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Phelps A, Pazos-Castro D, Urselli F, Grydziuszko E, Mann-Delany O, Fang A, Walker TD, Guruge RT, Tome-Amat J, Diaz-Perales A, Waserman S, Boonyaratanakornkit J, Jordana M, Taylor JJ, Koenig JFE. Production and use of antigen tetramers to study antigen-specific B cells. Nat Protoc 2024; 19:727-751. [PMID: 38243093 DOI: 10.1038/s41596-023-00930-8] [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: 05/16/2023] [Accepted: 10/20/2023] [Indexed: 01/21/2024]
Abstract
B cells generate antibodies that provide protection from infection, but also cause pathology in autoimmune and allergic conditions. Antigen-specific B cells can be detected by binding their surface antibody receptors with native antigens conjugated to fluorescent probes, a technique that has revealed substantial insight into B cell activation and function. This protocol describes the process of generating fluorescent antigen tetramer probes and delineates a process of enriching large samples based on antigen-specificity for high-resolution analyses of the antigen-specific B cell repertoire. Enrichment of tetramer-binding cells allows for detection of antigen-specific B cells as rare as 1 in 100 million cells, providing sufficient resolution to study naive B cells and IgE-expressing cells by flow cytometry. The generation of antigen tetramers involves antigen biotinylation, assessment of biotin:antigen ratio for optimal tetramer loading and polymerization around a streptavidin-fluorophore backbone. We also describe the construction of a control tetramer to exclude B cells binding to the tetramer backbone. We provide a framework to validate whether tetramer probes are detecting true antigen-specific B cells and discuss considerations for experimental design. This protocol can be performed by researchers trained in basic biomedical/immunological research techniques, using instrumentation commonly found in most laboratories. Constructing the antigen and control tetramers takes 9 h, though their specificity should be assessed before experimentation and may take weeks to months depending on the method of validation. Sample enrichment requires ~2 h but is generally time and cost neutral as fewer cells are run through the flow cytometer.
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Affiliation(s)
- Allyssa Phelps
- Department of Medicine, Schroeder Allergy and Immunology Research Institute, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Diego Pazos-Castro
- Department of Medicine, Schroeder Allergy and Immunology Research Institute, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (UPM-INIA/CSIC), Universidad Politécnica de Madrid, Madrid, Spain
- Department of Biotechnology-Plant Biology, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas (ETSIAAB), Universidad Politécnica de Madrid, Madrid, Spain
| | - Francesca Urselli
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Emily Grydziuszko
- Department of Medicine, Schroeder Allergy and Immunology Research Institute, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Olivia Mann-Delany
- Department of Medicine, Schroeder Allergy and Immunology Research Institute, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Allison Fang
- Department of Medicine, Schroeder Allergy and Immunology Research Institute, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Tina D Walker
- Department of Medicine, Schroeder Allergy and Immunology Research Institute, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Rangana Talpe Guruge
- Department of Medicine, Schroeder Allergy and Immunology Research Institute, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Jaime Tome-Amat
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (UPM-INIA/CSIC), Universidad Politécnica de Madrid, Madrid, Spain
| | - Araceli Diaz-Perales
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/Consejo Superior de Investigaciones Científicas (UPM-INIA/CSIC), Universidad Politécnica de Madrid, Madrid, Spain
- Department of Biotechnology-Plant Biology, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas (ETSIAAB), Universidad Politécnica de Madrid, Madrid, Spain
| | - Susan Waserman
- Department of Medicine, Schroeder Allergy and Immunology Research Institute, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Manel Jordana
- Department of Medicine, Schroeder Allergy and Immunology Research Institute, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Beirne B. Carter Center for Immunology Research, University of Virginia, Charlottesville, VA, USA.
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, USA.
| | - Joshua F E Koenig
- Department of Medicine, Schroeder Allergy and Immunology Research Institute, McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada.
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Bodansky A, Yu DJL, Rallistan A, Kalaycioglu M, Boonyaratanakornkit J, Green DJ, Gauthier J, Turtle CJ, Zorn K, O’Donovan B, Mandel-Brehm C, Asaki J, Kortbawi H, Kung AF, Rackaityte E, Wang CY, Saxena A, de Dios K, Masi G, Nowak RJ, O’Connor KC, Li H, Diaz VE, Casaletto KB, Gontrum EQ, Chan B, Kramer JH, Wilson MR, Utz PJ, Hill JA, Jackson SW, Anderson MS, DeRisi JL. Unveiling the autoreactome: Proteome-wide immunological fingerprints reveal the promise of plasma cell depleting therapy. medRxiv 2023:2023.12.19.23300188. [PMID: 38196603 PMCID: PMC10775319 DOI: 10.1101/2023.12.19.23300188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The prevalence and burden of autoimmune and autoantibody mediated disease is increasing worldwide, yet most disease etiologies remain unclear. Despite numerous new targeted immunomodulatory therapies, comprehensive approaches to apply and evaluate the effects of these treatments longitudinally are lacking. Here, we leverage advances in programmable-phage immunoprecipitation (PhIP-Seq) methodology to explore the modulation, or lack thereof, of proteome-wide autoantibody profiles in both health and disease. We demonstrate that each individual, regardless of disease state, possesses a distinct set of autoreactivities constituting a unique immunological fingerprint, or "autoreactome", that is remarkably stable over years. In addition to uncovering important new biology, the autoreactome can be used to better evaluate the relative effectiveness of various therapies in altering autoantibody repertoires. We find that therapies targeting B-Cell Maturation Antigen (BCMA) profoundly alter an individual's autoreactome, while anti-CD19 and CD-20 therapies have minimal effects, strongly suggesting a rationale for BCMA or other plasma cell targeted therapies in autoantibody mediated diseases.
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Affiliation(s)
- Aaron Bodansky
- Department of Pediatrics, Division of Critical Care, University of California San Francisco, San Francisco, CA
| | - David JL Yu
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA
| | - Alysa Rallistan
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305
| | - Muge Kalaycioglu
- Institute of Immunity, Transplantation, and Infection (ITI), Stanford University, Stanford, CA 94305
| | - Jim Boonyaratanakornkit
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- University of Washington School of Medicine, Seattle, WA, USA
| | - Damian J. Green
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- University of Washington School of Medicine, Seattle, WA, USA
| | - Jordan Gauthier
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- University of Washington School of Medicine, Seattle, WA, USA
| | - Cameron J. Turtle
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- University of Washington School of Medicine, Seattle, WA, USA
| | - Kelsey Zorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
| | - Brian O’Donovan
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
| | - James Asaki
- Biomedical Sciences Program, University of California San Francisco, San Francisco, CA
| | - Hannah Kortbawi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
- Medical Scientist Training Program, University of California San Francisco, San Francisco, CA
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA
| | - Elze Rackaityte
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
| | | | | | - Kimberly de Dios
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA
| | - Gianvito Masi
- Department of Neurology, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT
| | | | - Kevin C. O’Connor
- Department of Neurology, Yale School of Medicine, New Haven, CT
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT
| | - Hao Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
| | - Valentina E. Diaz
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Kaitlin B. Casaletto
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Eva Q. Gontrum
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Brandon Chan
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Joel H. Kramer
- Memory and Aging Center, Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Michael R. Wilson
- Weill Institute for Neurosciences, University of California San Francisco; San Francisco, CA
- Department of Neurology, University of California San Francisco; San Francisco, CA
| | - Paul J. Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305
| | - Joshua A. Hill
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- University of Washington School of Medicine, Seattle, WA, USA
| | - Shaun W. Jackson
- Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA
- Seattle Children’s Research Institute, Seattle, WA
- Pediatrics, University of Washington School of Medicine, Seattle, WA
| | - Mark S. Anderson
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub SF, San Francisco, CA
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3
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Fitzpatrick KS, Degefu HN, Poljakov K, Bibby MG, Remington AJ, Searles TG, Gray MD, Boonyaratanakornkit J, Rosato PC, Taylor JJ. Validation of Ligand Tetramers for the Detection of Antigen-Specific Lymphocytes. J Immunol 2023; 210:1156-1165. [PMID: 36883850 PMCID: PMC10073333 DOI: 10.4049/jimmunol.2200934] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/07/2023] [Indexed: 03/09/2023]
Abstract
The study of Ag-specific lymphocytes has been a key advancement in immunology over the past few decades. The development of multimerized probes containing Ags, peptide:MHC complexes, or other ligands was one innovation allowing the direct study of Ag-specific lymphocytes by flow cytometry. Although these types of study are now common and performed by thousands of laboratories, quality control and assessment of probe quality are often minimal. In fact, many of these types of probe are made in-house, and protocols vary between laboratories. Although peptide:MHC multimers can often be obtained from commercial sources or core facilities, few such services exist for Ag multimers. To ensure high quality and consistency with ligand probes, we have developed an easy and robust multiplexed approach using commercially available beads able to bind Abs specific for the ligand of interest. Using this assay, we have sensitively assessed the performance of peptide:MHC and Ag tetramers and have found considerable batch-to-batch variability in performance and stability over time more easily than using murine or human cell-based assays. This bead-based assay can also reveal common production errors such as miscalculation of Ag concentration. This work could set the stage for the development of standardized assays for all commonly used ligand probes to limit laboratory-to-laboratory technical variation and experimental failure caused by probe underperformance.
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Affiliation(s)
- Kristin S Fitzpatrick
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Molecular Medicine and Mechanisms of Disease PhD Program, University of Washington, Seattle, WA
| | - Hanna N Degefu
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Lebanon, NH
| | - Katrina Poljakov
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Madeleine G Bibby
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Allison J Remington
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA
| | - Tyler G Searles
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Lebanon, NH
| | - Matthew D Gray
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Jim Boonyaratanakornkit
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Pamela C Rosato
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Lebanon, NH
| | - Justin J Taylor
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Immunology, University of Washington, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
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4
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Hill JA, Kiem ES, Bhatti A, Liu W, Keane-Candib J, Fitzpatrick KS, Boonyaratanakornkit J, Gardner RA, Green DJ, Maloney DG, Turtle CJ, Smith JM, Gimferrer I, Blosser CD, Jackson SW. Anti-HLA antibodies in recipients of CD19 versus BCMA-targeted CAR T-cell therapy. Am J Transplant 2023; 23:416-422. [PMID: 36748802 PMCID: PMC10266802 DOI: 10.1016/j.ajt.2022.11.001] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/05/2022] [Accepted: 11/06/2022] [Indexed: 01/15/2023]
Abstract
Antibodies against foreign human leukocyte antigen (HLA) molecules are barriers to successful organ transplantation. B cell-depleting treatments are used to reduce anti-HLA antibodies but have limited efficacy. We hypothesized that the primary source for anti-HLA antibodies is long-lived plasma cells, which are ineffectively targeted by B cell depletion. To study this, we screened for anti-HLA antibodies in a prospectively enrolled cohort of 49 patients who received chimeric antigen receptor T-cell therapy (CARTx), targeting naïve and memory B cells (CD19-targeted, n = 21) or plasma cells (BCMA-targeted, n = 28) for hematologic malignancies. Longitudinal samples were collected before and up to 1 year after CARTx. All individuals were in sustained remission. We identified 4 participants with anti-HLA antibodies before CD19-CARTx. Despite B cell depletion, anti-HLA antibodies and calculated panel reactive antibody scores were stable for 1 year after CD19-CARTx. Only 1 BCMA-CARTx recipient had pre-CARTx low-level anti-HLA antibodies, with no follow-up samples available. These data implicate CD19neg long-lived plasma cells as an important source for anti-HLA antibodies, a model supported by infrequent HLA sensitization in BCMA-CARTx subjects receiving previous plasma cell-targeted therapies. Thus, plasma cell-targeted therapies may be more effective against HLA antibodies, thereby enabling improved access to organ transplantation and rejection management.
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Affiliation(s)
- Joshua A Hill
- Departments of Medicine, University of Washington School of Medicine, Seattle, Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
| | - Erika S Kiem
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Atif Bhatti
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Winnie Liu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jacob Keane-Candib
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Kristin S Fitzpatrick
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jim Boonyaratanakornkit
- Departments of Medicine, University of Washington School of Medicine, Seattle, Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Rebecca A Gardner
- Seattle Children's Research Institute, Seattle, Washington, USA; Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Damian J Green
- Departments of Medicine, University of Washington School of Medicine, Seattle, Washington, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - David G Maloney
- Departments of Medicine, University of Washington School of Medicine, Seattle, Washington, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Cameron J Turtle
- Departments of Medicine, University of Washington School of Medicine, Seattle, Washington, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jodi M Smith
- Seattle Children's Research Institute, Seattle, Washington, USA; Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Idoia Gimferrer
- Immunogenetics/HLA laboratory Bloodworks Northwest, Seattle, Washington, USA
| | - Christopher D Blosser
- Departments of Medicine, University of Washington School of Medicine, Seattle, Washington, USA; Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Shaun W Jackson
- Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA; Seattle Children's Research Institute, Seattle, Washington, USA; Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA.
