1
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Loos C, Coccia M, Didierlaurent AM, Essaghir A, Fallon JK, Lauffenburger D, Luedemann C, Michell A, van der Most R, Zhu AL, Alter G, Burny W. Systems serology-based comparison of antibody effector functions induced by adjuvanted vaccines to guide vaccine design. NPJ Vaccines 2023; 8:34. [PMID: 36890168 PMCID: PMC9992919 DOI: 10.1038/s41541-023-00613-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 01/27/2023] [Indexed: 03/10/2023] Open
Abstract
The mechanisms by which antibodies confer protection vary across vaccines, ranging from simple neutralization to functions requiring innate immune recruitment via Fc-dependent mechanisms. The role of adjuvants in shaping the maturation of antibody-effector functions remains under investigated. Using systems serology, we compared adjuvants in licensed vaccines (AS01B/AS01E/AS03/AS04/Alum) combined with a model antigen. Antigen-naive adults received two adjuvanted immunizations followed by late revaccination with fractional-dosed non-adjuvanted antigen ( NCT00805389 ). A dichotomy in response quantities/qualities emerged post-dose 2 between AS01B/AS01E/AS03 and AS04/Alum, based on four features related to immunoglobulin titers or Fc-effector functions. AS01B/E and AS03 induced similar robust responses that were boosted upon revaccination, suggesting that memory B-cell programming by the adjuvanted vaccinations dictated responses post non-adjuvanted boost. AS04 and Alum induced weaker responses, that were dissimilar with enhanced functionalities for AS04. Distinct adjuvant classes can be leveraged to tune antibody-effector functions, where selective vaccine formulation using adjuvants with different immunological properties may direct antigen-specific antibody functions.
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Affiliation(s)
- Carolin Loos
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | | | - Arnaud M Didierlaurent
- GSK, Rixensart, Belgium.,Center of Vaccinology, University of Geneva, Geneva, Switzerland
| | | | | | | | | | - Ashlin Michell
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | | | - Alex Lee Zhu
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Virology and Immunology Program, University of Duisburg-Essen, Essen, Germany
| | - Galit Alter
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
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2
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Nielsen CM, Barrett JR, Davis C, Fallon JK, Goh C, Michell AR, Griffin C, Kwok A, Loos C, Darko S, Laboune F, Tekman M, Diouf A, Miura K, Francica JR, Ransier A, Long CA, Silk SE, Payne RO, Minassian AM, Lauffenburger DA, Seder RA, Douek DC, Alter G, Draper SJ. Delayed boosting improves human antigen-specific Ig and B cell responses to the RH5.1/AS01B malaria vaccine. JCI Insight 2023; 8:163859. [PMID: 36692019 PMCID: PMC9977309 DOI: 10.1172/jci.insight.163859] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/30/2022] [Indexed: 01/24/2023] Open
Abstract
Modifications to vaccine delivery that increase serum antibody longevity are of great interest for maximizing efficacy. We have previously shown that a delayed fractional (DFx) dosing schedule (0-1-6 month) - using AS01B-adjuvanted RH5.1 malaria antigen - substantially improves serum IgG durability as compared with monthly dosing (0-1-2 month; NCT02927145). However, the underlying mechanism and whether there are wider immunological changes with DFx dosing were unclear. Here, PfRH5-specific Ig and B cell responses were analyzed in depth through standardized ELISAs, flow cytometry, systems serology, and single-cell RNA-Seq (scRNA-Seq). Data indicate that DFx dosing increases the magnitude and durability of circulating PfRH5-specific B cells and serum IgG1. At the peak antibody magnitude, DFx dosing was distinguished by a systems serology feature set comprising increased FcRn binding, IgG avidity, and proportion of G2B and G2S2F IgG Fc glycans, alongside decreased IgG3, antibody-dependent complement deposition, and proportion of G1S1F IgG Fc glycan. Concomitantly, scRNA-Seq data show a higher CDR3 percentage of mutation from germline and decreased plasma cell gene expression in circulating PfRH5-specific B cells. Our data, therefore, reveal a profound impact of DFx dosing on the humoral response and suggest plausible mechanisms that could enhance antibody longevity, including improved FcRn binding by serum Ig and a potential shift in the underlying cellular response from circulating short-lived plasma cells to nonperipheral long-lived plasma cells.
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Affiliation(s)
| | | | - Christine Davis
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
| | - Jonathan K. Fallon
- Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Boston, Massachusetts, USA
| | - Cyndi Goh
- University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Ashlin R. Michell
- Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Boston, Massachusetts, USA
| | - Catherine Griffin
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
| | - Andrew Kwok
- University of Oxford, Oxford, Oxfordshire, United Kingdom.,Wellcome Center for Human Genetics, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Carolin Loos
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA.,Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Boston, Massachusetts, USA
| | - Samuel Darko
- Vaccine Research Center, NIAID/NIH, Bethesda, Maryland, USA
| | - Farida Laboune
- Vaccine Research Center, NIAID/NIH, Bethesda, Maryland, USA
| | - Mehmet Tekman
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ababacar Diouf
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, Maryland, USA
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, Maryland, USA
| | | | - Amy Ransier
- Vaccine Research Center, NIAID/NIH, Bethesda, Maryland, USA
| | - Carole A. Long
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, Maryland, USA
| | - Sarah E. Silk
- University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Ruth O. Payne
- University of Oxford, Oxford, Oxfordshire, United Kingdom
| | | | | | | | | | - Galit Alter
- Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Boston, Massachusetts, USA
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3
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Poonam F, Loos C, Wells A, Ehsan A. Molecular Solid Tumor Algorithm – Simplified Patient-Centric/Cost-Effective Approach by Pathologists. Am J Clin Pathol 2022. [DOI: 10.1093/ajcp/aqac126.300] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract
Introduction/Objective
The process from the time the patient is diagnosed with cancer and receives their first treatment is complex and time-consuming. It requires adherence to national comprehensive cancer network (NCCN) guidelines; is challenged with limited tissue, how and when to order tests, and reimbursement timelines with pre- authorizations. We evaluated the role of the pathologists, who are an integral part of patient care, along with oncologists and surgeons.
Methods/Case Report
254 cases from various types of solid tumors (paraffin-embedded blocks) were collected from several pathology departments. Tests (two panels NGS-DNA/RNA expression, FISH, PD-L1, and IHC) were ordered as early as on the day of diagnosis to as late as 18 months following the diagnosis. Cancer cases reviewed were Colo-Rectal (72), Lung (48), Breast (24), Gastric (10), CNS (8), Melanoma (4), Head/Neck (20), GU (16), Sarcomas (8), Thyroid (6), Hepatic (8), Female Genital Tract (7) and Unknown Primary (23).
Results (if a Case Study enter NA)
We evaluated pathology reports, identified blocks, reviewed H&E slides, utilized NCCN guidelines in collaboration with oncologists. Tests were ordered using established billing criteria. Following tests were performed: PD-L1 (190 - 75%), FISH (50 - 20%), and NGS – two simple panel approach (215 - 85%). Using the aforesaid methods, our NGS results were successful in >95%. We were able to identify actionable and prognostic mutations in >80% of tumors.
Conclusion
Our algorithm has been designed considering NCCN guidelines and are updated frequently with new therapeutic targets and actionable mutations. The emphasis is to conserve diagnostic tissue and ensure timely ordering of tests as medically necessary. This can be adopted by pathologists in conjunction with clinical information, pathology reports, and be used as a part of diagnostic workups to reduce delays in treatment, avoid tissue loss, utilize current billing (inpatient/outpatient) practices, pre-authorization and eventually improving patient care as well as reduce overall healthcare costs.
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Affiliation(s)
- F Poonam
- Pathology, CorePath Laboratories , San Antonio, Texas , United States
| | - C Loos
- Pathology, CorePath Laboratories , San Antonio, Texas , United States
| | - A Wells
- Pathology, CorePath Laboratories , San Antonio, Texas , United States
| | - A Ehsan
- Pathology, CorePath Laboratories , San Antonio, Texas , United States
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4
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Dias AG, Atyeo C, Loos C, Montoya M, Roy V, Bos S, Narvekar P, Singh T, Katzelnick LC, Kuan G, Lauffenburger DA, Balmaseda A, Alter G, Harris E. Antibody Fc characteristics and effector functions correlate with protection from symptomatic dengue virus type 3 infection. Sci Transl Med 2022; 14:eabm3151. [PMID: 35767652 PMCID: PMC10115655 DOI: 10.1126/scitranslmed.abm3151] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Preexisting cross-reactive antibodies have been implicated in both protection and pathogenesis during subsequent infections with different dengue virus (DENV) serotypes (DENV1-4). Nonetheless, humoral immune correlates and mechanisms of protection have remained elusive. Using a systems serology approach to evaluate humoral responses, we profiled plasma collected before inapparent or symptomatic secondary DENV3 infection from our pediatric cohort in Nicaragua. Children protected from symptomatic infections had more anti-envelope (E) and anti-nonstructural protein 1 (NS1) total immunoglobulin G (IgG), IgG4, and greater Fc effector functions than those with symptoms. Fc effector functions were also associated with protection from hemorrhagic manifestations in the pre-symptomatic group. Furthermore, in vitro virological assays using these plasma samples revealed that protection mediated by antibody-dependent complement deposition was associated with both lysis of virions and DENV-infected cells. These data suggest that E- and NS1-specific Fc functions may serve as correlates of protection, which can be potentially applied toward the design and evaluation of dengue vaccines.
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Affiliation(s)
- Antonio G. Dias
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley; Berkeley, CA, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Magelda Montoya
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley; Berkeley, CA, USA
| | - Vicky Roy
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
| | - Sandra Bos
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley; Berkeley, CA, USA
| | - Parnal Narvekar
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley; Berkeley, CA, USA
| | - Tulika Singh
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley; Berkeley, CA, USA
| | - Leah C. Katzelnick
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley; Berkeley, CA, USA
- Viral Epidemiology and Immunity Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Guillermina Kuan
- Sustainable Sciences Institute, Managua, Nicaragua
- Centro de Salud Sócrates Flores Vivas, Ministerio de Salud, Managua, Nicaragua
| | | | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard; Cambridge, MA, USA
| | - Eva Harris
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley; Berkeley, CA, USA
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5
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Reyntiens P, Bossche SV, Loos C, Dekeyzer S. Two cases of symptomatic developmental venous anomalies: imaging findings and possible etiology. Acta Neurol Belg 2022; 122:1089-1092. [PMID: 35476293 DOI: 10.1007/s13760-022-01905-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/17/2022] [Indexed: 12/01/2022]
Affiliation(s)
- P Reyntiens
- Department of Radiology, Antwerp University Hospital (UZA), Drie Eikenstraat 655, 2650, Edegem, Belgium
| | - S Vanden Bossche
- Department of Radiology, Antwerp University Hospital (UZA), Drie Eikenstraat 655, 2650, Edegem, Belgium
| | - C Loos
- Department of Neurology, Antwerp University Hospital (UZA), Drie Eikenstraat 655, 2650, Edegem, Belgium
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - S Dekeyzer
- Department of Radiology, Antwerp University Hospital (UZA), Drie Eikenstraat 655, 2650, Edegem, Belgium.
