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Bello N, Hudu SA, Alshrari AS, Imam MU, Jimoh AO. Overview of Hepatitis B Vaccine Non-Response and Associated B Cell Amnesia: A Scoping Review. Pathogens 2024; 13:554. [PMID: 39057781 PMCID: PMC11279426 DOI: 10.3390/pathogens13070554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND The advent of the hepatitis B vaccine has achieved tremendous success in eradicating and reducing the burden of hepatitis B infection, which is the main culprit for hepatocellular carcinoma-one of the most fatal malignancies globally. Response to the vaccine is achieved in about 90-95% of healthy individuals and up to only 50% in immunocompromised patients. This review aimed to provide an overview of hepatitis B vaccine non-response, the mechanisms involved, B cell amnesia, and strategies to overcome it. METHODS Databases, including Google Scholar, PubMed, Scopus, Cochrane, and ClinicalTrials.org, were used to search and retrieve articles using keywords on hepatitis B vaccine non-response and B cell amnesia. The PRISMA guideline was followed in identifying studies, screening, selection, and reporting of findings. RESULTS A total of 133 studies on hepatitis B vaccine non-response, mechanisms, and prevention/management strategies were included in the review after screening and final selection. Factors responsible for hepatitis B vaccine non-response were found to include genetic, immunological factors, and B cell amnesia in healthy individuals. The genetic factors were sex, HLA haplotypes, and genetic polymorphisms in immune response markers (cytokines). Non-response was common in conditions of immunodeficiency, such as renal failure, haemodialysis, celiac disease, inflammatory bowel disease, hepatitis C co-infection, and latent hepatitis B infection. Others included diabetes mellitus and HIV infection. The mechanisms involved were impaired immune response by suppression of response (T helper cells) or induced suppression of response (through regulatory B and T cells). DISCUSSION A comprehensive and careful understanding of the patient factors and the nature of the vaccine contributes to developing effective preventive measures. These include revaccination or booster dose, vaccine administration through the intradermal route, and the use of adjuvants in the vaccine.
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Affiliation(s)
- Nura Bello
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto 840232, Nigeria;
- Department of Pharmacology and Therapeutics, Faculty of Pharmaceutical Sciences, Ahmadu Bello University, Zaria 810107, Nigeria
| | - Shuaibu A. Hudu
- Department of Basic Medical and Dental Sciences, Faculty of Dentistry, Zarqa University, Zarqa 13110, Jordan
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto 840232, Nigeria
| | - Ahmed S. Alshrari
- Medical Laboratory Technology Department, Faculty of Applied Medical Science, Northern Border University, Arar 91431, Saudi Arabia;
| | - Mustapha U. Imam
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, Sokoto 840232, Nigeria;
| | - Abdulgafar O. Jimoh
- Department of Pharmacology and Therapeutics, Faculty of Basic Clinical Sciences, College of Health Sciences, Usmanu Danfodiyo University, Sokoto 840232, Nigeria;
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Papadatou I, Geropeppa M, Piperi C, Spoulou V, Adamopoulos C, Papavassiliou AG. Deciphering Immune Responses to Immunization via Transcriptional Analysis: A Narrative Review of the Current Evidence towards Personalized Vaccination Strategies. Int J Mol Sci 2024; 25:7095. [PMID: 39000206 PMCID: PMC11240890 DOI: 10.3390/ijms25137095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
The development of vaccines has drastically reduced the mortality and morbidity of several diseases. Despite the great success of vaccines, the immunological processes involved in protective immunity are not fully understood and several issues remain to be elucidated. Recently, the advent of high-throughput technologies has enabled a more in-depth investigation of the immune system as a whole and the characterization of the interactions of numerous components of immunity. In the field of vaccinology, these tools allow for the exploration of the molecular mechanisms by which vaccines can induce protective immune responses. In this review, we aim to describe current data on transcriptional responses to vaccination, focusing on similarities and differences of vaccine-induced transcriptional responses among vaccines mostly in healthy adults, but also in high-risk populations, such as the elderly and children. Moreover, the identification of potential predictive biomarkers of vaccine immunogenicity, the effect of age on transcriptional response and future perspectives for the utilization of transcriptomics in the field of vaccinology will be discussed.
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Affiliation(s)
- Ioanna Papadatou
- Immunobiology and Vaccinology Research Laboratory, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (I.P.); (M.G.); (V.S.)
- First Department of Pediatrics, “Aghia Sophia” Children’s Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Maria Geropeppa
- Immunobiology and Vaccinology Research Laboratory, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (I.P.); (M.G.); (V.S.)
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.P.); (A.G.P.)
| | - Vana Spoulou
- Immunobiology and Vaccinology Research Laboratory, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (I.P.); (M.G.); (V.S.)
- First Department of Pediatrics, “Aghia Sophia” Children’s Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christos Adamopoulos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.P.); (A.G.P.)
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Athanasios G. Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.P.); (A.G.P.)
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Naidu A, Garg V, Balakrishnan D, C R V, Sundararajan V, Lulu S S. Systems and Computational Screening identifies SRC and NKIRAS2 as Baseline Correlates of Risk (CoR) for Live Attenuated Oral Typhoid Vaccine (TY21a) associated Protection. Mol Immunol 2024; 169:99-109. [PMID: 38552286 DOI: 10.1016/j.molimm.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/01/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
AIM We investigated the molecular underpinnings of variation in immune responses to the live attenuated typhoid vaccine (Ty21a) by analyzing the baseline immunological profile. We utilized gene expression datasets obtained from the Gene Expression Omnibus (GEO) database (accession number: GSE100665) before and after immunization. We then employed two distinct computational approaches to identify potential baseline biomarkers associated with responsiveness to the Ty21a vaccine. MAIN METHODS The first pipeline (knowledge-based) involved the retrieval of differentially expressed genes (DEGs), functional enrichment analysis, protein-protein interaction network construction, and topological network analysis of post-immunization datasets before gauging their pre-vaccination expression levels. The second pipeline utilized an unsupervised machine learning algorithm for data-driven feature selection on pre-immunization datasets. Supervised machine-learning classifiers were employed to computationally validate the identified biomarkers. KEY FINDINGS Baseline activation of NKIRAS2 (a negative regulator of NF-kB signalling) and SRC (an adaptor for immune receptor activation) was negatively associated with Ty21a vaccine responsiveness, whereas LOC100134365 exhibited a positive association. The Stochastic Gradient Descent (SGD) algorithm accurately distinguished vaccine responders and non-responders, with 88.8%, 70.3%, and 85.1% accuracy for the three identified genes, respectively. SIGNIFICANCE This dual-pronged novel analytical approach provides a comprehensive comparison between knowledge-based and data-driven methods for the prediction of baseline biomarkers associated with Ty21a vaccine responsiveness. The identified genes shed light on the intricate molecular mechanisms that influence vaccine efficacy from the host perspective while pushing the needle further towards the need for development of precise enteric vaccines and on the importance of pre-immunization screening.
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Affiliation(s)
- Akshayata Naidu
- Integrative Multi Omics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Varin Garg
- Integrative Multi Omics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Deepna Balakrishnan
- Integrative Multi Omics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Vinaya C R
- Integrative Multi Omics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Vino Sundararajan
- Integrative Multi Omics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India..
| | - Sajitha Lulu S
- Integrative Multi Omics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India..
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4
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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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5
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Orcel E, Hage H, Taha M, Boucher N, Chautard E, Courtois V, Saliou A. A single workflow for multi-species blood transcriptomics. BMC Genomics 2024; 25:282. [PMID: 38493105 PMCID: PMC10944614 DOI: 10.1186/s12864-024-10208-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Blood transcriptomic analysis is widely used to provide a detailed picture of a physiological state with potential outcomes for applications in diagnostics and monitoring of the immune response to vaccines. However, multi-species transcriptomic analysis is still a challenge from a technological point of view and a standardized workflow is urgently needed to allow interspecies comparisons. RESULTS Here, we propose a single and complete total RNA-Seq workflow to generate reliable transcriptomic data from blood samples from humans and from animals typically used in preclinical models. Blood samples from a maximum of six individuals and four different species (rabbit, non-human primate, mouse and human) were extracted and sequenced in triplicates. The workflow was evaluated using different wet-lab and dry-lab criteria, including RNA quality and quantity, the library molarity, the number of raw sequencing reads, the Phred-score quality, the GC content, the performance of ribosomal-RNA and globin depletion, the presence of residual DNA, the strandness, the percentage of coding genes, the number of genes expressed, and the presence of saturation plateau in rarefaction curves. We identified key criteria and their associated thresholds to be achieved for validating the transcriptomic workflow. In this study, we also generated an automated analysis of the transcriptomic data that streamlines the validation of the dataset generated. CONCLUSIONS Our study has developed an end-to-end workflow that should improve the standardization and the inter-species comparison in blood transcriptomics studies. In the context of vaccines and drug development, RNA sequencing data from preclinical models can be directly compared with clinical data and used to identify potential biomarkers of value to monitor safety and efficacy.
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Affiliation(s)
- Elody Orcel
- BIOASTER, 40 Avenue Tony Garnier, Lyon, 69007, France
| | - Hayat Hage
- BIOASTER, 40 Avenue Tony Garnier, Lyon, 69007, France
| | - May Taha
- BIOASTER, 40 Avenue Tony Garnier, Lyon, 69007, France
| | | | - Emilie Chautard
- SANOFI, 1541 Av. Marcel Mérieux, Marcy-L'Étoile, 69280, France
| | | | - Adrien Saliou
- BIOASTER, 40 Avenue Tony Garnier, Lyon, 69007, France.
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6
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Mura M, Misganaw B, Gautam A, Robinson T, Chaudhury S, Bansal N, Martins AJ, Tsang J, Hammamieh R, Bergmann-Leitner E. Human transcriptional signature of protection after Plasmodium falciparum immunization and infectious challenge via mosquito bites. Hum Vaccin Immunother 2023; 19:2282693. [PMID: 38010150 PMCID: PMC10760396 DOI: 10.1080/21645515.2023.2282693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
The identification of immune correlates of protection against infectious pathogens will accelerate the design and optimization of recombinant and subunit vaccines. Systematic analyses such as immunoprofiling including serological, cellular, and molecular assessments supported by computational tools are key to not only identify correlates of protection but also biomarkers of disease susceptibility. The current study expands our previous cellular and serological profiling of vaccine-induced responses to a whole parasite malaria vaccine. The irradiated sporozoite model was chosen as it is considered the most effective vaccine against malaria. In contrast to whole blood transcriptomics analysis, we stimulated peripheral blood mononuclear cells (PBMC) with sporozoites and enriched for antigen-specific cells prior to conducting transcriptomics analysis. By focusing on transcriptional events triggered by antigen-specific stimulation, we were able to uncover quantitative and qualitative differences between protected and non-protected individuals to controlled human malaria infections and identified differentially expressed genes associated with sporozoite-specific responses. Further analyses including pathway and gene set enrichment analysis revealed that vaccination with irradiated sporozoites induced a transcriptomic profile associated with Th1-responses, Interferon-signaling, antigen-presentation, and inflammation. Analyzing longitudinal time points not only post-vaccination but also post-controlled human malaria infection further revealed that the transcriptomic profile of protected vs non-protected individuals was not static but continued to diverge over time. The results lay the foundation for comparing protective immune signatures induced by various vaccine platforms to uncover immune correlates of protection that are common across platforms.
