1
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Wen M, Chen S, Zhang Y, Liu Y, Tang C, Zhang J, Sun J, Li X, Ding Y, Lu L, Long K, Nie Y, Li X, Li M, Ge L, Ma J. Diversity and host interaction of the gut microbiota in specific pathogen-free pigs. Front Microbiol 2024; 15:1402807. [PMID: 38800748 PMCID: PMC11122924 DOI: 10.3389/fmicb.2024.1402807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024] Open
Abstract
Pigs are widely used as animal models in various studies related to humans. The interaction between the gut microbiota and the host has significant effects on the host's health and disease status. However, although there have been many studies investigating the pig gut microbiota, the findings have been inconsistent due to variations in rearing conditions. Interactions between the gut microbiota and host have not been fully explored in pigs. Specific pathogen-free (SPF) pigs are ideal non-primate large animals to study the interactions between the gut microbiota and the host. In this study, we performed high-throughput sequencing analysis of the gut microbiota and the gut tissue transcriptome of six SPF pigs to provide a systematic understanding of the composition, function, and spatial distribution of gut microbiota in SPF pigs. We identified significant differences in microbial diversity and functionality among different gastrointestinal tract sites. Metagenomics data analysis revealed significant differences in alpha diversity and beta diversity of microbiota in different gastrointestinal sites of SPF pigs. Additionally, transcriptomic data indicated significant differences in gene expression as well as KEGG and GO functional enrichment between the small intestine and large intestine. Furthermore, by combining microbial metagenomics and host transcriptomics analyses, specific correlations were found between gut microbiota and host genes. These included a negative correlation between the TCN1 gene and Prevotella dentalis, possibly related to bacterial metabolic pathways involving vitamin B12, and a positive correlation between the BDH1 gene and Roseburia hominis, possibly because both are involved in fatty acid metabolism. These findings lay the groundwork for further exploration of the co-evolution between the microbiota and the host, specifically in relation to nutrition, metabolism, and immunity. In conclusion, we have elucidated the diversity of the gut microbiota in SPF pigs and conducted a detailed investigation into the interactions between the gut microbiota and host gene expression. These results contribute to our understanding of the intricate dynamics between the gut microbiota and the host, offering important references for advancements in life science research, bioproduct production, and sustainable development in animal husbandry.
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Affiliation(s)
- Mingxing Wen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shuangshuang Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yali Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yan Liu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chuang Tang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jinwei Zhang
- Chongqing Academy of Animal Sciences, Chongqing, China
- National Center of Technology Innovation for Pigs, Chongqing, China
- Ministry of Agriculture Key Laboratory of Pig Sciences, Chongqing Key Laboratory of Pig Sciences, Chongqing, China
| | - Jing Sun
- Chongqing Academy of Animal Sciences, Chongqing, China
- National Center of Technology Innovation for Pigs, Chongqing, China
- Ministry of Agriculture Key Laboratory of Pig Sciences, Chongqing Key Laboratory of Pig Sciences, Chongqing, China
| | - Xiaokai Li
- National Center of Technology Innovation for Pigs, Chongqing, China
- Ministry of Agriculture Key Laboratory of Pig Sciences, Chongqing Key Laboratory of Pig Sciences, Chongqing, China
| | - Yuchun Ding
- Chongqing Academy of Animal Sciences, Chongqing, China
- National Center of Technology Innovation for Pigs, Chongqing, China
- Ministry of Agriculture Key Laboratory of Pig Sciences, Chongqing Key Laboratory of Pig Sciences, Chongqing, China
| | - Lu Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Keren Long
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, China
| | - Xuewei Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Liangpeng Ge
- Chongqing Academy of Animal Sciences, Chongqing, China
- National Center of Technology Innovation for Pigs, Chongqing, China
- Ministry of Agriculture Key Laboratory of Pig Sciences, Chongqing Key Laboratory of Pig Sciences, Chongqing, China