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6
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Spatola M, Loos C, Cizmeci D, Webb N, Gorman MJ, Rossignol E, Shin S, Yuan D, Fontana L, Mukerji SS, Lauffenburger DA, Gabuzda D, Alter G. Functional compartmentalization of antibodies in the central nervous system during chronic HIV infection. J Infect Dis 2022; 226:738-750. [PMID: 35417540 PMCID: PMC9441210 DOI: 10.1093/infdis/jiac138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 04/07/2022] [Indexed: 11/30/2022] Open
Abstract
The central nervous system (CNS) has emerged as a critical HIV reservoir. Thus, interventions aimed at controlling and eliminating HIV must include CNS-targeted strategies. Given the inaccessibility of the brain, efforts have focused on cerebrospinal fluid (CSF), aimed at defining biomarkers of HIV-disease in the CNS, including HIV-specific antibodies. However, how antibodies traffic between the blood and CNS, and whether specific antibody profiles track with HIV-associated neurocognitive disorders (HAND) remains unclear. Here, we comprehensively profiled HIV-specific antibodies across plasma and CSF from 20 antiretroviral therapy (ART) naive or treated persons with HIV. CSF was populated by IgG1 and IgG3 antibodies, with reduced Fc-effector profiles. While ART improved plasma antibody functional coordination, CSF profiles were unaffected by ART and were unrelated to HAND severity. These data point to a functional sieving of antibodies across the blood-brain barrier, providing previously unappreciated insights for the development of next-generation therapeutics targeting the CNS reservoir.
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Affiliation(s)
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.,Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Deniz Cizmeci
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.,Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas Webb
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Evan Rossignol
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Sally Shin
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Dansu Yuan
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Laura Fontana
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | | | | | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
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7
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Herman JD, Wang C, Loos C, Yoon H, Rivera J, Eugenia Dieterle M, Haslwanter D, Jangra RK, Bortz RH, Bar KJ, Julg B, Chandran K, Lauffenburger D, Pirofski LA, Alter G. Functional convalescent plasma antibodies and pre-infusion titers shape the early severe COVID-19 immune response. Nat Commun 2021; 12:6853. [PMID: 34824251 PMCID: PMC8617042 DOI: 10.1038/s41467-021-27201-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/28/2021] [Indexed: 01/10/2023] Open
Abstract
Transfer of convalescent plasma (CP) had been proposed early during the SARS-CoV-2 pandemic as an accessible therapy, yet trial results worldwide have been mixed, potentially due to the heterogeneous nature of CP. Here we perform deep profiling of SARS-CoV-2-specific antibody titer, Fc-receptor binding, and Fc-mediated functional assays in CP units, as well as in plasma from hospitalized COVID-19 patients before and after CP administration. The profiling results show that, although all recipients exhibit expanded SARS-CoV-2-specific humoral immune responses, CP units contain more functional antibodies than recipient plasma. Meanwhile, CP functional profiles influence the evolution of recipient humoral immunity in conjuncture with the recipient's pre-existing SARS-CoV2-specific antibody titers: CP-derived SARS-CoV-2 nucleocapsid-specific antibody functions are associated with muted humoral immune evolution in patients with high titer anti-spike IgG. Our data thus provide insights into the unexpected impact of CP-derived functional anti-spike and anti-nucleocapsid antibodies on the evolution of SARS-CoV-2-specific response following severe infection.
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Affiliation(s)
- Jonathan D Herman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA, USA
| | - Chuangqi Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hyunah Yoon
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Johanna Rivera
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - M Eugenia Dieterle
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Denise Haslwanter
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rohit K Jangra
- Department of Microbiology and Immunology, Louisiana State University Health Science Center-Shreveport, Shreveport, LA, USA
| | - Robert H Bortz
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Katharine J Bar
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Boris Julg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Liise-Anne Pirofski
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA.
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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8
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Gorman MJ, Patel N, Guebre-Xabier M, Zhu AL, Atyeo C, Pullen KM, Loos C, Goez-Gazi Y, Carrion R, Tian JH, Yuan D, Bowman KA, Zhou B, Maciejewski S, McGrath ME, Logue J, Frieman MB, Montefiori D, Mann C, Schendel S, Amanat F, Krammer F, Saphire EO, Lauffenburger DA, Greene AM, Portnoff AD, Massare MJ, Ellingsworth L, Glenn G, Smith G, Alter G. Fab and Fc contribute to maximal protection against SARS-CoV-2 following NVX-CoV2373 subunit vaccine with Matrix-M vaccination. Cell Rep Med 2021; 2:100405. [PMID: 34485950 PMCID: PMC8405506 DOI: 10.1016/j.xcrm.2021.100405] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [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] [Received: 04/01/2021] [Revised: 06/30/2021] [Accepted: 08/24/2021] [Indexed: 12/16/2022]
Abstract
Recently approved vaccines have shown remarkable efficacy in limiting SARS-CoV-2-associated disease. However, with the variety of vaccines, immunization strategies, and waning antibody titers, defining the correlates of immunity across a spectrum of antibody titers is urgently required. Thus, we profiled the humoral immune response in a cohort of non-human primates immunized with a recombinant SARS-CoV-2 spike glycoprotein (NVX-CoV2373) at two doses, administered as a single- or two-dose regimen. Both antigen dose and boosting significantly altered neutralization titers and Fc-effector profiles, driving unique vaccine-induced antibody fingerprints. Combined differences in antibody effector functions and neutralization were associated with distinct levels of protection in the upper and lower respiratory tract. Moreover, NVX-CoV2373 elicited antibodies that functionally targeted emerging SARS-CoV-2 variants. Collectively, the data presented here suggest that a single dose may prevent disease via combined Fc/Fab functions but that two doses may be essential to block further transmission of SARS-CoV-2 and emerging variants.
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Affiliation(s)
| | - Nita Patel
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | - Alex L. Zhu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Virology and Immunology Program, University of Duisburg-Essen, Essen, Germany
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Krista M. Pullen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yenny Goez-Gazi
- Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX 78227, USA
| | - Ricardo Carrion
- Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX 78227, USA
| | - Jing-Hui Tian
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Dansu Yuan
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - Bin Zhou
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | - Marisa E. McGrath
- University of Maryland School of Medicine, 685 West Baltimore St, Baltimore, MD 21201, USA
| | - James Logue
- University of Maryland School of Medicine, 685 West Baltimore St, Baltimore, MD 21201, USA
| | - Matthew B. Frieman
- University of Maryland School of Medicine, 685 West Baltimore St, Baltimore, MD 21201, USA
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Colin Mann
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | | | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ann M. Greene
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | | | | | - Gregory Glenn
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Gale Smith
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
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9
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Minassian AM, Silk SE, Barrett JR, Nielsen CM, Miura K, Diouf A, Loos C, Fallon JK, Michell AR, White MT, Edwards NJ, Poulton ID, Mitton CH, Payne RO, Marks M, Maxwell-Scott H, Querol-Rubiera A, Bisnauthsing K, Batra R, Ogrina T, Brendish NJ, Themistocleous Y, Rawlinson TA, Ellis KJ, Quinkert D, Baker M, Lopez Ramon R, Ramos Lopez F, Barfod L, Folegatti PM, Silman D, Datoo M, Taylor IJ, Jin J, Pulido D, Douglas AD, de Jongh WA, Smith R, Berrie E, Noe AR, Diggs CL, Soisson LA, Ashfield R, Faust SN, Goodman AL, Lawrie AM, Nugent FL, Alter G, Long CA, Draper SJ. Reduced blood-stage malaria growth and immune correlates in humans following RH5 vaccination. Med (N Y) 2021; 2:701-719.e19. [PMID: 34223402 PMCID: PMC8240500 DOI: 10.1016/j.medj.2021.03.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background Development of an effective vaccine against the pathogenic blood-stage infection of human malaria has proved challenging, and no candidate vaccine has affected blood-stage parasitemia following controlled human malaria infection (CHMI) with blood-stage Plasmodium falciparum. Methods We undertook a phase I/IIa clinical trial in healthy adults in the United Kingdom of the RH5.1 recombinant protein vaccine, targeting the P. falciparum reticulocyte-binding protein homolog 5 (RH5), formulated in AS01B adjuvant. We assessed safety, immunogenicity, and efficacy against blood-stage CHMI. Trial registered at ClinicalTrials.gov, NCT02927145. Findings The RH5.1/AS01B formulation was administered using a range of RH5.1 protein vaccine doses (2, 10, and 50 μg) and was found to be safe and well tolerated. A regimen using a delayed and fractional third dose, in contrast to three doses given at monthly intervals, led to significantly improved antibody response longevity over ∼2 years of follow-up. Following primary and secondary CHMI of vaccinees with blood-stage P. falciparum, a significant reduction in parasite growth rate was observed, defining a milestone for the blood-stage malaria vaccine field. We show that growth inhibition activity measured in vitro using purified immunoglobulin G (IgG) antibody strongly correlates with in vivo reduction of the parasite growth rate and also identify other antibody feature sets by systems serology, including the plasma anti-RH5 IgA1 response, that are associated with challenge outcome. Conclusions Our data provide a new framework to guide rational design and delivery of next-generation vaccines to protect against malaria disease. Funding This study was supported by USAID, UK MRC, Wellcome Trust, NIAID, and the NIHR Oxford-BRC. The RH5.1/AS01B vaccine is safe, well tolerated, and immunogenic in healthy adults A delayed fractional third dose significantly improves antibody response longevity In vivo blood-stage P. falciparum growth rate is significantly lower in vaccinees In vitro IgG-mediated growth inhibition activity is associated with challenge outcome
A highly effective vaccine against the human malaria parasite Plasmodium falciparum is urgently needed. One vaccine strategy aims to prevent parasite growth in the blood, protecting against clinical disease; however, this has proved exceptionally challenging. Here we show that a candidate vaccine (reticulocyte-binding protein homolog 5.1 [RH5.1]/AS01B) is safe in a phase I/IIa clinical trial and identify a vaccination regimen that improves the durability of the human antibody response, which is critical for long-term protection. Following experimental challenge of vaccinated adults with malaria, we observed that the vaccine could reduce parasite growth in the blood and identified immune responses that could predict how well the vaccine performs. These data will help guide the design of improved vaccines in the future.
