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Wang B, Golubov J, Oswald EM, Poon P, Wei Q, Lett C, Shehadeh F, Kaczynski M, Felix LO, Mishra B, Mylona EK, Wipperman MF, Chio E, Hamon SC, Hooper AT, Somersan-Karakaya S, Musser BJ, Petro CD, Hamilton JD, Sleeman MA, Kalliolias GD, Mylonakis E, Skokos D. Potential immunomodulatory effects of CAS+IMD monoclonal antibody cocktail in hospitalized patients with COVID-19. EBioMedicine 2024; 108:105334. [PMID: 39270622 DOI: 10.1016/j.ebiom.2024.105334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 08/19/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Passive administration of SARS-CoV-2 neutralizing monoclonal antibodies (mAbs), such as CAS + IMD (Casirivimab + Imdevimab) antibody cocktail demonstrated beneficial effects on clinical outcomes in hospitalized patients with COVID-19 who were seronegative at baseline and outpatients. However, little is known about their impact on the host immunophenotypes. METHODS We conducted an immunoprofiling study in 46 patients from a single site of a multi-site trial of CAS + IMD in hospitalized patients. We collected longitudinal samples during October 2020 ∼ April 2021, prior to the emergence of the Delta and Omicron variants and the use of COVID-19 vaccines. All collected samples were analyzed without exclusion and post-hoc statistical analysis was performed. We examined the dynamic interplay of CAS + IMD with host immunity applying dimensional reduction approach on plasma proteomics and high dimensional flow cytometry data. FINDINGS Using an unbiased clustering method, we identified unique immunophenotypes associated with acute inflammation and disease resolution. Compared to placebo group, administration of CAS + IMD accelerated the transition from an acute inflammatory immunophenotype, to a less inflammatory or "resolving" immunophenotype, as characterized by reduced tissue injury, proinflammatory markers and restored lymphocyte/monocyte imbalance independent of baseline serostatus. Moreover, CAS + IMD did not impair the magnitude or the quality of host T cell immunity against SARS-CoV-2 spike protein. INTERPRETATION Our results identified immunophenotypic changes indicative of a possible SARS-CoV-2 neutralizing antibodies-induced anti-inflammatory effect, without an evident impairment of cellular antiviral immunity, suggesting that further studies of Mabs effects on SAS-CoV-2 or other viral mediated inflammation are warranted. FUNDING Regeneron Pharmaceuticals Inc and federal funds from the Department of Health and Human Services; Administration for Strategic Preparedness and Response; Biomedical Advanced Research and Development Authority, under OT number: HHSO100201700020C.
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Affiliation(s)
- Bei Wang
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | | | - Erin M Oswald
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | - Patrick Poon
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | - Qiaozhi Wei
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | - Clarissa Lett
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | - Fadi Shehadeh
- Division of Infectious Diseases, Department of Medicine, The Brown Alpert Medical School and the Miriam Hospital, Providence, RI, USA; Department of Medicine, Houston Methodist Academic Institute, Houston, TX, 77030, USA
| | - Matthew Kaczynski
- Division of Infectious Diseases, Department of Medicine, The Brown Alpert Medical School and the Miriam Hospital, Providence, RI, USA
| | - Lewis Oscar Felix
- Division of Infectious Diseases, Department of Medicine, The Brown Alpert Medical School and the Miriam Hospital, Providence, RI, USA; Department of Medicine, Houston Methodist Academic Institute, Houston, TX, 77030, USA
| | - Biswajit Mishra
- Division of Infectious Diseases, Department of Medicine, The Brown Alpert Medical School and the Miriam Hospital, Providence, RI, USA; Department of Medicine, Houston Methodist Academic Institute, Houston, TX, 77030, USA
| | - Evangelia K Mylona
- Division of Infectious Diseases, Department of Medicine, The Brown Alpert Medical School and the Miriam Hospital, Providence, RI, USA; Department of Medicine, Houston Methodist Academic Institute, Houston, TX, 77030, USA
| | | | - Erica Chio
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | - Sara C Hamon
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | - Andrea T Hooper
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | | | - Bret J Musser
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | | | | | - Matthew A Sleeman
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA
| | | | - Eleftherios Mylonakis
- Division of Infectious Diseases, Department of Medicine, The Brown Alpert Medical School and the Miriam Hospital, Providence, RI, USA; Department of Medicine, Houston Methodist Academic Institute, Houston, TX, 77030, USA
| | - Dimitris Skokos
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York, NY, 10591, USA.