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Affiliation(s)
- Marie Mura
- Immunology Core, Biologics Research & Development, WRAIR-Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Host-Pathogen Interactions, Microbiology and Infectious Diseases, IRBA-Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Burook Misganaw
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Vysnova Inc, Landover, MD, USA
| | - Aarti Gautam
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Tanisha Robinson
- Immunology Core, Biologics Research & Development, WRAIR-Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sidhartha Chaudhury
- Center of Enabling Capabilties, WRAIR-Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Neha Bansal
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Andrew J. Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - John Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Rasha Hammamieh
- Medical Readiness Systems Biology, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Elke Bergmann-Leitner
- Immunology Core, Biologics Research & Development, WRAIR-Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Gonzalez Dias Carvalho PC, Dominguez Crespo Hirata T, Mano Alves LY, Moscardini IF, do Nascimento APB, Costa-Martins AG, Sorgi S, Harandi AM, Ferreira DM, Vianello E, Haks MC, Ottenhoff THM, Santoro F, Martinez-Murillo P, Huttner A, Siegrist CA, Medaglini D, Nakaya HI. Baseline gene signatures of reactogenicity to Ebola vaccination: a machine learning approach across multiple cohorts. Front Immunol 2023; 14:1259197. [PMID: 38022684 PMCID: PMC10663260 DOI: 10.3389/fimmu.2023.1259197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The rVSVDG-ZEBOV-GP (Ervebo®) vaccine is both immunogenic and protective against Ebola. However, the vaccine can cause a broad range of transient adverse reactions, from headache to arthritis. Identifying baseline reactogenicity signatures can advance personalized vaccinology and increase our understanding of the molecular factors associated with such adverse events. Methods In this study, we developed a machine learning approach to integrate prevaccination gene expression data with adverse events that occurred within 14 days post-vaccination. Results and Discussion We analyzed the expression of 144 genes across 343 blood samples collected from participants of 4 phase I clinical trial cohorts: Switzerland, USA, Gabon, and Kenya. Our machine learning approach revealed 22 key genes associated with adverse events such as local reactions, fatigue, headache, myalgia, fever, chills, arthralgia, nausea, and arthritis, providing insights into potential biological mechanisms linked to vaccine reactogenicity.
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Affiliation(s)
| | - Thiago Dominguez Crespo Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Leandro Yukio Mano Alves
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | | | - André G. Costa-Martins
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Artificial Intelligence and Analytics Department, Institute for Technological Research, São Paulo, Brazil
| | - Sara Sorgi
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Ali M. Harandi
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Vaccine Evaluation Center, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Daniela M. Ferreira
- Oxford Vaccine Group, University of Oxford, Oxford, United Kingdom
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Eleonora Vianello
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Mariëlle C. Haks
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Tom H. M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Angela Huttner
- Centre for Vaccinology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Infectious Diseases Service, Geneva University Hospitals, Geneva, Switzerland
| | - Claire-Anne Siegrist
- Centre for Vaccinology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Donata Medaglini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Helder I. Nakaya
- Scientific Platform Pasteur-University of São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
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Nehar-Belaid D, Sokolowski M, Ravichandran S, Banchereau J, Chaussabel D, Ucar D. Baseline immune states (BIS) associated with vaccine responsiveness and factors that shape the BIS. Semin Immunol 2023; 70:101842. [PMID: 37717525 DOI: 10.1016/j.smim.2023.101842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
Vaccines are among the greatest inventions in medicine, leading to the elimination or control of numerous diseases, including smallpox, polio, measles, rubella, and, most recently, COVID-19. Yet, the effectiveness of vaccines varies among individuals. In fact, while some recipients mount a robust response to vaccination that protects them from the disease, others fail to respond. Multiple clinical and epidemiological factors contribute to this heterogeneity in responsiveness. Systems immunology studies fueled by advances in single-cell biology have been instrumental in uncovering pre-vaccination immune cell types and genomic features (i.e., the baseline immune state, BIS) that have been associated with vaccine responsiveness. Here, we review clinical factors that shape the BIS, and the characteristics of the BIS associated with responsiveness to frequently studied vaccines (i.e., influenza, COVID-19, bacterial pneumonia, malaria). Finally, we discuss potential strategies to enhance vaccine responsiveness in high-risk groups, focusing specifically on older adults.
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Affiliation(s)
| | - Mark Sokolowski
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | | | - Damien Chaussabel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
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9
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Mehta G, Riva A, Ballester MP, Uson E, Pujadas M, Carvalho-Gomes Â, Sahuco I, Bono A, D’Amico F, Viganò R, Diago E, Lanseros BT, Inglese E, Vazquez DM, Sharma R, Tsou HLP, Harris N, Broekhoven A, Kikkert M, Morales SPT, Myeni SK, Riveiro-Barciela M, Palom A, Zeni N, Brocca A, Cussigh A, Cmet S, Escudero-García D, Stocco M, Natola LA, Ieluzzi D, Paon V, Sangiovanni A, Farina E, di Benedetto C, Sánchez-Torrijos Y, Lucena-Varela A, Román E, Sánchez E, Sánchez-Aldehuelo R, López-Cardona J, Canas-Perez I, Eastgate C, Jeyanesan D, Morocho AE, Di Cola S, Lapenna L, Zaccherini G, Bongiovanni D, Zanaga P, Sayaf K, Hossain S, Crespo J, Robles-Díaz M, Madejón A, Degroote H, Fernández J, Korenjak M, Verhelst X, García-Samaniego J, Andrade RJ, Iruzubieta P, Wright G, Caraceni P, Merli M, Patel VC, Gander A, Albillos A, Soriano G, Donato MF, Sacerdoti D, Toniutto P, Buti M, Duvoux C, Grossi PA, Berg T, Polak WG, Puoti M, Bosch-Comas A, Belli L, Burra P, Russo FP, Coenraad M, Calleja JL, Perricone G, Berenguer M, Claria J, Moreau R, Arroyo V, Angeli P, Sánchez C, Ampuero J, Piano S, Chokshi S, Jalan R. Serological response and breakthrough infection after COVID-19 vaccination in patients with cirrhosis and post-liver transplant. Hepatol Commun 2023; 7:e0273. [PMID: 37870985 PMCID: PMC10586829 DOI: 10.1097/hc9.0000000000000273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/21/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Vaccine hesitancy and lack of access remain major issues in disseminating COVID-19 vaccination to liver patients globally. Factors predicting poor response to vaccination and risk of breakthrough infection are important data to target booster vaccine programs. The primary aim of the current study was to measure humoral responses to 2 doses of COVID-19 vaccine. Secondary aims included the determination of factors predicting breakthrough infection. METHODS COVID-19 vaccination and Biomarkers in cirrhosis And post-Liver Transplantation is a prospective, multicenter, observational case-control study. Participants were recruited at 4-10 weeks following first and second vaccine doses in cirrhosis [n = 325; 94% messenger RNA (mRNA) and 6% viral vaccine], autoimmune liver disease (AILD) (n = 120; 77% mRNA and 23% viral vaccine), post-liver transplant (LT) (n = 146; 96% mRNA and 3% viral vaccine), and healthy controls (n = 51; 72% mRNA, 24% viral and 4% heterologous combination). Serological end points were measured, and data regarding breakthrough SARS-CoV-2 infection were collected. RESULTS After adjusting by age, sex, and time of sample collection, anti-Spike IgG levels were the lowest in post-LT patients compared to cirrhosis (p < 0.0001), AILD (p < 0.0001), and control (p = 0.002). Factors predicting reduced responses included older age, Child-Turcotte-Pugh B/C, and elevated IL-6 in cirrhosis; non-mRNA vaccine in AILD; and coronary artery disease, use of mycophenolate and dysregulated B-call activating factor, and lymphotoxin-α levels in LT. Incident infection occurred in 6.6%, 10.6%, 7.4%, and 15.6% of cirrhosis, AILD, post-LT, and control, respectively. The only independent factor predicting infection in cirrhosis was low albumin level. CONCLUSIONS LT patients present the lowest response to the SARS-CoV-2 vaccine. In cirrhosis, the reduced response is associated with older age, stage of liver disease and systemic inflammation, and breakthrough infection with low albumin level.