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5
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Cabán M, Rodarte JV, Bibby M, Gray MD, Taylor JJ, Pancera M, Boonyaratanakornkit J. Cross-protective antibodies against common endemic respiratory viruses. Nat Commun 2023; 14:798. [PMID: 36781872 PMCID: PMC9923667 DOI: 10.1038/s41467-023-36459-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 06/27/2022] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
Respiratory syncytial virus (RSV), human metapneumovirus (HMPV), and human parainfluenza virus types one (HPIV1) and three (HPIV3) can cause severe disease and death in immunocompromised patients, the elderly, and those with underlying lung disease. A protective monoclonal antibody exists for RSV, but clinical use is limited to high-risk infant populations. Hence, therapeutic options for these viruses in vulnerable patient populations are currently limited. Here, we present the discovery, in vitro characterization, and in vivo efficacy testing of two cross-neutralizing monoclonal antibodies, one targeting both HPIV3 and HPIV1 and the other targeting both RSV and HMPV. The 3 × 1 antibody is capable of targeting multiple parainfluenza viruses; the MxR antibody shares features with other previously reported monoclonal antibodies that are capable of neutralizing both RSV and HMPV. We obtained structures using cryo-electron microscopy of these antibodies in complex with their antigens at 3.62 Å resolution for 3 × 1 bound to HPIV3 and at 2.24 Å for MxR bound to RSV, providing a structural basis for in vitro binding and neutralization. Together, a cocktail of 3 × 1 and MxR could have clinical utility in providing broad protection against four of the respiratory viruses that cause significant morbidity and mortality in at-risk individuals.
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Affiliation(s)
- Madelyn Cabán
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Immunology & Department of Global Health, University of Washington, Seattle, WA, USA
| | - Justas V Rodarte
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Madeleine Bibby
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Matthew D Gray
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Immunology & Department of Global Health, University of Washington, Seattle, WA, USA.
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Medicine, University of Washington, Seattle, WA, USA.
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Boonyaratanakornkit J, Wang Q, Nader A, Kimball LE, Levkova M, Nguyen J, Wright J, Ford ES, Mielcarek M, Han J, Boeckh MJ, Waghmare DA. Sotrovimab Pharmacokinetics and Covariate Effects in Hematopoietic Stem Cell Transplant Recipients. Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00504-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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7
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Doll MK, Waghmare A, Heit A, Levenson Shakoor B, Kimball LE, Ozbek N, Blazevic RL, Mose L, Boonyaratanakornkit J, Stevens-Ayers TL, Cornell K, Sheppard BD, Hampson E, Sharmin F, Goodwin B, Dan JM, Archie T, O’Connor T, Heckerman D, Schmitz F, Boeckh M, Crotty S. Acute and Postacute COVID-19 Outcomes Among Immunologically Naive Adults During Delta vs Omicron Waves. JAMA Netw Open 2023; 6:e231181. [PMID: 36853602 PMCID: PMC9975921 DOI: 10.1001/jamanetworkopen.2023.1181] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
IMPORTANCE The US arrival of the Omicron variant led to a rapid increase in SARS-CoV-2 infections. While numerous studies report characteristics of Omicron infections among vaccinated individuals or persons with previous infection, comprehensive data describing infections among adults who are immunologically naive are lacking. OBJECTIVES To examine COVID-19 acute and postacute clinical outcomes among a well-characterized cohort of unvaccinated and previously uninfected adults who contracted SARS-CoV-2 during the Omicron (BA.1/BA.2) surge, and to compare outcomes with infections that occurred during the Delta wave. DESIGN, SETTING, AND PARTICIPANTS This prospective multisite cohort study included community-dwelling adults undergoing high-resolution symptom and virologic monitoring in 8 US states between June 2021 and September 2022. Unvaccinated adults aged 30 to less than 65 years without an immunological history of SARS-CoV-2 who were at high risk of infection were recruited. Participants were followed for up to 48 weeks, submitting regular COVID-19 symptom surveys and nasal swabs for SARS-CoV-2 polymerase chain reaction (PCR) testing. Data were analyzed from May to October 2022. EXPOSURES Omicron (BA.1/BA.2 lineages) vs Delta SARS-CoV-2 infection, defined as a positive PCR test result that occurred during a period when the variant represented at least 50% of circulating SARS-CoV-2 variants in the participant's geographic region. MAIN OUTCOMES AND MEASURE(S) The main outcomes examined were the prevalence and severity of acute (≤28 days after onset) and postacute (≥5 weeks after onset) symptoms. RESULTS Among 274 participants who were immunologically naive (mean [SD] age, 49 [9.7] years; 186 [68%] female; 19 [7%] Hispanic participants; 242 [88%] White participants), 166 (61%) contracted SARS-CoV-2. Of these, 137 infections (83%) occurred during the Omicron-predominant period and 29 infections (17%) occurred during the Delta-predominant period. Asymptomatic infections occurred among 7% (95% CI, 3%-12%) of Omicron-wave infections and 0% (95% CI, 0%-12%) of Delta-wave infections. Health care use among individuals with Omicron-wave infections was 79% (95% CI, 43%-92%) lower relative to individuals with Delta-wave infections (P = .001). Compared with individuals infected during the Delta wave, individuals infected during the Omicron wave also experienced a 56% (95% CI, 26%-74%, P = .004) relative reduction in the risk of postacute symptoms and a 79% (95% CI, 54%-91%, P < .001) relative reduction in the rate of postacute symptoms. CONCLUSIONS AND RELEVANCE These findings suggest that among adults who were previously immunologically naive, few Omicron-wave (BA.1/BA.2) and Delta-wave infections were asymptomatic. Compared with individuals with Delta-wave infections, individuals with Omicron-wave infections were less likely to seek health care and experience postacute symptoms.
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Affiliation(s)
- Margaret K. Doll
- Department of Population Health Sciences, Albany College of Pharmacy & Health Sciences, Albany, New York
| | - Alpana Waghmare
- Division of Infectious Diseases, Department of Pediatrics, University of Washington, Seattle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | | | - Brianna Levenson Shakoor
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California
| | - Louise E. Kimball
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Nina Ozbek
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Rachel L. Blazevic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Larry Mose
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | | | - Terry L. Stevens-Ayers
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | | | | | | | - Faria Sharmin
- Department of Population Health Sciences, Albany College of Pharmacy & Health Sciences, Albany, New York
| | - Benjamin Goodwin
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California
| | - Jennifer M. Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla
| | - Tom Archie
- St Luke’s Medical Center, Ketchum, Idaho
| | - Terry O’Connor
- St Luke’s Medical Center, Ketchum, Idaho
- Department of Emergency Medicine, University of Washington, Seattle
| | | | | | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla
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8
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Doll MK, Waghmare A, Heit A, Levenson Shakoor B, Kimball LE, Ozbek N, Blazevic RL, Mose L, Boonyaratanakornkit J, Stevens-Ayers TL, Cornell K, Sheppard BD, Hampson E, Sharmin F, Goodwin B, Dan JM, Archie T, O'Connor T, Heckerman D, Schmitz F, Boeckh M, Crotty S. Acute and Post-Acute COVID-19 Outcomes Among Immunologically Naïve Adults During Delta Versus Omicron Waves. medRxiv 2022:2022.11.13.22282222. [PMID: 36425923 PMCID: PMC9685683 DOI: 10.1101/2022.11.13.22282222] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Importance The U.S. arrival of the Omicron variant led to a rapid increase in SARS-CoV-2 infections. While numerous studies report characteristics of Omicron infections among vaccinated individuals and/or persons with a prior history of infection, comprehensive data describing infections among immunologically naïve adults is lacking. Objective To examine COVID-19 acute and post-acute clinical outcomes among a well-characterized cohort of unvaccinated and previously uninfected adults who contracted SARS-CoV-2 during the Omicron (BA.1/BA.2) surge, and to compare outcomes with infections that occurred during the Delta wave. Design A prospective cohort undergoing high-resolution symptom and virologic monitoring between June 2021 and September 2022. Setting Multisite recruitment of community-dwelling adults in 8 U.S. states. Participants Healthy, unvaccinated adults between 30 to 64 years of age without an immunological history of SARS-CoV-2 who were at high-risk of infection were recruited. Participants were followed for up to 48 weeks, submitting regular COVID-19 symptom surveys and nasal swabs for SARS-CoV-2 PCR testing. Exposures Omicron (BA.1/BA.2 lineages) versus Delta SARS-CoV-2 infection, defined as a positive PCR that occurred during a period when the variant represented ≥50% of circulating SARS-CoV-2 variants in the participant's geographic region. Main Outcomes and Measures The main outcomes examined were the prevalence and severity of acute (≤28 days post-onset) and post-acute (≥5 weeks post-onset) symptoms. Results Among 274 immunologically naïve participants, 166 (61%) contracted SARS-CoV-2. Of these, 137 (83%) and 29 (17%) infections occurred during the Omicron- and Delta-predominant periods, respectively. Asymptomatic infections occurred among 6.7% (95% CI: 3.1%, 12.3%) of Omicron cases and 0.0% (95% CI: 0.0%, 11.9%) of Delta cases. Healthcare utilization among Omicron cases was 79% (95% CI: 43%, 92%, P =0.001) lower relative to Delta cases. Relative to Delta, Omicron infections also experienced a 56% (95% CI: 26%, 74%, P =0.004) and 79% (95% CI: 54%, 91%, P <0.001) reduction in the risk and rate of post-acute symptoms, respectively. Conclusions and Relevance These findings suggest that among previously immunologically naïve adults, few Omicron (BA.1/BA.2) and Delta infections are asymptomatic, and relative to Delta, Omicron infections were less likely to seek healthcare and experience post-acute symptoms.
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Affiliation(s)
- Margaret K Doll
- Department of Population Health Sciences, Albany College of Pharmacy & Health Sciences, Albany, NY, USA
| | - Alpana Waghmare
- Division of Infectious Diseases, Department of Pediatrics, University of Washington, Seattle, WA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Brianna Levenson Shakoor
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Louise E Kimball
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Nina Ozbek
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Rachel L Blazevic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Larry Mose
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Terry L Stevens-Ayers
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | | | | | - Faria Sharmin
- Department of Population Health Sciences, Albany College of Pharmacy & Health Sciences, Albany, NY, USA
| | - Benjamin Goodwin
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA.,Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Tom Archie
- St. Luke's Medical Center, Ketchum, ID, USA
| | - Terry O'Connor
- St. Luke's Medical Center, Ketchum, ID, USA.,Department of Emergency Medicine, University of Washington, Seattle, WA, USA
| | | | | | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.,Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA.,Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego, La Jolla, California, USA
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9
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Hayden RT, Su Y, Boonyaratanakornkit J, Cook L, Gu Z, Jerome KR, Pinsky BA, Sam SS, Tan SK, Zhu H, Tang L, Caliendo AM. Matrix Matters: Assessment of Commutability among BK Virus Assays and Standards. J Clin Microbiol 2022; 60:e0055522. [PMID: 35997500 PMCID: PMC9491175 DOI: 10.1128/jcm.00555-22] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
Quantitative testing of BK virus (BKPyV) nucleic acid has become the standard of care in transplant patients. While the relationship between interassay harmonization and commutability has been well characterized for other transplant-related viruses, it has been less well studied for BKPyV, particularly regarding differences in commutability between matrices. Here, interassay agreement was evaluated among six real-time nucleic acid amplification tests (NAATs) and one digital PCR (dPCR) BKPyV assay. Differences in the commutability of three quantitative standards was examined across all assays using a variety of statistical approaches. Panels, including 40 samples each of plasma and urine samples previously positive for BKPyV, together with one previously negative plasma sample and four previously negative urine samples, were tested using all assays, with each real-time NAAT utilizing its usual quantitative calibrators. Serial dilutions of WHO, National Institute for Standards and Technology (NIST), and commercially produced (Exact/Bio-Rad) reference materials were also run by each assay as unknowns. The agreement of the clinical sample values was assessed as a group and in a pairwise manner. The commutability was estimated using both relativistic and quantitative means. The quantitative agreement across assays in the urine samples was within a single log10 unit across all assays, while the results from the plasma samples varied by 2 to 3 log10 IU/mL. The commutability showed a similar disparity between the matrices. Recalibration using international standards diminished the resulting discrepancies in some but not all cases. Differences in the sample matrix can affect the commutability and interassay agreement of quantitative BKPyV assays. Differences in commutability between matrices may largely be due to factors other than those such as amplicon size, previously described as important in the case of cytomegalovirus. Continued efforts to standardize viral load measurements must address multiple sources of variability and account for differences in assay systems, quantitative standards, and sample matrices.
