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Shinde P, Soldevila F, Reyna J, Aoki M, Rasmussen M, Willemsen L, Kojima M, Ha B, Greenbaum JA, Overton JA, Guzman-Orozco H, Nili S, Orfield S, Gygi JP, da Silva Antunes R, Sette A, Grant B, Olsen LR, Konstorum A, Guan L, Ay F, Kleinstein SH, Peters B. A multi-omics systems vaccinology resource to develop and test computational models of immunity. CELL REPORTS METHODS 2024; 4:100731. [PMID: 38490204 PMCID: PMC10985234 DOI: 10.1016/j.crmeth.2024.100731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/04/2024] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Systems vaccinology studies have identified factors affecting individual vaccine responses, but comparing these findings is challenging due to varying study designs. To address this lack of reproducibility, we established a community resource for comparing Bordetella pertussis booster responses and to host annual contests for predicting patients' vaccination outcomes. We report here on our experiences with the "dry-run" prediction contest. We found that, among 20+ models adopted from the literature, the most successful model predicting vaccination outcome was based on age alone. This confirms our concerns about the reproducibility of conclusions between different vaccinology studies. Further, we found that, for newly trained models, handling of baseline information on the target variables was crucial. Overall, multiple co-inertia analysis gave the best results of the tested modeling approaches. Our goal is to engage community in these prediction challenges by making data and models available and opening a public contest in August 2024.
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Affiliation(s)
- Pramod Shinde
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ferran Soldevila
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Joaquin Reyna
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, San Diego, CA, USA
| | - Minori Aoki
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mikkel Rasmussen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lisa Willemsen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mari Kojima
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Brendan Ha
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jason A Greenbaum
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - James A Overton
- Knocean Inc., 107 Quebec Avenue, Toronto, Ontario M6P 2T3, Canada
| | - Hector Guzman-Orozco
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Somayeh Nili
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Shelby Orfield
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jeremy P Gygi
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Barry Grant
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Lars Rønn Olsen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Konstorum
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Leying Guan
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Ferhat Ay
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Steven H Kleinstein
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, San Diego, CA, USA.
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Shinde P, Soldevila F, Reyna J, Aoki M, Rasmussen M, Willemsen L, Kojima M, Ha B, Greenbaum JA, Overton JA, Guzman-Orozco H, Nili S, Orfield S, Gygi JP, da Silva Antunes R, Sette A, Grant B, Olsen LR, Konstorum A, Guan L, Ay F, Kleinstein SH, Peters B. A systems vaccinology resource to develop and test computational models of immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555193. [PMID: 37693565 PMCID: PMC10491180 DOI: 10.1101/2023.08.28.555193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Computational models that predict an individual's response to a vaccine offer the potential for mechanistic insights and personalized vaccination strategies. These models are increasingly derived from systems vaccinology studies that generate immune profiles from human cohorts pre- and post-vaccination. Most of these studies involve relatively small cohorts and profile the response to a single vaccine. The ability to assess the performance of the resulting models would be improved by comparing their performance on independent datasets, as has been done with great success in other areas of biology such as protein structure predictions. To transfer this approach to system vaccinology studies, we established a prototype platform that focuses on the evaluation of Computational Models of Immunity to Pertussis Booster vaccinations (CMI-PB). A community resource, CMI-PB generates experimental data for the explicit purpose of model evaluation, which is performed through a series of annual data releases and associated contests. We here report on our experience with the first such 'dry run' for a contest where the goal was to predict individual immune responses based on pre-vaccination multi-omic profiles. Over 30 models adopted from the literature were tested, but only one was predictive, and was based on age alone. The performance of new models built using CMI-PB training data was much better, but varied significantly based on the choice of pre-vaccination features used and the model building strategy. This suggests that previously published models developed for other vaccines do not generalize well to Pertussis Booster vaccination. Overall, these results reinforced the need for comparative analysis across models and datasets that CMI-PB aims to achieve. We are seeking wider community engagement for our first public prediction contest, which will open in early 2024.