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Affiliation(s)
- Gautam Mehta
- Institute for Liver and Digestive Heath, University College London, London, UK
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Royal Free London NHS Foundation Trust, London, UK
| | - Antonio Riva
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Maria Pilar Ballester
- Department of Gastroenterology and Hepatology, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Eva Uson
- European Foundation for the Study of Chronic Liver Failure (EF CLIF), EASL-CLIF Consortium and Grifols Chair, Barcelona, Spain
| | - Montserrat Pujadas
- European Foundation for the Study of Chronic Liver Failure (EF CLIF), EASL-CLIF Consortium and Grifols Chair, Barcelona, Spain
| | - Ângela Carvalho-Gomes
- Hepatology, HBP Surgery and Transplantation, Hepatology & Liver Transplant Unit, La Fe University Hospital, Valencia, Spain
- Ciberehd, Universidad de Valencia, Valencia, Spain
| | - Ivan Sahuco
- Hepatology, HBP Surgery and Transplantation, Hepatology & Liver Transplant Unit, La Fe University Hospital, Valencia, Spain
- Ciberehd, Universidad de Valencia, Valencia, Spain
| | - Ariadna Bono
- Hepatology, HBP Surgery and Transplantation, Hepatology & Liver Transplant Unit, La Fe University Hospital, Valencia, Spain
- Ciberehd, Universidad de Valencia, Valencia, Spain
| | - Federico D’Amico
- ASST Grande Ospedale Metropolitano Niguarda, Infectious Diseases Unit, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Postgraduate School of Clinical Pharmacology and Toxicology, University of Milan, Milan, Italy
| | - Raffaela Viganò
- ASST Grande Ospedale Metropolitano Niguarda, Hepatology and Gastroenterology Unit, Milan, Italy
| | - Elena Diago
- Department of Gastroenterology and Hepatology, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHIM, Madrid, Spain
- Central Unit of Clinical Research and Clinical Trials, Hospital Universitario La Paz, IdiPaz, Madrid, Spain
- CIBERehd, Madrid, Spain
| | - Beatriz Tormo Lanseros
- Department of Gastroenterology and Hepatology, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHIM, Madrid, Spain
- CIBERehd, Madrid, Spain
| | - Elvira Inglese
- ASST Grande Ospedale Metropolitano Niguarda, Hepatology and Gastroenterology Unit, Milan, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | | | - Rajni Sharma
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
| | - Hio Lam Phoebe Tsou
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
| | - Nicola Harris
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
| | - Annelotte Broekhoven
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, RC Leiden, the Netherlands
| | - Marjolein Kikkert
- Department of Medical Microbiology, Leiden University Medical Center, RC Leiden, the Netherlands
| | - Shessy P. Torres Morales
- Department of Medical Microbiology, Leiden University Medical Center, RC Leiden, the Netherlands
| | - Sebenzile K. Myeni
- Department of Medical Microbiology, Leiden University Medical Center, RC Leiden, the Netherlands
| | | | - Adriana Palom
- Liver Unit, Hospital Universitario Valle de Hebron, Barcelona, Spain
| | - Nicola Zeni
- Department of Medicine - DIMED, Unit of Internal Medicine and Hepatology (UIMH), University of Padova, Padova, Italy
| | - Alessandra Brocca
- Department of Medicine - DIMED, Unit of Internal Medicine and Hepatology (UIMH), University of Padova, Padova, Italy
| | - Annarosa Cussigh
- Hepatology and Liver Transplantation Unit, Azienda Sanitaria Universitaria Integrata, University of Udine, Udine, Italy
| | - Sara Cmet
- Hepatology and Liver Transplantation Unit, Azienda Sanitaria Universitaria Integrata, University of Udine, Udine, Italy
| | | | - Matteo Stocco
- Department of Gastroenterology and Hepatology, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | | | | | - Veronica Paon
- Azienda Ospedaiera Universitaria Integrata Verona, Verona Italy
| | - Angelo Sangiovanni
- Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Division of Gastroenterology and Hepatology, Milan, Italy
| | - Elisa Farina
- Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Division of Gastroenterology and Hepatology, Milan, Italy
| | - Clara di Benedetto
- Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Division of Gastroenterology and Hepatology, Milan, Italy
| | - Yolanda Sánchez-Torrijos
- Hospital Universitario Virgen del Rocio, Sevilla. Instituto de Biomedicina de Sevilla, Universidad de Sevilla, Sevilla, Spain
| | - Ana Lucena-Varela
- Hospital Universitario Virgen del Rocio, Sevilla. Instituto de Biomedicina de Sevilla, Universidad de Sevilla, Sevilla, Spain
| | - Eva Román
- Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- EUI-Sant Pau School of Nursing, Barcelona, Spain
| | - Elisabet Sánchez
- CIBERehd, Madrid, Spain
- Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Rubén Sánchez-Aldehuelo
- Servicio de Gastroenterología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto Salud Carlos III, Madrid, Spain
- Universidad de Alcalá, Madrid, Spain
| | - Julia López-Cardona
- Servicio de Gastroenterología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto Salud Carlos III, Madrid, Spain
| | | | | | - Dhaarica Jeyanesan
- Institute of Liver Studies, King’s College Hospital NHS Foundation Trust, London, UK
| | | | - Simone Di Cola
- Department of Translational and Precision Medicine, University of Rome Sapienza, Roma, Italy
| | - Lucia Lapenna
- Department of Translational and Precision Medicine, University of Rome Sapienza, Roma, Italy
| | - Giacomo Zaccherini
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Deborah Bongiovanni
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Paola Zanaga
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
- Gastroenterology and Multivisceral Transplant Units, Azienda Ospedale Università’ di Padova, Padova, Italy
| | - Katia Sayaf
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
- Gastroenterology and Multivisceral Transplant Units, Azienda Ospedale Università’ di Padova, Padova, Italy
| | - Sabir Hossain
- Mid & South Essex NHS Foundation Trust, Basildon, UK
| | - Javier Crespo
- Gastroenterology and Hepatology Department, Marqués de Valdecilla University Hospital, Santander, Spain
- Clinical and Traslational Digestive Research Group, Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain
| | - Mercedes Robles-Díaz
- CIBERehd, Madrid, Spain
- Servicio de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain
| | - Antonio Madejón
- Liver Unit, Hospital Universitario La Paz, CIBERehd, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Helena Degroote
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Belgium
- Liver Research Center Ghent, Ghent University, Belgium
- European Reference Network (ERN)RARE-LIVER
| | - Javier Fernández
- European Foundation for the Study of Chronic Liver Failure (EF CLIF), EASL-CLIF Consortium and Grifols Chair, Barcelona, Spain
- Liver Unit, Hospital Clínic, Universitat de Barcelona, Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS) and Centro de Investigación Biomèdica en Red (CIBEREHD), Barcelona, Spain
| | | | - Xavier Verhelst
- Department of Gastroenterology and Hepatology, Ghent University Hospital, Belgium
- Liver Research Center Ghent, Ghent University, Belgium
- European Reference Network (ERN)RARE-LIVER
| | - Javier García-Samaniego
- Liver Unit, Hospital Universitario La Paz, CIBERehd, IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Raúl J. Andrade
- CIBERehd, Madrid, Spain
- Servicio de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Málaga, Spain
| | - Paula Iruzubieta
- Gastroenterology and Hepatology Department, Marqués de Valdecilla University Hospital, Santander, Spain
- Clinical and Traslational Digestive Research Group, Instituto de Investigación Sanitaria Valdecilla (IDIVAL), Santander, Spain
| | - Gavin Wright
- Mid & South Essex NHS Foundation Trust, Basildon, UK
| | - Paolo Caraceni
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Unit of Semeiotics, Liver and Alcohol-related Diseases, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Manuela Merli
- Department of Translational and Precision Medicine, University of Rome Sapienza, Roma, Italy
| | - Vishal C Patel
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King’s College London, London, UK
- Institute of Liver Studies, King’s College Hospital NHS Foundation Trust, London, UK
| | - Amir Gander
- Royal Free London NHS Foundation Trust, London, UK
| | - Agustín Albillos
- Servicio de Gastroenterología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto Salud Carlos III, Madrid, Spain
| | - Germán Soriano
- CIBERehd, Madrid, Spain
- Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Maria Francesca Donato
- Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Division of Gastroenterology and Hepatology, Milan, Italy
| | - David Sacerdoti
- Azienda Ospedaiera Universitaria Integrata Verona, Verona Italy
| | - Pierluigi Toniutto
- Hepatology and Liver Transplantation Unit, Azienda Sanitaria Universitaria Integrata, University of Udine, Udine, Italy
| | - Maria Buti
- Liver Unit, Hospital Universitario Valle de Hebron, Barcelona, Spain
| | - Christophe Duvoux
- Department of Hepatogy-Liver Transplant Unit, Henri Mondor Hospital-APHP, Paris Est University, Paris, France
| | - Paolo Antonio Grossi
- Department of Medicine and Surgery, University of Insubria, Infectious and Tropical Diseases Unit, ASST Sette Laghim, Varese, Italy
| | - Thomas Berg
- European Association for the Study of the Liver (EASL)
| | - Wojciech G. Polak
- Department of Surgery, Division of HPB and Transplant Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Massimo Puoti
- University of Milano Bicocca, Infectious Diseases Niguarda Great Metropolitan Hospital, Milan, Italy
| | - Anna Bosch-Comas
- European Foundation for the Study of Chronic Liver Failure (EF CLIF), EASL-CLIF Consortium and Grifols Chair, Barcelona, Spain
| | - Luca Belli
- ASST Grande Ospedale Metropolitano Niguarda, Hepatology and Gastroenterology Unit, Milan, Italy
| | - Patrizia Burra
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
- Gastroenterology and Multivisceral Transplant Units, Azienda Ospedale Università’ di Padova, Padova, Italy
| | - Francesco Paolo Russo
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
- Gastroenterology and Multivisceral Transplant Units, Azienda Ospedale Università’ di Padova, Padova, Italy
| | - Minneke Coenraad
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, RC Leiden, the Netherlands
| | - José Luis Calleja
- Department of Gastroenterology and Hepatology, Hospital Universitario Puerta de Hierro Majadahonda, IDIPHIM, Madrid, Spain
- CIBERehd, Madrid, Spain
| | - Giovanni Perricone
- ASST Grande Ospedale Metropolitano Niguarda, Hepatology and Gastroenterology Unit, Milan, Italy
| | - Marina Berenguer
- Hepatology, HBP Surgery and Transplantation, Hepatology & Liver Transplant Unit, La Fe University Hospital, Valencia, Spain
- Ciberehd, Universidad de Valencia, Valencia, Spain
| | - Joan Claria
- European Foundation for the Study of Chronic Liver Failure (EF CLIF), EASL-CLIF Consortium and Grifols Chair, Barcelona, Spain
- Hospital Clínic, Institut d’Investigacions Biomèdiques August Pi-Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red (CIBERehd) and Universitat de Barcelona, Barcelona, Spain
| | - Richard Moreau
- European Foundation for the Study of Chronic Liver Failure (EF CLIF), EASL-CLIF Consortium and Grifols Chair, Barcelona, Spain
- INSERM and Université Paris Cité, Centre de Recherche sur l’inflammation (CRI), Paris, France
- APHP, Service d’hépatologie, Hôpital Beaujon, Clichy, France
| | - Vicente Arroyo
- European Foundation for the Study of Chronic Liver Failure (EF CLIF), EASL-CLIF Consortium and Grifols Chair, Barcelona, Spain
| | - Paolo Angeli
- Department of Medicine - DIMED, Unit of Internal Medicine and Hepatology (UIMH), University of Padova, Padova, Italy
| | - Cristina Sánchez
- European Foundation for the Study of Chronic Liver Failure (EF CLIF), EASL-CLIF Consortium and Grifols Chair, Barcelona, Spain
| | - Javier Ampuero
- Hospital Universitario Virgen del Rocio, Sevilla. Instituto de Biomedicina de Sevilla, Universidad de Sevilla, Sevilla, Spain
| | - Salvatore Piano
- Department of Medicine - DIMED, Unit of Internal Medicine and Hepatology (UIMH), University of Padova, Padova, Italy
| | - Shilpa Chokshi
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Rajiv Jalan
- Institute for Liver and Digestive Heath, University College London, London, UK
- Royal Free London NHS Foundation Trust, London, UK
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10
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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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11
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Affaticati F, Bartholomeus E, Mullan K, Damme PV, Beutels P, Ogunjimi B, Laukens K, Meysman P. Multi-View Learning to Unravel the Different Levels Underlying Hepatitis B Vaccine Response. Vaccines (Basel) 2023; 11:1236. [PMID: 37515051 PMCID: PMC10384938 DOI: 10.3390/vaccines11071236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
The immune system acts as an intricate apparatus that is dedicated to mounting a defense and ensures host survival from microbial threats. To engage this faceted immune response and provide protection against infectious diseases, vaccinations are a critical tool to be developed. However, vaccine responses are governed by levels that, when interrogated, separately only explain a fraction of the immune reaction. To address this knowledge gap, we conducted a feasibility study to determine if multi-view modeling could aid in gaining actionable insights on response markers shared across populations, capture the immune system's diversity, and disentangle confounders. We thus sought to assess this multi-view modeling capacity on the responsiveness to the Hepatitis B virus (HBV) vaccination. Seroconversion to vaccine-induced antibodies against the HBV surface antigen (anti-HBs) in early converters (n = 21; <2 months) and late converters (n = 9; <6 months) and was defined based on the anti-HBs titers (>10IU/L). The multi-view data encompassed bulk RNA-seq, CD4+ T-cell parameters (including T-cell receptor data), flow cytometry data, and clinical metadata (including age and gender). The modeling included testing single-view and multi-view joint dimensionality reductions. Multi-view joint dimensionality reduction outperformed single-view methods in terms of the area under the curve and balanced accuracy, confirming the increase in predictive power to be gained. The interpretation of these findings showed that age, gender, inflammation-related gene sets, and pre-existing vaccine-specific T-cells could be associated with vaccination responsiveness. This multi-view dimensionality reduction approach complements clinical seroconversion and all single modalities. Importantly, this modeling could identify what features could predict HBV vaccine response. This methodology could be extended to other vaccination trials to identify the key features regulating responsiveness.
