaccination were predictive of vaccine-induced pertussis and rotavirus antibody responses post 3 months of life. Collectively, HIV/ARV exposure disrupted the trajectory of innate and adaptive immunity from birth which may underlie relative vulnerability to infections in iHEU.
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Affiliation(s)
- Sonwabile Dzanibe
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Aaron J Wilk
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Susan Canny
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
- Division of Rheumatology, Department of Pediatrics, Seattle Children's Hospital, Seattle, WA, USA
| | - Thanmayi Ranganath
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Berenice Alinde
- Division of Immunology, Department of Biomedical Sciences, Biomedical Research Institute, Stellenbosch University, Cape Town, South Africa
| | - Florian Rubelt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Huang Huang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Heather B Jaspan
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Seattle Children's Research Institute and Department of Paediatrics and Global Health, University of Washington, Seattle, WA, USA.
| | - Catherine A Blish
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA.
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Clive M Gray
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Immunology, Department of Biomedical Sciences, Biomedical Research Institute, Stellenbosch University, Cape Town, South Africa.
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4
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Zhang M, Leong MW, Mitch WA, Blish CA, Boehm A. Persistence and free chlorine disinfection of human coronaviruses and their surrogates in water. Appl Environ Microbiol 2024; 90:e0005524. [PMID: 38511945 PMCID: PMC11022552 DOI: 10.1128/aem.00055-24] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
The coronavirus disease 2019 pandemic illustrates the importance of understanding the behavior and control of human pathogenic viruses in the environment. Exposure via water (drinking, bathing, and recreation) is a known route of transmission of viruses to humans, but the literature is relatively void of studies on the persistence of many viruses, especially coronaviruses, in water and their susceptibility to chlorine disinfection. To fill that knowledge gap, we evaluated the persistence and free chlorine disinfection of human coronavirus OC43 (HCoV-OC43) and its surrogates, murine hepatitis virus (MHV) and porcine transmissible gastroenteritis virus (TGEV), in drinking water and laboratory buffer using cell culture methods. The decay rate constants of human coronavirus and its surrogates in water varied, depending on virus and water matrix. In drinking water without disinfectant addition, MHV showed the largest decay rate constant (estimate ± standard error, 2.25 ± 0.09 day-1) followed by HCoV-OC43 (0.99 ± 0.12 day-1) and TGEV (0.65 ± 0.06 day-1), while in phosphate buffer without disinfectant addition, HCoV-OC43 (0.51 ± 0.10 day-1) had a larger decay rate constant than MHV (0.28 ± 0.03 day-1) and TGEV (0.24 ± 0.02 day-1). Upon free chlorine disinfection, the inactivation rates of coronaviruses were independent of free chlorine concentration and were not affected by water matrix, though they still varied between viruses. TGEV showed the highest susceptibility to free chlorine disinfection with the inactivation rate constant of 113.50 ± 7.50 mg-1 min-1 L, followed by MHV (81.33 ± 4.90 mg-1 min-1 L) and HCoV-OC43 (59.42 ± 4.41 mg-1 min-1 L). IMPORTANCE This study addresses an important knowledge gap on enveloped virus persistence and disinfection in water. Results have immediate practical applications for shaping evidence-based water policies, particularly in the development of disinfection strategies for pathogenic virus control.
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Affiliation(s)
- Mengyang Zhang
- Department of Civil and Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, California, USA
| | - Michelle Wei Leong
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - William A. Mitch
- Department of Civil and Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, California, USA
| | - Catherine A. Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Alexandria Boehm
- Department of Civil and Environmental Engineering, School of Engineering and Doerr School of Sustainability, Stanford University, Stanford, California, USA
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5
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Zaslavsky ME, Craig E, Michuda JK, Sehgal N, Ram-Mohan N, Lee JY, Nguyen KD, Hoh RA, Pham TD, Röltgen K, Lam B, Parsons ES, Macwana SR, DeJager W, Drapeau EM, Roskin KM, Cunningham-Rundles C, Moody MA, Haynes BF, Goldman JD, Heath JR, Nadeau KC, Pinsky BA, Blish CA, Hensley SE, Jensen K, Meyer E, Balboni I, Utz PJ, Merrill JT, Guthridge JM, James JA, Yang S, Tibshirani R, Kundaje A, Boyd SD. Disease diagnostics using machine learning of immune receptors. bioRxiv 2024:2022.04.26.489314. [PMID: 35547855 PMCID: PMC9094102 DOI: 10.1101/2022.04.26.489314] [Citation(s) in RCA: 1] [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: 11/25/2022]
Abstract
Clinical diagnosis typically incorporates physical examination, patient history, and various laboratory tests and imaging studies, but makes limited use of the human system's own record of antigen exposures encoded by receptors on B cells and T cells. We analyzed immune receptor datasets from 593 individuals to develop MAchine Learning for Immunological Diagnosis (Mal-ID) , an interpretive framework to screen for multiple illnesses simultaneously or precisely test for one condition. This approach detects specific infections, autoimmune disorders, vaccine responses, and disease severity differences. Human-interpretable features of the model recapitulate known immune responses to SARS-CoV-2, Influenza, and HIV, highlight antigen-specific receptors, and reveal distinct characteristics of Systemic Lupus Erythematosus and Type-1 Diabetes autoreactivity. This analysis framework has broad potential for scientific and clinical interpretation of human immune responses.
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Wilk AJ, Shalek AK, Holmes S, Blish CA. Comparative analysis of cell-cell communication at single-cell resolution. Nat Biotechnol 2024; 42:470-483. [PMID: 37169965 PMCID: PMC10638471 DOI: 10.1038/s41587-023-01782-z] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/05/2023] [Indexed: 05/13/2023]
Abstract
Inference of cell-cell communication from single-cell RNA sequencing data is a powerful technique to uncover intercellular communication pathways, yet existing methods perform this analysis at the level of the cell type or cluster, discarding single-cell-level information. Here we present Scriabin, a flexible and scalable framework for comparative analysis of cell-cell communication at single-cell resolution that is performed without cell aggregation or downsampling. We use multiple published atlas-scale datasets, genetic perturbation screens and direct experimental validation to show that Scriabin accurately recovers expected cell-cell communication edges and identifies communication networks that can be obscured by agglomerative methods. Additionally, we use spatial transcriptomic data to show that Scriabin can uncover spatial features of interaction from dissociated data alone. Finally, we demonstrate applications to longitudinal datasets to follow communication pathways operating between timepoints. Our approach represents a broadly applicable strategy to reveal the full structure of niche-phenotype relationships in health and disease.
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Affiliation(s)
- Aaron J Wilk
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA.
| | - Alex K Shalek
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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7
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Ratnasiri K, Zheng H, Toh J, Yao Z, Duran V, Donato M, Roederer M, Kamath M, Todd JPM, Gagne M, Foulds KE, Francica JR, Corbett KS, Douek DC, Seder RA, Einav S, Blish CA, Khatri P. Systems immunology of transcriptional responses to viral infection identifies conserved antiviral pathways across macaques and humans. Cell Rep 2024; 43:113706. [PMID: 38294906 PMCID: PMC10915397 DOI: 10.1016/j.celrep.2024.113706] [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: 07/03/2023] [Revised: 11/02/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Viral pandemics and epidemics pose a significant global threat. While macaque models of viral disease are routinely used, it remains unclear how conserved antiviral responses are between macaques and humans. Therefore, we conducted a cross-species analysis of transcriptomic data from over 6,088 blood samples from macaques and humans infected with one of 31 viruses. Our findings demonstrate that irrespective of primate or viral species, there are conserved antiviral responses that are consistent across infection phase (acute, chronic, or latent) and viral genome type (DNA or RNA viruses). Leveraging longitudinal data from experimental challenges, we identify virus-specific response kinetics such as host responses to Coronaviridae and Orthomyxoviridae infections peaking 1-3 days earlier than responses to Filoviridae and Arenaviridae viral infections. Our results underscore macaque studies as a powerful tool for understanding viral pathogenesis and immune responses that translate to humans, with implications for viral therapeutic development and pandemic preparedness.
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Affiliation(s)
- Kalani Ratnasiri
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jiaying Toh
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhiyuan Yao
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Veronica Duran
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA
| | - Michele Donato
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Megha Kamath
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul M Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph R Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirit Einav
- Department of Microbiology and Immunology, Stanford University, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.
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8
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Wilk AJ, Marceau JO, Kazer SW, Fleming I, Miao VN, Galvez-Reyes J, Kimata JT, Shalek AK, Holmes S, Overbaugh J, Blish CA. Pro-inflammatory feedback loops define immune responses to pathogenic Lentivirus infection. Genome Med 2024; 16:24. [PMID: 38317183 PMCID: PMC10840164 DOI: 10.1186/s13073-024-01290-y] [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: 04/17/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND The Lentivirus human immunodeficiency virus (HIV) causes chronic inflammation and AIDS in humans, with variable rates of disease progression between individuals driven by both host and viral factors. Similarly, simian lentiviruses vary in their pathogenicity based on characteristics of both the host species and the virus strain, yet the immune underpinnings that drive differential Lentivirus pathogenicity remain incompletely understood. METHODS We profile immune responses in a unique model of differential lentiviral pathogenicity where pig-tailed macaques are infected with highly genetically similar variants of SIV that differ in virulence. We apply longitudinal single-cell transcriptomics to this cohort, along with single-cell resolution cell-cell communication techniques, to understand the immune mechanisms underlying lentiviral pathogenicity. RESULTS Compared to a minimally pathogenic lentiviral variant, infection with a highly pathogenic variant results in a more delayed, broad, and sustained activation of inflammatory pathways, including an extensive global interferon signature. Conversely, individual cells infected with highly pathogenic Lentivirus upregulated fewer interferon-stimulated genes at a lower magnitude, indicating that highly pathogenic Lentivirus has evolved to partially escape from interferon responses. Further, we identify CXCL10 and CXCL16 as important molecular drivers of inflammatory pathways specifically in response to highly pathogenic Lentivirus infection. Immune responses to highly pathogenic Lentivirus infection are characterized by amplifying regulatory circuits of pro-inflammatory cytokines with dense longitudinal connectivity. CONCLUSIONS Our work presents a model of lentiviral pathogenicity where failures in early viral control mechanisms lead to delayed, sustained, and amplifying pro-inflammatory circuits, which in turn drives disease progression.
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Affiliation(s)
- Aaron J Wilk
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Joshua O Marceau
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Samuel W Kazer
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Ira Fleming
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Vincent N Miao
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Program in Health Sciences & Technology, Harvard Medical School & MIT, Boston, MA, 02115, USA
| | - Jennyfer Galvez-Reyes
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jason T Kimata
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Alex K Shalek
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA, 94305, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Catherine A Blish
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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9
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Li Z, Amaya L, Pi R, Wang SK, Ranjan A, Waymouth RM, Blish CA, Chang HY, Wender PA. Charge-altering releasable transporters enhance mRNA delivery in vitro and exhibit in vivo tropism. Nat Commun 2023; 14:6983. [PMID: 37914693 PMCID: PMC10620205 DOI: 10.1038/s41467-023-42672-x] [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: 01/26/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023] Open
Abstract
The introduction of more effective and selective mRNA delivery systems is required for the advancement of many emerging biomedical technologies including the development of prophylactic and therapeutic vaccines, immunotherapies for cancer and strategies for genome editing. While polymers and oligomers have served as promising mRNA delivery systems, their efficacy in hard-to-transfect cells such as primary T lymphocytes is often limited as is their cell and organ tropism. To address these problems, considerable attention has been placed on structural screening of various lipid and cation components of mRNA delivery systems. Here, we disclose a class of charge-altering releasable transporters (CARTs) that differ from previous CARTs based on their beta-amido carbonate backbone (bAC) and side chain spacing. These bAC-CARTs exhibit enhanced mRNA transfection in primary T lymphocytes in vitro and enhanced protein expression in vivo with highly selective spleen tropism, supporting their broader therapeutic use as effective polyanionic delivery systems.
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Affiliation(s)
- Zhijian Li
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Laura Amaya
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ruoxi Pi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford, CA, 94305, USA
| | - Sean K Wang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alok Ranjan
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Robert M Waymouth
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Catherine A Blish
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA
| | - Paul A Wender
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA.
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, 94305, USA.
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10
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Abstract
Natural killer (NK) cells are critical effectors of antiviral immunity. Researchers have therefore sought to characterize the NK cell response to coronavirus disease 2019 (COVID-19) and the virus that causes it, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The NK cells of patients with severe COVID-19 undergo extensive phenotypic and functional changes. For example, the NK cells from critically ill patients with COVID-19 are highly activated and exhausted, with poor cytotoxic function and cytokine production upon stimulation. The NK cell response to SARS-CoV-2 is also modulated by changes induced in virally infected cells, including the ability of a viral peptide to bind HLA-E, preventing NK cells from receiving inhibitory signals, and the downregulation of major histocompatibility complex class I and ligands for the activating receptor NKG2D. These changes have important implications for the ability of infected cells to escape NK cell killing. The implications of these findings for antibody-dependent NK cell activity in COVID-19 are also reviewed. Despite these advances in the understanding of the NK cell response to SARS-CoV-2, there remain critical gaps in our current understanding and a wealth of avenues for future research on this topic.
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Affiliation(s)
- Madeline J Lee
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA.
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11
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Núñez I, Gillard J, Fragoso-Saavedra S, Feyaerts D, Islas-Weinstein L, Gallegos-Guzmán AA, Valente-García U, Meyerowitz J, Kelly JD, Chen H, Ganio E, Benkendorff A, Flores-Gouyonnet J, Dammann-Beltrán P, Heredia-González JF, Rangel-Gutiérrez GA, Blish CA, Nadeau KC, Nolan G, Crispín JC, McIlwain DR, Gaudillière B, Valdés-Ferrer SI. Longitudinal clinical phenotyping of post COVID condition in Mexican adults recovering from severe COVID-19: a prospective cohort study. Front Med (Lausanne) 2023; 10:1236702. [PMID: 37727759 PMCID: PMC10505811 DOI: 10.3389/fmed.2023.1236702] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/08/2023] [Indexed: 09/21/2023] Open
Abstract
Introduction Few studies have evaluated the presence of Post COVID-19 conditions (PCC) in people from Latin America, a region that has been heavily afflicted by the COVID-19 pandemic. In this study, we describe the frequency, co-occurrence, predictors, and duration of 23 symptoms in a cohort of Mexican patients with PCC. Methods We prospectively enrolled and followed adult patients hospitalized for severe COVID-19 at a tertiary care centre in Mexico City. The incidence of PCC symptoms was determined using questionnaires. Unsupervised clustering of PCC symptom co-occurrence and Kaplan-Meier analyses of symptom persistence were performed. The effect of baseline clinical characteristics was evaluated using Cox regression models and reported with hazard ratios (HR). Results We found that amongst 192 patients with PCC, respiratory problems were the most prevalent and commonly co-occurred with functional activity impairment. 56% had ≥5 persistent symptoms. Symptom persistence probability at 360 days 0.78. Prior SARS-CoV-2 vaccination and infection during the Delta variant wave were associated with a shorter duration of PCC. Male sex was associated with a shorter duration of functional activity impairment and respiratory symptoms. Hypertension and diabetes were associated with a longer duration of functional impairment. Previous vaccination accelerated PCC recovery. Discussion In our cohort, PCC symptoms were frequent (particularly respiratory and neurocognitive ones) and persistent. Importantly, prior SARS-CoV-2 vaccination resulted in a shorter duration of PCC.