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Affiliation(s)
- R. T. Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Y. Su
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - L. Cook
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Z. Gu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - K. R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseaese Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - B. A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - S. S. Sam
- Division of Infectious Diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - S. K. Tan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - H. Zhu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - L. Tang
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - A. M. Caliendo
- Division of Infectious Diseases, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
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10
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Elyanow R, Snyder TM, Dalai SC, Gittelman RM, Boonyaratanakornkit J, Wald A, Selke S, Wener MH, Morishima C, Greninger AL, Gale M, Hsiang TY, Jing L, Holbrook MR, Kaplan IM, Zahid HJ, May DH, Carlson JM, Baldo L, Manley T, Robins HS, Koelle DM. T cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibodies and disease severity. JCI Insight 2022; 7:e150070. [PMID: 35439166 PMCID: PMC9220924 DOI: 10.1172/jci.insight.150070] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 04/15/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUNDMeasuring the immune response to SARS-CoV-2 enables assessment of past infection and protective immunity. SARS-CoV-2 infection induces humoral and T cell responses, but these responses vary with disease severity and individual characteristics.METHODSA T cell receptor (TCR) immunosequencing assay was conducted using small-volume blood samples from 302 individuals recovered from COVID-19. Correlations between the magnitude of the T cell response and neutralizing antibody (nAb) titers or indicators of disease severity were evaluated. Sensitivity of T cell testing was assessed and compared with serologic testing.RESULTSSARS-CoV-2-specific T cell responses were significantly correlated with nAb titers and clinical indicators of disease severity, including hospitalization, fever, and difficulty breathing. Despite modest declines in depth and breadth of T cell responses during convalescence, high sensitivity was observed until at least 6 months after infection, with overall sensitivity ~5% greater than serology tests for identifying prior SARS-CoV-2 infection. Improved performance of T cell testing was most apparent in recovered, nonhospitalized individuals sampled > 150 days after initial illness, suggesting greater sensitivity than serology at later time points and in individuals with less severe disease. T cell testing identified SARS-CoV-2 infection in 68% (55 of 81) of samples with undetectable nAb titers (<1:40) and in 37% (13 of 35) of samples classified as negative by 3 antibody assays.CONCLUSIONThese results support TCR-based testing as a scalable, reliable measure of past SARS-CoV-2 infection with clinical value beyond serology.TRIAL REGISTRATIONSpecimens were accrued under trial NCT04338360 accessible at clinicaltrials.gov.FUNDINGThis work was funded by Adaptive Biotechnologies, Frederick National Laboratory for Cancer Research, NIAID, Fred Hutchinson Joel Meyers Endowment, Fast Grants, and American Society for Transplantation and Cell Therapy.
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Affiliation(s)
| | | | - Sudeb C. Dalai
- Adaptive Biotechnologies, Seattle, Washington, USA
- Stanford University School of Medicine, Stanford, California, USA
| | | | - Jim Boonyaratanakornkit
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology
- Department of Laboratory Medicine and Pathology
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology
| | - Mark H. Wener
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology
| | | | | | - Michael Gale
- Department of Immunology
- Department of Microbiology, and
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Michael R. Holbrook
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, Frederick, Maryland, USA
| | | | | | - Damon H. May
- Adaptive Biotechnologies, Seattle, Washington, USA
| | | | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington, USA
| | | | | | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
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11
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Hurlburt NK, Homad LJ, Sinha I, Jennewein MF, MacCamy AJ, Wan YH, Boonyaratanakornkit J, Sholukh AM, Jackson AM, Zhou P, Burton DR, Andrabi R, Ozorowski G, Ward AB, Stamatatos L, Pancera M, McGuire AT. Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit. Commun Biol 2022; 5:342. [PMID: 35411021 PMCID: PMC9001700 DOI: 10.1038/s42003-022-03262-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [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: 01/10/2022] [Accepted: 03/11/2022] [Indexed: 12/11/2022] Open
Abstract
Three betacoronaviruses have crossed the species barrier and established human-to-human transmission causing significant morbidity and mortality in the past 20 years. The most current and widespread of these is SARS-CoV-2. The identification of CoVs with zoonotic potential in animal reservoirs suggests that additional outbreaks could occur. Monoclonal antibodies targeting conserved neutralizing epitopes on diverse CoVs can form the basis for prophylaxis and therapeutic treatments and enable the design of vaccines aimed at providing pan-CoV protection. We previously identified a neutralizing monoclonal antibody, CV3-25 that binds to the SARS-CoV-2 spike, neutralizes the SARS-CoV-2 Beta variant comparably to the ancestral Wuhan Hu-1 strain, cross neutralizes SARS-CoV-1 and binds to recombinant proteins derived from the spike-ectodomains of HCoV-OC43 and HCoV-HKU1. Here, we show that the neutralizing activity of CV3-25 is maintained against the Alpha, Delta, Gamma and Omicron variants of concern as well as a SARS-CoV-like bat coronavirus with zoonotic potential by binding to a conserved linear peptide in the stem-helix region. Negative stain electron microscopy and a 1.74 Å crystal structure of a CV3-25/peptide complex demonstrates that CV3-25 binds to the base of the stem helix at the HR2 boundary to an epitope that is distinct from other stem-helix directed neutralizing mAbs.
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Affiliation(s)
- Nicholas K Hurlburt
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Leah J Homad
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Irika Sinha
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Madeleine F Jennewein
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Anna J MacCamy
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Yu-Hsin Wan
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Jim Boonyaratanakornkit
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Anton M Sholukh
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Abigail M Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA. .,Department of Global Health, University of Washington, Seattle, WA, USA.
| | - Marie Pancera
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA. .,Vaccine Research Center, NAID, NIH, Bethesda, MD, USA.
| | - Andrew T McGuire
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA. .,Department of Global Health, University of Washington, Seattle, WA, USA. .,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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12
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Vick SC, Frutoso M, Mair F, Konecny AJ, Greene E, Wolf CR, Logue JK, Franko NM, Boonyaratanakornkit J, Gottardo R, Schiffer JT, Chu HY, Prlic M, Lund JM. A regulatory T cell signature distinguishes the immune landscape of COVID-19 patients from those with other respiratory infections. Sci Adv 2021; 7:eabj0274. [PMID: 34757794 PMCID: PMC8580318 DOI: 10.1126/sciadv.abj0274] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/22/2021] [Indexed: 06/01/2023]
Abstract
Despite recent studies of immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), little is known about how the immune response against SARS-CoV-2 differs from other respiratory infections. We compare the immune signature from hospitalized SARS-CoV-2–infected patients to patients hospitalized prepandemic with influenza or respiratory syncytial virus (RSV). Our in-depth profiling indicates that the immune landscape in SARS-CoV-2 patients is largely similar to flu or RSV patients. Unique to patients infected with SARS-CoV-2 who had the most critical clinical disease were changes in the regulatory T cell (Treg) compartment. A Treg signature including increased frequency, activation status, and migration markers was correlated COVID-19 severity. These findings are relevant as Tregs are considered for therapy to combat the severe inflammation seen in COVID-19 patients. Likewise, having defined the overlapping immune landscapes in SARS-CoV-2, existing knowledge of flu and RSV infections could be leveraged to identify common treatment strategies.
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Affiliation(s)
- Sarah C. Vick
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Marie Frutoso
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Florian Mair
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andrew J. Konecny
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Evan Greene
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Caitlin R. Wolf
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer K. Logue
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Nicholas M. Franko
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Martin Prlic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Jennifer M. Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
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13
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Cheon IS, Li C, Son YM, Goplen NP, Wu Y, Cassmann T, Wang Z, Wei X, Tang J, Li Y, Marlow H, Hughes S, Hammel L, Cox TM, Goddery E, Ayasoufi K, Weiskopf D, Boonyaratanakornkit J, Dong H, Li H, Chakraborty R, Johnson AJ, Edell E, Taylor JJ, Kaplan MH, Sette A, Bartholmai BJ, Kern R, Vassallo R, Sun J. Immune signatures underlying post-acute COVID-19 lung sequelae. Sci Immunol 2021; 6:eabk1741. [PMID: 34591653 DOI: 10.1126/sciimmunol.abk1741] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- I S Cheon
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - C Li
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Y M Son
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - N P Goplen
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Y Wu
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - T Cassmann
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Z Wang
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - X Wei
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - J Tang
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Y Li
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - H Marlow
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - S Hughes
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - L Hammel
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - T M Cox
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - E Goddery
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - K Ayasoufi
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - D Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - J Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - H Dong
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - H Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - R Chakraborty
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA.,Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - A J Johnson
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - E Edell
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - J J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - M H Kaplan
- Department of Microbiology and Immunology, Indiana University of School of Medicine, Indianapolis, IN 46202, USA
| | - A Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.,Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego (UCSD), La Jolla, CA 92037, USA
| | - B J Bartholmai
- Department of Radiology, Mayo Clinic, Rochester, MN 5590, USA
| | - R Kern
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - R Vassallo
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - J Sun
- Division of Pulmonary and Critical Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA.,Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA.,Carter Immunology Center, University of Virginia, Charlottesville, VA 22908, USA.,Division of Infectious Disease and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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14
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Boonyaratanakornkit J, Sholukh AM, Gray M, Bossard EL, Ford ES, Corbett KS, Corey L, Taylor JJ. Methods to Measure Antibody Neutralization of Live Human Coronavirus OC43. Viruses 2021; 13:2075. [PMID: 34696505 PMCID: PMC8540522 DOI: 10.3390/v13102075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 01/13/2023] Open
Abstract
The human Betacoronavirus OC43 is a common cause of respiratory viral infections in adults and children. Lung infections with OC43 are associated with mortality, especially in hematopoietic stem cell transplant recipients. Neutralizing antibodies play a major role in protection against many respiratory viral infections, but to date a live viral neutralization assay for OC43 has not been described. We isolated a human monoclonal antibody (OC2) that binds to the spike protein of OC43 and neutralizes the live virus derived from the original isolate of OC43. We used this monoclonal antibody to develop and test the performance of two readily accessible in vitro assays for measuring antibody neutralization, one utilizing cytopathic effect and another utilizing an ELISA of infected cells. We used both methods to measure the neutralizing activity of the OC2 monoclonal antibody and of human plasma. These assays could prove useful for studying humoral responses to OC43 and cross-neutralization with other medically important betacoronaviruses.