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Affiliation(s)
- Fabio Affaticati
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
| | - Esther Bartholomeus
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp (VAXINFECTIO), 2610 Antwerp, Belgium
| | - Kerry Mullan
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
| | - Pierre Van Damme
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
- Centre for the Evaluation of Vaccination (CEV), Vaccine and Infectious Disease Institute, University of Antwerp, 2610 Antwerp, Belgium
| | - Philippe Beutels
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Antwerp, Belgium
| | - Benson Ogunjimi
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
- Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute, University of Antwerp (VAXINFECTIO), 2610 Antwerp, Belgium
- Department of Paediatrics, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020 Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, 2020 Antwerp, Belgium
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12
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Van Breedam E, Buyle-Huybrecht T, Govaerts J, Meysman P, Bours A, Boeren M, Di Stefano J, Caers T, De Reu H, Dirkx L, Schippers J, Bartholomeus E, Lebrun M, Sadzot-Delvaux C, Rybakowska P, Alarcón-Riquelme ME, Marañón C, Laukens K, Delputte P, Ogunjimi B, Ponsaerts P. Lack of strong innate immune reactivity renders macrophages alone unable to control productive Varicella-Zoster Virus infection in an isogenic human iPSC-derived neuronal co-culture model. Front Immunol 2023; 14:1177245. [PMID: 37287975 PMCID: PMC10241998 DOI: 10.3389/fimmu.2023.1177245] [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: 03/01/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023] Open
Abstract
With Varicella-Zoster Virus (VZV) being an exclusive human pathogen, human induced pluripotent stem cell (hiPSC)-derived neural cell culture models are an emerging tool to investigate VZV neuro-immune interactions. Using a compartmentalized hiPSC-derived neuronal model allowing axonal VZV infection, we previously demonstrated that paracrine interferon (IFN)-α2 signalling is required to activate a broad spectrum of interferon-stimulated genes able to counteract a productive VZV infection in hiPSC-neurons. In this new study, we now investigated whether innate immune signalling by VZV-challenged macrophages was able to orchestrate an antiviral immune response in VZV-infected hiPSC-neurons. In order to establish an isogenic hiPSC-neuron/hiPSC-macrophage co-culture model, hiPSC-macrophages were generated and characterised for phenotype, gene expression, cytokine production and phagocytic capacity. Even though immunological competence of hiPSC-macrophages was shown following stimulation with the poly(dA:dT) or treatment with IFN-α2, hiPSC-macrophages in co-culture with VZV-infected hiPSC-neurons were unable to mount an antiviral immune response capable of suppressing a productive neuronal VZV infection. Subsequently, a comprehensive RNA-Seq analysis confirmed the lack of strong immune responsiveness by hiPSC-neurons and hiPSC-macrophages upon, respectively, VZV infection or challenge. This may suggest the need of other cell types, like T-cells or other innate immune cells, to (co-)orchestrate an efficient antiviral immune response against VZV-infected neurons.
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Affiliation(s)
- Elise Van Breedam
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Tamariche Buyle-Huybrecht
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Jonas Govaerts
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Andrea Bours
- Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Marlies Boeren
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Julia Di Stefano
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Thalissa Caers
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Hans De Reu
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Flow Cytometry and Cell Sorting Core Facility (FACSUA), Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Laura Dirkx
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Antwerp, Belgium
| | - Jolien Schippers
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Esther Bartholomeus
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Marielle Lebrun
- Laboratory of Virology and Immunology, Interdisciplinary Research Institute in the Biomedical Sciences GIGA-Infection, Inflammation and Immunity, University of Liège, Liège, Belgium
| | - Catherine Sadzot-Delvaux
- Laboratory of Virology and Immunology, Interdisciplinary Research Institute in the Biomedical Sciences GIGA-Infection, Inflammation and Immunity, University of Liège, Liège, Belgium
| | - Paulina Rybakowska
- Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Junta de Andalucía, Parque Tecnológico de la Salud (PTS), Granada, Spain
| | - Marta E. Alarcón-Riquelme
- Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Junta de Andalucía, Parque Tecnológico de la Salud (PTS), Granada, Spain
| | - Concepción Marañón
- Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Junta de Andalucía, Parque Tecnológico de la Salud (PTS), Granada, Spain
| | - Kris Laukens
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Peter Delputte
- Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
- Infla-Med, University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
- Centre for Health Economics Research & Modelling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Department of Paediatrics, Antwerp University Hospital, Antwerp, Belgium
| | - Peter Ponsaerts
- Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
- Flow Cytometry and Cell Sorting Core Facility (FACSUA), Laboratory of Experimental Hematology (LEH), Vaccine and Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
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13
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Hirota M, Tamai M, Yukawa S, Taira N, Matthews MM, Toma T, Seto Y, Yoshida M, Toguchi S, Miyagi M, Mori T, Tomori H, Tamai O, Kina M, Sakihara E, Yamashiro C, Miyagi M, Tamaki K, Wolf M, Collins MK, Kitano H, Ishikawa H. Human immune and gut microbial parameters associated with inter-individual variations in COVID-19 mRNA vaccine-induced immunity. Commun Biol 2023; 6:368. [PMID: 37081096 PMCID: PMC10119155 DOI: 10.1038/s42003-023-04755-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 03/24/2023] [Indexed: 04/22/2023] Open
Abstract
COVID-19 mRNA vaccines induce protective adaptive immunity against SARS-CoV-2 in most individuals, but there is wide variation in levels of vaccine-induced antibody and T-cell responses. However, the mechanisms underlying this inter-individual variation remain unclear. Here, using a systems biology approach based on multi-omics analyses of human blood and stool samples, we identified several factors that are associated with COVID-19 vaccine-induced adaptive immune responses. BNT162b2-induced T cell response is positively associated with late monocyte responses and inversely associated with baseline mRNA expression of activation protein 1 (AP-1) transcription factors. Interestingly, the gut microbial fucose/rhamnose degradation pathway is positively correlated with mRNA expression of AP-1, as well as a gene encoding an enzyme producing prostaglandin E2 (PGE2), which promotes AP-1 expression, and inversely correlated with BNT162b2-induced T-cell responses. These results suggest that baseline AP-1 expression, which is affected by commensal microbial activity, is a negative correlate of BNT162b2-induced T-cell responses.
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Affiliation(s)
- Masato Hirota
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Miho Tamai
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Sachie Yukawa
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
- Integrated Open Systems Unit, OIST, Onna-son, Okinawa, Japan
| | - Naoyuki Taira
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | | | - Takeshi Toma
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Yu Seto
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Makiko Yoshida
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Sakura Toguchi
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Mio Miyagi
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan
| | - Tomoari Mori
- Research Support Division, Occupational Health and Safety, OIST, Onna-son, Okinawa, Japan
| | | | | | | | - Eishin Sakihara
- Health Care Center of the Naha Medical Association, Naha-city, Okinawa, Japan
| | - Chiaki Yamashiro
- Yamashiro Orthopedic Surgery Ophthalmology Clinic, Naha-city, Okinawa, Japan
| | | | - Kentaro Tamaki
- Naha-Nishi Clinic, Department of Breast Surgery, Naha-city, Okinawa, Japan
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, OIST, Onna-son, Okinawa, Japan
| | - Mary K Collins
- Research Support Division, Office of the Provost, OIST, Onna-son, Okinawa, Japan
| | - Hiroaki Kitano
- Integrated Open Systems Unit, OIST, Onna-son, Okinawa, Japan
| | - Hiroki Ishikawa
- Immune Signal Unit, Okinawa Institute of Science and Technology, Graduate University (OIST), Onna-son, Okinawa, Japan.
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14
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Fourati S, Tomalin LE, Mulè MP, Chawla DG, Gerritsen B, Rychkov D, Henrich E, Miller HER, Hagan T, Diray-Arce J, Dunn P, Levy O, Gottardo R, Sarwal MM, Tsang JS, Suárez-Fariñas M, Pulendran B, Kleinstein SH, Sékaly RP. Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination. Nat Immunol 2022; 23:1777-1787. [PMID: 36316476 PMCID: PMC9747610 DOI: 10.1038/s41590-022-01329-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/12/2022] [Indexed: 11/05/2022]
Abstract
Several studies have shown that the pre-vaccination immune state is associated with the antibody response to vaccination. However, the generalizability and mechanisms that underlie this association remain poorly defined. Here, we sought to identify a common pre-vaccination signature and mechanisms that could predict the immune response across 13 different vaccines. Analysis of blood transcriptional profiles across studies revealed three distinct pre-vaccination endotypes, characterized by the differential expression of genes associated with a pro-inflammatory response, cell proliferation, and metabolism alterations. Importantly, individuals whose pre-vaccination endotype was enriched in pro-inflammatory response genes known to be downstream of nuclear factor-kappa B showed significantly higher serum antibody responses 1 month after vaccination. This pro-inflammatory pre-vaccination endotype showed gene expression characteristic of the innate activation state triggered by Toll-like receptor ligands or adjuvants. These results demonstrate that wide variations in the transcriptional state of the immune system in humans can be a key determinant of responsiveness to vaccination.
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Affiliation(s)
- Slim Fourati
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Lewis E Tomalin
- Center for Biostatistics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew P Mulè
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID and Center for Human Immunology (CHI), NIH, Bethesda, MD, USA
- NIH-Oxford-Cambridge Scholars Program, Cambridge University, Cambridge, UK
| | | | | | - Dmitry Rychkov
- Division of Transplant Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Evan Henrich
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Thomas Hagan
- Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | - Joann Diray-Arce
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Patrick Dunn
- ImmPort Curation Team, NG Health Solutions, Rockville, MD, USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Raphael Gottardo
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Biomedical Data Science Center, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Minnie M Sarwal
- Division of Transplant Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID and Center for Human Immunology (CHI), NIH, Bethesda, MD, USA
| | - Mayte Suárez-Fariñas
- Center for Biostatistics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bali Pulendran
- Stanford University School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Rafick-Pierre Sékaly
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.
