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Streng BMM, Van Coillie J, Wildenbeest JG, Binnendijk RS, Smits G, den Hartog G, Wang W, Nouta J, Linty F, Visser R, Wuhrer M, Vidarsson G, Bont LJ. IgG1 glycosylation highlights premature aging in Down syndrome. Aging Cell 2024:e14167. [PMID: 38616780 DOI: 10.1111/acel.14167] [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: 12/14/2023] [Revised: 03/12/2024] [Accepted: 03/24/2024] [Indexed: 04/16/2024] Open
Abstract
Down syndrome (DS) is characterized by lowered immune competence and premature aging. We previously showed decreased antibody response following SARS-CoV-2 vaccination in adults with DS. IgG1 Fc glycosylation patterns are known to affect the effector function of IgG and are associated with aging. Here, we compare total and anti-spike (S) IgG1 glycosylation patterns following SARS-CoV-2 vaccination in DS and healthy controls (HC). Total and anti-Spike IgG1 Fc N-glycan glycoprofiles were measured in non-exposed adults with DS and controls before and after SARS-CoV-2 vaccination by liquid chromatography-mass spectrometry (LC-MS) of Fc glycopeptides. We recruited N = 44 patients and N = 40 controls. We confirmed IgG glycosylation patterns associated with aging in HC and showed premature aging in DS. In DS, we found decreased galactosylation (50.2% vs. 59.0%) and sialylation (6.7% vs. 8.5%) as well as increased fucosylation (97.0% vs. 94.6%) of total IgG. Both cohorts showed similar bisecting GlcNAc of total and anti-S IgG1 with age. In contrast, anti-S IgG1 of DS and HC showed highly comparable glycosylation profiles 28 days post vaccination. The IgG1 glycoprofile in DS exhibits strong premature aging. The combination of an early decrease in IgG1 Fc galactosylation and sialylation and increase in fucosylation is predicted to reduce complement activity and decrease FcγRIII binding and subsequent activation, respectively. The altered glycosylation patterns, combined with decreased antibody concentrations, help us understand the susceptibility to severe infections in DS. The effect of premature aging highlights the need for individuals with DS to receive tailored vaccines and/or vaccination schedules.
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Affiliation(s)
- Bianca M M Streng
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Julie Van Coillie
- Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Joanne G Wildenbeest
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob S Binnendijk
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Gaby Smits
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Gerco den Hartog
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Wenjun Wang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Nouta
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Federica Linty
- Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Remco Visser
- Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gestur Vidarsson
- Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Louis J Bont
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
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2
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Hu Z, van der Ploeg K, Chakraborty S, Arunachalam PS, Mori DAM, Jacobson KB, Bonilla H, Parsonnet J, Andrews JR, Holubar M, Subramanian A, Khosla C, Maldonado Y, Hedlin H, de la Parte L, Press K, Ty M, Tan GS, Blish C, Takahashi S, Rodriguez-Barraquer I, Greenhouse B, Butte AJ, Singh U, Pulendran B, Wang TT, Jagannathan P. Early immune markers of clinical, virological, and immunological outcomes in patients with COVID-19: a multi-omics study. eLife 2022; 11:77943. [PMID: 36239699 PMCID: PMC9566856 DOI: 10.7554/elife.77943] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/22/2022] [Indexed: 01/29/2023] Open
Abstract
Background The great majority of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) infections are mild and uncomplicated, but some individuals with initially mild COVID-19 progressively develop more severe symptoms. Furthermore, there is substantial heterogeneity in SARS-CoV-2-specific memory immune responses following infection. There remains a critical need to identify host immune biomarkers predictive of clinical and immunological outcomes in SARS-CoV-2-infected patients. Methods Leveraging longitudinal samples and data from a clinical trial (N=108) in SARS-CoV-2-infected outpatients, we used host proteomics and transcriptomics to characterize the trajectory of the immune response in COVID-19 patients. We characterized the association between early immune markers and subsequent disease progression, control of viral shedding, and SARS-CoV-2-specific T cell and antibody responses measured up to 7 months after enrollment. We further compared associations between early immune markers and subsequent T cell and antibody responses following natural infection with those following mRNA vaccination. We developed machine-learning models to predict patient outcomes and validated the predictive model using data from 54 individuals enrolled in an independent clinical trial. Results We identify early immune signatures, including plasma RIG-I levels, early IFN signaling, and related cytokines (CXCL10, MCP1, MCP-2, and MCP-3) associated with subsequent disease progression, control of viral shedding, and the SARS-CoV-2-specific T cell and antibody response measured up to 7 months after enrollment. We found that several biomarkers for immunological outcomes are shared between individuals receiving BNT162b2 (Pfizer-BioNTech) vaccine and COVID-19 patients. Finally, we demonstrate that machine-learning models using 2-7 plasma protein markers measured early within the course of infection are able to accurately predict disease progression, T cell memory, and the antibody response post-infection in a second, independent dataset. Conclusions Early immune signatures following infection can accurately predict clinical and immunological outcomes in outpatients with COVID-19 using validated machine-learning models. Funding Support for the study was provided from National Institute of Health/National Institute of Allergy and Infectious Diseases (NIH/NIAID) (U01 AI150741-01S1 and T32-AI052073), the Stanford's Innovative Medicines Accelerator, National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA) DP1DA046089, and anonymous donors to Stanford University. Peginterferon lambda provided by Eiger BioPharmaceuticals.