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Affiliation(s)
- Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Anton M Sholukh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Matthew Gray
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Emily L Bossard
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Emily S Ford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Kizzmekia S Corbett
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
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15
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Walti CS, Loes AN, Shuey K, Krantz EM, Boonyaratanakornkit J, Keane-Candib J, Loeffelholz T, Wolf CR, Taylor JJ, Gardner RA, Green DJ, Cowan AJ, Maloney DG, Turtle CJ, Pergam SA, Chu HY, Bloom JD, Hill JA. Humoral immunogenicity of the seasonal influenza vaccine before and after CAR-T-cell therapy: a prospective observational study. J Immunother Cancer 2021; 9:jitc-2021-003428. [PMID: 34702753 PMCID: PMC8549667 DOI: 10.1136/jitc-2021-003428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Accepted: 09/30/2021] [Indexed: 11/23/2022] Open
Abstract
Recipients of chimeric antigen receptor-modified T (CAR-T) cell therapies for B cell malignancies have profound and prolonged immunodeficiencies and are at risk for serious infections, including respiratory virus infections. Vaccination may be important for infection prevention, but there are limited data on vaccine immunogenicity in this population. We conducted a prospective observational study of the humoral immunogenicity of commercially available 2019-2020 inactivated influenza vaccines in adults immediately prior to or while in durable remission after CD19-, CD20-, or B cell maturation antigen-targeted CAR-T-cell therapy, as well as controls. We tested for antibodies to all four vaccine strains using neutralization and hemagglutination inhibition (HAI) assays. Antibody responses were defined as at least fourfold titer increases from baseline. Seroprotection was defined as a HAI titer ≥40. Enrolled CAR-T-cell recipients were vaccinated 14-29 days prior to (n=5) or 13-57 months following therapy (n=13), and the majority had hypogammaglobulinemia and cellular immunodeficiencies prevaccination. Eight non-immunocompromised adults served as controls. Antibody responses to ≥1 vaccine strain occurred in 2 (40%) individuals before CAR-T-cell therapy and in 4 (31%) individuals vaccinated after CAR-T-cell therapy. An additional 1 (20%) and 6 (46%) individuals had at least twofold increases, respectively. One individual vaccinated prior to CAR-T-cell therapy maintained a response for >3 months following therapy. Across all tested vaccine strains, seroprotection was less frequent in CAR-T-cell recipients than in controls. There was evidence of immunogenicity even among individuals with low immunoglobulin, CD19+ B cell, and CD4+ T-cell counts. These data support consideration for vaccination before and after CAR-T-cell therapy for influenza and other relevant pathogens such as SARS-CoV-2, irrespective of hypogammaglobulinemia or B cell aplasia. However, relatively impaired humoral vaccine immunogenicity indicates the need for additional infection-prevention strategies. Larger studies are needed to refine our understanding of potential correlates of vaccine immunogenicity, and durability of immune responses, in CAR-T-cell therapy recipients.
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Affiliation(s)
- Carla S Walti
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Andrea N Loes
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, Washington, USA
| | - Kiel Shuey
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Elizabeth M Krantz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jacob Keane-Candib
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tillie Loeffelholz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Rebecca A Gardner
- Division of Hematology-Oncology, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Damian J Green
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Andrew J Cowan
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - David G Maloney
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Cameron J Turtle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Steven A Pergam
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, and Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jesse D Bloom
- Howard Hughes Medical Institute, Seattle, Washington, USA
- Basic Sciences Division, Computational Biology Program, and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Joshua A Hill
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, and Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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16
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Walti CS, Krantz EM, Maalouf J, Boonyaratanakornkit J, Keane-Candib J, Joncas-Schronce L, Stevens-Ayers T, Dasgupta S, Taylor JJ, Hirayama AV, Bar M, Gardner RA, Cowan AJ, Green DJ, Boeckh MJ, Maloney DG, Turtle CJ, Hill JA. Antibodies against vaccine-preventable infections after CAR-T cell therapy for B cell malignancies. JCI Insight 2021; 6:146743. [PMID: 33914708 PMCID: PMC8262349 DOI: 10.1172/jci.insight.146743] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/28/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Little is known about pathogen-specific humoral immunity after chimeric antigen receptor–modified T (CAR-T) cell therapy for B cell malignancies. METHODS We conducted a prospective cross-sectional study of CD19-targeted or B cell maturation antigen–targeted (BCMA-targeted) CAR-T cell therapy recipients at least 6 months posttreatment and in remission. We measured pathogen-specific IgG against 12 vaccine-preventable infections and the number of viral and bacterial epitopes to which IgG was detected (“epitope hits”) using a serological profiling assay. The primary outcome was the proportion of participants with IgG levels above a threshold correlated with seroprotection for vaccine-preventable infections. RESULTS We enrolled 65 children and adults a median of 20 months after CD19- (n = 54) or BCMA- (n = 11) CAR-T cell therapy. Among 30 adults without IgG replacement therapy (IGRT) in the prior 16 weeks, 27 (90%) had hypogammaglobulinemia. These individuals had seroprotection to a median of 67% (IQR, 59%–73%) of tested infections. Proportions of participants with seroprotection per pathogen were comparable to population-based studies, but most individuals lacked seroprotection to specific pathogens. Compared with CD19-CAR-T cell recipients, BCMA-CAR-T cell recipients were half as likely to have seroprotection (prevalence ratio, 0.47; 95% CI, 0.18–1.25) and had fewer pathogen-specific epitope hits (mean difference, –90 epitope hits; 95% CI, –157 to –22). CONCLUSION Seroprotection for vaccine-preventable infections in adult CD19-CAR-T cell recipients was comparable to the general population. BCMA-CAR-T cell recipients had fewer pathogen-specific antibodies. Deficits in both groups support the need for vaccine and immunoglobulin replacement therapy studies. FUNDING Swiss National Science Foundation (Early Postdoc Mobility grant P2BSP3_188162), NIH/National Cancer Institute (NIH/NCI) (U01CA247548 and P01CA018029), NIH/NCI Cancer Center Support Grants (P30CA0087-48 and P30CA015704-44), American Society for Transplantation and Cellular Therapy, and Juno Therapeutics/BMS. In this prospective study, we investigated antibodies against vaccine-preventable infections and other pathogen-specific antibodies in individuals with remission after CAR-T cell therapy for B lineage malignancies.
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Affiliation(s)
- Carla S Walti
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Elizabeth M Krantz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Joyce Maalouf
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jacob Keane-Candib
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Laurel Joncas-Schronce
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Terry Stevens-Ayers
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sayan Dasgupta
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Alexandre V Hirayama
- Clinical Research Division, and.,Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Merav Bar
- Department of Medicine, University of Washington, Seattle, Washington, USA.,Clinical Research Division, and.,Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Rebecca A Gardner
- Clinical Research Division, and.,Seattle Children's Hospital, Seattle, Washington, USA
| | - Andrew J Cowan
- Department of Medicine, University of Washington, Seattle, Washington, USA.,Clinical Research Division, and.,Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Damian J Green
- Department of Medicine, University of Washington, Seattle, Washington, USA.,Clinical Research Division, and.,Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael J Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA.,Clinical Research Division, and.,Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - David G Maloney
- Department of Medicine, University of Washington, Seattle, Washington, USA.,Clinical Research Division, and.,Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Cameron J Turtle
- Department of Medicine, University of Washington, Seattle, Washington, USA.,Clinical Research Division, and.,Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Joshua A Hill
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA.,Clinical Research Division, and.,Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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17
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Bhattacharyya P, Bryan A, Atluri V, Ma J, Durowoju L, Bandhlish A, Boonyaratanakornkit J. Fatal infection with enterocolitis from methicillin-resistant Staphylococcus aureus and the continued value of culture in the era of molecular diagnostics. Leuk Res Rep 2021; 15:100254. [PMID: 34136343 PMCID: PMC8178119 DOI: 10.1016/j.lrr.2021.100254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/15/2021] [Accepted: 05/23/2021] [Indexed: 01/03/2023] Open
Abstract
MRSA enterocolitis is under-recognized in the setting of PCR testing. In this case report, we describe risk factors, the importance of stool culture, and the third published case of MRSA enterocolitis in a patient with leukemia. In addition, we performed a retrospective analysis of all stool cultures at our institution that have grown Staphylococcus aureus, and we describe an additional five cases. We also report the diagnostic yield of organisms detected by culture, but not on the FilmArray panel. While rare, these cases demonstrate that MRSA in stool may indicate a severe and potentially life-threatening infection, particularly in immunocompromised persons.
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Affiliation(s)
- Pooja Bhattacharyya
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Research Center, Seattle, WA, 98109, USA
- Division of Oncology, University of Washington, Seattle, WA, 98109, USA
| | - Andrew Bryan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Vidya Atluri
- Division of Allergy and Infectious Disease, University of Washington, Seattle, WA, 98195, USA
| | - Jimmy Ma
- Division of Allergy and Infectious Disease, University of Washington, Seattle, WA, 98195, USA
| | - Lindsey Durowoju
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Anshu Bandhlish
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Research Center, Seattle, WA, 98109, USA
- Division of Allergy and Infectious Disease, University of Washington, Seattle, WA, 98195, USA
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18
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Walti CS, Loes AN, Shuey K, Krantz EM, Boonyaratanakornkit J, Keane-Candib J, Loeffelholz T, Wolf CR, Taylor JJ, Gardner RA, Green DJ, Cowan AJ, Maloney DG, Turtle CJ, Pergam SA, Chu HY, Bloom JD, Hill JA. Humoral immunogenicity of the seasonal influenza vaccine before and after CAR-T-cell therapy. medRxiv 2021. [PMID: 34013294 PMCID: PMC8132269 DOI: 10.1101/2021.05.10.21256634] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recipients of chimeric antigen receptor-modified T (CAR-T) cell therapies for B-cell malignancies are immunocompromised and at risk for serious infections. Vaccine immunogenicity is unknown in this population. We conducted a prospective observational study of the humoral immunogenicity of 2019-2020 inactivated influenza vaccines (IIV) in children and adults immediately prior to (n=7) or 13-57 months after (n=15) CD19-, CD20-, or BCMA-targeted CAR-T-cell therapy, as well as controls (n=8). Individuals post-CAR-T-cell therapy were in remission. We tested for antibodies to 4 vaccine strains at baseline and ≥1 time point after IIV using neutralization and hemagglutination inhibition assays. An antibody response was defined as a ≥4-fold titer increase from baseline at the first post-vaccine time point. Baseline A(H1N1) titers in the CAR-T cohorts were significantly lower compared to controls. Antibody responses to ≥1 vaccine strain occurred in 2 (29%) individuals before CAR-T-cell therapy; one individual maintained a response for >3 months post-CAR-T-cell therapy. Antibody responses to ≥1 vaccine strain occurred in 6 (40%) individuals vaccinated after CAR-T-cell therapy. An additional 2 (29%) and 6 (40%) individuals had ≥2-fold increases (at any time) in the pre- and post-CAR-T cohorts, respectively. There were no identified clinical or immunologic predictors of antibody responses. Neither severe hypogammaglobulinemia nor B-cell aplasia precluded antibody responses. These data support consideration for vaccination before and after CAR-T-cell therapy for influenza and other relevant pathogens such as SARS-CoV-2, irrespective of hypogammaglobulinemia or B-cell aplasia. Larger studies are needed to determine correlates of vaccine immunogenicity and durability in CAR-T-cell therapy recipients. Key Points Influenza vaccination was immunogenic pre- and post-CAR-T-cell therapy, despite hypogammaglobulinemia and B-cell aplasia.Vaccination with inactivated vaccines can be considered before CAR-T-cell therapy and in individuals with remission after therapy.
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19
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Boonyaratanakornkit J, Singh S, Weidle C, Rodarte J, Bakthavatsalam R, Perkins J, Stewart-Jones GBE, Kwong PD, McGuire AT, Pancera M, Taylor JJ. Protective antibodies against human parainfluenza virus type 3 infection. MAbs 2021; 13:1912884. [PMID: 33876699 PMCID: PMC8078717 DOI: 10.1080/19420862.2021.1912884] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human parainfluenza virus type III (HPIV3) is a common respiratory pathogen that afflicts children and can be fatal in vulnerable populations, including the immunocompromised. There are currently no effective vaccines or therapeutics available, resulting in tens of thousands of hospitalizations per year. In an effort to discover a protective antibody against HPIV3, we screened the B cell repertoires from peripheral blood, tonsils, and spleen from healthy children and adults. These analyses yielded five monoclonal antibodies that potently neutralized HPIV3 in vitro. These HPIV3-neutralizing antibodies targeted two non-overlapping epitopes of the HPIV3 F protein, with most targeting the apex. Prophylactic administration of one of these antibodies, PI3-E12, resulted in potent protection against HPIV3 infection in cotton rats. Additionally, PI3-E12 could also be used therapeutically to suppress HPIV3 in immunocompromised animals. These results demonstrate the potential clinical utility of PI3-E12 for the prevention or treatment of HPIV3 in both immunocompetent and immunocompromised individuals.