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15
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Subsequent AS01-adjuvanted vaccinations induce similar transcriptional responses in populations with different disease statuses. PLoS One 2022; 17:e0276505. [DOI: 10.1371/journal.pone.0276505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/07/2022] [Indexed: 11/12/2022] Open
Abstract
Transcriptional responses to adjuvanted vaccines can vary substantially among populations. Interindividual diversity in levels of pathogen exposure, and thus of cell-mediated immunological memory at baseline, may be an important determinant of population differences in vaccine responses. Adjuvant System AS01 is used in licensed or candidate vaccines for several diseases and populations, yet the impact of pre-existing immunity on its adjuvanticity remains to be elucidated. In this exploratory post-hoc analysis of clinical trial samples (clinicalTrials.gov: NCT01424501), we compared gene expression patterns elicited by two immunizations with the candidate tuberculosis (TB) vaccine M72/AS01, between three groups of individuals with different levels of memory responses to TB antigens before vaccination. Analyzed were one group of TB-disease-treated individuals, and two groups of TB-disease-naïve individuals who were (based on purified protein derivative [PPD] skin-test results) stratified into PPD-positive and PPD-negative groups. Although TB-disease-treated individuals displayed slightly stronger transcriptional responses after each vaccine dose, functional gene signatures were overall not distinctly different between groups. Considering the similarities with the signatures found previously for other AS01-adjuvanted vaccines, many features of the response appeared to be adjuvant-driven. Across groups, cell proliferation-related signals at 7 days post-dose 1 were associated with increased anti-M72 antibody response magnitudes. These early signals were stronger in the TB-disease-treated group as compared to both TB-disease-naïve groups. Interindividual homogeneity in gene expression levels was also higher for TB-disease-treated individuals post-dose 1, but increased in all groups post-dose 2 to attain similar levels between the three groups. Altogether, strong cell-mediated memory responses at baseline accelerated and amplified transcriptional responses to a single dose of this AS01-adjuvanted vaccine, resulting in more homogenous gene expression levels among the highly-primed individuals as compared to the disease-naïve individuals. However, after a second vaccination, response heterogeneity decreased and was similar across groups, irrespective of the degree of immune memory acquired at baseline. This information can support the design and analysis of future clinical trials evaluating AS01-adjuvanted vaccines.
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16
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Lipsit S, Facciuolo A, Scruten E, Wilkinson J, Plastow G, Kusalik A, Napper S. Signaling differences in peripheral blood mononuclear cells of high and low vaccine responders prior to, and following, vaccination in piglets. Vaccine X 2022; 11:100167. [PMID: 35692279 PMCID: PMC9175112 DOI: 10.1016/j.jvacx.2022.100167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 03/29/2022] [Accepted: 04/25/2022] [Indexed: 10/28/2022] Open
Abstract
Individual variability in responses to vaccination can result in vaccinated subjects failing to develop a protective immune response. Vaccine non-responders can remain susceptible to infection and may compromise efforts to achieve herd immunity. Biomarkers of vaccine unresponsiveness could aid vaccine research and development as well as strategically improve vaccine administration programs. We previously vaccinated piglets (n = 117) against a commercial Mycoplasma hyopneumoniae vaccine (RespiSure-One) and observed in low vaccine responder piglets, as defined by serum IgG antibody titers, differential phosphorylation of peptides involved in pro-inflammatory cytokine signaling within peripheral blood mononuclear cells (PBMCs) prior to vaccination, elevated plasma interferon-gamma concentrations, and lower birth weight compared to high vaccine responder piglets. In the current study, we use kinome analysis to investigate signaling events within PBMCs collected from the same high and low vaccine responders at 2 and 6 days post-vaccination. Furthermore, we evaluate the use of inflammatory plasma cytokines, birthweight, and signaling events as biomarkers of vaccine unresponsiveness in a validation cohort of high and low vaccine responders. Differential phosphorylation events (FDR < 0.05) within PBMCs are established between high and low responders at the time of vaccination and at six days post-vaccination. A subset of these phosphorylation events were determined to be consistently differentially phosphorylated (p < 0.05) in the validation cohort of high and low vaccine responders. In contrast, there were no differences in birth weight (p > 0.5) and plasma IFNγ concentrations at the time of vaccination (p > 0.6) between high and low responders within the validation cohort. The results in this study suggest, at least within this study population, phosphorylation biomarkers are more robust predictors of vaccine responsiveness than other physiological markers.
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Affiliation(s)
- Sean Lipsit
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Antonio Facciuolo
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Erin Scruten
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - James Wilkinson
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Anthony Kusalik
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Scott Napper
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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17
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Kiecolt-Glaser JK, Renna M, Peng J, Sheridan J, Lustberg M, Ramaswamy B, Wesolowski R, VanDeusen JB, Williams NO, Sardesai SD, Noonan AM, Reinbolt RE, Stover DG, Cherian MA, Malarkey WB, Andridge R. Breast cancer survivors' typhoid vaccine responses: Chemotherapy, obesity, and fitness make a difference. Brain Behav Immun 2022; 103:1-9. [PMID: 35378230 PMCID: PMC9149127 DOI: 10.1016/j.bbi.2022.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/24/2022] [Accepted: 03/31/2022] [Indexed: 02/05/2023] Open
Abstract
PURPOSE To investigate breast cancer survivors' inflammatory responses to typhoid vaccine as a window into their innate immune response to novel pathogens. METHODS This double-blind crossover trial randomized 158 breast cancer survivors to either the vaccine/saline placebo or the placebo/vaccine sequence. The relative contributions of age, cardiorespiratory fitness (VO2peak), type of cancer treatment, central obesity, and depression to interleukin (IL)-6, IL-1 receptor antagonist (IL-1Ra), and WBC vaccine responses were assessed pre-injection and 1.5, 3, 4.5, 6, and 7.5 h post-injection. RESULTS The vaccine produced larger IL-6, IL-1Ra, and WBC responses than placebo, ps < 0.0001. Prior chemotherapy, higher central obesity, and lower VO2peak were associated with smaller vaccine responses after controlling for baseline inflammation. Vaccine response was summarized by the percent increase in area under the curve (IL-6, WBC) or average post-injection mean (IL-1Ra) for vaccine relative to placebo. Women who received chemotherapy had smaller vaccine responses than women who did not for both IL-6 (44% vs 78%, p <.001) and WBC (26% vs 40%, p <.001); IL-1ra response was not significantly moderated by chemotherapy. Women whose central adiposity was one standard deviation above the mean had smaller vaccine responses than women with average adiposity for IL-6 (33% vs 54%, p <.001), WBC (20% vs 30%, p <.001), and IL-1Ra (2.0% vs 3.2%, p <.001). Women with an average level of VO2peak had smaller vaccine responses than women whose VO2peak was one standard deviation above the mean for IL-6 (54% vs 73%, p <.001), WBC (30% vs 40%, p <.001), and IL-1Ra (3.2% vs. 4.1%, p = 0.01). Age and depression did not significantly moderate vaccine responses. CONCLUSIONS This study provided novel data on chemotherapy's longer-term adverse immune consequences. The data also have an important public health message: even relatively low levels of fitness can benefit the innate immune response to a vaccine.
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Affiliation(s)
- Janice K. Kiecolt-Glaser
- Institute for Behavioral Medicine Research, The Ohio State University College of Medicine, Columbus, OH,Department of Psychiatry and Behavioral Health, The Ohio State University College of Medicine, Columbus, OH
| | - Megan Renna
- School of Psychology, University of Southern Mississippi, Hattiesburg, MS
| | - Juan Peng
- Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, College of Medicine, Columbus, OH
| | - John Sheridan
- Institute for Behavioral Medicine Research, The Ohio State University College of Medicine, Columbus, OH,Division of Biosciences, The Ohio State University College of Dentistry, Columbus, OH
| | | | - Bhuvaneswari Ramaswamy
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH,Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH
| | - Robert Wesolowski
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH,Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH
| | - Jeffrey B. VanDeusen
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH,Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH
| | - Nicole O. Williams
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH,Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH
| | - Sagar D. Sardesai
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH,Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH
| | - Anne M. Noonan
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH,Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH
| | - Raquel E. Reinbolt
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH,Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH
| | - Daniel G. Stover
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH,Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH
| | - Mathew A. Cherian
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH,Comprehensive Cancer Center, The Ohio State University College of Medicine, Columbus, OH
| | - William B. Malarkey
- Institute for Behavioral Medicine Research, The Ohio State University College of Medicine, Columbus, OH,Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH
| | - Rebecca Andridge
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH
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18
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Nong W, Huang F, Mao F, Lao D, Gong Z, Huang W. DCAF12 and HSPA1A May Serve as Potential Diagnostic Biomarkers for Myasthenia Gravis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8587273. [PMID: 35655486 PMCID: PMC9155969 DOI: 10.1155/2022/8587273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/11/2022] [Indexed: 12/20/2022]
Abstract
Background Myasthenia gravis (MG) is an autoimmune disease that severely affects the life quality of patients. This study explores the differences in immune cell types between MG and healthy control and the role of immune-related genes in the diagnosis of MG. Methods The GSE85452 dataset was downloaded from the Gene Expression Omnibus (GEO) database and analyzed using the limma package to determine differentially expressed genes (DEGs) between patients with MG and the control group. Differentially expressed immune cells were analyzed using single-sample gene set enrichment analysis (GSEA), while immune cell-associated modules were identified by weighted gene coexpression network analysis (WGCNA). Then, the expression of the identified hub genes was confirmed by RT-PCR in peripheral blood mononuclear cells (PBMCs) of MG patients. The R package pROC was used to plot the receiver operating characteristics (ROC) curves. Results The modules related to CD56bright natural killer cells were identified by GSEA and WGCNA. The proportion of CD56bright natural killer cells in the peripheral blood of MG patients is low. The results of RT-PCR showed that the levels of DDB1- and CUL4-associated factor 12 (DCAF12) and heat shock protein family A member 1A (HSPA1A) were significantly decreased in peripheral blood mononuclear cells of MG patients compared with healthy controls. The ROC curve results of DCAF12 and HSPA1A mRNA in MG diagnosis were 0.780 and 0.830, respectively. Conclusions CD56bright NK cell is lower in MG patients and may affect MG occurrence. DCAF12 and HSPA1A are lowly expressed in PBMCs of MG patients and may serve as the diagnostic biomarkers of MG.
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Affiliation(s)
- Weidong Nong
- Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, China 530021
| | - Fang Huang
- Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, China 530021
| | - Fengping Mao
- Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, China 530021
| | - Dayuan Lao
- Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, China 530021
| | - Zhuowei Gong
- Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, China 530021
| | - Wen Huang
- Department of Neurology, First Affiliated Hospital, Guangxi Medical University, Nanning, China 530021
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19
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Lee HK, Knabl L, Moliva JI, Knabl L, Werner AP, Boyoglu-Barnum S, Kapferer S, Pateter B, Walter M, Sullivan NJ, Furth PA, Hennighausen L. mRNA vaccination in octogenarians 15 and 20 months after recovery from COVID-19 elicits robust immune and antibody responses that include Omicron. Cell Rep 2022; 39:110680. [PMID: 35395191 PMCID: PMC8947943 DOI: 10.1016/j.celrep.2022.110680] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/16/2022] [Accepted: 03/23/2022] [Indexed: 01/20/2023] Open
Abstract
Knowledge about the impact of prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of the elderly on mRNA vaccination response is needed to appropriately address the demand for additional vaccinations in this vulnerable population. Here, we show that octogenarians, a high-risk population, mount a sustained SARS-CoV-2 spike-specific immunoglobulin G (IgG) antibody response for 15 months following infection. This response boosts antibody levels 35-fold upon receiving a single dose of BNT162b2 mRNA vaccine 15 months after recovery from coronavirus disease 2019 (COVID-19). In contrast, antibody responses in naive individuals boost only 6-fold after a second vaccine. Spike-specific angiotensin-converting enzyme 2 (ACE2) antibody binding responses in the previously infected octogenarians following two vaccine doses exceed those found in a naive cohort after two doses. RNA sequencing (RNA-seq) demonstrates activation of interferon-induced genetic programs, which persist only in the previously infected. A preferential increase of specific immunoglobulin G heavy chain variable (IGHV) clonal transcripts that are the basis of neutralizing antibodies is observed only in the previously infected nuns.