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Affiliation(s)
- Zicheng Hu
- Bakar Computational Health Sciences Institute, University of CaliforniaSan FranciscoUnited States
- Department of Microbiology and Immunology, University of CaliforniaSan FranciscoUnited States
| | | | | | - Prabhu S Arunachalam
- Institute for Immunity, Transplantation, and Infection, Stanford UniversityStanfordUnited States
| | - Diego AM Mori
- Department of Medicine, Stanford UniversityStanfordUnited States
| | - Karen B Jacobson
- Department of Medicine, Stanford UniversityStanfordUnited States
| | - Hector Bonilla
- Department of Medicine, Stanford UniversityStanfordUnited States
| | - Julie Parsonnet
- Department of Medicine, Stanford UniversityStanfordUnited States
- Department of Epidemiology and Population Health, Stanford UniversityStanfordUnited States
| | - Jason R Andrews
- Department of Medicine, Stanford UniversityStanfordUnited States
| | - Marisa Holubar
- Department of Medicine, Stanford UniversityStanfordUnited States
| | | | | | - Yvonne Maldonado
- Department of Pediatrics, Stanford UniversityStanfordUnited States
| | - Haley Hedlin
- Quantitative Sciences Unit, Stanford UniversityStanfordUnited States
| | | | - Kathleen Press
- Department of Medicine, Stanford UniversityStanfordUnited States
| | - Maureen Ty
- Department of Medicine, Stanford UniversityStanfordUnited States
| | - Gene S Tan
- J. Craig Venter InstituteSan DiegoUnited States
- Division of Infectious Diseases, Department of Medicine, University of CaliforniaSan DiegoUnited States
| | - Catherine Blish
- Department of Medicine, Stanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Saki Takahashi
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | | | - Bryan Greenhouse
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Department of Medicine, University of CaliforniaSan FranciscoUnited States
| | - Atul J Butte
- Bakar Computational Health Sciences Institute, University of CaliforniaSan FranciscoUnited States
| | - Upinder Singh
- Department of Medicine, Stanford UniversityStanfordUnited States
- Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
| | - Bali Pulendran
- Institute for Immunity, Transplantation, and Infection, Stanford UniversityStanfordUnited States
- Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
- Department of Pathology, Stanford UniversityStanfordUnited States
| | - Taia T Wang
- Department of Medicine, Stanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
| | - Prasanna Jagannathan
- Department of Medicine, Stanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
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3
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Sievers BL, Chakraborty S, Xue Y, Gelbart T, Gonzalez JC, Cassidy AG, Golan Y, Prahl M, Gaw SL, Arunachalam PS, Blish CA, Boyd SD, Davis MM, Jagannathan P, Nadeau KC, Pulendran B, Singh U, Scheuermann RH, Frieman MB, Vashee S, Wang TT, Tan GS. Antibodies elicited by SARS-CoV-2 infection or mRNA vaccines have reduced neutralizing activity against Beta and Omicron pseudoviruses. Sci Transl Med 2022; 14:eabn7842. [PMID: 35025672 PMCID: PMC8891085 DOI: 10.1126/scitranslmed.abn7842] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/07/2022] [Indexed: 01/29/2023]
Abstract
Multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that have mutations associated with increased transmission and antibody escape have arisen over the course of the current pandemic. Although the current vaccines have largely been effective against past variants, the number of mutations found on the Omicron (B.1.1.529) spike protein appear to diminish the protection conferred by preexisting immunity. Using vesicular stomatitis virus (VSV) pseudoparticles expressing the spike protein of several SARS-CoV-2 variants, we evaluated the magnitude and breadth of the neutralizing antibody response over time in individuals after infection and in mRNA-vaccinated individuals. We observed that boosting increases the magnitude of the antibody response to wild-type (D614), Beta, Delta, and Omicron variants; however, the Omicron variant was the most resistant to neutralization. We further observed that vaccinated healthy adults had robust and broad antibody responses, whereas responses may have been reduced in vaccinated pregnant women, underscoring the importance of learning how to maximize mRNA vaccine responses in pregnant populations. Findings from this study show substantial heterogeneity in the magnitude and breadth of responses after infection and mRNA vaccination and may support the addition of more conserved viral antigens to existing SARS-CoV-2 vaccines.