| | - Jideng Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Jensen KJ, Hansen MS, Skovgaard K, Svensson E, Larsen LE, Heegaard PMH, Benn CS, Jungersen G. Immunogenicity of Bacillus Calmette-Guérin in pigs: potential as a translational model of non-specific effects of BCG. Front Immunol 2023; 14:1219006. [PMID: 37520542 PMCID: PMC10374211 DOI: 10.3389/fimmu.2023.1219006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Background Clinical and immunological studies in humans show that the live attenuated Bacillus Calmette-Guérin (BCG) vaccine has beneficial non-specific effects, increasing resistance against diseases other than tuberculosis. The underlying mechanisms are currently being explored. The pig exhibits considerable physiological similarity to humans in anatomy and physiology, suggesting that similar responses to BCG could be expected. Studies of the non-specific effects of BCG in pigs are scarce. We investigated the feasibility of using pigs as a large animal model to investigate the non-specific immunological effects of BCG. Methods In a series of experiments, we randomized newborn or young piglets from conventional farms to receiving BCG or placebo and investigated the persistence of live BCG bacteria in various tissues, the immunogenicity of BCG in ex vivo blood and in vitro stimulation assays, and the acute phase protein and clinical responses to heterologous infectious challenge with influenza A virus or Actinobacillus pleuropneumoniae. Results The BCG vaccine was generally well tolerated. In contrast to humans, no skin reaction in the form of abscesses, ulcers, or scars was observed. Live BCG was recovered from draining lymph nodes in 2/13 animals 20 weeks after vaccination. Specific in vitro responses of IFN-γ to antigen-specific re-stimulation with mycobacterial antigen were increased but not TNF-responses to TLR2 or TLR4 agonists. A few genes were differentially expressed in blood after vaccination, including the antiviral genes RIG-I and CSF1, although the effect disappeared after correction for multiple testing. Clinical symptoms after heterologous bacterial or viral respiratory infections did not differ, nor did virus copies in nasopharyngeal samples after the challenge. However, the acute phase protein response was significantly reduced in BCG-vaccinated animals after influenza challenge but not after A. pleuropneumoniae challenge. Discussion BCG was safe in pigs, inducing specific immunological responses, but our model did not corroborate the innate immunological responsiveness to BCG seen in humans. The dose of BCG or the bacterial and viral challenges may have been sub-optimal. Even so, the acute phase protein response to influenza infection was significantly reduced in BCG-vaccinated animals.
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Affiliation(s)
- Kristoffer Jarlov Jensen
- Bandim Health Project, University of Southern Denmark, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
- Copenhagen Phase IV Unit, Center for Clinical Research and Prevention and Department of Clinical Pharmacology, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Frederiksberg, Denmark
| | - Mette Sif Hansen
- Institute for Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- Center for Diagnostics, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Erik Svensson
- Department of Tuberculosis and Mycobacteria, Statens Serum Institut, Copenhagen, Denmark
| | - Lars Erik Larsen
- Institute for Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Peter M. H. Heegaard
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christine Stabell Benn
- Bandim Health Project, University of Southern Denmark, Copenhagen, Denmark
- Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Gregers Jungersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
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3
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Burger S, Stenger T, Pierson M, Sridhar A, Huggins MA, Kucaba TA, Griffith TS, Hamilton SE, Schuldt NJ. Natural Microbial Exposure from the Earliest Natural Time Point Enhances Immune Development by Expanding Immune Cell Progenitors and Mature Immune Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1740-1751. [PMID: 37074206 PMCID: PMC10192123 DOI: 10.4049/jimmunol.2300061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/24/2023] [Indexed: 04/20/2023]
Abstract
Microbial experience fundamentally shapes immunity, particularly during the perinatal period when the immune system is underdeveloped, and novel microbial encounters are common. Most animal models are raised in specific pathogen-free (SPF) conditions with relatively uniform microbial communities. How SPF housing conditions alter early-life immune development relative to natural microbial exposure (NME) has not been thoroughly investigated. In this article, we compare immune development in SPF-raised mice with mice born from immunologically experienced mothers in microbially diverse environments. NME induced broad immune cell expansion, including naive cells, suggesting mechanisms besides activation-induced proliferation contribute to the increase in immune cell numbers. We found NME conditions also expanded immune cell progenitor cell populations in the bone marrow, suggesting microbial experience enhances immune development at the earliest stages of immune cell differentiation. Multiple immune functions characteristically impaired in infants were also enhanced by NME, including T cell memory and Th1 polarization, B cell class switching and Ab production, proinflammatory cytokine expression, and bacterial clearance after Listeria monocytogenes challenge. Collectively, our studies reveal numerous impairments in immune development in SPF conditions relative to natural immune development.