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2
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Ramirez SI, Lopez PG, Faraji F, Parikh UM, Heaps A, Ritz J, Moser C, Eron JJ, Wohl DA, Currier JS, Daar ES, Greninger AL, Klekotka P, Grifoni A, Weiskopf D, Sette A, Peters B, Hughes MD, Chew KW, Smith DM, Crotty S. Early antiviral CD4 and CD8 T cell responses and antibodies are associated with upper respiratory tract clearance of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.25.564014. [PMID: 37961119 PMCID: PMC10634820 DOI: 10.1101/2023.10.25.564014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
T cells are involved in protective immunity against numerous viral infections. Data regarding functional roles of human T cells in SARS-CoV-2 (SARS2) viral clearance in primary COVID-19 are limited. To address this knowledge gap, samples were assessed for associations between SARS2 upper respiratory tract viral RNA levels and early virus-specific adaptive immune responses for 95 unvaccinated clinical trial participants with acute primary COVID-19 aged 18-86 years old, approximately half of whom were considered high risk for progression to severe COVID-19. Functionality and magnitude of acute SARS2-specific CD4 and CD8 T cell responses were evaluated, in addition to antibody responses. Most individuals with acute COVID-19 developed SARS2-specific T cell responses within 6 days of COVID-19 symptom onset. Early CD4 T cell and CD8 T cell responses were polyfunctional, and both strongly associated with reduced upper respiratory tract SARS2 viral RNA, independent of neutralizing antibody titers. Overall, these findings provide evidence for protective roles for circulating SARS2-specific CD4 and CD8 T cells during acute COVID-19.
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3
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Ramirez SI, Faraji F, Hills LB, Lopez PG, Goodwin B, Stacey HD, Sutton HJ, Hastie KM, Saphire EO, Kim HJ, Mashoof S, Yan CH, DeConde AS, Levi G, Crotty S. Immunological memory diversity in the human upper airway. Nature 2024; 632:630-636. [PMID: 39085605 DOI: 10.1038/s41586-024-07748-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/24/2024] [Indexed: 08/02/2024]
Abstract
The upper airway is an important site of infection, but immune memory in the human upper airway is poorly understood, with implications for COVID-19 and many other human diseases1-4. Here we demonstrate that nasal and nasopharyngeal swabs can be used to obtain insights into these challenging problems, and define distinct immune cell populations, including antigen-specific memory B cells and T cells, in two adjacent anatomical sites in the upper airway. Upper airway immune cell populations seemed stable over time in healthy adults undergoing monthly swabs for more than 1 year, and prominent tissue resident memory T (TRM) cell and B (BRM) cell populations were defined. Unexpectedly, germinal centre cells were identified consistently in many nasopharyngeal swabs. In subjects with SARS-CoV-2 breakthrough infections, local virus-specific BRM cells, plasma cells and germinal centre B cells were identified, with evidence of local priming and an enrichment of IgA+ memory B cells in upper airway compartments compared with blood. Local plasma cell populations were identified with transcriptional profiles of longevity. Local virus-specific memory CD4+ TRM cells and CD8+ TRM cells were identified, with diverse additional virus-specific T cells. Age-dependent upper airway immunological shifts were observed. These findings provide new understanding of immune memory at a principal mucosal barrier tissue in humans.