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Affiliation(s)
| | - Sarah E Silk
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | | | | | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA
| | - Ababacar Diouf
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA
| | - Carolin Loos
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan K Fallon
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Ashlin R Michell
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Michael T White
- Department of Parasites and Insect Vectors, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Nick J Edwards
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Ian D Poulton
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Celia H Mitton
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Ruth O Payne
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Michael Marks
- Centre for Clinical Infection and Diagnostics Research, King's College London and Guy's & St Thomas' NHS Foundation Trust, Westminster Bridge Road, London SE1 7EH, UK
| | - Hector Maxwell-Scott
- Centre for Clinical Infection and Diagnostics Research, King's College London and Guy's & St Thomas' NHS Foundation Trust, Westminster Bridge Road, London SE1 7EH, UK
| | - Antonio Querol-Rubiera
- Centre for Clinical Infection and Diagnostics Research, King's College London and Guy's & St Thomas' NHS Foundation Trust, Westminster Bridge Road, London SE1 7EH, UK
| | - Karen Bisnauthsing
- Centre for Clinical Infection and Diagnostics Research, King's College London and Guy's & St Thomas' NHS Foundation Trust, Westminster Bridge Road, London SE1 7EH, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research, King's College London and Guy's & St Thomas' NHS Foundation Trust, Westminster Bridge Road, London SE1 7EH, UK
| | - Tatiana Ogrina
- NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Nathan J Brendish
- NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | | | | | | | - Doris Quinkert
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Megan Baker
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | | | | | - Lea Barfod
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Daniel Silman
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Mehreen Datoo
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Iona J Taylor
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Jing Jin
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - David Pulido
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Willem A de Jongh
- ExpreSion Biotechnologies, SCION-DTU Science Park, Agern Allé 1, Hørsholm 2970, Denmark
| | - Robert Smith
- Clinical BioManufacturing Facility, University of Oxford, Oxford OX3 7JT, UK
| | - Eleanor Berrie
- Clinical BioManufacturing Facility, University of Oxford, Oxford OX3 7JT, UK
| | - Amy R Noe
- Leidos Life Sciences, Fredrick, MD, USA
| | - Carter L Diggs
- USAID, 1300 Pennsylvania Ave. NW, Washington, DC 20004, USA
| | | | | | - Saul N Faust
- NIHR Wellcome Trust Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Anna L Goodman
- Centre for Clinical Infection and Diagnostics Research, King's College London and Guy's & St Thomas' NHS Foundation Trust, Westminster Bridge Road, London SE1 7EH, UK
| | - Alison M Lawrie
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Fay L Nugent
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
| | - Galit Alter
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Carole A Long
- Laboratory of Malaria and Vector Research, NIAID/NIH, Rockville, MD 20852, USA
| | - Simon J Draper
- The Jenner Institute, University of Oxford, Oxford OX3 7DQ, UK
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10
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Hauss A, Loos C, Gerritsen A, Urschel K, Pagan J. 61 Effect of branched-chain amino acid and N-acetylcysteine supplementation post-exercise on muscle mTOR signaling in exercising horses. J Equine Vet Sci 2021. [DOI: 10.1016/j.jevs.2021.103524] [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: 11/26/2022]
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11
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Stephenson KE, Le Gars M, Sadoff J, de Groot AM, Heerwegh D, Truyers C, Atyeo C, Loos C, Chandrashekar A, McMahan K, Tostanoski LH, Yu J, Gebre MS, Jacob-Dolan C, Li Z, Patel S, Peter L, Liu J, Borducchi EN, Nkolola JP, Souza M, Tan CS, Zash R, Julg B, Nathavitharana RR, Shapiro RL, Azim AA, Alonso CD, Jaegle K, Ansel JL, Kanjilal DG, Guiney CJ, Bradshaw C, Tyler A, Makoni T, Yanosick KE, Seaman MS, Lauffenburger DA, Alter G, Struyf F, Douoguih M, Van Hoof J, Schuitemaker H, Barouch DH. Immunogenicity of the Ad26.COV2.S Vaccine for COVID-19. JAMA 2021; 325:1535-1544. [PMID: 33704352 PMCID: PMC7953339 DOI: 10.1001/jama.2021.3645] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
IMPORTANCE Control of the global COVID-19 pandemic will require the development and deployment of safe and effective vaccines. OBJECTIVE To evaluate the immunogenicity of the Ad26.COV2.S vaccine (Janssen/Johnson & Johnson) in humans, including the kinetics, magnitude, and phenotype of SARS-CoV-2 spike-specific humoral and cellular immune responses. DESIGN, SETTING, AND PARTICIPANTS Twenty-five participants were enrolled from July 29, 2020, to August 7, 2020, and the follow-up for this day 71 interim analysis was completed on October 3, 2020; follow-up to assess durability will continue for 2 years. This study was conducted at a single clinical site in Boston, Massachusetts, as part of a randomized, double-blind, placebo-controlled phase 1 clinical trial of Ad26.COV2.S. INTERVENTIONS Participants were randomized to receive 1 or 2 intramuscular injections with 5 × 1010 viral particles or 1 × 1011 viral particles of Ad26.COV2.S vaccine or placebo administered on day 1 and day 57 (5 participants in each group). MAIN OUTCOMES AND MEASURES Humoral immune responses included binding and neutralizing antibody responses at multiple time points following immunization. Cellular immune responses included immunospot-based and intracellular cytokine staining assays to measure T-cell responses. RESULTS Twenty-five participants were randomized (median age, 42; age range, 22-52; 52% women, 44% male, 4% undifferentiated), and all completed the trial through the day 71 interim end point. Binding and neutralizing antibodies emerged rapidly by day 8 after initial immunization in 90% and 25% of vaccine recipients, respectively. By day 57, binding and neutralizing antibodies were detected in 100% of vaccine recipients after a single immunization. On day 71, the geometric mean titers of spike-specific binding antibodies were 2432 to 5729 and the geometric mean titers of neutralizing antibodies were 242 to 449 in the vaccinated groups. A variety of antibody subclasses, Fc receptor binding properties, and antiviral functions were induced. CD4+ and CD8+ T-cell responses were induced. CONCLUSION AND RELEVANCE In this phase 1 study, a single immunization with Ad26.COV2.S induced rapid binding and neutralization antibody responses as well as cellular immune responses. Two phase 3 clinical trials are currently underway to determine the efficacy of the Ad26.COV2.S vaccine. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT04436276.
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Affiliation(s)
- Kathryn E. Stephenson
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Jerald Sadoff
- Janssen Vaccines & Prevention, Leiden, the Netherlands
| | | | | | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Carolin Loos
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
- Massachusetts Institute of Technology, Cambridge
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Lisa H. Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Makda S. Gebre
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Zhenfeng Li
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Shivani Patel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Lauren Peter
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Erica N. Borducchi
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Joseph P. Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Morgana Souza
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Chen Sabrina Tan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Rebecca Zash
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Boris Julg
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | | | - Roger L. Shapiro
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Ahmed Abdul Azim
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Carolyn D. Alonso
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Kate Jaegle
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Jessica L. Ansel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Diane G. Kanjilal
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Caitlin J. Guiney
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Connor Bradshaw
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Anna Tyler
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Tatenda Makoni
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Katherine E. Yanosick
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | | | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Massachusetts Consortium on Pathogen Readiness, Boston
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12
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Yu KK, Fischinger S, Smith MT, Atyeo C, Cizmeci D, Wolf CR, Layton ED, Logue JK, Aguilar MS, Shuey K, Loos C, Yu J, Franko N, Choi RY, Wald A, Barouch DH, Koelle DM, Lauffenburger D, Chu HY, Alter G, Seshadri C. Comorbid illnesses are associated with altered adaptive immune responses to SARS-CoV-2. JCI Insight 2021; 6:146242. [PMID: 33621211 PMCID: PMC8026190 DOI: 10.1172/jci.insight.146242] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 11/19/2020] [Accepted: 02/17/2021] [Indexed: 12/16/2022] Open
Abstract
Comorbid medical illnesses, such as obesity and diabetes, are associated with more severe COVID-19, hospitalization, and death. However, the role of the immune system in mediating these clinical outcomes has not been determined. We used multiparameter flow cytometry and systems serology to comprehensively profile the functions of T cells and antibodies targeting spike, nucleocapsid, and envelope proteins in a convalescent cohort of COVID-19 subjects who were either hospitalized (n = 20) or not hospitalized (n = 40). To avoid confounding, subjects were matched by age, sex, ethnicity, and date of symptom onset. Surprisingly, we found that the magnitude and functional breadth of virus-specific CD4+ T cell and antibody responses were consistently higher among hospitalized subjects, particularly those with medical comorbidities. However, an integrated analysis identified more coordination between polyfunctional CD4+ T cells and antibodies targeting the S1 domain of spike among subjects who were not hospitalized. These data reveal a functionally diverse and coordinated response between T cells and antibodies targeting SARS-CoV-2, which is reduced in the presence of comorbid illnesses that are known risk factors for severe COVID-19.
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Affiliation(s)
- Krystle Kq Yu
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,PhD program in Immunology and Virology, University of Duisburg-Essen, Essen, Germany
| | - Malisa T Smith
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,PhD program in Virology, Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
| | - Deniz Cizmeci
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Erik D Layton
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jennifer K Logue
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Melissa S Aguilar
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kiel Shuey
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas Franko
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Anna Wald
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Epidemiology and.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Dan H Barouch
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - David M Koelle
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA.,Benaroya Research Institute, Seattle, Washington, USA
| | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
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13
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Herman JD, Wang C, Loos C, Yoon H, Rivera J, Dieterle ME, Haslwanter D, Jangra RK, Bortz RH, Bar KJ, Julg B, Chandran K, Lauffenburger D, Pirofski LA, Alter G. Functional Antibodies in COVID-19 Convalescent Plasma. medRxiv 2021:2021.03.08.21253157. [PMID: 33758875 PMCID: PMC7987034 DOI: 10.1101/2021.03.08.21253157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
In the absence of an effective vaccine or monoclonal therapeutic, transfer of convalescent plasma (CCP) was proposed early in the SARS-CoV-2 pandemic as an easily accessible therapy. However, despite the global excitement around this historically valuable therapeutic approach, results from CCP trials have been mixed and highly debated. Unlike other therapeutic interventions, CCP represents a heterogeneous drug. Each CCP unit is unique and collected from an individual recovered COVID-19 patient, making the interpretation of therapeutic benefit more complicated. While the prevailing view in the field would suggest that it is administration of neutralizing antibodies via CCP that centrally provides therapeutic benefit to newly infected COVID-19 patients, many hospitalized COVID-19 patients already possess neutralizing antibodies. Importantly, the therapeutic benefit of antibodies can extend far beyond their simple ability to bind and block infection, especially related to their ability to interact with the innate immune system. In our work we deeply profiled the SARS-CoV-2-specific Fc-response in CCP donors, along with the recipients prior to and after CCP transfer, revealing striking SARS-CoV-2 specific Fc-heterogeneity across CCP units and their recipients. However, CCP units possessed more functional antibodies than acute COVID-19 patients, that shaped the evolution of COVID-19 patient humoral profiles via distinct immunomodulatory effects that varied by pre-existing SARS-CoV-2 Spike (S)-specific IgG titers in the patients. Our analysis identified surprising influence of both S and Nucleocapsid (N) specific antibody functions not only in direct antiviral activity but also in anti-inflammatory effects. These findings offer insights for more comprehensive interpretation of correlates of immunity in ongoing large scale CCP trials and for the design of next generation therapeutic design.
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Affiliation(s)
- Jonathan D. Herman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Division of Infectious Disease, Brigham and Women’s Hospital, Boston, MA, USA
| | - Chuangqi Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hyunah Yoon
- Division of Infectious Diseases, Department of Medicine. Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY,USA
| | - Johanna Rivera
- Division of Infectious Diseases, Department of Medicine. Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY,USA
- Department of Microbiology and Immunology. Albert Einstein College of Medicine, Bronx, NY, USA
| | - M. Eugenia Dieterle
- Department of Microbiology and Immunology. Albert Einstein College of Medicine, Bronx, NY, USA
| | - Denise Haslwanter
- Department of Microbiology and Immunology. Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rohit K. Jangra
- Department of Microbiology and Immunology. Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert H. Bortz
- Department of Microbiology and Immunology. Albert Einstein College of Medicine, Bronx, NY, USA
| | - Katharine J. Bar
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Boris Julg
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology. Albert Einstein College of Medicine, Bronx, NY, USA
| | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Liise-anne Pirofski
- Division of Infectious Diseases, Department of Medicine. Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY,USA
- Department of Microbiology and Immunology. Albert Einstein College of Medicine, Bronx, NY, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
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14
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Alter G, Gorman M, Patel N, Guebre-Xabier M, Zhu A, Atyeo C, Pullen K, Loos C, Goez-Gazi Y, Carrion R, Tian JH, Yuan D, Bowman K, Zhou B, Maciejewski S, McGrath M, Logue J, Frieman M, Montefiori D, Schendel S, Saphire EO, Lauffenburger D, Greene A, Portnoff A, Massare M, Ellingsworth L, Glenn G, Smith G, Mann C, Amanat F, Krammer F. Collaboration between the Fab and Fc contribute to maximal protection against SARS-CoV-2 following NVX-CoV2373 subunit vaccine with Matrix-M™ vaccination. Res Sq 2021:rs.3.rs-200342. [PMID: 33619473 PMCID: PMC7899467 DOI: 10.21203/rs.3.rs-200342/v1] [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] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recently approved vaccines have already shown remarkable protection in limiting SARS-CoV-2 associated disease. However, immunologic mechanism(s) of protection, as well as how boosting alters immunity to wildtype and newly emerging strains, remain incompletely understood. Here we deeply profiled the humoral immune response in a cohort of non-human primates immunized with a stable recombinant full-length SARS-CoV-2 spike (S) glycoprotein (NVX-CoV2373) at two dose levels, administered as a single or two-dose regimen with a saponin-based adjuvant Matrix-M™. While antigen dose had some effect on Fc-effector profiles, both antigen dose and boosting significantly altered overall titers, neutralization and Fc-effector profiles, driving unique vaccine-induced antibody fingerprints. Combined differences in antibody effector functions and neutralization were strongly associated with distinct levels of protection in the upper and lower respiratory tract, pointing to the presence of combined, but distinct, compartment-specific neutralization and Fc-mechanisms as key determinants of protective immunity against infection. Moreover, NVX-CoV2373 elicited antibodies functionally target emerging SARS-CoV-2 variants, collectively pointing to the critical collaborative role for Fab and Fc in driving maximal protection against SARS-CoV-2. Collectively, the data presented here suggest that a single dose may prevent disease, but that two doses may be essential to block further transmission of SARS-CoV-2 and emerging variants.