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Affiliation(s)
- Isaac Núñez
- Department of Medical Education, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Division of Postrgraduate Studies, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Joshua Gillard
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Sergio Fragoso-Saavedra
- Department of Medical Education, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Division of Postrgraduate Studies, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Combined Study Plan in Medicine, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - León Islas-Weinstein
- Department of Neurology & Psychiatry, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Angel A. Gallegos-Guzmán
- Department of Neurology & Psychiatry, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Uriel Valente-García
- Department of Neurology & Psychiatry, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Justin Meyerowitz
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - J. Daniel Kelly
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA, United States
- Institute for Global Health Sciences, UCSF, San Francisco, CA, United States
- F.IProctor Foundation, UCSF, San Francisco, CA, United States
| | - Han Chen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Edward Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Alexander Benkendorff
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jaime Flores-Gouyonnet
- Department of Neurology & Psychiatry, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Pedro Dammann-Beltrán
- Department of Neurology & Psychiatry, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - Gabriela A. Rangel-Gutiérrez
- Combined Study Plan in Medicine, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Catherine A. Blish
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
- Division of Infectious Diseases, Stanford University, Stanford, CA, United States
| | - Kari C. Nadeau
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, CA, United States
- Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, Stanford, CA, United States
- Institute for Immunity, Transplantation, and Infectious Diseases, Stanford University, Stanford, CA, United States
| | - Garry Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Jose C. Crispín
- School of Medicine and Health Sciencies, Tecnologico de Monterrey, Mexico City, Mexico
- Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - David R. McIlwain
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Brice Gaudillière
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Sergio I. Valdés-Ferrer
- Department of Neurology & Psychiatry, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
- Center for Biomedical Science, Feinstein Institutes for Medical Research, New York, NY, United States
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12
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Dzanibe S, Wilk AJ, Canny S, Ranganath T, Alinde B, Rubelt F, Huang H, Davis MM, Holmes S, Jaspan HB, Blish CA, Gray CM. Disrupted memory T cell expansion in HIV-exposed uninfected infants is preceded by premature skewing of T cell receptor clonality. bioRxiv 2023:2023.05.19.540713. [PMID: 37292866 PMCID: PMC10245741 DOI: 10.1101/2023.05.19.540713] [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] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
While preventing vertical HIV transmission has been very successful, the increasing number of HIV-exposed uninfected infants (iHEU) experience an elevated risk to infections compared to HIV-unexposed and uninfected infants (iHUU). Immune developmental differences between iHEU and iHUU remains poorly understood and here we present a longitudinal multimodal analysis of infant immune ontogeny that highlights the impact of HIV/ARV exposure. Using mass cytometry, we show alterations and differences in the emergence of NK cell populations and T cell memory differentiation between iHEU and iHUU. Specific NK cells observed at birth were also predictive of acellular pertussis and rotavirus vaccine-induced IgG and IgA responses, respectively, at 3 and 9 months of life. T cell receptor Vβ clonotypic diversity was significantly and persistently lower in iHEU preceding the expansion of T cell memory. Our findings show that HIV/ARV exposure disrupts innate and adaptive immunity from birth which may underlie relative vulnerability to infections.
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Affiliation(s)
- Sonwabile Dzanibe
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Aaron J. Wilk
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Susan Canny
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA
- Division of Rheumatology, Department of Pediatrics, Seattle Children’s Hospital, Seattle, WA USA
| | - Thanmayi Ranganath
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Berenice Alinde
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Florian Rubelt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Huang Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M. Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, School of Medicine, Stanford University, Stanford, CA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Heather B. Jaspan
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Seattle Children’s Research Institute and Department of Paediatrics and Global Health, University of Washington, Seattle, WA
| | - Catherine A. Blish
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA
| | - Clive M. Gray
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
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13
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Choi SS, van Unen V, Zhang H, Rustagi A, Alwahabi SA, Santos AJ, Chan JE, Lam B, Solis D, Mah J, Röltgen K, Trope W, Guh-Siesel A, Lin Z, Beck A, Edwards C, Mallajosyula V, Martin BA, Dunn JCY, Shrager J, Baric RA, Pinsky B, Boyd SD, Blish CA, Davis MM, Kuo CJ. Organoid modeling of lung-resident immune responses to SARS-CoV-2 infection. Res Sq 2023:rs.3.rs-2870695. [PMID: 37205380 PMCID: PMC10187413 DOI: 10.21203/rs.3.rs-2870695/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Tissue-resident immunity underlies essential host defenses against pathogens, but analysis in humans has lacked in vitro model systems where epithelial infection and accompanying resident immune cell responses can be observed en bloc. Indeed, human primary epithelial organoid cultures typically omit immune cells, and human tissue resident-memory lymphocytes are conventionally assayed without an epithelial infection component, for instance from peripheral blood, or after extraction from organs. Further, the study of resident immunity in animals can be complicated by interchange between tissue and peripheral immune compartments. To study human tissue-resident infectious immune responses in isolation from secondary lymphoid organs, we generated adult human lung three-dimensional air-liquid interface (ALI) lung organoids from intact tissue fragments that co-preserve epithelial and stromal architecture alongside endogenous lung-resident immune subsets. These included T, B, NK and myeloid cells, with CD69+CD103+ tissue-resident and CCR7- and/or CD45RA- TRM and conservation of T cell receptor repertoires, all corresponding to matched fresh tissue. SARS-CoV-2 vigorously infected organoid lung epithelium, alongside secondary induction of innate cytokine production that was inhibited by antiviral agents. Notably, SARS-CoV-2-infected organoids manifested adaptive virus-specific T cell activation that was specific for seropositive and/or previously infected donor individuals. This holistic non-reconstitutive organoid system demonstrates the sufficiency of lung to autonomously mount adaptive T cell memory responses without a peripheral lymphoid component, and represents an enabling method for the study of human tissue-resident immunity.
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Affiliation(s)
- Shannon S. Choi
- Department of Medicine, Divisions of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Vincent van Unen
- Department of Medicine, Divisions of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Departments of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Huimin Zhang
- Department of Medicine, Divisions of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Arjun Rustagi
- Department of Infectious Disease and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samira A. Alwahabi
- Department of Medicine, Divisions of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - António J.M. Santos
- Department of Medicine, Divisions of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua E. Chan
- Department of Medicine, Divisions of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brandon Lam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel Solis
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jordan Mah
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Winston Trope
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Guh-Siesel
- Department of Medicine, Divisions of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zhongqi Lin
- Department of Medicine, Divisions of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aimee Beck
- Department of Infectious Disease and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caitlin Edwards
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill, Chapel Hill, NC 27599, USA
| | - Vamsee Mallajosyula
- Departments of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brock A. Martin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - James C. Y. Dunn
- Department of Pediatric Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph Shrager
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ralph A. Baric
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill, Chapel Hill, NC 27599, USA
| | - Benjamin Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Catherine A. Blish
- Stanford Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Infectious Disease and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Mark M. Davis
- Departments of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Calvin J. Kuo
- Department of Medicine, Divisions of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
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14
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Feng A, Yang EY, Moore AR, Dhingra S, Chang SE, Yin X, Pi R, Mack EK, Völkel S, Geßner R, Gündisch M, Neubauer A, Renz H, Tsiodras S, Fragkou PC, Asuni AA, Levitt JE, Wilson JG, Leong M, Lumb JH, Mao R, Pinedo K, Roque J, Richards CM, Stabile M, Swaminathan G, Salagianni ML, Triantafyllia V, Bertrams W, Blish CA, Carette JE, Frankovich J, Meffre E, Nadeau KC, Singh U, Wang TT, Luning Prak ET, Herold S, Andreakos E, Schmeck B, Skevaki C, Rogers AJ, Utz PJ. Autoantibodies are highly prevalent in non-SARS-CoV-2 respiratory infections and critical illness. JCI Insight 2023; 8:e163150. [PMID: 36752204 PMCID: PMC9977421 DOI: 10.1172/jci.insight.163150] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 07/13/2022] [Accepted: 12/14/2022] [Indexed: 02/09/2023] Open
Abstract
The widespread presence of autoantibodies in acute infection with SARS-CoV-2 is increasingly recognized, but the prevalence of autoantibodies in non-SARS-CoV-2 infections and critical illness has not yet been reported. We profiled IgG autoantibodies in 267 patients from 5 independent cohorts with non-SARS-CoV-2 viral, bacterial, and noninfectious critical illness. Serum samples were screened using Luminex arrays that included 58 cytokines and 55 autoantigens, many of which are associated with connective tissue diseases (CTDs). Samples positive for anti-cytokine antibodies were tested for receptor blocking activity using cell-based functional assays. Anti-cytokine antibodies were identified in > 50% of patients across all 5 acutely ill cohorts. In critically ill patients, anti-cytokine antibodies were far more common in infected versus uninfected patients. In cell-based functional assays, 11 of 39 samples positive for select anti-cytokine antibodies displayed receptor blocking activity against surface receptors for Type I IFN, GM-CSF, and IL-6. Autoantibodies against CTD-associated autoantigens were also commonly observed, including newly detected antibodies that emerged in longitudinal samples. These findings demonstrate that anti-cytokine and autoantibodies are common across different viral and nonviral infections and range in severity of illness.
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Affiliation(s)
- Allan Feng
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Emily Y. Yang
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Andrew Reese Moore
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | - Shaurya Dhingra
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Sarah Esther Chang
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Xihui Yin
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Ruoxi Pi
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Elisabeth K.M. Mack
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Sara Völkel
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Reinhard Geßner
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Margrit Gündisch
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Andreas Neubauer
- Department of Hematology, Oncology, Immunology, Philipps University Marburg, Marburg, Germany
| | - Harald Renz
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Sotirios Tsiodras
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
| | - Paraskevi C. Fragkou
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Attikon University Hospital, Athens, Greece
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Respiratory Viruses (ESGREV), Basel, Switzerland
| | - Adijat A. Asuni
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | - Joseph E. Levitt
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | | | - Michelle Leong
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Jennifer H. Lumb
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Rong Mao
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Kassandra Pinedo
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Jonasel Roque
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | - Christopher M. Richards
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Mikayla Stabile
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Gayathri Swaminathan
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
| | - Maria L. Salagianni
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Vasiliki Triantafyllia
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Wilhelm Bertrams
- Institute for Lung Research, UGMLC, Philipps University Marburg, Marburg, Germany
| | - Catherine A. Blish
- Institute for Immunity, Transplantation and Infection
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jan E. Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jennifer Frankovich
- Department of Pediatrics, Division of Allergy, Immunology, Rheumatology, Stanford University School of Medicine, Stanford, California, USA
| | - Eric Meffre
- Department of Immunobiology, Yale University, New Haven, Connecticut, USA
| | - Kari Christine Nadeau
- Institute for Immunity, Transplantation and Infection
- Department of Medicine, Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California, USA
| | - Upinder Singh
- Institute for Immunity, Transplantation and Infection
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Taia T. Wang
- Institute for Immunity, Transplantation and Infection
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine and
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Susanne Herold
- Department of Internal Medicine V, Infectious Diseases and Infection Control, UKGM, Justus Liebig University, and Institute for Lung Health (ILH), Giessen, Germany
- DZL and UGMLC, Giessen, Germany
| | - Evangelos Andreakos
- Laboratory of Immunobiology, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Bernd Schmeck
- Institute for Lung Research, UGMLC, Philipps University Marburg, Marburg, Germany
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Marburg, Marburg, Germany
- DZL, German Center for Infection Research (DZIF), Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Marburg, Germany
| | - Chrysanthi Skevaki
- Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, German Center for Lung Research (DZL), Marburg, Germany
| | - Angela J. Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, and
| | - Paul J. Utz
- Department of Medicine, Division of Immunology and Rheumatology
- Institute for Immunity, Transplantation and Infection
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15
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Ratnasiri K, Wilk AJ, Lee MJ, Khatri P, Blish CA. Single-cell RNA-seq methods to interrogate virus-host interactions. Semin Immunopathol 2023; 45:71-89. [PMID: 36414692 PMCID: PMC9684776 DOI: 10.1007/s00281-022-00972-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [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: 08/16/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The twenty-first century has seen the emergence of many epidemic and pandemic viruses, with the most recent being the SARS-CoV-2-driven COVID-19 pandemic. As obligate intracellular parasites, viruses rely on host cells to replicate and produce progeny, resulting in complex virus and host dynamics during an infection. Single-cell RNA sequencing (scRNA-seq), by enabling broad and simultaneous profiling of both host and virus transcripts, represents a powerful technology to unravel the delicate balance between host and virus. In this review, we summarize technological and methodological advances in scRNA-seq and their applications to antiviral immunity. We highlight key scRNA-seq applications that have enabled the understanding of viral genomic and host response heterogeneity, differential responses of infected versus bystander cells, and intercellular communication networks. We expect further development of scRNA-seq technologies and analytical methods, combined with measurements of additional multi-omic modalities and increased availability of publicly accessible scRNA-seq datasets, to enable a better understanding of viral pathogenesis and enhance the development of antiviral therapeutics strategies.
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Affiliation(s)
- Kalani Ratnasiri
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Aaron J. Wilk
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Madeline J. Lee
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Purvesh Khatri
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Medicine, Center for Biomedical Informatics Research, Stanford, CA, USA. .,Inflammatix, Inc., Sunnyvale, CA, 94085, USA.
| | - Catherine A. Blish
- grid.168010.e0000000419368956Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.499295.a0000 0004 9234 0175Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
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16
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Lee MJ, Leong MW, Rustagi A, Beck A, Zeng L, Holmes S, Qi LS, Blish CA. SARS-CoV-2 escapes direct NK cell killing through Nsp1-mediated downregulation of ligands for NKG2D. Cell Rep 2022; 41:111892. [PMID: 36543165 PMCID: PMC9742201 DOI: 10.1016/j.celrep.2022.111892] [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: 06/30/2022] [Revised: 11/09/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Natural killer (NK) cells are cytotoxic effector cells that target and lyse virally infected cells; many viruses therefore encode mechanisms to escape such NK cell killing. Here, we interrogate the ability of SARS-CoV-2 to modulate NK cell recognition and lysis of infected cells. We find that NK cells exhibit poor cytotoxic responses against SARS-CoV-2-infected targets, preferentially killing uninfected bystander cells. We demonstrate that this escape is driven by downregulation of ligands for the activating receptor NKG2D (NKG2D-L). Indeed, early in viral infection, prior to NKG2D-L downregulation, NK cells are able to target and kill infected cells; however, this ability is lost as viral proteins are expressed. Finally, we find that SARS-CoV-2 non-structural protein 1 (Nsp1) mediates downregulation of NKG2D-L and that Nsp1 alone is sufficient to confer resistance to NK cell killing. Collectively, our work demonstrates that SARS-CoV-2 evades direct NK cell cytotoxicity and describes a mechanism by which this occurs.
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Affiliation(s)
- Madeline J Lee
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michelle W Leong
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aimee Beck
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leiping Zeng
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Sarafan Chem-H, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94157, USA
| | - Catherine A Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94157, USA; Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA 94305, USA.
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17
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Ram-Mohan N, Rogers AJ, Blish CA, Nadeau KC, Zudock EJ, Kim D, Quinn JV, Sun L, Liesenfeld O, Yang S. Using a 29-mRNA Host Response Classifier To Detect Bacterial Coinfections and Predict Outcomes in COVID-19 Patients Presenting to the Emergency Department. Microbiol Spectr 2022; 10:e0230522. [PMID: 36250865 PMCID: PMC9769905 DOI: 10.1128/spectrum.02305-22] [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: 06/19/2022] [Accepted: 09/26/2022] [Indexed: 01/06/2023] Open
Abstract
Clinicians in the emergency department (ED) face challenges in concurrently assessing patients with suspected COVID-19 infection, detecting bacterial coinfection, and determining illness severity since current practices require separate workflows. Here, we explore the accuracy of the IMX-BVN-3/IMX-SEV-3 29 mRNA host response classifiers in simultaneously detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and bacterial coinfections and predicting clinical severity of COVID-19. A total of 161 patients with PCR-confirmed COVID-19 (52.2% female; median age, 50.0 years; 51% hospitalized; 5.6% deaths) were enrolled at the Stanford Hospital ED. RNA was extracted (2.5 mL whole blood in PAXgene blood RNA), and 29 host mRNAs in response to the infection were quantified using Nanostring nCounter. The IMX-BVN-3 classifier identified SARS-CoV-2 infection in 151 patients with a sensitivity of 93.8%. Six of 10 patients undetected by the classifier had positive COVID tests more than 9 days prior to enrollment, and the remaining patients oscillated between positive and negative results in subsequent tests. The classifier also predicted that 6 (3.7%) patients had a bacterial coinfection. Clinical adjudication confirmed that 5/6 (83.3%) of the patients had bacterial infections, i.e., Clostridioides difficile colitis (n = 1), urinary tract infection (n = 1), and clinically diagnosed bacterial infections (n = 3), for a specificity of 99.4%. Two of 101 (2.8%) patients in the IMX-SEV-3 "Low" severity classification and 7/60 (11.7%) in the "Moderate" severity classification died within 30 days of enrollment. IMX-BVN-3/IMX-SEV-3 classifiers accurately identified patients with COVID-19 and bacterial coinfections and predicted patients' risk of death. A point-of-care version of these classifiers, under development, could improve ED patient management, including more accurate treatment decisions and optimized resource utilization. IMPORTANCE We assay the utility of the single-test IMX-BVN-3/IMX-SEV-3 classifiers that require just 2.5 mL of patient blood in concurrently detecting viral and bacterial infections as well as predicting the severity and 30-day outcome from the infection. A point-of-care device, in development, will circumvent the need for blood culturing and drastically reduce the time needed to detect an infection. This will negate the need for empirical use of broad-spectrum antibiotics and allow for antibiotic use stewardship. Additionally, accurate classification of the severity of infection and the prediction of 30-day severe outcomes will allow for appropriate allocation of hospital resources.