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Affiliation(s)
| | - Saborni Chakraborty
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, 94305 USA
| | - Yong Xue
- J. Craig Venter Institute, La Jolla, CA, 92037 and Rockville, MD, 20850 USA
| | - Terri Gelbart
- J. Craig Venter Institute, La Jolla, CA, 92037 and Rockville, MD, 20850 USA
| | - Joseph C. Gonzalez
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, 94305 USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
| | - Arianna G. Cassidy
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94115 USA
| | - Yarden Golan
- Department of Bioengineering and Therapeutic Sciences, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94115 USA
| | - Mary Prahl
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of California, San Francisco, CA, 94115 USA
| | - Stephanie L. Gaw
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA, 94115 USA
| | - Prabhu S. Arunachalam
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, 94305 USA
| | - Catherine A. Blish
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, 94305 USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158 USA
| | - Scott D. Boyd
- Departments of Pathology and of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305 USA
- Sean N. Parker Center for Allergy and Asthma Research, Department of Medicine, Stanford, CA, 94305 USA
| | - Mark M. Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, 94305 USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Prasanna Jagannathan
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, 94305 USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Department of Medicine, Stanford, CA, 94305 USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, 94305 USA
| | - Upinder Singh
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, 94305 USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
| | | | - Matthew B. Frieman
- Department of Microbiology and Immunology, Center for Pathogen Research, University of Maryland School of Medicine, Baltimore, MD, 21201 USA
| | - Sanjay Vashee
- J. Craig Venter Institute, La Jolla, CA, 92037 and Rockville, MD, 20850 USA
| | - Taia T. Wang
- Department of Medicine, Division of Infectious Diseases, Stanford University, Stanford, CA, 94305 USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305 USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158 USA
| | - Gene S. Tan
- J. Craig Venter Institute, La Jolla, CA, 92037 and Rockville, MD, 20850 USA
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, 92037 USA
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4
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Smith N, Goncalves P, Charbit B, Grzelak L, Beretta M, Planchais C, Bruel T, Rouilly V, Bondet V, Hadjadj J, Yatim N, Pere H, Merkling SH, Ghozlane A, Kernéis S, Rieux-Laucat F, Terrier B, Schwartz O, Mouquet H, Duffy D, Di Santo JP. Distinct systemic and mucosal immune responses during acute SARS-CoV-2 infection. Nat Immunol 2021; 22:1428-1439. [PMID: 34471264 PMCID: PMC8553615 DOI: 10.1038/s41590-021-01028-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/12/2021] [Indexed: 01/20/2023]
Abstract
Coordinated local mucosal and systemic immune responses following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection either protect against coronavirus disease 2019 (COVID-19) pathologies or fail, leading to severe clinical outcomes. To understand this process, we performed an integrated analysis of SARS-CoV-2 spike-specific antibodies, cytokines, viral load and bacterial communities in paired nasopharyngeal swabs and plasma samples from a cohort of clinically distinct patients with COVID-19 during acute infection. Plasma viral load was associated with systemic inflammatory cytokines that were elevated in severe COVID-19, and also with spike-specific neutralizing antibodies. By contrast, nasopharyngeal viral load correlated with SARS-CoV-2 humoral responses but inversely with interferon responses, the latter associating with protective microbial communities. Potential pathogenic microorganisms, often implicated in secondary respiratory infections, were associated with mucosal inflammation and elevated in severe COVID-19. Our results demonstrate distinct tissue compartmentalization of SARS-CoV-2 immune responses and highlight a role for the nasopharyngeal microbiome in regulating local and systemic immunity that determines COVID-19 clinical outcomes.