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Affiliation(s)
- Hye Kyung Lee
- National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | | | - Juan I Moliva
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Anne P Werner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Mary Walter
- Clinical Core, National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Priscilla A Furth
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA.
| | - Lothar Hennighausen
- National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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20
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Bell MR, Kutzler MA. An old problem with new solutions: Strategies to improve vaccine efficacy in the elderly. Adv Drug Deliv Rev 2022; 183:114175. [PMID: 35202770 DOI: 10.1016/j.addr.2022.114175] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 11/01/2022]
Abstract
Vaccination is the most effective measure to protect against infections. However, with increasing age, there is a progressive decline in the ability of the immune system to both protect against infection and develop protective immunity from vaccination. This age-related decline of the immune system is due to age-related changes in both the innate and adaptive immune systems. With an aging world population and increased risk of pandemics, there is a need to continue to develop strategies to increase vaccine responses in the elderly. Here, the major age-related changes that occur in both the innate and adaptive immune responses that impair the response to vaccination in the elderly will be highlighted. Existing and future strategies to improve vaccine efficacy in the elderly will then be discussed, including adjuvants, delivery methods, and formulation. These strategies provide mechanisms to improve the efficacy of existing vaccines and develop novel vaccines for the elderly.
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21
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Abstract
ABSTRACT Metabolic changes represent the most common sign of aging and lead to increased risk of developing diseases typical of old age. Age-associated metabolic changes, such as decreased insulin sensitivity, decreased mitochondrial function, and dysregulated nutrient uptake, fuel the low-grade chronic systemic inflammation, known as inflammaging, a leading cause of morbidity and mortality, linked to the development of several diseases of old age. How aging affects the metabolic phenotype of immune cells, and B cells in particular, is not well known and is under intensive investigation by several groups. In this study, we summarized the few published results linking intrinsic B-cell metabolism and B-cell function in different groups of young and elderly individuals: healthy, with type-2 diabetes mellitus, or with HIV infection. Although preliminary, these results suggest the intriguing possibility that metabolic pathways can represent potential novel therapeutic targets to reduce inflammaging and improve humoral immunity.
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Affiliation(s)
- Daniela Frasca
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL; and
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL
| | - Suresh Pallikkuth
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL; and
| | - Savita Pahwa
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL; and
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22
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Preimmunization correlates of protection shared across malaria vaccine trials in adults. NPJ Vaccines 2022; 7:5. [PMID: 35031601 PMCID: PMC8760258 DOI: 10.1038/s41541-021-00425-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/02/2021] [Indexed: 12/15/2022] Open
Abstract
Identifying preimmunization biological characteristics that promote an effective vaccine response offers opportunities for illuminating the critical immunological mechanisms that confer vaccine-induced protection, for developing adjuvant strategies, and for tailoring vaccination regimens to individuals or groups. In the context of malaria vaccine research, studying preimmunization correlates of protection can help address the need for a widely effective malaria vaccine, which remains elusive. In this study, common preimmunization correlates of protection were identified using transcriptomic data from four independent, heterogeneous malaria vaccine trials in adults. Systems-based analyses showed that a moderately elevated inflammatory state prior to immunization was associated with protection against malaria challenge. Functional profiling of protection-associated genes revealed the importance of several inflammatory pathways, including TLR signaling. These findings, which echo previous studies that associated enhanced preimmunization inflammation with protection, illuminate common baseline characteristics that set the stage for an effective vaccine response across diverse malaria vaccine strategies in adults.
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23
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Aevermann BD, Shannon CP, Novotny M, Ben-Othman R, Cai B, Zhang Y, Ye JC, Kobor MS, Gladish N, Lee AHY, Blimkie TM, Hancock RE, Llibre A, Duffy D, Koff WC, Sadarangani M, Tebbutt SJ, Kollmann TR, Scheuermann RH. Machine Learning-Based Single Cell and Integrative Analysis Reveals That Baseline mDC Predisposition Correlates With Hepatitis B Vaccine Antibody Response. Front Immunol 2021; 12:690470. [PMID: 34777332 PMCID: PMC8588842 DOI: 10.3389/fimmu.2021.690470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/25/2021] [Indexed: 01/23/2023] Open
Abstract
Vaccination to prevent infectious disease is one of the most successful public health interventions ever developed. And yet, variability in individual vaccine effectiveness suggests that a better mechanistic understanding of vaccine-induced immune responses could improve vaccine design and efficacy. We have previously shown that protective antibody levels could be elicited in a subset of recipients with only a single dose of the hepatitis B virus (HBV) vaccine and that a wide range of antibody levels were elicited after three doses. The immune mechanisms responsible for this vaccine response variability is unclear. Using single cell RNA sequencing of sorted innate immune cell subsets, we identified two distinct myeloid dendritic cell subsets (NDRG1-expressing mDC2 and CDKN1C-expressing mDC4), the ratio of which at baseline (pre-vaccination) correlated with the immune response to a single dose of HBV vaccine. Our results suggest that the participants in our vaccine study were in one of two different dendritic cell dispositional states at baseline – an NDRG2-mDC2 state in which the vaccine elicited an antibody response after a single immunization or a CDKN1C-mDC4 state in which the vaccine required two or three doses for induction of antibody responses. To explore this correlation further, genes expressed in these mDC subsets were used for feature selection prior to the construction of predictive models using supervised canonical correlation machine learning. The resulting models showed an improved correlation with serum antibody titers in response to full vaccination. Taken together, these results suggest that the propensity of circulating dendritic cells toward either activation or suppression, their “dispositional endotype” at pre-vaccination baseline, could dictate response to vaccination.
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Affiliation(s)
- Brian D Aevermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada.,The University of British Columbia (UBC) Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
| | - Mark Novotny
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Rym Ben-Othman
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Bing Cai
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Yun Zhang
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Jamie C Ye
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada.,The University of British Columbia (UBC) Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
| | - Michael S Kobor
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Nicole Gladish
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Amy Huei-Yi Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Travis M Blimkie
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Robert E Hancock
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Alba Llibre
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Darragh Duffy
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Wayne C Koff
- Human Vaccines Project, New York, NY, United States
| | - Manish Sadarangani
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada.,The University of British Columbia (UBC) Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada.,Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tobias R Kollmann
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States.,Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
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24
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Lee HK, Knabl L, Knabl L, Kapferer S, Pateter B, Walter M, Furth PA, Hennighausen L. Robust immune response to the BNT162b mRNA vaccine in an elderly population vaccinated 15 months after recovery from COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.09.08.21263284. [PMID: 34545374 PMCID: PMC8452113 DOI: 10.1101/2021.09.08.21263284] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Knowledge about the impact of prior SARS-CoV-2 infection of the elderly on mRNA vaccination response is needed to appropriately address the need for booster vaccination in this vulnerable population. To address this, we investigated antibody and genomic immune responses in 16 elderly (avg. 81 yrs.) individuals that had received a single booster dose of BNT162b vaccine 15 months after recovering from COVID-19. Spike-specific IgG antibody levels increased in each of the study participants from an average of 710 U/ml prior to the vaccination to more than 40,000 U/ml within ten weeks after the vaccination. In contrast, anti-spike-specific IgG antibody levels averaged 2,190 U/ml in 14 healthy SARS-CoV-2-naïve individuals (avg. 58 yrs.) ten weeks after the second dose of BNT162b. RNA-seq conducted on PBMCs demonstrated the activation of interferon-activated genetic programs in both cohorts within one day. Unlike their transient induction in the younger naïve population, persistent activity and the initiation of additional cell cycle regulated programs were obtained in the older COVID-19 recovered population. Here we show that the elderly, a high-risk population, can mount a strong antibody and a persistent molecular immune response upon receiving a single dose of mRNA vaccine 15 months after recovery from COVID-19.
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Affiliation(s)
- Hye Kyung Lee
- National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | | | | | | | | | - Mary Walter
- Clinical Core, National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Priscilla A. Furth
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, MD 20892, USA
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25
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Abstract
Human responses to infection include transcriptional changes shared across diverse pathogens. To capture these common patterns, we establish the concept of, and the method for, the identification of “transfer signatures”: sets of genes defining human immunophenotypes. We demonstrate the usefulness of transfer signatures in two use cases: the progression of latent to active tuberculosis and the severity of viral respiratory infections. The modulation of the transcriptome is among the earliest responses to infection. However, defining the transcriptomic signatures of disease is challenging because logistic, technical, and cost factors limit the size and representativeness of samples in clinical studies. These limitations lead to a poor performance of signatures when applied to new datasets. Although the study focuses on infection, the central hypothesis of the work is the generalization of sets of signatures across diseases. We use a machine learning approach to identify common elements in datasets and then test empirically whether they are informative about a second dataset from a disease or process distinct from the original dataset. We identify sets of genes, which we name transfer signatures, that are predictive across diverse datasets and/or species (e.g., rhesus to humans). We demonstrate the usefulness of transfer signatures in two use cases: the progression of latent to active tuberculosis and the severity of COVID-19 and influenza A H1N1 infection. This indicates that transfer signatures can be deployed in settings that lack disease-specific biomarkers. The broad significance of our work lies in the concept that a small set of archetypal human immunophenotypes, captured by transfer signatures, can explain a larger set of responses to diverse diseases.
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26
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Abstract
Introduction: An effective vaccine against malaria forms a global health priority. Both naturally acquired immunity and sterile protection induced by irradiated sporozoite immunization were described decades ago. Still no vaccine exists that sufficiently protects children in endemic areas. Identifying immunological correlates of vaccine efficacy can inform rational vaccine design and potentially accelerate clinical development.Areas covered: We discuss recent research on immunological correlates of malaria vaccine efficacy, including: insights from state-of-the-art omics platforms and systems vaccinology analyses; functional anti-parasitic assays; pre-immunization predictors of vaccine efficacy; and comparison of correlates of vaccine efficacy against controlled human malaria infections (CHMI) and against naturally acquired infections.Expert Opinion: Effective vaccination may be achievable without necessarily understanding immunological correlates, but the relatively disappointing efficacy of malaria vaccine candidates in target populations is concerning. Hypothesis-generating omics and systems vaccinology analyses, alongside assessment of pre-immunization correlates, have the potential to bring about paradigm-shifts in malaria vaccinology. Functional assays may represent in vivo effector mechanisms, but have scarcely been formally assessed as correlates. Crucially, evidence is still meager that correlates of vaccine efficacy against CHMI correspond with those against naturally acquired infections in target populations. Finally, the diversity of immunological assays and efficacy endpoints across malaria vaccine trials remains a major confounder.