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Affiliation(s)
- Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Angela J. Rogers
- Department of Medicine—Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Catherine A. Blish
- Department of Medicine/Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
| | - Kari C. Nadeau
- Department of Medicine—Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Elizabeth J. Zudock
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - David Kim
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - James V. Quinn
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Lixian Sun
- Inflammatix, Inc., Burlingame, California, USA
| | | | - The Stanford COVID-19 Biobank Study Group
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine—Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine/Infectious Diseases, Stanford University School of Medicine, Stanford, California, USA
- Inflammatix, Inc., Burlingame, California, USA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California, USA
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18
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Martínez-Colón GJ, Ratnasiri K, Chen H, Jiang S, Zanley E, Rustagi A, Verma R, Chen H, Andrews JR, Mertz KD, Tzankov A, Azagury D, Boyd J, Nolan GP, Schürch CM, Matter MS, Blish CA, McLaughlin TL. SARS-CoV-2 infection drives an inflammatory response in human adipose tissue through infection of adipocytes and macrophages. Sci Transl Med 2022; 14:eabm9151. [PMID: 36137009 PMCID: PMC9529056 DOI: 10.1126/scitranslmed.abm9151] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 09/09/2022] [Indexed: 01/11/2023]
Abstract
Obesity, characterized by chronic low-grade inflammation of the adipose tissue, is associated with adverse coronavirus disease 2019 (COVID-19) outcomes, yet the underlying mechanism is unknown. To explore whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of adipose tissue contributes to pathogenesis, we evaluated COVID-19 autopsy cases and deeply profiled the response of adipose tissue to SARS-CoV-2 infection in vitro. In COVID-19 autopsy cases, we identified SARS-CoV-2 RNA in adipocytes with an associated inflammatory infiltrate. We identified two distinct cellular targets of infection: adipocytes and a subset of inflammatory adipose tissue-resident macrophages. Mature adipocytes were permissive to SARS-CoV-2 infection; although macrophages were abortively infected, SARS-CoV-2 initiated inflammatory responses within both the infected macrophages and bystander preadipocytes. These data suggest that SARS-CoV-2 infection of adipose tissue could contribute to COVID-19 severity through replication of virus within adipocytes and through induction of local and systemic inflammation driven by infection of adipose tissue-resident macrophages.
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Affiliation(s)
| | - Kalani Ratnasiri
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Heping Chen
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Elizabeth Zanley
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Renu Verma
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Han Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jason R. Andrews
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kirsten D. Mertz
- Institute of Pathology, Cantonal Hospital Baselland, 4410, Liestal, Switzerland
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital of Basel, University of Basel, 4056, Basel, Switzerland
| | - Dan Azagury
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jack Boyd
- Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Garry P. Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Christian M. Schürch
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, 72070, Tübingen, Germany
| | - Matthias S. Matter
- Institute of Medical Genetics and Pathology, University Hospital of Basel, University of Basel, 4056, Basel, Switzerland
| | - Catherine A. Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Tracey L. McLaughlin
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
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19
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Zhou X, Yu W, Dunham DM, Schuetz JP, Blish CA, DeKruyff RH, Nadeau KC. Cytometric analysis reveals an association between allergen-responsive natural killer cells and human peanut allergy. J Clin Invest 2022; 132:157962. [PMID: 36250466 PMCID: PMC9566921 DOI: 10.1172/jci157962] [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: 12/29/2021] [Accepted: 08/16/2022] [Indexed: 11/26/2022] Open
Abstract
Food allergies are a leading cause of anaphylaxis, and allergen-specific immune responses in both the innate and the adaptive immune system play key roles in its pathogenesis. We conducted a comprehensive phenotypic and functional investigation of immune cell responses from nonallergic (NA) and peanut allergic (PA) participants cultured with media alone or peanut protein and found, surprisingly, that NK cell activation was strongly associated with the immune response to allergen in PA participants. Peanut-responsive NK cells manifested a distinct expression pattern in PA participants compared with NA participants. Allergen-activated NK cells expressed both Th2 and immune regulatory cytokines, hinting at a potential functional role in mediating and regulating the Th2 allergic response. Depletion of CD3+ T cells attenuated the response of NK cells to peanut-allergen stimulation, suggesting that peanut-responsive NK cells are T cell dependent. We also showed that oral immune therapy was associated with decreased NK responses to peanut allergen stimulation in vitro. These results demonstrate that NK cells are associated with the food-allergic immune response, and the magnitude of this mobilized cell population suggests that they play a functional role in allergic immunity.
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Affiliation(s)
- Xiaoying Zhou
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, California, USA
| | - Wong Yu
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, California, USA
- Division of Allergy, Immunology and Blood and Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, California, USA
| | - Diane M. Dunham
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, California, USA
| | - Jackson P. Schuetz
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, California, USA
| | - Catherine A. Blish
- Program in Immunology and Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Rosemarie H. DeKruyff
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, California, USA
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford, California, USA
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20
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Richards CM, Jabs S, Qiao W, Varanese LD, Schweizer M, Mosen PR, Riley NM, Klüssendorf M, Zengel JR, Flynn RA, Rustagi A, Widen JC, Peters CE, Ooi YS, Xie X, Shi PY, Bartenschlager R, Puschnik AS, Bogyo M, Bertozzi CR, Blish CA, Winter D, Nagamine CM, Braulke T, Carette JE. The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection. Science 2022; 378:eabn5648. [PMID: 36074821 PMCID: PMC9547973 DOI: 10.1126/science.abn5648] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Lysosomes are key degradative compartments of the cell. Transport to lysosomes relies on GlcNAc-1-phosphotransferase-mediated tagging of soluble enzymes with mannose 6-phosphate (M6P). GlcNAc-1-phosphotransferase deficiency leads to the severe lysosomal storage disorder mucolipidosis II (MLII). Several viruses require lysosomal cathepsins to cleave structural proteins and thus depend on functional GlcNAc-1-phosphotransferase. Here, we used genome-scale CRISPR screens to identify Lysosomal Enzyme Trafficking factor (LYSET) as essential for infection by cathepsin-dependent viruses including SARS-CoV-2. LYSET deficiency resulted in global loss of M6P tagging and mislocalization of GlcNAc-1-phosphotransferase from the Golgi complex to lysosomes. Lyset knockout mice exhibited MLII-like phenotypes and human pathogenic LYSET alleles failed to restore lysosomal sorting defects. Thus, LYSET is required for correct functioning of the M6P trafficking machinery, and mutations in LYSET can explain the phenotype of the associated disorder.
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Affiliation(s)
- Christopher M Richards
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sabrina Jabs
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Wenjie Qiao
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauren D Varanese
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michaela Schweizer
- Department of Electron Microscopy, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter R Mosen
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | | | - Malte Klüssendorf
- Department of Osteology and Biomechanics, Cell Biology of Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - James R Zengel
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.,Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA, USA
| | - Arjun Rustagi
- Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - John C Widen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christine E Peters
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yaw Shin Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany.,Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Matthew Bogyo
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford, CA, USA
| | - Catherine A Blish
- Division of Infectious Disease and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Dominic Winter
- Institute for Biochemistry and Molecular Biology, Medical Faculty, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Claude M Nagamine
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas Braulke
- Department of Osteology and Biomechanics, Cell Biology of Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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21
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Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LI, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, Altman MC, Becker PM, Rouphael N, Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LI, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, McEnaney K, Barton B, Lentucci C, Saluvan M, Chang AC, Hoch A, Albert M, Shaheen T, Kho AT, Thomas S, Chen J, Murphy MD, Cooney M, Presnell S, Fragiadakis GK, Patel R, Guan L, Gygi J, Pawar S, Brito A, Khalil Z, Maguire C, Fourati S, Overton JA, Vita R, Westendorf K, Salehi-Rad R, Leligdowicz A, Matthay MA, Singer JP, Kangelaris KN, Hendrickson CM, Krummel MF, Langelier CR, Woodruff PG, Powell DL, Kim JN, Simmons B, Goonewardene IM, Smith CM, Martens M, Mosier J, Kimura H, Sherman AC, Walsh SR, Issa NC, Dela Cruz C, Farhadian S, Iwasaki A, Ko AI, Chinthrajah S, Ahuja N, Rogers AJ, Artandi M, Siegel SA, Lu Z, Drevets DA, Brown BR, Anderson ML, Guirgis FW, Thyagarajan RV, Rousseau JF, Wylie D, Busch J, Gandhi S, Triplett TA, Yendewa G, Giddings O, Anderson EJ, Mehta AK, Sevransky JE, Khor B, Rahman A, Stadlbauer D, Dutta J, Xie H, Kim-Schulze S, Gonzalez-Reiche AS, van de Guchte A, Farrugia K, Khan Z, Maecker HT, Elashoff D, Brook J, Ramires-Sanchez E, Llamas M, Rivera A, Perdomo C, Ward DC, Magyar CE, Fulcher JA, Abe-Jones Y, Asthana S, Beagle A, Bhide S, Carrillo SA, Chak S, Fragiadakis GK, Ghale R, Gonzalez A, Jauregui A, Jones N, Lea T, Lee D, Lota R, Milush J, Nguyen V, Pierce L, Prasad PA, Rao A, Samad B, Shaw C, Sigman A, Sinha P, Ward A, Willmore A, Zhan J, Rashid S, Rodriguez N, Tang K, Altamirano LT, Betancourt L, Curiel C, Sutter N, Paz MT, Tietje-Ulrich G, Leroux C, Connors J, Bernui M, Kutzler MA, Edwards C, Lee E, Lin E, Croen B, Semenza NC, Rogowski B, Melnyk N, Woloszczuk K, Cusimano G, Bell MR, Furukawa S, McLin R, Marrero P, Sheidy J, Tegos GP, Nagle C, Mege N, Ulring K, Seyfert-Margolis V, Conway M, Francisco D, Molzahn A, Erickson H, Wilson CC, Schunk R, Sierra B, Hughes T, Smolen K, Desjardins M, van Haren S, Mitre X, Cauley J, Li X, Tong A, Evans B, Montesano C, Licona JH, Krauss J, Chang JBP, Izaguirre N, Chaudhary O, Coppi A, Fournier J, Mohanty S, Muenker MC, Nelson A, Raddassi K, Rainone M, Ruff WE, Salahuddin S, Schulz WL, Vijayakumar P, Wang H, Wunder Jr. E, Young HP, Zhao Y, Saksena M, Altman D, Kojic E, Srivastava K, Eaker LQ, Bermúdez-González MC, Beach KF, Sominsky LA, Azad AR, Carreño JM, Singh G, Raskin A, Tcheou J, Bielak D, Kawabata H, Mulder LCF, Kleiner G, Lee AS, Do ED, Fernandes A, Manohar M, Hagan T, Blish CA, Din HN, Roque J, Yang S, Brunton A, Sullivan PE, Strnad M, Lyski ZL, Coulter FJ, Booth JL, Sinko LA, Moldawer LL, Borresen B, Roth-Manning B, Song LZ, Nelson E, Lewis-Smith M, Smith J, Tipan PG, Siles N, Bazzi S, Geltman J, Hurley K, Gabriele G, Sieg S, Vaysman T, Bristow L, Hussaini L, Hellmeister K, Samaha H, Cheng A, Spainhour C, Scherer EM, Johnson B, Bechnak A, Ciric CR, Hewitt L, Carter E, Mcnair N, Panganiban B, Huerta C, Usher J, Ribeiro SP, Altman MC, Becker PM, Rouphael N. Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. EBioMedicine 2022; 83:104208. [PMID: 35952496 PMCID: PMC9359694 DOI: 10.1016/j.ebiom.2022.104208] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/11/2022] [Accepted: 07/25/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Better understanding of the association between characteristics of patients hospitalized with coronavirus disease 2019 (COVID-19) and outcome is needed to further improve upon patient management. METHODS Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) is a prospective, observational study of 1164 patients from 20 hospitals across the United States. Disease severity was assessed using a 7-point ordinal scale based on degree of respiratory illness. Patients were prospectively surveyed for 1 year after discharge for post-acute sequalae of COVID-19 (PASC) through quarterly surveys. Demographics, comorbidities, radiographic findings, clinical laboratory values, SARS-CoV-2 PCR and serology were captured over a 28-day period. Multivariable logistic regression was performed. FINDINGS The median age was 59 years (interquartile range [IQR] 20); 711 (61%) were men; overall mortality was 14%, and 228 (20%) required invasive mechanical ventilation. Unsupervised clustering of ordinal score over time revealed distinct disease course trajectories. Risk factors associated with prolonged hospitalization or death by day 28 included age ≥ 65 years (odds ratio [OR], 2.01; 95% CI 1.28-3.17), Hispanic ethnicity (OR, 1.71; 95% CI 1.13-2.57), elevated baseline creatinine (OR 2.80; 95% CI 1.63- 4.80) or troponin (OR 1.89; 95% 1.03-3.47), baseline lymphopenia (OR 2.19; 95% CI 1.61-2.97), presence of infiltrate by chest imaging (OR 3.16; 95% CI 1.96-5.10), and high SARS-CoV2 viral load (OR 1.53; 95% CI 1.17-2.00). Fatal cases had the lowest ratio of SARS-CoV-2 antibody to viral load levels compared to other trajectories over time (p=0.001). 589 survivors (51%) completed at least one survey at follow-up with 305 (52%) having at least one symptom consistent with PASC, most commonly dyspnea (56% among symptomatic patients). Female sex was the only associated risk factor for PASC. INTERPRETATION Integration of PCR cycle threshold, and antibody values with demographics, comorbidities, and laboratory/radiographic findings identified risk factors for 28-day outcome severity, though only female sex was associated with PASC. Longitudinal clinical phenotyping offers important insights, and provides a framework for immunophenotyping for acute and long COVID-19. FUNDING NIH.