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Affiliation(s)
- Pramod Shinde
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ferran Soldevila
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Joaquin Reyna
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, CA, USA
| | - Minori Aoki
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mikkel Rasmussen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lisa Willemsen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mari Kojima
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Brendan Ha
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jason A Greenbaum
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - James A Overton
- Knocean Inc., 107 Quebec Ave. Toronto, Ontario, M6P 2T3, Canada
| | - Hector Guzman-Orozco
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Somayeh Nili
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Shelby Orfield
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jeremy P. Gygi
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Barry Grant
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Lars Rønn Olsen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Konstorum
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Leying Guan
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Ferhat Ay
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Steven H. Kleinstein
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, San Diego, CA, USA
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Yin Z, Zheng C, Fang Q, Wen T, Wang S, Li J, Gong X, Xiang Z. Comparing the pertussis antibody levels of healthy children immunized with four doses of DTap-IPV/Hib (Pentaxim) combination vaccine and DTaP vaccine in Quzhou, China. Front Immunol 2023; 13:1055677. [PMID: 36685526 PMCID: PMC9852981 DOI: 10.3389/fimmu.2022.1055677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/16/2022] [Indexed: 01/09/2023] Open
Abstract
Despite the high coverage of pertussis vaccines in high-income countries, pertussis resurgence has been reported in recent years, and has stimulated interest in the effects of vaccines and vaccination strategies. Immunoglobulin G (IgG) antibodies against pertussis toxoid (PT), filamentous hemagglutinin (FHA), and pertactin (PRN) after immunization with four doses of co-purified or component vaccines were determined by enzyme-linked immunosorbent assay (ELISA). Serological data of PT-IgG geometric mean concentrations (GMCs) over time since vaccination were used to fit the mathematical models. A total of 953 children were included in this study; 590 participants received four doses of the component acellular vaccine and 363 participants received four doses of the co-purified acellular vaccine. The GMCs and the seropositivity rate of pertussis IgG were significantly influenced by the production methods, and the immunogenicity of the component acellular vaccine was superior to that of the co-purified acellular vaccine. The fitted mathematical models for the component acellular vaccine and the co-purified acellular vaccine were Y=91.20e-0.039x and Y=37.71x-0.493, respectively. The initial GMCs of the component acellular vaccine was higher than that of the co-purified acellular vaccine, but both were similar at 72 months after immunization. Pertussis IgG levels waned over time after four doses of acellular pertussis vaccine, regardless of whether component or co-purified vaccine was used. The development and promotion of component acellular pertussis vaccines should be accelerated in China, and booster doses of pertussis vaccine in adolescents, adults, and pregnant women should be employed.
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Affiliation(s)
- Zhiying Yin
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang, China,School of Public Health, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China,*Correspondence: Zhiying Yin, ; Ziling Xiang,
| | - Canjie Zheng
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang, China
| | - Quanjun Fang
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang, China
| | - Tingcui Wen
- School of Public Health, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Shuangqing Wang
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang, China
| | - Junji Li
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang, China
| | - Xiaoying Gong
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang, China
| | - Ziling Xiang
- Department of Immunity, Quzhou Center for Disease Control and Prevention, Quzhou, Zhejiang, China,*Correspondence: Zhiying Yin, ; Ziling Xiang,
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Szwejser-Zawislak E, Wilk MM, Piszczek P, Krawczyk J, Wilczyńska D, Hozbor D. Evaluation of Whole-Cell and Acellular Pertussis Vaccines in the Context of Long-Term Herd Immunity. Vaccines (Basel) 2022; 11:vaccines11010001. [PMID: 36679846 PMCID: PMC9863224 DOI: 10.3390/vaccines11010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/04/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
After the pertussis vaccine had been introduced in the 1940s and was shown to be very successful in reducing the morbidity and mortality associated with the disease, the possibility of improving both vaccine composition and vaccination schedules has become the subject of continuous interest. As a result, we are witnessing a considerable heterogeneity in pertussis vaccination policies, which remains beyond universal consensus. Many pertussis-related deaths still occur in low- and middle-income countries; however, these deaths are attributable to gaps in vaccination coverage and limited access to healthcare in these countries, rather than to the poor efficacy of the first generation of pertussis vaccine consisting in inactivated and detoxified whole cell pathogen (wP). In many, particularly high-income countries, a switch was made in the 1990s to the use of acellular pertussis (aP) vaccine, to reduce the rate of post-vaccination adverse events and thereby achieve a higher percentage of children vaccinated. However the epidemiological data collected over the past few decades, even in those high-income countries, show an increase in pertussis prevalence and morbidity rates, triggering a wide-ranging debate on the causes of pertussis resurgence and the effectiveness of current pertussis prevention strategies, as well as on the efficacy of available pertussis vaccines and immunization schedules. The current article presents a systematic review of scientific reports on the evaluation of the use of whole-cell and acellular pertussis vaccines, in the context of long-term immunity and vaccines efficacy.