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Affiliation(s)
| | - Matthew B B McCall
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands.,Institut für Tropenmedizin, Universitätsklinikum Tübingen, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
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27
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Bosco N, Noti M. The aging gut microbiome and its impact on host immunity. Genes Immun 2021; 22:289-303. [PMID: 33875817 PMCID: PMC8054695 DOI: 10.1038/s41435-021-00126-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/11/2021] [Accepted: 03/25/2021] [Indexed: 02/01/2023]
Abstract
The microbiome plays a fundamental role in the maturation, function, and regulation of the host-immune system from birth to old age. In return, the immune system has co-evolved a mutualistic relationship with trillions of beneficial microbes residing our bodies while mounting efficient responses to fight invading pathogens. As we age, both the immune system and the gut microbiome undergo significant changes in composition and function that correlate with increased susceptibility to infectious diseases and reduced vaccination responses. Emerging studies suggest that targeting age-related dysbiosis can improve health- and lifespan, in part through reducing systemic low-grade inflammation and immunosenescence-two hallmarks of the aging process. However-a cause and effect relationship of age-related dysbiosis and associated functional declines in immune cell functioning have yet to be demonstrated in clinical settings. This review aims to (i) give an overview on hallmarks of the aging immune system and gut microbiome, (ii) discuss the impact of age-related changes in the gut commensal community structure (introduced as microb-aging) on host-immune fitness and health, and (iii) summarize prebiotic- and probiotic clinical intervention trials aiming to reinforce age-related declines in immune cell functioning through microbiome modulation or rejuvenation.
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Affiliation(s)
- Nabil Bosco
- grid.419905.00000 0001 0066 4948Nestlé Research, Nestlé Institute of Health Sciences, Department of Cell Biology, Cellular Metabolism, EPFL Innovation Park, Nestlé SA, Lausanne, Switzerland
| | - Mario Noti
- grid.419905.00000 0001 0066 4948Nestlé Research, Nestlé Institute of Health Sciences, Department of Gastrointestinal Health, Immunology, Vers-Chez-les-Blancs, Nestlé SA, Lausanne, Switzerland
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28
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De Mot L, Bechtold V, Bol V, Callegaro A, Coccia M, Essaghir A, Hasdemir D, Ulloa-Montoya F, Siena E, Smilde A, van den Berg RA, Didierlaurent AM, Burny W, van der Most RG. Transcriptional profiles of adjuvanted hepatitis B vaccines display variable interindividual homogeneity but a shared core signature. Sci Transl Med 2020; 12:12/569/eaay8618. [DOI: 10.1126/scitranslmed.aay8618] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/23/2020] [Indexed: 12/19/2022]
Abstract
The current routine use of adjuvants in human vaccines provides a strong incentive to increase our understanding of how adjuvants differ in their ability to stimulate innate immunity and consequently enhance vaccine immunogenicity. Here, we evaluated gene expression profiles in cells from whole blood elicited in naive subjects receiving the hepatitis B surface antigen formulated with different adjuvants. We identified a core innate gene signature emerging 1 day after the second vaccination and that was shared by the recipients of vaccines formulated with adjuvant systems AS01B, AS01E, or AS03. This core signature associated with the magnitude of the hepatitis B surface-specific antibody response and was characterized by positive regulation of genes associated with interferon-related responses or the innate cell compartment and by negative regulation of natural killer cell–associated genes. Analysis at the individual subject level revealed that the higher immunogenicity of AS01B-adjuvanted vaccine was linked to its ability to induce this signature in most vaccinees even after the first vaccination. Therefore, our data suggest that adjuvanticity is not strictly defined by the nature of the receptors or signaling pathways it activates but by the ability of the adjuvant to consistently induce a core inflammatory signature across individuals.
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Affiliation(s)
| | | | | | | | | | | | - Dicle Hasdemir
- Bioinformatics Laboratory, University of Amsterdam, 1012 WX Amsterdam, Netherlands
- Biosystems Data Analysis Group, University of Amsterdam, 1012 WX Amsterdam, Netherlands
| | | | | | - Age Smilde
- Biosystems Data Analysis Group, University of Amsterdam, 1012 WX Amsterdam, Netherlands
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29
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Pereira B, Xu XN, Akbar AN. Targeting Inflammation and Immunosenescence to Improve Vaccine Responses in the Elderly. Front Immunol 2020; 11:583019. [PMID: 33178213 PMCID: PMC7592394 DOI: 10.3389/fimmu.2020.583019] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
One of the most appreciated consequences of immunosenescence is an impaired response to vaccines with advanced age. While most studies report impaired antibody responses in older adults as a correlate of vaccine efficacy, it is now widely appreciated that this may fail to identify important changes occurring in the immune system with age that may affect vaccine efficacy. The impact of immunosenescence on vaccination goes beyond the defects on antibody responses as T cell-mediated responses are reshaped during aging and certainly affect vaccination. Likewise, age-related changes in the innate immune system may have important consequences on antigen presentation and priming of adaptive immune responses. Importantly, a low-level chronic inflammatory status known as inflammaging has been shown to inhibit immune responses to vaccination and pharmacological strategies aiming at blocking baseline inflammation can be potentially used to boost vaccine responses. Yet current strategies aiming at improving immunogenicity in the elderly have mainly focused on the use of adjuvants to promote local inflammation. More research is needed to understand the role of inflammation in vaccine responses and to reconcile these seemingly paradoxical observations. Alternative approaches to improve vaccine responses in the elderly include the use of higher vaccine doses or alternative routes of vaccination showing only limited benefits. This review will explore novel targets and potential new strategies for enhancing vaccine responses in older adults, including the use of anti-inflammatory drugs and immunomodulators.
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Affiliation(s)
- Branca Pereira
- HIV/GUM Directorate, Chelsea and Westminster Hospital NHS Foundation Trust, London, United Kingdom.,Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Xiao-Ning Xu
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Arne N Akbar
- Division of Medicine, University College London, London, United Kingdom
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30
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Cotugno N, Santilli V, Pascucci GR, Manno EC, De Armas L, Pallikkuth S, Deodati A, Amodio D, Zangari P, Zicari S, Ruggiero A, Fortin M, Bromley C, Pahwa R, Rossi P, Pahwa S, Palma P. Artificial Intelligence Applied to in vitro Gene Expression Testing (IVIGET) to Predict Trivalent Inactivated Influenza Vaccine Immunogenicity in HIV Infected Children. Front Immunol 2020; 11:559590. [PMID: 33123133 PMCID: PMC7569088 DOI: 10.3389/fimmu.2020.559590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/18/2020] [Indexed: 01/01/2023] Open
Abstract
The number of patients affected by chronic diseases with special vaccination needs is burgeoning. In this scenario, predictive markers of immunogenicity, as well as signatures of immune responses are typically missing even though it would especially improve the identification of personalized immunization practices in these populations. We aimed to develop a predictive score of immunogenicity to Influenza Trivalent Inactivated Vaccination (TIV) by applying deep machine learning algorithms using transcriptional data from sort-purified lymphocyte subsets after in vitro stimulation. Peripheral blood mononuclear cells (PBMCs) collected before TIV from 23 vertically HIV infected children under ART and virally controlled were stimulated in vitro with p09/H1N1 peptides (stim) or left unstimulated (med). A multiplexed-qPCR for 96 genes was made on fixed numbers of 3 B cell subsets, 3 T cell subsets and total PBMCs. The ability to respond to TIV was assessed through hemagglutination Inhibition Assay (HIV) and ELIspot and patients were classified as Responders (R) and Non Responders (NR). A predictive modeling framework was applied to the data set in order to define genes and conditions with the higher predicted probability able to inform the final score. Twelve NR and 11 R were analyzed for gene expression differences in all subsets and 3 conditions [med, stim or Δ (stim-med)]. Differentially expressed genes between R and NR were selected and tested with the Adaptive Boosting Model to build a prediction score. The score obtained from subsets revealed the best prediction score from 46 genes from 5 different subsets and conditions. Calculating a combined score based on these 5 categories, we achieved a model accuracy of 95.6% and only one misclassified patient. These data show how a predictive bioinformatic model applied to transcriptional analysis deriving from in-vitro stimulated lymphocytes subsets may predict poor or protective vaccination immune response in vulnerable populations, such as HIV-infected individuals. Future studies on larger cohorts are needed to validate such strategy in the context of vaccination trials.
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Affiliation(s)
- Nicola Cotugno
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy.,Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Veronica Santilli
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy
| | - Giuseppe Rubens Pascucci
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy
| | - Emma Concetta Manno
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy
| | - Lesley De Armas
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Suresh Pallikkuth
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Annalisa Deodati
- Academic Department of Pediatrics (DPUO), Research Unit of Growth Disorders, Bambino Gesù Children's Hospital, Rome, Italy
| | - Donato Amodio
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy.,Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Paola Zangari
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy
| | - Sonia Zicari
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy
| | - Alessandra Ruggiero
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy
| | | | | | - Rajendra Pahwa
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Paolo Rossi
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy.,Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Savita Pahwa
- Miami Center for AIDS Research, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Paolo Palma
- Academic Department of Pediatrics (DPUO), Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children's Hospital, Rome, Italy.,Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
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31
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Kinome profiling of peripheral blood mononuclear cells collected prior to vaccination reveals biomarkers and potential mechanisms of vaccine unresponsiveness in pigs. Sci Rep 2020; 10:11546. [PMID: 32665671 PMCID: PMC7360594 DOI: 10.1038/s41598-020-68039-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 05/17/2020] [Indexed: 01/21/2023] Open
Abstract
Inter-individual variance in host immune responses following vaccination can result in failure to develop protective immunity leaving individuals at risk for infection in addition to compromising herd immunity. While developing more efficacious vaccines is one strategy to mitigate this problem, predicting vaccine responsiveness prior to vaccination could inform which individuals require adjunct disease management strategies. To identify biomarkers of vaccine responsiveness, a cohort of pigs (n = 120) were vaccinated and pigs representing the high (n = 6; 90th percentile) and low (n = 6; 10th percentile) responders based on vaccine-specific antibody responses following vaccination were further analyzed. Kinase-mediated phosphorylation events within peripheral blood mononuclear cells collected prior to vaccination identified 53 differentially phosphorylated peptides when comparing low responders with high responders. Functional enrichment analysis revealed pro-inflammatory cytokine signaling pathways as dysregulated, and this was further substantiated by detection of higher (p < 0.01) concentrations of interferon-gamma in plasma of low responders compared to high responders prior to vaccination. In addition, low responder pigs with high plasma interferon-gamma showed lower (p < 0.01) birth weights than high responder pigs. These associations between vaccine responsiveness, cytokine signaling within peripheral immune cells, and body weight in pigs provide both evidence and insight into potential biomarkers for identifying low responders to vaccination.