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Affiliation(s)
- Sydney I Ramirez
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Farhoud Faraji
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, CA, USA
| | - L Benjamin Hills
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Paul G Lopez
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Benjamin Goodwin
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Hannah D Stacey
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Henry J Sutton
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kathryn M Hastie
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Erica Ollmann Saphire
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Hyun Jik Kim
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Otorhinolaryngology, College of Medicine, Seoul National University, Seoul, Korea
| | - Sara Mashoof
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Carol H Yan
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, CA, USA
| | - Adam S DeConde
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, CA, USA
| | - Gina Levi
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Shane Crotty
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA.
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4
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Bloom N, Ramirez SI, Cohn H, Parikh UM, Heaps A, Sieg SF, Greninger A, Ritz J, Moser C, Eron JJ, Bajic G, Currier JS, Klekotka P, Wohl DA, Daar ES, Li J, Hughes MD, Chew KW, Smith DM, Crotty S, Coelho CH. SARS-CoV-2 monoclonal antibody treatment followed by vaccination shifts human memory B cell epitope recognition suggesting antibody feedback. J Infect Dis 2024:jiae371. [PMID: 39036987 DOI: 10.1093/infdis/jiae371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 07/23/2024] Open
Abstract
Therapeutic monoclonal antibodies (mAbs) have been studied in humans, but the impact on immune memory of mAb treatment during an ongoing infection has remained unclear. We evaluated the effect of infusion of the anti-SARS-CoV-2 spike receptor binding domain (RBD) mAb bamlanivimab on memory B cells (MBCs) in SARS-CoV-2-infected individuals. Bamlanivimab treatment skewed the repertoire of memory B cells targeting Spike towards non-RBD epitopes. Furthermore, the relative affinity of RBD memory B cells was weaker in mAb-treated individuals compared to placebo-treated individuals over time. Subsequently, after mRNA COVID-19 vaccination, memory B cell differences persisted and mapped to a specific reduction in recognition of the class II RBD site, the same RBD epitope recognized by bamlanivimab. These findings indicate a substantial role of antibody feedback in regulating memory B cell responses to infection, and single mAb administration can continue to impact memory B cell responses to additional antigen exposures months later.
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Affiliation(s)
- Nathaniel Bloom
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - La Jolla, CA 92037, USA
| | - Sydney I Ramirez
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - 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
| | - Hallie Cohn
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Urvi M Parikh
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Amy Heaps
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Scott F Sieg
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve School of Medicine, Cleveland, Ohio, USA
| | - Alex Greninger
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Justin Ritz
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Carlee Moser
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Judith S Currier
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California, USA
| | | | - David A Wohl
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Eric S Daar
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jonathan Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael D Hughes
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kara W Chew
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California, USA
| | - Davey M Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, 92037, USA
| | - Shane Crotty
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - 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
| | - Camila H Coelho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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5
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Fumagalli V, Iannacone M. The interplay of drug therapeutics and immune responses to SARS-CoV-2. Cell Mol Immunol 2024; 21:197-200. [PMID: 37964122 PMCID: PMC10805708 DOI: 10.1038/s41423-023-01098-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/22/2023] [Indexed: 11/16/2023] Open
Abstract
The SARS-CoV-2 pandemic has necessitated rapid therapeutic and preventative responses. While vaccines form the frontline of defense, antiviral treatments such as nirmatrelvir have emerged as vital adjunctive measures, particularly for those unable or unwilling to be vaccinated. This review delves into the potential influence of nirmatrelvir on enduring immunity. In parallel, the potential of drug repurposing is explored, with bisphosphonates being examined for their possible effects against COVID-19 due to their immunomodulatory properties. The importance of rigorous clinical trials and careful interpretation of preliminary data is emphasized.
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Affiliation(s)
- Valeria Fumagalli
- Division of Immunology, Transplantation, and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Matteo Iannacone
- Division of Immunology, Transplantation, and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.