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Affiliation(s)
| | | | | | | | - Alex Zhu
- Ragon Institute of MGH, MIT, and Harvard
| | | | | | | | | | | | | | - Dansu Yuan
- Ragon Institute of MGH, MIT, and Harvard
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15
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Gorman MJ, Patel N, Guebre-Xabier M, Zhu A, Atyeo C, Pullen KM, Loos C, Goez-Gazi Y, Carrion R, Tian JH, Yaun D, Bowman K, Zhou B, Maciejewski S, McGrath ME, Logue J, Frieman MB, Montefiori D, Mann C, Schendel S, Amanat F, Krammer F, Saphire EO, Lauffenburger D, Greene AM, Portnoff AD, Massare MJ, Ellingsworth L, Glenn G, Smith G, Alter G. Collaboration between the Fab and Fc contribute to maximal protection against SARS-CoV-2 in nonhuman primates following NVX-CoV2373 subunit vaccine with Matrix-M™ vaccination. bioRxiv 2021:2021.02.05.429759. [PMID: 33564763 PMCID: PMC7872351 DOI: 10.1101/2021.02.05.429759] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recently approved vaccines have already shown remarkable protection in limiting SARS-CoV-2 associated disease. However, immunologic mechanism(s) of protection, as well as how boosting alters immunity to wildtype and newly emerging strains, remain incompletely understood. Here we deeply profiled the humoral immune response in a cohort of non-human primates immunized with a stable recombinant full-length SARS-CoV-2 spike (S) glycoprotein (NVX-CoV2373) at two dose levels, administered as a single or two-dose regimen with a saponin-based adjuvant Matrix-M™. While antigen dose had some effect on Fc-effector profiles, both antigen dose and boosting significantly altered overall titers, neutralization and Fc-effector profiles, driving unique vaccine-induced antibody fingerprints. Combined differences in antibody effector functions and neutralization were strongly associated with distinct levels of protection in the upper and lower respiratory tract, pointing to the presence of combined, but distinct, compartment-specific neutralization and Fc-mechanisms as key determinants of protective immunity against infection. Moreover, NVX-CoV2373 elicited antibodies functionally target emerging SARS-CoV-2 variants, collectively pointing to the critical collaborative role for Fab and Fc in driving maximal protection against SARS-CoV-2. Collectively, the data presented here suggest that a single dose may prevent disease, but that two doses may be essential to block further transmission of SARS-CoV-2 and emerging variants. HIGHLIGHTS NVX-CoV2373 subunit vaccine elicits receptor blocking, virus neutralizing antibodies, and Fc-effector functional antibodies.The vaccine protects against respiratory tract infection and virus shedding in non-human primates (NHPs).Both neutralizing and Fc-effector functions contribute to protection, potentially through different mechanisms in the upper and lower respiratory tract.Both macaque and human vaccine-induced antibodies exhibit altered Fc-receptor binding to emerging mutants.
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Affiliation(s)
- Matthew J Gorman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Nita Patel
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | - Alex Zhu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Krista M Pullen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yenny Goez-Gazi
- Texas Biomedical Research Institute. 8715 West Military Drive, San Antonio, TX 78227, USA
| | - Ricardo Carrion
- Texas Biomedical Research Institute. 8715 West Military Drive, San Antonio, TX 78227, USA
| | - Jing-Hui Tian
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Dansu Yaun
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Kathryn Bowman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Bin Zhou
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | - Marisa E McGrath
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD 21201, USA
| | - James Logue
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD 21201, USA
| | - Matthew B Frieman
- University of Maryland, School of Medicine, 685 West Baltimore St, Baltimore, MD 21201, USA
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Colin Mann
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | | | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ann M Greene
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | | | | | | | - Gregory Glenn
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Gale Smith
- Novavax, Inc., 21 Firstfield Road, Gaithersburg, MD 20878, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
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16
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Atyeo C, Pullen KM, Bordt EA, Fischinger S, Burke J, Michell A, Slein MD, Loos C, Shook LL, Boatin AA, Yockey LJ, Pepin D, Meinsohn MC, Nguyen NMP, Chauvin M, Roberts D, Goldfarb IT, Matute JD, James KE, Yonker LM, Bebell LM, Kaimal AJ, Gray KJ, Lauffenburger D, Edlow AG, Alter G. Compromised SARS-CoV-2-specific placental antibody transfer. Cell 2021; 184:628-642.e10. [PMID: 33476549 PMCID: PMC7755577 DOI: 10.1016/j.cell.2020.12.027] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [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: 08/28/2020] [Revised: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 infection causes more severe disease in pregnant women compared to age-matched non-pregnant women. Whether maternal infection causes changes in the transfer of immunity to infants remains unclear. Maternal infections have previously been associated with compromised placental antibody transfer, but the mechanism underlying this compromised transfer is not established. Here, we used systems serology to characterize the Fc profile of influenza-, pertussis-, and SARS-CoV-2-specific antibodies transferred across the placenta. Influenza- and pertussis-specific antibodies were actively transferred. However, SARS-CoV-2-specific antibody transfer was significantly reduced compared to influenza- and pertussis-specific antibodies, and cord titers and functional activity were lower than in maternal plasma. This effect was only observed in third-trimester infection. SARS-CoV-2-specific transfer was linked to altered SARS-CoV-2-antibody glycosylation profiles and was partially rescued by infection-induced increases in IgG and increased FCGR3A placental expression. These results point to unexpected compensatory mechanisms to boost immunity in neonates, providing insights for maternal vaccine design.
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Affiliation(s)
- Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA 02115, USA
| | - Krista M Pullen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Evan A Bordt
- Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; PhD Program in Immunology and Virology, University of Duisburg-Essen, Essen 47057, Germany
| | - John Burke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Ashlin Michell
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Matthew D Slein
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lydia L Shook
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Adeline A Boatin
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Laura J Yockey
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - David Pepin
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Marie-Charlotte Meinsohn
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ngoc Minh Phuong Nguyen
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Maeva Chauvin
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Drucilla Roberts
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ilona T Goldfarb
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Juan D Matute
- Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kaitlyn E James
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lael M Yonker
- Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lisa M Bebell
- Division of Infectious Diseases, Massachusetts General Hospital, MGH Global Health, and Harvard Medical School, Boston, MA 02114, USA
| | - Anjali J Kaimal
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kathryn J Gray
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrea G Edlow
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
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17
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Schmiester L, Schälte Y, Bergmann FT, Camba T, Dudkin E, Egert J, Fröhlich F, Fuhrmann L, Hauber AL, Kemmer S, Lakrisenko P, Loos C, Merkt S, Müller W, Pathirana D, Raimúndez E, Refisch L, Rosenblatt M, Stapor PL, Städter P, Wang D, Wieland FG, Banga JR, Timmer J, Villaverde AF, Sahle S, Kreutz C, Hasenauer J, Weindl D. PEtab-Interoperable specification of parameter estimation problems in systems biology. PLoS Comput Biol 2021; 17:e1008646. [PMID: 33497393 PMCID: PMC7864467 DOI: 10.1371/journal.pcbi.1008646] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 02/05/2021] [Accepted: 12/18/2020] [Indexed: 01/24/2023] Open
Abstract
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been-so far-no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies.
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Affiliation(s)
- Leonard Schmiester
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
| | - Yannik Schälte
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
| | | | - Tacio Camba
- Department of Applied Mathematics II, University of Vigo, Vigo, Galicia, Spain
- BioProcess Engineering Group, IIM-CSIC, Vigo, Galicia, Spain
| | - Erika Dudkin
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Janine Egert
- Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany
| | - Fabian Fröhlich
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lara Fuhrmann
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Adrian L. Hauber
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany
- Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Svenja Kemmer
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany
- Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Polina Lakrisenko
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
| | - Carolin Loos
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Simon Merkt
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Wolfgang Müller
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany
| | - Dilan Pathirana
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Elba Raimúndez
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Lukas Refisch
- Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany
| | - Marcus Rosenblatt
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany
- Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Paul L. Stapor
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
| | - Philipp Städter
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
| | - Dantong Wang
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
| | - Franz-Georg Wieland
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany
- Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Julio R. Banga
- BioProcess Engineering Group, IIM-CSIC, Vigo, Galicia, Spain
| | - Jens Timmer
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany
- Institute of Physics, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | | | - Sven Sahle
- BioQUANT/COS, Heidelberg University, Heidelberg, Germany
| | - Clemens Kreutz
- Faculty of Medicine and Medical Center, Institute of Medical Biometry and Statistics, University of Freiburg, Freiburg, Germany
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
- * E-mail:
| | - Daniel Weindl
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
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18
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Schuh L, Loos C, Pokrovsky D, Imhof A, Rupp RAW, Marr C. H4K20 Methylation Is Differently Regulated by Dilution and Demethylation in Proliferating and Cell-Cycle-Arrested Xenopus Embryos. Cell Syst 2020; 11:653-662.e8. [PMID: 33296683 DOI: 10.1016/j.cels.2020.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/05/2020] [Accepted: 11/11/2020] [Indexed: 11/26/2022]
Abstract
DNA replication during cell division leads to dilution of histone modifications and can thus affect chromatin-mediated gene regulation, raising the question of how the cell-cycle shapes the histone modification landscape, particularly during embryogenesis. We tackled this problem by manipulating the cell cycle during early Xenopus laevis embryogenesis and analyzing in vivo histone H4K20 methylation kinetics. The global distribution of un-, mono-, di-, and tri-methylated histone H4K20 was measured by mass spectrometry in normal and cell-cycle-arrested embryos over time. Using multi-start maximum likelihood optimization and quantitative model selection, we found that three specific biological methylation rate constants were required to explain the measured H4K20 methylation state kinetics. While demethylation is essential for regulating H4K20 methylation kinetics in non-cycling cells, demethylation is very likely dispensable in rapidly dividing cells of early embryos, suggesting that cell-cycle-mediated dilution of H4K20 methylation is an essential regulatory component for shaping its epigenetic landscape during early development. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Lea Schuh
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany; Department of Mathematics, Technical University of Munich, Garching 85748, Germany
| | - Carolin Loos
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany; Department of Mathematics, Technical University of Munich, Garching 85748, Germany; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniil Pokrovsky
- Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Axel Imhof
- Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Ralph A W Rupp
- Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Carsten Marr
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany.