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Affiliation(s)
- Al Ozonoff
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | - Joanna Schaenman
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, United States
| | | | - Carly E. Milliren
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | - Carolyn S. Calfee
- University of California San Francisco School of Medicine, San Francisco, CA, United States
| | - Charles B. Cairns
- Drexel University/Tower Health Hospital, Philadelphia, PA, United States
| | - Monica Kraft
- University of Arizona, Tucson, AZ, United States
| | - Lindsey R. Baden
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, United States
| | - Albert C. Shaw
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Denise A. Esserman
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Shanshan Liu
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David A. Hafler
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Ruth R. Montgomery
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Steven H. Kleinstein
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Ofer Levy
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, United States
| | | | - Elias K. Haddad
- Drexel University/Tower Health Hospital, Philadelphia, PA, United States
| | - David J. Erle
- University of California San Francisco School of Medicine, San Francisco, CA, United States
| | | | | | | | | | | | | | - Jordan P. Metcalf
- Oklahoma University Health Sciences Center, Oklahoma, OK, United States
| | - Mark A. Atkinson
- University of Florida, Gainesville and University of South Florida, Tampa, FL, United States
| | - Scott C. Brakenridge
- University of Florida, Gainesville and University of South Florida, Tampa, FL, United States
| | - David Corry
- Baylor College of Medicine, and the Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX, United States
| | - Farrah Kheradmand
- Baylor College of Medicine, and the Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX, United States
| | | | - Esther Melamed
- The University of Texas at Austin, Austin, TX, United States
| | | | - Rafick Sekaly
- Case Western Reserve University, Cleveland, OH, United States
| | - Joann Diray-Arce
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alison D. Augustine
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, United States
| | - Elaine F. Reed
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, United States
| | | | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, United States
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22
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Parikh VN, Ioannidis AG, Jimenez-Morales D, Gorzynski JE, De Jong HN, Liu X, Roque J, Cepeda-Espinoza VP, Osoegawa K, Hughes C, Sutton SC, Youlton N, Joshi R, Amar D, Tanigawa Y, Russo D, Wong J, Lauzon JT, Edelson J, Mas Montserrat D, Kwon Y, Rubinacci S, Delaneau O, Cappello L, Kim J, Shoura MJ, Raja AN, Watson N, Hammond N, Spiteri E, Mallempati KC, Montero-Martín G, Christle J, Kim J, Kirillova A, Seo K, Huang Y, Zhao C, Moreno-Grau S, Hershman SG, Dalton KP, Zhen J, Kamm J, Bhatt KD, Isakova A, Morri M, Ranganath T, Blish CA, Rogers AJ, Nadeau K, Yang S, Blomkalns A, O’Hara R, Neff NF, DeBoever C, Szalma S, Wheeler MT, Gates CM, Farh K, Schroth GP, Febbo P, deSouza F, Cornejo OE, Fernandez-Vina M, Kistler A, Palacios JA, Pinsky BA, Bustamante CD, Rivas MA, Ashley EA. Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy. Nat Commun 2022; 13:5107. [PMID: 36042219 PMCID: PMC9426371 DOI: 10.1038/s41467-022-32397-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 08/18/2021] [Accepted: 07/28/2022] [Indexed: 02/05/2023] Open
Abstract
The SARS-CoV-2 pandemic has differentially impacted populations across race and ethnicity. A multi-omic approach represents a powerful tool to examine risk across multi-ancestry genomes. We leverage a pandemic tracking strategy in which we sequence viral and host genomes and transcriptomes from nasopharyngeal swabs of 1049 individuals (736 SARS-CoV-2 positive and 313 SARS-CoV-2 negative) and integrate them with digital phenotypes from electronic health records from a diverse catchment area in Northern California. Genome-wide association disaggregated by admixture mapping reveals novel COVID-19-severity-associated regions containing previously reported markers of neurologic, pulmonary and viral disease susceptibility. Phylodynamic tracking of consensus viral genomes reveals no association with disease severity or inferred ancestry. Summary data from multiomic investigation reveals metagenomic and HLA associations with severe COVID-19. The wealth of data available from residual nasopharyngeal swabs in combination with clinical data abstracted automatically at scale highlights a powerful strategy for pandemic tracking, and reveals distinct epidemiologic, genetic, and biological associations for those at the highest risk.
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Affiliation(s)
- Victoria N. Parikh
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Alexander G. Ioannidis
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA USA
| | - David Jimenez-Morales
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - John E. Gorzynski
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
| | - Hannah N. De Jong
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
| | - Xiran Liu
- grid.168010.e0000000419368956Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA USA
| | - Jonasel Roque
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | | | - Kazutoyo Osoegawa
- grid.490568.60000 0004 5997 482XHistocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care, Stanford, USA
| | - Chris Hughes
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
| | - Shirley C. Sutton
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
| | - Nathan Youlton
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
| | - Ruchi Joshi
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - David Amar
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Yosuke Tanigawa
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Douglas Russo
- grid.168010.e0000000419368956Department of Statistics, Stanford University, Stanford, CA USA
| | - Justin Wong
- grid.168010.e0000000419368956Department of Statistics, Stanford University, Stanford, CA USA
| | - Jessie T. Lauzon
- grid.168010.e0000000419368956Department of Aeronautics and Astronautics, Stanford University, Stanford, CA USA
| | - Jacob Edelson
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Daniel Mas Montserrat
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Yongchan Kwon
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Simone Rubinacci
- grid.9851.50000 0001 2165 4204Department of Computational Biology and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Olivier Delaneau
- grid.9851.50000 0001 2165 4204Department of Computational Biology and Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Lorenzo Cappello
- grid.168010.e0000000419368956Department of Statistics, Stanford University, Stanford, CA USA
| | - Jaehee Kim
- grid.5386.8000000041936877XDepartment of Computational Biology, Cornell University, Ithaca, NY USA
| | - Massa J. Shoura
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, Stanford, CA USA
| | - Archana N. Raja
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Nathaniel Watson
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, Stanford, CA USA
| | - Nathan Hammond
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, Stanford, CA USA
| | - Elizabeth Spiteri
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, Stanford, CA USA
| | - Kalyan C. Mallempati
- grid.490568.60000 0004 5997 482XHistocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care, Stanford, USA
| | - Gonzalo Montero-Martín
- grid.490568.60000 0004 5997 482XHistocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care, Stanford, USA
| | - Jeffrey Christle
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Jennifer Kim
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Anna Kirillova
- grid.21925.3d0000 0004 1936 9000Medical Scientist Training Program, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, PA USA
| | - Kinya Seo
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Yong Huang
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Chunli Zhao
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Sonia Moreno-Grau
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Steven G. Hershman
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Karen P. Dalton
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Jimmy Zhen
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Jack Kamm
- grid.499295.a0000 0004 9234 0175Chan Zuckerburg Biohub, San Francisco, CA USA
| | - Karan D. Bhatt
- grid.499295.a0000 0004 9234 0175Chan Zuckerburg Biohub, San Francisco, CA USA
| | - Alina Isakova
- grid.168010.e0000000419368956Department of Bioengineering, Stanford University, Stanford, CA USA
| | - Maurizio Morri
- grid.499295.a0000 0004 9234 0175Chan Zuckerburg Biohub, San Francisco, CA USA
| | - Thanmayi Ranganath
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Catherine A. Blish
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Angela J. Rogers
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Kari Nadeau
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA USA
| | - Samuel Yang
- grid.168010.e0000000419368956Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Andra Blomkalns
- grid.168010.e0000000419368956Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA USA
| | - Ruth O’Hara
- grid.168010.e0000000419368956Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA USA
| | - Norma F. Neff
- grid.499295.a0000 0004 9234 0175Chan Zuckerburg Biohub, San Francisco, CA USA
| | | | - Sándor Szalma
- Takeda Development Center, Americas, Inc, San Diego, CA USA
| | - Matthew T. Wheeler
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA
| | | | - Kyle Farh
- grid.185669.50000 0004 0507 3954Illumina, Inc, San Diego, CA USA
| | - Gary P. Schroth
- grid.185669.50000 0004 0507 3954Illumina, Inc, San Diego, CA USA
| | - Phil Febbo
- grid.185669.50000 0004 0507 3954Illumina, Inc, San Diego, CA USA
| | - Francis deSouza
- grid.185669.50000 0004 0507 3954Illumina, Inc, San Diego, CA USA
| | - Omar E. Cornejo
- grid.30064.310000 0001 2157 6568School of Biological Sciences, Washington State University, Pullman, WA USA
| | - Marcelo Fernandez-Vina
- grid.490568.60000 0004 5997 482XHistocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Stanford Health Care, Stanford, USA ,grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, Stanford, CA USA
| | - Amy Kistler
- grid.499295.a0000 0004 9234 0175Chan Zuckerburg Biohub, San Francisco, CA USA
| | - Julia A. Palacios
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Department of Statistics, Stanford University, Stanford, CA USA
| | - Benjamin A. Pinsky
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, Stanford, CA USA
| | - Carlos D. Bustamante
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Manuel A. Rivas
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University, Stanford, CA USA
| | - Euan A. Ashley
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA
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Zhu C, Lee JY, Woo JZ, Xu L, Nguyenla X, Yamashiro LH, Ji F, Biering SB, Van Dis E, Gonzalez F, Fox D, Wehri E, Rustagi A, Pinsky BA, Schaletzky J, Blish CA, Chiu C, Harris E, Sadreyev RI, Stanley S, Kauppinen S, Rouskin S, Näär AM. An intranasal ASO therapeutic targeting SARS-CoV-2. Nat Commun 2022; 13:4503. [PMID: 35922434 PMCID: PMC9349213 DOI: 10.1038/s41467-022-32216-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 02/11/2022] [Accepted: 07/18/2022] [Indexed: 12/13/2022] Open
Abstract
The COVID-19 pandemic is exacting an increasing toll worldwide, with new SARS-CoV-2 variants emerging that exhibit higher infectivity rates and that may partially evade vaccine and antibody immunity. Rapid deployment of non-invasive therapeutic avenues capable of preventing infection by all SARS-CoV-2 variants could complement current vaccination efforts and help turn the tide on the COVID-19 pandemic. Here, we describe a novel therapeutic strategy targeting the SARS-CoV-2 RNA using locked nucleic acid antisense oligonucleotides (LNA ASOs). We identify an LNA ASO binding to the 5′ leader sequence of SARS-CoV-2 that disrupts a highly conserved stem-loop structure with nanomolar efficacy in preventing viral replication in human cells. Daily intranasal administration of this LNA ASO in the COVID-19 mouse model potently suppresses viral replication (>80-fold) in the lungs of infected mice. We find that the LNA ASO is efficacious in countering all SARS-CoV-2 “variants of concern” tested both in vitro and in vivo. Hence, inhaled LNA ASOs targeting SARS-CoV-2 represents a promising therapeutic approach to reduce or prevent transmission and decrease severity of COVID-19 in infected individuals. LNA ASOs are chemically stable and can be flexibly modified to target different viral RNA sequences and could be stockpiled for future coronavirus pandemics. Despite approved vaccines and anti-virals to prevent and treat SARS-CoV-2 infection, there is a need for further development of efficient antiviral therapeutic strategy. Here, Zhu et al. develop locked nucleic acid antisense oligonucleotides (LNA ASOs) targeting the 5’ leader sequence of SARS-CoV-2 RNA to interfere with replication of wildtype virus and variants of concern. Daily intranasal administration in K18-hACE2 humanized mice suppresses viral infection in lung.
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Affiliation(s)
- Chi Zhu
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Justin Y Lee
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jia Z Woo
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Lei Xu
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Xammy Nguyenla
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Livia H Yamashiro
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, USA
| | - Federico Gonzalez
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Douglas Fox
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Eddie Wehri
- The Henry Wheeler Center for Emerging and Neglected Diseases, University of California, Berkeley, CA, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Schaletzky
- The Henry Wheeler Center for Emerging and Neglected Diseases, University of California, Berkeley, CA, USA
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, School of Medicine, Stanford, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Sarah Stanley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, USA
| | - Sakari Kauppinen
- Center for RNA Medicine, Aalborg University, Copenhagen, Denmark
| | - Silvi Rouskin
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Anders M Näär
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, USA. .,Innovative Genomics Institute, University of California, Berkeley, CA, USA.
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24
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Wilk AJ, Shalek AK, Holmes S, Blish CA. Comparative analysis of cell-cell communication at single-cell resolution. bioRxiv 2022:2022.02.04.479209. [PMID: 35169794 PMCID: PMC8845414 DOI: 10.1101/2022.02.04.479209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Inference of cell-cell communication (CCC) from single-cell RNA-sequencing data is a powerful technique to uncover putative axes of multicellular coordination, yet existing methods perform this analysis at the level of the cell type or cluster, discarding single-cell level information. Here we present Scriabin â€" a flexible and scalable framework for comparative analysis of CCC at single-cell resolution. We leverage multiple published datasets to show that Scriabin recovers expected CCC edges and use spatial transcriptomic data, genetic perturbation screens, and direct experimental manipulation of receptor-ligand interactions to validate that the recovered edges are biologically meaningful. We then apply Scriabin to uncover co-expressed programs of CCC from atlas-scale datasets, validating known communication pathways required for maintaining the intestinal stem cell niche and revealing species-specific communication pathways. Finally, we utilize single-cell communication networks calculated using Scriabin to follow communication pathways that operate between timepoints in longitudinal datasets, highlighting bystander cells as important initiators of inflammatory reactions in acute SARS-CoV-2 infection. Our approach represents a broadly applicable strategy to leverage single-cell resolution data maximally toward uncovering CCC circuitry and rich niche-phenotype relationships in health and disease.
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25
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Jia X, Cao S, Lee AS, Manohar M, Sindher SB, Ahuja N, Artandi M, Blish CA, Blomkalns AL, Chang I, Collins WJ, Desai M, Din HN, Do E, Fernandes A, Geng LN, Rosenberg-Hasson Y, Mahoney MR, Glascock AL, Chan LY, Fong SY, Phelps M, Raeber O, Purington N, Röltgen K, Rogers AJ, Snow T, Wang TT, Solis D, Vaughan L, Verghese M, Maecker H, Wittman R, Puri R, Kistler A, Yang S, Boyd SD, Pinsky BA, Chinthrajah S, Nadeau KC. Anti-nucleocapsid antibody levels and pulmonary comorbid conditions are linked to post-COVID-19 syndrome. JCI Insight 2022; 7:156713. [PMID: 35801588 PMCID: PMC9310538 DOI: 10.1172/jci.insight.156713] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 11/18/2021] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUNDProlonged symptoms after SARS-CoV-2 infection are well documented. However, which factors influence development of long-term symptoms, how symptoms vary across ethnic groups, and whether long-term symptoms correlate with biomarkers are points that remain elusive.METHODSAdult SARS-CoV-2 reverse transcription PCR-positive (RT-PCR-positive) patients were recruited at Stanford from March 2020 to February 2021. Study participants were seen for in-person visits at diagnosis and every 1-3 months for up to 1 year after diagnosis; they completed symptom surveys and underwent blood draws and nasal swab collections at each visit.RESULTSOur cohort (n = 617) ranged from asymptomatic to critical COVID-19 infections. In total, 40% of participants reported at least 1 symptom associated with COVID-19 six months after diagnosis. Median time from diagnosis to first resolution of all symptoms was 44 days; median time from diagnosis to sustained symptom resolution with no recurring symptoms for 1 month or longer was 214 days. Anti-nucleocapsid IgG level in the first week after positive RT-PCR test and history of lung disease were associated with time to sustained symptom resolution. COVID-19 disease severity, ethnicity, age, sex, and remdesivir use did not affect time to sustained symptom resolution.CONCLUSIONWe found that all disease severities had a similar risk of developing post-COVID-19 syndrome in an ethnically diverse population. Comorbid lung disease and lower levels of initial IgG response to SARS-CoV-2 nucleocapsid antigen were associated with longer symptom duration.TRIAL REGISTRATIONClinicalTrials.gov, NCT04373148.FUNDINGNIH UL1TR003142 CTSA grant, NIH U54CA260517 grant, NIEHS R21 ES03304901, Sean N Parker Center for Allergy and Asthma Research at Stanford University, Chan Zuckerberg Biohub, Chan Zuckerberg Initiative, Sunshine Foundation, Crown Foundation, and Parker Foundation.