- Vita-Salute San Raffaele University, Milan, Italy.
- Experimental Imaging Centre, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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6
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Coelho CH, Bloom N, Ramirez SI, Parikh UM, Heaps A, Sieg SF, Greninger A, Ritz J, Moser C, Eron JJ, Currier JS, Klekotka P, Wohl DA, Daar ES, Li J, Hughes MD, Chew KW, Smith DM, Crotty S. SARS-CoV-2 monoclonal antibody treatment followed by vaccination shifts human memory B cell epitope recognition suggesting antibody feedback. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.567575. [PMID: 38045374 PMCID: PMC10690233 DOI: 10.1101/2023.11.21.567575] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Therapeutic anti-SARS-CoV-2 monoclonal antibodies (mAbs) have been extensively studied in humans, but the impact on immune memory of mAb treatment during an ongoing immune response has remained unclear. Here, we evaluated the effect of infusion of the anti-SARS-CoV-2 spike receptor binding domain (RBD) mAb bamlanivimab on memory B cells (MBCs) in SARS-CoV-2-infected individuals. Bamlanivimab treatment skewed the repertoire of memory B cells targeting Spike towards non-RBD epitopes. Furthermore, the relative affinity of RBD memory B cells was weaker in mAb-treated individuals compared to placebo-treated individuals over time. Subsequently, after mRNA COVID-19 vaccination, memory B cell differences persisted and mapped to a specific defect in recognition of the class II RBD site, the same RBD epitope recognized by bamlanivimab. These findings indicate a substantial role of antibody feedback in regulating human memory B cell responses, both to infection and vaccination. These data indicate that mAb administration can promote alterations in the epitopes recognized by the B cell repertoire, and the single administration of mAb can continue to determine the fate of B cells in response to additional antigen exposures months later.
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Affiliation(s)
- Camila H Coelho
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - La Jolla, CA 92037, USA
| | - Nathaniel Bloom
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - La Jolla, CA 92037, USA
| | - Sydney I Ramirez
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - 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
| | - Urvi M Parikh
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Amy Heaps
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Scott F Sieg
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve School of Medicine, Cleveland, Ohio, USA
| | - Alex Greninger
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Justin Ritz
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Carlee Moser
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Judith S Currier
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California, USA
| | | | - David A Wohl
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Eric S Daar
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jonathan Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael D Hughes
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kara W Chew
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California, USA
| | - Davey M Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, 92037, USA
| | - Shane Crotty
- Center for Vaccine Innovation - La Jolla Institute for Immunology (LJI) - 9420 Athena Circle - 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
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7
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da Silva Antunes R, Weiskopf D, Sidney J, Rubiro P, Peters B, Arlehamn CSL, Grifoni A, Sette A. The MegaPool Approach to Characterize Adaptive CD4+ and CD8+ T Cell Responses. Curr Protoc 2023; 3:e934. [PMID: 37966108 PMCID: PMC10662678 DOI: 10.1002/cpz1.934] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Epitopes recognized by T cells are a collection of short peptide fragments derived from specific antigens or proteins. Immunological research to study T cell responses is hindered by the extreme degree of heterogeneity of epitope targets, which are usually derived from multiple antigens; within a given antigen, hundreds of different T cell epitopes can be recognized, differing from one individual to the next because T cell epitope recognition is restricted by the epitopes' ability to bind to MHC molecules, which are extremely polymorphic in different individuals. Testing large pools encompassing hundreds of peptides is technically challenging because of logistical considerations regarding solvent-induced toxicity. To address this issue, we developed the MegaPool (MP) approach based on sequential lyophilization of large numbers of peptides that can be used in a variety of assays to measure T cell responses, including ELISPOT, intracellular cytokine staining, and activation-induced marker assays, and that has been validated in the study of infectious diseases, allergies, and autoimmunity. Here, we describe the procedures for generating and testing MPs, starting with peptide synthesis and lyophilization, as well as a step-by-step guide and recommendations for their handling and experimental usage. Overall, the MP approach is a powerful strategy for studying T cell responses and understanding the immune system's role in health and disease. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Generation of peptide pools ("MegaPools") Basic Protocol 2: MegaPool testing and quantitation of antigen-specific T cell responses.