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32
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Tsang JS, Dobaño C, VanDamme P, Moncunill G, Marchant A, Othman RB, Sadarangani M, Koff WC, Kollmann TR. Improving Vaccine-Induced Immunity: Can Baseline Predict Outcome? Trends Immunol 2020; 41:457-465. [PMID: 32340868 PMCID: PMC7142696 DOI: 10.1016/j.it.2020.04.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 12/21/2022]
Abstract
Immune signatures measured at baseline and immediately prior to vaccination may predict the immune response to vaccination. Such pre-vaccine assessment might allow not only population-based, but also more personalized vaccination strategies (‘precision vaccination’). If baseline immune signatures are predictive, the underlying mechanism they reflect may also determine vaccination outcome. Thus, baseline signatures might contribute to identifying interventional targets to be modulated prior to vaccination in order to improve vaccination responses. This concept has the potential to transform vaccination strategies and usher in a new approach to improve global health. Extensive baseline variability in immune responses (e.g., antibody titers) among individuals in given populations is increasingly being appreciated as a major contributor to vaccine response heterogeneity. The concept of ‘baseline may predict outcome’ has recently been reported for human influenza virus, yellow fever virus, and hepatitis B virus, as well as malaria vaccination. This concept might also apply to other vaccines. The ability to predict who might respond to immunization (and to what extent) might offer avenues for optimization of current vaccination strategies. We posit that this simple concept might be useful and significant for vaccine design: if ‘baseline determines outcome, then altering baseline prior to vaccination could alter outcome’. This approach could potentially lead to tailored (precision) vaccines ensuring that the majority, or all individuals vaccinated, respond by eliciting a protective immune response (i.e., devoid of non-responder individuals). Presumably, this approach might also allow the administration of fewer vaccine doses, potentially arriving at one vaccine dose only.
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Affiliation(s)
- John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID and Center for Human Immunology (CHI), NIH, Bethesda, MD, USA
| | - Carlota Dobaño
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Pierre VanDamme
- Centre for the Evaluation of Vaccination and Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Gemma Moncunill
- ISGlobal, Hospital Clínic, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Arnaud Marchant
- Institute for Medical Immunology, Université libre de Bruxelles, Charleroi, Belgium
| | - Rym Ben Othman
- Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute and Division of Infectious Diseases, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | | | - Tobias R Kollmann
- Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia.
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33
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Bartholomeus E, De Neuter N, Suls A, Elias G, van der Heijden S, Keersmaekers N, Jansens H, Van Tendeloo V, Beutels P, Laukens K, Ogunjimi B, Mortier G, Meysman P, Van Damme P. Transcriptomic profiling of different responder types in adults after a Priorix® vaccination. Vaccine 2020; 38:3218-3226. [PMID: 32165045 DOI: 10.1016/j.vaccine.2020.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/24/2020] [Accepted: 03/01/2020] [Indexed: 12/12/2022]
Abstract
Thanks to the recommendation of a combined Measles/Mumps/Rubella (MMR) vaccine, like Priorix®, these childhood diseases are less common now. This is beneficial to limit the spread of these diseases and work towards their elimination. However, the measles, mumps and rubella antibody titers show a large variability in short- and long-term immunity. The recent outbreaks worldwide of measles and mumps and previous studies, which mostly focused on only one of the three virus responses, illustrate that there is a clear need for better understanding the immune responses after vaccination. Our healthy cohort was already primed with the MMR antigens in their childhood. In this study, the adult volunteers received one Priorix® vaccine dose at day 0. First, we defined 4 different groups of responders, based on their antibody titers' evolution over 4 time points (Day 0, 21, 150 and 365). This showed a high variability within and between individuals. Second, we determined transcriptome profiles using 3'mRNA sequencing at day 0, 3 and 7. Using two analytical approaches, "one response group per time point" and "a time comparison per response group", we correlated the short-term gene expression profiles to the different response groups. In general, the list of differentially expressed genes is limited, however, most of them are clearly immune-related and upregulated at day 3 and 7, compared to the baseline day 0. Depending on the specific response group there are overlapping signatures for two of the three viruses. Antibody titers and transcriptomics data showed that an additional Priorix vaccination does not facilitate an equal immune response against the 3 viruses or among different vaccine recipients.
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Affiliation(s)
- Esther Bartholomeus
- Department of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium; AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.
| | - Nicolas De Neuter
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- Department of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium; AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - George Elias
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Sanne van der Heijden
- Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Nina Keersmaekers
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Hilde Jansens
- Department of Laboratory Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Viggo Van Tendeloo
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Philippe Beutels
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology (LEH), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium; Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium.
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium; AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp, Belgium
| | - Pierre Van Damme
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium; Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
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34
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Characterization of potential biomarkers of reactogenicity of licensed antiviral vaccines: randomized controlled clinical trials conducted by the BIOVACSAFE consortium. Sci Rep 2019; 9:20362. [PMID: 31889148 PMCID: PMC6937244 DOI: 10.1038/s41598-019-56994-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/10/2019] [Indexed: 02/08/2023] Open
Abstract
Biomarkers predictive of inflammatory events post-vaccination could accelerate vaccine development. Within the BIOVACSAFE framework, we conducted three identically designed, placebo-controlled inpatient/outpatient clinical studies (NCT01765413/NCT01771354/NCT01771367). Six antiviral vaccination strategies were evaluated to generate training data-sets of pre-/post-vaccination vital signs, blood changes and whole-blood gene transcripts, and to identify putative biomarkers of early inflammation/reactogenicity that could guide the design of subsequent focused confirmatory studies. Healthy adults (N = 123; 20-21/group) received one immunization at Day (D)0. Alum-adjuvanted hepatitis B vaccine elicited vital signs and inflammatory (CRP/innate cells) responses that were similar between primed/naive vaccinees, and low-level gene responses. MF59-adjuvanted trivalent influenza vaccine (ATIV) induced distinct physiological (temperature/heart rate/reactogenicity) response-patterns not seen with non-adjuvanted TIV or with the other vaccines. ATIV also elicited robust early (D1) activation of IFN-related genes (associated with serum IP-10 levels) and innate-cell-related genes, and changes in monocyte/neutrophil/lymphocyte counts, while TIV elicited similar but lower responses. Due to viral replication kinetics, innate gene activation by live yellow-fever or varicella-zoster virus (YFV/VZV) vaccines was more suspended, with early IFN-associated responses in naïve YFV-vaccine recipients but not in primed VZV-vaccine recipients. Inflammatory responses (physiological/serum markers, innate-signaling transcripts) are therefore a function of the vaccine type/composition and presence/absence of immune memory. The data reported here have guided the design of confirmatory Phase IV trials using ATIV to provide tools to identify inflammatory or reactogenicity biomarkers.
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35
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Bartholomeus E, De Neuter N, Lemay A, Pattyn L, Tuerlinckx D, Weynants D, Van Lede K, van Berlaer G, Bulckaert D, Boiy T, Vander Auwera A, Raes M, Van der Linden D, Verhelst H, Van Steijn S, Jonckheer T, Dehoorne J, Joos R, Jansens H, Suls A, Van Damme P, Laukens K, Mortier G, Meysman P, Ogunjimi B. Diagnosing enterovirus meningitis via blood transcriptomics: an alternative for lumbar puncture? J Transl Med 2019; 17:282. [PMID: 31443725 PMCID: PMC6708255 DOI: 10.1186/s12967-019-2037-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/18/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Meningitis can be caused by several viruses and bacteria. Identifying the causative pathogen as quickly as possible is crucial to initiate the most optimal therapy, as acute bacterial meningitis is associated with a significant morbidity and mortality. Bacterial meningitis requires antibiotics, as opposed to enteroviral meningitis, which only requires supportive therapy. Clinical presentation is usually not sufficient to differentiate between viral and bacterial meningitis, thereby necessitating cerebrospinal fluid (CSF) analysis by PCR and/or time-consuming bacterial cultures. However, collecting CSF in children is not always feasible and a rather invasive procedure. METHODS In 12 Belgian hospitals, we obtained acute blood samples from children with signs of meningitis (49 viral and 7 bacterial cases) (aged between 3 months and 16 years). After pathogen confirmation on CSF, the patient was asked to give a convalescent sample after recovery. 3' mRNA sequencing was performed to determine differentially expressed genes (DEGs) to create a host transcriptomic profile. RESULTS Enteroviral meningitis cases displayed the largest upregulated fold change enrichment in type I interferon production, response and signaling pathways. Patients with bacterial meningitis showed a significant upregulation of genes related to macrophage and neutrophil activation. We found several significantly DEGs between enteroviral and bacterial meningitis. Random forest classification showed that we were able to differentiate enteroviral from bacterial meningitis with an AUC of 0.982 on held-out samples. CONCLUSIONS Enteroviral meningitis has an innate immunity signature with type 1 interferons as key players. Our classifier, based on blood host transcriptomic profiles of different meningitis cases, is a possible strong alternative for diagnosing enteroviral meningitis.
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Affiliation(s)
- Esther Bartholomeus
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium.,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Nicolas De Neuter
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Annelies Lemay
- Department of Paediatrics, AZ Turnhout, Turnhout, Belgium
| | - Luc Pattyn
- Department of Paediatrics, AZ Turnhout, Turnhout, Belgium
| | - David Tuerlinckx
- Université Catholique de Louvain/CHU UCL Namur, Site Dinant, Service de Pédiatrie, Dinant, Belgium
| | - David Weynants
- Department of Paediatrics, CHU ULC Namur Ste Elisabeth, Namur, Belgium
| | - Koen Van Lede
- Department of Paediatrics, AZ Nikolaas, Sint-Niklaas, Belgium
| | - Gerlant van Berlaer
- Department of Emergency Medicine/Pediatric Care, University Hospital Brussels, Jette, Belgium
| | - Dominique Bulckaert
- Department of Emergency Medicine/Pediatric Care, University Hospital Brussels, Jette, Belgium
| | - Tine Boiy
- Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium
| | | | - Marc Raes
- Department of Paediatrics, Jessa Hospital, Hasselt, Belgium
| | - Dimitri Van der Linden
- Paediatric Infectious Diseases, Department of Paediatrics, CHU ULC Cliniques Universitaires Saint-Luc, UCLouvain, Brussels, Belgium
| | - Helene Verhelst
- Department of Paediatric Rheumatology, University Hospital, Ghent, Belgium
| | | | - Tijl Jonckheer
- Department of Paediatrics, GZA Sint-Vincentius, Antwerp, Belgium
| | - Joke Dehoorne
- Department of Paediatric Rheumatology, University Hospital, Ghent, Belgium
| | - Rik Joos
- Department of Paediatric Rheumatology, University Hospital, Ghent, Belgium.,Antwerp Center for Paediatric Rheumatology and AutoInflammatory Diseases, Antwerp, Belgium
| | - Hilde Jansens
- Department of Laboratory Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Arvid Suls
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium.,AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination (CEV), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Geert Mortier
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Edegem, Belgium
| | - Pieter Meysman
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium.,Adrem Data Lab, Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium.,Biomedical Informatics Research Network Antwerp (Biomina), University of Antwerp, Antwerp, Belgium
| | - Benson Ogunjimi
- AUDACIS, Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp, Antwerp, Belgium. .,Department of Paediatrics, Antwerp University Hospital, Edegem, Belgium. .,Antwerp Center for Paediatric Rheumatology and AutoInflammatory Diseases, Antwerp, Belgium. .,Centre for Health Economics Research & Modeling Infectious Diseases (CHERMID), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium. .,Antwerp Center for Translational Immunology and Virology (ACTIV), Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, 00323/8213251, Antwerp, Belgium. .,Department of Pediatrics, University Hospital Brussels, Jette, Belgium.
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