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Affiliation(s)
- Xiaolin Jia
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Division of Hospital Medicine
| | - Shu Cao
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research
| | - Alexandra S Lee
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research
| | - Monali Manohar
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research
| | - Sayantani B Sindher
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research
| | - Neera Ahuja
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Division of Hospital Medicine
| | - Maja Artandi
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Division of Primary Care and Population Health Stanford University, Stanford, California, USA
| | - Catherine A Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA.,Division of Infectious Diseases, Stanford University, Stanford, California, USA.,Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Andra L Blomkalns
- Department of Emergency Medicine, Stanford University, Stanford, California, USA
| | - Iris Chang
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research
| | - William J Collins
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Division of Hospital Medicine.,Sean N. Parker Center for Allergy and Asthma Research
| | - Manisha Desai
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research.,Quantitative Sciences Unit, Stanford University, Stanford, California, USA
| | - Hena Naz Din
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research
| | - Evan Do
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research
| | - Andrea Fernandes
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research
| | - Linda N Geng
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Division of Primary Care and Population Health Stanford University, Stanford, California, USA
| | - Yael Rosenberg-Hasson
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research
| | - Megan Ruth Mahoney
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Division of Primary Care and Population Health Stanford University, Stanford, California, USA
| | | | - Lienna Y Chan
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Sharon Y Fong
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | | | | | - Maira Phelps
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Olivia Raeber
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research
| | | | - Natasha Purington
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research.,Quantitative Sciences Unit, Stanford University, Stanford, California, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Angela J Rogers
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, Stanford, California, USA
| | - Theo Snow
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research
| | - Taia T Wang
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Division of Infectious Diseases, Stanford University, Stanford, California, USA.,Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Daniel Solis
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Laura Vaughan
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Division of Primary Care and Population Health Stanford University, Stanford, California, USA
| | - Michelle Verghese
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Holden Maecker
- Institute for Immunity, Transplantation, and Infectious Diseases, Stanford University, Stanford, California, USA
| | - Richard Wittman
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Division of Primary Care and Population Health Stanford University, Stanford, California, USA
| | - Rajan Puri
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Division of Primary Care and Population Health Stanford University, Stanford, California, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, Stanford, California, USA
| | - Scott D Boyd
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin A Pinsky
- Division of Infectious Diseases, Stanford University, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Sharon Chinthrajah
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research
| | - Kari C Nadeau
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research.,Division of Pulmonary, Allergy, and Critical Care Medicine, Stanford University, Stanford, California, USA.,Institute for Immunity, Transplantation, and Infectious Diseases, Stanford University, Stanford, California, USA
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26
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van der Ploeg K, Kirosingh AS, Mori DAM, Chakraborty S, Hu Z, Sievers BL, Jacobson KB, Bonilla H, Parsonnet J, Andrews JR, Press KD, Ty MC, Ruiz-Betancourt DR, de la Parte L, Tan GS, Blish CA, Takahashi S, Rodriguez-Barraquer I, Greenhouse B, Singh U, Wang TT, Jagannathan P. TNF-α + CD4 + T cells dominate the SARS-CoV-2 specific T cell response in COVID-19 outpatients and are associated with durable antibodies. Cell Rep Med 2022; 3:100640. [PMID: 35588734 PMCID: PMC9061140 DOI: 10.1016/j.xcrm.2022.100640] [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: 01/26/2022] [Revised: 03/26/2022] [Accepted: 04/27/2022] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific CD4+ T cells are likely important in immunity against coronavirus 2019 (COVID-19), but our understanding of CD4+ longitudinal dynamics following infection and of specific features that correlate with the maintenance of neutralizing antibodies remains limited. Here, we characterize SARS-CoV-2-specific CD4+ T cells in a longitudinal cohort of 109 COVID-19 outpatients enrolled during acute infection. The quality of the SARS-CoV-2-specific CD4+ response shifts from cells producing interferon gamma (IFNγ) to tumor necrosis factor alpha (TNF-α) from 5 days to 4 months post-enrollment, with IFNγ-IL-21-TNF-α+ CD4+ T cells the predominant population detected at later time points. Greater percentages of IFNγ-IL-21-TNF-α+ CD4+ T cells on day 28 correlate with SARS-CoV-2-neutralizing antibodies measured 7 months post-infection (⍴ = 0.4, p = 0.01). mRNA vaccination following SARS-CoV-2 infection boosts both IFNγ- and TNF-α-producing, spike-protein-specific CD4+ T cells. These data suggest that SARS-CoV-2-specific, TNF-α-producing CD4+ T cells may play an important role in antibody maintenance following COVID-19. SARS-CoV-2-specific CD4+ response shifts from cells producing IFNγ to TNF-α SARS-CoV-2-specific IFNγ−TNF-α+ CD4+ T cells predominate at later timepoints IFNγ-TNF-α+ CD4+ T cells correlate with durable SARS-CoV-2-neutralizing antibodies Post-infection mRNA vaccination boosts both IFNγ+ and TNF-α+ S-specific CD4+ T cells
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Affiliation(s)
- Kattria van der Ploeg
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Adam S Kirosingh
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Diego A M Mori
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Saborni Chakraborty
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Zicheng Hu
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Karen B Jacobson
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hector Bonilla
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julie Parsonnet
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Epidemiology and Population Health, Stanford University, Stanford, CA 94305, USA
| | - Jason R Andrews
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kathleen D Press
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maureen C Ty
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Lauren de la Parte
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gene S Tan
- J. Craig Venter Institute, La Jolla, CA 92037, USA; Division of Infectious Disease, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Catherine A Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Saki Takahashi
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | | | - Bryan Greenhouse
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Upinder Singh
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Taia T Wang
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Prasanna Jagannathan
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
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27
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Zeng L, Liu Y, Nguyenla XH, Abbott TR, Han M, Zhu Y, Chemparathy A, Lin X, Chen X, Wang H, Rane DA, Spatz JM, Jain S, Rustagi A, Pinsky B, Zepeda AE, Kadina AP, Walker JA, Holden K, Temperton N, Cochran JR, Barron AE, Connolly MD, Blish CA, Lewis DB, Stanley SA, La Russa MF, Qi LS. Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro. Nat Commun 2022; 13:2766. [PMID: 35589813 PMCID: PMC9119983 DOI: 10.1038/s41467-022-30546-7] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 05/06/2022] [Indexed: 12/13/2022] Open
Abstract
A major challenge in coronavirus vaccination and treatment is to counteract rapid viral evolution and mutations. Here we demonstrate that CRISPR-Cas13d offers a broad-spectrum antiviral (BSA) to inhibit many SARS-CoV-2 variants and diverse human coronavirus strains with >99% reduction of the viral titer. We show that Cas13d-mediated coronavirus inhibition is dependent on the crRNA cellular spatial colocalization with Cas13d and target viral RNA. Cas13d can significantly enhance the therapeutic effects of diverse small molecule drugs against coronaviruses for prophylaxis or treatment purposes, and the best combination reduced viral titer by over four orders of magnitude. Using lipid nanoparticle-mediated RNA delivery, we demonstrate that the Cas13d system can effectively treat infection from multiple variants of coronavirus, including Omicron SARS-CoV-2, in human primary airway epithelium air-liquid interface (ALI) cultures. Our study establishes CRISPR-Cas13 as a BSA which is highly complementary to existing vaccination and antiviral treatment strategies.
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Affiliation(s)
- Leiping Zeng
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Yanxia Liu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Xammy Huu Nguyenla
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA, 94720, USA
| | - Timothy R Abbott
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Mengting Han
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Yanyu Zhu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Xueqiu Lin
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Xinyi Chen
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Haifeng Wang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Draven A Rane
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Jordan M Spatz
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Saket Jain
- University of California San Francisco, San Francisco, CA, 94143, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Benjamin Pinsky
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | | | | | | | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, Chatham, Kent ME4 4TB, UK
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Annelise E Barron
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | | | - Catherine A Blish
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg BioHub, San Francisco, CA, 94158, USA
| | - David B Lewis
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Sarah A Stanley
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA, 94720, USA.
| | - Marie F La Russa
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg BioHub, San Francisco, CA, 94158, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA.
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28
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Nahass G, Salomon-Shulman R, Sheikh-Mohamed S, Blacker G, Haider K, Blish CA, Sanders E, Gommerman JL, Weissman IL, Tal MC. Low and transient salivary neutralizing antibodies after COVID vaccination. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.114.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Neutralizing activity found in the blood following intramuscular vaccination protects against systemic disease from SARS-CoV-2 infection. Mild breakthrough mucosal infections in vaccinated individuals can contribute to transmission chains of infection, and as such the contribution of intramuscular vaccination to mucosal immunity is important to understand. We assessed vesicular stomatitis virus (VSV) SARS-CoV-2 SPIKE protein neutralization activities as well as anti-viral spike and RBD IgG and IgA isotype antibody binding, in saliva from individuals who had recovered from SARS-CoV-2 infection and people who received immunization. The various vaccination strategies deployed globally showed key differences in the extent of neutralizing activity that could be measured. Even in subjects with significant peak activity 2–4 weeks following a second dose of mRNA vaccination, this neutralizing activity was transient and significantly reduced within 3–6 months. Among adenoviral vectors, ChAdOx1 elicited significantly more salivary neutralizing activity and antibody levels compared to Ad26.S. A large range of salivary neutralizing activity is induced following different intramuscular SARS-COV-2 vaccination strategies. All were orders of magnitude lower than neutralization levels observed in blood, and it remains to be determined if any of the observed neutralizing activity in the saliva can neutralize virus in the upper respiratory tract upon exposure. Based on studies where high levels of mucosal IgA antibodies were induced in response to stimulation with aerosol intranasal vaccines, such vaccines could be important in lowering transmission of SARS-COV-2.
Supported by The Fairbairn Foundation and SPARK
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Affiliation(s)
- Georgie Nahass
- 1University of Illinois College of Medicine
- 2Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine
| | | | | | - Grace Blacker
- 2Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine
| | - Kazim Haider
- 2Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine
| | | | | | | | - Irving L Weissman
- 2Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine
| | - Michal Caspi Tal
- 2Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine
- 5Massachusetts Institute of Technology
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29
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Yen M, Ren J, Liu Q, Glassman CR, Sheahan TP, Picton LK, Moreira FR, Rustagi A, Jude KM, Zhao X, Blish CA, Baric RS, Su LL, Garcia KC. Facile discovery of surrogate cytokine agonists. Cell 2022; 185:1414-1430.e19. [PMID: 35325595 PMCID: PMC9021867 DOI: 10.1016/j.cell.2022.02.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 10/19/2021] [Revised: 01/11/2022] [Accepted: 02/22/2022] [Indexed: 12/26/2022]
Abstract
Cytokines are powerful immune modulators that initiate signaling through receptor dimerization, but natural cytokines have structural limitations as therapeutics. We present a strategy to discover cytokine surrogate agonists by using modular ligands that exploit induced proximity and receptor dimer geometry as pharmacological metrics amenable to high-throughput screening. Using VHH and scFv to human interleukin-2/15, type-I interferon, and interleukin-10 receptors, we generated combinatorial matrices of single-chain bispecific ligands that exhibited diverse spectrums of functional activities, including potent inhibition of SARS-CoV-2 by surrogate interferons. Crystal structures of IL-2R:VHH complexes revealed that variation in receptor dimer geometries resulted in functionally diverse signaling outputs. This modular platform enabled engineering of surrogate ligands that compelled assembly of an IL-2R/IL-10R heterodimer, which does not naturally exist, that signaled through pSTAT5 on T and natural killer (NK) cells. This "cytokine med-chem" approach, rooted in principles of induced proximity, is generalizable for discovery of diversified agonists for many ligand-receptor systems.
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Affiliation(s)
- Michelle Yen
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Junming Ren
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Qingxiang Liu
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caleb R Glassman
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Timothy P Sheahan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lora K Picton
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Fernando R Moreira
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Arjun Rustagi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin M Jude
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xiang Zhao
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Catherine A Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Ralph S Baric
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leon L Su
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - K Christopher Garcia
- Departments of Molecular and Cellular Physiology, and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Ram-Mohan N, Rogers AJ, Blish CA, Nadeau KC, Zudock EJ, Kim D, Quinn JV, Sun L, Liesenfeld O, Yang S. Detection of bacterial co-infections and prediction of fatal outcomes in COVID-19 patients presenting to the emergency department using a 29 mRNA host response classifier. medRxiv 2022:2022.03.14.22272394. [PMID: 35313598 PMCID: PMC8936113 DOI: 10.1101/2022.03.14.22272394] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Objective Clinicians in the emergency department (ED) face challenges in concurrently assessing patients with suspected COVID-19 infection, detecting bacterial co-infection, and determining illness severity since current practices require separate workflows. Here we explore the accuracy of the IMX-BVN-3/IMX-SEV-3 29 mRNA host response classifiers in simultaneously detecting SARS-CoV-2 infection, bacterial co-infections, and predicting clinical severity of COVID-19. Methods 161 patients with PCR-confirmed COVID-19 (52.2% female, median age 50.0 years, 51% hospitalized, 5.6% deaths) were enrolled at the Stanford Hospital ED. RNA was extracted (2.5 mL whole blood in PAXgene Blood RNA) and 29 host mRNAs in response to the infection were quantified using Nanostring nCounter. Results The IMX-BVN-3 classifier identified SARS-CoV-2 infection in 151 patients with a sensitivity of 93.8%. Six of 10 patients undetected by the classifier had positive COVID tests more than 9 days prior to enrolment and the remaining oscillated between positive and negative results in subsequent tests. The classifier also predicted that 6 (3.7%) patients had a bacterial co-infection. Clinical adjudication confirmed that 5/6 (83.3%) of the patients had bacterial infections, i.e. Clostridioides difficile colitis (n=1), urinary tract infection (n=1), and clinically diagnosed bacterial infections (n=3) for a specificity of 99.4%. 2/101 (2.8%) patients in the IMX-SEV-3 Low and 7/60 (11.7%) in the Moderate severity classifications died within thirty days of enrollment. Conclusions IMX-BVN-3/IMX-SEV-3 classifiers accurately identified patients with COVID-19, bacterial co-infections, and predicted patients’ risk of death. A point-of-care version of these classifiers, under development, could improve ED patient management including more accurate treatment decisions and optimized resource utilization.
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Affiliation(s)
- Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Angela J. Rogers
- Department of Medicine-Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Catherine A. Blish
- Department of Medicine/Infectious Diseases, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Kari C. Nadeau
- Department of Medicine-Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Elizabeth J Zudock
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - David Kim
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - James V. Quinn
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | | | | | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
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31
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Valenzuela A, Rieger KE, Blish CA, Chung L, Fiorentino D. Gastrointestinal Perforation in a Patient With Antinuclear Matrix Protein 2 Antibody-Positive Dermatomyositis. Arthritis Care Res (Hoboken) 2022; 74:1409-1415. [PMID: 35287251 DOI: 10.1002/acr.24879] [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] [Received: 11/19/2021] [Revised: 02/23/2022] [Accepted: 03/08/2022] [Indexed: 11/08/2022]
Affiliation(s)
| | - Kerri E Rieger
- Stanford University School of Medicine, Redwood City, California
| | | | - Lorinda Chung
- Stanford University School of Medicine, Redwood City, California
| | - David Fiorentino
- Stanford University School of Medicine, Redwood City, California
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Abstract
Considerable research effort has been made worldwide to decipher the immune response triggered upon severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, identify the drivers of severe and fatal COVID-19, and understand what leads to the prolongation of symptoms after disease resolution. We review the results of almost 2 years of COVID-19 immunology research and discuss definitive findings and remaining questions regarding our understanding of COVID-19 pathophysiology. We discuss emerging understanding of differences in immune responses seen in those with and without Long Covid syndrome, also known as post-acute sequelae of SARS-CoV-2. We hope that the knowledge gained from this COVID-19 research will be applied in studies of inflammatory processes involved in critical and chronic illnesses, which remain a major unmet need.