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Affiliation(s)
- Nikaïa Smith
- grid.428999.70000 0001 2353 6535Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Pedro Goncalves
- grid.428999.70000 0001 2353 6535Innate Immunity Unit, Institut Pasteur, INSERM U1223, Paris, France
| | - Bruno Charbit
- grid.428999.70000 0001 2353 6535Cytometry and Biomarkers UTechS, Institut Pasteur, Paris, France
| | - Ludivine Grzelak
- grid.428999.70000 0001 2353 6535Virus and Immunity Unit, Institut Pasteur, Paris, France ,grid.508487.60000 0004 7885 7602Sorbonne Paris Cité, Université de Paris, Paris, France
| | - Maxime Beretta
- grid.428999.70000 0001 2353 6535Humoral Immunology Laboratory, Institut Pasteur, INSERM U1222, Paris, France
| | - Cyril Planchais
- grid.428999.70000 0001 2353 6535Humoral Immunology Laboratory, Institut Pasteur, INSERM U1222, Paris, France
| | - Timothée Bruel
- grid.428999.70000 0001 2353 6535Virus and Immunity Unit, Institut Pasteur, Paris, France
| | | | - Vincent Bondet
- grid.428999.70000 0001 2353 6535Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Jérôme Hadjadj
- grid.508487.60000 0004 7885 7602Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hôpitaux de Paris-Centre (APHP-CUP), Université de Paris, Paris, France ,grid.508487.60000 0004 7885 7602Imagine Institute, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Université de Paris, Paris, France
| | - Nader Yatim
- grid.428999.70000 0001 2353 6535Translational Immunology Lab, Institut Pasteur, Paris, France ,grid.508487.60000 0004 7885 7602Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hôpitaux de Paris-Centre (APHP-CUP), Université de Paris, Paris, France
| | - Helene Pere
- grid.417925.cUnité de Génomique Fonctionnelle des Tumeurs Solides, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Paris, France
| | - Sarah H. Merkling
- grid.428999.70000 0001 2353 6535Insect-Virus Interactions Unit, Institut Pasteur, CNRS UMR2000, Paris, France
| | - Amine Ghozlane
- grid.428999.70000 0001 2353 6535Hub de Bioinformatique et Biostatistique, Institut Pasteur, Paris, France
| | - Solen Kernéis
- grid.411784.f0000 0001 0274 3893Equipe Mobile d’Infectiologie, Hôpital Cochin, AP-HP, APHP-CUP, Paris, France ,Université de Paris, INSERM, IAME, Paris, France ,grid.428999.70000 0001 2353 6535Epidemiology and Antimicrobial Resistance Modeling Laboratory, Institut Pasteur, Paris, France
| | - Frederic Rieux-Laucat
- grid.508487.60000 0004 7885 7602Imagine Institute, Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Université de Paris, Paris, France
| | - Benjamin Terrier
- grid.508487.60000 0004 7885 7602Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hôpitaux de Paris-Centre (APHP-CUP), Université de Paris, Paris, France
| | - Olivier Schwartz
- grid.428999.70000 0001 2353 6535Virus and Immunity Unit, Institut Pasteur, Paris, France
| | - Hugo Mouquet
- grid.428999.70000 0001 2353 6535Humoral Immunology Laboratory, Institut Pasteur, INSERM U1222, Paris, France
| | - Darragh Duffy
- grid.428999.70000 0001 2353 6535Translational Immunology Lab, Institut Pasteur, Paris, France
| | - James P. Di Santo
- grid.428999.70000 0001 2353 6535Innate Immunity Unit, Institut Pasteur, INSERM U1223, Paris, France
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