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Affiliation(s)
- Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Suruchi Singh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Connor Weidle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Justas Rodarte
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Jonathan Perkins
- Department of Otolaryngology, University of Washington, Seattle, Washington, USA
| | - Guillaume B E Stewart-Jones
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Washington, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Washington, USA
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Washington, USA
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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20
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Vick SC, Frutoso M, Mair F, Konecny AJ, Greene E, Wolf CR, Logue JK, Boonyaratanakornkit J, Gottardo R, Schiffer JT, Chu HY, Prlic M, Lund JM. A differential regulatory T cell signature distinguishes the immune landscape of COVID-19 hospitalized patients from those hospitalized with other respiratory viral infections. medRxiv 2021:2021.03.25.21254376. [PMID: 33791720 PMCID: PMC8010752 DOI: 10.1101/2021.03.25.21254376] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
SARS-CoV-2 infection has caused a lasting global pandemic costing millions of lives and untold additional costs. Understanding the immune response to SARS-CoV-2 has been one of the main challenges in the past year in order to decipher mechanisms of host responses and interpret disease pathogenesis. Comparatively little is known in regard to how the immune response against SARS-CoV-2 differs from other respiratory infections. In our study, we compare the peripheral blood immune signature from SARS-CoV-2 infected patients to patients hospitalized pre-pandemic with Influenza Virus or Respiratory Syncytial Virus (RSV). Our in-depth profiling indicates that the immune landscape in patients infected by SARS-CoV-2 is largely similar to patients hospitalized with Flu or RSV. Similarly, serum cytokine and chemokine expression patterns were largely overlapping. Unique to patients infected with SARS-CoV-2 who had the most critical clinical disease state were changes in the regulatory T cell (Treg) compartment. A Treg signature including increased frequency, activation status, and migration markers was correlated with the severity of COVID-19 disease. These findings are particularly relevant as Tregs are being discussed as a therapy to combat the severe inflammation seen in COVID-19 patients. Likewise, having defined the overlapping immune landscapes in SARS-CoV-2, existing knowledge of Flu and RSV infections could be leveraged to identify common treatment strategies. HIGHLIGHTS The immune landscapes of hospitalized pre-pandemic RSV and influenza patients are similar to SARS-CoV-2 patientsSerum cytokine and chemokine expression patterns are largely similar between patients hospitalized with respiratory virus infections, including SARS-CoV-2, versus healthy donorsSARS-CoV-2 patients with the most critical disease displayed unique changes in the Treg compartmentadvances in understanding and treating SARS-CoV-2 could be leveraged for other common respiratory infections.
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Affiliation(s)
- Sarah C. Vick
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Marie Frutoso
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Florian Mair
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Andrew J. Konecny
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Evan Greene
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Caitlin R. Wolf
- Department of Medicine, University of Washington, Seattle, WA, 98195
| | - Jennifer K. Logue
- Department of Medicine, University of Washington, Seattle, WA, 98195
| | - Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Department of Medicine, University of Washington, Seattle, WA, 98195
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Department of Medicine, University of Washington, Seattle, WA, 98195
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, WA, 98195
| | - Martin Prlic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Department of Immunology, University of Washington, Seattle, WA, 98195
| | - Jennifer M. Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
- Department of Global Health, University of Washington, Seattle, WA 98195
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21
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Elyanow R, Snyder TM, Dalai SC, Gittelman RM, Boonyaratanakornkit J, Wald A, Selke S, Wener MH, Morishima C, Greninger AL, Holbrook MR, Kaplan IM, Zahid HJ, Carlson JM, Baldo L, Manley T, Robins HS, Koelle DM. T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity. medRxiv 2021:2021.03.19.21251426. [PMID: 33791723 PMCID: PMC8010755 DOI: 10.1101/2021.03.19.21251426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Measuring the adaptive immune response to SARS-CoV-2 can enable the assessment of past infection as well as protective immunity and the risk of reinfection. While neutralizing antibody (nAb) titers are one measure of protection, such assays are challenging to perform at a large scale and the longevity of the SARS-CoV-2 nAb response is not fully understood. Here, we apply a T-cell receptor (TCR) sequencing assay that can be performed on a small volume standard blood sample to assess the adaptive T-cell response to SARS-CoV-2 infection. Samples were collected from a cohort of 302 individuals recovered from COVID-19 up to 6 months after infection. Previously published findings in this cohort showed that two commercially available SARS-CoV-2 serologic assays correlate well with nAb testing. We demonstrate that the magnitude of the SARS-CoV-2-specific T-cell response strongly correlates with nAb titer, as well as clinical indicators of disease severity including hospitalization, fever, or difficulty breathing. While the depth and breadth of the T-cell response declines during convalescence, the T-cell signal remains well above background with high sensitivity up to at least 6 months following initial infection. Compared to serology tests detecting binding antibodies to SARS-CoV-2 spike and nucleoprotein, the overall sensitivity of the TCR-based assay across the entire cohort and all timepoints was approximately 5% greater for identifying prior SARS-CoV-2 infection. Notably, the improved performance of T-cell testing compared to serology was most apparent in recovered individuals who were not hospitalized and were sampled beyond 150 days of their initial illness, suggesting that antibody testing may have reduced sensitivity in individuals who experienced less severe COVID-19 illness and at later timepoints. Finally, T-cell testing was able to identify SARS-CoV-2 infection in 68% (55/81) of convalescent samples having nAb titers below the lower limit of detection, as well as 37% (13/35) of samples testing negative by all three antibody assays. These results demonstrate the utility of a TCR-based assay as a scalable, reliable measure of past SARS-CoV-2 infection across a spectrum of disease severity. Additionally, the TCR repertoire may be useful as a surrogate for protective immunity with additive clinical value beyond serologic or nAb testing methods.
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Affiliation(s)
| | | | - Sudeb C. Dalai
- Adaptive Biotechnologies, Seattle, Washington, USA
- Stanford University School of Medicine, Stanford, California, USA
| | | | - Jim Boonyaratanakornkit
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Mark H. Wener
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Chihiro Morishima
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Alex L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Michael R. Holbrook
- National Institute of Allergy and Infectious Diseases Integrated Research Facility, Frederick, Maryland, USA
| | | | | | | | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington, USA
| | | | | | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
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22
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Phan IQ, Subramanian S, Kim D, Murphy M, Pettie D, Carter L, Anishchenko I, Barrett LK, Craig J, Tillery L, Shek R, Harrington WE, Koelle DM, Wald A, Veesler D, King N, Boonyaratanakornkit J, Isoherranen N, Greninger AL, Jerome KR, Chu H, Staker B, Stewart L, Myler PJ, Van Voorhis WC. In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19. Sci Rep 2021; 11:4290. [PMID: 33619344 PMCID: PMC7900118 DOI: 10.1038/s41598-021-83730-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 02/03/2021] [Indexed: 02/07/2023] Open
Abstract
Rapid generation of diagnostics is paramount to understand epidemiology and to control the spread of emerging infectious diseases such as COVID-19. Computational methods to predict serodiagnostic epitopes that are specific for the pathogen could help accelerate the development of new diagnostics. A systematic survey of 27 SARS-CoV-2 proteins was conducted to assess whether existing B-cell epitope prediction methods, combined with comprehensive mining of sequence databases and structural data, could predict whether a particular protein would be suitable for serodiagnosis. Nine of the predictions were validated with recombinant SARS-CoV-2 proteins in the ELISA format using plasma and sera from patients with SARS-CoV-2 infection, and a further 11 predictions were compared to the recent literature. Results appeared to be in agreement with 12 of the predictions, in disagreement with 3, while a further 5 were deemed inconclusive. We showed that two of our top five candidates, the N-terminal fragment of the nucleoprotein and the receptor-binding domain of the spike protein, have the highest sensitivity and specificity and signal-to-noise ratio for detecting COVID-19 sera/plasma by ELISA. Mixing the two antigens together for coating ELISA plates led to a sensitivity of 94% (N = 80 samples from persons with RT-PCR confirmed SARS-CoV-2 infection), and a specificity of 97.2% (N = 106 control samples).
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Affiliation(s)
- Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - David Kim
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA
| | - Deleah Pettie
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA
| | - Ivan Anishchenko
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA
| | - Lynn K Barrett
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA
| | - Justin Craig
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA
| | - Logan Tillery
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA
| | - Roger Shek
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA
| | - Whitney E Harrington
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - David M Koelle
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Benaroya Research Institute, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
| | - Anna Wald
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Neil King
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA
| | - Jim Boonyaratanakornkit
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nina Isoherranen
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Helen Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA
| | - Bart Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Lance Stewart
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Medical Education and Biomedical Informatics & Department of Global Health, University of Washington, Seattle, WA, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. .,Department of Microbiology, University of Washington, Seattle, WA, USA. .,Department of Global Health, University of Washington, Seattle, WA, USA.
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23
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Boonyaratanakornkit J, Morishima C, Selke S, Zamora D, McGuffin S, Shapiro AE, Campbell VL, McClurkan CL, Jing L, Gross R, Liang J, Postnikova E, Mazur S, Lukin VV, Chaudhary A, Das MK, Fink SL, Bryan A, Greninger AL, Jerome KR, Holbrook MR, Gernsheimer TB, Wener MH, Wald A, Koelle DM. Clinical, laboratory, and temporal predictors of neutralizing antibodies against SARS-CoV-2 among COVID-19 convalescent plasma donor candidates. J Clin Invest 2021; 131:144930. [PMID: 33320842 PMCID: PMC7843229 DOI: 10.1172/jci144930] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUNDSARS-CoV-2-specific antibodies may protect from reinfection and disease, providing rationale for administration of plasma containing SARS-CoV-2-neutralizing antibodies (nAbs) as a treatment for COVID-19. Clinical factors and laboratory assays to streamline plasma donor selection, and the durability of nAb responses, are incompletely understood.METHODSPotential convalescent plasma donors with virologically documented SARS-CoV-2 infection were tested for serum IgG against SARS-CoV-2 spike protein S1 domain and against nucleoprotein (NP), and for nAb.RESULTSAmong 250 consecutive persons, including 27 (11%) requiring hospitalization, who were studied a median of 67 days since symptom onset, 97% were seropositive on 1 or more assays. Sixty percent of donors had nAb titers ≥1:80. Correlates of higher nAb titers included older age (adjusted OR [AOR] 1.03 per year of age, 95% CI 1.00-1.06), male sex (AOR 2.08, 95% CI 1.13-3.82), fever during illness (AOR 2.73, 95% CI 1.25-5.97), and disease severity represented by hospitalization (AOR 6.59, 95% CI 1.32-32.96). Receiver operating characteristic analyses of anti-S1 and anti-NP antibody results yielded cutoffs that corresponded well with nAb titers, with the anti-S1 assay being slightly more predictive. nAb titers declined in 37 of 41 paired specimens collected a median of 98 days (range 77-120) apart (P < 0.001). Seven individuals (2.8%) were persistently seronegative and lacked T cell responses.CONCLUSIONnAb titers correlated with COVID-19 severity, age, and sex. SARS-CoV-2 IgG results can serve as useful surrogates for nAb testing. Functional nAb levels declined, and a small proportion of convalescent individuals lacked adaptive immune responses.FUNDINGThe project was supported by the Frederick National Laboratory for Cancer Research with support from the NIAID under contract number 75N91019D00024, and was supported by the Fred Hutchinson Joel Meyers Endowment, Fast-Grants, a New Investigator award from the American Society for Transplantation and Cellular Therapy, and NIH contracts 75N93019C0063, 75N91019D00024, and HHSN272201800013C, and NIH grants T32-AI118690, T32-AI007044, K08-AI119142, and K23-AI140918.
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Affiliation(s)
- Jim Boonyaratanakornkit
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Seattle Cancer Care Alliance, Seattle, Washington, USA
| | | | - Stacy Selke
- Department of Laboratory Medicine and Pathology, and
| | - Danniel Zamora
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sarah McGuffin
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Adrienne E. Shapiro
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Robin Gross
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Frederick, Maryland, USA
| | - Janie Liang
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Frederick, Maryland, USA
| | - Elena Postnikova
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Frederick, Maryland, USA
| | - Steven Mazur
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Frederick, Maryland, USA
| | | | - Anu Chaudhary
- Department of Laboratory Medicine and Pathology, and
| | - Marie K. Das
- Department of Laboratory Medicine and Pathology, and
| | - Susan L. Fink
- Department of Laboratory Medicine and Pathology, and
| | - Andrew Bryan
- Department of Laboratory Medicine and Pathology, and
| | | | - Keith R. Jerome
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, and
| | - Michael R. Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Frederick, Maryland, USA
| | - Terry B. Gernsheimer
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Seattle Cancer Care Alliance, Seattle, Washington, USA
| | - Mark H. Wener
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, and
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, and
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
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24
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Walti CS, Maalouf J, Boonyaratanakornkit J, Keane-Candib J, Taylor JJ, Hirayama AV, Bar M, Gardner RA, Green DJ, Boeckh M, Maloney DG, Krantz EM, Turtle CJ, Hill JA. 196. Antibodies to Vaccine-preventable Infections After CAR-T Cell Immunotherapy for B Cell Malignancies. Open Forum Infect Dis 2020. [PMCID: PMC7776444 DOI: 10.1093/ofid/ofaa439.506] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Chimeric antigen receptor-modified T (CAR-T) cell immunotherapy for B cell hematologic malignancies results in prolonged B cell depletion. Little is known about the effects of CAR-T cell therapy on pre-existing pathogen-specific humoral immunity.