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19
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Zohar T, Loos C, Fischinger S, Atyeo C, Wang C, Slein MD, Burke J, Yu J, Feldman J, Hauser BM, Caradonna T, Schmidt AG, Cai Y, Streeck H, Ryan ET, Barouch DH, Charles RC, Lauffenburger DA, Alter G. Compromised Humoral Functional Evolution Tracks with SARS-CoV-2 Mortality. Cell 2020; 183:1508-1519.e12. [PMID: 33207184 PMCID: PMC7608014 DOI: 10.1016/j.cell.2020.10.052] [Citation(s) in RCA: 210] [Impact Index Per Article: 52.5] [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: 07/27/2020] [Revised: 09/15/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022]
Abstract
The urgent need for an effective SARS-CoV-2 vaccine has forced development to progress in the absence of well-defined correlates of immunity. While neutralization has been linked to protection against other pathogens, whether neutralization alone will be sufficient to drive protection against SARS-CoV-2 in the broader population remains unclear. Therefore, to fully define protective humoral immunity, we dissected the early evolution of the humoral response in 193 hospitalized individuals ranging from moderate to severe. Although robust IgM and IgA responses evolved in both survivors and non-survivors with severe disease, non-survivors showed attenuated IgG responses, accompanied by compromised Fcɣ receptor binding and Fc effector activity, pointing to deficient humoral development rather than disease-enhancing humoral immunity. In contrast, individuals with moderate disease exhibited delayed responses that ultimately matured. These data highlight distinct humoral trajectories associated with resolution of SARS-CoV-2 infection and the need for early functional humoral immunity.
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Affiliation(s)
- Tomer Zohar
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA,PhD Program in Immunology and Virology, University of Duisburg-Essen, Essen, Germany
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA,PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA, USA
| | - Chuangqi Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - John Burke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard, Medical School, Boston, MA 02215, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Tim Caradonna
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Yongfei Cai
- Division of Molecular Medicine, Boston Children’s Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Hendrik Streeck
- Institute of Virology, University Hospital, University of Bonn and German Center for Infection Research (DZIF), Bonn-Cologne, Bonn, Germany
| | - Edward T. Ryan
- Infectious Disease Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard, Medical School, Boston, MA 02215, USA
| | - Richelle C. Charles
- Infectious Disease Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA,Corresponding author
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA,Corresponding author
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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20
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McMahan K, Yu J, Mercado NB, Loos C, Tostanoski LH, Chandrashekar A, Liu J, Peter L, Atyeo C, Zhu A, Bondzie EA, Dagotto G, Gebre MS, Jacob-Dolan C, Li Z, Nampanya F, Patel S, Pessaint L, Van Ry A, Blade K, Yalley-Ogunro J, Cabus M, Brown R, Cook A, Teow E, Andersen H, Lewis MG, Lauffenburger DA, Alter G, Barouch DH. Correlates of protection against SARS-CoV-2 in rhesus macaques. Nature 2020; 590:630-634. [PMID: 33276369 PMCID: PMC7906955 DOI: 10.1038/s41586-020-03041-6] [Citation(s) in RCA: 801] [Impact Index Per Article: 200.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 11/25/2020] [Indexed: 12/04/2022]
Abstract
Recent studies have reported protective efficacy of both natural immunity1 and vaccine-induced immunity2–7 against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge in rhesus macaques. However, the importance of humoral and cellular immunity for protection against SARS-CoV-2 infection remains to be determined. Here we show that adoptive transfer of purified IgG from convalescent macaques protects naïve recipient rhesus macaques against SARS-CoV-2 challenge in a dose dependent fashion. Depletion of CD8+ T cells in convalescent animals partially abrogated the protective efficacy of natural immunity against SARS-CoV-2 re-challenge, suggesting the importance of cellular immunity in the context of waning or subprotective antibody titers. These data demonstrate that relatively low antibody titers are sufficient for protection against SARS-CoV-2 in rhesus macaques, and that cellular immune responses may also contribute to protection if antibody responses are suboptimal. We also show that higher antibody titers are required for therapy of SARS-CoV-2 infection in macaques. These findings have important implications for the development of SARS-CoV-2 vaccines and immune-based therapeutics.
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Affiliation(s)
- Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Noe B Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lisa H Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Lauren Peter
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Alex Zhu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Esther A Bondzie
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Gabriel Dagotto
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Makda S Gebre
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Zhenfeng Li
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Felix Nampanya
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shivani Patel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. .,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.
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21
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Yu KK, Fischinger S, Smith MT, Atyeo C, Cizmeci D, Wolf CR, Layton ED, Logue JK, Aguilar MS, Shuey K, Loos C, Yu J, Franko N, Choi RY, Wald A, Barouch DH, Koelle DM, Lauffenburger D, Chu HY, Alter G, Seshadri C. T cell and antibody functional correlates of severe COVID-19. medRxiv 2020:2020.11.25.20235150. [PMID: 33269369 PMCID: PMC7709190 DOI: 10.1101/2020.11.25.20235150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 01/09/2023]
Abstract
Comorbid medical illnesses, such as obesity and diabetes, are associated with more severe COVID-19, hospitalization, and death. However, the role of the immune system in mediating these clinical outcomes has not been determined. We used multi-parameter flow cytometry and systems serology to comprehensively profile the functions of T cells and antibodies targeting spike, nucleocapsid, and envelope proteins in a convalescent cohort of COVID-19 subjects who were either hospitalized (n=20) or not hospitalized (n=40). To avoid confounding, subjects were matched by age, sex, ethnicity, and date of symptom onset. Surprisingly, we found that the magnitude and functional breadth of virus-specific CD4 T cell and antibody responses were consistently higher among hospitalized subjects, particularly those with medical comorbidities. However, an integrated analysis identified more coordination between polyfunctional CD4 T-cells and antibodies targeting the S1 domain of spike among subjects that were not hospitalized. These data reveal a functionally diverse and coordinated response between T cells and antibodies targeting SARS-CoV-2 which is reduced in the presence of comorbid illnesses that are known risk factors for severe COVID-19. Our data suggest that isolated measurements of the magnitudes of spike-specific immune responses are likely insufficient to anticipate vaccine efficacy in high-risk populations.
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Affiliation(s)
- Krystle K.Q. Yu
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- PhD program in Immunology and Virology, University of Duisburg-Essen, Essen, Germany
| | - Malisa T. Smith
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- PhD program in Virology, Division of Medical Sciences, Harvard University, Boston, MA, USA
| | - Deniz Cizmeci
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caitlin R. Wolf
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Erik D. Layton
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Jennifer K. Logue
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Melissa S. Aguilar
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Kiel Shuey
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Nicholas Franko
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Anna Wald
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dan H. Barouch
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David M. Koelle
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Benaroya Research Institute, Seattle, WA, USA
| | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helen Y. Chu
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
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22
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Tostanoski LH, Wegmann F, Martinot AJ, Loos C, McMahan K, Mercado NB, Yu J, Chan CN, Bondoc S, Starke CE, Nekorchuk M, Busman-Sahay K, Piedra-Mora C, Wrijil LM, Ducat S, Custers J, Atyeo C, Fischinger S, Burke JS, Feldman J, Hauser BM, Caradonna TM, Bondzie EA, Dagotto G, Gebre MS, Jacob-Dolan C, Lin Z, Mahrokhian SH, Nampanya F, Nityanandam R, Pessaint L, Porto M, Ali V, Benetiene D, Tevi K, Andersen H, Lewis MG, Schmidt AG, Lauffenburger DA, Alter G, Estes JD, Schuitemaker H, Zahn R, Barouch DH. Ad26 vaccine protects against SARS-CoV-2 severe clinical disease in hamsters. Nat Med 2020; 26:1694-1700. [PMID: 32884153 PMCID: PMC7671939 DOI: 10.1038/s41591-020-1070-6] [Citation(s) in RCA: 228] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022]
Abstract
Coronavirus disease 2019 (COVID-19) in humans is often a clinically mild illness, but some individuals develop severe pneumonia, respiratory failure and death1-4. Studies of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in hamsters5-7 and nonhuman primates8-10 have generally reported mild clinical disease, and preclinical SARS-CoV-2 vaccine studies have demonstrated reduction of viral replication in the upper and lower respiratory tracts in nonhuman primates11-13. Here we show that high-dose intranasal SARS-CoV-2 infection in hamsters results in severe clinical disease, including high levels of virus replication in tissues, extensive pneumonia, weight loss and mortality in a subset of animals. A single immunization with an adenovirus serotype 26 vector-based vaccine expressing a stabilized SARS-CoV-2 spike protein elicited binding and neutralizing antibody responses and protected against SARS-CoV-2-induced weight loss, pneumonia and mortality. These data demonstrate vaccine protection against SARS-CoV-2 clinical disease. This model should prove useful for preclinical studies of SARS-CoV-2 vaccines, therapeutics and pathogenesis.
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Affiliation(s)
- Lisa H Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Frank Wegmann
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | - Amanda J Martinot
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Noe B Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Chi N Chan
- Oregon Health & Sciences University, Beaverton, OR, USA
| | | | | | | | | | - Cesar Piedra-Mora
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Linda M Wrijil
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | - Sarah Ducat
- Tufts University Cummings School of Veterinary Medicine, North Grafton, MA, USA
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - John S Burke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Timothy M Caradonna
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Esther A Bondzie
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Gabriel Dagotto
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Makda S Gebre
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Zijin Lin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shant H Mahrokhian
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Felix Nampanya
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Ramya Nityanandam
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | | | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Jacob D Estes
- Oregon Health & Sciences University, Beaverton, OR, USA
| | | | - Roland Zahn
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.
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23
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Roy V, Fischinger S, Atyeo C, Slein M, Loos C, Balazs A, Luedemann C, Astudillo MG, Yang D, Wesemann DR, Charles R, Lafrate AJ, Feldman J, Hauser B, Caradonna T, Miller TE, Murali MR, Baden L, Nilles E, Ryan E, Lauffenburger D, Beltran WG, Alter G. SARS-CoV-2-specific ELISA development. J Immunol Methods 2020; 484-485:112832. [PMID: 32780998 PMCID: PMC7414735 DOI: 10.1016/j.jim.2020.112832] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/20/2020] [Accepted: 07/30/2020] [Indexed: 12/16/2022]
Abstract
Critical to managing the spread of COVID-19 is the ability to diagnose infection and define the acquired immune response across the population. While genomic tests for the novel Several Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) detect the presence of viral RNA for a limited time frame, when the virus is shed in the upper respiratory tract, tests able to define exposure and infection beyond this short window of detectable viral replication are urgently needed. Following infection, antibodies are generated within days, providing a durable read-out and archive of exposure and infection. Several antibody tests have emerged to diagnose SARS-CoV-2. Here we report on a qualified quantitative ELISA assay that displays all the necessary characteristics for high-throughput sample analysis. Collectively, this test offers a quantitative opportunity to define both exposure and levels of immunity to SARS-CoV-2.
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Affiliation(s)
- Vicky Roy
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, United States of America
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, United States of America
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, United States of America
| | - Matthew Slein
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, United States of America
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, United States of America; Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Alejandro Balazs
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, United States of America
| | - Corinne Luedemann
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, United States of America
| | - Michael Gerino Astudillo
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States of America
| | - Diane Yang
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States of America
| | - Duane R Wesemann
- Brigham and Women's Hospital, Boston, MA 02115, United States of America
| | - Richelle Charles
- Division of Infectious Disease, Massachusetts General Hospital, Boston, MA 02114, United States of America
| | - A John Lafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States of America
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, United States of America
| | - Blake Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, United States of America
| | - Tim Caradonna
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, United States of America
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States of America
| | - Mandakolathur R Murali
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States of America
| | - Lindsey Baden
- Brigham and Women's Hospital, Boston, MA 02115, United States of America
| | - Eric Nilles
- Brigham and Women's Hospital, Boston, MA 02115, United States of America
| | - Edward Ryan
- Division of Infectious Disease, Massachusetts General Hospital, Boston, MA 02114, United States of America
| | - Douglas Lauffenburger
- Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America
| | - Wilfredo Garcia Beltran
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, United States of America; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, United States of America
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, United States of America.