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Affiliation(s)
- Miriam Merad
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Catherine A Blish
- Department of Medicine and Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Federica Sallusto
- Institute of Microbiology, ETH Zürich, 8093 Zürich, Switzerland.,Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
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Sievers BL, Chakraborty S, Xue Y, Gelbart T, Gonzalez JC, Cassidy AG, Golan Y, Prahl M, Gaw SL, Arunachalam PS, Blish CA, Boyd SD, Davis MM, Jagannathan P, Nadeau KC, Pulendran B, Singh U, Scheuermann RH, Frieman MB, Vashee S, Wang TT, Tan GS. Antibodies elicited by SARS-CoV-2 infection or mRNA vaccines have reduced neutralizing activity against Beta and Omicron pseudoviruses. Sci Transl Med 2022; 14:eabn7842. [PMID: 35025672 PMCID: PMC8891085 DOI: 10.1126/scitranslmed.abn7842] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/07/2022] [Indexed: 01/29/2023]
Abstract
Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that have mutations associated with increased transmission and antibody escape have arisen over the course of the current pandemic. Although the current vaccines have largely been effective against past variants, the number of mutations found on the Omicron (B.1.1.529) spike protein appear to diminish the protection conferred by preexisting immunity. Using vesicular stomatitis virus (VSV) pseudoparticles expressing the spike protein of several SARS-CoV-2 variants, we evaluated the magnitude and breadth of the neutralizing antibody response over time in individuals after infection and in mRNA-vaccinated individuals. We observed that boosting increases the magnitude of the antibody response to wild-type (D614), Beta, Delta, and Omicron variants; however, the Omicron variant was the most resistant to neutralization. We further observed that vaccinated healthy adults had robust and broad antibody responses, whereas responses may have been reduced in vaccinated pregnant women, underscoring the importance of learning how to maximize mRNA vaccine responses in pregnant populations. Findings from this study show substantial heterogeneity in the magnitude and breadth of responses after infection and mRNA vaccination and may support the addition of more conserved viral antigens to existing SARS-CoV-2 vaccines.
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Affiliation(s)
| | - Saborni Chakraborty
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, 94305 USA
| | - Yong Xue
- J. Craig Venter Institute, La Jolla, CA, 92037 and Rockville, MD, 20850 USA
| | - Terri Gelbart
- J. Craig Venter Institute, La Jolla, CA, 92037 and Rockville, MD, 20850 USA
| | - Joseph C. Gonzalez
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, 94305 USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
| | - Arianna G. Cassidy
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94115 USA
| | - Yarden Golan
- Department of Bioengineering and Therapeutic Sciences, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94115 USA
| | - Mary Prahl
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of California, San Francisco, CA, 94115 USA
| | - Stephanie L. Gaw
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94115 USA
| | - Prabhu S. Arunachalam
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, 94305 USA
| | - Catherine A. Blish
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, 94305 USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158 USA
| | - Scott D. Boyd
- Departments of Pathology and of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 USA
- Sean N. Parker Center for Allergy and Asthma Research, Department of Medicine, Stanford, CA, 94305 USA
| | - Mark M. 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 School of Medicine, Stanford, CA 94305, USA
| | - Prasanna Jagannathan
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, 94305 USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Department of Medicine, Stanford, CA, 94305 USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, 94305 USA
| | - Upinder Singh
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, 94305 USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
| | | | - Matthew B. Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, 21201 USA
| | - Sanjay Vashee
- J. Craig Venter Institute, La Jolla, CA, 92037 and Rockville, MD, 20850 USA
| | - Taia T. Wang
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, 94305 USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158 USA
| | - Gene S. Tan
- J. Craig Venter Institute, La Jolla, CA, 92037 and Rockville, MD, 20850 USA
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, 92037 USA
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Carroll T, Fox D, van Doremalen N, Ball E, Morris MK, Sotomayor-Gonzalez A, Servellita V, Rustagi A, Yinda CK, Fritts L, Port JR, Ma ZM, Holbrook MG, Schulz J, Blish CA, Hanson C, Chiu CY, Munster V, Stanley S, Miller CJ. The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters. PLoS Pathog 2022; 18:e1009914. [PMID: 35143587 PMCID: PMC8865701 DOI: 10.1371/journal.ppat.1009914] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 08/23/2021] [Revised: 02/23/2022] [Accepted: 01/22/2022] [Indexed: 12/13/2022] Open
Abstract
As novel SARS-CoV-2 variants continue to emerge, it is critical that their potential to cause severe disease and evade vaccine-induced immunity is rapidly assessed in humans and studied in animal models. In early January 2021, a novel SARS-CoV-2 variant designated B.1.429 comprising 2 lineages, B.1.427 and B.1.429, was originally detected in California (CA) and it was shown to have enhanced infectivity in vitro and decreased antibody neutralization by plasma from convalescent patients and vaccine recipients. Here we examine the virulence, transmissibility, and susceptibility to pre-existing immunity for B 1.427 and B 1.429 in the Syrian hamster model. We find that both variants exhibit enhanced virulence as measured by increased body weight loss compared to hamsters infected with ancestral B.1 (614G), with B.1.429 causing the most marked body weight loss among the 3 variants. Faster dissemination from airways to parenchyma and more severe lung pathology at both early and late stages were also observed with B.1.429 infections relative to B.1. (614G) and B.1.427 infections. In addition, subgenomic viral RNA (sgRNA) levels were highest in oral swabs of hamsters infected with B.1.429, however sgRNA levels in lungs were similar in all three variants. This demonstrates that B.1.429 replicates to higher levels than ancestral B.1 (614G) or B.1.427 in the oropharynx but not in the lungs. In multi-virus in-vivo competition experiments, we found that B.1. (614G), epsilon (B.1.427/B.1.429) and gamma (P.1) dramatically outcompete alpha (B.1.1.7), beta (B.1.351) and zeta (P.2) in the lungs. In the nasal cavity, B.1. (614G), gamma, and epsilon dominate, but the highly infectious alpha variant also maintains a moderate size niche. We did not observe significant differences in airborne transmission efficiency among the B.1.427, B.1.429 and ancestral B.1 (614G) and WA-1 variants in hamsters. These results demonstrate enhanced virulence and high relative oropharyngeal replication of the epsilon (B.1.427/B.1.429) variant in Syrian hamsters compared to an ancestral B.1 (614G) variant. In 2020 and 2021, new variants of SARS-CoV-2 were detected in the UK, South Africa, Brazil, India, California and beyond. New SARS-CoV-2 variants will continue to emerge for the foreseeable future in the human population and the potential for these new variants to produce severe disease and evade vaccines needs to be understood. In this study, we used the hamster model to determine the epsilon (B.1.427/429) SARS-CoV-2 variants that emerged in California in late 2020 cause more severe disease and infected hamsters have higher viral RNA levels in oral swabs compared to the prior B.1 (614G) variant. These findings are consistent with human clinical data and help explain the emergence and rapid spread of this variant in early 2021.
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Affiliation(s)
- Timothy Carroll
- California National Primate Research Center, University of California Davis, Davis, California, United States of America
- Center for Immunology and infectious Diseases, University of California Davis, Davis, California, United States of America
| | - Douglas Fox
- University of California, Berkeley, Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, Berkeley, California, United States of America
| | - Neeltje van Doremalen
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Erin Ball
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Mary Kate Morris
- Division of Viral and Rickettsial Diseases, California Department of Public Health, Richmond, California, United States of America
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, California, United States of America
| | - Claude Kwe Yinda
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Linda Fritts
- California National Primate Research Center, University of California Davis, Davis, California, United States of America
- Center for Immunology and infectious Diseases, University of California Davis, Davis, California, United States of America
| | - Julia Rebecca Port
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Zhong-Min Ma
- California National Primate Research Center, University of California Davis, Davis, California, United States of America
| | - Myndi G. Holbrook
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Jonathan Schulz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Catherine A. Blish
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Palo Alto, California, United States of America
| | - Carl Hanson
- Division of Viral and Rickettsial Diseases, California Department of Public Health, Richmond, California, United States of America
| | - Charles Y. Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail: (CYC); (VM); (SS); (CJM)
| | - Vincent Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail: (CYC); (VM); (SS); (CJM)
| | - Sarah Stanley
- University of California, Berkeley, Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, Berkeley, California, United States of America
- * E-mail: (CYC); (VM); (SS); (CJM)
| | - Christopher J. Miller
- California National Primate Research Center, University of California Davis, Davis, California, United States of America
- Center for Immunology and infectious Diseases, University of California Davis, Davis, California, United States of America
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- Division of Infectious Diseases, Department of Internal Medicine, School of Medicine, University of California Davis, Davis, California, United States of America
- * E-mail: (CYC); (VM); (SS); (CJM)
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Ram-Mohan N, Kim D, Rogers AJ, Blish CA, Nadeau K, Blomkalns AL, Yang S. Association Between SARS-CoV-2 RNAemia and Postacute Sequelae of COVID-19. Open Forum Infect Dis 2022; 9:ofab646. [PMID: 35111870 PMCID: PMC8802799 DOI: 10.1093/ofid/ofab646] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 10/08/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022] Open
Abstract
Determinants of Post-Acute Sequelae of COVID-19 are not known. Here we show that 83.3% of patients with viral RNA in blood (RNAemia) at presentation were symptomatic in the post-acute phase. RNAemia at presentation successfully predicted PASC, independent of patient demographics, worst disease severity, and length of symptoms.
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Affiliation(s)
- Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - David Kim
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Angela J Rogers
- Department of Medicine—Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Catherine A Blish
- Department of Medicine/Infectious Diseases, Stanford University School of Medicine, Palo Alto, California, USA
| | - Kari C Nadeau
- Department of Medicine—Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Andra L Blomkalns
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
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Ram-Mohan N, Kim D, Zudock EJ, Hashemi MM, Tjandra KC, Rogers AJ, Blish CA, Nadeau KC, Newberry JA, Quinn JV, O'Hara R, Ashley E, Nguyen H, Jiang L, Hung P, Blomkalns AL, Yang S. SARS-CoV-2 RNAemia Predicts Clinical Deterioration and Extrapulmonary Complications from COVID-19. Clin Infect Dis 2022; 74:218-226. [PMID: 33949665 PMCID: PMC8135992 DOI: 10.1093/cid/ciab394] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 02/14/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The determinants of coronavirus disease 2019 (COVID-19) disease severity and extrapulmonary complications (EPCs) are poorly understood. We characterized relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNAemia and disease severity, clinical deterioration, and specific EPCs. METHODS We used quantitative and digital polymerase chain reaction (qPCR and dPCR) to quantify SARS-CoV-2 RNA from plasma in 191 patients presenting to the emergency department with COVID-19. We recorded patient symptoms, laboratory markers, and clinical outcomes, with a focus on oxygen requirements over time. We collected longitudinal plasma samples from a subset of patients. We characterized the role of RNAemia in predicting clinical severity and EPCs using elastic net regression. RESULTS Of SARS-CoV-2-positive patients, 23.0% (44 of 191) had viral RNA detected in plasma by dPCR, compared with 1.4% (2 of 147) by qPCR. Most patients with serial measurements had undetectable RNAemia within 10 days of symptom onset, reached maximum clinical severity within 16 days, and symptom resolution within 33 days. Initially RNAemic patients were more likely to manifest severe disease (odds ratio, 6.72 [95% confidence interval, 2.45-19.79]), worsening of disease severity (2.43 [1.07-5.38]), and EPCs (2.81 [1.26-6.36]). RNA loads were correlated with maximum severity (r = 0.47 [95% confidence interval, .20-.67]). CONCLUSIONS dPCR is more sensitive than qPCR for the detection of SARS-CoV-2 RNAemia, which is a robust predictor of eventual COVID-19 severity and oxygen requirements, as well as EPCs. Because many COVID-19 therapies are initiated on the basis of oxygen requirements, RNAemia on presentation might serve to direct early initiation of appropriate therapies for the patients most likely to deteriorate.
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Affiliation(s)
- Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - David Kim
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Elizabeth J Zudock
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Marjan M Hashemi
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Kristel C Tjandra
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Angela J Rogers
- Department of Medicine-Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Catherine A Blish
- Department of Medicine/Infectious Diseases, Stanford University School of Medicine, Palo Alto, California, USA
| | - Kari C Nadeau
- Department of Medicine-Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Jennifer A Newberry
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - James V Quinn
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Ruth O'Hara
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, California, USA
| | - Euan Ashley
- Department of Medicine-Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | | | | | - Paul Hung
- Combinati Inc, Palo Alto, California, USA
| | - Andra L Blomkalns
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
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George AF, Luo X, Neidleman J, Hoh R, Vohra P, Thomas R, Shin MG, Lee MJ, Blish CA, Deeks S, Greene WC, Lee SA, Roan NR. Deep Phenotypic Analysis of Blood and Lymphoid T and NK Cells From HIV+ Controllers and ART-Suppressed Individuals. Front Immunol 2022; 13:803417. [PMID: 35154118 PMCID: PMC8829545 DOI: 10.3389/fimmu.2022.803417] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 12/03/2022] Open
Abstract
T and natural killer (NK) cells are effector cells with key roles in anti-HIV immunity, including in lymphoid tissues, the major site of HIV persistence. However, little is known about the features of these effector cells from people living with HIV (PLWH), particularly from those who initiated antiretroviral therapy (ART) during acute infection. Our study design was to use 42-parameter CyTOF to conduct deep phenotyping of paired blood- and lymph node (LN)-derived T and NK cells from three groups of HIV+ aviremic individuals: elite controllers (N = 5), and ART-suppressed individuals who had started therapy during chronic (N = 6) vs. acute infection (N = 8), the latter of which is associated with better outcomes. We found that acute-treated individuals are enriched for specific subsets of T and NK cells, including blood-derived CD56-CD16+ NK cells previously associated with HIV control, and LN-derived CD4+ T follicular helper cells with heightened expansion potential. An in-depth comparison of the features of the cells from blood vs. LNs of individuals from our cohort revealed that T cells from blood were more activated than those from LNs. By contrast, LNs were enriched for follicle-homing CXCR5+ CD8+ T cells, which expressed increased levels of inhibitory receptors and markers of survival and proliferation as compared to their CXCR5- counterparts. In addition, a subset of memory-like CD56brightTCF1+ NK cells was enriched in LNs relative to blood. These results together suggest unique T and NK cell features in acute-treated individuals, and highlight the importance of examining effector cells not only in blood but also the lymphoid tissue compartment, where the reservoir mostly persists, and where these cells take on distinct phenotypic features.
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Affiliation(s)
- Ashley F. George
- Gladstone Institute of Virology, San Francisco, CA, United States,Department of Urology, University of California San Francisco, San Francisco, CA, United States
| | - Xiaoyu Luo
- Gladstone Institute of Virology, San Francisco, CA, United States
| | - Jason Neidleman
- Gladstone Institute of Virology, San Francisco, CA, United States,Department of Urology, University of California San Francisco, San Francisco, CA, United States
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Poonam Vohra
- Department of Pathology, University of California San Francisco, San Francisco, CA, United States
| | - Reuben Thomas
- Gladstone Institutes, San Francisco, CA, United States
| | | | - Madeline J. Lee
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States,Program in Immunology, Stanford School of Medicine, Stanford, CA, United States
| | - Catherine A. Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States,Program in Immunology, Stanford School of Medicine, Stanford, CA, United States
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Warner C. Greene
- Gladstone Institute of Virology, San Francisco, CA, United States,Departments of Medicine, and Microbiology & Immunology, University of California San Francisco, San Francisco, CA, United States
| | - Sulggi A. Lee
- Zuckerberg San Francisco General Hospital and the University of California San Francisco, San Francisco, CA, United States,*Correspondence: Sulggi A. Lee, ; Nadia R. Roan,
| | - Nadia R. Roan
- Gladstone Institute of Virology, San Francisco, CA, United States,Department of Urology, University of California San Francisco, San Francisco, CA, United States,*Correspondence: Sulggi A. Lee, ; Nadia R. Roan,
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Cable J, Rappuoli R, Klemm EJ, Kang G, Mutreja A, Wright GJ, Pizza M, Castro SA, Hoffmann JP, Alter G, Carfi A, Pollard AJ, Krammer F, Gupta RK, Wagner CE, Machado V, Modjarrad K, Corey L, B Gilbert P, Dougan G, Lurie N, Bjorkman PJ, Chiu C, Nemes E, Gordon SB, Steer AC, Rudel T, Blish CA, Sandberg JT, Brennan K, Klugman KP, Stuart LM, Madhi SA, Karp CL. Innovative vaccine approaches-a Keystone Symposia report. Ann N Y Acad Sci 2022; 1511:59-86. [PMID: 35029310 DOI: 10.1111/nyas.14739] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/16/2022]
Abstract
The rapid development of COVID-19 vaccines was the result of decades of research to establish flexible vaccine platforms and understand pathogens with pandemic potential, as well as several novel changes to the vaccine discovery and development processes that partnered industry and governments. And while vaccines offer the potential to drastically improve global health, low-and-middle-income countries around the world often experience reduced access to vaccines and reduced vaccine efficacy. Addressing these issues will require novel vaccine approaches and platforms, deeper insight how vaccines mediate protection, and innovative trial designs and models. On June 28-30, 2021, experts in vaccine research, development, manufacturing, and deployment met virtually for the Keystone eSymposium "Innovative Vaccine Approaches" to discuss advances in vaccine research and development.