Methods
We conducted a prospective, cross-sectional study of children and adults treated with CD19- or BCMA-CAR-T cell therapy. Eligible patients were ≥ 6 months post-CAR-T cell infusion and in remission without subsequent chemoimmunotherapy. We measured total immunoglobulin G (IgG), pathogen-specific IgG levels for 12 vaccine-preventable infections, and B cell subsets from blood. Seroprotective antibody titers were based on standard thresholds. We described the proportion of patients with seroprotective titers and tested for associations between clinical factors and seroprotection using generalized estimating equations.
Results
We enrolled 65 patients who received CD19- (n=54) or BCMA- (n=11) CAR-T cell therapy. Seven patients were < 18 years old. Samples were collected a median of 20 months (range, 7–68) after CAR T cell infusion. Seroprotection to vaccine-preventable pathogens was generally comparable to the U.S. population (Fig 1) even though blood CD19+ B cell counts were low (< 20 cells/mm3) in 60% of patients. Among 30 patients without IgG replacement in the prior 16 weeks (4 half-lives of IgG), 27 (90%) had hypogammaglobulinemia. Despite this, these individuals had seroprotection to a median of 67% (IQR, 59%-73%) of tested pathogens (Fig 2A). The proportion of patients with seroprotection was lowest for mumps, hepatitis A and B, H. influenzae type B (Hib), S. pneumoniae, and B. pertussis. Patients receiving BCMA-CAR-T cells had seroprotection to fewer pathogens than those receiving CD19-CAR-T cells (Fig 2B), but the difference did not reach statistical significance (Fig 3). There were no significant differences by other variables.
Figure 1. Proportion of CAR-T cell recipients with seroprotection to vaccine-preventable infections compared to the U.S. population, stratified by receipt of IgG replacement in the previous 16 weeks.
Figure 2 A-B. Percentage of pathogens with seroprotective antibody titers among patients without IgG replacement in the previous 16 weeks.
Figure 3. Association of clinical factors with seroprotection to vaccine-preventable infections among patients without IgG replacement in the previous 16 weeks (n=30)
Conclusion
Seroprotection for vaccine-preventable infections after CD19-CAR-T cell therapy was comparable to the general population. BCMA-CAR-T cell recipients may benefit most from replacement IgG. Vaccinations after CAR-T cell therapy should be considered and prioritized for S. pneumoniae, Hib, hepatitis viruses, and B. pertussis.
Disclosures
Justin J. Taylor, PhD, Vir Biotechnology (Grant/Research Support) Damian J. Green, MD, Cellectar Biosciences (Grant/Research Support)GSK (Advisor or Review Panel member)Juno Therapeutics (Grant/Research Support, Advisor or Review Panel member, Other Financial or Material Support, Royalities)Seattle Genetics (Grant/Research Support, Advisor or Review Panel member) Michael Boeckh, MD PhD, AlloVir (Consultant)EvrysBio (Advisor or Review Panel member, Other Financial or Material Support, share options)Gilead (Consultant, Grant/Research Support)GSK (Consultant)Helocyte (Advisor or Review Panel member, Shareholder)Lophius (Grant/Research Support)Merck (Consultant, Grant/Research Support)SymBio (Consultant)VirBio (Consultant, Grant/Research Support) David G. Maloney, MD, PhD, A2 Biotherapeutics (Consultant, Other Financial or Material Support, Stock Options)Bioline Rx (Consultant)Celgene (Consultant, Grant/Research Support)Gilead (Consultant)Juno Therapeutics (Consultant, Research Grant or Support, Other Financial or Material Support, four pending patents, not issued, licensed, no royalities, no licensees)Kite Pharma (Consultant, Grant/Research Support)Novartis (Consultant)Pharmacyclics (Consultant) Cameron J. Turtle, MBBS, PhD, Allogene (Other Financial or Material Support, Ad hoc advisory board (last 12 months))ArsenalBio (Advisor or Review Panel member, Other Financial or Material Support, Stock/options)AstraZeneca (Grant/Research Support, Other Financial or Material Support, Ad hoc advisory board (last 12 months))Caribou Biosciences (Advisor or Review Panel member, Other Financial or Material Support, Stock/options)Century Therapeutics (Advisor or Review Panel member)Eureka Therapeutics (Advisor or Review Panel member, Other Financial or Material Support, Stock/options)Juno Therapeutics (Grant/Research Support, Other Financial or Material Support, Patent: Licensed to Juno Therapeutics)Myeloid Therapeutics (Advisor or Review Panel member, Other Financial or Material Support, Stock/options)Nektar Therapeutics (Grant/Research Support, Other Financial or Material Support, Ad hoc advisory board (last 12 months))PACT Pharma (Other Financial or Material Support, Ad hoc advisory board (last 12 months))Precision Biosciences (Advisor or Review Panel member, Other Financial or Material Support, Stock/options)TCR2 Therapeutics (Grant/Research Support)T-CURX (Advisor or Review Panel member) Joshua A. Hill, MD, Allogene (Consultant)Allovir (Consultant)Gilead (Consultant)Karius (Grant/Research Support, Scientific Research Study Investigator)Takeda (Grant/Research Support, Scientific Research Study Investigator)
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Affiliation(s)
- Carla S Walti
- Fred Hutchinson Cancer Research Center, Seattle, WA, Basel, Basel-Stadt, Switzerland
| | - Joyce Maalouf
- Fred Hutchinson Cancer Research Center, Seattle, WA, Basel, Basel-Stadt, Switzerland
| | | | - Jacob Keane-Candib
- Fred Hutchinson Cancer Research Center, Seattle, WA, Basel, Basel-Stadt, Switzerland
| | - Justin J Taylor
- Fred Hutchinson Cancer Research Center / University of Washington, Seattle, WA, Seattle, Washington
| | - Alexandre V Hirayama
- Fred Hutchinson Cancer Research Center, Seattle, WA, Basel, Basel-Stadt, Switzerland
| | - Merav Bar
- Fred Hutchinson Cancer Research Center / Department of Medicine University of Washington, Seattle, Washington
| | - Rebecca A Gardner
- University of Washington / Seattle Children’s Hospital / Ben Towne Center for Childhood Cancer Research, Seattle, Washington
| | - Damian J Green
- Fred Hutchinson Cancer Research Center / Seattle Care Cancer Alliance / University of Washington School of Medicine, Seattle, WA, Seattle, Washington
| | - Michael Boeckh
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - David G Maloney
- Fred Hutchinson Cancer Research Center / Seattle Care Cancer Alliance / University of Washington, Seattle, WA, Seattle, Washington
| | | | - Cameron J Turtle
- Fred Hutchinson Cancer Research Center / Seattle Care Cancer Alliance / University of Washington School of Medicine, Seattle, WA, Seattle, Washington
| | - Joshua A Hill
- Fred Hutchinson Cancer Research Center; University of Washington, Seattle, Washington
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25
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Boonyaratanakornkit J, Morishima C, Selke S, Zamora D, McGuffin S, Shapiro AE, Campbell VL, McClurkan CL, Jing L, Gross R, Liang J, Postnikova E, Mazur S, Chaudhary A, Das MK, Fink SL, Bryan A, Greninger AL, Jerome KR, Holbrook MR, Gernsheimer TB, Wener MH, Wald A, Koelle DM. Clinical, laboratory, and temporal predictors of neutralizing antibodies to SARS-CoV-2 after COVID-19. medRxiv 2020. [PMID: 33052361 DOI: 10.1101/2020.10.06.20207472] [Citation(s) in RCA: 4] [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: 01/06/2023]
Abstract
BACKGROUND SARS-CoV-2-specific antibodies may protect from reinfection and disease, providing the rationale for administration of plasma containing SARS-CoV-2 neutralizing antibodies (nAb) as a treatment for COVID-19. The clinical factors and laboratory assays to streamline plasma donor selection, and the durability of nAb responses, are incompletely understood. METHODS Adults with virologically-documented SARS-CoV-2 infection in a convalescent plasma donor screening program were tested for serum IgG to SARS-CoV-2 spike protein S1 domain, nucleoprotein (NP), and for nAb. RESULTS Amongst 250 consecutive persons studied a median of 67 days since symptom onset, 243/250 (97%) were seropositive on one or more assays. Sixty percent of donors had nAb titers ≥1:80. Correlates of higher nAb titer included older age (adjusted OR [AOR] 1.03/year of age, 95% CI 1.00-1.06), male sex (AOR 2.08, 95% CI 1.13-3.82), fever during acute illness (AOR 2.73, 95% CI 1.25-5.97), and disease severity represented by hospitalization (AOR 6.59, 95% CI 1.32-32.96). Receiver operating characteristic (ROC) analyses of anti-S1 and anti-NP antibody results yielded cutoffs that corresponded well with nAb titers, with the anti-S1 assay being slightly more predictive. NAb titers declined in 37 of 41 paired specimens collected a median of 98 days (range, 77-120) apart (P<0.001). Seven individuals (2.8%) were persistently seronegative and lacked T cell responses. CONCLUSIONS Nab titers correlated with COVID-19 severity, age, and sex. Standard commercially available SARS-CoV-2 IgG results can serve as useful surrogates for nAb testing. Functional nAb levels were found to decline and a small proportion of COVID-19 survivors lack adaptive immune responses.
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26
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Boonyaratanakornkit J, Vivek M, Xie H, Pergam SA, Cheng GS, Mielcarek M, Hill JA, Jerome KR, Limaye AP, Leisenring W, Boeckh MJ, Waghmare A. Predictive Value of Respiratory Viral Detection in the Upper Respiratory Tract for Infection of the Lower Respiratory Tract With Hematopoietic Stem Cell Transplantation. J Infect Dis 2020; 221:379-388. [PMID: 31541573 PMCID: PMC7107470 DOI: 10.1093/infdis/jiz470] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 08/05/2019] [Accepted: 09/11/2019] [Indexed: 12/30/2022] Open
Abstract
Background Hematopoietic cell transplant (HCT) recipients are frequently infected with respiratory viruses (RVs) in the upper respiratory tract (URT), but the concordance between URT and lower respiratory tract (LRT) RV detection is not well characterized. Methods Hematopoietic cell transplant candidates and recipients with respiratory symptoms and LRT and URT RV testing via multiplex PCR from 2009 to 2016 were included. Logistic regression models were used to analyze risk factors for LRT RV detection. Results Two-hundred thirty-five HCT candidates or recipients had URT and LRT RV testing within 3 days. Among 115 subjects (49%) positive for a RV, 37% (42 of 115) had discordant sample pairs. Forty percent (17 of 42) of discordant pairs were positive in the LRT but negative in the URT. Discordance was common for adenovirus (100%), metapneumovirus (44%), rhinovirus (34%), and parainfluenza virus type 3 (28%); respiratory syncytial virus was highly concordant (92%). Likelihood of LRT detection was increased with URT detection (oods ratio [OR] = 73.7; 95% confidence interval [CI], 26.7–204) and in cytomegalovirus-positive recipients (OR = 3.70; 95% CI, 1.30–10.0). Conclusions High rates of discordance were observed for certain RVs. Bronchoalveolar lavage sampling may provide useful diagnostic information to guide management in symptomatic HCT candidates and recipients.