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Affiliation(s)
- Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Paul Rubiro
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | | | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
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8
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Fumagalli V, Di Lucia P, Ravà M, Marotta D, Bono E, Grassi S, Donnici L, Cannalire R, Stefanelli I, Ferraro A, Esposito F, Pariani E, Inverso D, Montesano C, Delbue S, Perlman S, Tramontano E, De Francesco R, Summa V, Guidotti LG, Iannacone M. Nirmatrelvir treatment of SARS-CoV-2-infected mice blunts antiviral adaptive immune responses. EMBO Mol Med 2023; 15:e17580. [PMID: 36946379 PMCID: PMC10165354 DOI: 10.15252/emmm.202317580] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023] Open
Abstract
Alongside vaccines, antiviral drugs are becoming an integral part of our response to the SARS-CoV-2 pandemic. Nirmatrelvir-an orally available inhibitor of the 3-chymotrypsin-like cysteine protease-has been shown to reduce the risk of progression to severe COVID-19. However, the impact of nirmatrelvir treatment on the development of SARS-CoV-2-specific adaptive immune responses is unknown. Here, by using mouse models of SARS-CoV-2 infection, we show that nirmatrelvir administration blunts the development of SARS-CoV-2-specific antibody and T cell responses. Accordingly, upon secondary challenge, nirmatrelvir-treated mice recruited significantly fewer memory T and B cells to the infected lungs and mediastinal lymph nodes, respectively. Together, the data highlight a potential negative impact of nirmatrelvir treatment with important implications for clinical management and might help explain the virological and/or symptomatic relapse after treatment completion reported in some individuals.
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Affiliation(s)
- Valeria Fumagalli
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Pietro Di Lucia
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Micol Ravà
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Davide Marotta
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Elisa Bono
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Stefano Grassi
- Pathology UnitIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Lorena Donnici
- INGM ‐ Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”MilanItaly
| | - Rolando Cannalire
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Irina Stefanelli
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Anastasia Ferraro
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Francesca Esposito
- Dipartimento di Scienze della Vita e dell'AmbienteCittadella Universitaria di MonserratoCagliariItaly
| | - Elena Pariani
- Department of Biomedical Sciences for HealthUniversity of MilanMilanItaly
| | - Donato Inverso
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | | | - Serena Delbue
- Department of Biomedical, Surgical and Dental SciencesUniversity of MilanMilanItaly
| | - Stanley Perlman
- Department of Microbiology and ImmunologyUniversity of IowaIowa CityIAUSA
- Department of PediatricsUniversity of IowaIowa CityIAUSA
| | - Enzo Tramontano
- Dipartimento di Scienze della Vita e dell'AmbienteCittadella Universitaria di MonserratoCagliariItaly
| | - Raffaele De Francesco
- INGM ‐ Istituto Nazionale di Genetica Molecolare “Romeo ed Erica Invernizzi”MilanItaly
- Department of Pharmacological and Biomolecular SciencesUniversity of MilanMilanItaly
| | - Vincenzo Summa
- Department of Pharmacy, School of Medicine and SurgeryUniversity of Naples Federico IINaplesItaly
| | - Luca G Guidotti
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
| | - Matteo Iannacone
- Division of Immunology, Transplantation, and Infectious DiseasesIRCCS San Raffaele Scientific InstituteMilanItaly
- Vita‐Salute San Raffaele UniversityMilanItaly
- Experimental Imaging CenterIRCCS San Raffaele Scientific InstituteMilanItaly
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