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Affiliation(s)
- Sarah Burger
- Center for Immunology, Minneapolis, MN, USA
- Department of Pediatrics, Minneapolis, MN, USA
| | - Terran Stenger
- Center for Immunology, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, Minneapolis, MN, USA
| | - Mark Pierson
- Center for Immunology, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, Minneapolis, MN, USA
| | - Adhvaith Sridhar
- Center for Immunology, Minneapolis, MN, USA
- Department of Pediatrics, Minneapolis, MN, USA
| | - Matthew A. Huggins
- Center for Immunology, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, Minneapolis, MN, USA
| | | | - Thomas S. Griffith
- Center for Immunology, Minneapolis, MN, USA
- Department of Urology, Minneapolis, MN, USA
- Microbiology, Immunology, and Cancer Biology PhD Program, Minneapolis, MN, USA
- Masonic Cancer Center, Minneapolis, MN, USA
- Minneapolis VA Health Care System, Minneapolis, MN, USA
| | - Sara E. Hamilton
- Center for Immunology, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, Minneapolis, MN, USA
- Microbiology, Immunology, and Cancer Biology PhD Program, Minneapolis, MN, USA
- Masonic Cancer Center, Minneapolis, MN, USA
| | - Nathaniel J. Schuldt
- Center for Immunology, Minneapolis, MN, USA
- Department of Pediatrics, Minneapolis, MN, USA
- Masonic Cancer Center, Minneapolis, MN, USA
- Lead Contact
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4
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Carrisoza-Urbina J, Bedolla-Alva MA, Hernández-Pando R, López-Macías C, Huerta-Yepez S, Baay-Guzmán G, Juárez-Ramírez M, Gutiérrez-Pabello JA. Mycobacterium bovis naturally infected calves present a higher bacterial load and proinflammatory response than adult cattle. Front Vet Sci 2023; 10:1105716. [PMID: 37180066 PMCID: PMC10172680 DOI: 10.3389/fvets.2023.1105716] [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: 11/23/2022] [Accepted: 04/10/2023] [Indexed: 05/15/2023] Open
Abstract
Granulomas are characteristic bovine tuberculosis lesions; studying this structure has improved our understanding of tuberculosis pathogenesis. However, the immune response that develops in granulomas of young cattle naturally infected with Mycobacterium bovis (M. bovis) has not been fully studied. Our previous work described an atypical pattern in granulomatous lesions of cattle younger than 4 months (calves) naturally infected previously M. bovis that did not correspond to the histological classification previously proposed. Histologically, granulomas from calves lack a connective tissue capsule and have fewer multinucleated giant cells (MGCs) and more acid-fast bacilli (AFB) than the classic tuberculosis lesions found in cattle older than 1 year (adults); this suggests a deficient immune response against M. bovis infection in young animals. Therefore, we used IHC and digital pathology analysis to characterize the in situ immune response of granulomas from young and adult cattle. The immunolabeling quantification showed that granulomas from calves had more mycobacteria, CD3+ cells, IFN-γ, TNF-α, and inducible nitric oxide synthase (iNOS) than those of adult cattle. Furthermore, calf granulomas showed lower immunolabeling of MAC387+, CD79+, and WC1+ cells without connective tissue surrounding the lesion and were associated with less vimentin, Alpha Smooth Muscle Actin (α-SMA), and TGF-β compared with granulomas from adult cattle. Our results suggest that the immune responses in granulomas of cattle naturally infected with M. bovis may be age dependent. This implies that an exacerbated proinflammatory response may be associated with active tuberculosis, producing more necrosis and a lower microbicidal capacity in the granulomas of calves naturally infected with M. bovis.