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Affiliation(s)
- Jim Boonyaratanakornkit
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Meghana Vivek
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Hu Xie
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Steven A Pergam
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Guang-Shing Cheng
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Marco Mielcarek
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Joshua A Hill
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Keith R Jerome
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Ajit P Limaye
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Wendy Leisenring
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael J Boeckh
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Alpana Waghmare
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Seattle Children's Hospital, Seattle, Washington, USA
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27
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Steach HR, DeBuysscher BL, Schwartz A, Boonyaratanakornkit J, Baker ML, Tooley MR, Pease NA, Taylor JJ. Cross-Reactivity with Self-Antigen Tunes the Functional Potential of Naive B Cells Specific for Foreign Antigens. J Immunol 2019; 204:498-509. [PMID: 31882518 DOI: 10.4049/jimmunol.1900799] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/27/2019] [Indexed: 11/19/2022]
Abstract
Upon Ag exposure, naive B cells expressing BCR able to bind Ag can undergo robust proliferation and differentiation that can result in the production of Ab-secreting and memory B cells. The factors determining whether an individual naive B cell will proliferate following Ag encounter remains unclear. In this study, we found that polyclonal naive murine B cell populations specific for a variety of foreign Ags express high levels of the orphan nuclear receptor Nur77, which is known to be upregulated downstream of BCR signaling as a result of cross-reactivity with self-antigens in vivo. Similarly, a fraction of naive human B cells specific for clinically-relevant Ags derived from respiratory syncytial virus and HIV-1 also exhibited an IgMLOW IgD+ phenotype, which is associated with self-antigen cross-reactivity. Functionally, naive B cells expressing moderate levels of Nur77 are most likely to proliferate in vivo following Ag injection. Together, our data indicate that BCR cross-reactivity with self-antigen is a common feature of populations of naive B cells specific for foreign Ags and a moderate level of cross-reactivity primes individual cells for optimal proliferative responses following Ag exposure.
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Affiliation(s)
- Holly R Steach
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Blair L DeBuysscher
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Allison Schwartz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Melissa L Baker
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Marti R Tooley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Nicholas A Pease
- Molecular and Cellular Biology Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA 98195
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; .,Department of Global Health, University of Washington, Seattle, WA 98195; and.,Department of Immunology, University of Washington, Seattle, WA 98109
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Boonyaratanakornkit J, Ekici S, Magaret A, Gustafson K, Scott E, Haglund M, Kuypers J, Pergamit R, Lynch J, Chu HY. Respiratory Syncytial Virus Infection in Homeless Populations, Washington, USA. Emerg Infect Dis 2019; 25:1408-1411. [PMID: 31211675 PMCID: PMC6590761 DOI: 10.3201/eid2507.181261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Homelessness has not previously been identified as a risk factor for respiratory syncytial virus (RSV) infection. We conducted an observational study at an urban safety-net hospital in Washington, USA, during 2012–2017. Hospitalized adults with RSV were more likely to be homeless, and several clinical outcome measures were worse with RSV than with influenza.
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Affiliation(s)
- Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Abstract
Antibodies against foreign antigens are a critical component of the overall immune response and can facilitate pathogen clearance during a primary infection and also protect against subsequent infections. Dysregulation of the antibody response can lead to an autoimmune disease, malignancy, or enhanced infection. Since the experimental delineation of a distinct B cell lineage in 1965, various methods have been developed to understand antigen-specific B cell responses in the context of autoimmune diseases, primary immunodeficiencies, infection, and vaccination. In this review, we summarize the established techniques and discuss new and emerging technologies for probing the B cell response in vitro and in vivo by taking advantage of the specificity of B cell receptor (BCR)-associated and secreted antibodies. These include ELISPOT, flow cytometry, mass cytometry, and fluorescence microscopy to identify and/or isolate primary antigen-specific B cells. We also present our approach to identify rare antigen-specific B cells using magnetic enrichment followed by flow cytometry. Once these cells are isolated, in vitro proliferation assays and adoptive transfer experiments in mice can be used to further characterize antigen-specific B cell activation, function, and fate. Transgenic mouse models of B cells targeting model antigens and of B cell signaling have also significantly advanced our understanding of antigen-specific B cell responses in vivo.
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Affiliation(s)
- Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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Moffett HF, Harms CK, Fitzpatrick KS, Tooley MR, Boonyaratanakornkit J, Taylor JJ. B cells engineered to express pathogen-specific antibodies protect against infection. Sci Immunol 2019; 4:eaax0644. [PMID: 31101673 PMCID: PMC6913193 DOI: 10.1126/sciimmunol.aax0644] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [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: 02/19/2019] [Accepted: 03/29/2019] [Indexed: 01/02/2023]
Abstract
Effective vaccines inducing lifelong protection against many important infections such as respiratory syncytial virus (RSV), HIV, influenza virus, and Epstein-Barr virus (EBV) are not yet available despite decades of research. As an alternative to a protective vaccine, we developed a genetic engineering strategy in which CRISPR-Cas9 was used to replace endogenously encoded antibodies with antibodies targeting RSV, HIV, influenza virus, or EBV in primary human B cells. The engineered antibodies were expressed efficiently in primary B cells under the control of endogenous regulatory elements, which maintained normal antibody expression and secretion. Using engineered mouse B cells, we demonstrated that a single transfer of B cells engineered to express an antibody against RSV resulted in potent and durable protection against RSV infection in RAG1-deficient mice. This approach offers the opportunity to achieve sterilizing immunity against pathogens for which traditional vaccination has failed to induce or maintain protective antibody responses.
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Affiliation(s)
- Howell F Moffett
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. Seattle, WA 98109, USA
| | - Carson K Harms
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. Seattle, WA 98109, USA
| | - Kristin S Fitzpatrick
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. Seattle, WA 98109, USA
| | - Marti R Tooley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. Seattle, WA 98109, USA
| | - Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. Seattle, WA 98109, USA
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. Seattle, WA 98109, USA.
- Department of Global Health, University of Washington, 1510 San Juan Road, Seattle, WA 98195, USA
- Department of Immunology, University of Washington, 750 Republican St., Seattle, WA 98109, USA
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Boonyaratanakornkit J, Englund JA, Magaret AS, Bu Y, Tielsch JM, Khatry SK, Katz J, Kuypers J, Shrestha L, LeClerq SC, Steinhoff MC, Chu HY. Primary and Repeated Respiratory Viral Infections Among Infants in Rural Nepal. J Pediatric Infect Dis Soc 2018; 9:21-29. [PMID: 30423150 PMCID: PMC7317152 DOI: 10.1093/jpids/piy107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 10/10/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND Respiratory viruses cause significant morbidity and death in infants; 99% of such deaths occur in resource-limited settings. Risk factors for initial and repeated respiratory viral infections in young infants in resource-limited settings have not been well described. METHODS From 2011 to 2014, a birth cohort of infants in rural Nepal was enrolled and followed with weekly household-based active surveillance for respiratory symptoms until 6 months of age. Respiratory illness was defined as having any of the following: fever, cough, wheeze, difficulty breathing, and/or a draining ear. We tested nasal swabs of infants with respiratory illness for multiple respiratory viruses by using a reverse transcription polymerase chain reaction assay. The risk of primary and repeated infections with the same virus was evaluated using Poisson regression. RESULTS Of 3528 infants, 1726 (49%) had a primary infection, and 419 (12%) had a repeated infection. The incidences of respiratory viral infection in infants were 1816 per 1000 person-years for primary infections and 1204 per 1000 person-years for repeated infection with the same virus. Exposure to other children and male sex were each associated with an increased risk for primary infection (risk ratios, 1.13 [95% confidence interval (CI), 1.06-1.20] and 1.14 [95% CI, 1.02-1.27], respectively), whereas higher maternal education was associated with a decreased risk for both primary and repeated infections (risk ratio, 0.96 [95% CI, 0.95-0.98]). The incidence of subsequent infection did not change when previous infection with the same or another respiratory virus occurred. Illness duration and severity were not significantly different in the infants between the first and second episodes for any respiratory virus tested. CONCLUSIONS In infants in rural Nepal, repeated respiratory virus infections were frequent, and we found no decrease in illness severity with repeated infections and no evidence of replacement with another virus. Vaccine strategies and public health interventions that provide durable protection in the first 6 months of life could decrease the burden of repeated infections by multiple respiratory viruses, particularly in low-resource countries.
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Affiliation(s)
| | - Janet A Englund
- Department of Pediatrics, Seattle Children’s Hospital, University of Washington, Seattle
| | - Amalia S Magaret
- Department of Laboratory Medicine, University of Washington, Seattle,Department of Biostatistics, University of Washington, Seattle
| | - Yunqi Bu
- Department of Biostatistics, University of Washington, Seattle
| | - James M Tielsch
- Department of Global Health, Milken School of Public Health, George Washington University, Washington, DC
| | | | - Joanne Katz
- Department of International Health, Johns Hopkins University, Baltimore, Maryland
| | - Jane Kuypers
- Department of Laboratory Medicine, University of Washington, Seattle
| | - Laxman Shrestha
- Department of Pediatrics and Child Health, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Steven C LeClerq
- Department of Pediatrics and Child Health, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | | | - Helen Y Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle,Correspondence: H. Y. Chu, MD, MPH, University of Washington, Division of Allergy and Infectious Diseases, 325 9th Ave., MS 359779, Seattle, WA 98104 ()
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Sabo MC, Boonyaratanakornkit J, Cybulski R, Kopmar NE, Freeman RV, Fang FC, Graham SM. Getting to the Heart of the Matter: A 20-Year-Old Man With Fever, Rash, and Chest Pain. Open Forum Infect Dis 2018; 5:ofx272. [PMID: 29399597 PMCID: PMC5788053 DOI: 10.1093/ofid/ofx272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 10/26/2017] [Accepted: 12/19/2017] [Indexed: 02/05/2023] Open
Abstract
Infection with Helicobacter cinaedi can encompass a wide spectrum of clinical manifestations, including fever, rash, endocarditis, osteomyelitis, and meningitis. The present case demonstrates the ability of H cinaedi to masquerade as acute rheumatic fever and represents the first reported case of cardiac tamponade caused by H cinaedi.
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Affiliation(s)
- Michelle C Sabo
- Department of Laboratory Medicine, University of Washington, Seattle
| | | | - Robert Cybulski
- Department of Laboratory Medicine, University of Washington, Seattle
| | - Noam E Kopmar
- Department of Medicine, University of Washington, Seattle
| | | | - Ferric C Fang
- Department of Medicine, University of Washington, Seattle.,Department of Laboratory Medicine, University of Washington, Seattle
| | - Susan M Graham
- Department of Medicine, University of Washington, Seattle.,Department of Global Health, University of Washington, Seattle.,Department of Epidemiology, University of Washington, Seattle, University of Washington, Seattle
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Barouch-Bentov R, Neveu G, Xiao F, Beer M, Bekerman E, Schor S, Campbell J, Boonyaratanakornkit J, Lindenbach B, Lu A, Jacob Y, Einav S. Hepatitis C Virus Proteins Interact with the Endosomal Sorting Complex Required for Transport (ESCRT) Machinery via Ubiquitination To Facilitate Viral Envelopment. mBio 2016; 7:e01456-16. [PMID: 27803188 PMCID: PMC5090039 DOI: 10.1128/mbio.01456-16] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [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: 08/08/2016] [Accepted: 10/07/2016] [Indexed: 02/07/2023] Open
Abstract
Enveloped viruses commonly utilize late-domain motifs, sometimes cooperatively with ubiquitin, to hijack the endosomal sorting complex required for transport (ESCRT) machinery for budding at the plasma membrane. However, the mechanisms underlying budding of viruses lacking defined late-domain motifs and budding into intracellular compartments are poorly characterized. Here, we map a network of hepatitis C virus (HCV) protein interactions with the ESCRT machinery using a mammalian-cell-based protein interaction screen and reveal nine novel interactions. We identify HRS (hepatocyte growth factor-regulated tyrosine kinase substrate), an ESCRT-0 complex component, as an important entry point for HCV into the ESCRT pathway and validate its interactions with the HCV nonstructural (NS) proteins NS2 and NS5A in HCV-infected cells. Infectivity assays indicate that HRS is an important factor for efficient HCV assembly. Specifically, by integrating capsid oligomerization assays, biophysical analysis of intracellular viral particles by continuous gradient centrifugations, proteolytic digestion protection, and RNase digestion protection assays, we show that HCV co-opts HRS to mediate a late assembly step, namely, envelopment. In the absence of defined late-domain motifs, K63-linked polyubiquitinated lysine residues in the HCV NS2 protein bind the HRS ubiquitin-interacting motif to facilitate assembly. Finally, ESCRT-III and VPS/VTA1 components are also recruited by HCV proteins to mediate assembly. These data uncover involvement of ESCRT proteins in intracellular budding of a virus lacking defined late-domain motifs and a novel mechanism by which HCV gains entry into the ESCRT network, with potential implications for other viruses. IMPORTANCE Viruses commonly bud at the plasma membrane by recruiting the host ESCRT machinery via conserved motifs termed late domains. The mechanism by which some viruses, such as HCV, bud intracellularly is, however, poorly characterized. Moreover, whether envelopment of HCV and other viruses lacking defined late domains is ESCRT mediated and, if so, what the entry points into the ESCRT pathway are remain unknown. Here, we report the interaction network of HCV with the ESCRT machinery and a critical role for HRS, an ESCRT-0 complex component, in HCV envelopment. Viral protein ubiquitination was discovered to be a signal for HRS binding and HCV assembly, thereby functionally compensating for the absence of late domains. These findings characterize how a virus lacking defined late domains co-opts ESCRT to bud intracellularly. Since the ESCRT machinery is essential for the life cycle of multiple viruses, better understanding of this virus-host interplay may yield targets for broad-spectrum antiviral therapies.