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24
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Yu J, Tostanoski LH, Peter L, Mercado NB, McMahan K, Mahrokhian SH, Nkolola JP, Liu J, Li Z, Chandrashekar A, Martinez DR, Loos C, Atyeo C, Fischinger S, Burke JS, Slein MD, Chen Y, Zuiani A, Lelis FJN, Travers M, Habibi S, Pessaint L, Van Ry A, Blade K, Brown R, Cook A, Finneyfrock B, Dodson A, Teow E, Velasco J, Zahn R, Wegmann F, Bondzie EA, Dagotto G, Gebre MS, He X, Jacob-Dolan C, Kirilova M, Kordana N, Lin Z, Maxfield LF, Nampanya F, Nityanandam R, Ventura JD, Wan H, Cai Y, Chen B, Schmidt AG, Wesemann DR, Baric RS, Alter G, Andersen H, Lewis MG, Barouch DH. DNA vaccine protection against SARS-CoV-2 in rhesus macaques. Science 2020; 369:806-811. [PMID: 32434945 PMCID: PMC7243363 DOI: 10.1126/science.abc6284] [Citation(s) in RCA: 817] [Impact Index Per Article: 204.3] [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: 05/05/2020] [Accepted: 05/16/2020] [Indexed: 12/22/2022]
Abstract
The global coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made the development of a vaccine a top biomedical priority. In this study, we developed a series of DNA vaccine candidates expressing different forms of the SARS-CoV-2 spike (S) protein and evaluated them in 35 rhesus macaques. Vaccinated animals developed humoral and cellular immune responses, including neutralizing antibody titers at levels comparable to those found in convalescent humans and macaques infected with SARS-CoV-2. After vaccination, all animals were challenged with SARS-CoV-2, and the vaccine encoding the full-length S protein resulted in >3.1 and >3.7 log10 reductions in median viral loads in bronchoalveolar lavage and nasal mucosa, respectively, as compared with viral loads in sham controls. Vaccine-elicited neutralizing antibody titers correlated with protective efficacy, suggesting an immune correlate of protection. These data demonstrate vaccine protection against SARS-CoV-2 in nonhuman primates.
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MESH Headings
- Adjuvants, Immunologic
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Betacoronavirus/immunology
- Betacoronavirus/physiology
- Bronchoalveolar Lavage Fluid/virology
- COVID-19
- COVID-19 Vaccines
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/virology
- Disease Models, Animal
- Female
- Humans
- Immunity, Cellular
- Immunity, Humoral
- Immunization, Secondary
- Immunogenicity, Vaccine
- Immunologic Memory
- Macaca mulatta
- Male
- Mutant Proteins/chemistry
- Mutant Proteins/immunology
- Nasal Mucosa/virology
- Pandemics/prevention & control
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/virology
- Protein Domains
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Vaccination
- Vaccines, DNA/administration & dosage
- Vaccines, DNA/immunology
- Viral Load
- Viral Vaccines/administration & dosage
- Viral Vaccines/immunology
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Affiliation(s)
- Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lisa H Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lauren Peter
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Noe B Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Shant H Mahrokhian
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Joseph P Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Zhenfeng Li
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | | | - John S Burke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Matthew D Slein
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Yuezhou Chen
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Adam Zuiani
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Felipe J N Lelis
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Meghan Travers
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shaghayegh Habibi
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | | | | - Roland Zahn
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | - Frank Wegmann
- Janssen Vaccines & Prevention BV, Leiden, Netherlands
| | - Esther A Bondzie
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Gabriel Dagotto
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Makda S Gebre
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Xuan He
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Marinela Kirilova
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Nicole Kordana
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Zijin Lin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lori F Maxfield
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Felix Nampanya
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ramya Nityanandam
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - John D Ventura
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | - Bing Chen
- Children's Hospital, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02215, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02215, USA
| | - Duane R Wesemann
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02215, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02215, USA
| | | | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02215, USA
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25
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Loos C, Lauffenburger DA, Alter G. Dissecting the antibody-OME: past, present, and future. Curr Opin Immunol 2020; 65:89-96. [PMID: 32755751 DOI: 10.1016/j.coi.2020.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/24/2020] [Indexed: 02/08/2023]
Abstract
Humoral immunity is key to protection for nearly all licensed vaccines. Yet, the design of vaccines has been more difficult for some of our most deadly killers (e.g. HIV, influenza, Dengue virus, etc.), likely due to our incomplete understanding of the precise immunological mechanisms associated with protection. Humoral immunity is governed both by B-cells and their bi-functional secreted antibodies, all of which have a unique capacity to evolve during an immune response. Current OMIC technologies capture individual features of the humoral immune response, providing a glimpse into humoral components (Fab/Fc/B-cell-omic), but fail to provide a wholistic view of the humoral response as a collective functional arm. Here, we dissect current OMIC strategies reviewing experimental and computational approaches, that if integrated could provide a true systems-level view of the humoral immune response.
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Affiliation(s)
- Carolin Loos
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Galit Alter
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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26
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Atyeo C, Fischinger S, Zohar T, Slein MD, Burke J, Loos C, McCulloch DJ, Newman KL, Wolf C, Yu J, Shuey K, Feldman J, Hauser BM, Caradonna T, Schmidt AG, Suscovich TJ, Linde C, Cai Y, Barouch D, Ryan ET, Charles RC, Lauffenburger D, Chu H, Alter G. Distinct Early Serological Signatures Track with SARS-CoV-2 Survival. Immunity 2020; 53:524-532.e4. [PMID: 32783920 PMCID: PMC7392190 DOI: 10.1016/j.immuni.2020.07.020] [Citation(s) in RCA: 266] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/29/2020] [Accepted: 07/23/2020] [Indexed: 10/27/2022]
Abstract
As SARS-CoV-2 infections and death counts continue to rise, it remains unclear why some individuals recover from infection, whereas others rapidly progress and die. Although the immunological mechanisms that underlie different clinical trajectories remain poorly defined, pathogen-specific antibodies often point to immunological mechanisms of protection. Here, we profiled SARS-CoV-2-specific humoral responses in a cohort of 22 hospitalized individuals. Despite inter-individual heterogeneity, distinct antibody signatures resolved individuals with different outcomes. Although no differences in SARS-CoV-2-specific IgG levels were observed, spike-specific humoral responses were enriched among convalescent individuals, whereas functional antibody responses to the nucleocapsid were elevated in deceased individuals. Furthermore, this enriched immunodominant spike-specific antibody profile in convalescents was confirmed in a larger validation cohort. These results demonstrate that early antigen-specific and qualitative features of SARS-CoV-2-specific antibodies point to differences in disease trajectory, highlighting the potential importance of functional antigen-specific humoral immunity to guide patient care and vaccine development.
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Affiliation(s)
- Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; PhD Program in Immunology and Virology, University of Duisburg-Essen, Essen, Germany
| | - Tomer Zohar
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew D Slein
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - John Burke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Kira L Newman
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Caitlin Wolf
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kiel Shuey
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Tim Caradonna
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | | | - Yongfei Cai
- Division of Molecular Medicine, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Dan Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Edward T Ryan
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Richelle C Charles
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helen Chu
- Department of Medicine, University of Washington, Seattle, WA, USA.
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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27
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Mercado NB, Zahn R, Wegmann F, Loos C, Chandrashekar A, Yu J, Liu J, Peter L, McMahan K, Tostanoski LH, He X, Martinez DR, Rutten L, Bos R, van Manen D, Vellinga J, Custers J, Langedijk JP, Kwaks T, Bakkers MJG, Zuijdgeest D, Rosendahl Huber SK, Atyeo C, Fischinger S, Burke JS, Feldman J, Hauser BM, Caradonna TM, Bondzie EA, Dagotto G, Gebre MS, Hoffman E, Jacob-Dolan C, Kirilova M, Li Z, Lin Z, Mahrokhian SH, Maxfield LF, Nampanya F, Nityanandam R, Nkolola JP, Patel S, Ventura JD, Verrington K, Wan H, Pessaint L, Van Ry A, Blade K, Strasbaugh A, Cabus M, Brown R, Cook A, Zouantchangadou S, Teow E, Andersen H, Lewis MG, Cai Y, Chen B, Schmidt AG, Reeves RK, Baric RS, Lauffenburger DA, Alter G, Stoffels P, Mammen M, Van Hoof J, Schuitemaker H, Barouch DH. Single-shot Ad26 vaccine protects against SARS-CoV-2 in rhesus macaques. Nature 2020; 586:583-588. [PMID: 32731257 PMCID: PMC7581548 DOI: 10.1038/s41586-020-2607-z] [Citation(s) in RCA: 637] [Impact Index Per Article: 159.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 07/24/2020] [Indexed: 11/09/2022]
Abstract
A safe and effective vaccine for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be required to end the coronavirus disease 2019 (COVID-19) pandemic1-8. For global deployment and pandemic control, a vaccine that requires only a single immunization would be optimal. Here we show the immunogenicity and protective efficacy of a single dose of adenovirus serotype 26 (Ad26) vector-based vaccines expressing the SARS-CoV-2 spike (S) protein in non-human primates. Fifty-two rhesus macaques (Macaca mulatta) were immunized with Ad26 vectors that encoded S variants or sham control, and then challenged with SARS-CoV-2 by the intranasal and intratracheal routes9,10. The optimal Ad26 vaccine induced robust neutralizing antibody responses and provided complete or near-complete protection in bronchoalveolar lavage and nasal swabs after SARS-CoV-2 challenge. Titres of vaccine-elicited neutralizing antibodies correlated with protective efficacy, suggesting an immune correlate of protection. These data demonstrate robust single-shot vaccine protection against SARS-CoV-2 in non-human primates. The optimal Ad26 vector-based vaccine for SARS-CoV-2, termed Ad26.COV2.S, is currently being evaluated in clinical trials.
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Affiliation(s)
- Noe B Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Roland Zahn
- Janssen Vaccines and Prevention BV, Leiden, The Netherlands
| | - Frank Wegmann
- Janssen Vaccines and Prevention BV, Leiden, The Netherlands
| | - Carolin Loos
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Lauren Peter
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Lisa H Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xuan He
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - David R Martinez
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lucy Rutten
- Janssen Vaccines and Prevention BV, Leiden, The Netherlands
| | - Rinke Bos
- Janssen Vaccines and Prevention BV, Leiden, The Netherlands
| | | | - Jort Vellinga
- Janssen Vaccines and Prevention BV, Leiden, The Netherlands
| | - Jerome Custers
- Janssen Vaccines and Prevention BV, Leiden, The Netherlands
| | | | - Ted Kwaks
- Janssen Vaccines and Prevention BV, Leiden, The Netherlands
| | | | | | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - John S Burke
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Timothy M Caradonna
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Esther A Bondzie
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Gabriel Dagotto
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Makda S Gebre
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Emily Hoffman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Marinela Kirilova
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Zhenfeng Li
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Zijin Lin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shant H Mahrokhian
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Lori F Maxfield
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Felix Nampanya
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Ramya Nityanandam
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Joseph P Nkolola
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shivani Patel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - John D Ventura
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kaylee Verrington
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Bing Chen
- Children's Hospital, Boston, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - R Keith Reeves
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Ralph S Baric
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Paul Stoffels
- Janssen Vaccines and Prevention BV, Leiden, The Netherlands
| | - Mathai Mammen
- Janssen Vaccines and Prevention BV, Leiden, The Netherlands
| | - Johan Van Hoof
- Janssen Vaccines and Prevention BV, Leiden, The Netherlands
| | | | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA. .,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.