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Affiliation(s)
| | | | | | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Hinxton, UK.,Department of Biology, Hull York Medical School, and York Biomedical Research Institute, University of York, York, UK
| | | | - Sowmya Ajay Castro
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Joseph P Hoffmann
- Departments of Pediatrics and Medicine, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, Louisiana
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts.,Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Florian Krammer
- The Tisch Cancer Institute and Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) and Department of Medicine, University of Cambridge, Cambridge, UK.,Africa Health Research Institute, Durban, South Africa
| | - Caroline E Wagner
- Department of Bioengineering, McGill University, Montreal, Quebec, Canada
| | - Viviane Machado
- Measles and Respiratory Viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Lawrence Corey
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington.,Department of Medicine, University of Washington School of Medicine, Seattle, Washington.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Peter B Gilbert
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) and Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicole Lurie
- Coalition for Epidemic Preparedness Innovations, Oslo, Norway.,Harvard Medical School, Boston, Massachusetts
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Christopher Chiu
- Department of Infectious Disease, Imperial College London, London, UK
| | - Elisa Nemes
- Division of Immunology, Department of Pathology, South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Andrew C Steer
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia.,Department of General Medicine, The Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Thomas Rudel
- Microbiology Biocenter, University of Würzburg, Würzburg, Germany
| | - Catherine A Blish
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford Immunology Program, Stanford University School of Medicine, Stanford, California.,Chan Zuckerberg Biohub, San Francisco, California
| | - John Tyler Sandberg
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kiva Brennan
- National Children's Research Centre, Crumlin and School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Lynda M Stuart
- Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington.,Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
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Ivison GT, Vendrame E, Martínez-Colón GJ, Ranganath T, Vergara R, Zhao NQ, Martin MP, Bendall SC, Carrington M, Cyktor JC, McMahon DK, Eron J, Jones RB, Mellors JW, Bosch RJ, Gandhi RT, Holmes S, Blish CA. Natural Killer Cell Receptors and Ligands Are Associated With Markers of HIV-1 Persistence in Chronically Infected ART Suppressed Patients. Front Cell Infect Microbiol 2022; 12:757846. [PMID: 35223535 PMCID: PMC8866573 DOI: 10.3389/fcimb.2022.757846] [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: 08/12/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
The latent HIV-1 reservoir represents a major barrier to achieving a long-term antiretroviral therapy (ART)-free remission or cure for HIV-1. Natural Killer (NK) cells are innate immune cells that play a critical role in controlling viral infections and have been shown to be involved in preventing HIV-1 infection and, in those who are infected, delaying time to progression to AIDS. However, their role in limiting HIV-1 persistence on long term ART is still uncharacterized. To identify associations between markers of HIV-1 persistence and the NK cell receptor-ligand repertoire, we used twin mass cytometry panels to characterize the peripheral blood NK receptor-ligand repertoire in individuals with long-term antiretroviral suppression enrolled in the AIDS Clinical Trial Group A5321 study. At the time of testing, participants had been on ART for a median of 7 years, with virological suppression <50 copies/mL since at most 48 weeks on ART. We found that the NK cell receptor and ligand repertoires did not change across three longitudinal samples over one year-a median of 25 weeks and 50 weeks after the initial sampling. To determine the features of the receptor-ligand repertoire that associate with markers of HIV-1 persistence, we performed a LASSO normalized regression. This analysis revealed that the NK cell ligands CD58, HLA-B, and CRACC, as well as the killer cell immunoglobulin-like receptors (KIRs) KIR2DL1, KIR2DL3, and KIR2DS4 were robustly predictive of markers of HIV-1 persistence, as measured by total HIV-1 cell-associated DNA, HIV-1 cell-associated RNA, and single copy HIV-RNA assays. To characterize the roles of cell populations defined by multiple markers, we augmented the LASSO analysis with FlowSOM clustering. This analysis found that a less mature NK cell phenotype (CD16+CD56dimCD57-LILRB1-NKG2C-) was associated with lower HIV-1 cell associated DNA. Finally, we found that surface expression of HLA-Bw6 measured by CyTOF was associated with lower HIV-1 persistence. Genetic analysis revealed that this was driven by lower HIV-1 persistence in HLA-Bw4/6 heterozygotes. These findings suggest that there may be a role for NK cells in controlling HIV-1 persistence in individuals on long-term ART, which must be corroborated by future studies.
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Affiliation(s)
- Geoffrey T Ivison
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States.,Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Elena Vendrame
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Giovanny J Martínez-Colón
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Thanmayi Ranganath
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Rosemary Vergara
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Nancy Q Zhao
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Maureen P Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National, Cancer Institute, Frederick, MD, United States.,Laboratory of Integrative Cancer, Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National, Cancer Institute, Frederick, MD, United States.,Laboratory of Integrative Cancer, Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States.,Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Boston, MA, United States
| | - Joshua C Cyktor
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States
| | - Deborah K McMahon
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States
| | - Joseph Eron
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ronald J Bosch
- Center for Biostatistics in AIDS Research, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Rajesh T Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Center for AIDS Research, Harvard University, Boston, MA, United States
| | - Susan Holmes
- Department of Statistics, School of Humanities and Sciences, Stanford University, Stanford, CA, United States
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Chan Zuckerberg Biohub, San Francisco, CA, United States
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Dzanibe S, Lennard K, Kiravu A, Seabrook MSS, Alinde B, Holmes SP, Blish CA, Jaspan HB, Gray CM. Stereotypic Expansion of T Regulatory and Th17 Cells during Infancy Is Disrupted by HIV Exposure and Gut Epithelial Damage. J Immunol 2022; 208:27-37. [PMID: 34819390 PMCID: PMC8702481 DOI: 10.4049/jimmunol.2100503] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/01/2021] [Indexed: 01/03/2023]
Abstract
Few studies have investigated immune cell ontogeny throughout the neonatal and early pediatric period, when there is often increased vulnerability to infections. In this study, we evaluated the dynamics of two critical T cell populations, T regulatory (Treg) cells and Th17 cells, over the first 36 wk of human life. First, we observed distinct CD4+ T cells phenotypes between cord blood and peripheral blood, collected within 12 h of birth, showing that cord blood is not a surrogate for newborn blood. Second, both Treg and Th17 cells expanded in a synchronous fashion over 36 wk of life. However, comparing infants exposed to HIV in utero, but remaining uninfected, with HIV-unexposed uninfected control infants, there was a lower frequency of peripheral blood Treg cells at birth, resulting in a delayed expansion, and then declining again at 36 wk. Focusing on birth events, we found that Treg cells coexpressing CCR4 and α4β7 inversely correlated with plasma concentrations of CCL17 (the ligand for CCR4) and intestinal fatty acid binding protein, IL-7, and CCL20. This was in contrast with Th17 cells, which showed a positive association with these plasma analytes. Thus, despite the stereotypic expansion of both cell subsets over the first few months of life, there was a disruption in the balance of Th17 to Treg cells at birth likely being a result of gut damage and homing of newborn Treg cells from the blood circulation to the gut.
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Affiliation(s)
- Sonwabile Dzanibe
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa;
| | - Katie Lennard
- Division of Computational Biology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Agano Kiravu
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Melanie S S Seabrook
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Berenice Alinde
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Susan P Holmes
- Department of Statistic, Stanford University, Stanford, CA
| | - Catherine A Blish
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA
- Chan Zuckerberg Biohub, San Francisco, CA
| | - Heather B Jaspan
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Seattle Children's Research Institute and Departments of Paediatrics and Global Health, University of Washington, Seattle, WA; and
| | - Clive M Gray
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa;
- Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
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41
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Wirz OF, Röltgen K, Stevens BA, Pandey S, Sahoo MK, Tolentino L, Verghese M, Nguyen K, Hunter M, Snow TT, Singh AR, Blish CA, Cochran JR, Zehnder JL, Nadeau KC, Pinsky BA, Pham TD, Boyd SD. Use of Outpatient-Derived COVID-19 Convalescent Plasma in COVID-19 Patients Before Seroconversion. Front Immunol 2021; 12:739037. [PMID: 34594341 PMCID: PMC8477649 DOI: 10.3389/fimmu.2021.739037] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
Background Transfusion of COVID-19 convalescent plasma (CCP) containing high titers of anti-SARS-CoV-2 antibodies serves as therapy for COVID-19 patients. Transfusions early during disease course was found to be beneficial. Lessons from the SARS-CoV-2 pandemic could inform early responses to future pandemics and may continue to be relevant in lower resource settings. We sought to identify factors correlating to high antibody titers in convalescent plasma donors and understand the magnitude and pharmacokinetic time course of both transfused antibody titers and the endogenous antibody titers in transfused recipients. Methods Plasma samples were collected up to 174 days after convalescence from 93 CCP donors with mild disease, and from 16 COVID-19 patients before and after transfusion. Using ELISA, anti-SARS-CoV-2 Spike RBD, S1, and N-protein antibodies, as well as capacity of antibodies to block ACE2 from binding to RBD was measured in an in vitro assay. As an estimate for viral load, viral RNA and N-protein plasma levels were assessed in COVID-19 patients. Results Anti-SARS-CoV-2 antibody levels and RBD-ACE2 blocking capacity were highest within the first 60 days after symptom resolution and markedly decreased after 120 days. Highest antibody titers were found in CCP donors that experienced fever. Effect of transfused CCP was detectable in COVID-19 patients who received high-titer CCP and had not seroconverted at the time of transfusion. Decrease in viral RNA was seen in two of these patients. Conclusion Our results suggest that high titer CCP should be collected within 60 days after recovery from donors with past fever. The much lower titers conferred by transfused antibodies compared to endogenous production in the patient underscore the importance of providing CCP prior to endogenous seroconversion.
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Affiliation(s)
- Oliver F. Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Bryan A. Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Suchitra Pandey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Blood Center, Palo Alto, CA, United States
| | - Malaya K. Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | | | - Michelle Verghese
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Khoa Nguyen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | | | - Theo Thomas Snow
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, United States
| | - Abhay Raj Singh
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, United States
| | - Catherine A. Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Jennifer R. Cochran
- Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - James L. Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, United States
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA, United States
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, United States
| | - Tho D. Pham
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Stanford Blood Center, Palo Alto, CA, United States
| | - Scott D. Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, United States
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Ram-Mohan N, Kim D, Rogers AJ, Blish CA, Nadeau KC, Blomkalns AL, Yang S. Association Between SARS-CoV-2 RNAemia and Post-Acute Sequelae of COVID-19. medRxiv 2021:2021.09.03.21262934. [PMID: 34518843 PMCID: PMC8437320 DOI: 10.1101/2021.09.03.21262934] [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] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Determinants of Post-Acute Sequelae of COVID-19 are not known. Here we show that 75% of patients with viral RNA in blood (RNAemia) at presentation were symptomatic in the post-acute phase. RNAemia at presentation successfully predicted PASC, independent of patient demographics, initial disease severity, and length of symptoms.
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Affiliation(s)
- Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto CA 94305 USA
| | - David Kim
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto CA 94305 USA
| | - Angela J Rogers
- Department of Medicine - Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Palo Alto CA 94305 USA
| | - Catherine A Blish
- Department of Medicine/Infectious Diseases, Stanford University School of Medicine, Palo Alto CA 94305 USA
| | - Kari C Nadeau
- Department of Medicine - Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Palo Alto CA 94305 USA
| | - Andra L Blomkalns
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto CA 94305 USA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto CA 94305 USA
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Carroll T, Fox D, van Doremalen N, Ball E, Morris MK, Sotomayor-Gonzalez A, Servellita V, Rustagi A, Yinda CK, Fritts L, Port JR, Ma ZM, Holbrook M, Schulz J, Blish CA, Hanson C, Chiu CY, Munster V, Stanley S, Miller CJ. The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters. bioRxiv 2021. [PMID: 34462750 PMCID: PMC8404898 DOI: 10.1101/2021.08.25.457626] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
As novel SARS-CoV-2 variants continue to emerge, it is critical that their potential to cause severe disease and evade vaccine-induced immunity is rapidly assessed in humans and studied in animal models. In early January 2021, a novel variant of concern (VOC) designated B.1.429 comprising 2 lineages, B.1.427 and B.1.429, was originally detected in California (CA) and shown to enhance infectivity in vitro and decrease antibody neutralization by plasma from convalescent patients and vaccine recipients. Here we examine the virulence, transmissibility, and susceptibility to pre-existing immunity for B 1.427 and B 1.429 in the Syrian hamster model. We find that both strains exhibit enhanced virulence as measured by increased body weight loss compared to hamsters infected with ancestral B.1 (614G), with B.1.429 causing the most body weight loss among all 3 lineages. Faster dissemination from airways to parenchyma and more severe lung pathology at both early and late stages were also observed with B.1.429 infections relative to B.1. (614G) and B.1.427 infections. In addition, subgenomic viral RNA (sgRNA) levels were highest in oral swabs of hamsters infected with B.1.429, however sgRNA levels in lungs were similar in all three strains. This demonstrates that B.1.429 replicates to higher levels than ancestral B.1 (614G) or B.1.427 in the upper respiratory tract (URT) but not in the lungs. In multi-virus in-vivo competition experiments, we found that epsilon (B.1.427/B.1.429) and gamma (P.1) dramatically outcompete alpha (B.1.1.7), beta (B.1.351) and zeta (P.2) in the lungs. In the URT gamma, and epsilon dominate, but the highly infectious alpha variant also maintains a moderate size niche. We did not observe significant differences in airborne transmission efficiency among the B.1.427, B.1.429 and ancestral B.1 (614G) variants in hamsters. These results demonstrate enhanced virulence and high relative fitness of the epsilon (B.1.427/B.1.429) variant in Syrian hamsters compared to an ancestral B.1 (614G) strain. In the last 12 months new variants of SARS-CoV-2 have arisen in the UK, South Africa, Brazil, India, and California. New SARS-CoV-2 variants will continue to emerge for the foreseeable future in the human population and the potential for these new variants to produce severe disease and evade vaccines needs to be understood. In this study, we used the hamster model to determine the epsilon (B.1.427/429) SARS-CoV-2 strains that emerged in California in late 2020 cause more severe disease and infected hamsters have higher viral loads in the upper respiratory tract compared to the prior B.1 (614G) strain. These findings are consistent with human clinical data and help explain the emergence and rapid spread of this strain in early 2021.
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44
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Wilk AJ, Lee MJ, Wei B, Parks B, Pi R, Martínez-Colón GJ, Ranganath T, Zhao NQ, Taylor S, Becker W, Jimenez-Morales D, Blomkalns AL, O’Hara R, Ashley EA, Nadeau KC, Yang S, Holmes S, Rabinovitch M, Rogers AJ, Greenleaf WJ, Blish CA. Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19. J Exp Med 2021; 218:e20210582. [PMID: 34128959 PMCID: PMC8210586 DOI: 10.1084/jem.20210582] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [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: 03/12/2021] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 12/20/2022] Open
Abstract
Our understanding of protective versus pathological immune responses to SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is limited by inadequate profiling of patients at the extremes of the disease severity spectrum. Here, we performed multi-omic single-cell immune profiling of 64 COVID-19 patients across the full range of disease severity, from outpatients with mild disease to fatal cases. Our transcriptomic, epigenomic, and proteomic analyses revealed widespread dysfunction of peripheral innate immunity in severe and fatal COVID-19, including prominent hyperactivation signatures in neutrophils and NK cells. We also identified chromatin accessibility changes at NF-κB binding sites within cytokine gene loci as a potential mechanism for the striking lack of pro-inflammatory cytokine production observed in monocytes in severe and fatal COVID-19. We further demonstrated that emergency myelopoiesis is a prominent feature of fatal COVID-19. Collectively, our results reveal disease severity-associated immune phenotypes in COVID-19 and identify pathogenesis-associated pathways that are potential targets for therapeutic intervention.