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Affiliation(s)
- Rina Barouch-Bentov
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Gregory Neveu
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Fei Xiao
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Melanie Beer
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Elena Bekerman
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Stanford Schor
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Joseph Campbell
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jim Boonyaratanakornkit
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Brett Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Albert Lu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Yves Jacob
- Département de Virologie, Unité de Génétique Moléculaire des Virus ARN (GMVR), Institut Pasteur, Centre national de la recherche scientifique, and Université Paris Diderot, Paris, France
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
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Boonyaratanakornkit J, Schomacker H, Collins P, Schmidt A. Alix serves as an adaptor that allows human parainfluenza virus type 1 to interact with the host cell ESCRT system. PLoS One 2013; 8:e59462. [PMID: 23527201 PMCID: PMC3602193 DOI: 10.1371/journal.pone.0059462] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 07/25/2012] [Accepted: 02/18/2013] [Indexed: 12/19/2022] Open
Abstract
The cellular ESCRT (endosomal sorting complex required for transport) system functions in cargo-sorting, in the formation of intraluminal vesicles that comprise multivesicular bodies (MVB), and in cytokinesis, and this system can be hijacked by a number of enveloped viruses to promote budding. The respiratory pathogen human parainfluenza virus type I (HPIV1) encodes a nested set of accessory C proteins that play important roles in down-regulating viral transcription and replication, in suppressing the type I interferon (IFN) response, and in suppressing apoptosis. Deletion or mutation of the C proteins attenuates HPIV1 in vivo, and such mutants are being evaluated preclinically and clinically as vaccines. We show here that the C proteins interact and co-localize with the cellular protein Alix, which is a member of the class E vacuolar protein sorting (Vps) proteins that assemble at endosomal membranes into ESCRT complexes. The HPIV1 C proteins interact with the Bro1 domain of Alix at a site that is also required for the interaction between Alix and Chmp4b, a subunit of ESCRT-III. The C proteins are ubiquitinated and subjected to proteasome-mediated degradation, but the interaction with AlixBro1 protects the C proteins from degradation. Neither over-expression nor knock-down of Alix expression had an effect on HPIV1 replication, although this might be due to the large redundancy of Alix-like proteins. In contrast, knocking down the expression of Chmp4 led to an approximately 100-fold reduction in viral titer during infection with wild-type (WT) HPIV1. This level of reduction was similar to that observed for the viral mutant, P(C-) HPIV1, in which expression of the C proteins were knocked out. Chmp4 is capable of out-competing the HPIV1 C proteins for binding Alix. Together, this suggests a possible model in which Chmp4, through Alix, recruits the C proteins to a common site on intracellular membranes and facilitates budding.
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Affiliation(s)
- Jim Boonyaratanakornkit
- Laboratory of Infectious Diseases, RNA Viruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Henrick Schomacker
- Laboratory of Infectious Diseases, RNA Viruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter Collins
- Laboratory of Infectious Diseases, RNA Viruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alexander Schmidt
- Laboratory of Infectious Diseases, RNA Viruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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36
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Chang TT, Walther I, Li CF, Boonyaratanakornkit J, Galleri G, Meloni MA, Pippia P, Cogoli A, Hughes-Fulford M. The Rel/NF-κB pathway and transcription of immediate early genes in T cell activation are inhibited by microgravity. J Leukoc Biol 2012; 92:1133-45. [PMID: 22750545 DOI: 10.1189/jlb.0312157] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
This study tested the hypothesis that transcription of immediate early genes is inhibited in T cells activated in μg. Immunosuppression during spaceflight is a major barrier to safe, long-term human space habitation and travel. The goals of these experiments were to prove that μg was the cause of impaired T cell activation during spaceflight, as well as understand the mechanisms controlling early T cell activation. T cells from four human donors were stimulated with Con A and anti-CD28 on board the ISS. An on-board centrifuge was used to generate a 1g simultaneous control to isolate the effects of μg from other variables of spaceflight. Microarray expression analysis after 1.5 h of activation demonstrated that μg- and 1g-activated T cells had distinct patterns of global gene expression and identified 47 genes that were significantly, differentially down-regulated in μg. Importantly, several key immediate early genes were inhibited in μg. In particular, transactivation of Rel/NF-κB, CREB, and SRF gene targets were down-regulated. Expression of cREL gene targets were significantly inhibited, and transcription of cREL itself was reduced significantly in μg and upon anti-CD3/anti-CD28 stimulation in simulated μg. Analysis of gene connectivity indicated that the TNF pathway is a major early downstream effector pathway inhibited in μg and may lead to ineffective proinflammatory host defenses against infectious pathogens during spaceflight. Results from these experiments indicate that μg was the causative factor for impaired T cell activation during spaceflight by inhibiting transactivation of key immediate early genes.
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Affiliation(s)
- Tammy T Chang
- Department of Surgery, University of California, San Francisco, CA, USA.
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Schmidt AC, Schaap-Nutt A, Bartlett EJ, Schomacker H, Boonyaratanakornkit J, Karron RA, Collins PL. Progress in the development of human parainfluenza virus vaccines. Expert Rev Respir Med 2011; 5:515-26. [PMID: 21859271 DOI: 10.1586/ers.11.32] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In children under 5 years of age, human parainfluenza viruses (HPIVs) as a group are the second most common etiology of acute respiratory illness leading to hospitalization, surpassed only by respiratory syncytial virus but ahead of influenza viruses. Using reverse genetics systems for HPIV serotypes 1, 2 and 3 (HPIV1, 2 and 3), several live-attenuated HPIVs have been generated and evaluated as intranasal vaccines in adults and in children. Two vaccines against HPIV3 were found to be well tolerated, infectious and immunogenic in Phase I trials in HPIV3-seronegative infants and children and should progress to proof-of-concept trials. Vaccines against HPIV1 and HPIV2 are less advanced and have just entered pediatric trials.
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Affiliation(s)
- Alexander C Schmidt
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Bartlett EJ, Cruz AM, Boonyaratanakornkit J, Esker J, Castaño A, Skiadopoulos MH, Collins PL, Murphy BR, Schmidt AC. A novel human parainfluenza virus type 1 (HPIV1) with separated P and C genes is useful for generating C gene mutants for evaluation as live-attenuated virus vaccine candidates. Vaccine 2009; 28:767-79. [PMID: 19857454 DOI: 10.1016/j.vaccine.2009.10.069] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 08/26/2009] [Accepted: 10/13/2009] [Indexed: 01/12/2023]
Abstract
A novel recombinant human parainfluenza virus type 1 (rHPIV1), rHPIV1-C+P, in which the overlapping open reading frames of the C and P genes were separated in order to introduce mutations into the C gene without affecting P, was generated. Infectious rHPIV1-C+P was readily recovered and replicated as efficiently as HPIV1 wild type (wt) in vitro and in African green monkeys (AGMs). rHPIV1-C+P expressed increased levels of C protein and, surprisingly, activated the type I IFN and apoptosis responses more strongly than HPIV1 wt. rHPIV1-C+P provided a useful backbone for recovering an attenuated P/C gene mutation (Delta 84-85), which was previously unrecoverable, likely due to detrimental effects of the deletion on the P protein. rHPIV1-C(Delta 84-85)+P and an additional mutant, rHPIV1-C(Delta 169-170)+P, were found to replicate to similar titers in vitro and to activate the type I IFN and apoptosis responses to a similar degree as rHPIV1-C+P. rHPIV1-C(Delta 84-85)+P was found to be highly attenuated in AGMs, and all viruses were immunogenic and effective in protecting AGMs against challenge with HPIV1 wt. rHPIV1-C(Delta 84-85)+P will be investigated as a potential live-attenuated vaccine candidate for HPIV1.
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Affiliation(s)
- Emmalene J Bartlett
- Laboratory of Infectious Diseases, RNA Viruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892-2007, USA
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Hughes-Fulford M, Li CF, Boonyaratanakornkit J, Sayyah S. Arachidonic Acid Activates Phosphatidylinositol 3-Kinase Signaling and Induces Gene Expression in Prostate Cancer. Cancer Res 2006; 66:1427-33. [PMID: 16452198 DOI: 10.1158/0008-5472.can-05-0914] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Essential fatty acids are not only energy-rich molecules; they are also an important component of the membrane bilayer and recently have been implicated in induction of fatty acid synthase and other genes. Using gene chip analysis, we have found that arachidonic acid, an omega-6 fatty acid, induced 11 genes that are regulated by nuclear factor-kappaB (NF-kappaB). We verified gene induction by omega-6 fatty acid, including COX-2, IkappaBalpha, NF-kappaB, GM-CSF, IL-1beta, CXCL-1, TNF-alpha, IL-6, LTA, IL-8, PPARgamma, and ICAM-1, using quantitative reverse transcription-PCR. Prostaglandin E(2) (PGE(2)) synthesis was increased within 5 minutes of addition of arachidonic acid. Analysis of upstream signal transduction showed that within 5 minutes of fatty acid addition, phosphatidylinositol 3-kinase (PI3K) was significantly activated followed by activation of Akt at 30 minutes. Extracellular signal-regulated kinase 1 and 2, p38 and stress-activated protein kinase/c-Jun-NH(2)-kinase were not phosphorylated after omega-6 fatty acid addition. Thirty minutes after fatty acid addition, we found a significant 3-fold increase in translocation of NF-kappaB transcription factor to the nucleus. Addition of a nonsteroidal anti-inflammatory drug (NSAID) caused a decrease in COX-2 protein synthesis, PGE(2) synthesis, as well as inhibition of PI3K activation. We have previously shown that NSAIDs cause an inhibition of arachidonic acid-induced proliferation; here, we have shown that arachidonic acid-induced proliferation is also blocked (P < 0.001) by PI3K inhibitor LY294002. LY294002 also significantly inhibited the arachidonic acid-induced gene expression of COX-2, IL-1beta, GM-CSF, and ICAM1. Taken together, the data suggest that arachidonic acid via conversion to PGE(2) plays an important role in stimulation of growth-related genes and proliferation via PI3K signaling and NF-kappaB translocation to the nucleus.
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Affiliation(s)
- Millie Hughes-Fulford
- Department of Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, CA 91421, USA.
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Cho K, Pham TN, Chamberlain T, Boonyaratanakornkit J, Greenhalgh DG. CD14-mediated alterations in transcription and splicing of endogenous retroviruses after injury. Arch Virol 2004; 149:2215-33. [PMID: 15503208 DOI: 10.1007/s00705-004-0358-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Accepted: 04/07/2004] [Indexed: 11/26/2022]
Abstract
Increase in systemic levels of lipopolysaccharide (LPS) contributes to the pathogenesis of distant organ injury after burn. Stress signals elicited from burn influence transcriptional activities of mouse endogenous retroviruses (MuERVs) in various distant organs. The involvement of LPS pathways in the burn-mediated regulation of MuERVs in the spleen was investigated in this study. Spleen harbors substantial numbers of tissue macrophages, a key responder to LPS stimulation. Spleen tissues collected from CD14 (LPS receptor) knockout (KO) and wild type (WT) mice after burn were subjected to RT-PCR analysis of MuERV expression. There was a substantial induction of 2 bands and a marked downregulation of a band in CD14 KO mice compared to WT mice after burn. Sequence analysis of these CD14- and burn-dependent bands identified 3 new alternatively spliced and 2 defective env transcripts of MuERVs as well as novel splicing signals. Chromosomal loci of putative MuERVs sharing the unique U3 sequences of these transcripts were mapped by surveying the entire genome of C57BL/6J mice. In addition, coding potentials, transcriptional regulatory elements, and adjacent cellular genes of these putative MuERVs were analyzed. The results from these studies suggest that injury-triggered LPS/CD14 signaling events play roles in the transcriptional regulation of certain MuERVs carrying unique U3 promoter sequences.
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Affiliation(s)
- K Cho
- Burn Research, Shriners Hospitals for Children Northern California and Department of Surgery, University of California at Davis, Sacramento, CA, USA
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