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28
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Hass H, Loos C, Raimúndez-Álvarez E, Timmer J, Hasenauer J, Kreutz C. Benchmark problems for dynamic modeling of intracellular processes. Bioinformatics 2020; 35:3073-3082. [PMID: 30624608 PMCID: PMC6735869 DOI: 10.1093/bioinformatics/btz020] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/19/2018] [Accepted: 01/06/2019] [Indexed: 12/19/2022] Open
Abstract
Motivation Dynamic models are used in systems biology to study and understand cellular processes like gene regulation or signal transduction. Frequently, ordinary differential equation (ODE) models are used to model the time and dose dependency of the abundances of molecular compounds as well as interactions and translocations. A multitude of computational approaches, e.g. for parameter estimation or uncertainty analysis have been developed within recent years. However, many of these approaches lack proper testing in application settings because a comprehensive set of benchmark problems is yet missing. Results We present a collection of 20 benchmark problems in order to evaluate new and existing methodologies, where an ODE model with corresponding experimental data is referred to as problem. In addition to the equations of the dynamical system, the benchmark collection provides observation functions as well as assumptions about measurement noise distributions and parameters. The presented benchmark models comprise problems of different size, complexity and numerical demands. Important characteristics of the models and methodological requirements are summarized, estimated parameters are provided, and some example studies were performed for illustrating the capabilities of the presented benchmark collection. Availability and implementation The models are provided in several standardized formats, including an easy-to-use human readable form and machine-readable SBML files. The data is provided as Excel sheets. All files are available at https://github.com/Benchmarking-Initiative/Benchmark-Models, including step-by-step explanations and MATLAB code to process and simulate the models. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Helge Hass
- Center for Systems Biology (ZBSA), University of Freiburg, Freiburg 79104, Germany.,Institute of Physics, University of Freiburg, Freiburg 79104, Germany
| | - Carolin Loos
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg 85764, Germany.,Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Garching 85748, Germany
| | - Elba Raimúndez-Álvarez
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg 85764, Germany.,Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Garching 85748, Germany
| | - Jens Timmer
- Center for Systems Biology (ZBSA), University of Freiburg, Freiburg 79104, Germany.,Institute of Physics, University of Freiburg, Freiburg 79104, Germany.,Center for Data Analysis and Modelling (FDM), University of Freiburg, Freiburg 79104, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg 79104, Germany
| | - Jan Hasenauer
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg 85764, Germany.,Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Garching 85748, Germany
| | - Clemens Kreutz
- Center for Systems Biology (ZBSA), University of Freiburg, Freiburg 79104, Germany.,Institute of Physics, University of Freiburg, Freiburg 79104, Germany.,Center for Data Analysis and Modelling (FDM), University of Freiburg, Freiburg 79104, Germany
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29
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Loos C, Krause S, Hasenauer J. Hierarchical optimization for the efficient parametrization of ODE models. Bioinformatics 2019; 34:4266-4273. [PMID: 30010716 PMCID: PMC6289139 DOI: 10.1093/bioinformatics/bty514] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 01/14/2018] [Accepted: 07/10/2018] [Indexed: 11/14/2022] Open
Abstract
Motivation Mathematical models are nowadays important tools for analyzing dynamics of cellular processes. The unknown model parameters are usually estimated from experimental data. These data often only provide information about the relative changes between conditions, hence, the observables contain scaling parameters. The unknown scaling parameters and corresponding noise parameters have to be inferred along with the dynamic parameters. The nuisance parameters often increase the dimensionality of the estimation problem substantially and cause convergence problems. Results In this manuscript, we propose a hierarchical optimization approach for estimating the parameters for ordinary differential equation (ODE) models from relative data. Our approach restructures the optimization problem into an inner and outer subproblem. These subproblems possess lower dimensions than the original optimization problem, and the inner problem can be solved analytically. We evaluated accuracy, robustness and computational efficiency of the hierarchical approach by studying three signaling pathways. The proposed approach achieved better convergence than the standard approach and required a lower computation time. As the hierarchical optimization approach is widely applicable, it provides a powerful alternative to established approaches. Availability and implementation The code is included in the MATLAB toolbox PESTO which is available at http://github.com/ICB-DCM/PESTO. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Carolin Loos
- Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Chair of Mathematical Modeling of Biological Systems, Center for Mathematics, Technische Universität München, Garching, Germany
| | - Sabrina Krause
- Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Chair of Mathematical Modeling of Biological Systems, Center for Mathematics, Technische Universität München, Garching, Germany
| | - Jan Hasenauer
- Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Chair of Mathematical Modeling of Biological Systems, Center for Mathematics, Technische Universität München, Garching, Germany
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30
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Stratton S, Gerritsen A, Loos C, Urschel K. Effect of forage type and ration balancer protein content on measures of whole-body protein metabolism in growing horses consuming a predominantly forage diet. J Equine Vet Sci 2019. [DOI: 10.1016/j.jevs.2019.03.095] [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: 10/26/2022]
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31
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Loos C, Dorsch S, Gerritsen A, Urschel K. Effects of dietary protein level on muscle protein signaling pathways in horses. J Equine Vet Sci 2019. [DOI: 10.1016/j.jevs.2019.03.087] [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: 10/26/2022]
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32
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Stapor P, Weindl D, Ballnus B, Hug S, Loos C, Fiedler A, Krause S, Hroß S, Fröhlich F, Hasenauer J. PESTO: Parameter EStimation TOolbox. Bioinformatics 2019; 34:705-707. [PMID: 29069312 PMCID: PMC5860618 DOI: 10.1093/bioinformatics/btx676] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/20/2017] [Indexed: 11/15/2022] Open
Abstract
Summary PESTO is a widely applicable and highly customizable toolbox for parameter estimation in MathWorks MATLAB. It offers scalable algorithms for optimization, uncertainty and identifiability analysis, which work in a very generic manner, treating the objective function as a black box. Hence, PESTO can be used for any parameter estimation problem, for which the user can provide a deterministic objective function in MATLAB. Availability and implementation PESTO is a MATLAB toolbox, freely available under the BSD license. The source code, along with extensive documentation and example code, can be downloaded from https://github.com/ICB-DCM/PESTO/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Paul Stapor
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Center for Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Daniel Weindl
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Benjamin Ballnus
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Center for Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Sabine Hug
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Center for Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Carolin Loos
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Center for Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Anna Fiedler
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Center for Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Sabrina Krause
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Center for Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Sabrina Hroß
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Center for Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Fabian Fröhlich
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Center for Mathematics, Technische Universität München, 85748 Garching, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Center for Mathematics, Technische Universität München, 85748 Garching, Germany
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33
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Abstract
Ordinary differential equation models have become a standard tool for the mechanistic description of biochemical processes. If parameters are inferred from experimental data, such mechanistic models can provide accurate predictions about the behavior of latent variables or the process under new experimental conditions. Complementarily, inference of model structure can be used to identify the most plausible model structure from a set of candidates, and, thus, gain novel biological insight. Several toolboxes can infer model parameters and structure for small- to medium-scale mechanistic models out of the box. However, models for highly multiplexed datasets can require hundreds to thousands of state variables and parameters. For the analysis of such large-scale models, most algorithms require intractably high computation times. This chapter provides an overview of the state-of-the-art methods for parameter and model inference, with an emphasis on scalability.
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Affiliation(s)
- Fabian Fröhlich
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
| | - Carolin Loos
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Center for Mathematics, Technische Universität München, Garching, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany.
- Center for Mathematics, Technische Universität München, Garching, Germany.
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34
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Loos C, Dorsch S, Barnes T, Elzinga S, Adams A, Urschel K. PSXVI-5 A high protein meal affects plasma insulin concentrations and amino acid metabolism in horses with equine metabolic syndrome. J Anim Sci 2018. [DOI: 10.1093/jas/sky404.560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- C Loos
- University of Kentucky,Lexington, KY, United States
| | - S Dorsch
- University of Kentucky,Lexington, KY, United States
| | - T Barnes
- University of Kentucky,Lexington, KY, United States
| | - S Elzinga
- University of Michigan, East Lansing, MI, United States
| | - A Adams
- University of Kentucky,Lexington, KY, United States
| | - K Urschel
- University of Kentucky,Lexington, KY, United States
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35
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Loos C, Dorsch S, Gerritsen A, Barnes T, Urschel K. PSXIII-10 Effects of short-term dexamethasone administration on glucose and insulin dynamics and muscle protein signaling in horses after the consumption of a high protein meal. J Anim Sci 2018. [DOI: 10.1093/jas/sky404.548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- C Loos
- University of Kentucky,Lexington, KY, United States
| | - S Dorsch
- University of Kentucky,Lexington, KY, United States
| | - A Gerritsen
- University of Kentucky,Lexington, KY, United States
| | - T Barnes
- University of Kentucky,Lexington, KY, United States
| | - K Urschel
- University of Kentucky,Lexington, KY, United States
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36
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Loos C, Moeller K, Fröhlich F, Hucho T, Hasenauer J. A Hierarchical, Data-Driven Approach to Modeling Single-Cell Populations Predicts Latent Causes of Cell-To-Cell Variability. Cell Syst 2018; 6:593-603.e13. [DOI: 10.1016/j.cels.2018.04.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/28/2017] [Accepted: 04/10/2018] [Indexed: 12/23/2022]
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37
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Maier C, Loos C, Hasenauer J. Robust parameter estimation for dynamical systems from outlier-corrupted data. Bioinformatics 2017; 33:718-725. [PMID: 28062444 DOI: 10.1093/bioinformatics/btw703] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 11/04/2016] [Indexed: 11/13/2022] Open
Abstract
Motivation Dynamics of cellular processes are often studied using mechanistic mathematical models. These models possess unknown parameters which are generally estimated from experimental data assuming normally distributed measurement noise. Outlier corruption of datasets often cannot be avoided. These outliers may distort the parameter estimates, resulting in incorrect model predictions. Robust parameter estimation methods are required which provide reliable parameter estimates in the presence of outliers. Results In this manuscript, we propose and evaluate methods for estimating the parameters of ordinary differential equation models from outlier-corrupted data. As alternatives to the normal distribution as noise distribution, we consider the Laplace, the Huber, the Cauchy and the Student's t distribution. We assess accuracy, robustness and computational efficiency of estimators using these different distribution assumptions. To this end, we consider artificial data of a conversion process, as well as published experimental data for Epo-induced JAK/STAT signaling. We study how well the methods can compensate and discover artificially introduced outliers. Our evaluation reveals that using alternative distributions improves the robustness of parameter estimates. Availability and Implementation The MATLAB implementation of the likelihood functions using the distribution assumptions is available at Bioinformatics online. Contact jan.hasenauer@helmholtz-muenchen.de. Supplementary information Supplementary material are available at Bioinformatics online.