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Affiliation(s)
- Aaron J. Wilk
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Madeline J. Lee
- Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Bei Wei
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Benjamin Parks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
- Graduate Program in Computer Science, Stanford University School of Medicine, Stanford, CA
| | - Ruoxi Pi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | | | - Thanmayi Ranganath
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Nancy Q. Zhao
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Shalina Taylor
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA
| | - Winston Becker
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | | | | | - Andra L. Blomkalns
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA
| | - Ruth O’Hara
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA
| | - Euan A. Ashley
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - Kari C. Nadeau
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, CA
| | - Marlene Rabinovitch
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
- Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
- Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, CA
| | - Angela J. Rogers
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
| | - William J. Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
- Department of Applied Physics, Stanford University, Stanford, CA
| | - Catherine A. Blish
- Stanford Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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45
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Verma R, Kim E, Martínez-Colón GJ, Jagannathan P, Rustagi A, Parsonnet J, Bonilla H, Khosla C, Holubar M, Subramanian A, Singh U, Maldonado Y, Blish CA, Andrews JR. SARS-CoV-2 Subgenomic RNA Kinetics in Longitudinal Clinical Samples. Open Forum Infect Dis 2021; 8:ofab310. [PMID: 34295944 PMCID: PMC8291522 DOI: 10.1093/ofid/ofab310] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 05/20/2021] [Accepted: 06/09/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Given the persistence of viral RNA in clinically recovered coronavirus disease 2019 (COVID-19) patients, subgenomic RNAs (sgRNAs) have been reported as potential molecular viability markers for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, few data are available on their longitudinal kinetics, compared with genomic RNA (gRNA), in clinical samples. METHODS We analyzed 536 samples from 205 patients with COVID-19 from placebo-controlled, outpatient trials of peginterferon Lambda-1a (Lambda; n = 177) and favipiravir (n = 359). Nasal swabs were collected at 3 time points in the Lambda (days 1, 4, and 6) and favipiravir (days 1, 5, and 10) trials. N-gene gRNA and sgRNA were quantified by quantitative reverse transcription polymerase chain reaction. To investigate the decay kinetics in vitro, we measured gRNA and sgRNA in A549ACE2+ cells infected with SARS-CoV-2, following treatment with remdesivir or dimethylsulfoxide control. RESULTS At 6 days in the Lambda trial and 10 days in the favipiravir trial, sgRNA remained detectable in 51.6% (32/62) and 49.5% (51/106) of the samples, respectively. Cycle threshold (Ct) values for gRNA and sgRNA were highly linearly correlated (marginal R 2 = 0.83), and the rate of increase did not differ significantly in the Lambda trial (1.36 cycles/d vs 1.36 cycles/d; P = .97) or the favipiravir trial (1.03 cycles/d vs 0.94 cycles/d; P = .26). From samples collected 15-21 days after symptom onset, sgRNA was detectable in 48.1% (40/83) of participants. In SARS-CoV-2-infected A549ACE2+ cells treated with remdesivir, the rate of Ct increase did not differ between gRNA and sgRNA. CONCLUSIONS In clinical samples and in vitro, sgRNA was highly correlated with gRNA and did not demonstrate different decay patterns to support its application as a viability marker.
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Affiliation(s)
- Renu Verma
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Eugene Kim
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Giovanny Joel Martínez-Colón
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Prasanna Jagannathan
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Arjun Rustagi
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Julie Parsonnet
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, California, USA
| | - Hector Bonilla
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Chaitan Khosla
- Departments of Chemistry and Chemical Engineering, Stanford University, Stanford, California, USA
| | - Marisa Holubar
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Aruna Subramanian
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Upinder Singh
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Yvonne Maldonado
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Catherine A Blish
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
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46
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Hao Y, Hao S, Andersen-Nissen E, Mauck WM, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M, Hoffman P, Stoeckius M, Papalexi E, Mimitou EP, Jain J, Srivastava A, Stuart T, Fleming LM, Yeung B, Rogers AJ, McElrath JM, Blish CA, Gottardo R, Smibert P, Satija R. Integrated analysis of multimodal single-cell data. Cell 2021; 184:3573-3587.e29. [PMID: 34062119 PMCID: PMC8238499 DOI: 10.1016/j.cell.2021.04.048] [Citation(s) in RCA: 4627] [Impact Index Per Article: 1542.3] [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: 11/03/2020] [Revised: 03/03/2021] [Accepted: 04/28/2021] [Indexed: 02/08/2023]
Abstract
The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce "weighted-nearest neighbor" analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of 211,000 human peripheral blood mononuclear cells (PBMCs) with panels extending to 228 antibodies to construct a multimodal reference atlas of the circulating immune system. Multimodal analysis substantially improves our ability to resolve cell states, allowing us to identify and validate previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets and to interpret immune responses to vaccination and coronavirus disease 2019 (COVID-19). Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets and to look beyond the transcriptome toward a unified and multimodal definition of cellular identity.
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Affiliation(s)
- Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; New York Genome Center, New York, NY 10013, USA
| | - Stephanie Hao
- Technology Innovation Lab, New York Genome Center, New York, NY 10013, USA
| | - Erica Andersen-Nissen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Cape Town HVTN Immunology Lab, Hutchinson Cancer Research Institute of South Africa, Cape Town 8001, South Africa
| | - William M Mauck
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Shiwei Zheng
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; New York Genome Center, New York, NY 10013, USA
| | - Andrew Butler
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; New York Genome Center, New York, NY 10013, USA
| | - Maddie J Lee
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Aaron J Wilk
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charlotte Darby
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michael Zager
- Center for Data Visualization, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Paul Hoffman
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Marlon Stoeckius
- Technology Innovation Lab, New York Genome Center, New York, NY 10013, USA
| | - Efthymia Papalexi
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; New York Genome Center, New York, NY 10013, USA
| | - Eleni P Mimitou
- Technology Innovation Lab, New York Genome Center, New York, NY 10013, USA
| | - Jaison Jain
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Avi Srivastava
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Tim Stuart
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Lamar M Fleming
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Angela J Rogers
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Juliana M McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Catherine A Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94063, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Peter Smibert
- Technology Innovation Lab, New York Genome Center, New York, NY 10013, USA.
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; New York Genome Center, New York, NY 10013, USA.
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47
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Rubin SJS, Falkson SR, Degner NR, Blish CA. Safety of ACE-I and ARB medications in COVID-19: A retrospective cohort study of inpatients and outpatients in California. J Clin Transl Sci 2021; 5:e8. [PMID: 34611496 PMCID: PMC7605244 DOI: 10.1017/cts.2020.489] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION There is significant interest in the use of angiotensin converting enzyme inhibitors (ACE-I) and angiotensin II receptor blockers (ARB) in coronavirus disease 2019 (COVID-19) and concern over potential adverse effects since these medications upregulate the severe acute respiratory syndrome coronavirus 2 host cell entry receptor ACE2. Recent studies on ACE-I and ARB in COVID-19 were limited by excluding outpatients, excluding patients by age, analyzing ACE-I and ARB together, imputing missing data, and/or diagnosing COVID-19 by chest computed tomography without definitive reverse transcription polymerase chain reaction (RT-PCR), all of which are addressed here. METHODS We performed a retrospective cohort study of 1023 COVID-19 patients diagnosed by RT-PCR at Stanford Hospital through April 8, 2020 with a minimum follow-up time of 14 days to investigate the association between ACE-I or ARB use with outcomes. RESULTS Use of ACE-I or ARB medications was not associated with increased risk of hospitalization, intensive care unit admission, or death. Compared to patients with charted past medical history, there was a lower risk of hospitalization for patients on ACE-I (odds ratio (OR) 0.43; 95% confidence interval (CI) 0.19-0.97; P = 0.0426) and ARB (OR 0.39; 95% CI 0.17-0.90; P = 0.0270). Compared to patients with hypertension not on ACE-I or ARB, patients on ARB medications had a lower risk of hospitalization (OR 0.09; 95% CI 0.01-0.88; P = 0.0381). CONCLUSIONS These findings suggest that the use of ACE-I and ARB is not associated with adverse outcomes and may be associated with improved outcomes in COVID-19, which is immediately relevant to care of the many patients on these medications.
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Affiliation(s)
- Samuel J. S. Rubin
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Samuel R. Falkson
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas R. Degner
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A. Blish
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA, USA
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48
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Delaveris C, Wilk AJ, Riley NM, Stark JC, Yang SS, Rogers AJ, Ranganath T, Nadeau KC, Blish CA, Bertozzi CR. Synthetic Siglec-9 Agonists Inhibit Neutrophil Activation Associated with COVID-19. ACS Cent Sci 2021; 7:650-657. [PMID: 34056095 PMCID: PMC8009098 DOI: 10.1021/acscentsci.0c01669] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Indexed: 05/02/2023]
Abstract
Severe cases of coronavirus disease 2019 (COVID-19), caused by infection with SARS-CoV-2, are characterized by a hyperinflammatory immune response that leads to numerous complications. Production of proinflammatory neutrophil extracellular traps (NETs) has been suggested to be a key factor in inducing a hyperinflammatory signaling cascade, allegedly causing both pulmonary tissue damage and peripheral inflammation. Accordingly, therapeutic blockage of neutrophil activation and NETosis, the cell death pathway accompanying NET formation, could limit respiratory damage and death from severe COVID-19. Here, we demonstrate that synthetic glycopolymers that activate signaling of the neutrophil checkpoint receptor Siglec-9 suppress NETosis induced by agonists of viral toll-like receptors (TLRs) and plasma from patients with severe COVID-19. Thus, Siglec-9 agonism is a promising therapeutic strategy to curb neutrophilic hyperinflammation in COVID-19.
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Affiliation(s)
- Corleone
S. Delaveris
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- ChEM-H, Stanford University, Stanford, California 94305, United States
| | - Aaron J. Wilk
- Stanford
Medical Scientist Training Program, Stanford
University, Stanford, California 94305, United States
- Stanford
Immunology Program, Stanford University, Stanford, California 94305, United States
- Department
of Medicine, Stanford University, Stanford, California 94305, United States
| | - Nicholas M. Riley
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jessica C. Stark
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Samuel S. Yang
- Department
of Emergency Medicine, Stanford University, Stanford, California 94305, United States
| | - Angela J. Rogers
- Department
of Medicine, Stanford University, Stanford, California 94305, United States
| | - Thanmayi Ranganath
- Department
of Medicine, Stanford University, Stanford, California 94305, United States
| | - Kari C. Nadeau
- Department
of Medicine, Stanford University, Stanford, California 94305, United States
- Sean
N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, California 94305, United States
| | | | - Catherine A. Blish
- Department
of Medicine, Stanford University, Stanford, California 94305, United States
- Chan
Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Carolyn R. Bertozzi
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- ChEM-H, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford, California 94305, United States
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49
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Seiler C, Ferreira AM, Kronstad LM, Simpson LJ, Le Gars M, Vendrame E, Blish CA, Holmes S. CytoGLMM: conditional differential analysis for flow and mass cytometry experiments. BMC Bioinformatics 2021; 22:137. [PMID: 33752595 PMCID: PMC7983283 DOI: 10.1186/s12859-021-04067-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/03/2021] [Indexed: 11/10/2022] Open
Abstract
Background Flow and mass cytometry are important modern immunology tools for measuring expression levels of multiple proteins on single cells. The goal is to better understand the mechanisms of responses on a single cell basis by studying differential expression of proteins. Most current data analysis tools compare expressions across many computationally discovered cell types. Our goal is to focus on just one cell type. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. Results Differential analysis of marker expressions can be difficult due to marker correlations and inter-subject heterogeneity, particularly for studies of human immunology. We address these challenges with two multiple regression strategies: a bootstrapped generalized linear model and a generalized linear mixed model. On simulated datasets, we compare the robustness towards marker correlations and heterogeneity of both strategies. For paired experiments, we find that both strategies maintain the target false discovery rate under medium correlations and that mixed models are statistically more powerful under the correct model specification. For unpaired experiments, our results indicate that much larger patient sample sizes are required to detect differences. We illustrate the CytoGLMM R package and workflow for both strategies on a pregnancy dataset. Conclusion Our approach to finding differential proteins in flow and mass cytometry data reduces biases arising from marker correlations and safeguards against false discoveries induced by patient heterogeneity.
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Affiliation(s)
- Christof Seiler
- Department of Data Science and Knowledge Engineering, Maastricht University, Maastricht, The Netherlands. .,Mathematics Centre Maastricht, Maastricht University, Maastricht, The Netherlands. .,Department of Statistics, Stanford University, Stanford, USA.
| | | | - Lisa M Kronstad
- Immunology Program, Stanford University School of Medicine, Stanford, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, USA.,Department of Microbiology and Immunology, Midwestern University, Downers Grove, USA
| | - Laura J Simpson
- Immunology Program, Stanford University School of Medicine, Stanford, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, USA
| | - Mathieu Le Gars
- Immunology Program, Stanford University School of Medicine, Stanford, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, USA
| | - Elena Vendrame
- Immunology Program, Stanford University School of Medicine, Stanford, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, USA
| | - Catherine A Blish
- Immunology Program, Stanford University School of Medicine, Stanford, USA.,Department of Medicine, Stanford University School of Medicine, Stanford, USA.,Chan Zuckerberg Biohub, San Francisco, USA
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, USA
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50
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Chakraborty S, Gonzalez J, Edwards K, Mallajosyula V, Buzzanco AS, Sherwood R, Buffone C, Kathale N, Providenza S, Xie MM, Andrews JR, Blish CA, Singh U, Dugan H, Wilson PC, Pham TD, Boyd SD, Nadeau KC, Pinsky BA, Zhang S, Memoli MJ, Taubenberger JK, Morales T, Schapiro JM, Tan GS, Jagannathan P, Wang TT. Proinflammatory IgG Fc structures in patients with severe COVID-19. Nat Immunol 2021; 22:67-73. [PMID: 33169014 PMCID: PMC8130642 DOI: 10.1038/s41590-020-00828-7] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [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: 08/31/2020] [Accepted: 10/26/2020] [Indexed: 12/30/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 infections can cause coronavirus disease 2019 (COVID-19), which manifests with a range of severities from mild illness to life-threatening pneumonia and multi-organ failure. Severe COVID-19 is characterized by an inflammatory signature, including high levels of inflammatory cytokines, alveolar inflammatory infiltrates and vascular microthrombi. Here we show that patients with severe COVID-19 produced a unique serologic signature, including an increased likelihood of IgG1 with afucosylated Fc glycans. This Fc modification on severe acute respiratory syndrome coronavirus 2 IgGs enhanced interactions with the activating Fcγ receptor FcγRIIIa; when incorporated into immune complexes, Fc afucosylation enhanced production of inflammatory cytokines by monocytes, including interleukin-6 and tumor necrosis factor. These results show that disease severity in COVID-19 correlates with the presence of proinflammatory IgG Fc structures, including afucosylated IgG1.
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Affiliation(s)
- Saborni Chakraborty
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Joseph Gonzalez
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Karlie Edwards
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Anthony S Buzzanco
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Robert Sherwood
- Proteomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Cindy Buffone
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Nimish Kathale
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Susan Providenza
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Markus M Xie
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Jason R Andrews
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Upinder Singh
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Haley Dugan
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL, USA
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology, University of Chicago, Chicago, IL, USA
| | - Tho D Pham
- Stanford Blood Center, Palo Alto, CA, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sheng Zhang
- Proteomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Matthew J Memoli
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeffery K Taubenberger
- LID Clinical Studies Unit, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Tasha Morales
- TPMG Regional Reference Laboratory, Kaiser Permanente Northern California, Berkeley, CA, USA
| | - Jeffrey M Schapiro
- TPMG Regional Reference Laboratory, Kaiser Permanente Northern California, Berkeley, CA, USA
| | - Gene S Tan
- J. Craig Venter Institute, La Jolla, CA, USA
- Department of Infectious Diseases, University of California, San Diego, La Jolla, CA, USA
| | - Prasanna Jagannathan
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
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