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Affiliation(s)
- Jacobo Carrisoza-Urbina
- Laboratorio de Investigación en Tuberculosis y Brucelosis, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mario A. Bedolla-Alva
- Departamento de Patología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rogelio Hernández-Pando
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubiran, Mexico City, Mexico
| | - Constantino López-Macías
- Unidad de Investigación Médica en Inmunoquímica, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI. Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Sara Huerta-Yepez
- Unidad de Investigación en Enfermedades Oncológicas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Guillermina Baay-Guzmán
- Unidad de Investigación en Enfermedades Oncológicas, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Mireya Juárez-Ramírez
- Departamento de Patología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - José A. Gutiérrez-Pabello
- Laboratorio de Investigación en Tuberculosis y Brucelosis, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: José A. Gutiérrez-Pabello,
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5
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Binns C, Low WY, Shunnmugam B. The Year of the Rabbit and the COVID Pandemic. Asia Pac J Public Health 2023; 35:5-6. [PMID: 36694949 PMCID: PMC9895313 DOI: 10.1177/10105395221150836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Colin Binns
- School of Population Health, Faculty of
Health Sciences, Curtin University, Perth, WA, Australia,Colin Binns, School of Population Health,
Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845,
Australia.
| | - Wah Yun Low
- Faculty of Medicine, Universiti Malaya,
Kuala Lumpur, Malaysia
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6
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Lunney JK, Van Goor A, Walker KE, Hailstock T, Franklin J, Dai C. Importance of the pig as a human biomedical model. Sci Transl Med 2021; 13:eabd5758. [PMID: 34818055 DOI: 10.1126/scitranslmed.abd5758] [Citation(s) in RCA: 242] [Impact Index Per Article: 80.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Joan K Lunney
- Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA, Beltsville, MD 20705, USA
| | - Angelica Van Goor
- Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA, Beltsville, MD 20705, USA
| | - Kristen E Walker
- Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA, Beltsville, MD 20705, USA
| | - Taylor Hailstock
- Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA, Beltsville, MD 20705, USA
| | - Jasmine Franklin
- Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA, Beltsville, MD 20705, USA
| | - Chaohui Dai
- Animal Parasitic Diseases Laboratory, BARC, NEA, ARS, USDA, Beltsville, MD 20705, USA.,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
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7
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Sarfas C, White AD, Sibley L, Morrison AL, Gullick J, Lawrence S, Dennis MJ, Marsh PD, Fletcher HA, Sharpe SA. Characterization of the Infant Immune System and the Influence and Immunogenicity of BCG Vaccination in Infant and Adult Rhesus Macaques. Front Immunol 2021; 12:754589. [PMID: 34707617 PMCID: PMC8542880 DOI: 10.3389/fimmu.2021.754589] [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: 08/06/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
In many countries where tuberculosis (TB) is endemic, the Bacillus Calmette–Guérin (BCG) vaccine is given as close to birth as possible to protect infants and children from severe forms of TB. However, BCG has variable efficacy and is not as effective against adult pulmonary TB. At present, most animal models used to study novel TB vaccine candidates rely on the use of adult animals. Human studies show that the infant immune system is different to that of an adult. Understanding how the phenotypic profile and functional ability of the immature host immune system compares to that of a mature adult, together with the subsequent BCG immune response, is critical to ensuring that new TB vaccines are tested in the most appropriate models. BCG-specific immune responses were detected in macaques vaccinated within a week of birth from six weeks after immunization indicating that neonatal macaques are able to generate a functional cellular response to the vaccine. However, the responses measured were significantly lower than those typically observed following BCG vaccination in adult rhesus macaques and infant profiles were skewed towards the activation and attraction of macrophages and monocytes and the synthesis in addition to release of pro-inflammatory cytokines such as IL-1, IL-6 and TNF-α. The frequency of specific immune cell populations changed significantly through the first three years of life as the infants developed into young adult macaques. Notably, the CD4:CD8 ratio significantly declined as the macaques aged due to a significant decrease in the proportion of CD4+ T-cells relative to a significant increase in CD8+ T-cells. Also, the frequency of both CD4+ and CD8+ T-cells expressing the memory marker CD95, and memory subset populations including effector memory, central memory and stem cell memory, increased significantly as animals matured. Infant macaques, vaccinated with BCG within a week of birth, possessed a significantly higher frequency of CD14+ classical monocytes and granulocytes which remained different throughout the first three years of life compared to unvaccinated age matched animals. These findings, along with the increase in monokines following vaccination in infants, may provide an insight into the mechanism by which vaccination with BCG is able to provide non-specific immunity against non-mycobacterial organisms.