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Affiliation(s)
- Corinna Maier
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg 85764, Germany.,Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Garching 85748, Germany
| | - Carolin Loos
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg 85764, Germany.,Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Garching 85748, Germany
| | - Jan Hasenauer
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg 85764, Germany.,Technische Universität München, Center for Mathematics, Chair of Mathematical Modeling of Biological Systems, Garching 85748, Germany
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Fuchs A, Syrovets T, Loos C, Haas K, Simmet T. Nanoparticle treatment inhibits macrophage polarization towards the anti-inflammatory M2 subset. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)32794-0] [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: 11/26/2022]
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Runge CE, MacKenzie A, Loos C, Waller M, Gabbett M, Mills R, Eley D. Characteristics of Queensland physicians and the influence of rural exposure on practice location. Intern Med J 2016; 46:981-5. [DOI: 10.1111/imj.13156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 11/30/2022]
Affiliation(s)
- C. E. Runge
- Schools of Medicine; The University of Queensland; Brisbane Queensland Australia
| | - A. MacKenzie
- Schools of Public Health; The University of Queensland; Brisbane Queensland Australia
| | - C. Loos
- Schools of Public Health; The University of Queensland; Brisbane Queensland Australia
| | - M. Waller
- Schools of Public Health; The University of Queensland; Brisbane Queensland Australia
| | - M. Gabbett
- Schools of Medicine; The University of Queensland; Brisbane Queensland Australia
- Genetic Health Queensland; Royal Brisbane & Women's Hospital; Brisbane Queensland Australia
- The Royal Australasian College of Physicians; Sydney New South Wales Australia
- School of Medicine; Griffith University; Nathan Queensland Australia
| | - R. Mills
- Office of the Principal Medical Officer; Queensland Health; Brisbane Queensland Australia
| | - D. Eley
- Schools of Medicine; The University of Queensland; Brisbane Queensland Australia
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Loos C, Buhr H, Blendl C. Investigation of the performance of digital mammographic X-ray equipment: determination of noise equivalent quanta (NEQQC) and detective quantum efficiency (DQEQC) compared with the automated analysis of CDMAM test images with CDCOM and CDIC programs. ROFO-FORTSCHR RONTG 2013; 185:635-43. [PMID: 23801376 DOI: 10.1055/s-0033-1335220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
PURPOSE The purpose of this study was to determine the values for noise equivalent quanta, detective quantum efficiency, modulation transfer function, noise power spectrum, and the values for the parameters for automated CDMAM test phantom analyses required to achieve satisfactory quality of digital mammograms. MATERIALS AND METHODS During the course of tests according to PAS 1054 (8 CR and 12 DR systems), test images were made with a test phantom insertion plate containing two lead edges in nearly horizontal and vertical directions. Only original data were processed with a program that was developed at the Cologne University of Applied Sciences (FH-Köln). All equipment systems complied with the requirements regarding visual recognition of gold-plated mammo detail test objects. CDMAM test images were also evaluated using the CDIC (CUAS) and CDCOM (EUREF) programs. RESULTS CDMAM test images show comparable values for the parameters, precision, sensitivity and specificity. DR systems require about half the dose used for CR systems for similar results. The NEQ values achieved with the dose used for the CDMAM test images show larger scatter ranges. The MTF of the different equipment system types differ significantly from each other. CONCLUSION Visual evaluation of CDMAM test images can be replaced by automated evaluation. Limiting values were determined for each parameter. Automated evaluation of CDMAM test phantom images should be used to determine the physical parameter NEQQC. This method is much more sensitive to noise and sharpness influences and has a higher validity than diagnostic methods. Automated evaluation objectivizes testing.
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Affiliation(s)
- C Loos
- Institut für Medien- und Phototechnik, Fachhochschule, Köln, Betzdorfer Str. 2, 50679 Köln, Germany.
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Redon E, Bursztejn AC, Loos C, Barbaud A, Schmutz JL. [A retrospective efficacy and safety study of UVB-TL01 phototherapy and PUVA therapy in palmoplantar psoriasis]. Ann Dermatol Venereol 2010; 137:597-603. [PMID: 20932438 DOI: 10.1016/j.annder.2010.06.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Revised: 05/31/2010] [Accepted: 06/22/2010] [Indexed: 11/30/2022]
Abstract
BACKGROUND Topical therapy is generally insufficient in palmoplantar psoriasis. UVBTL01 phototherapy is a therapeutic alternative and we conducted a retrospective study of the efficacy and safety of this approach and of PUVA therapy in palmoplantar psoriasis. PATIENTS AND METHODS All patients treated with UVBTL01 or PUVA therapy from November 2001 to April 2008 were included in the study. Phototherapy was given three times a week. Evaluation was performed after 20 sessions, again after 30 sessions and then at the end of the treatment. Therapeutic outcome was classed as "failure", "slight improvement" or "improvement or clear skin". RESULTS UVBTL01 phototherapy and PUVA therapy were effective, with "improvement or clear skin" in respectively 52% and 61% of cases and "slight improvement" in 16% and 23% of cases at the end of the treatment. With UVBTL01, adverse effects occurred in 20% of cases (erythema 18%, first-degree burns 7%) and treatment was discontinued as a result in only 4% of cases. Adverse effects occurred in 50% in patients on PUVA therapy, mainly due to methoxypsoralen intake. CONCLUSION UVBTL01 phototherapy and PUVA therapy are efficacious treatments in palmoplantar psoriasis; UVBTL01 phototherapy involves fewer constraints and has fewer adverse effects.
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Affiliation(s)
- E Redon
- Hôpital Fournier, CHU de Nancy, France.
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Abstract
PURPOSE To test the sensitivity of automatic methods for evaluating CDMAM test images with respect to noise. MATERIALS AND METHODS CDMAM test images were analyzed with two computer programs. The images were made with different tube loads [mAs]. The other exposure conditions remained constant. They were analyzed with the CDCOM program, which is offered by the EUREF as a free download, and with the CDMAM Image Checker (CDIC), which was developed by the authors. RESULTS The determination of the sensitivity in one image always delivers the same result when the same type of computer program is used. This means that the precision of both programs is sufficient. The dose sensitivity of CDIC is two times higher than the sensitivity of CDCOM. However, the required entrance dose (ESAK) for a faultless evaluation with the CDIC program is in the range of 10 mGy. The nominal sensitivity values for the CDCOM program attain a higher level. Differences in dose of more than 5 % should be detectable by both programs. CONCLUSION Methods that dispense with visual inspections to determine the performance of X-ray units for mammography can be applied in the acceptance test or the yearly constancy tests according to the German X-ray directive ( section sign 16). The CDCOM program cannot be characterized fully because the data is not complete. Finally the detection methods are not clear. Therefore, the CDCOM program can be called a black box method, while the CDIC has to be called an open source method (general public license).
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Affiliation(s)
- C Blendl
- Institut für Medien- und Phototechnik, Fachhochschule Köln.
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Perret-Guillaume C, Loos C, Erpelding M, Frimat L, Briancon S, Leplege A. Le WHOQOL-OLD, un nouvel outil pour évaluer la qualité de vie des sujets âgés : application à des patients insuffisants rénaux dialysés. Rev Med Interne 2009. [DOI: 10.1016/j.revmed.2009.03.041] [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: 11/30/2022]
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Abstract
This paper describes the planning of a community-based approach to injury control and safety promotion, the Kolan Injury Prevention Program. The process involved the establishment of a local steering committee, 11 months of injury surveillance, a critical review of the evidence base, community consultations and assessment of community resources. There were 412 recorded injury cases during the surveillance period, with higher rates among men, manual workers, those aged 15-34 years, sport/leisure activities and around the home and farm. Salient issues for residents included a lack of access to safety information and skills, particularly with regard to first aid and bush fire for isolated residents and rurally inexperienced new residents. While injury prevention was identified as an important issue for the community, the rapidly changing size and nature of the community and its infrastructure made this a particularly challenging issue. Challenges included limited availability of volunteers from key sectors, lack of formal data collection systems, difficulties in mobilising support for a broad issue like injury, limited communication networks and the negative impact of distance and role uncertainty on community ownership of the program. This case study illustrates the steps involved in an effective community-based needs assessment addressing injury prevention. Such an approach, if carried out systematically, will help ensure that the strategies and programs developed will be both appropriate and likely to obtain the support of the local community.
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Affiliation(s)
- C Loos
- Department of Social and Preventive Medicine, University of Queensland, School of Public Health, Queensland University of Technology and University of the Sunshine Coast, Queensland, Australia
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McGrath P, Patterson C, Yates P, Treloar S, Oldenburg B, Loos C. A study of postdiagnosis breast cancer concerns for women living in rural and remote Queensland. Part II: Support issues. Aust J Rural Health 1999; 7:43-52. [PMID: 10373815 DOI: 10.1046/j.1440-1584.1999.00216.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This paper presents the recent findings from a study on the postdiagnosis support needs of women with breast cancer living in rural and remote Queensland. The findings presented in this discussion focus on support needs from the perspective of the women experiencing breast cancer as well as health service providers. The tyranny of distance imposes unique hardships, such as separation from family and friends, during a time of great vulnerability for treatment, the need to travel long distances for support and follow-up services, and extra financial burdens, which can combine to cause strains on the marital relationship and family cohesion. Positive indications are, however, that the rural communities operate on strong, informal networks of support. This network of family, friends and community can, and does, play an active role in the provision of emotional and practical support.
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Affiliation(s)
- P McGrath
- Centre for Public Health Research, Queensland University of Technology, Kelvin Grove, Red Hill, Australia.
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McGrath P, Patterson C, Yates P, Treloar S, Oldenburg B, Loos C. A study of postdiagnosis breast cancer concerns for women living in rural and remote Queensland. Part I: Personal concerns. Aust J Rural Health 1999; 7:34-42. [PMID: 10373814 DOI: 10.1046/j.1440-1584.1999.00214.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The findings presented in this paper are part of a research project designed to provide a preliminary indication of the support needs of postdiagnosis women with breast cancer in remote and isolated areas in Queensland. This discussion will present data that focuses on the women's expressed personal concerns. For participants in this research a diagnosis of breast cancer involves a confrontation with their own mortality and the possibility of a reduced life span. This is a definite life crisis, creating shock and needing considerable adjustment. Along with these generic issues the participants also articulated significant issues in relation to their experience as women in a rural setting. These concerns centred around worries about how their partner and families cope during their absences for treatment, the additional burden on the family of having to cope with running the property or farm during the participant's absence or illness, added financial strain brought about by the cost of travel for treatment, maintenance of properties during absences, and problems created by time off from properties or self-employment. These findings accord with other reports of health and welfare services for rural Australian and the generic literature on psycho-oncology studies of breast cancer.
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Affiliation(s)
- P McGrath
- Centre for Public Health Research, Queensland University of Technology, Kelvin Grove, Red Hill, Australia.
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Abstract
A conceptual model for planning adolescent prenatal programs was developed that anticipated future trends, was easily modifiable, and fostered community self-direction (Loos & Morton, 1996). However, the model's reliability with diverse groups in atypical settings required testing. Validation of its reliability focused on adolescent Aboriginal women living in an isolated northern community. Use of the model helped identify modifications in program design, implementation, and evaluation to meet the ethno-cultural, socioeconomic, and age-related needs differences of this population, suggesting that this model is an effective tool for program development.
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Affiliation(s)
- C Loos
- C ynthia L oos is a Professor and A
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Loos C, Bowd A. Caregivers of persons with Alzheimer's disease: some neglected implications of the experience of personal loss and grief. Death Stud 1997; 21:501-514. [PMID: 10175165 DOI: 10.1080/074811897201840] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
This article questions some traditional conceptualizations of caregivers of persons with Alzheimer's disease and related dementias (AD). The phenomenology of caregiving in rural and isolated regions of northern Canada is examined within a framework developed from the constructs of personal loss and grief. Sixty-eight caregivers for persons with AD shared their thoughts and feelings about personal losses perceived to have occurred in their lives with the advent of the caregiving role. Four themes were identified suggesting a role perceived by caregivers as one in which they become subsumed to the needs of the person in care. Diminution of self in the caregiver role has been neglected in the literature.
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Affiliation(s)
- C Loos
- School of Nursing, Lakehead University, Thunder Bay, Ontario, Canada
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Morton AM, Loos C. Does universal health care coverage mean universal accessibility? Examining the Canadian experience of poor, prenatal women. Womens Health Issues 1995; 5:139-42. [PMID: 7549492 DOI: 10.1016/1049-3867(95)00037-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- A M Morton
- School of Nursing, Lakehead University, Thunder Bay, Ontario, Canada
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Favuzzi C, Maggi G, Nappi E, Posa F, Ranieri A, Selvaggi G, Spinelli P, Bamberger A, Fuchs M, Heck W, Loos C, Marx R, Runge K, Skodzek E, Weber C, Wülker M, Zetsche F, Artemiev V, Galaktionov Y, Gordeev A, Gorodkov Y, Kamyshkov Y, Plyaskin V, Pojidaev V, Shevchenko V, Shumilov E, Tchudakov V, Bunn J, Fent J, Freund P, Gebauer J, Glas M, Polakos P, Pretzl K, Schouten T, Seyboth P, Seyerlein J, Vesztergombi G. Measurement of the production of high-mass gamma gamma, pi 0 pi 0, and gamma pi 0 pairs in pi -p, pi +p, and pp collisions at 300 GeV/c. Phys Rev D Part Fields 1990; 42:748-758. [PMID: 10012895 DOI: 10.1103/physrevd.42.748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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