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Affiliation(s)
- Ewa Szwejser-Zawislak
- Institute of Biotechnology of Serums and Vaccines Biomed, Al. Sosnowa 8, 30-224 Krakow, Poland
| | - Mieszko M. Wilk
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Piotr Piszczek
- Institute of Biotechnology of Serums and Vaccines Biomed, Al. Sosnowa 8, 30-224 Krakow, Poland
| | - Justyna Krawczyk
- Institute of Biotechnology of Serums and Vaccines Biomed, Al. Sosnowa 8, 30-224 Krakow, Poland
| | - Daria Wilczyńska
- Institute of Biotechnology of Serums and Vaccines Biomed, Al. Sosnowa 8, 30-224 Krakow, Poland
| | - Daniela Hozbor
- VacSal Laboratory, Institute of Biotechnology and Molecular Biology, Faculty of Sciences, National University of La Plata (UNLP), National Council for Scientific and Technical Research (CONICET), La Plata 1900, Argentina
- Correspondence:
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da Silva Antunes R, Soldevila F, Pomaznoy M, Babor M, Bennett J, Tian Y, Khalil N, Qian Y, Mandava A, Scheuermann RH, Cortese M, Pulendran B, Petro CD, Gilkes AP, Purcell LA, Sette A, Peters B. A system-view of Bordetella pertussis booster vaccine responses in adults primed with whole-cell versus acellular vaccine in infancy. JCI Insight 2021; 6:141023. [PMID: 33690224 PMCID: PMC8119213 DOI: 10.1172/jci.insight.141023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 03/03/2021] [Indexed: 01/26/2023] Open
Abstract
The increased incidence of whooping cough worldwide suggests that current vaccination against Bordetella pertussis infection has limitations in quality and duration of protection. The resurgence of infection has been linked to the introduction of acellular vaccines (aP), which have an improved safety profile compared with the previously used whole-cell (wP) vaccines. To determine immunological differences between aP and wP priming in infancy, we performed a systems approach of the immune response to booster vaccination. Transcriptomic, proteomic, cytometric, and serologic profiling revealed multiple shared immune responses with different kinetics across cohorts, including an increase of blood monocyte frequencies and strong antigen-specific IgG responses. Additionally, we found a prominent subset of aP-primed individuals (30%) with a strong differential signature, including higher levels of expression for CCL3, NFKBIA, and ICAM1. Contrary to the wP individuals, this subset displayed increased PT-specific IgE responses after boost and higher antigen-specific IgG4 and IgG3 antibodies against FHA and FIM2/3 at baseline and after boost. Overall, the results show that, while broad immune response patterns to Tdap boost overlap between aP- and wP-primed individuals, a subset of aP-primed individuals present a divergent response. These findings provide candidate targets to study the causes and correlates of waning immunity after aP vaccination.
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Affiliation(s)
- Ricardo da Silva Antunes
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Ferran Soldevila
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Mikhail Pomaznoy
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Mariana Babor
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Jason Bennett
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Yuan Tian
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Natalie Khalil
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Yu Qian
- J. Craig Venter Institute, La Jolla, California, USA
| | | | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, California, USA
- University of California San Diego School of Medicine, La Jolla, California, USA
| | - Mario Cortese
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Bali Pulendran
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | | | | | | | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
- University of California San Diego School of Medicine, La Jolla, California, USA
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