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Affiliation(s)
- Charlotte Sarfas
- National Infection Service, UK Health Security Agency, Salisbury, United Kingdom
| | - Andrew D White
- National Infection Service, UK Health Security Agency, Salisbury, United Kingdom
| | - Laura Sibley
- National Infection Service, UK Health Security Agency, Salisbury, United Kingdom
| | - Alexandra L Morrison
- National Infection Service, UK Health Security Agency, Salisbury, United Kingdom
| | - Jennie Gullick
- National Infection Service, UK Health Security Agency, Salisbury, United Kingdom
| | - Steve Lawrence
- National Infection Service, UK Health Security Agency, Salisbury, United Kingdom
| | - Mike J Dennis
- National Infection Service, UK Health Security Agency, Salisbury, United Kingdom
| | - Philip D Marsh
- National Infection Service, UK Health Security Agency, Salisbury, United Kingdom
| | - Helen A Fletcher
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sally A Sharpe
- National Infection Service, UK Health Security Agency, Salisbury, United Kingdom
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8
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Van Tilbeurgh M, Lemdani K, Beignon AS, Chapon C, Tchitchek N, Cheraitia L, Marcos Lopez E, Pascal Q, Le Grand R, Maisonnasse P, Manet C. Predictive Markers of Immunogenicity and Efficacy for Human Vaccines. Vaccines (Basel) 2021; 9:579. [PMID: 34205932 PMCID: PMC8226531 DOI: 10.3390/vaccines9060579] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
Vaccines represent one of the major advances of modern medicine. Despite the many successes of vaccination, continuous efforts to design new vaccines are needed to fight "old" pandemics, such as tuberculosis and malaria, as well as emerging pathogens, such as Zika virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Vaccination aims at reaching sterilizing immunity, however assessing vaccine efficacy is still challenging and underscores the need for a better understanding of immune protective responses. Identifying reliable predictive markers of immunogenicity can help to select and develop promising vaccine candidates during early preclinical studies and can lead to improved, personalized, vaccination strategies. A systems biology approach is increasingly being adopted to address these major challenges using multiple high-dimensional technologies combined with in silico models. Although the goal is to develop predictive models of vaccine efficacy in humans, applying this approach to animal models empowers basic and translational vaccine research. In this review, we provide an overview of vaccine immune signatures in preclinical models, as well as in target human populations. We also discuss high-throughput technologies used to probe vaccine-induced responses, along with data analysis and computational methodologies applied to the predictive modeling of vaccine efficacy.
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Affiliation(s)
- Matthieu Van Tilbeurgh
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Katia Lemdani
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Anne-Sophie Beignon
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Catherine Chapon
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Nicolas Tchitchek
- Unité de Recherche i3, Inserm UMR-S 959, Bâtiment CERVI, Hôpital de la Pitié-Salpêtrière, 75013 Paris, France;
| | - Lina Cheraitia
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Ernesto Marcos Lopez
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Quentin Pascal
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Roger Le Grand
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Pauline Maisonnasse
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Caroline Manet
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
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